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 19-Nov-2009 by GMC.
242. 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
241. Church GM (2011) Intellectual property rights. Prometheus 29: (in press Oct 2011)
240. Church GM (2011) Evolving Engineering. (The Scientist in press).
239. Wang HH, Kim H, Cong L, Jeong J, Bang D, Church GM (2011) Genome-scale Promoter Engineering by Co-Selection MAGE (submitted)
238. Wang HH, Church GM (2011) Multiplexed genome engineering and genotyping methods applications for synthetic biology and metabolic engineering. Methods Enzymol. 498:409-26.
237. 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. 2011 Sep;7(9):e1002280. PMID: 21935354 PMCID: PMC3174201
236. 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. doi:10.1093/nar/gkr18.
235. Church G (2011) Non-Inherent Inheritance. Edge World Question (Jan 2011).
234. Carmi S, Church GM, Levanon E (2011) Large scale DNA editing of retrotransposons accelerates mammalian genome evolution (submitted)
233. Douglas SM, Bachelet I, Church GM (2011) A logic-gated nanorobot for targeted transport of molecular payloads. (submitted)
232. 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. PMID: 21248753
231. 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
230b. 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.
230a. 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.
230. 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.
229. Strong M, Sandgren A, Galagan JE, Borowsky M, Church GM, Murray MB (2011) Structural Meta-Analysis of the Mycobacterium tuberculosis Antibiotic Resistome (in revision)
228. Schwartz D, Church GM (2010) Collection and Motif-Based Prediction of Phosphorylation Sites in Human Viruses. Science Signaling 3(137):rs2. PMID: 20807955
227. 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.
226. 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
225. 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.
224. 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
223. 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.
222. Mosberg JA, Lajoie MJ, Church GM (2010) Lambda Red Recombination of Double-Stranded DNA in Escherichia coli Proceeds Through a Fully Single-Stranded Intermediate. Genetics 10.1534/genetics.110.120782 PMID: 20813883
221. Robertson DE, Jacobson S, Morgan F, Berry D, Church GM, Afeyan N (2010) A New Dawn for Industrial Photosynthesis. Photosyn Res. DOI 10.1007/s11120-011-9631-7.
220. 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.
219. Carr PA, Wang HH, Sterling B, Isaacs FJ, Xu G, Church GM, Jacobson JM (2011) Enhanced Multiplex Genome Engineering through Oligonucleotide Co-selection (in revision)
218. 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
217. Umbarger MA, Wright MA, Porreca GJ, Bay D, Toro E, Shapiro L, Marti-Renom MA, Dekker J, Church GM (2010) The 3D Architecture of a Bacterial Genome. (submitted)
216. 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
215. 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
214. Krueger AS, Sommer MOA, Hoffstrom B, Hsu C, Rampuria A, Borisy AA, Church GM, Dantas G, Lehar J (2010) Overcoming bacterial robustness using complex drug mixtures. (in revision)
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. Vigneault F, Laserson U, Simen BB, Lieberman-Aiden E, Egholm M, Church GM (2010) Tracking the dynamics of a human antibody repertoire. (in revision)
210. Church GM (2010) Synthetic Biology. Nature 463: 26-32.
209. Church G (2010) How Has The Internet Changed The Way You Think?. Edge World Question (Jan 2010).
208. Jewett MC, Church GM (2010) In vitro integration of ribosomal RNA synthesis, ribosome self-assembly and protein synthesis. Nature (in revision).
207. Thakuria JV, Ball MP*, Clegg T*, Rosenbaum AM*, Wu X*, Zaranek AW*, Angrist M, Berry GT, Bhak J, Browning MF, Callow MJ, Chou MF, Chung WK, Cox G, Douglas SM, Ge D, Ho Ghang H, Gore A, Hulick P, Kim BC, Kim JI, Kim T, Lee MS, Lee S, Li Z, Nilsen GB, Rienhoff HY, Robasky K, Shianna K, Wheeler MT, Yang JL, Yang L, Aach J, Ashley EA, Drmanac R, Kim SJ, Li JB, Murray M, Quake R, Seidman CE, Seo JS, Zhang K, Rehm H, Church GM (2010) Clinical Analysis of Public Genomes. (in revision)
206. Drmanac R, Burns NL, Callow MJ, Carnevali P, Dahl F, Fernandez A, Halpern AL, Kermani BG, Nazarenko I, Nilsen GB, Pant KP, Sparks AB, Staker B, Yeung G, Baccash J, Borcherding AP, Brownley A, Cedeno R, Chen L, Chernikoff D, Cheung A, Chirita R, Curson B, Ebert J, Hacker CR, Hartlage R, Hauser B, Huang S, Jiang Y, Karpinchyk V, Koenig M, Kong C, Landers T, Le C, Liu J, McBride CE, Morenzoni M, Morey RE, Mutch K, Perazich H, Perry K, Peters BA, Peterson J, Pethiyagoda CL, Pothuraju K, Richter C, Rosenbaum AM, Roy S, Shafto J, Shananhovich V, Shannon KW, Sheppy CG, Sun M, Thakuria JV, Tran A, Vu D, Wu X, Zaranek AW, Drmanac S, Oliphant AR, Banyai WC, Martin B, Ballinger DG, Church GM, Reid CA (2009) Human Genome Sequencing Using Unchained Base Reads on Self-assembling DNA Nanoarrays. Science 2010 Jan 1;327(5961):78-81. Epub 2009 Nov 5; Supplement. PMID: 19892942
205. Sommer MO, Dantas G, Church GM (2009) Functional Characterization of the Antibiotic Resistance Reservoir in the Human Microflora Science Aug 28; 325 (5944) 1128-31. PMID: 19713526
204. Friedland AE, Lu TK, Wang X, Shi D, Church GM, Collins J (2009) Synthetic Gene Networks that Count. Science. Jun 14; 324(5931):1199-202. PMID: 19478183 PMC2690711
203. Wang HH, Isaacs FJ, Carr PA, Sun ZZ, Xu G, Forest CR, Church GM (2009) Programming cells by multiplex genome engineering and accelerated evolution. Nature. Jul 26; 460(7257):894-8. PMID: 19633652
202a. Dietz H, Douglas SM, Shih WH.(2009) Folding DNA into twisted and curved nanoscale shapes. Science. Aug 7; 325(5941):725-30.
202. Li JB, Levanon EY, Yoon J-K, Aach J, Xie B, LeProust E, Zhang K, Gao Y, Church GM (2009) Genome-wide Identification of Human RNA Editing Sites by Parallel DNA Capturing and Sequencing. Science. Jun 14; 324(5931):1210-3. PMID: 19478186
201. Kim JI, Ju YS, Park HS, Kim S, Lee S, Yi JH, Mudge J, Miller NA, Hong D, Bell CJ, Kim HS, Chung IS, Seo SH, Yun JY, Woo HN, Lee H, Suh D, Lee S, Park H, Kim JY, Gokcumen O, Mills RE, Zaranek AW, Thakuria J, Wu X, Kim RW, Huntley JJ, Luo S, Schroth GP, Wu TD, Yang KS, Kim H, Church GM, Lee C, Kingsmore SF, Seo JS (2009) A highly annotated whole genome sequence of a Korean Individual. Nature Jul 8; 460(7258):1011-5. PMID: 19587683.
200a. 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.
200. Church G (2009) The Genome Generation Newsweek (Dec).
199. Lunshof JE, Bobe J, Aach J, Angrist M, Thakuria JV, Vorhaus DB, Hoehe MR, Church GM (2010) Personal genomes in progress: from the human genome project to the personal genome project. Dialogues Clin Neurosci. 2010;12(1):47-60. PMID: 20373666
198a. Guo JU, Ma DK, Mo H, Ball MP, Jang MH, Bonaguidi MA, Balazer JA, Eaves HL, Xie B, Ford E, Zhang K, Ming GL, Gao Y, Song H (2011) Neuronal activity modifies DNA methylation landscape in the adult brain. Nature Neuroscience
198. Prisic S, Dankwa S, Schwartz D, Chou M, Locasale JW, Kang CM, Bemis G, Church G, Steen H, Husson RN (2010) Extensive phosphorylation with overlapping specificity by Mycobacterium tuberculosis serine/threonine protein kinases. PNAS Apr 20;107(16):7521-6. PMID: 20368441
197. P3G Consortium, Church G, Heeney C, Hawkins N, de Vries J, Boddington P, Kaye J, Bobrow M, Weir B (2009) Public access to genome-wide data: five views on balancing research with privacy and protection. PLoS Genet. 2009 Oct; 5(10):e1000665. PMID: 19798440
196. Sullivan GJ, Hay DC, Park IH, Fletcher J, Hannoun Z, Payne CM, Dalgetty D, Black JR, Ross J, Samuel K, Wang G, Daley GQ, Lee JH, Church GM, Forbes SJ, Iredale JP, Wilmut I (2010) Generation of Functional Human Hepatic Endoderm from Human iPS cells. Hepatology Jan;51(1):329-35. PMID: 19877180
195. Sommer MOA, Church GM, Dantas G (2010) A functional metagenomic approach for expanding the synthetic biology toolbox for biomass conversion. Molecular Systems Biology 6:360. PMID: 20393580
194. Zaranek AW, Levanon EY, Zecharia T, Clegg T, Church GM (2010) A Survey of Genomic Traces Reveals a Common Sequencing Error, RNA Editing and DNA Editing. PLoS Genetics May 20;6(5):e1000954. PMID: 20531933
193. Fuller CW, Middendorf LR, Benner SA, Church GM, Harris T, Huang X, Jovanovich SB, Nelson JR, Schloss JA, Schwartz DC, Vezenov DV (2009) Challenges of Sequencing by Synthesis. Nature Biotech. Nov; PMID: 19898456
192. Tolonen A, Chilaka AC, Church GM (2009) Targeted gene inactivation in Clostridium phytofermentans shows that cellulose degradation requires the family 9 hydrolase Cphy3367. Mol Microbiol Dec;74(6):1300-13. PMID: 19775243
191. Lun DS, Rockwell G, Guido NJ, Baym M, Kelner JA, Galagan JE, Church GM (2009) Large-Scale Identification of Genetic Design Strategies using Local Search. Nature EMBO MSB 5:296. PMID: 19690565
190. Khoury MJ, McBride C, Schully SD, Ioannidis JPA, Feero WG, Janssens ACJW, Gwinn M, Simons-Morton DG, Bernhardt JM, Cargill M, Chanock SJ, Church GM, Coates RJ, Collins FS, Croyle RT, Davis BR, Downing GJ, DuRoss A, Friedman S, Gail MH, Ginsburg GS, Green RC, Greene MH, Greenland P, Gulcher JR, Hsu A, Hudson KL, Kardia SLR, Kimmel PL, Lauer MS, Miller AM, Offit K, Ransohoff DF, Roberts S, Rasooly RS, Stefansson K, Terry SF, Teutsch SM, Trepanier A, Wanke KL, Witte JS, Xu J (2009) The Scientific Foundation for Personal Genomics. Genetics in Medicine Jul 16; PMID: 19617843.
189. Zhang K, Li JB, Gao Y, Egli D, Xie B, Lee JH, Aach J, LeProust E, Eggan K, Church GM (2009) Digital RNA Allelotyping Reveals Tissue-specific and Allele-specific Gene Expression in Human. Nature Methods Aug;6(8):613-8. PMID: 19620972 PMC2742772
188. Lee J, Park IH, Gao Y, Li JB, Li Z, Daley G, Zhang K, Church GM (2009) A Robust Approach to Identifying Tissue-specific Gene Expression Regulatory Variants Using Personalized Human Induced Pluripotent Stem Cells. PLoS Genetics Nov;5(11):e1000718. PMID: 19911041 PMC2766639
187. Sandgren A, Strong M, Muthukrishnan P, Weiner BK, Church GM, Murray MB. Tuberculosis drug resistance mutation database. PLoS Med. 2009 Feb 10;6(2):e2. PMID: 19209951
186. de Magalhaes JP, Curado J, Church GM (2009) Meta-analysis of age-related gene expression profiles identifies common signatures of aging. Bioinformatics. Feb 2. PMID: 19189975
185. Li JB, Gao Y, Aach J, Zhang K, Kryukov GV, Xie B, Ahlford A, Yoon J-K, Rosenbaum AM, Zaranek AW, LeProust E, Sunyaev SR, Church GM (2009) Multiplex padlock capturing and sequencing reveal human hypermutable CpG variations. Genome Research Sep;19(9):1606-15. PMID: 19525355.
184. Douglas SM, Marblestone A, Teerapittayanon S, Vazquez A, Church GM, Shih WH (2009) Rapid prototyping of three-dimensional DNA-origami shapes with caDNAno Nucleic Acids Res doi:10.1093/nar/gkp436 (software) PMID: 19531737 PMC2731887
183. Reppas NB, Lin X, Shendure J, Porreca GJ, Church GM (2009) Engineering and Laboratory Evolution of a Cooperative Microbial System (in prep)
182. Carr P, Church GM (2009) Genome Engineering. Nature Biotech. Dec;27(12):1151-62. PMID: 20010598
181. 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
180. 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
179. Reppas N, Lin X, Church GM (2004) Experimental and Theoretical Studies of Artificial Microbial Symbiosis. American Institute of Chemical Engineers (AIChE) 2004.
178. 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
177a. 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.
177. Church GM (2009) Safeguarding Biology. Seed 20:84-86.
176a. Church GM (2008) Evolution of Faith In Experiments Edge World Question (Jan 2008).
176. Zaranek AW, Clegg T, Vandewege W, Church GM (2008) Free Factories: Unified Infrastructure for Data Intensive Web Services. USENIX Annual Technical Conference 2008: 391-404. PMID: 20514356 PMC2877279
175a. Chiang CW, Derti A, Schwartz D, Chou MF, Hirschhorn JN, Wu CT (2008) Ultraconserved elements: analyses of dosage sensitivity, motifs and boundaries. Genetics 180, 2277-93.
175. Shendure JA, Porreca GJ, Church GM (2008) Overview of DNA sequencing strategies. Curr Protoc Mol Biol. 2008 Jan;Unit 7.1. PMID: 18231983
174a. Kim DS, Ross SE, Trimarchi JM, Aach J, Greenberg ME, Cepko CL (2008). Identification of molecular markers of bipolar cells in the murine retina J Comp Neurol. 2008 Apr 10;507(5):1795-810.
174. Schwartz D, Chou MF, Church GM (2008) Predicting protein post-translational modifications using meta-analysis of proteome-scale data sets. Mol Cell Proteomics. 8(2):365-79. web resource PMID: 18974045 PMC2634583
173. Lunshof JE, Chadwick R, Church GM (2008) Hippocrates revisited? Old ideals and new realities. Genomic Med. 2(1-2):1-3. PMID 18716915 PMC2518662
172. Snitkin ES, Dudley AM, Janse DM, Wong K, Church GM, Segre D (2008). Model-driven analysis of experimentally determined growth phenotypes for 465 yeast gene deletion mutants under 16 different conditions. Genome Biology 9:R140. PMID: 18808699 PMC2592718
171. Isenbarger TA, Finney M, Church GM, Gilbert W, Carr CE, Zuber MT, Ruvkun G (2008) The most conserved genome segments for life detection on Earth and other planets. Orig Life Evol Biosph. 38(6):517-33. PMID: 18853276
170. Forest CR, Rosenbaum AM, Church GM (2008) DNA Sequencing By Ligation On Surface-Bound Beads In A Microchannel Environment MicroTAS 2008
169. Vigneault F, Sismour AM, Church GM (2008) Efficient microRNA capture and barcoding via enzymatic oligonucleotide adenylation. Nature Methods 5, 777 - 779. PMID: 18711363
168. Church GM, Porreca GJ, Terry RC, Lares M (2008) High-speed imaging for DNA sequencing. Biophotonics
167. Dantas G, Sommer MO, Oluwasegun RD, Church GM (2008) Bacteria subsisting on antibiotics. Science. 2008 Apr 4;320(5872):100-3. PMID: 18388292
163. 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
166. Bang D, Church GM (2008) Gene synthesis by circular assembly amplification. Nat Methods. 2008 Jan;5(1):37-9. PMID: 18037891
165. 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. Patterns and Implications of Gene Gain and Loss in the Evolution of Prochlorococcus. PLoS Genet. 2007 Dec 21;3(12):e231. PMID: 18159947 PMC2151091
164a. 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
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
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. Global gene expression of Prochlorococcus ecotypes in response to changes in nitrogen availability. Mol Syst Biol. 2006;2:53. Epub 2006 Oct 3. 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 W, Liu F, Jenssen T, Trimarchi J, Punzo C, Lombardi M, Sarang J, Maysuria M, Serikawa K, Lee SY, McCrann D, Kang J, Shearstone J, Burke J, Park D, Choi S, Perrin S, Church GM, Bumgarner R, Cepko C (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.
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.
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 .
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).
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.
18. Richterich P, Church GM (1993) DNA sequencing with direct transfer electrophoresis and non-radioactive detection. Methods in Enzymology 218, 187-222.
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.
16. Wang M, Church GM (1992) A whole genome approach to in vivo DNA-protein interactions in Escherichia coli. Nature 360: 606-610.
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).
14b. 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.
14a. 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.
14. Sikorav JL, Church GM (1991) Accelerated DNA renaturation: Complementary recognition in condensed DNA J. Mol. Biol. 222: 1085-1108.
13e. 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.
13d. 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.
13c. 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.
13b. 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.
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.
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.
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.
6. Sutcliffe JG, Church GM (1978) The cleavage site of the restriction endonuclease Ava II. Nucleic Acids Res. 5: 2313-2319.
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
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.
34. Agresti J, Chu L-Y, Weitz DA, Kim J-W, Rowat A, Sommer M, Dantas G, Church G (2008) WO/2008/109176 Assays and Other Reactions Involving Droplets (Harvard)
33. Church G, Sismour M (2008) WO 2008/151127 Compounds and Methods for Chemical Ligation (Harvard)
32. Church G, Zhang K, Shendure J (2008) WO 2008/127901 Region-Specific Hyperbranched Amplification (Harvard)
31. Jacobson JM, Church G, Baynes BM (2008) WO 2008/127283 Engineered Metabolic Pathways (Codon Devices)
30. Church G, Bang D (2008) WO 2008/112683 Gene Synthesis by Circular Assembly Amplification (Harvard)
29. Church G, Wang HH, Isaacs FJ (2008) WO 2008/052101 Multiplex Automated Genome Engineering (Harvard)
28. Kim JB, Porreca GJ, Church GM, Seidman JG (2008) WO 2008/039998 Methods for Sequencing DNA(SbL bead arrays) (Harvard)
27. Church G, Zhang K (2007) WO 2007/136874 Genomic Library Construction (Harvard)
26. Church G, Baynes B (2007) WO 2007/136835 Methods and Cells for Creating Functional Diversity and Uses Thereof (Codon Devices)
25. Church G, Jacobson JM, Baynes BM (2007) WO 2007/136833 Methods and Compositions for Aptamer Production and Uses Thereof (Codon Devices)
24. 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.)
23. Church G, Porreca G, Shendure J, Rosenbaum A (2007) WO 2007/120208 Nanogrid Rolling Circle DNA Sequencing (Harvard)
22. Church G, Zhang K, Chou J (2007) WO 2007/092538 Methods for Making Nucleotide Probes for Sequencing and Synthesis (Harvard)
21. Church G, Liu D (2007) WO 2007/075438 Polypeptides Comprising Unnatural Amino Acids, Methods for Their Production and Uses Therefor (Codon Devices)
20. Gao X, Bear DM, Church GM, Zhou X (2007) WO 2007/021971 Labeling Compositions and Methods of Use for Deterrent Trackability (Pharmorx Inc.)
19. Church G, Baynes B, Pitcher ER (2007) WO 2007/005053 Hierarchical Assembly Methods for Genome Engineering (Codon Devices)
18. Church G, Cerrina F, Baynes B, Pitcher ER (2007) WO 2007/136736 A2 Methods For Nucleic Acid Sorting and Synthesis (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, Janse D (2005) US Patent Appl # 2005/0152888 Targeted polypeptide degradation. (Harvard)
10. 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)
9. Church GM, Bulyk ML, Choo Y (2002) WO 02/18648 Analysis of binding interactions (Harvard)
8. Church GM, Shendure J (2002) US Patent Appl #2010 0099080 Nucleic acid memory device (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)