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

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 in bold font). Updated 23-Nov-2014 by GMC.

388. Noble C, Jason Olejarz J, …, Esvelt KM, Church GM, Nowak MA (2015) in prep.

387. Soares AE, Novak BJ, Haile J, Gilbert MTP, … Poinar H, Church GM, Shapiro B (2015) in prep.

386. Zhirnov V, Zadegan RM, Sandhu GS, Church GM, and William L. Hughes WL (2015) NAM – Nucleic Acid Memory. Submitted

385. 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 in press.

384. 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) in prep.

383. 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

382. 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

381. 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 (2015) In preparation.

380. 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

379. Chavez A, Scheiman J, Vora S, Pruitt BW, Tuttle M, P R Iyer E, 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

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

377. 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

376. 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

375. Tsioris K, Gupta NT, Ogunniyi AO, Zimnisky RM, Qian F, Vigneault F, Stern JNH,Yao Y, Wang X, Karpikov A, Chari R, Church GM, Garcia MN, Murray KO, Montgomery RR, Kleinstein SH, Love JC (2015) In prep.

374. Chew WL, Tabebordbar M, Mali P, Wu EY, Wagers AJ, Church GM (2015)

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

372. 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

371. 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.

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

369. 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. In press.

368. 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).

367. 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

366. Yang L, Monroe MR, Ayturk DG, Pan J, Grishin D, Cepko C, Church GM (2015) Submitted

365. Yang L, Monroe MR, Huang P, Dhadwar SS, Grishin D, Church GM (2015) Submitted

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

363. 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

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

361. Chari R, Mali P, Moosburner M, Church GM (2015) Unraveling CRISPR-Cas9 genome engineering parameters via a library-on-library approach. Nature Methods

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

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

358. 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.

357. 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

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

355. 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. PMID: 25425480

354. Krueger AS, Munck C, Dantas G, Church GM, Galagan J, Joseph Lehar J, Sommer MOA (2014) Predicting drug .. In revision.

353. 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

352. 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.

351. 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

350. 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

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

348. 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

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

346. 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.

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

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

343. 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

342. 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

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

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

339. 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

338. 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

337. 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.

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

335a. 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

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

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

333. 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

332. Stern JNH, Yaari G, Vander Heiden JA, Church G, Donahue W, Rogier Q. Hintzen RQ, Huttner AJ, Jon D. Laman, 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.

331. 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

330. 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).

329. 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

328. 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

327. Chatterjee A, Lajoie MJ, Han Xiao H, Church GM, Schultz PG (2014) A Bacterial Strain with a Unique Quadruplet Codon Specifying Non-native Amino Acids. ChemBioChem in press. PMID: 24867343

326. 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

325a.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

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

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

323. 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

322. 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

321. 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)

320. 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

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

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

317. 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

316. Church GM, Marblestone A, Kalhor R (2014) Rosetta Brain. In press. Book: The Future of the Brain.

315. 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

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

313. 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

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

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

310. Church G. Please reanimate. (2013) Sci Am. 309(3):12. PMID: 24003542.

309. 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

308. 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

307. 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

306. 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 three-dimensional subcellular transcriptome sequencing in situ. Science 343(6177):1360-3. PMID: 24578530 Supplement

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

304. 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

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

302. 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

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

300. 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

299. 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.

298. 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.

297a. Lunshof JE, Ball MP (2013) Our genomes today: time to be clear. Genome Medicine 5:52. PMID: 23806003

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

296. 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

295. Friedland AE, Tzur YB, Esvelt KM, Colaiacovo 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

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

293. Umbarger MA, Kennedy CJ, Saunders P, Breton B, Niru Chennagiri M.S., John Emhoff, Valerie Greger , Stephanie Hallam , David Maganzini, Cynthia Micale , Marcia M. Nizzari M.S., Charles F. Towne CF, Church GM, Porreca GJ (2013) Next-Generation Carrier Screening. Genetics in Medicine. PMID: 23765052

292. 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

291. 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

290. 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

289. 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

288. 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

287. 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

286. 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

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

284. 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. 2012 Nov;30(11):1081-3. PMID: 23138307

283a. Mee MT, Wang HH. (2012) Engineering ecosystems and synthetic ecologies. Mol Biosyst. 8(10):2470-83.

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

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

281a. Esvelt KM, Wang HH (2012) Genome-scale engineering for systems and synthetic biology Molecular Systems Biology MSB 9:641. PMID: 23340847

281. 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

280. 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

279. Mali P, John Aach J, Lee J, Levner D, Nip L, Church GM (2013) Barcoding cells using cell-surface programmable DNA-binding domains. Nature Methods. Supplement

278. 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

277. 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

276. 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, Jan 3. 339(6121): 823-6. Supplement PMID: 23287722 Addgene: hCas9, D10A, Vector

275a. 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

275. 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

274a. Beliveau BJ, Joyce EF, Apostolopoulos N, Yilmaz F, Fonseka CY, McCole RB, Yiming Chang Y, Li JB, Senaratne TN, Williams BR, Rouillard JM, and Wu CT (2012) A versatile design and synthesis platform for visualizing genomes with Oligopaint FISH probes. PNAS 109: 21301-6. PMID: 23236188

274. 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

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

273. 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

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

271. 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

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

269. 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

268. 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

267a. 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

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

266a. 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

266. 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

265. 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

264. 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

263. 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

262. 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

261. 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

260. 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.

259. 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

258a. Kosuri S, Sismour M (2012) When It Rains, It Pores. ACS Synth. Biol. 2012, 1, 109-110. (

258. 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

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

256. 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. PMID: 24639495.Supplement

255. 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

254. 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

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

252. 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

251. 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

250. 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)

249. 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

248. 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

247. 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

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

245. 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

244. 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.

243. 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

242. 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

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

240. 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

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

238. 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

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

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

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

234. 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

233. 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

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

231. 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

230. 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

229a. 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

229. 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

228. 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

227. 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

226a. 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.

226. 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.

225. 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)

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

223. 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.

222. 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

221. 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

220. 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

219. 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.

218. 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

217. 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

216. 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.

215. 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

214. 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

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

212. 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

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

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

209. 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

208. 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

207. 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

206. 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. Jul 26; 460(7257):894-8. PMID: 19633652

205a. Dietz H, Douglas SM, Shih WH.(2009) Folding DNA into twisted and curved nanoscale shapes. Science. Aug 7; 325(5941):725-30.

205. 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

204. 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 Jul 8; 460(7258):1011-5. PMID: 19587683

203a. 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.

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

202. 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

201a. 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

201. 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

200. 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

199. 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 Jan;51(1):329-35. PMID: 19877180

198. 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

197. 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

196. 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. Nov; PMID: 19898456

195. 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 Dec;74(6):1300-13. PMID: 19775243

194. 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

193. 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

192. 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 Aug;6(8):613-8. PMID: 19620972 PMC2742772

191. 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 Nov;5(11):e1000718. PMID: 19911041 PMC2766639

190. 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

189. 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

188. 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 Sep;19(9):1606-15. PMID: 19525355

187. 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

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

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

184. 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

183. 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

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

181. 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

180a. 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.

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

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

178. 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

177a. 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.

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

176a. 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.

176. 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

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

174. 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

173. 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

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

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

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

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

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

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

166. 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

165. 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) .

164. 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. 2007 Nov;4(11):931-6. (Supplement) PMID: 17934468

163a. Douglas SM, Chou JJ, Shih WM. (2007) DNA-nanotube-induced alignment of membrane proteins for NMR structure determination. Proc Natl Acad Sci U S A. 104(16):6644-8. PMID: 17404217

163. 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

162a. Church GM (2007) Formulae for the 21st Century. Edge/Serpentine Gallery.

162. 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

161. 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

160. 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

159. 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

158. 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

157. 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

156. 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

155. 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

154. 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

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

152. 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?)

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

150. 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

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

148a. Nguyen DH, D'haeseleer P. (2006) Deciphering principles of transcription regulation in eukaryotic genomes . Mol Syst Biol. 2: 2006.0012.

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

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

146. 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

145. 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

144. 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

143. 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. Jun;3(6):439-45. PMID: 16721377 PMC2690135

142. 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

141. 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

140. 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

139. 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. Jul;24(7):832-840. PMID: 16823376

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

137. 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

136. 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 Mar; 38(3):382-7. PMID: 16493423

135. 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

134. Medico E, D'Alessandro L, Gentile A, Montemurro F, Church GM, Comoglio PM (2006) A genomic signature for the invasive growth program. Submitted.

133. 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

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

131. 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

130. 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

129. 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

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

127. 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

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

125. 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

124. 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

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

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

121. 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

120. 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

119. 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

118. 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

117a. Church GM (2004) A Synthetic Biohazard Non-proliferation Proposal.

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

116. 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

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

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

113a. Pe'er D (2005) Bayesian network analysis of signaling networks: a primer. Sci STKE. 2005 Apr 26;2005(281):pl4.

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

112a. 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.

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

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

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

109. 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. Oct;186(20):6938-43.

108. 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

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

106. 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.

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

104. 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 Feb;14(2):201-8.

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

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

101. 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.

100. 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.

99. Gao Y, Church GM (2004) FLEXMOTIF: A Generic Flexible Motif Discovery Algorithm for Unaligned Sequences. Submitted to RECOMB2004.

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

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)

92. King OD, Lee JC, Dudley AM, Janse DM, Church GM, Roth FP (2003) Predicting Phenotype from Patterns of Annotation. ISMB 2003; Bioinformatics. 2003 Jul;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 May;11(5):1253-63.

90. Merritt J, DiTonno JR, Mitra RD, Church GM, Edwards JS (2003) Functional characterization of mutant yeast PGK1 within the context of the whole cell. Nucleic Acids Research 2003 Aug 1;31(15):e84. .

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.

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.

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 Feb;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 Feb;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. 2002 Nov;184(22):6225-34.

75. Wright M, Church GM (2002) An Open-source Oligonucleotide Microarray Probe Standard for Human and Mouse . Nat Biotechnol. 2002 Nov;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. 2002 Aug;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. 2002 May;13(5):1608-14.

69. Lee M-LT, 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.

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

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.

66. Weber G, Shendure J, Tanenbaum DM, Church GM, Meyerson M (2002) Microbial sequence identification by computational subtraction of the human transcriptome. Nature Genetics 30(2):141-2.

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 2001 Dec;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, Dec;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. 8(6):571-583.

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

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-)

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 Oct;26(2):183-186.

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

43. Mitra R, Church GM (1999) In situ localized amplification and contact replication of many individual DNA moleculesNucleic 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 pumpsJ. 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.

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

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.

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.

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

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

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.

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.

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.

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.

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).

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.

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.

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.

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

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.

PATENTS (priority date - publication date):

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 (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 (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 droplet (Harvard)

65.Church GM (2012-2014) Methods of storing information using nucleic acids (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 App 20120142540. 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 (2010) US Pat. App. 20100093064. Metagenomic Functional Selection (Harvard)

41. Church GM, Sismour AM (2010) US Pat. App. 20100081140. Chemically Cleavable Phosphoramidite Linkers For Sequencing By Ligation (Harvard)

40. Church GM, Vigneault F, Sismour AM (2010) US Pat. App. 20100062494. Enzymatic Oligonucleotide Pre-Adenylation (Harvard)

39. Baynes B, Church GM, Pitcher E (2010) US 7723077. Hierarchical Assembly of Polynucleotides (Harvard)

38. Church GM, Shendure J (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 (2008) US Pat. Appl. 20100136544 Assays and Other Reactions Involving Droplets (Harvard)

36. Church G, Sismour M (2008) WO 2008/151127 Compounds and Methods for Chemical Ligation (Harvard)

35. Church G, Zhang K, Shendure J (2008) WO 2008/127901 Region-Specific Hyperbranched Amplification (Harvard)

34. Jacobson JM, Church G, Baynes BM (2008) WO 2008/127283 Engineered Metabolic Pathways (Codon Devices)

33. Church G, Bang D (2008) WO 2008/112683 Gene Synthesis by Circular Assembly Amplification (Harvard)

32. Church G, Wang HH, Isaacs FJ (2008) WO 2008/052101 Multiplex Automated Genome Engineering (Harvard)

31. Kim JB, Porreca GJ, Church GM, Seidman JG (2008) WO 2008/039998 Methods for Sequencing DNA (SbL bead arrays) (Harvard)

30. Church GM, Shendure J, Porreca GJ, Reppas N (2008) US Pat. App. 20080269068. Multiplex Decoding Of Sequence Tags in Barcodes

29. Church GM, Shendure J, Porreca GJ, Zhu J (2007) US Pat. App. 20070087362. Polony fluorescent in situ sequencing beads

28. Church G, Zhang K (2007) WO 2007/136874 Genomic Library Construction (Harvard)

27. Church G, Baynes B (2007) WO 2007/136835 Methods and Cells for Creating Functional Diversity and Uses Thereof (Codon Devices)

26. Church G, Jacobson JM, Baynes BM (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 (2007) WO 2007/136762 Production of Fatty Acids and Derivatives Thereof (LS9, Inc.)

24. Church G, Porreca G, Shendure J, Rosenbaum A (2007) WO 2007/120208 Nanogrid Rolling Circle DNA Sequencing (Harvard)

23. Church G, Zhang K, Chou J (2007) WO 2007/092538 Methods for Making Nucleotide Probes for Sequencing and Synthesis (Harvard)

22. Church G, Liu D (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 (2007) WO 2007/005053 Hierarchical Assembly Methods for Genome Engineering (Codon Devices)

19. Church G, Cerrina F, Baynes B, Pitcher ER (2007) WO 2007/136736 A2 Methods For Nucleic Acid Sorting and Synthesis (Codon Devices)

18. Church GM, Pitcher ER (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 (2006) WO 2006/127423 Methods of Producing Polynucleotide Libraries Using Scarless Ligation (Codon Devices)

16. Church G, Baynes B (2006) WO 2006/076679 Compositions and Methods for Protein Design (Codon Devices)

15. Church G, Reppas N (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 (2006) WO 2006/044956 Methods for Assembly of High Fidelity Synthetic Polynucleotides (Codon Devices)

13. Church GM, Porreca G, Shendure J (2006) Patent Appl # WO/2006/073504 Wobble Sequencing (Harvard)

12. Church GM, Zhang K (2006) US Patent Appl # 2006/0014167 Amplification of trace amounts of nucleic acids. (Harvard)

11. Church GM, Tian J (2006) US Pat. App. 20060127920. Polynucleotide synthesis (Harvard)

10. Church GM, Janse D (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 (2002) US Patent Appl # 2002/0192721A1 Modular Molecular Clasps and uses thereof. (EnGeneOS)

8. Church GM, Bulyk ML, Choo Y (2002) WO 02/18648 Analysis of binding interactions (Harvard)

7. Church GM, Bulyk ML (2001) US # 6,548,021 & # 6,326,489 Surface-bound, bimolecular, double-stranded DNA arrays (Harvard)

6. Church GM (2001) WO 01/68671 Method of making protein arrays (Harvard)

5. Church GM, Mitra R (2000) WO 00/53812 Replica amplification of nucleic acid arrays. (also US # 6,432,360) (Harvard)

4. Church GM, Deamer DW, Branton D, Baldarelli R, Kasianowicz J (1998) US # 5,795,782 Characterization of individual polymer molecules based on monomer-interface interactions. (Harvard)

3. Church GM, Kieffer-Higgins S (1992) WO 92/21079A1 Parallel Sequential Reactor. (Harvard)

2. Church GM, Kieffer-Higgins S (1992) US # 5,149,625 Multiplex analysis of DNA (Harvard)

1. Church GM, Kieffer-Higgins S (1989) US # 4,924,124 & EPO# 0303459A2 Multiplex sequencing. (Harvard)

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