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-Jun-2009 by GMC.
200. Fuller CW, Middendorf LR, Benner SA, Church GM, Harris T, Huang X, Jovanovich SB, Nelson JR, Schloss JA, Schwartz DC, Vezenov DV. Challenges of Sequencing by Synthesis (Nature Biotech in press)
199. Tolonen A, Chilaka AC, Church GM (2009) Targeted gene inactivation in Clostridium phytofermentans shows that cellulose degradation requires hydrolase. (submitted)
198. Friedland AE, Lu TK, Wang X, Shi D, Church GM, Collins J (2009) Synthetic Gene Networks that Count. Science 324(5931):1199-202.
197. Wang HH, Isaacs FJ, Forest CR, Sun ZZ, Xu G, Church GM (2009) Multiplexed Genome Engineering and Directed Evolution (Nature in press)
196. 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 Massively Parallel DNA Capturing and Sequencing. Science 324(5931):1210-3.
195. Kim JI, Young Seok Ju, 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 in press)
194a. Douglas SM, Dietz H, Liedl T, Hogberg B, Graf F, Shih WM (2009) Self-assembly of DNA into nanoscale three-dimensional shapes. Nature 459(7245):414-8.
194. Lun DS, Rockwell G, Guido NJ, Baym M, Kelner JA, Galagan JE, and Church GM (2009) Large-Scale Identification of Genetic Design Strategies using Local Search. Nature EMBO MSB in press.
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 in press
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 (submitted to Nature Methods)
191. Lee J, Park IH, Gao Y, Li JB, Li Z, Daley G, Zhang K, Church GM (2009) Changes in Allele-specific Gene Expression In Human Induced Pluripotent Stem Cells (submitted to Nature Genetics)
190. 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.
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 in press)
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
186. Reppas NB, Lin X, Shendure J, Porreca GJ, Church GM (2009) Engineering and Laboratory Evolution of a Cooperative Microbial System (in prep)
185. Thakuria JV, Wu X, Zaranek AW, Rosenbaum AM, Li J, Hulick P, Murray M, Browning MF, Rienhoff HY, Cox G , Rehm H, Berry G , Church GM (2009) Clinical interpretation of variants in seven individual human genomes (submitted)
184. Ball MP, Li JB, Gao Y, Lee J, LeProust E, Park I-H, Xie B, Daley GQ, Church GM (2009) Targeted and whole-genome methylomics reveals gene-body signatures in human cell lines. Nature Biotechnol 27:361-8
183. Zaranek AW, Levanon EY, Church GM (2009) Evidence for editing events in genomic traces (in prep)
182. 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 (submitted to NAR).
181. Lee J, Park IH, Maherali N, Li J, Deng J, Li JB, Hochedlinger K, Daley G, Zhang K, Church GM (2009) Induction of Developmental and Inflammatory Transcriptomes Using Pluripotent Stem Cell Factors for the Personal Genome Project (submitted)
180. Sommer MO, Dantas G, Church GM. (2009) Human-associated microbiome is a mobilizable reservoir of antibiotic resistance (submitted)
179. Sommer MO, Dantas G, Church GM. (2009) Functional metagenomic mining for synthetic biology parts and for biomass utilization conversion (submitted to MSB)
178. Zaranek AW, Clegg T, Vandewege W, Church GM. Free Factories: Unified Infrastructure for Data Intensive Web Services. USENIX Annual Technical Conference 2008: 391-404
177. 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.
176. Church GM (Feb 2009) Seed 20:84-86. Safeguarding Biology.
175a. 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 (submitted)
175. Shendure JA, Porreca GJ, Church GM. Overview of DNA sequencing strategies. Curr Protoc Mol Biol. 2008 Jan;Unit 7.1.
174. Schwartz D, Chou MF, Church GM (2008) Predicting protein post-translational modifications using meta-analysis of proteome-scale data sets. Mol Cell Proteomics. Oct 28. web resource
173. Lunshof JE, Chadwick R, Church GM (May 2008) Hippocrates revisited? Old ideals and new realities. Genomic Med. 2(1-2):1-3. PMID 18716915 - PMCID: PMC2518662
172. Snitkin ES, Dudley AM, Janse DM, Wong K, Church GM, Daniel Segre D (Sep 2008). Model-driven analysis of experimentally determined growth phenotypes for 465 yeast gene deletion mutants under 16 different conditions. Genome Biology 9:R140.
171. Isenbarger TA, Finney M, Church GM, Gilbert W, Carr CE, Zuber MT, Ruvkun G. The most conserved genome segments for life detection on Earth and other planets. Orig Life Evol Biosph. 2008 Oct 14.
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. (Sep 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. Bacteria subsisting on antibiotics. Science. 2008 Apr 4;320(5872):100-3. PMID: 18388292
163. Lunshof JE, Chadwick R, Vorhaus DB, Church GM. From genetic privacy to open consent. Nat Rev Genet. 2008 May;9(5):406-11.
166. Bang D, Church GM. Gene synthesis by circular assembly amplification. Nat Methods. 2008 Jan;5(1):37-9.
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
164. Porreca GJ, Zhang K, Li JB, Xie B, Austin D, Vassallo SL, LeProust EM, Peck BJ, Emig CJ, Dahl F, Yuan Gao Y, Church GM, Shendure, J (2007) Multiplex amplification of large sets of human exons. Nat Methods. 2007 Nov;4(11):931-6. (Supplement)
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
162. Nardi V, Raz T, Chao X, Wu CJ, Stone RM, Cortes J, Deininger MWN, Church GM, Zhu J and Daley GQ (2007) Monitoring resistance to kinase inhibitors with polony technology: towards personalized therapy for CML patients. Oncogene 27(6):775-82. (Supplement)
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..
160. Wright MA, Kharchenko P, Church GM, Segre D. Chromosomal periodicity of evolutionarily conserved gene pairs. Proc Natl Acad Sci U S A. 2007 Jun 19;104(25):10559-64.
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).
158. Bugl H, Danner JP, Molinari RJ, Mulligan JT, Park H-O, 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.
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.
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
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.
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.
153. Strong M, Church G.Gem of an idea for a unique machine. Nature. 2007 May 3;447(7140):112.
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. Polony DNA sequencing. Curr Protoc Mol Biol. 2006 Nov;Unit 7.8.
150. The BIO FAB Group -- Baker, D, Church G, Collins, J, Endy, D, Jacobson, J, Jay Keasling, J, Modrich, P, Smolke, C, and Weiss, R (2006) Building a Fab for Biology . Scientific American. June 2006.
149. Church GM, Shendure J, Porreca G (2006) Sequencing thoroughbreds Nature Biotech 24: 139.
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.
147. Forster AC, Church GM. (2007) Synthetic biology projects in vitro. Genome Res. 17(1):1-6.
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
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.
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.
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.
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;
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
140. Yang A, Zhu Z, Kapranov P, McKeon F, Church GM, Gingeras TR, and Kevin 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.
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.
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.
137. Forster AC & Church, GM (2006) Toward Synthesis of a Minimal Cell. Nature-EMBO-Molecular Systems Biology 2 doi:10.1038/msb4100090. (supplement).
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.
135. Kharchenko P, Chen L, Freund Y, Vitkup D, Church GM. Identifying metabolic enzymes with multiple types of association evidence. BMC Bioinformatics. 2006 Mar 29;7(1):177
134. Medico E, D'Alessandro L, Gentile A, Montemurro F, Church GM, and 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
132. deMagalhaes J, Church GM (2006) Cells discover fire: employing reactive oxygen species in development and aging. Experimental Gerontology Oct 11.
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.
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.
128. Gao Y & Church G (2005) Improving molecular cancer class discovery through sparse non-negative matrix factorization. Bioinformatics 21: 3970-5.
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.
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 .
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.
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.
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.
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.
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.
117. Segre D, DeLuna A, Church GM, Kishony R (2004) Modular epistasis in yeast metabolism (Nature Genetics Dec 12).
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, H Kim T, O Barrera L, Qu C, Van Calcar S, Luna R, K Glass C, G Rosenfeld M, Guigo R, E Antonarakis S, Birney E, Brent M, Pachter L, Reymond A, T Dermitzakis E, Dewey C, Keefe D, Denoeud F, Lagarde J, Ashurst J, Hubbard T, J 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, C Zody M, 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.
115. Church GM (2005) Let us go forth and safely multiply. Nature 438: 423.
114. Church GM (2005) The Personal Genome Project. Nature EMBO Molecular Systems Biology doi:10.1038/msb4100040
113. Aach J, Church GM. Accommodation or prediction? Science. 2005 Jun 3;308(5727):1409-12; author reply 1409-12.
112b. Pe'er D. 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. 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).
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.
109. Grainger DC, Overton TW, Reppas N, Wade JT, Tamai E, Hobman JL, Constantinidou C, Struhl K, Church G and 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. 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 U S A. 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, Le Crom S, Devaux F, Vialette S, Church GM, Jacq C and Marc P (2004) yMGV : a cross-species expression data mining tool. Nucleic Acids Res. 90001 D323-D325.
97. Aach JA and 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 Mol Endocrinol. 17(4):610-27.
85. Masuda N. and 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, and 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, and 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. and 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 and 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 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, and 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. 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 and 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 and 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. and 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 and 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, and 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, and 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, M.R. Kopke, K, Wendel,B, Rohde, K, Flachmeier, C, Kidd, KK, Berrettini,WH and 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, and 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, F.J., Furukawa, T., Steffen, M.A., Church, G.M., and Cepko, C.L., (2000) Microarray analysis of the transcriptional network controlled by the photoreceptor homeobox gene Crx . Current Biology 10: 301-310.
53. Mcguire, A.M. and Church, G.M., (2000) Predicting regulons and their cis-regulatory motifs by comparative genomics. Nucleic Acids Research 28:4523-30.
52. Goldmark,J.P., Fazzio,T.G., Estep,P.W., Church,G.M., and Tsukiyama, T. (2000) The Isw2 chromatin remodeling complex represses early meiotic genes upon recruitment by Ume6p , Cell 103: 423.
51. Jelinsky, S.A., Estep, P., Church, G.M., Samson, L.D. (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, A.M., Hughes, J.D., and Church, G.M. (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, G.M. (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, J.M. and Church, G.M. (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. and Church, G.M. (2000) Biclustering of expresssion data. ISMB 2000. (Supplement. & Java version).
45. Hughes, J.D., Estep, P.W., Tavazoie, S. and Church, G.M. (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, G.M. (2000) Systematic management and analysis of yeast gene expression data . Genome Research 10: 431-445.ExpressDB
43. Mitra, R. and Church, G.M. (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, and 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, A.M., De Wulf, P., Church, G.M., and Lin, E.C. (1999) A weight matrix for binding recognition by the redox-response regulator ArcA-P of Escherichia coli . Mol Microbiol 32: 219-21.
39. Johnson, J.M. and Church, G.M. (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, K.R., McGuire, A.M., and Church, G.M. (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. and Church, G.M. (1998) Quantitative Whole-genome analysis of DNA-protein interactions by in vivo methylase protection in E.coli. Nature Biotechnology 16: 566-571.
36. Roth, F.P., Hughes, J.D., Estep, P.W. and Church, G.M. (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, and 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, and 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 and 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 and 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, and 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 and 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 N.D., Lee H.-M., Mao J., Smith D., and Church G.M. (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, and 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, and 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 and 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, and Richterich P (1994) Automated Multiplex Sequencing. Automated DNA sequencing and analysis techniques, pp. 11-16. (eds. Adams MD, Fields C and Venter JC (Academic Press, San Diego).
19. Roth JR, Lawrence JG, Rubenfield M, Kieffer-Higgins S, and Church GM (1993) Characterization of the cobalamin (Vitamin B12) biosynthetic genes in Salmonella typhimurium. J. Bacteriology 175: 3303-3316.
18. Richterich P and 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, and Tabin C. (1992) The dispersion of neuronal clones across the cerebral cortex. Science 258: 317-320. supplement.
16. Wang M and Church GM (1992) A whole genome approach to in vivo DNA-protein interactions in Escherichia coli. Nature 360: 606-610.
15. Church, GM and 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 and 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, A.J., Furlong, D., and 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 and Church GM (1991) Accelerated DNA renaturation: Complementary recognition in condensed DNA. J. Mol. Biol. 222: 1085-1108.
13e. Carlone, R.L., Boulianne, R.P., and Link, A.J. (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, J.W., Smoller, D.A., Jones, R.W., Carulli, J.P., Vellek, A.E., Garza, D., Link, A.J., Duncan, I.W., and Hartl, D.L. (1991) Drosophila genome project: one-hit coverage in yeast artificial chromosomes. Chromosoma 100: 495-509.
13c. Kafatos, F.C., Louis, C., Savakis, C., Glover, D.M., Ashburner, M., Link, A.J., Siden-Kiamos, I., and Saunder, R.D.C. (1991) Integrated maps of the Drosophila genome: progress and prospects. Trends in Genetics 7: 155-161.
13b. Danilevskaya, O.N., Kurenova, E.V., Pavlova, M.N., Bebehov, D.V., Link, A.J., Koga, A., Vellek, A., and Hartl, D.L. (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, and 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 and Kieffer-Higgins S. (1988) Multiplex DNA sequencing . Science 240: 185-188.
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, and 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 and 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, and Gilbert W. (1984) Genomic Sequencing. Proc. Nat. Acad. Sci. USA 81: 1991-1995.
8. Church GM, and Gilbert W (1980) Yeast mitochondrial intron products required in trans for RNA splicing. In Mobilization and Reassembly of Genetic Information, eds. Joseph, D.R., Schultz, J., Scott, W.A., and 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 and 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, and Kim S-H (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, and Kim S-H (1977) RNA-ligand interactions: (I) magnesium binding sites in yeast tRNA phe. Nucleic Acids Res. 4: 2811-2820.
3. Sussman JL, Holbrook SR, Church GM, and Kim S-H (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, and Kim S-H (1977) Secondary structural complementarity between DNA and proteins. Proc. Nat. Acad. Sci. USA 74: 1458-1462.
1. Kim SH, Sussman JL, and 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. and Rao, S.T. (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 GJ, 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 (2001) US Patent Appl #2003/0228611 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 and Kieffer-Higgins S. (1992) WO 92/21079A1 Parallel Sequential Reactor. (Harvard)
2. Church GM and Kieffer-Higgins S. (1992) US # 5,149,625 Multiplex analysis of DNA. (Harvard)
1. Church GM and Kieffer-Higgins S (1989) US # 4,924,124 & EPO# 0303459A2 Multiplex sequencing. (Harvard)