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 1-Jul-2012 by GMC.
294. Petit E, Coppi MV, Hayes J, Tolonen A, Warnick T, Latouf W, Amisano D, Biddle A, Mukherjee S, Ivanova N, Lykidis A, Land M, Hauser L, Kyrpides N, Henrissat B, Lau J, Schnell D, Church G, Leschine S, Blanchard J (2013) Genome and transcriptome of Clostridium phytofermentans, catalyst for the direct conversion of plant feedstocks to fuels. Submitted
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.
292. Yang L, Mali P, Kim-Kiselak C, Church G (2013) CRISPR-Cas mediated targeted genome editing in human cells. Methods in Molecular Biology.
291. Mali P, Aach J, Stranges PB, Esvelt KM, Moosburner M, Kosuri S, Yang L, Church GM (2013) submitted.
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.
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 DOI: 10.1126/science.1236939
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, submitted.
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. Submitted.
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
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 MSB 9:642. PMID: 23340848
281a. Esvelt KM, Wang HH (2012) Genome-scale engineering for systems and synthetic biology MSB 9:641. PMID: 23340847
281. Lajoie MJ, Kosuri S, Mosberg JA, Gregg CJ, Zhang D, Church GM (2013) Towards a radically reassigned genetic code. Submitted.
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. Submitted.
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.
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). An Efficient Pipeline for Scarless Genome Editing of Human Stem Cells. Submitted.
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. 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, TyoK, Boyden E, Church GM (2012) Measuring Cation Dependent DNA Polymerase Fidelity Landscapes by Deep Sequencing PLoS ONE 7(8):e43876, PMID: 22928047 Supplementary data
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.
269a. 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: 2222279
269. Drukier A, Freese K, Spergel D, Cantor C, Church G, Sano T (2012) New Dark Matter Detectors using DNA for Nanometer Tracking ArXiv.
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 (2012) PLATO: Parallel Analysis of in vitro Translated ORF libraries. Nature Biotech. doi: 10.1038/nbt.2539.
265. Larman HB, Laserson U, Gutierrez LQ, Verhaeghen K, Solimini NL, Xu G, Klarenbeek PL, Church GM, Hafler DA, Plenge RM, Nigrovic PA, De Jager PL, Martens GA, O'Connor KC, Elledge SJ (2012) Submitted.
264. Gu L, Li C, Aach J, Church GM (2012) Submitted.
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, In-Hyun 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.
258a. Kosuri S, Sismour M (2012) When It Rains, It Pores. ACS Synth. Biol. 2012, 1, 109-110. (dx.doi.org/10.1021/sb300015f)
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. Vigneault F, Laserson U, Simen BB, Lieberman-Aiden E, Egholm M, Church GM (2012) Tracking the dynamics of a human antibody repertoire. (in revision)
255. Jewett MC, Fritz BR, Timmerman LE, Church GM (2012) In vitro integration of ribosomal RNA synthesis, ribosome assembly and translation. (in revision).
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 (2012) Structural Meta-Analysis of the Mycobacterium tuberculosis Antibiotic Resistome (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. Nature 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.
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 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. Nature EMBO 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 U S
A 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
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 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.
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 msb4100004-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
113. Aach J, Church GM (2005) Accommodation or prediction?
Science. 2005 Jun 3;308(5727):1409-12; author reply 1409-12.
112b. Pe'er D (2005) Bayesian
network analysis of signaling networks: a primer. Sci STKE. 2005 Apr
26;2005(281):pl4.
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
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 molecules.
Nucleic
Acids Res. 27(24):e34; pp.1-6. 42. Tavazoie S, Hughes JD, Campbell MJ, Cho RJ, Church GM (1999)
Systematic determination
of genetic network architecture. Nature
Genetics 22:281-5. 41. Bulyk ML, Gentalen E, Lockhart DJ, Church GM (1999) Quantifying DNA-protein
interactions by double-stranded DNA arrays. Nature
Biotechnology 17: 573-7. 40. McGuire AM, De Wulf P, Church GM, Lin EC (1999) A weight
matrix for binding recognition by the redox-response regulator ArcA-P of Escherichia
coli . Mol
Microbiol 32: 219-21. 39. Johnson JM, Church GM (1999) Alignment and structure
prediction of divergent protein families: periplasmic and outer membrane
proteins of bacterial efflux pumps. J.
Molec. Biol. 287: 695-715. (Supplement). 38. Robison KR, McGuire AM, Church GM (1998) A comprehensive library of
DNA-binding site matrices for 55 proteins applied to the complete Escherichia
coli K-12 genome. J.
Molec. Biol. 284: 241-254. 37. Tavazoie S, Church GM (1998) Quantitative Whole-genome
analysis of DNA-protein interactions by in vivo methylase protection in E.coli.
Nature
Biotechnology 16: 566-571. 36. Roth FP, Hughes JD, Estep PW, Church GM (1998) Finding DNA regulatory motifs
within unaligned non-coding sequences by whole-genome mRNA quantitation. Nature
Biotechnology 16: 939-945. 35. Chen T, He HL, Church GM (1999) Modeling Gene Expression with
Differential Equations. Pac Symp Biocomput-1999:29-40.
34. Collins FS, Patrinos A, Jordan E, Chakravarti A, Gesteland R, Walters L(with Fearon E, Hartwell L, Langley CH, Mathies RA, Olson M, Pawson AJ, Pollard T, Williamson A, Wold B, Buetow K, Branscomb E, Capecchi M,
Church G, Garner H, Gibbs RA, Hawkins T, Hodgson K, Knotek M, Meisler M, Rubin GM, Smith LM, Smith RF, Westerfield M, Clayton EW, Fisher NL, Lerman CE, McInerney JD, Nebo W, Press N, Valle D)
(1998) New goals for
the U.S. Human Genome Project: 1998-2003. Science
282(5389):682-9. 33. Smith DR, Doucette-Stamm LA, Deloughery C, Lee H, Dubois J,
Aldredge T, Bashirzadeh R, Blakely D, Cook R, Gilbert K, Harrison
D, Hoang L, Keagle P, Lumm W, Pothier B, Qiu D, Spadafora R,
Vicaire R, Wang Y, Wierzbowski J, Gibson R, Jiwani N, Caruso A,
Bush D, Safer H, Patwell D, Prabhakar S, McDougall S, Shimer G,
Goyal A, Pietrokovski S, Church GM, Daniels CJ, Mao J,
Rice P, Nolling J, Reeve JN (1997)
The Complete Genome
Sequence of Methanobacterium thermoautotrophicum Strain delta-H: Functional
Analysis and Comparative Genomics . J.
Bacteriol. Nov. 179: 7135-7155. 32. Bian N, Wang P, Wang Z, Church GM, Giese RW (1997)
Detection via Laser Desorption and Mass Spectrometry of Multiplex
Electrophore-Labeled Albumin. Rapid
Commun. Mass Spectrom. 11: 1781-1784. 31. Link AJ, Phillips D, Church GM (1997)
Methods for generating precise deletions and insertions in the genome of
wild-type Escherichia coli: Application to open reading frame characterization.
J.
Bacteriol. 179: 6228-6237. PMID: 9335267 Addgene: pKOV
30. Link AJ, Robison K, Church GM (1997)
Comparing the predicted
and observed properties of proteins encoded in the genome of Escherichia coli. Electrophoresis
18 (8):1259-1313 . PMID: 9298646
29. Xu L, Bian N, Wang Z, Abdel-Baky S, Pillai S, Magiera D,
Murugaiah V, Giese RW, Wang P, O'Keeffe T, Abushamaa H, Kutney L,
Church GM, Carson S, Smith D, Park M, Wronka J, Laukien F (1997) Electrophore Mass Tag Dideoxy
DNA Sequencing. Analytical Chemistry 69: 3595-3602. 28. Smith DR, Richterich P, Rubenfield M, Rice PW, Butler C,
Lee HM, Kirst S, Gundersen K, Abendschan K, Xu Q, Chung M, Deloughery C,
Aldredge T, Maher J, Lundstrom R, Tulig C, Falls K, Imrich J, Torrey D,
Engelstein M, Breton G, Madan D, Nietupski R, Seitz B, Connelly S,
McDougall S, Safer H, Gibson R, Doucette-Stamm L, Eiglmeier K, Bergh S,
Cole ST, Robison K, Richterich L, Johnson J, Church GM, Mao J
(1997) Multiplex
sequencing of 1.5 Mb of the Mycobacterium leprae genome. NCBI Accession
numbers: L01095, L01263, L01536, L04666, U00010
to U00023,
U15180 to U15184, U15186, U15187. Genome
Research 7: 802-819. 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 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.
56. Church G, Skraly FA, Green BD, Harrison JC (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 (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 (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 (2012) US Pat App 20120171720 Method of Making Ribosomes (Harvard)
52. Akeson M, Branton D, Church G, Deamer D (2012) US Pat App. 20120160687 Characterization of Individual Polymer Molecules based on monomer-interface interactions. (Harvard)
51. Adesokan A, Church GM (2012) EP 2464753 A1 Biodetection methods and compositions. (Harvard)
50. Church GM, Cong L, Kosuri S, Zhang F (2012)
US Pat App. 20120270273.
Transcription activator-like effectors (Harvard)
49. Wu CT, Church GM (2011) US Pat App 20120142540. Methods For Sequencing Nucleic Acid Molecules (Harvard)
48. Church GM, Bang D, Li J (2011) US Pat. App. 20110039304. Methods to Generate Oligonucleotide Pools and Enrich Target Nucleic Acid Sequences (Harvard)
47. Church GM, Yang L (2011) US Pat. App. 20110104787. Fusion Peptides That Bind to and Modify Target Nucleic Acid Sequences (Harvard)
46. Jacobson J, Church G, Chu L (2011) US Pat. App. 20110172127. Methods and Devices for High Fidelity Polynucleotide Synthesis (Codon Devices)
45. Wu Ct, Church GM, Williams BR (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 (2010) US Pat. App. 20100159565. 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. Church GM (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)
PATENTS: