Harvard Molecular Technologies	Contact	Calendar	Courses	G.Church	Lab photos & List	News	Publications

Publications by George Church & colleagues. (Skip to Patents). (Skip to Papers in prep).

Click on titles for full text pdf files (for fair use) or click on the literature citation for pubmed abstract and journal links. Jump down to patents. Lab members names are in bold font. Suffix "s" on numbers means submitted, but not yet published. Suffix "a" means additional publications from the lab. Updated 4-Oct-02024 by GMC. 655 ORCID works ; Google Scholar citations=177895; h-index=205. Academic Chemistry Tree, Genetics Tree. As of 1-Feb-2022, 3615 co-authors on this page. (Erdős number = 4) Chemistry: #6(world), #1(Harvard)

722. Li L, Tang Z, Portillo X, Arora R, Yang M, Mintzer E, Han P, Zhang Z, Majewski DD, Titelman AA, Plesa AM, Shadpour M, McNamee S, Zheng Y, Li X, Tam J, McGee J, Sol S, Boncimino F, Zhang Y, Mandinova A, Murphy G, Kupper T, Ma S, Church GM (2024) Human skin rejuvenation via mRNA. Biorxiv

721. Abbott KL, Subudhi S, Ferreira R, Gültekin Y, Steinbuch SC, Munim MB, Honeder SE, Kumar AS, Ramesh DL, Wu M, Hansen JA, Sivanand S, Riedmayr LM, Duquette M, Ali A, Henning N, Shevzov-Zebrun A, Gourgue F, Barbeau AM, Waite M, Kunchok T, Ferraro GB, Do BT, Spanoudaki V, Sánchez-Rivera FJ, Jin X, Church GM, Jain RK, Vander Heiden MG (2024) Site of breast cancer metastasis is independent of single nutrient levels. bioRxiv PMID: 39484531

720. Islam M, Yang Y, Simmons AJ, Shah VM, Musale KP, Xu Y, Tasneem N, Chen Z, Trinh LT, Molina P, Ramirez-Solano MA, Sadien ID, Dou J, Rolong A, Chen K, Magnuson MA, Rathmell JC, Macara IG, Winton DJ, Liu Q, Zafar H, Kalhor R, Church GM, Shrubsole MJ, Coffey RJ, Lau KS (2024) Temporal recording of mammalian development and precancer. Nature. 634(8036):1187-1195. PMID: 39478207

719. Gilboa T, Ter-Ovanesyan D, Wang SC, Whiteman S, Kannarkat GT, Church GM, Chen-Plotkin AS, Walt DR (2024) Measurement of α-synuclein as protein cargo in plasma extracellular vesicles. PNAS. PMID: 39475636

718. Labade AS, Chiang ZD, Comenho C, Reginato PL, Payne AC, Earl AS, Shrestha R, Duarte FM, Habibi E, Zhang R, Church GM, Boyden ES, Chen F, Buenrostro JD (2024) Expansion in situ genome sequencing links nuclear abnormalities to hotspots of aberrant euchromatin repression. bioRxiv PMID: 39386718

717. Haspel G, Baker B, Beets I, Boyden E, Brown J, Church G, Cohen N, Colon-Ramos D, Dyer E, Fang-Yen C, Flavell S, Goodman M, Hart A, Izquierdo E, Kagias K, Lockery S, Lu Y, Marblestone A, Matelsky J, Mensh B, Pereira T, Pfister H, Rajan K, Rotstein H, Scholz M, Shaevitz J, Shlizerman E, Simeon Q, Skuhersky M, Tiruvadi V, Venkatachalam V, Wei D, Wester B, Yang G, Yemini E, Zimmer M, Kording K (2024) The time is ripe to reverse engineer an entire nervous system: simulating behavior from neural interactions. Arxiv.

716. McKenzie AT, Zeleznikow-Johnston A, Sparks JS, Nnadi O, Smart J, Wiley K, Cerullo MA, de Wolf A, Minerva F, Risco R, Church GM, de Magalhães JP, Kendziorra EF (2024) Structural brain preservation: a potential bridge to future medical technologies. Front Med Technol. 6:1400615. PMID: 39315362

715. Short E, Adcock IM, Al-Sarireh B, Ager A, Ajjan R, Akbar N, Akeroyd MA, Alsaleh G, Al-Sharbatee G, Alavian K, Amoaku W, Andersen J, Antoniades C, Arends MJ, Astley S, Atan D, Attanoos R, Attems J, Bain S, Balaskas K, Balmus G, Bance M, Barber TM, Bardhan A, Barker K, Barnes P, Basatemur G, Bateman A, Bauer ME, Bellamy C, van Beek E, Bellantuono I, Benbow E, Bhandari S, Bhatnagar R, Bloom P, Bowdish D, Bowerman M, Burke M, Carare R, Carrington EV, Castillo-Quan JI, Clegg P, Cole J, Cota C, Chazot P, Chen C, Cheong Y, Christopher G, Church G, Clancy D, Cool P, Del Galdo F, Dalakoti M, Dasgupta S, Deane C, Dhasmana D, Dojcinov S, Di Prete M, Du H, Duggal NA, Ellmers T, Emanueli C, Emberton M, Erusalimsky JD, Feldmeyer L, Fleming A, Forbes K, Foster TC, Frasca D, Frayling I, Freedman D, Fülöp T, Ellison-Hughes G, Gazzard G, George C, Gil J, Glassock R, Goldin R, Green J, Guymer R, Haboubi H, Harries L, Hart S, Hartley D, Hasaballa S, Henein C, Helliwell M, Henderson E, Heer R, Holte K, Idris I, Isenburg D, Jylhävä J, Iqbal A, Jones SW, Kalaria R, Kanamarlapudi V, Kempf W, Kermack AJ, Kerns J, Koulman A, Khan AH, Kinross J, Klaucane K, Krishna Y, Gill HS, Lakatta E, Laconi E, Lazar A, Leeuwenburgh C, Leung S, Li X, Linde I, Lopes L, Lorenzini A, Lotery A, Machado P, Mackie S, Madeddu P, Maier A, Mukkanna K, Manousou P, Markey O, Mauro C, McDonnell B, Medina R, Meran S, Metzler-Baddeley C, Meglinksi I, Milman N, Mitteldorf C, Montgomery R, Morris A, Mühleisen B, Mukherkee A, Murray A, Nelson S, Nicolaou A, Nirenberg A, Noble S, Nolan L, Nus M, On C, Osei-Lah V, Peffers M, Palmer A, Palmer D, Palmer L, Parry-Smith W, Pawelec G, Peleg S, Perera R, Pitsillides A, Plack C, Progatzsky F, Pyott S, Rajput K, Rashid S, Ratnayaka J, Ratnayake S, Rodriguez-Justo M, Rosa A, Rule A, Sanger G, Sayers I, Saykin A, Selvarajah D, Sethi J, Shanahan C, Shen-Orr S, Sheridan C, Shiels P, Sidlauskas K, Sivaprasad S, Sluimer J, Small G, Smith P, Smith R, Snelling S, Spyridopoulos I, Raghavan R, Steel D, Steel K, Stewart C, Stone K, Subbarayan S, Sussman M, Svensson J, Tadanki V, Tan A, Tanzi R, Tatler A, Tavares A, Mohd T, Tiganescu A, Timmons J, Tree J, Trivedi D, Tsochatzis E, Tsimpida D, Vinke E, Whittaker A, Vallabh N, Veighey K, Venables Z, Reddy V, Vernooij M, Verschoor C, Vinciguerra M, Vukanovic V, Vyazovskiy V, Walker J, Wakefield R, Watkins A, Webster A, Weight C, Weinberger B, Whitney S, Willis R, Witkowski J, Yeo L, Chung T, Yu E, Zemel M, Calimport S, Bentley B (2024) Defining an Ageing-Related Pathology, Disease or Syndrome: International Consensus Statement. MedRxiv. Geroscience. PMID: 39304617

714. Zheng Y, Koh HY, Yang M, Li L, May LT, Webb GI, Pan S, Church G (2024) Large Language Models in Drug Discovery and Development: From Disease Mechanisms to Clinical Trials. Arxiv

713. Weinstein EN, Gollub MG, Slabodkin A, Gardner CL, Dobbs K, Cui XB, Amin AN, Church GM, Wood EB (2024) Manufacturing-Aware Generative Model Architectures Enable Biological Sequence Design and Synthesis at Petascale. Preprint

712. Appleton E, Mehdipour N, Daifuku T, Briers D, Haghighi I, Moret M, Chao G, Wannier T, Chiappino-Pepe A, Huang J, Belta C, Church GM (2024) Algorithms for Autonomous Formation of Multicellular Shapes from Single Cells. ACS Synth Biol. PMID: 39194023

711. Maxim DS, Wu DW, Johnson NS, Charu V, Carter JN, Anand S, Church GM, Bhalla V (2024) EditABLE: A Simple Web Application for Designing Genome Editing Experiments. Research Square. PMID: 39184070

710. McIntyre CA, Grimont A, Park J, Meng Y, Sisso WJ, Seier K, Jang GH, Walch H, Aveson VG, Falvo DJ, Fall WB, Chan CW, Wenger A, Ecker BL, Pulvirenti A, Gelfer R, Zafra MP, Schultz N, Park W, O'Reilly EM, Houlihan SL, Alonso A, Hissong E, Church GM, Mason CE, Siolas D, Notta F, Gonen M, Dow LE, Jarnagin WR, Chandwani R (2024) Distinct clinical outcomes and biological features of specific KRAS mutants in human pancreatic cancer. Cancer Cell. PMID: 39214094

709. Liu W, Li Y, Patrinos GP, Xu S, Thong MK, Chen Z, Crawley FP, Li L, Ekmekci PE, Drmanac R, Cheong W, Benamouzig R, Nguyen Q, Volchkov P, Reichardt JKV, Carninci P, Majumder P, Jin X, Church G, Wang J, Xu X (2024) The 1% gift to humanity: The Human Genome Project II. Cell Res. PMID: 39261573

708. Kuru E, Rittichier J, de Puig H, Flores A, Rout S, Han I, Reese AE, Bartlett TM, De Moliner F, Bernier SG, Galpin JD, Marchand J, Bedell W, Robinson-McCarthy L, Ahern CA, Bernhardt TG, Rudner DZ, Collins JJ, Vendrell M, Church GM (2024) Rapid discovery and evolution of nanosensors containing fluorogenic amino acids. Nature Comm. PMID: 39237489

707. Karpinski E, Badey N, Mintzer E, Ashkenazy-Titelman A, Church GM (2024) Engineering Asian elephant TP53: TP53 retrogene knockouts activate common and unique cancer-relevant pathways. Biorxiv

706. Chiappino-Pepe A, Radford F, Budnik B, Tas H, Augustin TL, Burgess HM, Moret M, Dharani AM, Zeng Q, Fan W, Afrikawala MM, Thapa S, Kuru E, Narasimhan K, Marchand JA, Perrotta RM, Stokes JM, Lunshof JE, Aach J, Tam JM, Church GM. Preventing escape and malfunction of recoded cells due to tRNA base changes. bioRxiv

705. Wang Y, Liu X, Zeng Y, Saka SK, Xie W, Goldaracena I, Kohman RE, Yin P, Church GM (2024) Multiplexed in situ protein imaging using DNA-barcoded antibodies with extended hybridization chain reactions. Nucleic Acids Res. PMID:38966983

704. Nyerges A, Chiappino-Pepe A, Budnik B, Baas-Thomas M, Flynn R, Yan S, Ostrov N, Liu M, Wang M, Zheng Q, Hu F, Chen K, Rudolph A, Chen D, Ahn J, Spencer O, Ayalavarapu V, Tarver A, Harmon-Smith M, Hamilton M, Blaby I, Yoshikuni Y, Hajian B, Jin A, Kintses B, Szamel M, Seregi V, Shen Y, Li Z, Church GM (2024) Synthetic genomes unveil the effects of synonymous recoding. Biorxiv. PMID: 38915524

703. De Los Angeles A, Hug CB, Gladyshev VN, Church GM, Velychko S (2024) Sendai virus persistence questions the transient naive reprogramming method for iPSC generation. PMID: 38559172

702. Zheng Z, Xu L, Gao Y, Dou H, Zhou Y, Feng X, He X, Tian Z, Song L, Mo G, Hu J, Zhao H, Wei H, Church GM, Yang L (2024) Testing multiplexed anti-ASFV CRISPR-Cas9 in reducing African swine fever virus. Microbiology Spectrum. PMID: 38563791

701. Smela M, Adams J, Ma C, Breimann L, Widocki U, Shioda T, Church GM (2024) Induction of Meiosis from Human Pluripotent Stem Cells. bioRxiv PMID: 38854076

702. Overbey EG, Kim J, Tierney BT, Park J, Houerbi N, Lucaci AG, Medina SG, Damle N, Najjar D, Grigorev K, Afshin EE, Ryon KA, Sienkiewicz K, Patras L, Klotz R, Ortiz V, MacKay M, Schweickart A, Chin CR, Sierra MA, Valenzuela MF, Dantas E, Nelson TM, Cekanaviciute E, Deards G, Foox J, Narayanan SA, Schmidt CM, Schmidt MA, Schmidt JC, Mullane S, Tigchelaar SS, Levitte S, Westover C, Bhattacharya C, Lucotti S, Hirschberg JW, Proszynski J, Burke M, Kleinman A, Butler DJ, Loy C, Mzava O, Lenz J, Paul D, Mozsary C, Sanders LM, Taylor LE, Patel CO, Khan SA, Suhail M, Byhaqui SG, Aslam B, Gajadhar AS, Williamson L, Tandel P, Yang Q, Chu J, Benz RW, Siddiqui A, Hornburg D, Blease K, Moreno J, Boddicker A, Zhao J, Lajoie B, Scott RT, Gilbert RR, Polo SL, Altomare A, Kruglyak S, Levy S, Ariyapala I, Beer J, Zhang B, Hudson BM, Rininger A, Church SE, Beheshti A, Church GM, Smith SM, Crucian BE, Zwart SR, Matei I, Lyden DC, Garrett-Bakelman F, Krumsiek J, Chen Q, Miller D, Shuga J, Williams S, Nemec C, Trudel G, Pelchat M, Laneuville O, De Vlaminck I, Gross S, Bolton KL, Bailey SM, Granstein R, Furman D, Melnick AM, Costes SV, Shirah B, Yu M, Menon AS, Mateus J, Meydan C, Mason CE (2024) The Space Omics and Medical Atlas (SOMA) and international astronaut biobank. Nature. PMID: 38862028

700. Tierney BT, Kim J, Overbey EG, Ryon KA, Foox J, Sierra MA, Bhattacharya C, Damle N, Najjar D, Park J, Garcia Medina JS, Houerbi N, Meydan C, Wain Hirschberg J, Qiu J, Kleinman AS, Al-Ghalith GA, MacKay M, Afshin EE, Dhir R, Borg J, Gatt C, Brereton N, Readhead BP, Beyaz S, Venkateswaran KJ, Wiseman K, Moreno J, Boddicker AM, Zhao J, Lajoie BR, Scott RT, Altomare A, Kruglyak S, Levy S, Church GM, Mason CE (2024) Longitudinal multi-omics analysis of host microbiome architecture and immune responses during short-term spaceflight. Nat Microbiol. PMID: 38862604

699. Mason CE, Green J, Adamopoulos KI, Afshin EE, Baechle JJ, Basner M, Bailey SM, Bielski L, Borg J, Borg J, Broddrick JT, Burke M, Caicedo A, Castañeda V, Chatterjee S, Chin C, Church G, Costes SV, De Vlaminck I, Desai RI, Dhir R, Diaz JE, Etlin SM, Feinstein Z, Furman D, Garcia-Medina JS, Garrett-Bakelman F, Giacomello S, Gupta A, Hassanin A, Houerbi N, Irby I, Javorsky E, Jirak P, Jones CW, Kamal KY, Kangas BD, Karouia F, Kim J, Kim JH, Kleinman A, Lam T, Lawler JM, Lee JA, Limoli CL, Lucaci A, MacKay M, McDonald JT, Melnick AM, Meydan C, Mieczkowski J, Muratani M, Najjar D, Othman MA, Overbey EG, Paar V, Park J, Paul AM, Perdyan A, Proszynski J, Reynolds RJ, Ronca AE, Rubins K, Ryon KA, Sanders LM, Glowe PS, Shevde Y, Schmidt MA, Scott RT, Shirah B, Sienkiewicz K, Sierra M, Siew K, Theriot CA, Tierney BT, Venkateswaran K, Hirschberg JW, Walsh SB, Walter C, Winer DA, Yu M, Zea L, Mateus J, Beheshti A. (2024) A Second Space Age Spanning Omics, Platforms, and Medicine Across Orbits Nature PMID: 38862027

698. Ulicevic J, Shao Z, Jasnovidova O, Bressin A, Martyna Gajos, Ng AHM, Annaldasula S, Meierhofer D, Church GM, Busskamp V, Mayer A (2024) Uncovering the dynamics and consequences of RNA isoform changes during neuronal differentiation. Mol Syst Biol.

697. Poquérusse J, Brown GC, Gaillard C, Doughty C, Dalén L, Gallagher AJ, Wooller M, Zimov N, Church GM, Lamm B, Hysolli E (2024) Assessing contemporary Arctic habitat availability for a woolly mammoth proxy Nature Scientific Reports.

696. Ter-Ovanesyan D, Whiteman S, Gilboa T, Kowal EJK, Trieu W, Iyer S, Budnik B, Babila CM, Heimberg M, Burgess MW, Keshishian H, Carr SA, Regev A, Church GM, Walt DR(2024) Identification of markers for the isolation of neuron-specific extracellular vesicles Biorxiv.

695. CAGI Consortium, Jain S, ... Ball MP, Bobe JR, Church GM, ... Zook JM (2024) CAGI, the Critical Assessment of Genome Interpretation, establishes progress and prospects for computational genetic variant interpretation methods. Genome Biol. 25(1):53. PMID: 38389099

694. Appleton E, Hong K, Rodriguez C, Tanaka Y, Ashkenazy-Titelman A, Bhide K, Rasmussen-Ivey C, Ambriz-Pena X, Korover N, Bai H, Quieroz A, Nelson J, Rathod G, Knox G, Morgan M, Malviya N, Zhang K, Kehler J, KowalczykA, Bow A, McLendon B, Cantarel BL, James M, Mason CE, Gray C, Koehler K, Pearson V, Lamm B, Church G, Hysolli E (2024) Derivation of Elephant Pluripotent Stem Cells. Biorxiv

693. Smela MP, Kramme CC, Fortuna PRJ, Wolf B, Kavirayuni VS, Adams J, Ma C, Velychko S, Widocki U, Goel S, Chen T, Vincoff S, Dong E, Kohman RE, Kobayashi M, Shioda T, Church GM, Chatterjee P (2024) Rapid Human Oogonia-like Cell Specification via Combinatorial Transcription Factor-Directed Differentiation. Biorxiv.

692. Wang X, Li XF, Zhao J, Li Y, Shin SR, Ligresti G, Ng AHM, Bromberg JS, Church G, Lemos DR, Abdi R.(2024) Rapid Generation of Hpsc-Derived High Endothelial Venule Organoids with In Vivo Ectopic Lymphoid Tissue Capabilities. Adv Mater. PMID: 38306610

691. Stein J, Ericsson M, Nofal M, Magni L, Aufmkolk S, McMillan RB, Breimann L, Herlihy CP, Lee SD, Willemin A, Wohlmann J, Arguedas-Jimenez L, Yin P, Pombo A, Church GM, Wu CT (2024) Cryosectioning-enabled super-resolution microscopy for studying nuclear architecture at the single protein level. Biorxiv. PMID: 38370628

690. Sengupta A, Bandyopadhyay A, Sarkar D, Hendry JI, Schubert MG, Liu D, Church GM, Maranas CD, Pakrasi HB (2024) Genome streamlining to improve performance of a fast-growing cyanobacterium Synechococcus elongatus UTEX 2973. mBio 15(3):e0353023. Biorxiv. PMID: 38358263

699. Callisto A, Strutz J, Leeper K, Kalhor R, Church G, Tyo KEJ, Bhan N (2024) Post-translation digital data encoding into the genomes of mammalian cell populations. bioRxiv PMID: 38765976

689. Koeppel J, Ferreira R, Vanderstichele T, Riedmayr LM, Peets EM, Girling G, Weller J, Liberante FG, Ellis T, Church GM, Parts L (2024) Randomizing the human genome by engineering recombination between repeat elements. Biorxiv.

688a. Macip CC, Hasan R, Hoznek V, Kim J, Lu YR, Metzger LE 4th, Sethna S, Davidsohn N. Gene Therapy-Mediated Partial Reprogramming Extends Lifespan and Reverses Age-Related Changes in Aged Mice. Cell Reprogram. 26(1):24-32. PMID: 38381405

688. Baker D, Church G (2024) Protein design meets biosecurity. Science 383:349. PMID: 38271530

687. Islam M, Yang Y, Simmons AJ, Shah VM, Pavan MK, Xu Y, Tasneem N, Chen Z, Trinh LT, Molina P, Ramirez-Solano MA, Sadien I, Dou J, Chen K, Magnuson MA, Rathmell JC, Macara IG, Winton D, Liu Q, Zafar H, Kalhor R, Church GM, Shrubsole MJ, Coffey RJ, Lau KS (2023) Temporal recording of mammalian development and precancer. bioRxiv. PMID: 38187699

686. Li L, Hajam I, McGee JS, Tang Z, Zhang Y, Badey N, Mintzer E, Zhang Z, Liu GY, Church GM, Wang Y (2023) Comparative Transcriptome Analysis of Acne vulgaris, Rosacea, and Hidradenitis Suppurativa Supports High Dose Dietary Zinc as a Therapeutic Agent. MedRxiv. PMID: 38076983

685. Lei A, Yu H, Lu S, Lu H, Ding X, Tan T, Zhang H, Zhu M, Tian L, Wang X, Su S, Xue D, Zhang S, Zhao W, Chen Y, Xie W, Zhang L, Zhu Y, Zhao J, Jiang W, Church G, Chan FK, Gao Z, Zhang J (2023) A second-generation M1-polarized CAR macrophage with antitumor efficacy. Nature Immunology. PMID: 38012418

684a. Jiang K, Koob J, Chen XD, Krajeski RN, Zhang Y, Volf V, Zhou W, Sgrizzi SR, Villiger L, Gootenberg JS, Chen F, Abudayyeh OO (2022) Programmable eukaryotic protein synthesis with RNA sensors by harnessing ADAR. Nature Biotechnology 41:698–707. PMID: 36302988

684. MacCarthy CM, Wu G, Malik V, Menuchin-Lasowski Y, Velychko T, Keshet G, Fan R, Bedzhov I, Church GM, Jauch R, Cojocaru V, Schöler HR, Velychko S (2023) Highly cooperative chimeric super-SOX induces naive pluripotency across species. Cell Stem Cell. PMID: 38141611

683. Tierney BT, Kim J, Overbey EG, Ryon KA, Foox J, Sierra M, Bhattacharya C, Damle N, Najjar D, Park J, Garcia Medina S, Houerbi N, Meydan C, Wain Hershberg J, Qiu J, Kleinman A, Al Ghalith G, MacKay M, Afshin EE, Dhir R, Borg J, Gatt C, Brereton N, Readhead B, Beyaz S, Venkateswaran KJ, Blease K, Moreno J, Boddicker A, Zhao J, Lajoie B, Scott RT, Altomare A, Kruglyak S, Levy S, Church G, Mason CE (2023) Viral activation and ecological restructuring characterize a microbiome axis of spaceflight-associated immune activation. Research Square PMID: 37886447

682. Plesa AM, Jung S, Wang HH, Omar F, Shadpour M, Buentello DC, Perez-Matos MC, Horwitz N, Cai G, Ngian ZK, de Magalhaes CV, Wagers AJ, Mair WB, del Sol A, Church GM (2023) Transcriptomic reprogramming screen identifies SRSF1 as rejuvenation factor. BioRxiv

681. Volf V, Zhang S, Song KM, Qian S, Chen F, Church G (2023) Cryptography in the DNA of living cells enabled by multi-site base editing Biorxiv.

680. Jain NK, Ogden PJ, Church GM (2023) Comprehensive mutagenesis maps the effect of all single codon mutations in the AAV2 rep gene on AAV production. Biorxiv.

679. Wiegand DJ, Rittichier J, Meyer E, Lee H, Conway NJ, Ahlstedt D, Yurtsever Z, Rainone D, Kuru E, Church GM (2023) Template-Independent Enzymatic Synthesis of RNA Oligonucleotides. Biorxiv. Nature Biotech. PMID: 38997579

678. Meyer K, Ling KH, Yeo PL, Spathopoulou A, Drake D, Choi J, Aron L, Garcia-Corral M, Ko T, Lee EA, Tam JM, Perlis RH, Church GM, Tsai LH, Yankner BA (2023) Impaired neural stress resistance and loss of REST in bipolar disorder. Molecular Psychiatry. PMID: 37938767

677. Biggs BW, de Paz AM, Bhan NJ, Cybulski TR, Church GM, Tyo KEJ (2023) Engineering Ca2+-Dependent DNA Polymerase Activity. ACS Synth Biol. bioRxiv. PMID: 37856140

676. Smela MP, Pepe V, Church GM (2023) SeqVerify: A quality-assurance pipeline for whole-genome sequencing data. bioRxiv. PMID: 37829615

675a. Piechota S, Marchante M, Giovannini A, Paulsen B, Potts KS, Rockwell G, Aschenberger C, Noblett AD, Figueroa AB, Sanchez M, Barrachina F, Wiemer K, Guzman L, Belchin P, Smela MP, Fortuna PRJ, Chatterjee P, Tran ND, Kelk DA, Forti M, Marcinyshyn S, Smith T, McCulloh DH, Fernandez-Gonzalez MJ, Abittan B, Ortiz S, Klein JU, Klatsky P, Ordonez-Perez D, Kramme CC (2023) Human-induced pluripotent stem cell-derived ovarian support cell co-culture improves oocyte maturation invitro after abbreviated gonadotropin stimulation. Hum Reprod. PMID: 37815487

675. Anand RP, Layer JV, Heja D, Hirose T, Lassiter G, Firl DJ, Paragas VB, Akkad A, Chhangawala S, Colvin RB, Ernst RJ, Esch N, Getchell K, Griffin AK, Guo X, Hall KC, Hamilton P, Kalekar LA, Kan Y, Karadagi A, Li F, Low SC, Matheson R, Nehring C, Otsuka R, Pandelakis M, Policastro RA, Pols R, Queiroz L, Rosales IA, Serkin WT, Stiede K, Tomosugi T, Xue Y, Zentner GE, Angeles-Albores D, Chao JC, N. Crabtree JN, Harken S, Hinkle N, Lemos T, Li M, Pantano L, Stevens D, Subedar OD, Tan X, Yin S, Anwar IJ, Aufhauser D, Capuano S, Kaufman DB, Knechtle SJ, Kwun J, Shanmuganayagam D, Markmann JF, Church GM, Curtis M, Kawai T, Youd ME, Qin W (2023) Design and testing of a humanized porcine donor for xenotransplantation. Nature. PMID: 37821590

674. Smullen M, Olson MN, Reichert JM, Dawes P, Murray LF, Baer CE, Wang Q, Readhead B, Church GM, Lim ET, Chan Y (2023) Reliable multiplex generation of pooled induced pluripotent stem cells. Cell Reports Methods. PMID: 37751688

673. Chao G, Zukin S, Fortuna PRJ, Boettner B, Church GM (2023) Progress and limitations in engineering cellular adhesion for research and therapeutics. Trends Cell Biol. 12:S0962-8924(23)00140-X. PMID: 37580241

672. Elias KM, Ng NW, Dam KU, Milne A, Disler ER, Gockley A, Holub N, Seshan ML, Church GM, Ginsburg ES, Anchan RM (2023) Fertility restoration in mice with chemotherapy induced ovarian failure using differentiated iPSCs. EBioMedicine 94:104715. PMID: 37482511

671. Smidler AL, Paton DG, Church GM, Esvelt KM, Shaw WR, Catteruccia F (2023) CRISPR-mediated germline mutagenesis for genetic sterilization of Anopheles gambiae males. Scientific Reports 14:4057. bioRxiv. PMID: 38374393

670. Tierney BT, Foox J, Ryon KA, Butler D, Damle N, Young BG, Mozsary C, Babler KM, Yin X, Carattini Y, Andrews D, Solle NS, Kumar N, Shukla B, Vidovic D, Currall B, Williams SL, Schürer SC, Stevenson M, Amirali A, Beaver CC, Kobetz E, Boone MM, Reding B, Laine J, Comerford S, Lamar WE, Tallon JJ, Hirschberg JW, Proszynski J, Sharkey ME, Church GM, Grills GS, Solo-Gabriele HM, Mason CE (2023) Geospatially-resolved public-health surveillance via wastewater sequencing. medRxiv. 05.31.23290781. PMID: 37398062

669. Smullen M, Olson MN, Murray LF, Suresh M, Yan G, Dawes P, Barton NJ, Mason JN, Zhang Y, Fernandez-Fontaine AA, Church GM, Mastroeni D, Wang Q, Lim ET, Chan Y, Readhead B (2023) Modeling of mitochondrial genetic polymorphisms reveals induction of heteroplasmy by pleiotropic disease locus 10398AtoG. Sci Rep. 13(1):10405. PMID: 37369829

668. Rudolph A, Nyerges A, Chiappino-Pepe A, Landon M, Baas-Thomas M, Church G (2023) Strategies to identify and edit improvements in synthetic genome segments episomally. Nucleic Acids Research, gkad692 PMID: 37615546

667. Schubert MG, Tang TC, Goodchild-Michelman I, Ryon K, Henriksen J, Chavkin T, Wu Y, Miettinen T, Spatafora D, Turco G, Manalis S, Quatrini P, Milazzo M, Mason CE, Church GM, Tierney BT (2023) Cyanobacteria newly isolated from marine volcanic seeps display rapid sinking and robust high density growth. Biorxiv Applied and Industrial Microbiology.

666. Zhao L, Koseki SRT, Silversteim RA, Amrani N, Peng C, Kramme C, Savic N, Pacesa M, Rodríguez TC, Stan T, Tysinger E, Hong L, Yudistyra V, Ponnapati MR, Jacobson JM, Church GM, Jakimo N, Truant R, Jinek M, Kleinstiver BP, Sontheimer EJ, Chatterjee P (2023) PAM-Flexible Genome Editing with an Engineered Chimeric Cas9 Nature Comm. PMID: 36945419

665. Rutter LA, MacKay MJ, Cope H, Szewczyk NJ, Kim J, Overbey E, Tierney BT, Muratani M, Lamm B, Bezdan D, Paul AM, Church GM, Giacomello S, Mason CE (2024) Protective alleles and precision healthcare in crewed spaceflight. Nat Commun. 15(1):6158. PMID: 39039045

664. Jain VS, Schubert MG, Pritam P, Sarnaik AP, Jaiswal D, Church GM, Wangikar PP (2024) De novo genome assembly and pan-genome analysis of the fast-growing Indian isolates of Synechococcus elongatus: Potential chassis for bioproduction. The Microbe 2: 100048.

663. Park J, Overbey EG, Narayanan SA, Kim J, Tierney BT, Damle1 N, Deena Najjar D, Ryon KA, Proszynski J, Kleinman A, Hirschberg JW, MacKay M, Afshin EE, Meydan C, Granstein R, Gurvitch J, Hudson BM, Rininger A, Mullane S, Church SE, Church G, Beheshti A, Mateus J, Mason CE (2024) Spatial multi-omics of human skin reveals KRAS and inflammatory responses to spaceflight. Nat Commun. PMID: 38862494

662. Haspel G, Boyden ES, Brown J, Church G, Cohen N, Fang-Yen C, Flavell S, Goodman M, Hart AC, Hobert O, Kagias K, Lockery S, Lu Y, Marblestone A, Matelsky J, Pfister H, Rotstein H, Scholz M, Shlizerman E, Simeon Q, Skuhersky MA, Venkatachalam V, Yang GR, Yemini E, Zimmer M, Kording KP (2023) To reverse engineer an entire nervous system. Arxiv.

661. Sengupta A, Bandyopadhyay A, Schubert MG, Church GM, Pakrasi HB (2023) Antenna Modification in a Fast-Growing Cyanobacterium Synechococcus elongatus UTEX 2973 Leads to Improved Efficiency and Carbon-Neutral Productivity. Microbiol Spectr.

660. Vijg J, Schumacher B, Abakir A, Antonov M, Bradley C, Cagan A, Church G, Gladyshev VN, Gorbunova V, Maslov AY, Reik W, Sharifi S, Suh Y, Walsh K (2023) Mitigating age-related somatic mutation burden. Trends Mol Med. PMID: 37121869

659. Plesa AM, Shadpour M, Boyden E, Church GM (2023) Transcriptomic reprogramming for neuronal age reversal. Hum Genet. 1:1-10. PMID: 37004545

658. Dec E, Clement J, Cheng K, Church GM, Fossel MB, Rehkopf DH, Rosero-Bixby L, Kobor MS, Lin DT, Lu AT, Fei Z, Guo W, Chew YC, Yang X, Putra SED, Reiner AP, Correa A, Vilalta A, Pirazzini C, Passarino G, Monti D, Arosio B, Garagnani P, Franceschi C, Horvath S (2023) Centenarian clocks: epigenetic clocks for validating claims of exceptional longevity. Geroscience. PMID: 36964402

657. Nyerges A, Vinke S, Flynn R, Owen SV, Rand EA, Budnik B, Keen E, Narasimhan K, Marchand JA, Baas-Thomas M, Liu M, Chen K, Chiappino-Pepe A, Hu F, Baym M, Church GM (2023) Swapped genetic code prevents viral infections and gene transfer. Nature. 8-Jul-2022 Biorxiv. PMID: 36922599

656. Goodchild-Michelman IM, Church GM, Schubert MG, Tang TC (2023) Light and carbon: Synthetic biology toward new cyanobacteria-based living biomaterials. Mater Today Bio. PMID: 36846306

655. Dawes P, Murray LF, Olson MN, Barton NJ, Smullen M, Suresh M, Yan G, Zhang Y, Fernandez-Fontaine A, English J, Uddin M, Pak C, Church GM, Chan Y, Lim ET (2023) oFlowSeq: a quantitative approach to identify protein coding mutations affecting cell type enrichment using mosaic CRISPR-Cas9 edited cerebral organoids. Hum Genet. PMID: 36877372

654. Ter-Ovanesyan D, Gilboa T, Budnik B, Nikitina A, Whiteman S, Lazarovits R, Trieu W, Kalish D, Church GM, Walt DR(2023) Improved Isolation of Extracellular Vesicles by Removal of Both Free Proteins and Lipoproteins Biorxiv. Elife. PMID: 37252755

653. Smela MP, Kramme C, Fortuna P, Adams J, Su R, Dong E, Kobayashi M, Brixi G, Kavirayuni VS, Tysinger E, Kohman RE, Shioda T, Chatterjee P, Church GM (2022) Directed Differentiation of Human iPSCs to functional ovarian granulosa-like cells via transcription factor overexpression. eLife. Biorxiv PMID: 36803359

652. Jo C, Zhang J, Tam JM, Church GM, Khalil AS, Segre D, Tang TC(2023) Unlocking the magic in mycelium: Using synthetic biology to optimize filamentous fungi for biomanufacturing and sustainability. Materials Today Bio 19: 100560. PMID: 36756210

651. An B, Wang Y, Huang Y, Wang X, Liu Y, Xun D, Church GM, Dai Z, Yi X, Tang TC, Zhong C (2022) Chem Rev. Engineered Living Materials For Sustainability. PMID: 36512650

650. Oliynyk RT, Church GM (2022) Commun Biol. 21;5(1):1393. Efficient modification and preparation of circular DNA for expression in cell culture PMID: 36543890

649. Resnik DB, Medina RF, Gould F, Church G, Kuzma J (2022) Pathog Glob Health. 22:1-10. Genes drive organisms and slippery slopes. PMID: 36562087

648. Perry E, Weber J, Pataranutaporn P, Volf V, Gonzalez LM, Nejad S, Angleton C, Chen JE, Gabo A, Jammalamadaka MSS, Kuru E, Fortuna P, Rico A, Sulich K, Wawrzyniak D, Jacobson J, Church G, Kong D (2022) How to grow (almost) anything: a hybrid distance learning model for global laboratory-based synthetic biology education. Nat Biotechnol. PMID: 36510008

647. Church G (2022) Picogram-Scale Interstellar Probes via Bioinspired Engineering. Astrobiology. 22(12):1452-1458.PMID: 36475966

646. Wang H, Li L, Ma J, Chi L, Yang J, Tao G, Wu J, Zhao Z, Church GM (2022) An Interpretable Deep Embedding Model for Few and Imbalanced Biomedical Data. IEEE J Biomed Health Inform. PMID: 36409803

645. Liu S, Li L, Zhang F, van Sambeek B, Appleton E, Ng A, Khoshakhlagh P, Chen Y, Garcia-Corral M, Wu CT, Huang J, Tan Y, Chao G, Aach J, Tam J, Lim E, Raychaudhuri S, Church GM (2022) Characterizing gene regulation and hiPSC differentiation from pooled transcription factors library. Bioriv.

644. Appleton E, Tao J, Fonseca G, Liu S, Glass C, Church G (2022) Machine-guided cell-fate engineering. Biorxiv.

643. Hyun I, Scharf-Deering JC, Sullivan S, Aach JD, Arlotta P, Baum ML, Church GM, Goldenberg A, Greely HT, Khoshakhlagh P, Kohman RE, Lopes M, Lowenthal C, Lu A, Ng AHM, Pasca SP, Paulsen B, Pigoni M, Scott CT, Silbersweig DA, Skylar-Scott MA, Truog RD, Lunshof JE (2022) How collaboration between bioethicists and neuroscientists can advance research. Nat Neurosci. doi: 10.1038/s41593-022-01187-2. PMID: 36258039

642. Yeo NC, Church GM (2022) Perturbation of Gene Regulation by Genome Editing. Methods Mol Biol. 2594:59-68. doi: 10.1007/978-1-0716-2815-7_5. PMID: 36264488

641. Yilmaz S, Nyerges A, John van der Oost J, Church GM, Claassens NJ (2022) Towards next-generation cell factories by rational genome-scale engineering. Nature Catalysis

640. De Los Angeles A, Regenberg A, Mascetti V, Benvenisty N, Church G, Deng H, Izpisua Belmonte JC, Ji W, Koplin J, Loh YH, Niu Y, Pei D, Pera M, Pho N, Pinzon-Arteaga C, Saitou M, Silva JCR, Tao T, Trounson A, Warrier T, Zambidis ET (2022) Why it is important to study human-monkey embryonic chimeras in a dish. Nature Methods. PMID: 35879609

639. Lim D, Zhou Q, Cox KJ, Law BK, Lee M, Kokkonda P, Sreekanth V, Pergu R, Chaudhary SK, Gangopadhyay SA, Maji B, Lai S, Amako Y, Thompson DB, Subramanian HKK, Mesleh MF, Dančík V, Clemons PA, Wagner BK, Woo CM, Church GM, Choudhary A (2022) A general approach to identify cell-permeable and synthetic anti-CRISPR small molecules. Nature Cell Biology. PMID: 36396978

638. Bhattarai-Kline S, Lear SK, Fishman CB, Lopez SC, Lockshin E, Schubert MG, Nivala J, Church G, Shipman SL (2022) Recording gene expression order in DNA by CRISPR addition of retron barcodes.. Nature. PMID: 35896746

637. Goodwin DR, Vaughan A, Leible D, Alon S, Henry GL, Cheng A, Chen X, Zhang R, Xue AG, Wassie AT, Sinha A, Bando Y, Kajita A, Marblestone AH, Zador AM, Boyden ES, Church GM, Kohman RE (2022) Expansion Sequencing of RNA Barcoded Neurons in the Mammalian Brain: Progress and Implications for Molecularly Annotated Connectomics. Biorxiv.

636. Kramme C, Smela MP, Wolf B, Fortuna PR, Brixi G, Palepu K, Dong E, Adams JL, Bhat S, Koseki S, Tysinger E, Stan T, Kohman RE, Liu S, Kobayashi M, Shioda T, Church GM, Chatterjee P (2022) Efficient Human Germ Cell Specification from Stem Cells via Combinatorial Expression of Transcription Factors. Biorxiv.

635. Zheng Z, Xu L, Dou H, Zhou Y, Feng X, He X, Tian Z, Song L, Gao Y, Mo G, Hu J, Zhao H, Wei H, Church GM, Yang L (2022) Multiplex CRISPR strategy targeting viral genome for agriculture and clinical use. Biorxiv.

634. Oliynyk R, Church GM, et al. (2022) Efficient Modification and Preparation of Circular DNA for Expression in Cell Culture. Biorxiv.

633. Rudolph A, Nyerges A, Chiappino-Pepe A, Landon M, Baas-Thomas M, Church GM (2022) Strategies to Identify and Edit Improvements in Synthetic Genome Segments Episomally. Biorxiv

632. Lim ET, Chan Y, Dawes P, Guo X, Erdin S, Tai DJC, Liu S, Reichert JM, Burns MJ, Chan YK, Chiang JJ, Meyer K, Zhang X, Walsh CA, Yankner BA, Raychaudhuri S, Hirschhorn JN, Gusella JF, Talkowski ME, Church GM (2022) Orgo-Seq integrates single-cell and bulk transcriptomic data to identify cell type specific-driver genes associated with autism spectrum disorder. Nat Commun. 2022 Jun 10;13(1):3243. PMID: 35688811

631. Pan X, Qu K, Yuan H, Xiang X, Anthon C, Pashkova L, Liang X, Han P, Corsi G, Xu F, Liu P, Zhong J, Zhou Y, Ma T, Jiang H, Liu J, Wang J, Jessen N, Bolund L, Yang H, Xu X, Church G, Gorodkin J, Lin L, Luo Y (2022) Massively Targeted Evaluation Of Therapeutic Crispr Off-Targets In Cells. Nature Comm. 13(1):4049. PMID: 35831290

630. Baas-Thomas MS, Oehm SB, Ostrov N, Church GM (2022) Characterization of ColE1 Production for Robust tolC Plate Dual-Selection in E. coli. ACS Synth Biol. PMID: 35666547

629. Li Y, Hu X, Lin R, Zhou G, Zhao L, Zhao D, Zhang Y, Li W, Zhang Y, Ma P, Ren H, Liao X, Niu P, Wang T, Zhang X, Wang W, Gao R, Li Q, Church G, He J, Chen Y (2022) Single-cell landscape reveals active cell subtypes and their interaction in the tumor microenvironment of gastric cancer. Theranostics. 12(8):3818-3833. PMID: 35664061

628. Ping Z, Chen S, Zhou G, Huang X, Zhu SJ, Zhang H, Lee HH, Lan Z, Cui J, Chen T, Zhang W, Yan Hg, Xu X, Church GM, Shen Y (2022) Towards practical and robust DNA-based data archiving using the yin–yang codec system. Nature Computational Science 2:234–242 PMID:

627. Chao G, Wannier TM, Travis C, Borders NC, Appleton E, Chadha A, Lebar T, Church GM (2022) helixCAM: A Platform for Programmable Cellular Assembly in Bacteria and Human Cells Cell 185: 3551-3567 Biorxiv PMID: 36055250

626. Kobayashi M, Kobayashi M, Odajima J, Shioda K, Hwang YS, Sasaki K, Chatterjee P, Kramme C, Kohman RE, Church GM, Loehr AR, Weiss RS, Jüppner H, Gell JJ, Lau CC, Shioda T (2022) Expanding homogeneous culture of human primordial germ cell-like cells maintaining germline features without serum or feeder layers. Stem Cell Reports. PMID: 35148847

625. Tian S, Liu Y, Appleton E, Wang H, Church GM, Dong M (2022) Targeted intracellular delivery of Cas13 and Cas9 nucleases using bacterial toxin-based platforms. Cell Reports. PMID: 35263584

624. Fuller CW, Padayatti PS, Abderrahim H, Adamiak L, Alagar N, Ananth N, Baek J, Chinni S, Choi C, Delaney KJ, Dubielzig R, Frkanec J, Garcia C, Gardner C, Gebhardt D, Geiser T, Gutierrez Z, Hall D, Hodges AP, Hou G, Jain S, Jones T, Lobaton R, Majzik Z, Marte A, Mohan P, Mola II P, Mudondo P, Mullinix J, Nguyen T, Ollinger F, Orr S, Ouyang Y, Pan P, Park N, Porras D, Prabhu K, Reese C, Ruel T, Sauerbrey T, Sawyer JR, Sinha P, Tu J, Venkatesh A, VijayKumar S, Zheng L, Jin S, Tour JM, Church GM, Mola PW, Merriman B (2022). Molecular Electronics Sensors on a Scalable CMOS Chip: A Platform for Single-Molecule Measurement of Binding Kinetics & Enzyme Activity. PNAS 119 (5) e2112812119. PMID: 35074874

623. Hanley BP, Brewer K, Church G (2021) Results of a 5 year N-of-1 GHRH gene therapy experiment. Rejuvenation Res. PMID: 34841890

622. Grishin D, Raisaro JL, Troncoso-Pastoriza JR, Obbad K, Quinn K, Misbach M, Gollhardt J, Sa J, Fellay J, Church GM, Hubaux JP (2021) Citizen-Centered, Auditable, and Privacy-Preserving Population Genomics. Nature Computational Science 1:192–198 Bioriv 2019 PMID: 38183193

621. Lane J, Keasling J, Church G, Arnold F (2021) ABLC Forum: Aspirations for a Fragile Planet. Industrial Biotechnology 17:3

620. Xiang X, Qu K, Pan X, Wang J, Han P, Dong Z, Liu L, Zhong J, Ma T, Wang Y, Yu J, Zhao X, Li S, Xu Z, Wang J, Zhang X, Jiang H, Xu F, Zou L, Teng H, Liu X, Xu X, Wang J, Yang H, Bolund L, Church GM, Lin L, Gorodkin J, Luo Y (2021) Massively parallel quantification of CRISPR editing in cells by TRAP-seq enables better design of Cas9, ABE, CBE gRNAs of high efficiency and accuracy. Biorxiv.

619. Kramme C, Plesa AM, Wang HH, Wolf B, Smela MP, Guo X, Kohman RE, Chatterjee P, Church GM (2021) MegaGate: A toxin-less gateway molecular cloning tool. STAR Protoc. 2(4):100907. PMID: 34746865

618. Sinai S, Jain N, Church GM, Kelsic ED (2021) Generative AAV capsid diversification by latent interpolation. Biorxiv.

617. Ter-Ovanesyan D, Norman M, Lazarovits R, Trieu W, Lee JH, Church GM, Walt DR (2021) Framework for Rapid Comparison of Extracellular Vesicle Isolation Methods. Biorxiv. eLife PMID: 34783650

616. Aznauryan E, Yermanos A, Kinzina E, Kapetanovic E, Milanova D, Church GM, Reddy ST (2021) Discovery and validation of novel human genomic safe harbor sites for gene and cell therapies. Cell Reports Methods. Biorxiv PMID: 35474867

615. Chowdhury R, Bouatta N, Biswas S, Rochereau C, Church GM, Sorger PK, AlQuraishi M (2021) Single-sequence protein structure prediction using a language model and deep learning. Biorxiv. Nature Biotech. (2022) "RGN2 outperforms AlphaFold2 and RoseTTAFold on orphan proteins &... designed proteins ... [million]-fold reduction in compute time"

614. Chen Y, Hysolli E, Chen A, Casper S, Liu S, Yang K, Liu C, Church G (2022) Multiplex base editing to convert TAG into TAA codons in the human genome Biorxiv. Nature Comm. PMID: 35918324

613. Kramme C, Plesa AM, Wang HH, Wolf B, Smela MP, Guo X, Kohman RE, Chatterjee P, Church GM (2021) An integrated pipeline for mammalian genetic screening. Cell Reports Methods. PMID: 35474898

612. Kim HS, Kim C, Church G, Bhak J (2021) PGP1 personal genome assembly - a hybrid assembly dataset using ONT’s PromethION and PacBio’s HiFi sequencing. Biorxiv.

611. Sun B, Yang X, Hou F, Yu X, Wang Q, Oh HS, Raja P, Pesola JM, Vanni EAH, McCarron S, Morris-Love J, Ng AHM, Church GM, Knipe DM, Coen DM, Pan D (2021) Regulation of host and virus genes by neuronal miR-138 favours herpes simplex virus 1 latency. Nature Microbiol. PMID: 33558653

610. Robinson-McCarthy LR, Mijalis AJ, Filsinger GT, de Puig H, Donghia NM, Schaus TE, Rasmussen RA, Ferreira R, Lunshof JE, Chao G, Ter-Ovanesyan D, Dodd O, Kuru E, Sesay AM, Rainbow J, Pawlowski AC, Wannier TM, Angenent-Mari NM, Najjar D, Yin P, Ingber DE, Tam JM, Church GM (2021) Laboratory-Generated DNA Can Cause Anomalous Pathogen Diagnostic Test Results. Microbiol Spectr. PMID: 34523989

609. Stork DA, Squyres GR, Kuru E, Gromek KA, Rittichier J, Jog A, Burton BM, Church GM, Garner EC, Kunjapur AM (2021) Designing efficient genetic code expansion in Bacillus subtilis to gain biological insights. Nat Commun. 14;12(1):5429. PMID: 34521822

608. Liu S, Striebel J, Pasquini G, Ng AHM, Khoshakhlagh P, Church GM, Busskamp V (2021) Neuronal Cell-type Engineering by Transcriptional Activation. Front. Genome Editing. PMID: 34713262

607. Zaki MM, Lesha E, Said K, Kiaee K, Robinson-McCarthy L, George H, Hanna A, Appleton E, Liu S, Ng AHM, Khoshakhlagh P, Church GM (2021) Cell therapy strategies for COVID-19: Current approaches and potential applications. Sci Adv. PMID: 34380619

606. Chao G, Travis C, Church G. (2021) Measurement of large serine integrase enzymatic characteristics in HEK293 cells reveals variability and influence on downstream reporter expression. FEBS J. PMID: 34043859

605. Chen Y, Hysolli E, Chen A, Casper S, Liu S, Yang K, Liu C, Church G (2021) Multiplex base editing to convert TAG into TAA codons in the human genome. Biorxiv. doi.org/10.1101/2021.07.13.452007

604. Bhattarai-Kline S, Lockshin E, Schubert MG, Nivala J, Church G, Shipman SL (2021) Reconstructing transcriptional histories by CRISPR acquisition of retron-based genetic barcodes. Biorxiv.

603. Yonker LM, Gilboa T, Ogata AF, Senussi Y, Lazarovits R, Boribong BP, Bartsch YC, Loiselle M, Rivas MN, Porritt RA, Lima R, Davis JP, Farkas EJ, Burns MD, Young N, Mahajan VS, Hajizadeh S, Lopez XIH, Kreuzer J, Morris R, Martinez EE, Han I, Griswold K, Barry NC, Thompson DB, Church G, Edlow AG, Haas W, Pillai S, Arditi M, Alter G, Walt DR, Fasano A (2021) Multisystem inflammatory syndrome in children is driven by zonulin-dependent loss of gut mucosal barrier. J Clin Invest. 131(14):e149633. PMID: 34032635

602. Garruss AS, Collins KM, Church GM (2021) Deep representation learning improves prediction of LacI-mediated transcriptional repression. PNAS 118(27):e2022838118. PMID: 34187888

601. Kunjapur AM, Napolitano MG, Hysolli E, Noguera K, Appleton EM, Schubert MG, Jones MA, Iyer S, Mandell DJ, Church GM (2021) Synthetic auxotrophy remains stable after continuous evolution and in coculture with mammalian cells. Sci Adv. 7(27):eabf5851. PMID: 34215581

600. Jaijyan DK, Selariu A, Cruz-Cosme R, Tong M, Yang S, Church G, Kekich D, Fallah A, Sadoshima J, Tang Q, Parrish E, Zhu H (2021) New intranasal and injectable gene therapy for healthy life extension Biorxiv. PNAS. PMID: 35537048

599. Abong AE, Bosley K, Casebourn C, Chan P, Chen J, Chen M, Church G, Cumbers J, de Wouters T, Dewey-Hagborg H, Duportet X, Elizondo A, Farrar J, Gates B, Gatto F, Giwa S, Godec J, Gold S, LeProust E, Lunshof J, Martucci E, Heath MM, Mellad J, Oudova V, Oxman N, Regev A, Richardson S, Scott CT, Sherkow J, Sibener L, Tarragó T, Terry S, Venter JC, Wang S, Wickramasekara S, Yadi H, Yang L, Zhao B. (2021) Voices of biotech leaders. Nat Biotechnol. 39(6):654-660. PMID: 34113035

598. Xiang X, Corsi GI, Anthon C, Qu K, Pan X, Liang X, Han P, Dong Z, Liu L, Zhong J, Ma T, Wang J, Zhang X, Jiang H, Xu F, Liu X, Xu X, Wang J, Yang H, Bolund L, Church GM, Lin L, Gorodkin J, Luo Y (2021) Enhancing CRISPR-Cas9 gRNA efficiency prediction by data integration and deep learning. Nat Commun. 12(1): 3238. PMID: 34050182

597. Dai M, Ma W, Kang H, Sonnett M, Church GM, Kirschner M (2021) One-Seq: A Highly Scalable Sequencing-Based Diagnostic for SARS-CoV-2 and Other Single-Stranded Viruses. MedRxiv.

596. Liu S, Punthambaker S, Iyer EPR, Ferrante T, Goodwin D, Fürth D, Pawlowski AC, Jindal K, Tam JM, Mifflin L, Alon S, Sinha A, Wassie AT, Chen F, Cheng A, Willocq V, Meyer K, Ling KH, Camplisson CK, Kohman RE, Aach J, Lee JH, Yankner BA, Boyden ES, Church GM (2021) Barcoded Oligonucleotides Ligated On RNA Amplified for Multiplexed and parallel In Situ analyses.(BOLORAMIS) Nucleic Acids Res. PMID: 33693773

595. Leeper K, Kalhor K, Vernet A, Graveline A, Church GM, Mali P, Kalhor R (2021) Lineage barcoding in mice with homing CRISPR. Nat Protoc. PMID: 33692551

594. Jung S, Appleton E, Ali M, Church G, del Sol A (2021) A computer-guided design tool to increase the efficiency of cellular conversions. Nature Comm. PMID: 33712564

593. Ping Y, Church GM (2021) Delivery of biomacromolecules for therapeutic genome editing. Adv Drug Deliv Rev. PMID: 33482978

592. Chan YK, Wang SK, Chu CJ, Copland DA, Letizia AJ, Costa Verdera H, Chiang JJ, Sethi M, Wang MK, Neidermyer WJ Jr, Chan Y, Lim ET, Graveline AR, Sanchez M, Boyd RF, Vihtelic TS, Inciong RGCO, Slain JM, Alphonse PJ, Xue Y, Robinson-McCarthy LR, Tam JM, Jabbar MH, Sahu B, Adeniran JF, Muhuri M, Tai PWL, Xie J, Krause TB, Vernet A, Pezone M, Xiao R, Liu T, Wang W, Kaplan HJ, Gao G, Dick AD, Mingozzi F, McCall MA, Cepko CL, Church GM (2021) Engineering adeno-associated viral vectors to evade innate immune and inflammatory responses. Science Transl Med. PMID: 33568518

591. Yang L, Church G, Zhao HY, Huang L, Yang G, Gao Y, Wei HJ (2021) Germline Genome Engineering. PNAS 118(22):e2004836117. PMID: 34050015

590. Kemp L, Adam L, Boehm CR, Casagrande R, Church G, Dando M, Dijkeng A, Evans N, Hammond R, Hills K, Holt L, Kuiken T, Markotić A, Millett P, Napier JA, Nelson C, Ó hÉigeartaigh S, Osbourne A, Palmer M, Patron NJ, Perello E, Piyawattanametha W, Restrepo-Schild V, Rios-Rajas C, Rhodes C, Roessing A, Scott D, Shapira P, Simuntala C, Smith R, Sundaram L, Takano E, Uttmark M, Veerakumarasivam A, Wintle B, Zahra N, Sutherland WJ (2020) Bioengineering Horizon Scan 2020. eLIfe

589. Tierney BT, He Y, Church GM, Segal E, Kostic AD, Chirag J, Patel CJ (2020) The predictive power of the microbiome exceeds that of genome-wide association studies in discrimination of human disease. Biorxiv.

588. Heller D, Vingron M, Church G, Li H, Garg S (2020) SDip: A novel graph-based approach to haplotype-aware assembly based structural variant calling in targeted segmental duplications sequencing. Biorxiv.

587. Stedman H, Herzog R, Gao G, Church G, Chan YK (2020) High dose systemic gene therapy: emerging trends on safety and efficacy. Cell & Gene Therapy Insights 2020; 6(4), 569–575

586. Ostrov N, Nyerges A, Chiappino-Pepe A, Rudolph A, Baas-Thomas M, Church GM (2020) Synthetic genomes with altered genetic codes. Current Opinion in Systems Biology 24:32-40.

585. Venkatakrishnan AJ, Kayal N, Anand P, Badley AD, Church GM, Soundararajan V (2020) Benchmarking evolutionary tinkering underlying human-viral molecular mimicry shows multiple host pulmonary-arterial peptides mimicked by SARS-CoV-2. Cell Death Discov. 6(1):96. PMID: 34599152

584. Lim ET, Chan Y, Burns MJ, Guo X, Erdin S, Tai DJC, Reichert JM, Chan YK, Chiang JJ, Meyers K, Zhang X, Walsh CA, Yankner BA, Raychaudhuri S, Hirschhorn JN, Gusella JF, Talkowski ME, Church GM (2020) Identifying cell type specific driver genes in autism-associated copy number loci from cerebral organoids. Biorxiv.

583. Bryant D, Bashir A, Sinai S, Jain N, Ogden P, Riley P, Church G, Colwell L, Kelsic E (2020) Massively parallel deep diversification of AAV capsid proteins by machine learning. Nature Biotech. PMID: 33574611

582. Alley EC, Turpin M, Liu AB, Kulp-McDowall T, Swett J, Edison R, Von Stetina SE, Church GM, Esvelt KM (2020) A machine learning toolkit for genetic engineering attribution to facilitate biosecurity. Nature Comm. PMID: 33293535

581. DeLisi C, Patrinos A, MacCracken M, Drell D, Annas G, Arkin A, George Church, Cook-Deegan R, Jacoby H, Lidstrom M, Melillo J, Milo R, Paustian K, Reilly J, Roberts R, Segrè D, Solomon S, Woolf D, Wullschleger SD, Yang X (2020) The Role of Synthetic Biology in Atmospheric Greenhouse Gas Reduction: Prospects and Challenges. BioDesign Research.

580. Lewis G, Jordan JL, Relman DA, Koblentz GD, Leung J, Dafoe A, Nelson C, Epstein GL, Katz R, Montague M, Alley EC, Filone CM, Luby S, Church GM, Millett P, Esvelt KM, Cameron EE, Inglesby TV (2020) The biosecurity benefits of genetic engineering attribution. Nat Commun. PMID: 33293537

579. Palla M, Punthambaker S, Stranges B, Vigneault F, Nivala J, Wiegand D, Ayer A, Craig T, Gremyachinskiy D, Franklin H, Sun S, Pollard J, Trans A, Arnold C, Schwab C, Mcgaw C, Sarvabhowman P, Dalal D, Thai E, Amato E, Lederman I, Taing M, Kelley S, Qwan A, Fuller CW, Roever S, Church GM (2020). Multiplex Single-Molecule Kinetics of Nanopore-Coupled Polymerases. ACS Nano. PMID: 33370106

578. Payne AC, Chiang ZD, Reginato P, Mangiameli SM, Murray EM, Yao CC, Markoulaki S, Earl AS, Labade A, Jaenisch R, Church GM, Boyden ES, Buenrostro JD, Chen F (2020) In situ genome sequencing resolves DNA sequence and structure in intact biological samples. Science. PMID: 33384301

577. Long KC, Alphey L, Annas GJ, Bloss CS, Campbell KJ, Champer J, Chen CH, Choudhary A, Church GM, Collins JP, Cooper KL, Delborne JA, Edwards OR, Emerson CI, Esvelt K, Evans SW, Friedman RM, Gantz VM, Gould F, Hartley S, Heitman E, Hemingway J, Kanuka H, Kuzma J, Lavery JV, Lee Y, Lorenzen M, Lunshof JE, Marshall JM, Messer PW, Montell C, Oye KA, Palmer MJ, Papathanos PA, Paradkar PN, Piaggio AJ, Rasgon JL, Rašić G, Rudenko L, Saah JR, Scott MJ, Sutton JT, Vorsino AE, Akbari OS. (2020) Core commitments for field trials of gene drive organisms. Science. PMID: 33335055

576. Estep PW, Church GM (2020 ) Transparency is key to ethical vaccine research. Science. PMID: 33335056

575. Lu Y, Brommer B, Tian X, Krishnan A, Meer M, Wang C, Vera DL, Zeng Q, Yu D, Bonkowski MS, Yang JH, Zhou S, Hoffmann E, Karg MM, Schultz MB, Davidsohn N, Korobkina E, Chwalek K, Rajman L, Church GM, Hochedlinger K, Gladyshev VN, Horvath S, Levine ME, Gregory-Ksander M, Ksander BR, He Z, Sinclair DA (2020) Reprogramming to recover youthful epigenetic information and restore vision. Nature. 588(7836):124-129. PMID: 33268865

574. Garg S, Fungtammasan A, Carroll A, Chou M, Schmitt A, Zhou X, Mac S, Peluso P, Hatas E, Ghurye J, Maguire J, Mahmoud M, Cheng H, Heller D, Zook JM, Moemke T, Marschall T, Sedlazeck FJ, Aach J, Chin CS, Church GM, Li H (2020) Chromosome-scale, haplotype-resolved assembly of human genomes. Nat Biotechnol. PMID: 33288905

573. Chatterjee P, Ponnapati M, Kramme C, Plesa A, Church GM, Jacobson JM (2020) Targeted Intracellular Degradation of SARS-CoV-2 via Computationally-Optimized Peptide Fusions. Commun Biol. 3(1):715. PMID: 33230174

572. Wannier T, Ciaccia P, Ellington A, Filsinger G, Isaacs F, Javanmardi K, Jones M, Kunjapur A, Nyerges A, Pal C, Schubert M, Church G (2020) Recombineering and MAGE. Nature Rev. Meth. Primers.

571. Robinson-McCarthy LR, Mijalis AJ, Filsinger GT, de Puig H, Donghia NM, Schaus TE, Rasmussen RA, Ferreira R, Lunshof JE, Chao G, Ter-Ovanesyan D, Dodd O, Kuru E, Sesay AM, Rainbow J, Pawlowski AC, Wannier TM, Yin P, Collins JJ, Ingber DE, Tam JM, Church GM (2020) New recommended policies for pathogen surveillance testing of researchers and improved stewardship of diagnostic DNA. Anomalous COVID-19 tests hinder researchers Science. PMID: 33446547

570. Angrist M, Barrangou R, Baylis F, Brokowski C, Burgio G, Caplan A, Chapman CR, Church GM, Cook-Deegan R, Cwik B, Doudna JA, Evans JH, Greely HT, Hercher L, Hurlbut JB, Hynes RO, Ishii T, Kiani S, Lee LH, Levrier G, Liu DR, Lunshof JE, Macintosh KL, Mathews DJH, Meslin EM, Mills PHR, Montoliu L, Musunuru K, Nicol D, O'Neill H, Qiu R, Ranisch R, Sherkow JS, Soni S, Terry S, Topol E, Williamson R, Zhang F, Davies K (2020) Reactions to the National Academies/Royal Society Report on Heritable Human Genome Editing. CRISPR J. PMID: 33095048

569. Venkatakrishnan AJ, Kayal N, Anand P, Badley AD, Church GM, Soundararajan V (2020) Benchmarking evolutionary tinkering underlying human-viral molecular mimicry shows multiple host pulmonary-arterial peptides mimicked by SARS-CoV-2. Cell Death Discov. 2020 Oct 2;6:96. PMID: 33024578

568. Yue Y, Xu W, Kan Y, Zhao HY, Zhou Y, Song X, Wu J, Xiong J, Goswami D, Yang M, Lamriben L , Xu M, Qi Zhang , Luo Y, Guo J, Mao S, Jiao D, Nguyen TD, Li Z, Layer JV, Li M, Paragas V, Youd ME, Sun Z, Ding Y, Wang W, Dou H, Song L, Wang X, Le L, Fang X, George H, Anand R, Wang SY, Westlin WF, Guell M, Markmann J, Qin W, Gao Y, Wei H, Church GM, Yang L (2020) Extensive Germline Genome Engineering in Pigs. Nature Biomed. Eng. biorxiv. PMID: 32958897

567. Dryzek JS, Nicol D, Niemeyer S, Pemberton S, Curato N, Bächtiger A, Batterham P, Bedsted B, Burall S, Burgess M, Burgio G, Castelfranchi Y, Chneiweiss H, Church G, Crossley M, de Vries J, Farooque M, Hammond M, He B, Mendonça R, Merchant J, Middleton A, Rasko J, Van Hoyweghen I, Vergne A (2020) Global Citizen Deliberation on Genome Editing. Science. PMID: 32943515

566. Norman M, Ter-Ovanesyan D, Trieu W, Lazarovits R, Kowal EJK, Lee JH, Chen-Plotkin AS, Regev A, Church GM, Walt DR (2020) L1CAM is not Associated with Extracellular Vesicles in Human Cerebrospinal Fluid or Plasma. Biorxiv. Nat Methods. 18(6):631-634. PMID: 34092791

565. Gopalkrishnan N, Punthambaker S, Schaus TE, Church GM, Yin P (2020) A DNA nanoscope that identifies and precisely localizes over a hundred unique molecular features with nanometer accuracy. Biorxiv.

564. Schubert MG, Goodman DB, Wannier TM, Kaur D, Farzadfard F, Lu TK, Shipman SL, Church GM (2020-1) High throughput functional variant screens via in-vivo production of single-stranded DNA. PNAS Biorxiv PMID: 33906944

563. MacKay MJ, Hooker AC, Afshinnekoo E, Salit M, Kelly J, Feldstein JV, Haft N, Schenkel D, Nambi S, Cai Y, Zhang F, Church G, Dai J, Wang CL, Levy S, Huber J, Ji HP, Kriegel A, Wyllie AL, Mason CE (2020) The COVID-19 XPRIZE and the need for scalable, fast, and widespread testing Nature Biotech. PMID: 32820257

562. Ng AHM, Khoshakhlagh P, Arias JER, Pasquini G, Wang K, Swiersy A, Shipman S, Appleton E, Kiaee K, Kohman R, Vernet K, Dysart M, Leeper K, Saylor W, Huang J, Graveline A, Taipale J, Hill D, Vidal M, Melero-Martin JM, Busskamp V, Church GM (2020) A comprehensive library of human transcription factors for cell fate engineering. Nature Biotech. Nov-2020. PMID: 33257861

561. Weber JA, Park SG, Luria V, Jeon S, Kim HM, Jeon Y, Bhak Y, Jun JH, Kim SW, Hong WH, Lee S, Cho YS, Karger A, Cain JW, Manica A, Kim S, Kim JH, Edwards JS, Bhak J, Church GM (2020) The whale shark genome reveals how genomic and physiological properties scale with body size. PNAS. PMID: 32753383

560. Jeon S, Bhak Y, Choi Y, Jeon Y, Kim S, Jang J, Jang J, Blazyte A, Kim C, Kim Y, Shim J, Kim N, Kim YJ, Park SG, Kim J, Cho YS, Park Y, Kim HM, Kim BC, Park NH, Shin ES, Kim BC, Bolser D, Manica A, Edwards JS, Church G, Lee S, Bhak J (2020) Korean Genome Project: 1094 Korean personal genomes with clinical information. Science Advances 6(22):eaaz7835. PMID: 32766443

559. Kuru E, Määttälä RM, Noguera K, Stork DA, Narasimhan K, Rittichier J, Wiegand D, Church GM (2020) Release factor inhibiting antimicrobial peptides improve non-standard amino acid incorporation in wild-type bacterial cells. ACS Chem Biol. 2020 Jul 17;15(7):1852-1861. PMID: 32603088

558. Afonin KA, Dobrovolskaia MA, Church G, Bathe M (2020) Opportunities, Barriers, and a Strategy for Overcoming Translational Challenges to Therapeutic Nucleic Acid Nanotechnology. ACS Nano. PMID: 32706238

557. Eroshenko N, Gill T, Keaveney M, Church GM, Trevejo J, Rajaniemi H (2020) Implications of antibody-dependent enhancement of infection for SARS-CoV-2 countermeasures. Nature Biotech. PMID: 32504046

556. Marchand JA, Smela MDP, Jordan THH, Narasimhan K, Church G (2020) TBDB: A database of structurally annotated T-box riboswitch-tRNA pairs. Biorxiv. Nucleic Acids Res. PMID: 32882008

555. Skylar-Scott MA, Huang J, Lu A, Ng AHM, Duenki T, Liu S, Nam LL, Damaraju S, Church GM, Lewis JA (2020-2) Orthogonally induced differentiation of stem cells for the programmatic patterning of vascularized organoids and bioprinted tissues Nat Biomed Eng. Biorxiv. PMID: 35332307

554. Alon S, Goodwin DR, Sinha A, Wassie AT, Chen F, Daugharthy E, Bando Y, Kajita A, Xue A, Marrett K, Prior R, Cui Y, Payne AC, Yao C, Suk H, Wang R, Yu C, Tillberg P, Reginato P, Pak N, Liu S, Punthambaker S, Iyer EPR, Kohman R, Miller J, Lein E, Lako A, Cullen N, Rodig S, Helvie K, Abravanel D, Wagle N, Johnson B, Klughammer J, Slyper M, Waldman J, Jané-Valbuena J, Rozenblatt-Rosen O, Regev A, IMAXT Consortium, Church GM, Marblestone AH, Boyd ES (2020) Expansion Sequencing: Spatially Precise In Situ Transcriptomics in Intact Biological Systems. Biorxiv. Science. PMID: 33509999

553. Vaidyanathan P, Appleton E, Tran D, Vahid A, Church G, Densmore D (2020) Algorithms for the selection of fluorescent reporters Biorxiv. Commun. Biol. PMID: 33500520

552. Turczyk BM, Busby M, Martin AL, Daugharthy ER, Myung D, Terry RC, Inverso SA, Church GM (2020) Spatial Sequencing: A Perspective. J. Biomolecular Techniques 31. PMID: 32382252

551. Nguyen HQ, Chattoraj S, Castillo D, Nguyen SC, Nir G, Martins NMC, Reginato PR, Hannan M, Church GM, Daugharthy ER, Marti-Renom MA, Wu CT (2020) 3D mapping and accelerated super-resolution imaging of the human genome using in situ sequencing. Nature Methods. PMID: 32719531

550. Kelsic ED, Church GM (2019) Challenges and opportunities of machine-guided capsid engineering for gene therapy. Cell & Gene Therapy Insights 2019; 5(4), 523-536.

549. Wan T, Niu D, Wu C, Xu FJ, Church G, Wan T, Ping Y (2019) Material Solutions for Delivery of CRISPR/Cas-Based Genome Editing Tools: Current Status and Future Outlook. Materials today. doi.org/10.1016/j.mattod.2018.12.003

548. Ping Z, Chen S, Huang X, Zhu SJ, Chai C, Zhang H, Lee H, Zhou G, Chiu TY, Chen T, Yang H, Xu X, Church GM, Shen Y (2019) Towards Practical and Robust DNA-based Data Archiving by Codec System Named ‘Yin-Yang’. Biorxiv.

547. Castanon O, Smith CJ, Khoshakhlagh P, Ferreira R, Güell M, Said K, Yildiz R, Dysart M, Wang S, Thompson D, Myllykallio H, Church GM (2019) CRISPR mediated Biocontainment. Biorxiv.

546. Kohman RE, Church GM (2020) Fluorescent in situ sequencing of DNA barcoded antibodies. Biorxiv.

545. Filsinger G, Wannier T, Pedersen FB, Zhang J, Lutz I, Stork D, Debnath A, Gozzi K, Kuchwara H, Volf V, Wang S, Rios X, Gregg C, Lajoie M, Shipman S, Aach J, Laub M, Church G (2020-1) Characterizing the portability of RecT-mediated oligonucleotide recombination. Biorxiv. Nat Chem Biol. PMID: 33462496

544. Niu D, Ma X, Yuan T, Niu Y, Xu Y, Sun Z, Ping Y, Li W, Zhang J, Wang T, Church GM (2020) Porcine genome engineering for xenotransplantation. Advanced Drug Delivery Reviews; PMID: 32275950

543. Hanley BP, Keen S, Church G (2020) A call for a three tiered pandemic public health strategy in context of SARS-CoV-2. Rejuvenation Res. doi: 10.1089/rej.2020.2363. PMID: 32539623

542. Zhang L, Tian L, Dai X, Yu H, Wang J, Lei A, Zhao W, Zhu Y, Sun Z, Zhang H, Church G, Huang H, Weng Q, Zhang J (2020) Induced Pluripotent Stem Cell-derived CAR-Macrophage Cells with Antigen-dependent Anti-Cancer Cell Functions for Liquid and Solid Tumors. Biorxiv J Hematol Oncol. PMID: 33176869

541. Wang K, Lin RZ, Hong X, Ng A, Lee CN, Neumeyer J, Wang G, Wang X, Ma M, Pu W, Church G, Melero-Martin J. (2020) Robust differentiation of human pluripotent stem cells into endothelial cells via temporal modulation of ETV2 with modified mRNA. Biorxiv. Sci Adv. 2020 Jul 24;6(30):eaba7606 PMID: 32832668

540. Stokes JM, Yang K, Swanson K, Jin W, Cubillos-Ruiz A, Donghia NM, MacNair CR, French S, Carfrae LA, Bloom-Ackerman Z, Tran VM, Chiappino-Pepe A, Badran AH, Andrews IW, Chory EJ, Church GM, Brown ED, Jaakkola TS, Barzilay R, Collins JJ (2020) A Deep Learning Approach to Antibiotic Discovery. Cell. 180(4):688-702.e13. PMID: 32084340

539. Lee H, Wiegand DJ, Griswold K, Punthambaker S, Chun H, Kohman RE, Church GM (2020) Photon-directed Multiplexed Enzymatic DNA Synthesis for Molecular Digital Data Storage. Biorxiv. Nat Comm. PMID: 33067441

538. Davis J, Bisson-Filho A, Kadyrov D, De Kort T, Biamonte M, Thattai M, Thutupalli S, Church G (2020) In vivo multi-dimensional information-keeping in Halobacterium salinarum. Biorxiv

537. Biswas S, Alley EC, Khimulya G, Esvelt KM, Church GM (2020) Low-N protein engineering with data-efficient deep learning. Nature Methods. Biorxiv. PMID: 33828272

536. Wannier TM, Nyerges A, Kuchwara HM, Czikkely M, Balogh D, Filsinger GT, Borders NC, Gregg CJ, Lajoie MJ, Rios X, Pál C, Church GM (2019) Improved bacterial recombineering by parallelized protein discovery. Biorxiv.

535. Martinez-Redondo P, Guillen-Guillen I, Davidsohn N, Wang C, Prieto J, Kurita M, Hatanaka F, Reddy P, Zhong C, Hernandez-Benitez R, Hishida T, Sakamoto A, Schwarz M, Nemeth A, Rodriguez-Esteban C, Shojima K, Huang L, Shokhirev M, Nuñez-Delicado E, Guillen-Vicente I, Rodriguez-Iñigo E, Lopez-Alcorocho JM, Guillen-Vicente M, Guillen-Garcia P, Church G, Belmonte JCI (2020) αKLOTHO and sTGFβR2 treatment counteract the osteoarthritic phenotype developed in a rat model. Protein Cell. doi: 10.1007/s13238-019-00685-7. PMID: 31950348

534. Angenent-Mari NM, Garruss AS, Soenksen LR, Church GM, Collins JJ (2019) Deep Learning for RNA Synthetic Biology. Biorxiv. Nature Comm. PMID: 33028812

533. Davies K, Church GM (2019) Radical Technology Meets Radical Application. CRISPR J. 2(6):346-351. PMID: 31860351

532. Yue Y, Kan Y, Xu W, Zhao HY, Zhou Y, Song X, Wu J, Xiong J, Goswami D, Meng Yang , Lamriben L , Xu M, Zhang Q, Luo Y, Guo J, Mao S, Jiao D, Nguyen TD, Li Z, Layer JV, Li M, Paragas V, Youd ME, Sun Z, Ding Y, Wang W, Dou H, Song L, Wang X, Le L, Fang X, George H, Anand R, Wang SY, Westlin WF, Guell M, Markmann J, Qin W, Gao Y, Wei H, Church GM, Yang L (2019) Extensive Mammalian Germline Genome Engineering Biorxiv. Nature Biomed. Eng. PMID: 32958897

529s. Tierney BT, Kostic AD, Patel CJ, Church GM, et al. (2019) Individual privacy in human microbiome and genomic data; in prep

529s. Rittichier J, Kuru E, West A, Booherb G, Yevsikova A, Church GM, VanNiewhenze M (2019) Design and synthesis of a photoinduced electron-transfer quenched fluorogenic amino acid. in prep.

531. Bobe J, Meyer MN, Church GM (2019) Privacy and Agency are Critical to a Flourishing Biomedical Research Enterprise: Misconceptions About the Role of CLIA. SSRN FL Law Review.

530. Ogden PJ, Kelsic ED, Sinai S, Church GM (2019) Comprehensive AAV capsid fitness landscape reveals a viral gene and enables machine-guided design. Science. PMID: 31780559

529. Kalhor K, Church GM (2019) Single-Cell CRISPR-Based Lineage Tracing in Mice. Biochemistry. doi: 10.1021/acs.biochem.9b00688. PMID: 31730337

528. Zhang HS, Schaefer A, Wang Y, Hodge R, Blake D, Diehl J, Papageorge A, Stachler M, Liao J, Zhou J, Wu Z, Fahire A, de Klerk L, Derks S, Pierobon M, Hoadley K, Wang T, Church G, Wong KK, Petricoin E, Cox A, Lowy D, Der C, Bass A (2019) Gain-of-Function RHOA Mutations Promote Focal Adhesion Kinase Activation and Dependency in Diffuse Gastric Cancer. Cancer Discovery. PMID: 31771969

527. Calimport SRG, Bentley BL, Stewart C, Pawelec G, Scuteri A, Lakatta EG, Marchant G, Fleming GA, Nikolich K, Antebi A, Vinciguer M, Slack C, Magalhães JP, Harries L, Chen D, Conboy M, Conboy I, Small G, Gil J, Richardson A, Rosen C, Wyss-Coray T, Goronzy J, Steinman L, Montine T, Campisi J, Church G (2019) To help aging populations, classify organismal senescence. Science. PMID: 31672885

526. Zullo J, Drake D, Aron L, O’Hern P, Dhamne SC, Davidsohn N, Mao CA, Klein WH, Rotenberg A, Bennett DA, Church GM, Colaiácovo MP, Yankner BA (2019) Regulation of Lifespan by Neural Excitation and REST. Nature 574(7778):359-364. PMID: 31619788

525. Godehardt AW, Fischer N, Rauch P, Gulich B, Boller K, Church GM, Tönjes RR (2019) PERV inactivated pig cells are resistant to pig endogenous retroviral superinfection. Xenotransplantation. PMID: 31667881

524. Ostrov N, Beal J, Ellis T, Gordon DB, Karas BJ, Lee HH, Lenaghan S, Schloss JA, Stracquadanio G, Trefzer A, Bader JS, Church GM, Coelho CM, Efcavitch JW, Guell M, Mitchell LA, Nielsen AAK, Peck B, Smith AC, Stewart CN, Tekotte H (2019) Technological challenges and milestones for writing genomes. Science. 366(6463):310-312. PMID: 31624201

523. Garg S, Fungtammasan A, Carroll A, Chou M, Schmitt A, Zhou X, Mac S, Peluso P, Hatas E, Ghurye J, Maguire J, Mahmoud M, Cheng H, Heller D, Zook JM, Moemke T, Marschall T, Sedlazeck FJ, Aach J, Chin CS, Church GM, Li H (2019) Efficient chromosome-scale haplotype-resolved assembly of human genomes. Biorxiv.

522. Appleton E, Mehdipour N, Daifuku T, Briers D, Haghighi I, Moret M, Chao G, Wannier T, Chiappino-Pepe A, Belta C, Church GM (2019) Genetic design automation for autonomous formation of multicellular shapes from a single cell progenitor. Biorxiv.

521. Grishin D, Obbad K, Church GM (2019) Data privacy in the age of personal genomics; Nat Biotechnol. doi: 10.1038/s41587-019-0271-3. PMID: 31537915

520. Davidsohn N, Pezzone M, Vernet A, Graveline A, Oliver D, Slomovic S, Punthambaker S, Sun X, Liao R, Bonventre JV, Church G (2019) A single combination gene therapy treats multiple age-related diseases. PNAS (4-Nov-2019). PMID: 31685628

519. Lu Y, Krishnan A, Brommer B, Tian X, Meer M, Vera DL, Wang C, Yu D, Zeng Q, Bonkowski MS, Yang JH, Hoffmann E, Zhou S, Korobkina E, Davidsohn N, Schultz MB, Chwalek K, Rajman L, Church GM, Hochedlinger K, Gladyshev VN, Horvath S, Gregory-Ksander M, Ksander BR, He Z, Sinclair DA (2019) Reversal of ageing- and injury-induced vision loss by Tet-dependent epigenetic reprogramming. Biorxiv.

518. Bhan NJ, Callisto A, Strutz J, Glaser J, Kalhor R, Boyden E, Church G, Kording K, Tyo EJK (2019-21). Recording Temporal Signals with Minutes Resolution Using Enzymatic DNA Synthesis. J Am Chem Soc. PMID: 34591459 Biorxiv.

517. Zhavoronkov A, Church G (2019) The Advent of Human Life Data Economics Trends in Molecular Medicine. PMID: 31257078

516. Saka SK, Wang Y, Kishi JY, Zhu A, Zeng Y, Xie W, Kirli K, Yapp C, Cicconet M, Beliveau BJ, Lapan SW, Yin S, Lin M, Boyden ES, Kaeser PS, Pihan G, Church GM, Yin P (2019) Immuno-SABER enables highly multiplexed and amplified protein imaging in tissues Nature Biotechnology. PMID: 31427819

515. Zook JM, Hansen NF, Olson ND, Chapman LM, Mullikin JC, Xiao C, Sherry S, Koren S, Phillippy AM, Boutros PC, Ebrahim SM, Huang V, Rouette A, Alexander N, Mason CC, Hajirasouliha IC, Ricketts CC, Lee J, Tearle R, Fiddes IT, Barrio AM, Wala J, Carroll A, Ghaffari NC, Rodriguez OL, Bashir A, Jackman S, Farrell JJ, Wenger AM, Alkan C, Soylev A, Schatz MC, Garg S, Church G, Marschall T, Chen K, Fan X, English AC, Rosenfeld JD, Zhou W, Mills RE, Sage JM, Davis JR, Kaiser MD, Oliver JS, Catalano AP, Spies N, Chaisson MJ, Sedlazeck FJ, Salit M, Genome in a Bottle Consortium (2019) A robust benchmark for germline structural variant detection BioRxiv. Nat Biotechnol. PMID: 32541955

514. Xiao Y, Muhuri M, Li S, Qin W, Xu G, Luo L, Li J, Letizia AJ, Wang SK, Chan YK, Wang C, Fuchs SP, Wang D, Su Q, Nahid MA, Church GM, Farzan M, Yang L, Wei Y, Desrosiers RC, Mueller C, Tai PW, Gao G (2019) Circumventing cellular immunity by miR142-mediated regulation sufficiently supports rAAV-delivered OVA expression without activating humoral immunity. JCI Insight. PMID: 31112525

513. Lee HH, Kalhor R, Goela N, Bolot J, Church GM. (2019) Terminator-free template-independent enzymatic DNA synthesis for digital information storage. Nat Commun. 2019 Jun 3;10(1):2383. PMID: 31160595

512. Alley EC, Khimulya G, Biswas S, AlQuraishi M, Church GM (2019) Unified rational protein engineering with sequence-only deep representation learning. Nat Methods PMID: 31636460 Biorxiv

511. Lee HH, Ostrov N, Wong BG, Gold MA, Khalil AS, Church GM (2019) Functional genomics of the rapidly replicating bacterium Vibrio natriegens by CRISPRi. Nature Microbiology. PMID: 30962569

510. Strauss SK, Schirman D, Jona G, Brooks AN, Kunjapur AM, Nguyen Ba AN, Flint A, Solt A, Mershin A, Dixit A, Yona AH, Csörgő B, Busby BP, Hennig BP, Pál C, Schraivogel D, Schultz D, Wernick DG, Agashe D, Levi D, Zabezhinsky D, Russ D, Sass E, Tamar E, Herz E, Levy ED, Church GM, Yelin I, Nachman I, Gerst JE, Georgeson JM, Adamala KP, Steinmetz LM, Rübsam M, Ralser M, Klutstein M, Desai MM, Walunjkar N, Yin N, Hefetz NA, Jakimo N, Snitser O, Adini O, Kumar P, Soo Hoo Smith R, Zeidan R, Hazan R, Rak R, Kishony R, Johnson S, Nouriel S, Vonesch SC, Foster S, Dagan T, Wein T, Karydis T, Wannier TM, Stiles T, Olin-Sandoval V, Mueller WF, Bar-On YM, Dahan O, Pilpel Y (2019) Evolthon: A community endeavor to evolve lab evolution PLoS Biol. PMID: 30925180

509. Mackey TK , Clauson K, Kuo TT, Gummadi B, Church G, Grishin D, Obbad K, Barkovich R, Palombini M (2019) Fit-for-Purpose?: Challenges and Opportunities for Applications of Blockchain Technology in the Future of Healthcare. BMC Medicine. PMID: 30914045

508. Garg S, Aach J, Li H, Sebenius I, Durbin R, Church G (2019) A haplotype-aware de novo assembly of related individuals using pedigree graph. Bioinformatics 36(8):2385-2392.Biorxiv. PMID: 31860070

507. Smith CJ, Castanon O, Said K, Khoshakhlagh P, Volf V, Hornick A, Ferreira R, Wu CT, Güell M, Myllykallio H, Church GM (2020) Enabling large-scale genome editing by reducing DNA nicking. Nucleic Acids Res Biorxiv. PMID: 32315033

506. Church GM (2019) A Bill of Rights for the Age of Artificial Intelligence OneZero.Medium. Also as a book Chapter in Possible Minds.

505. Minev D, Guerra R, Kishi JY, Smith C, Krieg E, Said K, Hornick A, Sasaki HM, Filsinger G, Beliveau BJ, Yin P, Church GM, Shih WM (2019) Rapid and scalable production of single-stranded DNA. Nucleic Acids Res 2019 Nov 12. pii: gkz998. doi: 10.1093/nar/gkz998. Biorxiv PMID: 31713635

504. Caldwell BJ, Zakharova E, Filsinger GT, Wannier TM, Hempfling JP, Chun-Der L, Pei D, Church GM, Bell CE (2019) Crystal structure of the Redβ C-terminal domain in complex with λ Exonuclease reveals an unexpected homology with λ Orf and an interaction with Escherichia coli single stranded DNA binding protein. Nucleic Acids Res doi: 10.1093/nar/gky1309. PMID: 30624736

503. Scheiman J, Luber JM, Chavkin TA, MacDonald T, Tung A, Pham LD, Wibowo MC, Wurth RC, Punthambaker S, Tierney BT, Yang Z, Hattab M, Avila-Pacheco J, Clish CB, Lessard S, Church GM, Kostic AD (2019) Meta-omics analysis of elite athletes identifies a performance-enhancing microbe that functions via lactate metabolism. Nature medicine. PMID: 31235964

502. Zoltick ES, Linderman MD, McGinniss MA, Ramos E, Ball MP, Church GM, Leonard DGB, Pereira S, McGuire AL, Caskey CT, Sanderson SC, Schadt EE, Nielsen DE, Crawford SD, Green RC (2018) Predispositional Genome Sequencing in Healthy Adults: Design, Participant Characteristics, and Early Outcomes of the PeopleSeq Consortium. Genome Medicine. PMID: 30808425

501. Wiegand DJ, Lee HH, Ostrov N, Church GM (2018) Cell-free protein expression using the rapidly growing bacterium Vibrio natriegens. Jove. J.Vis.Exp. PMID: 30933074

500. Brunk E, Chang RL, Xia J, Hefzi H, Yurkovich J, Kim D, Buckmiller E, Wang H, Yang C, Palsson BO, Church GM, Lewis NE (2018) Characterizing post-translational modifications in prokaryotic metabolism using a multi-scale workflow. PNAS. PMID: 30301795

499. Saka SK, Wang Y, Kishi JY, Zhu A, Zeng Y, Xie W, Kirli K, Yapp C, Cicconet M, Beliveau BJ, Lapan SW, Yin S, Lin M, Boyden ES, Kaeser PS, Pihan G, Church GM, Yin P (2018) Highly multiplexed in situ protein imaging with signal amplification by Immuno-SABER. Biorxiv.

498. Grishin D, Obbad K, Estep P, Quinn K, Zaranek SW, Zaranek AW, Vandewege W, Clegg T, César N, Cifric M, Church G (2018) Accelerating Genomic Data Generation and Facilitating Genomic Data Access Using Decentralization, Privacy-Preserving Technologies and Equitable Compensation. Blockchain in HealthCare Today.

497. Meyer K, Feldman HM, Lu T, Drake D, Lim ET, King-Hwa L, Bishop NA, Pan Y, Seo J, Su SC, Church GM, Tsai LH, Yankner BA (2018) REST and Neural Gene Network Dysregulation in iPSC Models of Alzheimer’s Disease. Cell Reports PMID: 30699343

496. Biswas S, Kuznetsov G, Ogden PJ, Conway NJ, Adams RP, Church GM (2018) Toward machine-guided design of proteins Biorxiv.

495. Nageshwaran S, Chavez A, Yeo NC, Guo X, Lance-Byrne A, Tung A, Collins JJ, Church GM (2018) CRISPR Guide RNA Cloning for Mammalian Systems J Vis Exp. & Jove PMID: 30346403

494. Sinai S, Kelsic E, Church GM, Nowak MA (2017) Variational auto-encoding of protein sequences. Arxiv.

493. Brunk E, Chang RL, Xia J, Hefzi H, Yurkovich JT, Kim D,Buckmiller E, Wang H, Chen Yang C, Palsson BO, Church GM, Lewis NE (2017) Systemic post-translational control of bacterial metabolism regulates adaptation in dynamic environments. Biorxiv.

492. Porsdam Mann S, Mitchell C, Bradley VJ, Chou MF, Church G, Mann M, Donders Y, Porsdam H (2017) Advocating for science progress as a human right. PNAS 115(43):10820-10823. doi.org/10.1073/pnas.1816320115 PMID: 30352870

491. Wiegand D, Lee HH, Ostrov N, Church GM (2018) Establishing a cell-free Vibrio natriegens expression system. ACS Synth Biol. Biorxiv. PMID: 30160938

490. Madison AC, Royal MW, Vigneault F, Chen L, Griffin PB, Horowitz M, Church GM, Fair RB (2017) A Scalable Device for Automated Microbial Electrotransformation in a Digital Microfluidic Platform. ACS Synth Biol. 2017 Jun 7. PMID: 28569062

489. Musah S, Dimitrakakis N, Camacho DM, Church GM, Ingber DE (2018) Directed differentiation of human induced pluripotent stem cells into mature kidney podocytes and establishment of a Glomerulus Chip. Nat Protoc. 13(7):1662-1685. PMID: 29995874

488. Lubner JM, Balsbaugh JL, Church GM, Chou MF, Schwartz D (2018) Characterizing Protein Kinase Substrate Specificity Using the Proteomic Peptide Library (ProPeL) Approach. Curr Protoc Chem Biol. 10(2):e38. PMID: 29927115

487. Hanley BP, Bains W, Church G (2018) Review of Scientific Self-experimentation: ethics history, regulation, scenarios, and views among ethics committees and prominent scientists. Rejuvenation Res PMID: 29926769

486. Clarke R, Heler R, MacDougall MS, Yeo NC, Chavez A, Regan M, Hanakai L, Church GM, Marraffini LA, Merrill BJ (2018) Enhanced bacterial immunity and mammalian genome editing via RNA polymerase-mediated via RNA-Polymerase-Mediated Dislodging of Cas9 from Double-Strand DNA Breaks. Mol Cell. 71(1):42-55. PMID: 29979968

485. Saha K, Hurlbut JB, Jasanoff S, Ahmed A, Appiah A, Bartholet E, Baylis F, Bennett G, Church G, Cohen IG, Daley G, Finneran K, Hurlbut W, Jaenisch R, Lwoff L, Kimes JP, Mills P, Moses J, Park BS, Parens E, Salzman R, Saxena A, Simmet H, Simoncelli T, Snead OC, Rajan KS, Truog RD, Williams P, Woopen C(2018) Building Capacity for a Global Genome Editing Observatory: Institutional Design. Trends Biotechnol. PMID: 29891181

484. Lee HH, Kalhor R, Goela N, Bolot J, Church GM (2018) Enzymatic DNA synthesis for digital information storage. Biorxiv.

483. McDonald D, Hyde E, Debelius JW, Morton JT, Gonzalez A, Ackermann G, Aksenov AA, Behsaz B, Brennan C, Chen Y, Goldasich LD, Dorrestein PC, Dunn RR, Fahimipour AK, Gaffney J, Gilbert JA, Gogul G, Green JL, Hugenholtz P, Humphrey G, Huttenhower C, Jackson MA, Janssen S, Jeste DV, Jiang L, Kelley ST, Knights D, Kosciolek T, Ladau J, Leach J, Marotz C, Meleshko D, Melnik AV, Metcalf JL, Mohimani H, Montassier E, Navas-Molina J, Nguyen TT, Peddada S, Pevzner P, Pollard KS, Rahnavard G, Robbins-Pianka A, Sangwan N, Shorenstein J, Smarr L, Song S, Spector T, Swafford AD, Thackray VG, Thompson LR, Tripathi A, Vázquez-Baeza Y, Vrbanac A, Wischmeyer P, Wolfe E, Zhu Q, [ Mann AE, Amir A, Frazier A, Martino C, Lebrilla C, Lozupone C, Lewis Jr. CM, Raison C, Zhang C, Lauber CL, Warinner C, Lowry CA, Callewaert C, Bloss C, Willner D, Galzerani DD, Gonzalez DJ, Mills DA, Chopra D, Gevers D, Berg-Lyons D, Sears DD, Wendel D, Lovelace E, Pierce E, TerAvest E, Bolyen E, Bushman FD, Wu GD, Church GM, Saxe G, Holscher HD, Ugrina I, German JB, Caporaso JG, Wozniak JM, Kerr J, Ravel J, Lewis JD, Suchodolski JS, Jansson JK, HamptonMarcell JT, Bobe J, Raes J, Chase JH, Eisen JA, Monk J, Clemente JC, Petrosino J, Goodrich J, Gauglitz J, Jacobs J, Zengler K, Swanson KS, Lewis K, Mayer K, Bittinger K, Dillon L, Zaramela LS, Schriml LM, Dominguez-Bello MG, Jankowska MM, Blaser M, Pirrung M, Minson M, Kurisu M, Ajami N, Gottel NR, Chia N, Fierer N, White O, Cani PD, Gajer P, Strandwitz P, Kashyap P, Dutton R, Park RS, Xavier RJ, Mills RH, Krajmalnik-Brown R, Ley R, Owens SM, Klemmer S, Matamoros S, Mirarab S, Moorman S, Holmes S, Schwartz T, Eshoo-Anton TW, Vigers T, Pandey V, Treuren WV, Fang X, Xu ZZ, Jarmusch A, Geier J, Reeve N, Silva R, Kopylova E, Nguyen D, Sanders K, Salido Benitez RA, Heale AC, Abramson M, Waldispühl J, Butyaev A, Drogaris C, Nazarova E, Ball M, Gunderson B,] Knight R (2018) American Gut: an Open Platform for Citizen-Science Microbiome Research . mSystems PMID: 29795809

482. Hurlbut JB, Jasanoff S , Saha K, Ahmed A, Appiah A, Bartholet E, Baylis F, Bennett G, Church G, Cohen IG, Daley G, Finneran K, Hurlbut W, Jaenisch R, Lwoff L, Kimes JP, Mills P, Moses J, Park BS, Parens E, Salzman R, Saxena A, Simmet H, Simoncelli T, Snead OC, Rajan KS, Truog RD, Williams P, Woopen C (2018) Building Capacity for a Global Genome Editing Observatory: Conceptual Challenges. Trends in Biotechnology. PMID: 29871776

481. Frumkin I, Lajoie MJ, Gregg, Hornung G, Church GM, Pilpel Y (2018) Codon Usage of Highly Expressed Genes Affects Proteome-Wide Translation Efficiency. PNAS PMID: 29735666

480. de Paz AM, Cybulski TR, Marblestone AH, Zamft BM, Church GM, Boyden ES, Kording KP, Tyo KEJ (2018) High-resolution mapping of DNA polymerase fidelity using nucleotide imbalances and next-generation sequencing. Nucleic Acids Res PMID: 29718339

479. Henikoff S, Church GM (2018) Simultaneous discovery of cell-free DNA and the nucleosome ladder. Genetics 209: 27-29. PMID: 29716984

478. Farahany NA, Greely HT, Koroshetz W, Gordon JA, Hyman S, Koch C, Eberwine J, Grady C, Pașca SP, Arlotta P, Sestan N, Ramos K, Rommelfanger KS, Lunshof JE, Iyer EPR, Hyun I, Johnson LSM, Capestany BH, Church GM, Huang H, Bernat J, Ting J, Song H (2018) The ethics of experimenting with human brain tissue. Nature 556(7702):429-432. PMID: 29691509

477. Chan Y, Chan YK, Goodman DB, Chavez A, Lim ET, Church GM (2018) Multiplexed testing of pooled donor cells using SNPs and NGS. Genome Medicine 10:31. PMID: 29673390

476. Møller HD, Lin L, Xi X, Petersen TS, Huang J, Yang L, Nielsen K, Jensen UB, Zhang X, Xu X, Wang J, Yang H, Church GM, Bolund L, Regenberg B, Luo Y (2018) Circularization of genes and chromosome by CRISPR in human cells. Nucleic Acids Res BioRxiv PMID: 30551175

475. Yeo NC, Chavez A, Lance-Byrne A, Chan Y, Menn D, Milanova D, Kuo CC, Guo X, Sharma S, Tung A, Cecchi RJ, Tuttle M, Pradhan S, Lim ET, Davidsohn N, Ebrahimkhani MR, Collins JJ, Lewis NE, Kiani S, Church GM (2018) An enhanced CRISPR repressor for targeted mammalian gene regulation. Nat Methods PMID: 30013045

474. Vora S, Cheng J, Xiao R, VanDusen N, Quintino L, Pu W, Vandenberghe L, Chavez A, Church G (2018) Rational design of a compact CRISPR-­‐Cas9 activator for AAV-mediated delivery. Biorxiv.

473. Iyer EP, Punthambaker S, Liu S, Jindal K, Farrell M, Murn J, Ferrante T, Rudnicki S, Kohman RE, Wassie AT, Goodwin D, Chen F, Alon S, Sinha A, Milanova D, Aron L, Camplisson C, Skrynnyk A, Reginato PL, Conway N, Aach J, Yankner B, Boyden ES, Church GM (2018) Barcoded oligonucleotides ligated on RNA amplified for multiplex and parallel in-situ analyses Biorxiv

472. Church GM (2018) Genome Reading and Editing Tools for All Leapsmag.

471. Kalhor R, Kalhor K, Leeper K, Graveline A, Mali P, Church GM (2018) A homing CRISPR mouse resource for barcoding and lineage tracing. Science. Biorxiv. PMID: 30093604

470. Wang Y, Xie W, Kohman RE, Church GM (2018) Multiplexed imaging using same species primary antibodies with signal amplification. BioRxiv

469. Grishin D, Obbad K, Estep P, Cifric M, Zhao Y, Church G (2018) Blockchain-enabled genomic data sharing and analysis platform v4.52.

468. Nivala J, Shipman SL, Church GM (2018) Spontaneous CRISPR loci generation in vivo by non-canonical spacer integration. Nature Microbiol. PMID: 29379209

467. Juárez JF, Lecube-Azpeitia B, Brown SL, Church GM (2017). Biosensor libraries harness large classes of binding domains for allosteric transcription regulators. Nature Communications BioRxiv doi: 10.1101/193029. PMID: 30082754

466. Kunjapur AM, Stork DA, Kuru E, Vargas-Rodriguez O, Landon M, Söll D, Church GM (2017) Engineering post-translational proofreading to discriminate non-standard amino acids. BioRxiv PNAS PMID: 29301968

465. Hoehe MR, Herwig R, Mao Q, Peters BA, Drmanac R, Church GM, Huebsch T (2019) Significant abundance of cis configurations of mutations in diploid human genomes. Nucleic Acids Res Biorxiv 2017. PMID: 30698752

464. Thompson DB, Aboulhouda S, Hysolli E, Smith C, Wang S, Castanon O, Church GM (2017) The future of multiplexed eukaryotic genome engineering. ACS Chem. Biol. PMID: 29241002

463. Noble C, Adlam B, Church GM, Esvelt KM, Nowak MA (2017) Current CRISPR gene drive systems are likely to be highly invasive in wild populations BioRxiv. Elife. PMID: 29916367

462. Church GM (2017) Compelling Reasons for Repairing Human Germlines NEJM 377:1909-1911. PMID: 29141159

461. Güell M, Niu D, Kan Y, George H, Wang T, Lee IH, Wang G, Church G, Yang L. (2017) PERV inactivation is necessary to guarantee absence of pig-to-patient PERVs transmission in xenotransplantation. Xenotransplantation. 2017 Nov;24(6). doi: 10.1111/xen.12366. PMID: 29171094

460. Labun K, Guo X, Chavez A, Church G, Gagnon J, Valen E (2017) Automated analysis of genuine CRISPR editing events with ampliCan. Genome Res. Biorxiv PMID: 30850374

534a. Chen H, Liu S, Padula S, Lesman D, Griswold K, Lin A, Zhao T, Marshall JL, Chen F (2019) Efficient, continuous mutagenesis in human cells using a pseudo-random DNA editor. Nature Biotech. PMID: 31844291

521a. Holtzman SH, Cohen R, Levin JM, Maraganore J; Signatories to the Statement (2019) Chinese scientists and US leadership in the life sciences. Nat Biotechnol. 37(11):1261-1263. PMID: 31582856

514a. Kishi JY, Lapan SW, Beliveau BJ, West ER, Zhu A, Sasaki HM, Saka SK, Wang Y, Cepko CL, Yin P (2019) SABER amplifies FISH: enhanced multiplexed imaging of RNA and DNA in cells and tissues. Nat Methods. 16(6):533-544. PMID: 31110282

494a. Marie R, Pedersen JN, Bærlocher L, Koprowska K, Pødenphant M, Sabatel C, Zalkovskij M, Mironov A, Bilenberg B, Ashley N, Flyvbjerg H, Bodmer WF, Kristensen A, Mir KU (2018) Single-molecule DNA-mapping and whole-genome sequencing of individual cells. PNAS 115(44):11192-11197. PMID: 30322920

474a. Chu WK, Edge P, Lee HS, Bansal V, Bafna V, Huang X, Zhang K (2017) Ultraaccurate genome sequencing and haplotyping of single human cells PNAS 114(47):12512-12517. Suppl. Seq. data PMID: 29078313

469a. Wolpe PR, Rommelfanger KS, Delegates of the BEINGS Working Groups. (2017) Ethical principles for the use of human cellular biotechnologies. Nat Biotechnol. 2017 Nov 9;35(11):1050-1058. PMID: 29121024

466a. Min J, Smidler AL,Najjar D, Esvelt KM (2017) Harnessing gene drive. Journal of Responsible Innovation.

459a. Min J, Noble C, Najjar D, Esvelt KM (2017) Daisy quorum drives for the genetic restoration of wild populations. Biorxiv.

459. Grigaityte K, Carter J, Briggs AW, Goldfless SJ, Timberlake S, Koppstein D, Hause R, Church GM, Vigneault F, Atwal G (2017) Single-cell sequencing reveals αβ chain pairing shapes the T cell repertoire. Biorxiv.

458. Guo X, Chavez A, Tung A, Chan Y, Cecchi R, Garnier SL, Kaas C, Kelsic E, Schubert M, DiCarlo JE, Collins JJ, Church GM (2017) High-throughput creation and functional profiling of eukaryotic DNA sequence variant libraries using CRISPR/Cas9. Biorxiv. Nature Biotech. PMID: 29786095

457. Fang L, Guell M, Church GM, Pfeifer BA (2017) Heterologous Erythromycin Production across Strain and Plasmid Construction. Biotechnol Prog. 2017 Sep 28. doi: 10.1002/btpr.2567. PMID: 28960932

456. Huang PY, Narasimhan K, Chatman K, Aach J, Trauger SA, Spoering R, Church GM (2017) Toward D-peptide biosynthesis: Elongation Factor P enables ribosomal incorporation of consecutive D-amino acids. BioRxiv.

455. Chari R, Church GM (2017) Beyond editing to writing large genomes. Nat Rev Genet. doi: 10.1038/nrg.2017.59. PMID: 28852223

454. Egli D, Zuccaro M, Kosicki M, Church G, Bradley A, Jasin M (2017) Inter-homologue repair in fertilized human eggs? BioRxiv. Nature. PMID: 30089924

453. Ter-Ovanesyan D, Kowal EJK, Regev A, Church GM, Cocucci E (2017) Imaging of Isolated Extracellular Vesicles Using Fluorescence Microscopy. Methods Mol Biol. 1660:233-241. PMID: 28828661

452. Kowal EJK, Ter-Ovanesyan D, Regev A, Church GM (2017) Extracellular Vesicle Isolation and Analysis by Western Blotting. Methods Mol Biol. 1660:143-152. PMID: 28828654

451. Shapiro RS, Chavez A, Porter CBM, Hamblin M, Kaas CS, DiCarlo JE, Zeng G, Xu X, Revtovich AV, Kirienko NV, Wang Y, Church GM, Collins JJ (2017) A CRISPR Cas9-based gene drive platform for genetic interaction analysis in Candida albicans. Nat Microbiol. PMID: 29062088

450. Chen X, Sun YC, Church GM, Lee JH, Zador AM (2017) Efficient in situ barcode sequencing using padlock-probe-based BaristaSeq. Nucleic Acids Res. doi: 10.1093/nar/gkx1206. Biorxiv. PMID: 29190363

449. Kohman RE, Kunjapur AM, Hysolli E, Wang Y, Church GM (2017) From Designing the Molecules of Life to Designing Life: Future Applications Derived from Advances in DNA Technologies. Angew Chem Int Ed Engl. PMID: 29316123

448. Lim ET, Uddin M, De Rubeis S, Chan Y, Kamumbu AS, Zhang X, D'Gama AM, Kim S, Hill RS, Goldberg AP, Poultney C, Minshew NJ, Kushima I, Aleksic B, Ozaki N, Parellada M, Arango C, Penzol MJ, Carracedo A, Kolevzon A, Hultman CM, Weiss LA, Fromer M, Chiocchetti AG, Freitag CM, Autism Sequencing Consortium, Church GM, Scherer SW, Buxbaum JD, Walsh CA (2017) Rates, Distribution, and Implications of Post-zygotic Mosaic Mutations in Autism Spectrum Disorder. Nature Neuroscience. PMID: 28714951

447. Wannier TM, Kunjapur AM, Rice DP, McDonald MJ, Desai MM, Church GM (2017) Adaptive evolution of genomically recoded Escherichia coli. BioRxiv. PNAS. PMID: 29440500

446. Carter AC, Chang HY, Church G, Dombkowski A, Ecker J, Gil E, Giresi PG, Greely H, Greenleaf WJ, Hacohen N, He C, Hill DE, Ko J, Kohane IS, Kundaje A, Palmer M, Snyder M, Tung J, Urban AE, Vidal M, Wong W (2017) Challenges and recommendations for epigenomics in precision health. Nat Biotechnol. 35(12):1128-1132. PMID: 29220033

445a. Plesa C, Sidore AM, Lubock NB, Zhang D, Kosuri S (2017) Multiplexed Gene Synthesis in Emulsions for Exploring Protein Functional Landscapes. Science. 2018 Jan 19;359(6373):343-347. PMID: 29301959

445. Aach J, Lunshof J, Iyer E, Church GM (2017) Addressing the ethical issues raised by synthetic human entities with embryo-like features. ELife 6:e20674. PMID: 28494857

444. Soares AE, Novak BJ, Haile J, Fjeldsa J, Gilbert MTP, Poinar H, Church GM, Shapiro B (2016) BMC Evol Biol. 16(1):230. PMID: 27782796

443a. Ma NJ, Isaacs FJ (2016) Genomic Recoding Broadly Obstructs the Propagation of Horizontally Transferred Genetic Elements. Cell Syst. 3(2): 199–207. PMC5568630

443. Carr CE, Mojarro A, Tani J, Bhattaru SA, Zuber MT, Doebler R, Brown M, Herrington K, Talbot R, Fuller CW, Finney M, Church G, Ruvkun G (2016) Advancing the Search for Extra-Terrestrial Genomes. IEEE Aerospace.

442a. Linderman MD, Nielsen DE, Green RC (2016) Personal Genome Sequencing in Ostensibly Healthy Individuals and the PeopleSeq Consortium Personal Genome Sequencing in Ostensibly Healthy Individuals and the PeopleSeq Consortium J Pers Med. PMID: 27023617

442. Cai B, Li B, Kiga N, Thusberg J, Bergquist T, Chen Y, Niknafs N, Carter H, Tokheim C, Beleva-Guthrie V, Douville C, Bhattacharya R, Yeo HTG, Fan J, Sengupta S, Kim D, Cline M, Turner T, Diekhans M, Zaucha J, Pal L, Cao C, Yu C, Yin Y, Carraro M, Giollo M, Ferrari C, Leonardi E, Tosatto SCE, Bobe J, Ball M, Hoskins R, Repo S, Church G, Brenner S, Moult J, Gough J, Stanke M, Karchin R, Mooney SD (2016) Matching Phenotypes to Whole Genomes: Lessons Learned from Three Iterations of the Personal Genome Project Community Challenges. Hum Mutat. PMID: 28544481

441. Wilson CJ, Fenell T, Bothmer A, Maeder ML, Reyon D, Cotta-Ramusino C, Fernandez CA, Marco E, Barrera LA, Jayaram H, Albright CF, Cox GF, Church GM, Myer VE (2017) The experimental design and data interpretation in “Unexpected mutations after CRISPR–Cas9 editing in vivo” by Schaefer et al. are insufficient to support the conclusions drawn by the authors . BioRxiv. Nat Methods15:236-237. PMID: 29600989

440. Shipman SL, Nivala J, Macklis JD, Church GM (2017) CRISPR-Cas encoding of a digital movie into the genomes of a population of living bacteria. Nature. PMID: 28700573.

439. Bester AC, Chavez A, Lee YR, Vora S, Monteleone E, Lee J, Victor J, Sauvageau M, Rinn J, Provero P, Clohessy JG, Church GM, Pandolfi PP (2018) An Integrated Genome-wide CRISPRa Approach to Functionalize lncRNAs in Drug Resistance. Cell. 173(3):649-664. PMID: 29677511

438.Goodman DB, Kuznetsov G, Lajoie M, Ahern BW, Napolitano M, Chen K, Chen C, Church G (2017) Millstone: Software for Multiplex Microbial Genome Analysis and Engineering. Genome Biology 18(1):101. PMID: 28545559

437. Kuznetsov G, Goodman DB, Filsinger GT, Landon M, Rohland N, Aach J, Lajoie MJ, Church GM (2017) Optimizing complex phenotypes through model-guided multiplex genome engineering. Genome Biology. 18(1):100. PMID: 28545477

436. Briggs AW, Goldfless SJ, Timberlake S, Clouser CR, Belmont BJ, Sok D, Heiden JV, Broering TJ, Tammimen MV, Kleinstein SH, Burton DR, Church GM, Vigneault F (2017) Tumor-infiltrating immune repertoires captured by single-cell barcoding in emulsion. BioRxiv.

435. Cybulski TR, Boyden ES, Church GM, Tyo KEJ, Kording KP (2016) Nucleotide-Time Alignment for Molecular Recorders. PLoS Comput Biol. 13(5):e1005483. PMID: 28459860

434. Giwa S, Lewis JK, Alvarez L, Langer R, Roth A, Church GM, Markmann J, Sachs D, Rothblatt M, Boyden E, Eidbo E, Pomahac B, Lee A, Brandacher G, Weinstock DM, Elliott G, Nelson D, Acker J, Uygun MK, Schmalz B, Weegman B, Tocchio A, Fahy G, Storey K, Rubinsky B, Bischof J, Elliott JAW, Woodruff T, Morris J, Demirci U, Brockbank K, Woods E, Ben R, Baust JG, Gao D, Fuller B, Rabin Y, Kravitz D, Taylor MJ, Toner M (2017) The Promise of Organ and Tissue Preservation to Transform Medicine. Nature Biotechnology, 35(6):530-542. PMID: 28591112

433. Niu D, Wei, H, Lin L, George H, Wang T, Lee IH, Wang Y, Kan Y, Shrock E, Lesha E, Wang G, Luo Y, Qing Y, Jiao D, Zhao H, Zhao H, Zhou X, Wang S, Wei H, Guell M, Church GM, Yang L (2017) Inactivation of porcine endogenous retrovirus in pigs using CRISPR-Cas9. Science 357, 1303–1307. PMID: 28798043

432. Lee HH, Ostrov N, Gold MA, Church GM (2017) Recombineering in Vibrio natriegens. Biorxiv.

431. Chan Y, Tung M, Garruss AS, Zaranek SW, Chan YK, Lunshof JE, Zaranek AW, Ball MP, Chou MF, Lim ET, Church GM (2017) An unbiased index to quantify participant's phenotypic contribution to an open-access cohort. Sci Rep. 7:46148. PMID: 28387241

430. Li J, Haas W, Jackson K, Kuru E, Jewett MC, Fan ZH, Gygi S, Church GM (2017) Co-generating synthetic parts toward a self-replicating system. ACS Synth Biol. PMID: 28330337

429. Li J, Zhang C, Huang P, Kuru E, Forster-Benson ETC, Li T, Church GM (2017) Dissecting limiting factors of the Protein synthesis Using Recombinant Elements (PURE) system. BioRxiv, Translation 5(1):e1327006. PMID: 28702280

428a. Agasti SS, Wang Y, Schueder F, Sukumar A, Jungmann R, Yin P (2017) DNA-barcoded labeling probes for highly multiplexed Exchange-PAINT imaging. Chem Sci. 8(4):3080-3091. PMID: 28451377

428. Wang Y, Woehrstein JB, Donoghue N, Dai M, Avendaño MS, Schackmann RCJ, Zoeller JJ, Wang SSH, Tillberg PW, Park D, Lapan SW, Boyden ES, Brugge JS, Kaeser PS, Church GM, Agasti SS, Jungmann R, Yin P (2017) Rapid sequential in situ multiplexing with DNA Exchange Imaging in Neuronal Cells and Tissues. BioRxiv. Nano Lett. PMID: 28933153

427. Rock JM, Hopkins FF, Chavez A, Diallo M, Chase MR, Gerrick ER, Pritchard JR, Church GM, Rubin EJ, Sassetti CM, Schnappinger D, Fortune SM (2017) Programmable transcriptional repression in mycobacteria using an orthogonal CRISPR interference platform. Nat Microbiol. 2:16274. PMID: 28165460

426. Chari R, Yeo NC, Chavez A, Church GM (2017) sgRNA Scorer 2.0 - a species independent model to predict CRISPR/Cas9 activity. ACS Synth Biol. doi: 10.1021/acssynbio.6b00343. PMID: 28146356

425. Lubock N, Zhang D, Church G, Kosuri S (2017) A systematic comparison of error correction enzymes by next-generation sequencing. BioRxiv Nucleic Acids Res.45(15):9206-9217. PMID: 28911123

424. Church G (2017) DNA Edge World Question (Jan 2017)

423. Lubner JM, Dodge-Kafka KL, Carlson CR, Church GM, Chou MF, Schwartz D (2016) Reprogramming protein kinase substrate specificity through synthetic mutations. Biorxiv. Current Protocols in Chemical Biology. Characterizing Protein Kinase Substrate Specificity Using the Proteomic Peptide Library (ProPeL) Approach.

422. Lubner JM, Dodge-Kafka KL, Carlson CR, Church GM, Chou MF, Schwartz D (2016) Cushing’s Syndrome Mutant PKAL205R Exhibits Altered Substrate Specificity. Biorxiv. FEBS Lett. 2017 Jan 18. doi: 10.1002/1873-3468.12562. PMID: 28100013

421. Mao Q, Ciotlos S, Zhang RY, Ball MP, Chin R, Carnevali P, Barua N, Nguyen S, Agarwal MR, Clegg T, Connelly A, Vandewege W, Zaranek AW, Estep PW, Church GM, Drmanac R, Peters BA (2016). The whole genome sequences and experimentally phased haplotypes of over 100 personal genomes. Gigascience. 5(1):42. PMID: 27724973

420. Moore JA, Nemat-Gorgani M, Madison AC, Sandahl MA, Punnamaraju S, Eckhardt AE, Pollack MG, Vigneault F, Church GM, Fair RB, Horowitz MA, Griffin PB (2017) Automated electrotransformation of Escherichia coli on a digital microfluidic platform using bioactivated magnetic beads. Biomicrofluidics 11(1):014110. PMID: 28191268

419. Shendure J, Balasubramanian S, Church GM, Gilbert W, Rogers J, Schloss JA, Waterston RH (2017) DNA sequencing at 40: past, present and future. Nature. PMID: 29019985

418. Cho YS, Kim H, Kim HM, Jho S, Jun J, Lee YJ, Chae KS, Kim CG, Kim S, Eriksson A, Edwards JS, Lee S, Kim BC, Manica A, Church GM, Bhak J (2016) Ethnically relevant consensus Korean reference genome towards personal reference genomes. BioRxiv. Nature Comm. PMID: 27882922

417. Vogelstein JT, Amunts K, Andreou A, Angelaki D, Ascoli G, Bargmann C, Burns R, Cali C, Chance F, Chun M, Church G, Cline H, Coleman T, de La Rochefoucauld S, Denk W, Belen Elgoyhen AB, Cummings RE, Evans A, Harris K, Hausser M, Hill S, Inverso S, Jackson C, Jain V, Kass R, Kasthuri B, Kording K, Koushika S, Krakauer J, Landis S, Layton J, Luo Q, Marblestone A, Markowitz D, McArthur J, Mensh B, Milham M, Mitra P, Neskovic P, Nicolelis M, O'Brien R, Oliva A, Orban G, Peng H, Picchini­Schaffer A, Picciotto M, Poline JB, Poo M, Pouget A, Raghavachari S, Roskams J, Sejnowski T, Sommer F, Spruston N, Swanson L, Toga A, Vogelstein RJ, Yuste R, Zador A, Huganir R, Miller M (2016) Grand Challenges for Global Brain Sciences. Arxiv.

416. Norville JE, Gardner CL, Aponte E, Camplisson CK, Gonzales A, Barclay DK, Turner KA, Longe V, Mincheva M, Teramoto J, Tominaga K, Sugimoto R, Dicarlo JE, Guell M, Hysolli E, Aach J, Gregg CJ, Wanner BL, Church GM (2016) Assembly of Radically Recoded E. coli Genome Segments. BioRxiv.

415. Yang L, Briggs A, Chew WL, Mali P, Guell M, Aach J, Goodman D, Cox D, Kan Y, Lesha E, Soundararajan V, Zhang F, Church G (28-Jul-2016) Engineering and optimising deaminase fusions for genome editing Biorxiv. Nature Comm. (2-Nov-2016) PMID: 27804970

414. Vasiliou S, Diamandis EP, Church G, Greely HT, Baylis F, Thompson C, Schmitt‐Ulms G (2016) CRISPR-Cas9 system: Opportunities and Concerns. Clinical Chemistry. PMID: 27551006.

413. Chen F, Wassie AT, Cote AJ, Sinha A, Alon S, Asano S, Daugharthy ER, Chang JB, Marblestone A, Church GM, Raj A, Boyden ES (2016) Nanoscale imaging of RNA with expansion microscopy. Nat Methods 13(8):679-84. PMID: 27376770

412. Boeke JD, Church G, Hessel A, Kelley NJ, Arkin A, Cai Y, Carlson R, Chakravarti A, Cornish VW, Holt L, Isaacs FJ, Kuiken T, Lajoie M, Lessor T, Lunshof J, Maurano MT, Mitchell LA, Rine J, Rosser S, Sanjana NE, Silver PA, Valle D, Wang H, Way JC, Yang L (2016) Science 353(6295):126-7. The Genome Project-Write. supplement. resources. PMID: 27256881

411. Vora S, Tuttle M, Cheng J, Church G. (2016) Next stop for the CRISPR revolution: RNA guided epigenetic regulators. FEBS J. PMID: 27248712

410. Kalhor R, Mali P, Church GM (2016) Rapidly evolving homing CRISPR barcodes. BioRxiv. Nat Methods. PMID: 27918539

409. Noble C, Min J, Olejarz J, Buchthal J, Chavez A, Smidler AL, DeBenedictis EA, Church GM, Nowak MA, Esvelt KM (2019) Daisy-chain gene drives for the alteration of local populations. PNAS 116(17):8275-8282. BioRxiv. PMID: 30940750

408. Lee HH, Ostrov N, Wong BG, Gold MA, Khalil A, Church GM (2016) Vibrio natriegens, a new genomic powerhouse. BioRxiv.

407. Blawat M, Gaedke K, Huetter I, Chen XM, Turczyk B, Inverso S, Pruitt B, Church G (2016) Forward Error Correction for DNA Data Storage. In International Conference on Computational Science (BBC Jun-2016).

406. Rogers JK, Taylor ND, Church GM (2016) Biosensor-based engineering of biosynthetic pathways Current Opinion in Biotechnology 2016, 42:84–91. PMID: 26998575

405. Braff JL, Yaung SJ, Esvelt KM, Church GM (2016) Characterization of Cas9 - Guide RNA Orthologs. in CRISPR-Cas A Laboratory Manual CSH Protocols. PMID: 27140923

404. Soares AR, Novak BJ, Haile J, Heupink TH, Fjeldså J, Gilbert MT, Poinar H, Church GM, Shapiro B (2016) Complete mitochondrial genomes of living and extinct pigeons revise the timing of the Columbiform radiation. BMC Evol Biol. 16(1):230. PMID: 27782796

403. Zheng Y, Lajoie MJ, Italia JS, Chin M, Church GM, Chatterjee A (2016) Performance of optimized noncanonical amino acid mutagenesis systems in the absence of release factor 1. Mol Biosyst. 2016 Mar 30. PMID: 27027374

402. Chavez A, Pruitt BW, Tuttle M, Shapiro RS, Cecchi RJ, Winston J, Turczyk BM, Tung M, Collins JJ, Church GM (2018) Precise Cas9 targeting enables genomic mutation prevention PNAS. PMID: 29555762 BioRxiv 2016.

401. Ostrov N, Landon M, Guell M, Kuznetsov G, Teramoto J, Cervantes N, Zhou M, Singh K, Napolitano MG, Moosburner M, Shrock E, Pruitt BW, Conway N, Goodman DB, Gardner C, Tyree G, Gonzales A, Wanner BL, Norville J, Lajoie M, Church G (2016) Design, Synthesis and Testing Towards a 57-Codon Genome. Science 353(6301):819-22. supplement. PMID: 27540174

400. Musah S, Mammoto T, Mammoto A, Ferrente TC, Hirano-Kobayashi M, Roberts K, Chung S, Novak R, Ingram M, Fatanat-Didar T, Weaver JC, Church GM, Ingber DE (2017) Mature induced-pluripotent-stem-cell-derived human podocytes reconstitute kidney glomerular-capillary-wall function on a chip. Nat Biomed Eng. PMID: 29038743 suppl

399. Shipman SL, Nivala J, Macklis JD, Church GM (2016) Molecular recordings by directed CRISPR spacer acquisition Science. PMID: 27284167

398. Krueger AS, Munck C, Dantas G, Church GM, Galagan J, Lehar J, Sommer MOA (2016) Simulating serial-target antibacterial drug synergies using flux balance analysis. PLos One. PMID: 26821252

397. Church G. (2015) Perspective: Encourage the innovators. Nature. 528(7580):S7. PMID: 26630599

396. Chavez A, Tuttle M, Pruitt BW, Ewen-Campen B, Chari R, Ter-Ovanesyan D, Haque SJ, Cecchi RJ, Kowal EJK, Buchthal J, Housden BE, Perrimon N, Collins JJ, Church G (23-May-2016) Comparison of Cas9 Activators in Multiple Species. Nat Methods. 13(7):563-7. PMID: 27214048

395. Wang G, Yang L, Grishin D, Ye LL, Li K, Zhang D, Hu Y, Church GM, Pu WT (2016). Efficient, footprint-free human iPSC genome editing by consolidation of Cas9/CRISPR and piggybac technologies. Nat Protoc. 2017 Jan;12(1):88-103. PMID: 27929521

394. Stranges PB*, Palla M*, Kalachikov S, Nivala J, Dorwart M, Trans A, Kumar S, Porel M, Chien M, Tao C, Morozova I, Li Z, Shi S, Aberra A, Arnold C, Yang A, Aguirre A, Harada T, Korenblum D, Pollard J, Bhat A, Gremyachinskiy D, Bibillo A, Chen R, Davis R, Russo JJ, Fuller CW, Roever S, Ju J, Church GM (2016) Design and characterization of a nanopore-coupled polymerase for single molecule DNA sequencing by synthesis on an electrode array. PNAS. pii: 201608271. PMID: 27729524

393. Fuller CW, Kumar S, Porel M, Chien M, Bibillo A, Stranges PB, Dorwart M, Tao C, Li Z, Guo W, Shi S, Korenblum D, Trans A, Aguirre A, Liu E, Harada T, Pollard J, Bhat A, Cech C, Yang A, Spilman C, Palla M, Hovis JS, Chen R, Morozova I, Kalachikov S, Russo JJ, Kasianowicz J, Davis R, Roever S, Church GM, Ju J (2016) Real-Time Single Molecule Electronic DNA Sequencing by Synthesis Using Polymer Tagged Nucleotides on a Nanopore Array. Proc Natl Acad Sci USA 113(19):5233-8. PMID: 27091962

392. Church G (2016) Nootropic Neural News Edge World Question (Jan 2016)

391. Braff JL, Yaung SJ, Esvelt KM, Church GM (2016) Characterizing Cas9 Protospacer-Adjacent Motifs with High-Throughput Sequencing of Library Depletion Experiments. Cold Spring Harb Protoc. 2016 May 2;2016(5):pdb.prot090183. PMID: 27140916

390. Biteen JS, Blainey PC, Cardon ZG, Chun M, Church G, Dorrestein PC, Fraser SE, Gilbert J, Jansson JK, Knight R, Miller JF, Ozcan A, Prather KA, Taha S, van den Engh G, Quake S, Ruby EG, Silver P, Weiss PS, Wong GCL, Wright AT, Xie XS, Young TD (2015) Tools for the Microbiome: Nano and Beyond. ACS Nano. PMID: 26695070

389a. Lunshof J (2016) World View: Regulate gene editing in wild animals. Nature 521:127.

389. DiCarlo JE, Chavez A, Dietz SL, Esvelt KM, Church GM (2015) Safeguarding CRISPR-Cas9 gene drives in yeast. Nat Biotechnol. PMID: 26571100

388a. Lunshof J (2016) Human germ line editing—roles and responsibilities Protein Cell. 7(1):7–10. PMID: 26511643

388. Rogers JK, Church GM (2016) Multiplexed Engineering in Biology. Trends in Biotechnology. Jan 11. pii: S0167-7799(15)00261-9. PMID: 26897356

387. Rogers JK, Church GM (2015) Genetically encoded sensors enable real-time observation of metabolite production. PNAS. PMID: 26858408

386a. Lunshof J (2015) World View: Regulate gene editing in wild animals. Nature 521:127. PMID: 25971471

386. Ho JM, Reynolds NM, Rivera K, Connolly M, Guo LT, Ling J, Pappin DJ, Church GM, Soll DD (2015) Efficient reassignment of a frequent serine codon in wild-type Escherichia coli. ACS Synth Biol. PMID: 26544153

385. Napolitano MG, Gregg CJ, Lajoie MJ, Landon MM, Govindarajan LN, Mosberg JA, Kuznetsov G, Goodman DB, Vargas O, Isaacs FJ, Soll D, Church GM (2015) Emergent rules for codon choice elucidated by editing rare arginine codons in E. coli. PNAS. BioRxiv. PMID: 27601680

384. Feng J, Jester BW, Tinberg CE, Mandell DJ, Antunes MS, Chari R, Morey KJ, Xavier Rios, Medford JI, Church G, Fields S, Baker D (2015) A general strategy to construct small molecule biosensors in eukaryotes. ELife. PMID: 26714111

383. Taylor ND, Garruss AS, Moretti R, Chan S, Arbing M, Cascio D, Rogers RK, Isaacs FJ, Kosuri S, Baker D, Fields S, Church GM, Raman S (2015) Engineering an allosteric transcription factor to respond to new ligands. Nat Methods. PMID: 26689263

382. Alivisatos AP, Chun M, Church GM, Greenspan RJ, Roukes ML, Yuste R (2015) A National Network of Neurotechnology Centers for the BRAIN Initiative. Neuron 88(3):445-8. PMID: 26481036

381. Yetisen AK, Davis J, Coskun AF, Church GM, Yun SH (2015) Bioart. Trends in Biotech. PMID: 26617334

380. Zook JM, Catoe D, McDaniel J, Vang L, Spies N, Sidow A, Weng Z, Liu Y, Mason C, Alexander N, Henaff E, Chen F, Jaeger E, Moshrefi A, Pham K, Stedman W, Liang T, Saghbini M, Dzakula Z, Hastie A, Cao H, Deikus G, Schadt E, Sebra R, Bashir A, Truty RM, Chang CC, Gulbahce N, Zhao K, Ghosh S, Hyland F, Fu Y, Chaisson M, Xiao C, Trow J, Sherry ST, Zaranek AW, Ball M, Bobe J, Estep P, Church GM, Marks P, Kyriazopoulou-Panagiotopoulou S, Zheng GXY, Schnall-Levin M, Ordonez HS, Mudivarti PA, Giorda K, Salit M (2015) Extensive sequencing of seven human genomes to characterize benchmark reference materials. bioRxiv. Sci Data PMID: 27271295

379. Tabebordbar M, Zhu K, Cheng JKW, Chew WL , Maesner C, Widrick JJ, Wu EY, Xiao R , Ran FA, Cong L, Yan WX, Zhang F, Vandenberghe LH, Church GM, Wagers AJ (2015) In vivo gene editing in dystrophic mouse muscle and muscle stem cells. Science. PMID: 26721686

378. Lajoie MJ, Söll D, Church GM (2015) Overcoming challenges in engineering the genetic code. J. Mol. Biol. PMID: 26348789

377. Noble C, Olejarz J, Esvelt KM, Church GM, Nowak MA (2016) Evolutionary dynamics of CRISPR gene drives. BioRxiv. Science Advances PMID: 28435878

376. Zhirnov V, Zadegan RM, Sandhu GS, Church GM, Hughes WL (2016) NAM – Nucleic Acid Memory. Nat Mater. 2016 Mar 23;15(4):366-70. PMID: 27005909

375. Kiani S, Chavez A, Tuttle M, Hall RN, Chari R, Beal J, Vora S, Buchthal J, Ebrahimkhani MR, Collins JJ, Weiss R, Church G (2015) Cas9 gRNA engineering for selectable genome editing, activation and repression. Nature Methods. PMID: 26344044

374. Yang L, Güell M, Niu D , George H, Lesha E, Grishin D, Weihong Xu, Poci J, Shrock E, Cortazio R, Wilkinson RA, Fishman JA, Church G (2015) Genome-wide inactivation of porcine endogenous retroviruses (PERVs). Science 350:1101-1104. PMID: 26456528

373. Rogers JK, Guzman CD, Taylor ND, Raman S, Anderson K, Church GM (2015) Synthetic biosensors for precise gene control and real-time monitoring of metabolites Nucleic Acids Research. PMID: 26152303

372. Petit E, Coppi MV, Hayes JC, Tolonen AC, Warnick T, Latouf WG, Amisano D, Biddle A, Mukherjee S, Ivanova N, Lykidis A, Land M, Hauser L, Kyrpides N, Henrissat B, Lau J, Schnell DJ, Church GM, Leschine SB, Blanchard JL (2015) Genome and Transcriptome of Clostridium phytofermentans, Catalyst for the Direct Conversion of Plant Feedstocks to Fuels. PLoS One. 10(6):e0118285 PMID: 26035711

371. Akbari OS, Bellen HJ, Bier E, Bullock SL, Burt A, Church GM, Cook KR, Duchek P, Edwards OR, Esvelt KM, Gantz VM, Golic KG, Gratz SJ, Harrison MM, Hayes KR, Kaufman TC, Knoblich J, Malik HS, Matthews KA, O'Connor-Giles KM, Parks AL, Perrimon N, Port F, Russell S, Wildonger J, Ueda R (2015) Safeguarding gene drive experiments in the laboratory. Science. PMID: 26229113

370. Chavez A, Scheiman J, Vora S, Pruitt BW, Tuttle M, Iyer EPR, Lin S, Kiani S, Guzman CD, Wiegand DJ, Ter-Ovanesyan D, Braff JL, Davidsohn N, Housden BE, Perrimon N, Weiss R, Aach J, Collins JJ, Church GM (2015) Highly efficient Cas9-mediated transcriptional programming. Nat Methods. 12(4):326-8. PMID: 25730490

369. Church GM (2015) Precision Chemistry for Precision Medicine. ACS Central Science 1: 11-13.

368. Yaung SJ, Deng L, Li N, Braff JL, Church GM, Lynn Bry L, Wang HH, Gerber GK (2015) Improving microbial fitness in the mammalian gut by in vivo temporal functional metagenomics. Mol Syst Biol 11(3). PMID: 26148351

367. Baltimore D, Berg P, Botchan M, Carroll D, Charo A, Church G, Daley G, Doudna J, Fenner M, Greely H, Jinek M, Martin G, Penhoet E, Puck J, Sternberg S, Weissman J, Yamamoto K (2015) A Prudent Path Forward for Genomic Engineering and Germ Line Gene Modification. Science. PMID: 25791083

366. Tsioris K, Gupta NT, Ogunniyi AO, Zimnisky RM, Qian F, Yao Y, Wang X, Stern JN, Chari R, Briggs AW, Clouser CR, Vigneault F, Church GM, Garcia MN, Murray KO, Montgomery RR, Kleinstein SH, Love JC (2015) Neutralizing antibodies against West Nile virus identified directly from human B cells by single-cell analysis and next generation sequencing. Integr Biol (Camb). PMID: 26481611

365. Chew WL, Tabebordbar M, Cheng JKW, Mali P, Wu EY, Ng A, Zhu K, Wagers AJ, Church GM (2016) A multifunctional AAV–CRISPR–Cas9 and its host response. Nature Methods. PMID: 27595405

364. Glaser JI, Zamft BM, Church GM, Kording KP (2015) Puzzle Imaging: Using Large-scale Dimensionality Reduction Algorithms for Localization. Arxiv. PLoS One. PMID: 26192446

363. Cybulski TR, Glaser JI, Marblestone AH, Zamft BM, Boyden ES, Church GM, Kording KP (2015) Spatial information in large-scale neural recordings. Front Comput Neurosci. 8:172. PMID: 25653613

362. Yaung SJ, Esvelt KM, Church GM (2014)Complete Genome Sequences of T4-Like Bacteriophages RB3, RB5, RB6, RB7, RB9, RB10, RB27, RB33, RB55, RB59, and RB68. Genome Announcements ASM. PMID: 25555735

361. Church GM (2015) What Do You Care What Other Machines Think? Edge World Question (Jan 2015)

360. Hinson JT, Chopra A, Nafissi N, Polacheck WJ, Benson CC, Swist S, Gorham J, Yang L, Schafer S, Hubner N, Church G, Linke WA, Chen CS, Seidman JG, Seidman CE (2015) Titin Mutations in iPS cells define Sarcomere Insufficiency as Mechanism for Dilated Cardiomyopathy. Science 349(6251):982-6. PMID: 26315439

359. Drmanac R, Peters BA, Church GM, Reid CA, Xu X (5-Dec-2014)Accurate Whole-Genome Sequencing as the Ultimate Genetic Test. Clin Chem. pii: clinchem.2014.224907. PMID: 25479756

358. Byrne SM, Mali P, Church GM (2014) Genome editing in human stem cells. Methods Enzymol. 546:119-38. PMID: 25398338

357. Bhatt S, Gupta MK, Martinez R, Gritsenko MA, Wagner BK, Guye P, Busskamp V, Khamaisi M, Takatani T, Wu G, El Ouaamari A, Dirice E, Liew CW, Keenan HA, Smith RD, Church G, Wagers AJ, Weiss R, Qian WJ, King GL, Kulkarni RN (2014) Preserved DNA Damage Checkpoint Pathway Protects against Complications in Long-Standing Type 1 Diabetes. Cell Metab. 2015 Aug 4;22(2):239-52. PMID: 26244933

356. Byrne SM, Ortiz L, Mali P, Aach J, Church GM. (2014) Multi-kilobase homozygous targeted gene replacement in human induced pluripotent stem cells. Nucleic Acids Research 43(3):e21. PMID: 25414332

355. Chari R, Mali P, Moosburner M, Church GM (2015) Unraveling CRISPR-Cas9 genome engineering parameters via a library-on-library approach. Nature Methods 12(9):823-6. PMID: 26167643

354. Raman S, Rogers JK, Taylor ND, Church GM (2014) Evolution-guided optimization of biosynthetic pathways. PNAS 111(50):17803-8. PMID: 25453111

353. DiCarlo JE, Chavez A, Dietz SL, Esvelt KM, Church GM (2014) RNA-guided gene drives can efficiently bias inheritance in yeast. BioRxiv.

352. Chavez A, Scheiman J, Vora S, Pruitt BW, Tuttle M, Iyer E, Ter-Ovanesyan D, Kiani S, Guzman CD, Wiegand DJ, Davidsohn N, Braff JL, Weiss R, Aach J, Collins JJ, Church GM (2014) Highly-efficient Cas9-mediated transcriptional programming. BioRxiv.

351. Hoehe MR, Church GM, Lehrach H, Kroslak T, Palczewski S, Nowick K, Schulz S, Suk EK, Huebsch T (2014) Multiple haplotype-resolved genomes reveal population patterns of gene and protein diplotypes. Nature Comm. PMID: 25424553

350. Raman S, Taylor N, Genuth N , Fields S, Church GM (2014) Engineering Allostery. Trends in Genetics. PMID: 25306102

349. Yang L, Grishin D, Zhang CZ, Wang G, Homsy J, Cai X, Zhao Y, Fan JB, Seidman C, Seidman J, Pu W, Church G (2014) Targeted and genome-wide sequencing reveal single nucleotide variations impacting specificity of Cas9 in human stem cells. Nature Comm. 5:5507. PMID: 25425480

348. Keane M, Craig T, Alfoldi J, Berlin AM, Johnson J, Seluanov A, Gorbunova V, Di Palma F, Lindblad-Toh K, Church GM, de Magalhaes JP (2014) The Naked Mole Rat Genome Resource: facilitating analyses of cancer and longevity-related adaptations. Bioinformatics pii: btu579. PMID: 25172923

347. Keane M, Semeiks J, Webb AE, Li YI, Quesada V, Craig T, Madsen LB, Brawand D, Marques PI, Michalak P, Kang L, Bhak J, Yim HS, Grishin N, Nielsen NH, Heide-Jorgensen MP, Oziolor EM, Matson CW, Church G, Stuart G, Patton J, George C, Suydam R, Larsen K, Lopez-Otin C, O'Connell MJ, Bickham J, Thomsen B, de Magalhaes JP (2014) Insights into the evolution of longevity from the bowhead whale genome. Cell Reports. PMID: 25565328

346. Esvelt KM, Smidler AL, Catteruccia F, Church GM (2014) Concerning RNA-Guided Gene Drives for the Alteration of Wild Populations. eLife 3:e03401. PMID: 25035423

345. Oye KA, Esvelt K, Appleton E, Catteruccia F, Church G, Kuiken T, Lightfoot SBY, McNamara J, Smidler A, Collins JP (2014) Regulating Gene Drives. Regulatory gaps must be filled before gene drives are used in the wild. Science. PMID: 250354

344. Esvelt K, Church G, Lunshof J (Jul 2014) Gene Drives and CRISPR Could Revolutionize Ecosystem Management. Scientific American.

343. Yang L, Yang JL, Byrne S, Pan J, Church GM (2014) CRISPR/Cas9-Directed Genome Editing of Cultured Cells. Curr Protoc Mol Biol. 107:31.1.1-31.1.17. PMID: 24984853

342. Guell M, Yang L, Church G (2014) Genome Editing Assessment using CRISPR Genome Analyzer (CRISPR-GA) Bioinformatics pii: btu427. PMID: 24990609

341. Lee J, Daugharthy ER, Scheiman J, Kalhor R, Ferrente TC, Terry R, Turczyk B, Yang JL, Lee HS, Aach J, Zhang K, Church GM (2015) Fluorescent in situ sequencing (FISSEQ) of RNA for gene expression profiling in intact cells and tissues. Nature Protocols. PMID: 25675209

340. Li J, Gu L, Aach J, Church GM (2014). Improved cell-free RNA and protein synthesis system. PLoS One 9(9):e106232. PMID: 25180701

339. Yaung SJ, Esvelt KM, Church GM (2014) CRISPR/Cas9-Mediated Phage Resistance Is Not Impeded by the DNA Modifications of Phage T4. PLoS One. 9: e98811. PMID: 24886988

338. Bonde M, Kosuri S, Genee H, Sarup-Lytzen K, Church G, Sommer M, Wang H (2014) Direct Mutagenesis of Thousands of Genomic Targets using Microarray-derived Oligonucleotides. ACS Synthetic Biology. PMID: 24856730

337. Mee MT, Collins JJ, Church GM, Wang HH. (Apr 2014) Syntrophic exchange in synthetic microbial communities. Proc Natl Acad Sci PMID: 24778240

336. Kosuri S, Church GM (May 2014) Large-scale de novo DNA synthesis: technologies and applications. Nature Methods 11 (5): 499-507. PMID: 24781323

335. Marblestone A, Daugharthy E, Kalhor R, Peikon I, Kebschull J, Shipman S, Mishchenko Y, Lee J, Kording KP, Boyden ES, Zador AM, Church GM (2014) Rosetta Brains: A Strategy for Molecularly-Annotated Connectomics. ArXiv. 22-Apr-2014

334. Drukier AK, Cantor C, Chonofsky M, Church GM, Fagaly RL, Freese K, Lopez A, Sano T, Savage C, Wong WP (2014) New class of biological detectors for WIMPs. ArXiv. 31-Mar-2014. New class of biological detectors for WIMPs, Int. J. Mod. Phys. A 29 1443007 [1403.8154].

333. Mandell DJ, Lajoie MJ, Mee MT, Takeuchi R, Kuznetsov G, Norville J, Gregg CJ, Stoddard BL, Church GM (2015) Biocontainment of genetically modified organisms by synthetic protein design. Nature 518: 55–60. PMID: 25607366

332. Aach J, Mali P, Church GM (2014) CasFinder: Flexible Algorithm for Identifying Specific Cas9 Targets in Genomes. BioRxiv.

331a. Amir Y, Ben-Ishay E, Levner D, Ittah S, Abu-Horowitz A, Bachelet I (2014) Universal computing by DNA origami robots in a living animal Nature Biotech. PMID: 24705510 Supplement

331. Lunshof JE, Church GM, Prainsack B. (28-Feb-2014) Raw data: access to inaccuracy--response. Science 343(6174):969. PMID: 24578564

330. Yuste R, Church GM (Mar 2014) The New Century of the Brain. Scientific American. PMID: 24660326

329. Church GM, Elowitz M, Smolke CD, Voigt CA, Weiss R (2014) Realizing the potential of synthetic biology. Nature Reviews of Molec. Cell Bio. PMID: 24622617

328. Stern JNH, Yaari G, Vander Heiden JA, Church G, Donahue W, Rogier Q. Hintzen RQ, Huttner AJ, Laman JD, Nylander A, Pitt D, Ramanan S, Siddiqui BA, Vigneault F, Kleinstein SH , Hafler DA, O'Connor KC (2014) B cells populating the multiple sclerosis brain mature in the draining cervical lymph nodes. Science Transl. Medicine 6: 248ra07. PMID: 25100741

327. Ball MP, Bobe JR, Chou MF, Clegg T, Estep PW, Lunshof JE, Vandewege W, Zaranek AW, Church GM (2014) Harvard Personal Genome Project: Lessons from Participatory Public Research. Genome Medicine. PMID: 24713084

326. Davis R, Bibillo A, Fuller C, Dorwart M, Chen R, Kumar S, Kalachikov S, Russo J, Porel M, Chien M, Morozova I, Tao C, Li Z, Guo W, Korenblum D, Trans A, Aguirre A, Liu E, Harada T, Pollard J, Hu J, Cech C, Yang A, Spilman C, Thai E, Rode T, Walgren M, Lai M, De Cuir C, Hovis J, Bhat A, Stranges PB, Kasianowicz J, Church GM, Ju J (2014) Sequencing on a Genia Nanopore Chip: Proof of Principle. Advances in Genome Biology and Technology (AGBT).

325. Cybulski TR, Glaser JI, Marblestone AH, Zamft BM, Boyden ES, Church GM, Kording KP (2014) Spatial information in large-scale neural recordings. ArXiv. 14-Feb-2014

324. Montague TG, Cruz JM, Gagnon JA, Church GM, Valen E (2014) CHOPCHOP: a CRISPR/Cas9 and TALEN web tool for genome editing. Nucleic Acids Res. . PMID: 24861617

323. Chatterjee A, Lajoie MJ, Xiao H, Church GM, Schultz PG (2014) A Bacterial Strain with a Unique Quadruplet Codon Specifying Non-native Amino Acids. ChemBioChem 15(12):1782-6. PMID: 24867343

322. Tolonen AC, Cerisy T, El-Sayyed H, Boutard M, Salanoubat M, Church GM (2014) Fungal lysis by a bacterium fermenting cellulose. Environ Microbiol. PMID: 24798076

321a.Yaari G, Vander Heiden JA, Uduman M, Gadala-Maria D, Gupta N, Stern JN, O'Connor KC, Hafler DA, Laserson U, Vigneault F, Kleinstein SH (2013) Models of somatic hypermutation targeting and substitution based on synonymous mutations from high-throughput immunoglobulin sequencing data; Front Immunol. 4:358. PMID: 24298272

321. Lunshof JE, Church GM, Prainsack B (2013) Raw Personal Data: Providing Access and Agency. Science 343(6169):373-4. PMID: 24458627

320a. Church G (2013) World View: Genomics is mired in misunderstanding. Nature 502:143.

320. Robasky K, Lewis NE, Church GM (2013) The role of replicates for error mitigation in next-generation sequencing. Nature Rev Gen. 15(1):56-62. PMID: 24322726

319. Uduman M, Shlomchik MJ, Vigneault F, Church GM, Kleinstein SH (2013) Integrating B Cell Lineage Information into Statistical Tests for Detecting Selection in Ig Sequences. J. Immunology 192(3):867-74. PMID: 24376267

318. Brocker MJ, Ho JML, Church GM, Soll D, O'Donoghue P (2013) Recoding the Genetic Code with Selenocysteine. Angewandte Chemie 53(1):319-23. PMID: 24511637

317. Marblestone AH, Daugharthy E, Kalhor R, Peikon I, Kebschull J, Shipman S, Mishchenko Y, Dalrymple DA, Zamft BM, Kording KP, Boyden ES, Zador AM, Church GM (2013) Conneconomics: The Economics of Large-Scale Neural Connectomics. bioRxiv (16-Dec-2013)

316. Sok D*, Laserson U*, Laserson J*, Liu Y*, Vigneault F, Julien JP, Briney B, Ramos A, Saye KF, Le K, Mahan A, Wang S, Kardar M, Yaari G, Walker LM, Simen BB, St John EP, Chan-Hui PY, Swiderek K, Kleinstein SH, Alter G, Seaman MS, Chakraborty AK, Koller D, Wilson IA, Church GM, Burton DR, Poignard P (2013) The Effects of Somatic Hypermutation on Neutralization and Binding in the PGT121 Family of Broadly Neutralizing HIV Antibodies. PLoS Pathogens. PDB: 4NPY PMID: 24385895 PMCID: PMC3875691

315. Church GM (2013) BRAIN: innovative neurotechnologies for imaging and therapeutics Dialogues Clin Neurosci. 15(3):241-3. PMID: 24174897

314. Church GM (2013) Improving Genome Understanding Nature 502:143. PMID: 24108012

313. O'Shea J, Chou MF, Quader S, Ryan J, Church GM, Schwartz D (2013) pLogo: a probabilistic approach to visualizing sequence motifs. Nature Methods. doi: 10.1038/nmeth.2646. PMID: 24097270

312. Church GM, Marblestone A, Kalhor R (2014) Rosetta Brain. in The Future of the Brain. Editors Marcus G and Freeman J.

311. Wang G, McCain ML, Yang L, He A, Pasqualini FS, Agarwal A, Yuan H, Jiang D, Zhang D, Zangi L, Geva J, Roberts AE, Ma Q, Ding J, Chen J, Wang DZ, Li K, Wang J, Wanders RJ, Kulik W, Vaz FM, Laflamme MA, Murry CE, Chien KR, Kelley RI, Church GM, Parker KK, Pu WT. (2014) Modeling the mitochondrial cardiomyopathy of Barth syndrome with induced pluripotent stem cell and heart-on-chip technologies. Nature Medicine 20: 616-23. PMID: 24813252

310. Eroshenko N, Church GM (2013) Mutants of Cre recombinase with improved accuracy. Nature Communications 4:2509. PMID: 24056590

309. Gregg CJ, Lajoie MJ, Napolitano MG, Mosberg JA, Goodman DB, Aach J, Isaacs FJ, Church GM (2014) Rational Optimization of tolC as a Powerful Dual Selectable Marker for Genome Engineering. Nucleic Acids Research. PMID: 24452804

308. Ling J, Daoud R, Lajoie MJ, Church GM, Soll D, Lang BF (2013) Natural reassignment of CUU and CUA sense codons to alanine in Ashbya mitochondria. Nucleic Acids Research. PMID: 24049072

307. Tzur YB, Friedland AE, Nadarajan S, Church GM, Calarco JA, Colaiácovo MP (2013) Heritable Custom Genomic Modifications in Caenorhabditis elegans via a CRISPR-Cas9 System. Genetics. PMID: 23979579

306. Church G. Please reanimate (De-Extinction Is a Good Idea) (2013) Scientific American 309(3):12. PMID: 24003542.

305. Li JB, Church GM (2013) Deciphering the functions and regulation of brain-enriched A-to-I RNA editing. Nat Neurosci. 16(11):1518-22. PMID: 24165678

304. Marblestone AH, Zamft BM, Maguire YG, Shapiro MG, Cybulski T, Glaser JI, Amodei D, Stranges B, Kalhor R, Dalrymple DA, Seo D, Alon E, Maharbiz MM, Carmena JM,Rabaey JM, Boyden E, Church GM, Kording KP (2013) Physical Principles for Scalable Neural Recording. Frontiers in Neuroscience. (Hypothesis & Theory section). PMID: 24187539 PMCID: PMC3807567

303. Lo C, Liu R, Lee J, Robasky K, Byrne S, Lucchesi C, Aach J, Church G, Bafna V, Zhang K (2013) On the design of clone-based haplotyping Genome Biology 14(9):R100. PMID: 24028704

302. Lee J, Daugharthy E, Scheiman J, Kalhor R, Yang JL, Ferrente TC, Terry R, Jeanty SSF, Li C,Amamoto R, Peters DT, Turczyk BM, Marblestone A, Inverso S, Bernard A, Mali P, Rios X, Aach J, Church GM (2014) Highly multiplexed subcellular RNA sequencing in situ. Science 343(6177):1360-3. PMID: 24578530 Supplement

301. DiCarlo JE, Conley A, Penttil M, Jantti J, Wang HH, Church GM (2013) Yeast Oligo-mediated Genome Engineering (YOGE). ACS Synthetic Biology. PMID: 24160921

300. Li JF, Norville JE, Aach J, McCormack M, Zhang D, Bush J, Church GM, Sheen J (2013) Multiplex and homologous recombination-mediated genome editing in Arabidopsis and Nicotiana benthamiana using guide RNA and Cas9. Nat Biotechnol. 31(8):688-91. PMID: 23929339

299. Goodman DB, Church GM, Kosuri S (2013) Causes and effects of N-terminal codon bias in bacterial genes. Science 342:475-9. PMID: 24072823

298. Eminaga S, Christodoulou DC, Vigneault F, Church GM, Seidman JG. (2013) Quantification of microRNA Expression with Next-Generation Sequencing. Curr Protoc Mol Biol. Chapter 4:Unit4.17. doi: 10.1002/0471142727.mb0417s103. PMID: 23821442

297. Mali P, Esvelt KM, Church GM (2013) Cas9 as a Versatile Tool for Engineering Biology. Nature Methods 10:957-963. PMID: 24076990

296. Busskamp V, Lewis NE, Guye P, Ng AHM, Shipman S, Byrne SS, Sanjana NE, Li Y, Weiss R, Church GM (2014) Rapid neurogenesis through transcriptional activation in human stem cells. Molecular Systems Biology MSB 10:760: 1-21. PMID: 25403753

295. Marblestone AH, Zamft BM, Maguire YG, Shapiro MG, Cybulski T, Glaser JI, Stranges B, Kalhor R, Dalrymple DA, Boyden E, Church GM, Kording KP (2013) Physical Principles for Scalable Neural Recording. ArXiv. 24-Jun-2013.

294. Esvelt KM, Mali P, Braff J, Moosburner M, Yaung S, Church GM (2013) Orthogonal Cas9 proteins for RNA-guided gene regulation and editing. Nature Methods.

293a. Lunshof JE, Ball MP (2013) Our genomes today: time to be clear. Genome Medicine 5:52. PMID: 23806003

293. Glaser J, Zamft B, Marblestone A, Moffitt JR, Boyden E, Church GM, Kording K. (2013) Statistical analysis of molecular signal recording. PLoS Computational Biology. PMID: 23874187

292. Konermann S, Brigham MD, Trevino A, Hsu PD, Heidenreich M, Cong L, Platt RJ, Scott DA, Church GM, Zhang FM (2013) Optical Control of Mammalian Endogenous Transcription. Nature. PMID: 23877069

291. Friedland AE, Tzur YB, Esvelt KM, Colaiácovo MP, Church GM, Calarco JA (2013) Heritable genome editing in C. elegans via a CRISPR-Cas9 system. Nat Methods. 10(8):741-3. PMID: 23817069

290. Yaung SJ, Church GM, Wang HH (2013) Recent Progress in Engineering Human-associated Microbiomes. Methods Mol Biol. 2014;1151:3-25. PMID: 24838875

289. Umbarger MA, Kennedy CJ, Saunders P, Breton B, Chennagiri N, Emhoff J, Greger V, Hallam S, Maganzini D, Micale C, Nizzari MM, Towne CF, Church GM, Porreca GJ (2013) Next-Generation Carrier Screening. Genetics in Medicine. PMID: 23765052

288. Yang L, Mali P, Kim-Kiselak C, Church G (2013) CRISPR-Cas mediated targeted genome editing in human cells. Methods in Molecular Biology. PMID: 24557908

287. Mali P, Aach J, Stranges PB, Esvelt KM, Moosburner M, Kosuri S, Yang L, Church GM (2013) CAS9 transcriptional activators for target specificity screening and paired nickases for cooperative genome engineering. Nature Biotech 31(9):833-8. PMID: 23907171 Supplementary info

286. Alivisatos AP, Andrews A, Boyden E, Chun M, Church G, Deisseroth K, Donoghue J, Fraser S, Lippincott-Schwartz J, Looger L, Masmanidis S, McEuen P, Nurmikko A, Park H, Peterka D, Reid C, Roukes M, Scherer A, Schnitzer M, Sejnowski T, Shepard K, Tsao D, Turrigiano G, Weiss P, Xu C, Yuste R, Zhuang X (2013) Nanotools for Neuroscience and Brain Activity Mapping. ACS Nano 7(3):1850-66. PMID: 23514423

285. Alivisatos AP, Chun M, Church GM, Deisseroth K, Donoghue JP, Greenspan RJ, McEuen PL, Roukes ML, Sejnowski TJ, Weiss PS, Yuste R (2013) The Brain Activity Map Science 339(6125):1284-5. PMID: 23470729

284. Payne A, Andregg M, Kemmish K, Hamalainen M, Bowell C, Bleloch A, Klejwa N, Lehrach W, Schatz K, Stark H, Marblestone A, Church G, Own CS, Andregg W (2013) Molecular threading: mechanical extraction, stretching and placement of DNA molecules from a liquid-air interface. PLoS One 8(7):e69058. PMID: 23935923

283. Kosuri S, Goodman DB, Cambray G, Mutalik VK, Gao Y, Arkin AP, Endy D, Church GM. (2013) Composability of regulatory sequences controlling transcription and translation in E. coli. PNAS. PMID: 23924614

282. DiCarlo J, Norville J, Mali P, Rios X, Aach J, Church G (2013) Genome Engineering in Saccharomyces cerevisiae using CRISPR-Cas systems. Nucleic Acids Res. PMID: 23460208

281. Rockwell G, Guido NJ, Church GM (2013) Redirector: designing cell factories by reconstructing the metabolic objective. PLoS Comput Biol. 9(1):e1002882. PMID: 23341769

280. Baker S, Joecker A, Church G, Snyder M, West J, Salzberg S, Worthey E, Smith T, Wang J, Reid JG (2012) Genome interpretation and assembly -- recent progress and next steps. Nat Biotechnol. 30(11):1081-3. PMID: 23138307

281a. Church G (2012) Technologies for Reading and Writing Omes. Journal of Biomolecular Techniques 23:S1-S2. PMC3630559

280a. Church G, Olejnik J, Werner M, Guggenheim E, DiMeo J, Marma MS, Visalakshi V, Hagerott T, Golaski E, Veatch P, Stoops D, Gordon S (2012) Clinical DNA Sequencer for Ultra-Low Cost Testing. Journal of Biomolecular Techniques 23:S9-S9 PMC3630694

279a. Mee MT, Wang HH. (2012) Engineering ecosystems and synthetic ecologies. Mol Biosyst. 8(10):2470-83.

279. Wang HH, Mee MT, Church GM (2013) Applications of Engineered Synthetic Ecosystems. Chapter 17. Synthetic Biology. doi

278. Church GM (2012) Reading and writing omes Molecular Systems Biology MSB 9:642. PMID: 23340848

277a. Esvelt KM, Wang HH (2012) Genome-scale engineering for systems and synthetic biology Molecular Systems Biology MSB 9:641. PMID: 23340847

277. Lajoie MJ, Kosuri S, Mosberg JA, Gregg CJ, Zhang D, Church GM (2013) Probing the limits of genetic recoding in essential genes. Science 342: 361-3. PMID: 24136967 Supplement

276. Lajoie MJ, Rovner AJ, Goodman DB, Aerni HR, Haimovich AD, Mercer JA, Wang HH, Carr PA, Mosberg JA, Rohland N, Schultz PG, Jacobson JM, Rinehart J, Church GM, Isaacs FI (2013) Genomically Recoded Organisms Impart New Biological Functions. Science 342: 357-60. PMID: 24136966

275. Mali P, Aach J, Lee J, Levner D, Nip L, Church GM (2013) Barcoding cells using cell-surface programmable DNA-binding domains. Nature Methods 10(5):403-6. Supplement PMID: 23503053

274. Yang L, Guell M, Byrne S, Yang J, De Los Angeles A, Mali P, Aach J, Briggs A, Rios X, Huang PY, Daley G, Church GM (2013). Optimization of Scarless Human Stem Cell Genome Editing. Nucleic Acids Res. PMID: 23907390

273. Plank M, Hu G, Silva AS, Wood SH, Hesketh EE, Janssens G, Macedo A, de Magalhaes JP, Church GM (2012) An analysis and validation pipeline for large-scale RNAi-based screens. Scientific Reports 3:1076. doi: 10.1038/srep01076. PMID: 23326633

272. Mali P, Yang L, Esvelt KM, Aach J, Guell M, DiCarlo JE, Norville J, Church GM (2013) RNA-guided human genome engineering via Cas9. Science 339: 823-6. Supplement PMID: 23287722 Addgene: hCas9, D10A, Vector

271a. Cong L, Ran FA, Cox D, Lin S, Barretto R, Habib N, Hsu PD, Wu X, Jiang W, Marraffini LA, Zhang F (2013) Multiplex Genome Engineering Using CRISPR/Cas Systems. Science Jan 3. PMID: 23287718

271. Lin C, Jungmann R, Leifer AM, Li C, Levner D, Church GM, Shih WM, Yin P(2012) Submicrometre geometrically encoded fluorescent barcodes self-assembled from DNA. Nat Chem. 4(10):832-839. PMID: 23000997

270a. Beliveau BJ, Joyce EF, Apostolopoulos N, Yilmaz F, Fonseka CY, McCole RB, Yiming Chang Y, Li JB, Senaratne TN, Williams BR, Rouillard JM, Wu CT (2012) A versatile design and synthesis platform for visualizing genomes with Oligopaint FISH probes. PNAS 109: 21301-6. PMID: 23236188

270. Zamft B, Marblestone A, Kording K, Schmidt D, Martin-Alarcon D, Tyo K, Boyden E, Church GM (2012) Measuring Cation Dependent DNA Polymerase Fidelity Landscapes by Deep Sequencing PLoS One 7(8):e43876, PMID: 22928047 Supplementary data

269. Rios X, Briggs AW, Christodoulou D, Gorham JM, Seidman JG, Church GM (2012) Stable gene targeting in human cells using single-strand oligonucleotides with modified bases. PLoS One. 7:e36697. PMID: 22615794

268. Regis E, Church G (2012) The Recipe For Immortality Discover Magazine. 17-Oct-2012.

267. Dreyfuss JM, Levner D, Galagan JE, Church GM, Ramoni MF (2012) How accurate can genetic predictions be? BMC Genomics 13(1):340. PMID: 22827772

266. Briggs AW, Rios X, Chari R, Yang L, Zhang F, Mali P, Church GM. (2012) Iterative capped assembly: rapid and scalable synthesis of repeat-module DNA such as TAL effectors from individual monomers. Nucleic Acids Res. PMID: 22740649

265. Church GM, Regis E (2012) Regenesis: How Synthetic Biology Will Reinvent Nature and Ourselves 288 pages. Basic Books, publisher.

264. Drukier A, Freese K, Spergel D, Cantor C, Church G, Sano T (2012) New Dark Matter Detectors using DNA for Nanometer Tracking ArXiv. 29-Jun-2012

263. Alivisatos AP, Chun M, Church GM, Greenspan RJ, Roukes ML, Yuste R (2012) The Brain Activity Map Project and the Challenge of Functional Connectomics. Neuron. 74: 970-4. PMID: 22726828

262a. Cong L, Zhou R, Kuo YC, Cunniff M, Zhang F. (2012) Comprehensive interrogation of natural TALE DNA-binding modules and transcriptional repressor domains. Nat Commun. 3:968. PMID: 22828628

262. Church GM, Gao Y, Kosuri S (2012) Next-generation Digital Information Storage in DNA. Science DOI: 10.1126/science.1226355 supplement PMID: 22903519

261a. Sanjana NE, Cong L, Zhou Y, Cunniff MM, Feng G, Zhang F (2012) A transcription activator-like effector toolbox for genome engineering. Nat Protoc. 7(1):171-92. PMID: 22222791

261. Zhu J, Larman HB, Gao G, Somwar R, Zhang Z, Laserson U, Ciccia A, Pavlova N, Church G, Zhang W, Kesari S, Elledge SJ (2013) PLATO: Parallel Analysis of in vitro Translated ORF libraries. Nature Biotech. doi: 10.1038/nbt.2539. PMID: 23503679

260. Larman HB, Laserson U, Querol L, Verhaeghen K, Solimini NL, Xu G, Klarenbeek PL, Church GM, Hafler DA, Plenge RM, Nigrovic PA, De Jager PL, Weets I, Martens GA, O'Connor KC, Elledge SJ (2013) PhIP-Seq characterization of autoantibodies from patients with multiple sclerosis, type 1 diabetes and rheumatoid arthritis. J Autoimmun. 43:1-9. PMID: 23497938

259. Gu L, Li C, Aach J, Hill DE, Vidal M, Church GM (2014) Multiplex single-molecule interaction profiling of DNA barcoded proteins. Nature doi: 10.1038/nature13761. PMID: 25252978 Supplement

258. Chou MF, Prisic S, Lubner JM, Church GM, Husson RN, Schwartz D (2012) Using bacteria to determine protein kinase specificity and predict target substrates. PLoS One 7(12):e52747. PMID: 23300758

257. Mosberg Ja, Gregg CJ, Lajoie MJ, Wang HH, Church GM (2012) Improving Lambda Red Genome Engineering via Rational Removal of Endogenous Nucleases. PLoS One 7(9):e44638. PMID: 22957093

256. Lajoie MJ, Gregg CJ, Mosberg JA, Washington GC, Church GM (2012) Manipulating Replisome Dynamics to Enhance Lambda Red-Mediated Multiplex Genome Engineering Nucleic Acids Research 40(22):e170. PMID: 22904085

255. Eroshenko N, Kosuri S, Marblestone AH, Conway N, Church GM (2012) Gene Assembly from Chip-Synthesized Oligonucleotides. Current Protocols in Chemical Biology 4: 1-17. PMID: 25077042

254a. Kosuri S, Sismour M (2012) When It Rains, It Pores. ACS Synth. Biol. 2012, 1, 109-110. (dx.doi.org/10.1021/sb300015f)

254. Alon S, Mor E, Vigneault F, Church G, Locatelli F, Galeano F, Gallo A, Shomron N, Eisenberg E. (2012) Systematic identification of edited microRNAs in the human brain. Genome Res. PMID: 22499667

253. Vigneault F, Ter-Ovanesyan D, Alon S, Eminaga S, Christodoulou DC, Seidman JG, Eisenberg E, Church G (2012) High-Throughput Multiplex Sequencing of miRNA; Curr Protoc Hum Genet. Chapter 11: Unit 11.12.

252. Laserson U, Vigneault F, Gadala-Maria D, Yaari G, Uduman M, Vander Heiden J, Kelton W, Jung ST, Liu Y, Laserson J, Chari R, Lee J, Bachelet I, Hickey B, Lieberman-Aiden E, Hanczaruk B, Simen BB, Egholm M, Koller D, Georgiou G, Kleinstein S, Church GM (2014) High-resolution antibody dynamics of vaccine-induced immune responses. PNAS 111(13):4928-33. PMID: 24639495.Supplement Amazon s3://flu-antibody-data

251. Jewett MC, Fritz BR, Timmerman LE, Church GM (2013) In vitro integration of ribosomal RNA synthesis, ribosome assembly and translation. Molecular Systems Biology MSB 9:678. PMID: 23799452

250. Carr PA, Wang HH, Sterling B, Isaacs FJ, Xu G, Church GM, Jacobson JM (2012) Enhanced Multiplex Genome Engineering through Co-operative Oligonucleotide Co-selection. Nucleic Acids Res. PMID: 22638574

249. Juhas M, Eberl L, Church GM (2012) Essential genes as antimicrobial targets and cornerstones of synthetic biology. Trends Biotechnol. PMID: 22951051

248. Boyle PM, Burrill DR, Inniss MC, Agapakis CM, Deardon A, DeWerd JG, Gedeon MA, Quinn JY, Paull ML, Raman AM, Theilmann MR, Wang L, Winn JC, Medvedik O, Schellenberg K, Haynes KA, Viel A, Brenner TJ, Mathews S, Church GM, Shah JV, Silver PA (2012) A BioBrick compatible strategy for genetic modification of plants. J Biol Eng. 6:8. PMID: 22716313

247. Ball MP*, Thakuria JV*, Zaranek AW*, Clegg T, Rosenbaum AM, Wu X, Angrist M, Bhak J, Bobe J, Callow M, Cano C, Chou MF, Chung WK, Douglas SM, Estep P, Gore A, Hulick P, Labarga A, Lee J, Lunshof J, Kim BC, Kim JI, Li Z, Murray MF, Nilsen GB, Peters B, Raman AM, Reinhoff HY, Robasky K, Wheeler M, Vandewege W, Vorhaus D, Yang JL, Yang L, Aach J, Ashley EA, Drmanac R, Kim SJ, Li JB, Peshkin L, Seidman CE, Seo JS, Zhang K, Rehm HL, Church GM (2012) A Public Resource Facilitating Clinical Use of Genomes. Proc Natl Acad Sci USA 109(30):11920-7 (inaugural article) PMID: 22797899

246. Peters BA, Kermani BG, Sparks AB, Alferov O, Hong P, Alexeev A, Jiang Y, Dahl F, Tang YT, Hass J, Robasky K, Zaranek AW, Lee JH, Ball MP, Peterson JE, Perazich H, Yeung G, Liu J, Chen L, Pothuraju K, Konvicka K, Tsoupko-Sitnikov M, Pant KP, Ebert J, Nilsen G, Baccash J, Halpern AL, Church GM, Drmanac R (2012) Accurate whole genome sequencing and haplotyping from 10-20 human cells. Nature 487: 190-195. (supplement) PMID: 22785314

245. Wang HH, Kim H, Cong L, Jeong J, Bang D, Church GM (2012) Genome-scale Promoter Engineering by Coselection MAGE. Nature Methods Apr 8. doi: 10.1038/nmeth.1971 PMID: 22484848

244. Wang HH, Huang PY, Xu G, Haas W, Marblestone A, Li J, Gygi S, Forster A, Jewett MC, Church GM (2012) Multiplexed in vivo His-tagging of enzyme pathways for in vitro single-pot multi-enzyme catalysis. ACS Synthetic Biology 1(2):43-52. PMID: 22737598

243. Thakuria JV, Zaranek AW, Church GM, Berry GT. (2012) Back to the future: From genome to metabolome. Hum Mutat. 2012 Mar 16. doi: 10.1002/humu.22073. PMID: 22431014

242. Douglas SM, Bachelet I, Church GM (2012) A logic-gated nanorobot for targeted transport of molecular payloads. Science 335, 831-834. PMID: 22344439. Supplement

241. Gianoulis TA, Griffin MA, Spakowicz DJ, Dunican BF, Alpha CJ, Sboner A, Sismour AM, Kodira C, Egholm M, Church GM, Gerstein MB, Strobel SA (2012) Genomic Analysis of the Hydrocarbon-Producing, Cellulolytic, Endophytic Fungus Ascocoryne sarcoides. PLoS Genet. 8(3):e1002558. PMID: 22396667

240. Nelson FK, Snyder M,Gardner AF, Hendrickson CL, Shendure JA, Porreca GJ, Church GM, Ausubel FM, Ju J, Kieleczawa J, Slatko BE (2011) Overview of DNA sequencing strategies. Curr Protoc Mol Biol. Chapter 7:Unit7.0.

239. Shendure JA, Porreca GJ, Church GM, Gardner AF, Hendrickson CL, Kieleczawa J, Slatko BE (2011) Overview of DNA sequencing strategies. Curr Protoc Mol Biol. Chapter 7:Unit7.1. PMID: 21987056

238. Ji J, Ng SH, Sharma V, Neculai D, Hussein S, Sam M, Trinh Q, Church GM, McPherson JD, Nagy A, Batada NN (2011) Elevated Coding Mutation Rate During the Reprogramming of Human Somatic Cells into Induced Pluripotent Stem Cells. Stem Cells. 2011 Dec 12. doi: 10.1002/stem.1011. PMID: 22162363

237. Church GM (2012) Elegant=Complex. Edge World Question (Jan 2012).

236. Yu C, Li Y, Holmes A, Szafranski K, Faulkes CG, Coen CW, Buffenstein R, Platzer M, de Magalhaes JP, Church GM (2011). RNA sequencing reveals differential expression of mitochondrial and oxidation reduction genes in the long-lived naked mole-rat when compared to mice. PLoS One 6(11):e26729. PMID: 22073188

235. Church GM (2011) New technologies for integrating genomic, environmental and trait data. J Clin Sleep Med. 7(5 Suppl):S43-4. PMID: 22003332

234. Alon S, Vigneault F, Eminaga S, Christodoulou DC, Seidman JG, Church GM, Eisenberg E. (2011) Barcoding bias in high-throughput multiplex sequencing of miRNA. Genome Res. 2011 Sep;21(9):1506-11. PMID: 21750102

233. Church GM (2011) Thoughts on the Manchester Manifesto. Prometheus 29 (3):343-344.

232. Church GM (2011) Evolving Engineering. The Scientist Oct-2011.

231. Wang HH, Church GM (2011) Multiplexed genome engineering and genotyping methods applications for synthetic biology and metabolic engineering. Methods Enzymol. 498:409-26.

230. Dewey FE, Chen R, Cordero SP, Ormond KE, Caleshu C, Karczewski KJ, Carrillo MW, Wheeler MT, Dudley JT, Byrnes JK, Cornejo OE, Knowles JW, Woon M, Sangkuhl K, Gong L, Thorn CF, Hebert JM, Capriotti E, David SP, Pavlovic A, West A, West JS, Thakuria JV, Ball MP, Zaranek AW, Rehm HL, Church GM, Bustamante CD, Snyder MP, Altman RB, Klein TE, Butte AJ, Ashley EA (2011) Phased whole genome genetic risk in a family quartet. PLoS Genet. 7(9):e1002280. PMID: 21935354 PMCID: PMC3174201

229. Wang HH, Xu G, Vonner A, Church GM (2011) Modified Bases Enable High-efficiency Oligonucleotide-Mediated Allelic Replacement via Mismatch Repair Evasion. Nucleic Acids Res. 39(16):7336-47. PMID: 21609953

228. Church G (2011) Non-Inherent Inheritance. Edge World Question (Jan 2011).

227. Carmi S, Church GM, Levanon EY (2011) Large-scale DNA editing of retrotransposons accelerates mammalian genome evolution. Nat Commun. 2011 Nov 1;2:519. doi: 10.1038/ncomms1525. PMID: 22044998

226. Zhang F, Cong L, Lodato S, Kosuri S, Church GM, Arlotta P (2011) Programmable Sequence-Specific Regulation of Mammalian Gene Expression Using Designer TAL Effectors. Nature Biotech 29(2):149-153. supplement PMID: 21248753

225a. Gore A, Li Z, Fung HL, Young J, Agarwal S, Antosiewicz-Bourget J, Canto I, Israel M, Kiskinis E, Lee JH, Loh YH, Manos P, Montserrat N, Wilbert M, Yu J, Kirkness E, Belmonte JCI, Daley GQ, Eggan K, Rossi DJ, Thomson J, Goldstein LSB, Zhang K (2011) Somatic coding mutations in human induced pluripotent stem cells. Nature 471, 63-67. PMID: 21368825

225. Larman HB, Zhao Z, Laserson U, Li M, Ciccia A, Martinez A, Church GM, Kesari S, LeProust E, Solimini NL, Elledge SJ (2011) Autoantigen discovery with a synthetic peptidome. Nature Biotech. doi:10.1038/nbt.1856 PMID: 21602805 . Supplement

224. Robertson DE, Jacobson S, Morgan F, Berry D, Church GM, Afeyan N (2011) A New Dawn for Industrial Photosynthesis. Photosyn Res. DOI 10.1007/s11120-011-9631-7. PMID: 21318462

223. Isaacs FJ, Carr PA, Wang HH, Lajoie MJ,Sterling B, Kraal L, Tolonen A, Gianoulis T, Goodman D, Reppas NB, Emig CJ, Bang D, Hwang SJ, Jewett MC, Jacobson JM, Church GM (2011) Precise Manipulation of Chromosomes in vivo Enables Genome-wide Codon Replacement Science 333(6040):348-53. PMID: 21764749

222a. Jacobs B, Roffenbender J, Collmann J, Cherry K, Bitsoi LL, Bassett K, Evans CH (2010) Bridging the Divide between Genomic Science and Indigenous Peoples. J. Law, Medicine & Ethics. 684-696.

222. Hauser RM, Church GM, Duncan GT, Greely HT, Gutmann MP, Levine RJ, Quackenbush J, Reiter JP, Wallace RB, Weinstein M, Cohen B, Pool R, Desiderio UV, Sovde JR (2010) Conducting Biosocial Surveys: Collecting, Storing, Accessing, and Protecting Biospecimens and Biodata NAS Press National Research Council.

221. Schwartz D, Church GM (2010) Collection and Motif-Based Prediction of Phosphorylation Sites in Human Viruses. Science Signaling 3(137):rs2. PMID: 20807955

220. Shee K, Strong M, Guido NJ, Lue R, Church GM, Viel A (2010) Research, Collaboration, and Open Science using Web 2.0 Journal of Microbiology and Biology Education 11:2, p130-134, 2010.

219. Tolonen AC, Haas W, Chilaka AC, Aach J, Gygi SP, Church GM (2010) Proteome-wide systems analysis of a cellulosic biofuel producing microbe. Molecular Systems Biology MSB 7:461. PMID: 21245846

218. Kosuri S, Eroshenko N, LeProust E, Super M, Way J, Li JB, Church GM (2010) A Scalable Gene Synthesis Platform Using High-Fidelity DNA Microchips. Nature Biotech. 28(12):1295-9. PMID: 21113165.Supplement

217. Matzas M, Stahler PF, Kefer N, Siebelt N, Boisguirin V, Leonard JT, Keller A, Stahler CF, Haberle P, Gharizadeh B, Babrzadeh F, Church GM (2010) High-fidelity gene synthesis by retrieval of sequence-verified DNA identified using high-throughput pyrosequencing. Nature Biotech 28(12):1291-4. PMID: 21113166

216. Vigneault F, Woods M, Buzon M, Li C, Pereyra F, Church G, Martinez-Picado J, Rosenberg ES, Telenti A, Yu XG, Lichterfeld M (2010) Transcriptional profiling of CD4 T cells identifies distinct subgroups of HIV-1 elite controllers. J.Virol. PMID: 21177805.

215. Mosberg JA, Lajoie MJ, Church GM (2010) Lambda red recombineering in Escherichia coli occurs through a fully single-stranded intermediate.. Genetics 186(3):791-9. PMID: 20813883

214. Loh YH, Hartung O, Li H, Guo C, Sahalie JM, Manos PD,Urbach A, Heffner GC,Grskovic M, Vigneault F, Lensch MW, Park IH, Agarwal S, Church GM, Collins JJ, Irion S, Daley GQ (2010) Reprogramming of T Cells from Human Peripheral Blood. Cell Stem Cell Jul 2;7(1):15-9. PMID: 20621044

213. Umbarger MA, Wright MA, Porreca GJ, Bay D, Toro E, Shapiro L, Marti-Renom MA, Dekker J, Church GM (2011) The 3D Architecture of a Bacterial Genome. Mol Cell. 2011 Oct 21;44(2):252-64. Supplement

212. Ashley EA, Butte AJ, Wheeler MT, Chen R, Klein TE, Dewey FE, Dudley JT, Ormond KE, Pavlovic A, Morgan AA, Pushkarev D,Neff NF ,Hudgins L, Gong L, Hodges LM, Berlin DS, Thorn CF, Sangkuhl K, Hebert JM, Woon M, Sagreiya H, Whaley R, Knowles JW, Chou MF, Thakuria JV, Rosenbaum AM, Zaranek AW, Church GM, Greely HT, Quake SR, Altman RB (2010) Clinical assessment incorporating a personal genome. Lancet 375: 1525-35. PMID: 20435227

211. Sommer MO, Church GM, Dantas G (2010) The human microbiome harbors a diverse reservoir of antibiotic resistance genes. Virulence. 1(4):299-303. PMID: 21178459

210. Church G (2010) Life after the synthetic cell. Nature May 27;465(7297):422-4. PMID: 20495545

209. Fabsitz RR, McGuire A, Sharp RR, Hudson K, Pandey M, Beskow LM, Biesecker LG, Bookman E, Burke W, Burchard EG, Church G, Clayton EW, Eckfeldt J, Fernandez C, Fisher R, Fullerton SM, Gabriel S, James C, Jarvik G, Kittles R, Leib J, O'Donnell C, O'Rourke PP, Rodriguez LL, Romero F, Schully SD, Shuldiner AR, Shurin S, Sze RKF, Thakuria J, Wolf S, Burke G (2010) Ethical and Practical Guidelines for Reporting Genetic Research Results To Study Participants: Updated Guidelines from an NHLBI Working Group. Circ Cardiovasc Genet. 3(6):574-80. PMID: 21156933

208. Church GM (2010) Synthetic Biology. Nature 463: 26-32.

207. Church G (2010) How Has The Internet Changed The Way You Think?. Edge World Question (Jan 2010).

206. Drmanac R, Burns NL, Callow MJ, Carnevali P, Dahl F, Fernandez A, Halpern AL, Kermani BG, Nazarenko I, Nilsen GB, Pant KP, Sparks AB, Staker B, Yeung G, Baccash J, Borcherding AP, Brownley A, Cedeno R, Chen L, Chernikoff D, Cheung A, Chirita R, Curson B, Ebert J, Hacker CR, Hartlage R, Hauser B, Huang S, Jiang Y, Karpinchyk V, Koenig M, Kong C, Landers T, Le C, Liu J, McBride CE, Morenzoni M, Morey RE, Mutch K, Perazich H, Perry K, Peters BA, Peterson J, Pethiyagoda CL, Pothuraju K, Richter C, Rosenbaum AM, Roy S, Shafto J, Shananhovich V, Shannon KW, Sheppy CG, Sun M, Thakuria JV, Tran A, Vu D, Wu X, Zaranek AW, Drmanac S, Oliphant AR, Banyai WC, Martin B, Ballinger DG, Church GM, Reid CA (2009) Human Genome Sequencing Using Unchained Base Reads on Self-assembling DNA Nanoarrays. Science 2010 Jan 1;327(5961):78-81. Epub 2009 Nov 5; Supplement. PMID: 19892942

205. Sommer MO, Dantas G, Church GM (2009) Functional Characterization of the Antibiotic Resistance Reservoir in the Human Microflora Science Aug 28; 325 (5944) 1128-31. PMID: 19713526 . supplement

204. Friedland AE, Lu TK, Wang X, Shi D, Church GM, Collins J (2009) Synthetic Gene Networks that Count. Science. Jun 14; 324(5931):1199-202. PMID: 19478183 PMCID: 2690711

203. Wang HH, Isaacs FJ, Carr PA, Sun ZZ, Xu G, Forest CR, Church GM (2009) Programming cells by multiplex genome engineering and accelerated evolution. Nature. 460:894-8. PMID: 19633652

202a. Dietz H, Douglas SM, Shih WH.(2009) Folding DNA into twisted and curved nanoscale shapes. Science. Aug 7; 325(5941):725-30.

202. Li JB, Levanon EY, Yoon J-K, Aach J, Xie B, LeProust E, Zhang K, Gao Y, Church GM (2009) Genome-wide Identification of Human RNA Editing Sites by Parallel DNA Capturing and Sequencing. Science. Jun 14; 324(5931):1210-3. PMID: 19478186

201. Kim JI, Ju YS, Park HS, Kim S, Lee S, Yi JH, Mudge J, Miller NA, Hong D, Bell CJ, Kim HS, Chung IS, Seo SH, Yun JY, Woo HN, Lee H, Suh D, Lee S, Park H, Kim JY, Gokcumen O, Mills RE, Zaranek AW, Thakuria J, Wu X, Kim RW, Huntley JJ, Luo S, Schroth GP, Wu TD, Yang KS, Kim H, Church GM, Lee C, Kingsmore SF, Seo JS (2009) A highly annotated whole genome sequence of a Korean Individual. Nature. 2009 Jul 8; 460(7258):1011-5. PMID: 19587683

200a. Ahn SM, Kim TH, Lee S, Kim D, Ghang H, Kim DS, Kim BC, Kim SY, Kim WY, Kim C, Park D, Lee YS, Kim S, Reja R, Jho S, Kim CG, Cha JY, Kim KH, Lee B, Bhak J, Kim SJ. (2009) The first Korean genome sequence and analysis: full genome sequencing for a socio-ethnic group. Genome Res. 2009 May 26;19(9):1622-9. doi: 10.1101/gr.092197.109. PMID: 19470904

200. Church G (2009) The Genome Generation Newsweek (Dec).

199a. Douglas SM, Dietz H, Liedl T, Hogberg B, Graf F, Shih WM (2009) Self-assembly of DNA into nanoscale three-dimensional shapes. Nature May 21; 459(7245):414-8.

199. Lunshof JE, Bobe J, Aach J, Angrist M, Thakuria JV, Vorhaus DB, Hoehe MR, Church GM (2010) Personal genomes in progress: from the human genome project to the personal genome project. Dialogues Clin Neurosci. 2010;12(1):47-60. PMID: 20373666

198a. Guo JU, Ma DK, Mo H, Ball MP, Jang MH, Bonaguidi MA, Balazer JA, Eaves HL, Xie B, Ford E, Zhang K, Ming GL, Gao Y, Song H (2011) Neuronal activity modifies DNA methylation landscape in the adult brain. Nature Neuroscience

198. Prisic S, Dankwa S, Schwartz D, Chou M, Locasale JW, Kang CM, Bemis G, Church G, Steen H, Husson RN (2010) Extensive phosphorylation with overlapping specificity by Mycobacterium tuberculosis serine/threonine protein kinases. PNAS Apr 20;107(16):7521-6. PMID: 20368441

197. P3G Consortium, Church G, Heeney C, Hawkins N, de Vries J, Boddington P, Kaye J, Bobrow M, Weir B (2009) Public access to genome-wide data: five views on balancing research with privacy and protection. PLoS Genet. 2009 Oct; 5(10):e1000665. PMID: 19798440

196. Sullivan GJ, Hay DC, Park IH, Fletcher J, Hannoun Z, Payne CM, Dalgetty D, Black JR, Ross J, Samuel K, Wang G, Daley GQ, Lee JH, Church GM, Forbes SJ, Iredale JP, Wilmut I (2010) Generation of Functional Human Hepatic Endoderm from Human iPS cells. Hepatology 51(1):329-35. PMID: 19877180

195. Sommer MOA, Church GM, Dantas G (2010) A functional metagenomic approach for expanding the synthetic biology toolbox for biomass conversion. Molecular Systems Biology MSB 6:360. PMID: 20393580

194. Zaranek AW, Levanon EY, Zecharia T, Clegg T, Church GM (2010) A Survey of Genomic Traces Reveals a Common Sequencing Error, RNA Editing and DNA Editing. PLoS Genetics May 20;6(5):e1000954. PMID: 20531933

193. Fuller CW, Middendorf LR, Benner SA, Church GM, Harris T, Huang X, Jovanovich SB, Nelson JR, Schloss JA, Schwartz DC, Vezenov DV (2009) Challenges of Sequencing by Synthesis. Nature Biotech. 27(11):1013-23. PMID: 19898456

192. Tolonen A, Chilaka AC, Church GM (2009) Targeted gene inactivation in Clostridium phytofermentans shows that cellulose degradation requires the family 9 hydrolase Cphy3367. Mol Microbiol. 74(6):1300-13. PMID: 19775243

191. Lun DS, Rockwell G, Guido NJ, Baym M, Kelner JA, Galagan JE, Church GM (2009) Large-Scale Identification of Genetic Design Strategies using Local Search. Molecular Systems Biology MSB 5:296. PMID: 19690565

190. Khoury MJ, McBride C, Schully SD, Ioannidis JPA, Feero WG, Janssens ACJW, Gwinn M, Simons-Morton DG, Bernhardt JM, Cargill M, Chanock SJ, Church GM, Coates RJ, Collins FS, Croyle RT, Davis BR, Downing GJ, DuRoss A, Friedman S, Gail MH, Ginsburg GS, Green RC, Greene MH, Greenland P, Gulcher JR, Hsu A, Hudson KL, Kardia SLR, Kimmel PL, Lauer MS, Miller AM, Offit K, Ransohoff DF, Roberts S, Rasooly RS, Stefansson K, Terry SF, Teutsch SM, Trepanier A, Wanke KL, Witte JS, Xu J (2009) The Scientific Foundation for Personal Genomics. Genetics in Medicine Jul 16; PMID: 19617843

189. Zhang K, Li JB, Gao Y, Egli D, Xie B, Lee JH, Aach J, LeProust E, Eggan K, Church GM (2009) Digital RNA Allelotyping Reveals Tissue-specific and Allele-specific Gene Expression in Human. Nature Methods 6(8):613-8. PMID: 19620972 PMC2742772

188. Lee J, Park IH, Gao Y, Li JB, Li Z, Daley G, Zhang K, Church GM (2009) A Robust Approach to Identifying Tissue-specific Gene Expression Regulatory Variants Using Personalized Human Induced Pluripotent Stem Cells. PLoS Genetics 5(11):e1000718. PMID: 19911041 PMC2766639

187. Sandgren A, Strong M, Muthukrishnan P, Weiner BK, Church GM, Murray MB (2009) Tuberculosis drug resistance mutation database. PLoS Med. 6(2):e2. PMID: 19209951

186. de Magalhaes JP, Curado J, Church GM (2009) Meta-analysis of age-related gene expression profiles identifies common signatures of aging. Bioinformatics. Feb 2. PMID: 19189975

185. Li JB, Gao Y, Aach J, Zhang K, Kryukov GV, Xie B, Ahlford A, Yoon J-K, Rosenbaum AM, Zaranek AW, LeProust E, Sunyaev SR, Church GM (2009) Multiplex padlock capturing and sequencing reveal human hypermutable CpG variations. Genome Research 19(9):1606-15. PMID: 19525355

184. Douglas SM, Marblestone A, Teerapittayanon S, Vazquez A, Church GM, Shih WH (2009) Rapid prototyping of three-dimensional DNA-origami shapes with caDNAno Nucleic Acids Res doi:10.1093/nar/gkp436 (software) PMID: 19531737 PMC2731887

183. Carr P, Church GM (2009) Genome Engineering. Nature Biotech. 27(12):1151-62. PMID: 20010598 , supplement

182. Ball MP, Li JB, Gao Y, Lee J, LeProust E, Park IH, Xie B, Daley GQ, Church GM (2009) Targeted and genome-scale strategies reveal gene-body methylation signatures in human cells. Nature Biotechnol 27:361-8. PMID: 19329998 . Supplement

181. Barak M, Levanon EY, Eisenberg E, Paz N, Rechavi G, Church GM, Mehr R (2009) Evidence for Large Diversity in the Human Transcriptome Created by Alu RNA Editing. Nucleic Acids Res. PMID: 19740767 PMC2777429

180. Reppas N, Lin X, Church GM (2004) Experimental and Theoretical Studies of Artificial Microbial Symbiosis. American Institute of Chemical Engineers (AIChE) 2004.

179. de Magalhaes JP, Budovsky A, Lehmann G, Costa J, Li Y, Fraifeld V, Church GM (2009) Human Ageing Genomic Resources: online databases and tools for biogerontologists. Aging Cell 8(1):65-72. PMID: 18986374 PMC2635494

178a. Whiteford N, Skelly T, Curtis C, Ritchie M, Lohr A, Zaranek AW, Abnizove I, Brown C, (2009) Swift: Primary Data Analysis for the Illumina Solexa Sequencing Platform Bioinformatics 2009 25(17):2194-2199.

178. Church GM (2009) Safeguarding Biology. Seed 20:84-86.

177. Church GM (2008) Evolution of Faith In Experiments Edge World Question (Jan 2008).

176. Zaranek AW, Clegg T, Vandewege W, Church GM (2008) Free Factories: Unified Infrastructure for Data Intensive Web Services. USENIX Annual Technical Conference 2008: 391-404. PMID: 20514356 PMC2877279

175a. Chiang CW, Derti A, Schwartz D, Chou MF, Hirschhorn JN, Wu CT (2008) Ultraconserved elements: analyses of dosage sensitivity, motifs and boundaries. Genetics 180, 2277-93.

175. Shendure JA, Porreca GJ, Church GM (2008) Overview of DNA sequencing strategies. Curr Protoc Mol Biol. Unit 7.1. PMID: 18231983

174a. Kim DS, Ross SE, Trimarchi JM, Aach J, Greenberg ME, Cepko CL (2008). Identification of molecular markers of bipolar cells in the murine retina J Comp Neurol. 2008 Apr 10;507(5):1795-810.

174. Schwartz D, Chou MF, Church GM (2008) Predicting protein post-translational modifications using meta-analysis of proteome-scale data sets. Mol Cell Proteomics. 8(2):365-79. web resource PMID: 18974045 PMC2634583

173. Lunshof JE, Chadwick R, Church GM (2008) Hippocrates revisited? Old ideals and new realities. Genomic Med. 2(1-2):1-3. PMID 18716915 PMC2518662

172. Snitkin ES, Dudley AM, Janse DM, Wong K, Church GM, Segre D (2008). Model-driven analysis of experimentally determined growth phenotypes for 465 yeast gene deletion mutants under 16 different conditions. Genome Biology 9:R140. PMID: 18808699 PMC2592718

171. Isenbarger TA, Finney M, Church GM, Gilbert W, Carr CE, Zuber MT, Ruvkun G (2008) The most conserved genome segments for life detection on Earth and other planets. Orig Life Evol Biosph. 38(6):517-33. PMID: 18853276

170. Forest CR, Rosenbaum AM, Church GM (2008) DNA Sequencing By Ligation On Surface-Bound Beads In A Microchannel Environment MicroTAS 2008

169. Vigneault F, Sismour AM, Church GM (2008) Efficient microRNA capture and barcoding via enzymatic oligonucleotide adenylation. Nature Methods 5: 777 - 779. PMID: 18711363

168. Church GM, Porreca GJ, Terry RC, Lares M (2008) High-speed imaging for DNA sequencing. Biophotonics

167. Dantas G, Sommer MO, Oluwasegun RD, Church GM (2008) Bacteria subsisting on antibiotics. Science. 2008 Apr 4;320(5872):100-3. PMID: 18388292

166. Lunshof JE, Chadwick R, Vorhaus DB, Church GM (2008) From genetic privacy to open consent. Nat Rev Genet. 9(5):406-11. PMID: 18379574

165. Bang D, Church GM (2008) Gene synthesis by circular assembly amplification. Nat Methods. 5(1):37-9. PMID: 18037891

164. Kettler GC, Martiny AC, Huang K, Zucker J, Coleman ML, Rodrigue S, Chen F, Lapidus A, Ferriera S, Johnson J, Steglich C, Church GM, Richardson P, Chisholm SW (2007) Patterns and Implications of Gene Gain and Loss in the Evolution of Prochlorococcus. PLoS Genet. 3(12):e231. PMID: 18159947 PMC2151091

163. Church GM (2007) Personal Genomics Will Arrive This Year, and With It a Revolutionary Wave of Volunteerism and Self-Knowledge Edge World Question (Jan 2007) .

162. Porreca GJ, Zhang K, Li JB, Xie B, Austin D, Vassallo SL, LeProust EM, Peck BJ, Emig CJ, Dahl F, Gao Y, Church GM, Shendure J (2007) Multiplex amplification of large sets of human exons. Nat Methods 4(11):931-6. (Supplement) PMID: 17934468

161a. Douglas SM, Chou JJ, Shih WM. (2007) DNA-nanotube-induced alignment of membrane proteins for NMR structure determination. Proc Natl Acad Sci USA 104(16):6644-8. PMID: 17404217

161. de Magalhaes JP, Sedivy JM, Finch CE, Austad SN, Church GM (2007). A Proposal to Sequence Genomes of Unique Interest for Research on Aging. J Gerontol A Biol Sci Med Sci. 62: 583-584. PMID: 17595413 Proposal to Sequence an Organism of Unique Interest for Research on Aging: Heterocephalus glaber, the Naked Mole-Rat

160a. Church GM (2007) Formulae for the 21st Century. Edge/Serpentine Gallery.

160. Nardi V, Raz T, Chao X, Wu CJ, Stone RM, Cortes J, Deininger MWN, Church GM, Zhu J, Daley GQ (2007) Quantitative monitoring by polymerase colony assay of known mutations resistant to ABL kinase inhibitors. Oncogene 27(6):775-82. (Supplement) PMID: 17684485

159. Conrad C, Zhu J, Conrad C, Schoenfeld D, Fang Z, Ingelsson M, Stamm S, Church G, Hyman BT (2007) Single Molecule Profiling of tau Gene Expression in Alzheimer's Disease. J. Neurochem 103(3):1228-36. PMID: 17727636

158. Wright MA, Kharchenko P, Church GM, Segre D (2007) Chromosomal periodicity of evolutionarily conserved gene pairs. Proc Natl Acad Sci USA 2007 Jun 19;104(25):10559-64. PMID: 17563360 PMC1890563

157. Lindell D, Jaffe JD, Coleman ML, Futschik ME, Axmann IM, Rector T, Kettler G, Sullivan MB, Steen R, Hess WR, Church GM, Chisholm SW (2007) Genome-Wide Expression Dynamics of a Marine Virus and its Host Reveal Features of Co-evolution. Nature. 449(7158):83-6. (Supplement). PMID: 17805294

156. Bugl H, Danner JP, Molinari RJ, Mulligan JT, Park HO, Reichert B, Roth DA, Wagner R, Budowle B, Scripp RM, Smith JAL, Steele SJ, Church G, Endy D (2007) DNA synthesis and biological security Nat Biotechnol. 25(6):627-629. PMID: 17557094

155. Kim JB, Porreca GJ, Gorham JM, Church GM, Seidman CE, Seidman JG (2007) Polony multiplex analysis of gene expression (PMAGE) in a mouse model of hypertrophic cardiomyopathy. Science Jun 8; 316(5830):1481-4. PMID: 17556586

154. Bakal C, Aach J, Church GM, Perrimon N (2007) Defining the Components Of Local Signaling Networks That Regulate Cell Morphology Using Quantitative Morphological Signatures. Science Jun 22; 316(5832):1753-6. Supplement PMID: 17588932

153. de Magalhaes JP, Church GM (2007) Analyses of human-chimpanzee orthologous gene pairs to explore evolutionary hypotheses of aging. Mech Ageing Dev. 128(5-6):355-64. PMID: 17459455

152. de Magalhaes JP, Costa J, Church GM (2007) An analysis of the relation between metabolism, developmental schedules, and longevity using phylogenetic independent contrasts. J Gerontol A Biol Sci Med Sci. 62(2):149-60. PMID: 17339640 PMC2288695

151. Strong M, Church G (2007) Gem of an idea for a unique machine. Nature. 2007 May 3;447(7140):112. PMID: 17508434

150. Church G (2007) The Personal Exome Project (Nature Genetics Question of the Year: What would you do if it became possible to sequence the equivalent of a full human genome for only $1,000?)

149. Porreca GJ, Shendure J, Church GM (2006) Polony DNA sequencing.Current Protoc Mol Biol. Unit 7.8. PMID: 18265387

148. The BIO FAB Group -- Baker D, Church G, Collins J, Endy D, Jacobson J, Keasling J, Modrich P, Smolke C, Weiss R (2006) Building a Fab for Biology. Scientific American. June 2006. PMID: 16711359

147. Church GM, Shendure J, Porreca G (2006) Sequencing thoroughbreds Nature Biotech 24: 139. PMID: 16465149

146a. Nguyen DH, D'haeseleer P. (2006) Deciphering principles of transcription regulation in eukaryotic genomes . Mol Syst Biol. 2: 2006.0012.

146. Church GM (2006) Genomes for all . Scientific American Jan 2006. PMID: 16468433

145. Forster AC, Church GM (2007) Synthetic biology projects in vitro. Genome Res. 17(1):1-6. PMID: 17151344

144. Reppas NB, Wade JT, Church GM, Struhl K (2006) The Transition between Transcriptional Initiation and Elongation in E. coli Is Highly Variable and Often Rate Limiting. Molecular Cell 24(5):747-757. PMID: 17157257

143. Tolonen AC, Aach J, Lindell D, Johnson ZI, Rector T, Steen R, Church GM, Chisholm SW (2006) Global gene expression of Prochlorococcus ecotypes in response to changes in nitrogen availability. Mol Syst Biol. 2:53. PMID: 17016519 PMC1682016

142. Derti A, Roth FP, Church GM, Wu CT (2006) Mammalian ultraconserved elements are strongly depleted among segmental duplications and copy number variants. Nat Genet. 38(10):1216-20. PMID: 16998490

141. Turner DJ, Shendure J, Porreca G, Church G, Green P, Tyler-Smith C, Hurles ME (2006) Assaying chromosomal inversions by single-molecule haplotyping. Nat Methods. 3(6):439-45. PMID: 16721377 PMC2690135

140. Jaffe J, Mani DR, Leptos K, Church GM, Carr SA (2006) PEPPeR: A platform for experimental proteomic pattern recognition. Mol Cell Proteomics. 2006 Jul 19; PMID: 16857664

139. Lee S-I, Pe'er D, Dudley AM, Church GM, Koller D (2006) Identifying Regulatory Mechanisms using Individual Variation Reveals Key Role for Chromatin Modification. Proc Natl Acad Sci USA 103(38):14062-7. PMID: 16968785 Supplement

138. Yang A, Zhu Z, Kapranov P, McKeon F, Church GM, Gingeras TR, Struhl K (2006) Relationships between p63 binding, DNA sequence, transcription activity, and biological function in human cells. Mol Cell. 2006 Nov 17;24(4):593-602. PMID: 17188034

137. Kuo WP, Liu F, Trimarchi J, Punzo C, Lombardi M, Sarang J, Whipple ME, Maysuria M, Serikawa K, Lee SY, McCrann D, Kang J, Shearstone J, Burke J, Park D, Wang X, Rector TL, Riccardi-Gastagnoli P, Perrin S, Choi S, Bumgarner R, Kim JH, Short GF, Freeman MW, Seed B, Jensen R, Church GM, Hovig E, Cepko CL, Park P, Ohno-Machado L, Jenssen TK (2006) A sequence-oriented comparison of gene expression measurements across different hybridization-based technologies. Nature Biotech. 24(7):832-840. PMID: 16823376

136. Zhang K, Martiny AC, Reppas NB, Barry KW, Malek J, Chisholm SW, Church GM (2006) Sequencing genomes from single cells by polymerase clones. Nature Biotech. 24(6):680-6. PMID: 16732271

135. Forster AC, Church GM (2006) Toward Synthesis of a Minimal Cell. Nature-EMBO Molecular Systems Biology MSB 2 doi:10.1038/msb4100090. (supplement). PMID: 16924266

134. Zhang K, Zhu J, Shendure J, Porreca GJ, Aach JD, Mitra RD, Church GM (2006) Long-range polony haplotyping of individual human chromosome molecules. Nature Genetics 38(3):382-7. PMID: 16493423

133. Kharchenko P, Chen L, Freund Y, Vitkup D, Church GM (2006) Identifying metabolic enzymes with multiple types of association evidence. BMC Bioinformatics. 2006 Mar 29;7(1):177. PMID: 16571130 PMC1450304

132. Estrada B, Choe SE, Gisselbrecht SS, Michaud S, Raj L, Busser BW, Halfon MS, Church GM, Michelson AM (2006) An Integrated Strategy for Analyzing the Unique Developmental Programs of Different Myoblast Subtypes. PLoS Genet. 2(2):e16. PMID: 16493423

131. de Magalhaes J, Church GM (2006) Cells discover fire: employing reactive oxygen species in development and aging. Experimental Gerontology Oct 11. PMID: 16226003

130. Leptos KC, Sarracino DA, Church GM (2006) MapQuant: Open-Source Software for Large-Scale Protein Quantitation. Proteomics 6(6):1770-82. PMID: 16470651. Data and software supplement. PMID: 16470651

129. Shendure J, Porreca GJ, Reppas NB, Lin X, McCutcheon JP, Rosenbaum AM, Wang MD, Zhang K, Mitra RD, Church GM (2005) Accurate Multiplex Polony Sequencing of an Evolved Bacterial Genome Science 309(5741):1728-32. PMID: 16081699 Supplement

128. Wade JT, Reppas NB, Church GM, Struhl K (2005) Genomic analysis of LexA binding reveals the permissive nature of the Escherichia coli genome and identifies unconventional target sites. Genes Dev. 2005 Nov 1;19(21):2619-30. PMID: 16264194

127. Gao Y, Church G (2005) Improving molecular cancer class discovery through sparse non-negative matrix factorization. Bioinformatics 21: 3970-5. PMID: 16244221

126. Lindell D, Jaffe JD, Johnson ZI, Church GM, Chisholm SW (2005) Photosynthesis genes in marine viruses yield proteins during host infection. Nature 438:86-9. PMID: 16222247

125. de Magalhaes JP, Church GM (2005) Genomes optimize reproduction: aging as a consequence of the developmental program. Physiology 20:252-9.

124. Ahmad R, Nguyen DH, Wingerd MA, Church GM, Steffen MA (2005) Molecular Weight Assessment of Proteins in Total Proteome Profiles Using 1D-PAGE and LC/MS/MS. Proteome Sci. 3(1):6

123. Kharchenko P, Vitkup D, Church GM (2005) Expression dynamics of a cellular metabolic network. Nature-EMBO MSB doi:10.1038/msb4100023, 2-Aug-2005. PMID: 16729051

122. Zhu Z, Shendure J, Church GM (2005) Discovering Functional Transcription Factor Combinations in the Human Cell Cycle. Genome Research 15(6):848-55.

121. Petti A, Church GM (2005) A Network of Transcriptionally Coordinated Functional Modules in Saccharomyces cerevisiae. Genome Research 15(9):1298-306. PMID: 16222247 PMC1199545

120. Dudley A, Janse D, Church GM (2005) A global view of pleiotropy and phenotypically derived gene function in yeast. Nature-EMBO Molecular Systems Biology MSB 4100004-E1-E11. PMID: 16729036 PMC1681449

119. Choe SE, Boutros M, Michelson AM, Church GM, Halfon MS (2005) Preferred analysis methods for Affymetrix GeneChips revealed by a wholly defined control dataset. Genome Biol. 6(2):R16. PMID: 15693945

118. Tompa M, Li N, Bailey TL, Church GM, De Moor B, Eskin E, Favorov AV, Frith MC, Fu Y, Kent WJ, Makeev VJ, Mironov AA, Noble WS, Pavesi G, Pesole G, Rignier M, Simonis N, Sinha S, Thijs G, van Helden J, Vandenbogaert M, Weng Z, Workman C, Ye C, Zhu Z (2005) An Assessment of Computational Tools for the Discovery of Transcription Factor Binding Sites. Nature Biotechnology 23(1):137-44. PMID: 15637633

117. Tian J, Gong H, Sheng N, Zhou X, Gulari E, Gao X, Church GM (2004) Accurate Multiplex Gene Synthesis from Programmable DNA Chips. Nature 432: 1050-4. Supplement. PMID: 15616567

116a. Church GM (2004) A Synthetic Biohazard Non-proliferation Proposal. (web.archive.org)

116. Segre D, DeLuna A, Church GM, Kishony R (2004) Modular epistasis in yeast metabolism Nature Genetics 37(1):77-83. PMID: 15592468

115. Feingold EA, Good PJ, Guyer MS, Kamholz S, Liefer L, Wetterstrand K, Collins FS, Gingeras TR, Kampa D, Sekinger EA, Cheng J, Hirsch H, Ghosh S, Zhu Z, Patel S, Piccolboni A, Yang A, Tammana H, Bekiranov S, Kapranov P, Harrison R, Church G, Struhl K, Ren B, Kim TH, Barrera LO, Qu C, Van Calcar S, Luna R, Glass CK, Rosenfeld MG, Guigo R, Antonarakis SE, Birney E, Brent M, Pachter L, Reymond A, Dermitzakis ET, Dewey C, Keefe D, Denoeud F, Lagarde J, Ashurst J, Hubbard T, Wesselink J, Castelo R, Eyras E, Myers RM, Sidow A, Batzoglou S, Trinklein ND, Hartman SJ, Aldred SF, Anton E, Schroeder DI, Marticke SS, Nguyen L, Schmutz J, Grimwood J, Dickson M, Cooper GM, Stone EA, Asimenos G, Brudno M, Dutta A, Karnani N, Taylor CM, Kim HK, Robins G, Stamatoyannopoulos G, Stamatoyannopoulos JA, Dorschner M, Sabo P, Hawrylycz M, Humbert R, Wallace J, Yu M, Navas PA, McArthur M, Noble WS, Dunham I, Koch CM, Andrews RM, Clelland GK, Wilcox S, Fowler JC, James KD, Groth P, Dovey OM, Ellis PD, Wraight VL, Mungall AJ, Dhami P, Fiegler H, Langford CF, Carter NP, Vetrie D, Snyder M, Euskirchen G, Urban AE, Nagalakshmi U, Rinn J, Popescu G, Bertone P, Hartman S, Rozowsky J, Emanuelsson O, Royce T, Chung S, Gerstein M, Lian Z, Lian J, Nakayama Y, Weissman S, Stolc V, Tongprasit W, Sethi H, Jones S, Marra M, Shin H, Schein J, Clamp M, Lindblad-Toh K, Chang J, Jaffe DB, Kamal M, Lander ES, Mikkelsen TS, Vinson J, Zody MC, deJong PJ, Osoegawa K, Nefedov M, Zhu B, Baxevanis AD, Wolfsberg TG, Crawford GE, Whittle J, Holt IE, Vasicek TJ, Zhou D, Luo S, Green ED, Bouffard GG, Margulies EH, Portnoy ME, Hansen NF, Thomas PJ, McDowell JC, Maskeri B, Young AC, Idol JR, Blakesley RW, Schuler G, Miller W, Hardison R, Elnitski L, Shah P, Salzberg SL, Pertea M, Majoros WH, Haussler D, Thomas D, Rosenbloom KR, Clawson H, Siepel A, Kent WJ, Weng Z, Jin S, Halees A, Burden H, Karaoz U, Fu Y, Yu Y, Ding C, Cantor CR, Kingston RE, Dennis J, Green RD, Singer MA, Richmond TA, Norton JE, Farnham PJ, Oberley MJ, Inman DR, McCormick MR, Kim H, Middle CL, Pirrung MC, Fu XD, Kwon YS, Ye Z, Dekker J, Tabuchi TM, Gheldof N, Dostie J, Harvey SC (2004) The ENCODE (ENCyclopedia Of DNA Elements) Project. Science 306: 636-40. PMID: 15499007

114. Church GM (2005) Let us go forth and safely multiply. Nature 438: 423. PMID: 16306966

113. Church GM (2005) The Personal Genome Project. Nature EMBO Molecular Systems Biology doi:10.1038/msb4100040. PMID: 16729065

112a. Pe'er D (2005) Bayesian network analysis of signaling networks: a primer. Sci STKE. 2005 Apr 26;2005(281):pl4.

112. Aach J, Church GM (2005) Accommodation or prediction? Science. 2005 Jun 3;308(5727):1409-12; author reply 1409-12.

111a. Sachs K, Perez O, Pe'er D, Lauffenburger DA, Nolan GP (2005) Causal protein-signaling networks derived from multiparameter single-cell data Science. 2005 Apr 22;308(5721):523-9.

111. Church GM (2005) From systems biology to synthetic biology. Molecular Systems Biology doi:10.1038/msb4100007 (open access). PMID: 16729067

110. Church GM (2004) The Future of Human Nature pp. 41-44

109. D'haeseleer P, Church GM (2004) Estimating and improving protein interaction error rates. Proc IEEE Comput Syst Bioinform Conf. 2004:216-23. PMID: 16448015

108. Grainger DC, Overton TW, Reppas N, Wade JT, Tamai E, Hobman JL, Constantinidou C, Struhl K, Church G, Busby SJW (2004) Genomic studies with Escherichia coli MelR protein: applications of chromatin immunoprecipitation and microarrays. J Bacteriol. 186(20):6938-43.

107. Jaffe JD, Stange-Thomann N, Smith C, DeCaprio D, Fisher S, Butler J, Calvo S, Elkins T, FitzGerald MG, Hafez N, Kodira CD, Major J, Wang S, Wilkinson J, Nicol R, Nusbaum C, Birren B, Berg HC, Church GM (2004) The complete genome and proteome of Mycoplasma mobile. Genome Research 14: 1447-1461. supplement PMID: 15289470

106. Shendure J, Mitra R, Varma C, Church GM (2004) Advanced Sequencing Technologies: Methods and Goals. Nature Reviews of Genetics 5(5):335-44. Supplement. PMID: 15143316

105. Mikkilineni V, Mitra RD, Merritt J, DiTonno JR, Church GM, Ogunnaike B, Edwards JS (2004) Digital quantitative measurements of gene expression. Biotechnol Bioeng. 2004 Apr 20;86(2):117-24. PMID: 15052631

104. Catic A, Collins C, Church GM, Ploegh HL (2004) Preferred in vivo ubiquitination sites. Bioinformatics Jul 15.

103. Bulyk ML, McGuire AM, Masuda N, Church GM (2004) A Motif Co-Occurrence Approach for Genome-Wide Prediction of Transcription-Factor-Binding Sites in Escherichia coli Genome Research 14(2):201-8.

102. Kharchenko P, Church GM, Vitkup D (2004) Filling gaps in a metabolic network using expression information. Bioinformatics Aug 4;20 Suppl 1:I178-I185.

101. Janse DM, Crosas B, Finley D, Church GM (2004) Localization to the Proteasome is Sufficient for Degradation. J. Biol Chem 279 (20):21415-20.

100. Grad YH, Roth FP, Halfon MS, Church GM (2004) Prediction of similarly-acting cis-regulatory modules by subsequence profiling and comparative genomics in D. melanogaster and D. pseudoobscura. Bioinformatics, May 14.

99. Kim J, Kirchevsky A, Grad Y, Hayes GD, Kosik KS, Church GM, Ruvkun G (2004) Identification of many microRNAs that copurify with polyribosomes in mammalian neurons. Proc Natl Acad Sci USA 101(1): 360-5.

98. Lelandais G, LeCrom S, Devaux F, Vialette S, Church GM, Jacq C, Marc P (2004) yMGV: a cross-species expression data mining tool. Nucleic Acids Res. 90001 D323-D325.

97. Aach J, Church GM (2004)Mathematical models of diffusion-constrained polymerase chain reactions: basis of high-throughput nucleic acid assays and simple self-organizing systems. J Theor. Biol. May 7;228(1):31-46. supplemental material

96. Jaffe JD, Berg HC, Church GM (2004) Proteogenomic mapping reveals genomic structure and novel proteins undetected by computational algorithms. Proteomics 4(1): 59-77. supplement PMID: 14730672

95. Vitkup D, Sander C, Church GM (2003) The Amino-acid Mutational Spectrum of Human Genetic Disease. Genome Biol. 4: R72.

94. Segre D, Zucker J, Katz J, Lin X, D'haeseleer P, Rindone W, Karchenko P, Nguyen D, Wright M, Church GM (2003) From annotated genomes to metabolic flux models and kinetic parameter fitting. Omics 7:301-16. (Biospice special issue)

93. Zhu J, Shendure J, Mitra RD, Church GM (2003) Single Molecule Profiling of Alternative Pre-mRNA Splicing. Science. 2003 Aug 8;301(5634):836-8. (Supplement) PMID: 12907803

92. King OD, Lee JC, Dudley AM, Janse DM, Church GM, Roth FP (2003) Predicting Phenotype from Patterns of Annotation. ISMB 2003; Bioinformatics. 19 Suppl 1:I183-I189.

91. Grad Y, Kim J, Aach J, Hayes G, Reinhart B, Church GM, Ruvkun G (2003) Computational and Experimental Identification of C. elegans microRNAs Molecular Cell 11(5):1253-63.

90. Merritt J, DiTonno JR, Mitra RD, Church GM, Edwards JS (2003) Parallel competition analysis of Saccharomyces cerevisiae strains differing by a single base using polymerase colonies. Nucleic Acids Research 2003 Aug 1;31(15):e84. . PMID: 12888536

89. Anderson LM, Choe SE, Yukhananov RY, Hopfner RL, Church GM, Pratt RE, Dzau VJ (2003) Identification of a novel set of genes regulated by a unique LXRalpha-mediated Transcription Mechanism. J. biol. Chem. Apr 25;278(17):15252-60. Epub 2003 Jan 27.

88. Mitra RD, Shendure J, Olejnik J, Olejnik EK, Church GM (2003) Fluorescent in situ Sequencing on Polymerase Colonies. >Analyt. Biochem. 320:55-65. Protocol & software supplements. PMID: 12895469

87. Mitra RD, Butty V, Shendure J, Williams BR, Housman DE, Church GM (2003) Digital Genotyping and Haplotyping with Polymerase Colonies. Proc Natl Acad Sci USA May 13;100(10):5926-31. PMID: 12730373

86. Yao MWM, Lim H, Schust DJ, Choe SE, Farago A, Ding Y, Michaud S, Church GM, Maas RL (2003) Gene expression profiling reveals progesterone-mediated cell cycle and immunoregulatory roles of Hoxa-10 in the pre-implantation uterus. Molecular Endocrinology 17(4):610-27.

85. Masuda N, Church GM (2003) Regulatory Network of acid resistances genes in Escherichia coli. Molecular Microbiology 48 (3), 699-712.

84. Selinger DW, Saxena RM, Cheung KJ, Church GM, Rosenow C (2003) Global RNA half-life analysis in Escherichia coli reveals positional patterns of transcript degradation . Genome Research 13(2):216-23.

83. Selinger D, Wright M, Church GM (2003) On the complete determination of biological systems . Trends in Biotechnology 21: 251-4.

82. Wright M, Segre D, Church G (2002) 4-D Model of Bacterial Chromosome Structure . ICSB 2002, 3rd International Conference on System Biology, pp. 229-230

81. Church GM (2002) Foreword in Scientific American's "Understanding the Genome".

80. Cheung KJ, Badarinarayana V, Selinger D, Janse D, Church GM (2002) A microarray-based antibiotic screen identifies a regulatory role for supercoiling in the osmotic stress response of Escherichia coli . Genome Research 13(2):206-15.

79. Segre D, Vitkup D, Church GM (2002) Analysis of optimality in natural and perturbed metabolic networks . Proc. Nat. Acad. Sci USA 99: 15112-7. Supplement (MOMA)

78. Sudarsanam P, Pilpel Y, Church GM (2002) Genome-wide co-occurrence of promoter elements reveals a cis-regulatory cassette of rRNA transcription motifs in S. cerevisiae. Genome Research 12: 1723-1731

77. Steffen M, Petti A, D'haeseleer P, Aach J, Church GM (2002) Automated Modelling of Signal Transduction Networks. BMC Bioinformatics 3:34-44.

76. Masuda N, Church GM (2002) Global Analysis of Escherichia coli Gene Expression during the Overexpression of the Response Regulator EvgA . J Bacteriol. 184(22):6225-34.

75. Wright M, Church GM (2002) An Open-source Oligonucleotide Microarray Probe Standard for Human and Mouse . Nat Biotechnol. 20(11):1082-3.. Supplement

74. Shendure J, Church GM (2002) Computational discovery of sense-antisense transcription in the mouse and human genomes . Genome Biology 3:1-14 . Supplements: antisense & HumMus.

73. Halfon MS, Grad Y, Church GM, Michelson AM (2002) Computation-based discovery of related transcriptional regulatory modules and motifs from a combinatorial model. Genome Research 12: 1019-1028.

72. Schilling CH, Covert MW, Famili I, Church GM, Edwards JS, Palsson BO (2002) Genome-scale metabolic model of Helicobacter pylori 26695. J Bacteriol. 184(16):4582-93.

71. Dudley AM, Aach J, Steffen MA, Church GM (2002) Measuring absolute expression with microarrays using a calibrated reference sample and an extended signal intensity range. Proc. Nat. Acad. Sci. USA 99:7554-7559. Supplement.

70. Cohen B, Pilpel Y, Mitra R, Church GM (2002) Discrimination between Paralogs using Microarray Analysis: Application to the Yap1p and Yap2p Transcriptional Networks. Mol Biol Cell 13(5):1608-14. PMID: 12006656

69. Lee ML, Bulyk ML, Whitmore GA, Church GM (2002) A statistical model for investigating binding probabilities of DNA nucleotide sequences using microarrays . Biometrics 58(4):981-8. PMID: 12495153

68. Zhu Z, Pilpel Y, Church GM (2002) Computational Identification of Transcription Factor Binding Sites via a Transcription-factor-centric Clustering (TFCC) Algorithm. J. Molec. Biol. 318: 71-81. PMID: 12054769

67. Bulyk ML, Johnson PLF, Church GM (2002) Nucleotides of transcription factor binding sites exert interdependent effects on the binding affinities of transcription factors. Nucleic Acids Research 30:1255-1261. PMID: 11861919

66. Weber G, Shendure J, Tanenbaum DM, Church GM, Meyerson M (2002) Identification of foreign gene sequences by transcript filtering against the human genome. Nature Genetics 30(2):141-2. PMID: 11788827

65a. Brazma A, Hingamp P, Quackenbush J, Sherlock G, Spellman P, Stoeckert C, Aach J, Ansorge W, Ball CA, Causton HC, Gaasterland T, Glenisson P, Holstege FC, Kim IF, Markowitz V, Matese JC, Parkinson H, Robinson A, Sarkans U, Schulze-Kremer S, Stewart J, Taylor R, Vilo J, Vingron M (2001) Minimum information about a microarray experiment (MIAME) -toward standards for microarray data Nat Genet. 29(4):365-71

65. Badarinarayana V, Estep PW, Shendure J, Edwards J, Tavazoie S, Lam F, Church GM (2001) Selection analyses of insertional mutants using subgenic-resolution arrays; Nature Biotechnology 19: 1060-5.(web supplement)

64. Ge H, Church GM, Vidal M (2001) Correlation between transcriptome and interactome data obtained from S. cerevisiae. Nature Genetics 29(4):482-6.

63. Pilpel Y, Sudarsanam P, Church GM (2001) Identifying regulatory networks by combinatorial analysis of promoter elements . Nature Genetics 29(2):153-9. (Supplementary info).

62. Chen T, Jaffe JD, Church GM (2001) Algorithms for Identifying Protein Cross-links via Tandem Mass Spectrometry . RECOMB 2001. J Comput Biol. J Comput Biol. 8(6):571-583. PMID: 11747613

61. Aach J, Church GM (2001) Aligning gene expression time series with time warping algorithms. Bioinformatics 17:495-508. (web supplement) 1-8. PMID: 11395426

60. Bulyk ML, Choo Y, Huang X, Church GM (2001) Exploring DNA binding specificities of zinc fingers with DNA microarrays . Proc. Nat. Acad. Sci USA 98: 7158-7163. Supplement.

59. Aach J, Bulyk ML, Church GM, Comander J, Derti A, Shendure J (2001) Computational comparison of two draft sequences of the human genome. Nature 409, 856-859. (web supplements -software- & -doc-) PMID: 11237010

58. Selinger D, Cheung K, Mei R, Johanson EM, Richmond C, Blattner FR, Lockhart D, Church GM (2000) RNA expression analysis using a 30 base pair resolution Escherichia coli genome array. Nature Biotechnology 18, 1262-7. (Suppl. data and software)

57. Jamshidi N, Edwards JS, Fahland T, Church GM, Palsson BO (2001) Dynamic simulation of the human red blood cell metabolic network. Bioinformatics 17: 286-287. (Supplementary software)

56. Hoehe MR, Kopke K, Wendel B, Rohde K, Flachmeier C, Kidd KK, Berrettini WH, Church GM (2000) Sequence Variability and Candidate Gene Analysis in Complex Disease: Association of mu Opioid Receptor Gene Variation with Substance Dependence. Human Molec. Genetics 9: 2895-2908. (Software)

55. Cohen BA, Mitra RD, Hughes JD, Church GM (2000) A computational analysis of whole genome expression data reveals chromosomal domains of gene expression. Nature Genetics 26(2):183-186. PMID: 11017073

54. Livesey FJ, Furukawa T, Steffen MA, Church GM, Cepko CL (2000) Microarray analysis of the transcriptional network controlled by the photoreceptor homeobox gene Crx . Current Biology 10: 301-310.

53. Mcguire AM, Church GM (2000) Predicting regulons and their cis-regulatory motifs by comparative genomics. Nucleic Acids Research 28:4523-30.

52. Goldmark JP, Fazzio TG, Estep PW, Church GM, Tsukiyama T (2000) The Isw2 chromatin remodeling complex represses early meiotic genes upon recruitment by Ume6p , Cell 103: 423.

51. Jelinsky SA, Estep P, Church GM, Samson LD (2000) Regulatory networks revealed by transcriptional profiling of damaged Saccharomyces cerevisiae cells: Rpn4 links base excision repair with proteasomes. Molecular and Cellular Biol. 20:8157-8167.

50. McGuire AM, Hughes JD, Church GM (2000) Conservation of DNA regulatory motifs and discovery of new motifs in microbial genomes. Genome Res. 2000;10 744-757 supplementary info

49. Chen T, Kao M, Tepel M, Rush J, Church GM (2000) A dynamic programming approach to de novo peptide sequencing via tandem mass spectrometry. 11th Annual ACM-SIAM Symp. of Discrete Algorithms pp. 389-398.

48. Johnson JM, Church GM (2000) Predicting ligand-binding function in families of bacterial receptors. . Proc. Nat. Acad. Sci USA 97(8):3965-70. (Supplement).

47. Teichmann SA, Chothia C, Church GM, Park J (2000) Fast assignment of protein structures to sequences using the intermediate sequence library PDB-ISL. Bioinformatics 16: 117-124.

46. Cheng Y, Church GM (2000) Biclustering of expresssion data ISMB 2000. (Supplement. & Java version).

45. Hughes JD, Estep PW, Tavazoie S, Church GM (2000) Computational identification of cis-regulatory elements associated with functionally coherent groups of genes in Saccharomyces cerevisiae. J. Molec. Biol. 296: 1205-1214.

44. Aach J, Rindone W, Church GM (2000) Systematic management and analysis of yeast gene expression data Genome Research 10: 431-445.ExpressDB PMID: 10779484

43. Mitra R, Church GM (1999) In situ localized amplification and contact replication of many individual DNA molecules.  Nucleic Acids Res. 27(24):e34; pp.1-6.

42. Tavazoie S, Hughes JD, Campbell MJ, Cho RJ, Church GM (1999) Systematic determination of genetic network architecture. Nature Genetics 22:281-5.

41. Bulyk ML, Gentalen E, Lockhart DJ, Church GM (1999) Quantifying DNA-protein interactions by double-stranded DNA arrays. Nature Biotechnology 17: 573-7.

40. McGuire AM, De Wulf P, Church GM, Lin EC (1999) A weight matrix for binding recognition by the redox-response regulator ArcA-P of Escherichia coli . Mol Microbiol 32: 219-21.

39. Johnson JM, Church GM (1999) Alignment and structure prediction of divergent protein families: periplasmic and outer membrane proteins of bacterial efflux pumps.  J. Molec. Biol. 287: 695-715. (Supplement).

38. Robison KR, McGuire AM, Church GM (1998) A comprehensive library of DNA-binding site matrices for 55 proteins applied to the complete Escherichia coli K-12 genome. J. Molec. Biol. 284: 241-254.

37. Tavazoie S, Church GM (1998) Quantitative Whole-genome analysis of DNA-protein interactions by in vivo methylase protection in E.coli. Nature Biotechnology 16: 566-571.

36. Roth FP, Hughes JD, Estep PW, Church GM (1998) Finding DNA regulatory motifs within unaligned non-coding sequences by whole-genome mRNA quantitation. Nature Biotechnology 16: 939-945.

35. Chen T, He HL, Church GM (1999) Modeling Gene Expression with Differential Equations. Pac Symp Biocomput-1999:29-40.

34. Collins FS, Patrinos A, Jordan E, Chakravarti A, Gesteland R, Walters L (with Fearon E, Hartwell L, Langley CH, Mathies RA, Olson M, Pawson AJ, Pollard T, Williamson A, Wold B, Buetow K, Branscomb E, Capecchi M, Church G, Garner H, Gibbs RA, Hawkins T, Hodgson K, Knotek M, Meisler M, Rubin GM, Smith LM, Smith RF, Westerfield M, Clayton EW, Fisher NL, Lerman CE, McInerney JD, Nebo W, Press N, Valle D) (1998) New goals for the U.S. Human Genome Project: 1998-2003. Science 282(5389):682-9.

33. Smith DR, Doucette-Stamm LA, Deloughery C, Lee H, Dubois J, Aldredge T, Bashirzadeh R, Blakely D, Cook R, Gilbert K, Harrison D, Hoang L, Keagle P, Lumm W, Pothier B, Qiu D, Spadafora R, Vicaire R, Wang Y, Wierzbowski J, Gibson R, Jiwani N, Caruso A, Bush D, Safer H, Patwell D, Prabhakar S, McDougall S, Shimer G, Goyal A, Pietrokovski S, Church GM, Daniels CJ, Mao J, Rice P, Nolling J, Reeve JN (1997) The Complete Genome Sequence of Methanobacterium thermoautotrophicum Strain delta-H: Functional Analysis and Comparative Genomics . J. Bacteriol. Nov. 179: 7135-7155.

32. Bian N, Wang P, Wang Z, Church GM, Giese RW (1997) Detection via Laser Desorption and Mass Spectrometry of Multiplex Electrophore-Labeled Albumin. Rapid Commun. Mass Spectrom. 11: 1781-1784.

31. Link AJ, Phillips D, Church GM (1997)Methods for generating precise deletions and insertions in the genome of wild-type Escherichia coli: Application to open reading frame characterization. J. Bacteriol. 179: 6228-6237. PMID: 9335267 Addgene: pKOV

30. Link AJ, Robison K, Church GM (1997) Comparing the predicted and observed properties of proteins encoded in the genome of Escherichia coli. Electrophoresis 18 (8):1259-1313 . PMID: 9298646

29. Xu L, Bian N, Wang Z, Abdel-Baky S, Pillai S, Magiera D, Murugaiah V, Giese RW, Wang P, O'Keeffe T, Abushamaa H, Kutney L, Church GM, Carson S, Smith D, Park M, Wronka J, Laukien F (1997) Electrophore Mass Tag Dideoxy DNA Sequencing. Analytical Chemistry 69: 3595-3602.

28. Smith DR, Richterich P, Rubenfield M, Rice PW, Butler C, Lee HM, Kirst S, Gundersen K, Abendschan K, Xu Q, Chung M, Deloughery C, Aldredge T, Maher J, Lundstrom R, Tulig C, Falls K, Imrich J, Torrey D, Engelstein M, Breton G, Madan D, Nietupski R, Seitz B, Connelly S, McDougall S, Safer H, Gibson R, Doucette-Stamm L, Eiglmeier K, Bergh S, Cole ST, Robison K, Richterich L, Johnson J, Church GM, Mao J (1997) Multiplex sequencing of 1.5 Mb of the Mycobacterium leprae genome. NCBI Accession numbers: L01095, L01263, L01536, L04666, U00010 to U00023, U15180 to U15184, U15186, U15187. Genome Research 7: 802-819. PMID: 9267804

27. Church GM (1996) Databases for Gene Expression. Nature Biotechnology 14: 828. PMID: 9631002

26. Goodman HM, Gallant P, Keifer-Higgins S, Rubenfield M, Church GM (1996) A 37.5 Kb sequence from Arabidopsis thaliana chromosome I. Genbank Accession number: U53501.

25. Robison K, Gilbert W, Church GM (1996) More Haemophilus and Mycoplasma genes. Science 271: 1302-1304. PMID: 8638118

24. Richterich P, Lakey ND, Lee HM, Mao J, Smith D, Church GM (1995) Cytosine specific DNA sequencing with hydrogen peroxide. Nucl. Acids. Res. 23:4922-4923. PMID: 8532538

23. Chae HZ, Robison K, Poole LB, Church GM, Storz G, Rhee SG (1994) Cloning and sequencing of the thiol-specific antioxidant from mammalian brain: Alkyl hydroperoxide reductase and thiol-specific antioxidant define a large family of antioxidant enzymes. Proc. Nat. Acad. Sci. USA 91: 7017-7021 PMID: 8041738

22. Robison K, Gilbert W, Church GM (1994) Large scale bacterial gene discovery by similarity search. Nature Genetics 7: 205-214. Data Archive PMID: 7920643

21. Richterich P, Lakey N, Gryan G, Jaehn L, Mintz L, Robison K, Church GM (1994) Automated multiplex sequencing of E.coli genomic and plasmid DNA, Genbank accession numbers: U00007, U00008, U00009,U43659, U39483-4, U38811, U38702, U38659-60, U35065-7, U34308, U30459, U26536, U27210-1, U00003.

20. Church GM, Gryan G, Lakey N, Kieffer-Higgins S, Mintz L, Temple M, Rubenfield M, Jaehn L, Ghazizadeh H, Robison K, Richterich P (1994) Automated Multiplex Sequencing. Automated DNA sequencing and analysis techniques, pp. 11-16. (eds. Adams MD, Fields C, Venter JC (Academic Press, San Diego).

19a. Hudson TJ, Engelstein M, Lee MK, Ho EC, Rubenfield MJ, Adams CP, Housman DE, Dracopoli NC (1992) Isolation and chromosomal assignment of 100 highly informative human simple sequence repeat polymorphisms. Genomics. 13(3):622-9. PMID: 1639389

19. Roth JR, Lawrence JG, Rubenfield M, Kieffer-Higgins S, Church GM (1993) Characterization of the cobalamin (Vitamin B12) biosynthetic genes in Salmonella typhimurium. J. Bacteriology 175: 3303-3316. PMID: 8501034

18a. Carlone RL, Boulianne RP, Link AJ (1992) Identification of proteins potentially involved in proximal-distal pattern formation in the regenerating forelimb of the newt. Biochem Cell Biol. 70: 285-290.

18. Richterich P, Church GM (1993) DNA sequencing with direct transfer electrophoresis and non-radioactive detection. Methods in Enzymology 218, 187-222. PMID: 8510533

17a. Almiron M, Link AJ, Furlong D, Kolter R (1992) A novel DNA binding protein with regulatory and protective roles in starved E.coli. Genes and Development 6: 2646-2654.

17. Walsh C, Ryder L, Cepko C, Church GM, Tabin C (1992) The dispersion of neuronal clones across the cerebral cortex. Science 258: 317-320. supplement.

16a. Kafatos FC, Louis C, Savakis C, Glover DM, Ashburner M, Link AJ, Siden-Kiamos I, Saunder RDC (1991) Integrated maps of the Drosophila genome: progress and prospects. Trends in Genetics 7: 155-161.

16. Wang M, Church GM (1992) A whole genome approach to in vivo DNA-protein interactions in Escherichia coli. Nature 360: 606-610. PMID: 1334233

15a. Danilevskaya ON, Kurenova EV, Pavlova MN, Bebehov DV, Link AJ, Koga A, Vellek A, Hartl DL (1991) He-T family DNA sequences in the Y chromosome of Drosophila melanogaster share homology with the X-linked Stellate genes. Chromosoma 100: 118-124.

15. Church GM, Mintz L (1992) REPLICA: Automatic DNA sequencing from films using multiplex internal standards, sequence assembly, and image databases. (A 40,000 line Fortran and "C" program distributed by HMS-OTL). Gryan G, Church GM (1992) GTAC: DNA sequence assembly software for shotgun and directed strategies: New algorithms and tests on megabase sized data sets. (A 30,000 line "C" program distributed by HMS-OTL).
br>14a. Link AJ, Olson MV (1991) Genome-wide mapping and cryo-EM structural analyses of the overlapping tri-nucleosome composed of hexasome-hexasome-octasome moieties.

14a. Ajioka JW, Smoller DA, Jones RW, Carulli JP, Vellek AE, Garza D, Link AJ, Duncan IW, Hartl DL (1991) Drosophila genome project: one-hit coverage in yeast artificial chromosomes. Chromosoma 100: 495-509.

14. Sikorav JL, Church GM (1991) Accelerated DNA renaturation: Complementary recognition in condensed DNA J. Mol. Biol. 222: 1085-1108. PMID: 1837060

13a. Tempst P, Link AJ, Riviere LR, Fleming M, Elicone C (1990) Internal sequence analysis of proteins separated on polyacrylamide gels at the sub-microgram level: Improved methods, applications and gene cloning strategies. Electrophoresis 11: 537-553. PMID: 2226409

13. Church GM, Kieffer-Higgins S(1988) Multiplex DNA sequencing . Science 240: 185-8. PMID: 3353714

12. Church GM, Ephrussi A, Gilbert W, Tonegawa S (1985) Cell-type specific contacts to immunoglobulin enhancers in nuclei. Nature 313: 798-801. PMID: 3919308

12a. Delehanty J, White RL, Mendelsohn ML (with Branscomb E, Botstein D, Cantor C, Caskey T, Church GM, Hood L, Lerman L, Myers R, Neel JV, Olson M, Weissman S) (1986) International Commission for Protection Against Environmental Mutagens and Carcinogens. ICPEMC Meeting Report No. 2. Approaches to determining mutation rates in human DNA Mutat Res 167(3):215-32

11. Church GM, Gilbert W (1985) The genomic sequencing technique. Prog Clin Biol Res 177:17-21. PMID: 2989835

10. Ephrussi A, Church GM, Tonegawa S, Gilbert W (1985) B Lineage-specific interactions of an immunoglobulin enhancer with cellular factors in vivo. Science 227: 134-140. NCBI DNA accession#: M12827 PMID: 3917574

9. Church GM, Gilbert W (1984) Genomic Sequencing. Proc. Nat. Acad. Sci. USA 81: 1991-1995. PMID: 6326095

8. Church GM, Gilbert W (1980) Yeast mitochondrial intron products required in trans for RNA splicing. In Mobilization and Reassembly of Genetic Information, eds. Joseph DR, Schultz J, Scott WA, Werner R (Academic Press, New York) pp. 379-395.

7. Church GM, Slonimski PS, Gilbert W (1979) Pleiotropic mutations within two yeast mitochondrial cytochrome genes block mRNA processing. Cell 18: 1209-1215. PMID: 229970

6. Sutcliffe JG, Church GM (1978) The cleavage site of the restriction endonuclease Ava II. Nucleic Acids Res. 5: 2313-2319. PMID: 97636

5. Sussman JL, Holbrook SR, Warrant RW, Church GM, Kim SH (1978) Crystal structure of yeast phenylalanine transfer RNA I. Crystallographic refinement. J. Mol. Biol. 123: 607-630. PDB ID: 6TNA PMID: 357742

4. Holbrook SR, Sussman JL, Warrant RW, Church GM, Kim SH (1977) RNA-ligand interactions: (I) magnesium binding sites in yeast tRNA phe. Nucleic Acids Res. 4: 2811-2820. PMID: 333395

3. Sussman JL, Holbrook SR, Church GM, Kim SH (1977) A structure factor least-squares refinement procedure for macromolecular structures using constrained and restrained parameters . Acta Cryst. A33: 800-804.

2. Church GM, Sussman JL, Kim SH (1977) Secondary structural complementarity between DNA and proteins. Proc. Nat. Acad. Sci. USA 74: 1458-1462. PMID: 266187

1. Kim SH, Sussman JL, Church GM (1975) A model for recognition scheme between double stranded DNA and proteins. In Structure and Conformation of Nucleic Acids and Protein-Nucleic Acid Interactions, eds. Sundaralingam M, Rao ST (Univ. Park Press, Baltimore, MD), pp. 571-575.

---

Papers submitted or in prep (not yet published)

551s. MacKay MJ, Hooker A, Afshinnekoo E, Feldstein J, Haft N, Kelly J, Boeke J, Salit M, Zhang F, Church G, Vallone P, Huber J, Hanlee Ji, Wyllie A, Mason CE (2020) Technologies to Enable Continual, Widespread COVID-19 Testing. In prep.

550s. Kunjapur AM, Napolitano MG, Hysolli E, Noguera K, Appleton EM, Schubert MG, Jones MA, Mandell DJ, Church GM (2020) Automated continuous evolution of a synthetic auxotroph. in prep.

519s. Dong M, Appleton E, Church G (2019) The first-in-class post-exposure countermeasure against botulinum neurotoxins and a novel drug delivery platform for treating motor neuron degenerative diseases. In prep.

510s. Sinai S, Tam A, Church GM, Kelsic E, Nowak MA (2019) Super-Darwinian exploration of fitness landscapes with model-guided targeted mutagenesis. in prep.

500s. Wang K, Lin RZ, Ng AH, Hong X, Lee CN, Neumeyer J, Wang G, Pu WT, Church GM, Melero-Martin JM (2018) Robust and highly efficient differentiation of human induced pluripotent stem cells into endothelial cells using synthetic modified mRNA encoding transcription factor. in prep.

466s. Goela N, Lee HH, Kalhor R, Bolot J, Church GM (2017) DNA data... in prep.

427s. Yeo NC, Guo X, Chavez A, Chari R, Shen CH, Sami R, Tung A, Lance-Byrne A, Cecchi R, Buchthal J, Collins JJ, Church GM (2017) A flexible Cas9 toolkit for facile genome engineering. submitted.

423s. Rios X, Gregg CJ, Lajoie MJ, Chung MY, Cruz J, Govindarajan LN, Wapinski I, Konieczka J, Church GM (2016) Facilitating Recombinase Discovery in Non-Standard Model Organisms. In prep.

400s. Wu J, De Paz A, Zamft BM, Marblestone AH, Boyden ES, Church G, Kording KP, Tyo KEJ (2016) DNA binding activity increases the processivity of a Y-Family DNA polymerase. In prep.

360s. Drukier A, Freese K, Spergel D, Cantor C, Church G, Sano T (2015) New Dark Matter Detectors using DNA or RNA for Nanometer Tracking. PNAS (submitted).

359s. Yang L, Monroe MR, Ayturk DG, Pan J, Grishin D, Cepko C, Church GM (2015) Ttago DNA-guided gene editing and regulation (see patent 100)

358s. Yang L, Monroe MR, Huang P, Dhadwar SS, Grishin D, Church GM (2015) Mitochondrial genome editing. (see patent 101)

341s. Li J, Haas W, Wassie B, Aach J, Gygi SP, Church GM (2014). Submitted.

256s. Rho J, Kuoy E, Huo H, Kim KY, Lensch MW, Bang D, Church GM, Daley GQ, Park IH (2012) Analysis of Retroviral Insertion Sites for Generation of Transgene-Free Human Induced Pluripotent Stem Cells. submitted to PLoS One.

222s. Strong M, Sandgren A, Galagan JE, Borowsky M, Church GM, Murray MB (2013) Comprehensive Structural Analysis of Drug-Resistant Mutations in Mycobacterium tuberculosis (in revision)

183s. Reppas NB, Lin X, Shendure J, Porreca GJ, Church GM (2009) Engineering and Laboratory Evolution of a Cooperative Microbial System (in prep)

132s. Medico E, D'Alessandro L, Gentile A, Montemurro F, Church GM, Comoglio PM (2006) A genomic signature for the invasive growth program. Submitted.

---

Patent publications (priority date - publication date)

165. Bradley C, Church GM, Sharifi MS (2021-2023) DNA Revertase (MatterBio)

164. Church GM, Conway N, Kohman RE, Kuru E, Rittichier J, Wiegand DJ (2018-2020) Compositions and methods comprising mutants of terminal deoxynucleotidyl (Harvard)

163. Han I, Kuru E, Church GM, de Puig H, Rittichier J (2021-2022) Fluorogenic sensors for detecting antigens (Harvard)    

162. Rittichier J, Wiegand DJ, Lee H, Kuru E, Church GM (2022-2023) Fluorogenic nucleosides (Harvard)

161. Kuru E, Rittichier J, Church GM (2020-2021) Fluorogenic amino acids (Harvard)

160. Church GM, Wiegand DJ, Kohman RE, Kuru E, Rittichier J, Conway N (2019-2022) Enzymatic RNA synthesis (Harvard)

159. Church GM, Yang L, Guell M (2016-2022) Multiplexed genome editing (Harvard)

158. Dai M, Kirschner MW, Church GM (2022-2023) Single-molecule protein identification via stretching (Harvard)

157. Church GM, Hysolli E, Weber J, Chatterjee P, Smith C (2021-2022) Compositions and methods for gene editing with woolly mammoth alleles (Harvard)

156. Church G, Skraly FA, Green BD, Harrison JC (2010-2015) Methods and compositions for limiting viability of a modified host cell outside of designated process conditions (Joule Unlimited)

155. Milanova DM, Church GM, Davidsohn N, Schoellhammer C, Langer RS, Mandinova AI, Traverso CG (2017-2018) Systemic delivery of polypeptides (Harvard)

154. Milanova DM, Church GM, Davidsohn N, Schoellhammer C, Langer RS, Mandinova AI, Traverso CG, Li L (2017-2018) Systemic delivery of polypeptides (Harvard)

153. Kalhor R, Lee HHY, Church GM (2017-2018) Enzymatic DNA synthesis using the terminal transferase activity of template-dependent DNA polymerases (Harvard)

152. Kohman R, Church GM (2017-2018) Targeted expansion fluorescent in situ sequencing (Harvard)

151. Kunjapur AM, Church GM, Stork DAO, Kuru E (2017-2019) Synthetase variants for incorporation of biphenylalanine into a peptide (Harvard)

150. Wiegand DJ, Ostrov N, Church GM (2017-2019) High-throughput system using a cell-free expression system and in situ sequencing (Harvard)

149. Ayer A, Church GM, Palla M, Pepin F, Punthambaker SSRA, Stranges PB (2017-2019) Enzyme screening methods (Harvard)

148. Khoshaklagh P, Ng AHM, Church GM (2017-2019) Methods and compositions for the production of oligodendrocyte progenitor cells (Harvard)

147. Chan YK, Church G (2016-2020) Engineered viral vector reduces induction of inflammatory and immune responses (Harvard)

146. Chan YK, Church G (2017-2019) Compositions and methods for inhibiting viral vector-induced inflammatory responses (Harvard)

145.Chan YK, Chiang JJS, Church GM (2017-2020) Enhanced Immunogenicity of mRNA with Co-Encoded Adjuvant Sequences (Harvard)

144. Ng AHM, Church GM, Khoshaklagh P (2018-2019) Methods of identifying combinations of transcription factors (Harvard)

143. Church GM, Kelsic E, Ogden P, Sinai S (2018-2019) Viral vectors exhibiting improved gene delivery properties (Harvard)

142. Griswold KJF, Turczyk BM, Wiegand DJ, Church GM, Garruss A (2016-2018) Processive template independent dna polymerase variants (Harvard)

141. Church GM, Lee JH, Terry RC, Daugharthy ER (2013-2018) Method for Generating A Three-Dimensional Nucleic Acid Containing Matrix (Harvard)

140. Griswold KJF, Kohman R, Church GM, Rittichier J (2017-2018) Cleavable nucleotide analogs and uses thereof (Harvard)

139. Kalhor R, Mali PG, Church GM (2017-2018) Engineered guide rna sequences for in situ detection and sequencing (Harvard)

138. Shrock EL, Church GM, Hysolli E (2017-2018) Methods of genome engineering by nuclease-transposase fusion proteins (Harvard)

137. Debnath A, Juarez JF, Lee HH, Church GM (2017-2018) Methods of regulating gene expression in a cell (Harvard)

136. Shipman SL, Nivala JM, Church GM, Schubert M (2017-2018) Method of recording multiplexed biological information into a crispr array using a retron (Harvard)

135. Nivala JM, Shipman SL, Church GM (2017-2018) Method of off-target recording of spacer sequences within a cell in vivo (Harvard)

134. Griswold K, Lee H, Church GM (2016-2018) Modulation of enzymatic polynucleotide synthesis using chelated divalent cations (Harvard)

133. Church GM, Yang L (2017-2018) Methods for increasing efficiency of gene editing in cells (Harvard)

132. Kunjapur A, Church GM (2017-2018) Methods of making proteins with non-standard amino acids (Harvard)

131. Church GM, Shrock E, Kan Y (2017-2018) Methods of genetic modification of a cell (Harvard)

130. Church GM, Yang L, Guell M (2015-2016) Multiplexed genome editing (Harvard)

129. Zhang F, Cong L, Kosuri S, Church GM (2011-2017) Transcription Activator-Like Effectors (Harvard)

128. Daugharthy ER, Terry RC, Lee JH, Church GM, Pruitt BW (2016-2017) Method and apparatus for volumetric imaging of a three-dimensional nucleic acid containing matrix (Harvard)

127. Church GM, Gregg CJ, Lajoie MJ, Rios X (2016-2017) Recombinase genome editing (Harvard)

126. Church GM, Rogers JK, Guell M, Garruss A (2016-2017) Methods and systems of cell-free enzyme discovery and optimization (Harvard)

125. Church GM, Mandell DJ, Feng J (2016-2017) Protein stability-based small molecule biosensors and methods (Harvard)

124. Church GM, Griswold KJF (2016-2017) Method of making polynucleotides using closed-loop verification (Harvard)

123. Daugharthy ER, Nguyen SC, Wu CT, Church GM (2016-2017) Methods for detecting and identifying genomic nucleic acids (Harvard)

122. Church GM, Pruitt BW, Terry RC (2016-2017) Methods and compositions for the single tube preparation of sequencing libraries using cas9 (Harvard)

121. Lee HH, Kalhor R, Church GM (2016-2017) Enzymatic nucleic acid synthesis (Harvard)

120. Scheiman J, Church GM (2016-2017) Probiotic formulations for improving athletic performance (Harvard)

119. Church GM, Palla M, Stranges PB, Nivala JM (2016-2017) Method and system of nanopore-based information encoding (Harvard)

118. Church GM, Byrne SM (2016-2017) Methods for increasing efficiency of nuclease-mediated gene editing in stem cells (Harvard)

117. Daugharthy ER, Church GM (2016-2017) Hybridization chain reaction methods for in situ molecular detection (Harvard)

116. Lee HH, Kalhor R, Church GM (2016-2017) Enzymatic nucleic acid synthesis

115. Lee HH, Kalhor R, Church GM (2016-2017) Method of secure communication via nucleotide polymers (Harvard)

114. Church GM, Chew WL (2016-2017) AAV split cas9 genome editing and transcriptional regulation (Harvard)

113. Church GM, Daugharthy ER, Terry RC (2016-2018) Methods of combining the detection of biomolecules into a single assay using fluorescent in situ sequencing (Harvard)

112. Church GM, Daugharthy ER, Terry RC, Pruitt BW, Turczyk B (2016-2018) Methods of generating libraries of nucleic acid sequences for detection via fluorescent in situ sequencing (Harvard)

111. Ng AHM, Church GM, Busskamp V (2016-2018) Transcription factors controlling differentiation of stem cells (Harvard)

110. Church GM, Lee HH, Ostrov N (2016-2018) Methods of crispr mediated genome modulation in V. natriegens (Harvard)

109. Way JC, Church GM (2018) Organisms, Molecules And Methods For the Reduction of Horizontal Gene Transfer (64-x.com)

108. Davidsohn N, Church GM (2016-2017) Gene therapy methods for age-related diseases and conditions (Harvard)

107. Chan YK, Church GM (2016-2017) Engineered viral vector reduces induction of inflammatory and immune responses. (Harvard)

106. Kuznetsov G, Lajoie MJ, Landon MM, Napolitano MG, Goodman DB, Gregg CJ, Church GM, Ostrov N (2016-2017) Methods for rule-based genome design (Harvard)

105. Kalhor R, Juarez JF, Lee HH, Church GM (2016-2017) Frequency-based modulation of diverse species in a nucleic acid library (Harvard)

104. Church GM, Kalhor R, Mali PG (2016-2017) Self-targeting guide RNAs in CRISPR system (Harvard)

103. Church GM, Iyer E, Camplisson C (2016-2017) Multiplex alteration of cells using a pooled nucleic acid library and analysis thereof. (Harvard)

102. Church GM, Huang PY (2016-2017) Methods for making polypeptides including D-amino acids. (Harvard)

101. Rogers JK, Church GM (2016-2017) Production of Acrylate in Cells. (Harvard)

100. Church GM, Yang L, Monroe MR, Huang PY (2016-2017) Mitochondrial genome editing and regulation. (Harvard)

99. Church GM, Yang L, Monroe MR (2016-2017) DNA-guided gene editing and regulation. (Harvard)

98. Church GM, Lee H, Palla M (2016-2017) Method of making polynucleotides using an anion toroidal vortex. (Harvard)

97. Church GM, Shipman SL, Macklis JD, Nivala JM (2016-2017) Methods and systems of molecular recording by CRISPR-Cas system. (Harvard)

96. Church GM (2015-2019) Methods for Retrievable Information Storage Using Nucleic Acids. US10289801B2 (Harvard)

95. Daugharthy ER, Dasari V, Church GM (2015-2016) Systems and methods for processing spatially related sequence data received from a sequencing device. (Harvard)

94. Ter-Ovanesyan, Kowal EJK, Church GM, Regev A (2015-2016) Exosomes and uses thereof (Broad Inst, Harvard, MIT)

93. Church GM, Chew WL (2015-2016) Split cas9 proteins (Harvard)

92. Boyden ES, Chen F, Alon S, Church G, Tillberg PW, Marblestone A, Daugharthy E (2015-2016) In situ nucleic acid sequencing of expanded biological samples (Harvard & MIT)

91. Lewis JA, Skylar-Scott MS, Kolesky DB, Homan KA, Ng SHM, Church GM. (2015-2016) Methods of generating functional human tissue (Harvard)

90. Rogers J, Church GM (2015-2016) Production and monitoring of metabolites in cells (Harvard)

89. Levner D, Lee J, Church GM, Super M (2011-2014) Compositions and methods for analyte detection (Harvard)

88. Umbarger M, Porreca G, Towne C, Church GM (2012-2016) Capture reactions (Good Start Genetics)

87. Church GM, Mali P (2012-2015) Polynucleotide-binding domains as a means of cell labeling, cell organization and polymer sequencing (Harvard)

86. Eroshenko NA, Church GM (2013-2016) Mutants of cre recombinase (Harvard)

85. Church GM, Lee JH, Terry RC, Daugharthy ER (2013-2016) Method of generating a three-dimensional nucleic acid containing matrix (Harvard)

84. Church GM, Esvelt K, Mali P (2013-2015) Orthogonal Cas9 Proteins for RNA-Guided Gene Regulation and Editing (Harvard)

83. Church GM, Dicarlo J (2013-2016) Multiplex RNA-guided genome engineering (Harvard)

82. Church GM, Raman S, Taylor ND (2014-2015) De novo design of allosteric proteins. (Harvard)

81. Elf J, Öhman O, Church G (2014-2016) Phenotypic characterization and in situ genotyping of a library of genetically different cells (Johan Elf)

80. Church GM, Gu L (2014-2015) Barcoded protein array for multiplex single-molecule interaction profiling. (Harvard)

79. Church GM, Lee JH, Daugharthy ER (2014-2016) Methods for high-throughput labelling and detection of biological features in situ using microscopy (Harvard)

78. Wagers AJ, Tabebordbar M, Chew WL, Church GM (2014-2016) RNA-guided systems for in vivo gene editing (Harvard)

77. Church GM, Vigneault F, Mir KU (2014-2016) RNA-guided systems for probing and mapping of nucleic acids (Harvard)

76. Church GM, Gregg CJ, Lajoie MJ, Mandell DJ (2014-2016) Methods of making polypeptides with non-standard amino acids using genomically recoded organisms. (Harvard)

75. Church GM, Feng J, Mandell DJ Baker D, Fields SF, Jester BW, Tinberg CE (2016) Biosensors Engineered from Conditionally Stable Ligand-Binding Domains (Harvard, U. Washington)

74. Lajoie MJ, Gregg CJ, Mosberg JA, Church GM (2012-2014) Methods of Introducing Nucleic Acids into Cellular DNA (Harvard)

73. Church GM, Mali P, Esvelt KM (2013-2014) RNA-Guided Transcriptional Regulation (Harvard)

72. Chavez A, Poelwijk F, Church GM (2013-2015) Mutant cas9 proteins (Harvard)

71. Byrne SM, Church GM (2013-2015) Large gene excision and insertion (Harvard)

70. Church GM, Mandell DJ, Lajoie MJ (2013-2015) Recombinant cells and organisms having persistent nonstandard amino acid dependence and methods of making them (Harvard)

69. Church GM, Vigneault F (2010-2013) High-throughput single cell barcoding (Harvard)

68. Mali PG, Church GM, Yang L (2012-2014) RNA-Guided Human Genome Engineering (FokI)(Harvard)

67. Church GM, Raman S, Taylor ND, Rogers J (2013-2014) Methods for selecting microbes from a genetically modified library to detect and optimize the production of metabolites (Harvard)

66. Church GM, Yang L, Guell-Cargol M , Yang JL (2013-2015) Genome engineering (TALEN & Cas9, co-localization of donor DNA) (Harvard)

65. Agresti J, Chu LY, Weitz DA, Kim JW, Rowat A, Sommer M, Dantas G, Church G (2007-2014) Assay and other reactions involving droplets (Harvard)

65. Church GM (2012-2016) Methods of storing information using nucleic acids US9384320B2 (Harvard)

64. Jacobson J, Church GM, Chu LLY (2008-2014) Methods and devices for high fidelity polynucleotide synthesis (Gen9)

63. Church GM, Terry RC, Vigneault F (2010-2013) Spatial sequencing of nucleic acids using DNA origami probes (Harvard)

62. Church GM, Terry RC, Kosuri S, Zhang D (2012-2013) Assembly of nucleic acid sequences in emulsions (Harvard)

61. Church GM, Vigneault F (2010-2013) High-Throughput Single Cell Barcoding (Harvard)

60. Church GM, Kosuri S, Eroshenko N (2010-2012) Orthogonal Amplification And Assembly Of Nucleic Acid Sequences (Harvard)

59. Church GM, Terry RC, Vigneault F, Vigneault F (2011-2013) Sequencing by Structure Assembly (Harvard)

58. Bachelet I, Church G, Douglas S (2010-2012) DNA Origami Devices (Harvard)

57. Bachelet I, Church G, Laserson U, Vigneault F (2010-2012) High-throughput Immune Sequencing. (Harvard)

56. Church G, Skraly FA, Green BD, Harrison JC (2010-2012) US Pat App 20120077273 Methods and composition for limiting viability of a modified host cell (Joule Unlimited)

55. Porreca G, Umbarger M, Church G (2010-2012) US Pat App 20120164630 Methods for maintaining the integrity and identification of a nucleic acid template in a multiplex sequencing reaction. (Good Start Genetics)

54. Jacobson J, Church G (2009-2012) US Pat App 20120315670 Compositions and Methods for the Regulation of Multiple Genes of Interest in a Cell (Gen9)

53. Church GM, Jewett MC (2009-2012) US Pat App 20120171720 Method of Making Ribosomes (Harvard)

52. Akeson M, Branton D, Church G, Deamer D (1995-2012) US Pat App. 20120160687 Characterization of Individual Polymer Molecules based on monomer-interface interactions. (Harvard)

51. Adesokan A, Church GM (2009-2012) EP 2464753 A1 Biodetection methods and compositions. (Harvard)

50. Church GM, Cong L, Kosuri S, Zhang F (2011-2012) US Pat App. 20120270273. Transcription activator-like effectors (Harvard)

49. Wu CT, Church GM (2010-2012) US Pat 8865404 B2. Methods For Sequencing Nucleic Acid Molecules (Harvard)

48. Church GM, Bang D, Li J (2009-2011) US Pat. App. 20110039304. Methods to Generate Oligonucleotide Pools and Enrich Target Nucleic Acid Sequences (Harvard)

47. Church GM, Yang L (2009-2011) US Pat. App. 20110104787. Fusion Peptides That Bind to and Modify Target Nucleic Acid Sequences (Harvard)

46. Jacobson J, Church G, Chu L (2008-2011) US Pat. App. 20110172127. Methods and Devices for High Fidelity Polynucleotide Synthesis (Codon Devices)

45. Wu Ct, Church GM, Williams BR (2009-2010) US Pat. App. 20100304994. Oligonucleotide Paints (Harvard)

44. Church GM, Ball MP, Li J (2010) US Pat. App. 20100273164. Targeted and Whole-Genome Technologies to Profile DNA Cytosine Methylation (Harvard)

43. Church GM, Dantas G, Sommer MO (2008-2014) US 8658416 Toxin-Eating Bacteria and Bioremediation (Harvard)

42. Church GM, Sommer MO, Dantas G (2008-2010) US Pat. App. 20100093064. Metagenomic Functional Selection (Harvard)

41. Church GM, Sismour AM (2008-2010) US Pat. App. 20100081140. Chemically Cleavable Phosphoramidite Linkers For Sequencing By Ligation (Harvard)

40. Church GM, Vigneault F, Sismour AM (2008-2010) US Pat. App. 20100062494. Enzymatic Oligonucleotide Pre-Adenylation (Harvard)

39. Church GM (2008-2010) US 7723077. Hierarchical Assembly of Polynucleotides (Harvard)

38. Church GM, Shendure J (2002-2010) US Pat. App. 20100099080 Nucleic acid memory device (Harvard)

37. Agresti J, Chu L-Y, Weitz DA, Kim J-W, Rowat A, Sommer M, Dantas G, Church G (2007-2010) US Pat. Appl. 20100136544 Assays and Other Reactions Involving Droplets (Harvard)

36. Church G, Sismour M (2007-2008) WO 2008/151127 Compounds and Methods for Chemical Ligation (Harvard)

35. Church G, Zhang K, Shendure J (2007-2008) WO 2008/127901 Region-Specific Hyperbranched Amplification (Harvard)

34. Jacobson JM, Church G, Baynes BM (2006-2008) WO 2008/127283 Engineered Metabolic Pathways (Codon Devices)

33. Church G, Bang D (2007-2008) WO 2008/112683 Gene Synthesis by Circular Assembly Amplification (Harvard)

32. Church G, Wang HH, Isaacs FJ (2006-2008) WO 2008/052101 Multiplex Automated Genome Engineering (Harvard)

31. Kim JB, Porreca GJ, Church GM, Seidman JG (2006-2008) WO 2008/039998 Methods for Sequencing DNA (SbL bead arrays) (Harvard)

30. Church GM, Shendure J, Porreca GJ, Reppas N (2007-2008) US Pat. App. 20080269068. Multiplex Decoding Of Sequence Tags in Barcodes

29. Church GM, Shendure J, Porreca GJ, Zhu J (2004-2007) US Pat. App. 20070087362. Polony fluorescent in situ sequencing beads

28. Church G, Zhang K (2006-2007) WO 2007/136874 Genomic Library Construction (Harvard)

27. Church G, Baynes B (2006-2007) WO 2007/136835 Methods and Cells for Creating Functional Diversity and Uses Thereof (Codon Devices)

26. Church G, Jacobson JM, Baynes BM (2006-2007) WO 2007/136833 Methods and Compositions for Aptamer Production and Uses Thereof (Codon Devices)

25. Keasling JD, Hu Z, Somerville C, Church G, Berry D, Friedman L, Schirmer A, Brubaker S, Del Cardayre SB (2006-2007) WO 2007/136762 Production of Fatty Acids and Derivatives Thereof (LS9, Inc.)

24. Church G, Porreca G, Shendure J, Rosenbaum A (2005-2007) WO 2007/120208 Nanogrid Rolling Circle DNA Sequencing (Harvard)

23. Church G, Zhang K, Chou J (2006-2007) WO 2007/092538 Methods for Making Nucleotide Probes for Sequencing and Synthesis (Harvard)

22. Church G, Liu D (2005-2007) WO 2007/075438 Polypeptides Comprising Unnatural Amino Acids, Methods for Their Production and Uses Therefor (Codon Devices)

21. Gao X, Bear DM, Church GM, Zhou X (2006-2011) US 7874489 Labeling Compositions and Methods of Use for Deterrent Trackability (Pharmorx Inc.)

20. Church G, Baynes B, Pitcher ER (2005-2007) WO 2007/005053 Hierarchical Assembly Methods for Genome Engineering (Codon Devices)

19. Church G, Cerrina F, Baynes B, Pitcher ER (2006-2007) WO 2007/136736 A2 Methods For Nucleic Acid Sorting and Synthesis (Codon Devices)

18. Church GM, Pitcher ER (2005-2006) US Pat. App. 20060281113. Accessible polynucleotide libraries and methods of use thereof. Junction Oligonucleotides for Polynucleotide Assembly. (Codon Devices)

17. Church G, Pitcher ER (2005-2006) WO 2006/127423 Methods of Producing Polynucleotide Libraries Using Scarless Ligation (Codon Devices)

16. Church G, Baynes B (2005-2006) WO 2006/076679 Compositions and Methods for Protein Design (Codon Devices)

15. Church G, Reppas N (2004-2006) WO 2006/055836 In Vivo Alteration of Cellular DNA (Harvard)

14. Afeyan N, Church G, Jacobson J, Baynes BM, Nesmith KG, Chapman BA, Strack-Logue B (2004-2006) WO 2006/044956 Methods for Assembly of High Fidelity Synthetic Polynucleotides (Codon Devices)

13. Church GM, Porreca G, Shendure J (2004-2006) Patent Appl # WO/2006/073504 Wobble Sequencing (Harvard)

12. Church GM, Zhang K (2004-2006) US # 7,387,876 Amplification of trace amounts of nucleic acids. (Harvard)

11. Church GM, Tian J (2004-2006) US Pat. App. 20060127920. Polynucleotide synthesis (Harvard)

10. Church GM, Janse D (2003-2005) US Patent Appl # 2005/0152888 Targeted polypeptide degradation. (Harvard)

9. Rizzuto C, Afeyan N, Lee F, Church GM, Gupta RD, Schwartz JJ, Zhang B, Lugovskoy A (2001-2002) US Patent Appl # 2002/0192721A1 Modular Molecular Clasps and uses thereof. (EnGeneOS)

8. Church GM, Bulyk ML, Choo Y (2000-2002) WO 02/18648 Analysis of binding interactions (Harvard)

7. Church GM, Bulyk ML (1997-2001) US # 6,548,021 & # 6,326,489 Surface-bound, bimolecular, double-stranded DNA arrays (Harvard)

6. Church GM (2000-2001) WO 01/68671 Method of making protein arrays (Harvard)

5. Church GM, Mitra R (1997-2002) US # 6,432,360 Replica amplification of nucleic acid arrays. (Harvard)

4. Church GM, Deamer DW, Branton D, Baldarelli R, Kasianowicz J (1995-1998) US # 5,795,782 Characterization of individual polymer molecules based on monomer-interface interactions. (Harvard)

3. Church GM, Kieffer-Higgins S (1991-1992) WO 92/21079A1 Parallel Sequential Reactor. (Harvard)

2. Church GM, Kieffer-Higgins S (1990-1992) US # 5,149,625 Multiplex analysis of DNA (Harvard)

1. Church GM (1987-1989) US # 4,942,124 Multiplex sequencing. (Harvard)

21a. Wu CT, Kalhor R (2013-2014) Methods of Hybridizing Probes to Genomic DNA (Harvard)

20a. Esvelt KM, Yaung S (2016) Precise microbiota engineering at the cellular level (Harvard)

19a. Esvelt KM, Smidler AL (2016) RNA-Guided Gene Drives (Harvard)

18a. Chavez A, Pruitt B (2016) CAS Discrimination Using Tuned Guide RNA (Harvard)

17a. Chavez A, Hu JH (2016) Methods of Making Guide RNA (Harvard)

16a. Chavez A, Tuttle M (2016) Cas9 Genome Editing and Transcriptional Regulation (Harvard)

15a. Esvelt KM, Min J (2016) Dependent Component Genome Editing Gene Drives (Harvard)

14a. Mandell DJ, Feng J, Rios Villanueva X, Chari R (2016) Small Molecules Biosensors (Harvard)

13a. Chavez A (2016) Mutant Cas Proteins (Harvard)

12a. Griswold K, Fang N (2016) Method of Determining the Molecular Binding Between Libraries of Molecules (Harvard)

11a. Guo X, Chavez A, Schubert M, Kelsic E (2016) Library-scale engineering of metabolic pathways (Harvard)

10a. Kaas CS, Chavez A (2016) Methods of Screening Using Barcoded Libraries (Harvard)

9a. Kaas CS, Chavez A, Guo X (2016) Methods of Genetically Altering Yeast to Produce Yeast Variants (Harvard)

8a. Vora S, Chavez A, Ching J, Pruitt BW (2016) Methods of Modulating Expression of Target Nucleic Acid Sequences in a Cell (Harvard)

7a. Chavez A, Yeo NC (2016) Cas9-Based Transcription Modulation Systems (dCas9-Krab-MECP2) (Harvard)

6a. Sinclair D, Lu Y, Davidsohn N (2016) Mutant Reverse Tetracycline Transactivators for Expression of Genes (Harvard)

5a. Alley E (2018) Unified rational protein engineering with sequence-only deep representation learning (Harvard)

4a. Armon R, Lajoie M, Jensen KF, Langer RS (2015-2018) Gene Editing Through Microfluidic Delivery (MIT, Harvard)

3a. Chen F, Payne A, Buenrostro JD, Reginato P, Boyden ES (2016) In Situ ATAC Sequencing (MIT)

2a. Chen F, Alon S, Payne A, Wassie A, Goodwin D, Boyden ES (2016) Augmenting in situ Nucleic Acid Sequencing of Expanded Biological Samples with in vitro Sequence Information (MIT, Harvard)

1a. Gregg CJ, Mandell DJ, Thyer R, Ellington AD, Stranges B (2016) Production of Seleno-Biologics in Genomically Recoded Organisms (Harvard)

Return to Church Lab Homepage