152. Dantas G, Sommer MO, Oluwasegun RD, Church GM. Bacteria subsisting on antibiotics. Science. 2008 Apr 4;320(5872):100-3.
151. Lunshof JE, Chadwick R, Vorhaus DB, Church GM. From genetic privacy to open consent. Nat Rev Genet. 2008
150. Bang D, Church GM. Gene synthesis by circular assembly amplification. Nat Methods. 2008 Jan;5(1):37-9.
149. 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
148. 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)
147. 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
146. Nardi V, Raz T, Chao X, Wu CJ, Stone RM, Cortes J, Deininger MWN, Church G, 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)
145. 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..
144. 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.
143. Debbie Lindell D, Jaffe JD, Coleman ML, Futschik ME, Axmann IM, Rector T, Kettler G, Sullivan MB, Steen R, Hess WR, Church GM, Sallie W. 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).
142. 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.
141. 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.
140. 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
139. 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.
138. Forster AC, Church GM. (2006) Synthetic biology projects in vitro. Genome Res. 17(1):1-6.
137. 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
136. 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.
135. 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.
134. 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.
133. 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.
132. 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;
131. Su-In Lee, S-I, Pe'er, D, Dudley, AM, Church, GM, Daphne Koller D (2006) Identifying Regulatory Mechanisms using Individual Variation Reveals Key Role for Chromatin Modification. Proc Natl Acad Sci USA 103(38):14062-7
130. 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.
129. 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.
128. Lin, X. Gao, Y, Yaoyun Shi, Y, Church, GM (2006) Submitted.
127. 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.
126. Forster, AC & Church, GM (2005) Toward Synthesis of a Minimal Cell. Nature-EMBO-Molecular Systems Biology 2 doi:10.1038/msb4100090. (supplement).
125. 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.
124. 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
123. Medico, E, D'Alessandro, L, Gentile, A, Montemurro, F, Church, GM, and Comoglio, PM (2006) A genomic signature for the invasive growth program. Submitted.
122. 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
121. deMagalhaes, J, Church, GM (2006) Cells discover fire: employing reactive oxygen species in development and aging. Experimental Gerontology Oct 11.
120. 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.
119. 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.
118. Gao, Y & Church G (2005) Improving molecular cancer class discovery through sparse non-negative matrix factorization. Bioinformatics 21: 3970-5.
117. 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.
116. de Magalhaes JP, Church GM. (2005) Genomes optimize reproduction: aging as a consequence of the developmental program. Physiology 20:252-9.
115. 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
114. Kharchenko, P, Vitkup, D & Church, GM (2005) Expression dynamics of a cellular metabolic network. Nature-EMBO MSB doi:10.1038/msb4100023, 2-Aug-2005 .
113. Zhu, Z, Shendure J, & Church, GM (2005) Discovering Functional Transcription Factor Combinations in the Human Cell Cycle. Genome Research 15(6):848-55.
112. Petti,A & Church, GM (2005) A Network of Transcriptionally Coordinated Functional Modules in Saccharomyces cerevisiae. Genome Research Sep;15(9):1298-306.
111. 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 (open access).
110. 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.
109. 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.
108. Segre, D, DeLuna, A, Church, GM, Kishony, R (2004) Modular epistasis in yeast metabolism (Nature Genetics Dec 12).
107. Feingold, EA, et al. (2004) The ENCODE (ENCyclopedia Of DNA Elements) Project. Science 306: 636-40.
106. Tompa, M. et al (2005) An Assessment of Computational Tools for the Discovery of Transcription Factor Binding Sites. Nature Biotechnology 23(1):137-44.
105. 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.
104. D'haeseleer P, Church GM. (2004) Estimating and improving protein interaction error rates. Proc IEEE Comput Syst Bioinform Conf. 2004:216-23.
103. 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.
102. Jaffe, JD, Stange-Thomann, N, Smith, C, DeCaprio, D, Sheila 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
101. 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.
100.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.
99. Catic, A, Collins, C, Church, GM and Hidde L. Ploegh, HL (2004) Preferred in vivo ubiquitination sites. Bioinformatics Jul 15.
98. Bulyk,ML, McGuire, AM, Masuda,N, and 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.
97. Kharchenko, P, Church, GM, Vitkup, D. (2004) Filling gaps in a metabolic network using expression information. Bioinformatics Aug 4;20 Suppl 1:I178-I185.
96. Janse, DM, Crosas,B Finley,D & Church, GM (2004) Localization to the Proteasome is Sufficient for Degradation. J. Biol Chem 279 (20):21415-20.
95. 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.
94. 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.
93. Gao,Y & Church, GM (2004) FLEXMOTIF: A Generic Flexible Motif Discovery Algorithm for Unaligned Sequences. Submitted to RECOMB2004.
92. 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.
91. 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
90. Steffen, M, Jaffe, JD, & Church, GM (2004-5) Analysis of DNA-Binding Proteins by Mass Spectrometry. Submitted.
89. 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
88. Vitkup,D, Sander,C, Church,GM (2003) The Amino-acid Mutational Spectrum of Human Genetic Disease. Genome Biol. 4: R72.
87. Segre, D, Zucker, J, Katz, J, Lin, X, D'haeseleer, P, Rindone, W, Karchenko, P, Nguyen, D, Wright, M, and Church, GM (2003) From annotated genomes to metabolic flux models and kinetic parameter fitting. Omics 7:301-16. (Biospice special issue)
86. 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.
85. 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.
84. 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.
83. 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. .
82. Anderson, LM, Choe,SE, Yukhananov, RY, Hopfner, RL, Church, GM, Pratt, RE, and 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.
81. Mitra,RD, Shendure,J, Olejnik,J, Olejnik,EK, and Church,GM (2003) Fluorescent in situ Sequencing on Polymerase Colonies. Analyt. Biochem. 320:55-65 Protocol & software supplements.
80.Mitra, RD, Butty, V, Shendure, J, Williams, BR, Housman, DE, and Church, GM (2003) Digital Genotyping and Haplotyping with Polymerase Colonies. Proc Natl Acad Sci USA. May 13;100(10):5926-31.
79. 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.
78. Masuda N. and Church GM (2003) Regulatory Network of acid resistances genes in Escherichia coli. Molecular Microbiology 48 (3), 699-712.
77. 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.
76. 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.
75. Segre, D, Vitkup, D, and Church, GM (2002) Analysis of optimality in natural and perturbed metabolic networks . Proc. Nat. Acad. Sci USA 99: 15112-7. Supplement
74. Sudarsanam,P., Pilpel,Y, and Church, G.M. (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
73. Steffen, M, Petti, A, D'haeseleer, P, Aach,J, and Church, GM (2002) Automated Modelling of Signal Transduction Networks. BMC Bioinformatics 3:34-44.
72. 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.
71. 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
70. 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.
69. Halfon, MS, Grad, Y, Church, GM, and Michelson, AM (2002) Computation-based discovery of related transcriptional regulatory modules and motifs from a combinatorial model. Genome Research 12: 1019-1028.
68. 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.
67. Dudley, AM, Aach, J, Steffen, MA, and 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.
66. 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.
65. 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.
64. Zhu, Z, Pilpel, Y, and Church, GM (2002) Computational Identification of Transcription Factor Binding Sites via a Transcription-factor-centric Clustering (TFCC) Algorithm. J. Molec. Biol. 318: 71-81
63. 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.
62. 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.
61. 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)
60. Ge, H, Church, GM, Vidal, M (2001) Correlation between transcriptome and interactome data obtained from S. cerevisiae. Nature Genetics, Dec;29(4):482-6.
59. 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).
58. 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.
57. Aach, J and Church, GM (2001) Aligning gene expression time series with time warping algorithms. Bioinformatics 17:495-508. (web supplement) 1-8.
56. Bulyk, ML, Choo, Y., Huang, X, and Church, G.M. (2001) Exploring DNA binding specificities of zinc fingers with DNA microarrays . Proc. Nat. Acad. Sci USA 98: 7158-7163. Supplement.
55. 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-)
54. Selinger, D., Cheung, K., Mei, R., Johanson, E.M., Richmond, C., Blattner, F.R., Lockhart, D., and Church, G.M. (2000) RNA expression analysis using a 30 base pair resolution Escherichia coli genome array. Nature Biotechnology 18, 1262-7. (Suppl. data and software)
53. Jamshidi, N., Edwards, J.S., Fahland, T, Church, G.M., Palsson, B.O. (2001) Dynamic simulation of the human red blood cell metabolic network. Bioinformatics 17: 286-287. (Supplementary software)
52. 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)
51. Cohen, B.A., Mitra, R.D., Hughes, J.D., and Church, G.M. (2000) A computational analysis of whole genome expression data reveals chromosomal domains of gene expression. Nature Genetics Oct;26(2):183-186.
50. 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.
49. Mcguire, A.M. and Church, G.M., (2000) Predicting regulons and their cis-regulatory motifs by comparative genomics. Nucleic Acids Research 28:4523-30.
48. 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.
47. 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.
46. 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
45. 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.
44. 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).
43. Teichmann, S.A., Chothia, C., Church, G.M., Park, J. (2000) Fast assignment of protein structures to sequences using the intermediate sequence library PDB-ISL. Bioinformatics 16: 117-124.
42. Cheng, Y. and Church, G.M. (2000) Biclustering of expresssion data. ISMB 2000. (Supplement. & Java version).
41. 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.
40. Aach, J., Rindone, W., Church, G.M. (2000) Systematic management and analysis of yeast gene expression data . Genome Research 10: 431-445.ExpressDB
39. 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.
38. Tavazoie, S., Hughes, J.D., Campbell, M.J., Cho, R.J., and Church, G.M. (1999) Systematic determination of genetic network architecture. Nature Genetics 22:281-5.
37. Bulyk, M.L., Gentalen, E. Lockhart, D.J., Church, G.M. (1999) Quantifying DNA-protein interactions by double-stranded DNA arrays. Nature Biotechnology 17: 573-7.
36. 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.
35. 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).
34. 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.
33. 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.
32. 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.
31. Chen, T. Hongyu L. He, Church, G.M. (1999) Modeling Gene Expression with Differential Equations. PSB-1999:29-40.
30. Smith, D.R., Doucette-Stamm, L.A., 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, G.M., Daniels, C.J., Mao, J., Rice, P., Nolling, J., and Reeve, J.N. (1997) The Complete Genome Sequence of Methanobacterium thermoautotrophicum Strain delta-H: Functional Analysis and Comparative Genomics . J. Bacteriol. Nov. 179: 7135-7155.
29. Bian, N., Wang, P., Wang, Z., Church, G.M., and Giese, R.W. (1997) Detection via Laser Desorption and Mass Spectrometry of Multiplex Electrophore-Labeled Albumin. Rapid Commun. Mass Spectrom. 11: 1781-1784.
28. Link, A.J., Phillips, D. and Church, G.M. (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.
27. Link, A.J., Robison, K. and Church, G.M. (1997) Comparing the predicted and observed properties of proteins encoded in the genome of Escherichia coli. Electrophoresis 18 (8):1259-1313 .
26. L. Xu, N. Bian, Z. Wang, S. Abdel-Baky, S. Pillai, D. Magiera, V. Murugaiah, R.W. Giese, P. Wang, T. O'Keeffe, H. Abushamaa, L. Kutney, G.M. Church, S. Carson, D. Smith, M. Park, J. Wronka, F. Laukien. (1997) Electrophore Mass Tag Dideoxy DNA Sequencing. Analytical Chemistry 69: 3595-3602.
25. Smith, D.R. P. Richterich, M. Rubenfield, P.W. Rice, C. Butler, H.-M. Lee, S. Kirst, K. Gundersen, K. Abendschan, Q. Xu, M. Chung, C. Deloughery, T. Aldredge, J. Maher, R. Lundstrom, C. Tulig, K. Falls, J. Imrich, D. Torrey, M. Engelstein, G. Breton, D. Madan, R. Nietupski, B. Seitz, S. Connelly, S. McDougall, H. Safer, R. Gibson, L. Doucette-Stamm, K. Eiglmeier, S. Bergh, S. T. Cole, K. Robison, L. Richterich, J. Johnson, G. M. Church, and J. Mao. (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.
24. Goodman, H.M., Gallant,P., Keifer-Higgins,S., Rubenfield,M. and Church,G.M. (1996) A 37.5 Kb sequence from Arabidopsis thaliana chromosome I. Genbank Accession number: U53501.
23. Robison, K., Gilbert, W., Church, G.M. (1996) More Haemophilus and Mycoplasma genes. Science 271: 1302-1304.
22. 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.
21. Richterich,P., Lakey,N., Gryan,G., Jaehn,L., Mintz,L., Robison,K. and Church,G.M. (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. Chae, H.Z., Robison, K., Poole, L.B., Church, G.M., Storz, G., and Rhee, S.G. (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
19. Robison, K., Gilbert, W., and Church, G.M. (1994) Large scale bacterial gene discovery by similarity search. Nature Genetics 7: 205-214. Data Archive
18. Church, G.M., 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, M.D., Fields, C., and Venter, J.C. (Academic Press, San Diego).
17. Roth, J.R., Lawrence, J.G., Rubenfield, M., Kieffer-Higgins, S., and Church, G.M. (1993) Characterization of the cobalamin (Vitamin B12) biosynthetic genes in Salmonella typhimurium. J. Bacteriology 175: 3303-3316.
16. Richterich, P. and Church, G.M. (1993) DNA sequencing with direct transfer electrophoresis and non-radioactive detection. Methods in Enzymology 218, 187-222.
15. Walsh, C., Ryder, L., Cepko, C., Church, G.M., and Tabin, C. (1992) The dispersion of neuronal clones across the cerebral cortex. Science 258: 317-320. supplement.
14. Wang, M. and Church, G.M. (1992) A whole genome approach to in vivo DNA-protein interactions in Escherichia coli. Nature 360: 606-610.
13. Church, G.M. 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, G.M. (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).
12. Sikorav, J.-L. and Church, G.M. (1991) Accelerated DNA renaturation: Complementary recognition in condensed DNA. J. Mol. Biol. 222: 1085-1108.
11. Church, G.M., and Kieffer-Higgins, S. (1988) Multiplex DNA sequencing . Science 240: 185-188.
10. Church, G.M., Ephrussi, A., Gilbert, W., and Tonegawa, S. (1985) Cell-type specific contacts to immunoglobulin enhancers in nuclei. Nature 313: 798-801.
9. Ephrussi, A., Church, G.M., Tonegawa, S., and Gilbert, W. (1985) B Lineage-specific interactions of an immunoglobulin enhancer with cellular factors in vivo. Science 227: 134-140. NCBI DNA accession#: M12827
8. Church, G.M., and Gilbert, W. (1984) Genomic Sequencing. Proc. Nat. Acad. Sci. USA 81: 1991-1995.
6. Church, G.M., 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, G.M., Slonimski, P.S., and Gilbert, W. (1979) Pleiotropic mutations within two yeast mitochondrial cytochrome genes block mRNA processing. Cell 18: 1209-1215.
6. Sutcliffe, J.G., and Church, G.M. (1978) The cleavage site of the restriction endonuclease Ava II. Nucleic Acids Res. 5: 2313-2319.
5. Sussman, J.L., Holbrook, S.R., Warrant, R.W., Church, G.M., 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, S.R., Sussman, J.L., Warrant, R.W., Church, G.M., and Kim, S.-H. (1977) RNA-ligand interactions: (I) magnesium binding sites in yeast tRNA phe. Nucleic Acids Res. 4: 2811-2820.
3. Sussman, J.L., Holbrook, S.R., Church, G.M., 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, G.M., Sussman, J.L., and Kim, S.-H. (1977) Secondary structural complementarity between DNA and proteins. Proc. Nat. Acad. Sci. USA 74: 1458-1462.
1. Kim, S.H., Sussman, J.L., and Church, G.M. (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.
Church GM & Zhang K (2006) US Patent Appl # 2006/0014167 Amplification of trace amounts of nucleic acids
Church GM & Janse D (2005) US Patent Appl # 2005/0152888 Targeted polypeptide degradation.
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.
Church, G.M., Bulyk, M.L., & Choo, Y (2002) WO 02/18648 Analysis of binding interactions
Church, G.M. & Shendure J (2001) US Patent Appl #2003/0228611 Nucleic acid memory device
Church, G.M. & Bulyk, M.L. (2001) US # 6,548,021 & # 6,326,489 Surface-bound, bimolecular, double-stranded DNA arrays
Church, G.M. (2001) WO 01/68671 Method of making protein arrays
Church, G.M. & Mitra (2000) WO 00/53812 Replica amplification of nucleic acid arrays. (also US # 6,432,360)
Church, G.M., Deamer, D.W., Branton, D., Baldarelli, R., Kasianowicz, J. (1998) US # 5,795,782 Characterization of individual polymer molecules based on monomer-interface interactions.
Church, G.M. and Kieffer-Higgins, S. (1992) WO 92/21079A1 Parallel Sequential Reactor.
Church, G.M. and Kieffer-Higgins, S. (1992) US # 5,149,625 Multiplex analysis of DNA.
Church, G.M., and Kieffer-Higgins, S. (1989) US # 4,924,124 & EPO# 0303459A2 Multiplex sequencing.
Shendure JA, Porreca GJ, Church GM. Overview of DNA sequencing strategies. Curr Protoc Mol Biol. 2008 Jan;Unit 7.1.
Porreca GJ, Shendure J, Church GM. Polony DNA sequencing. Curr Protoc Mol Biol. 2006 Nov;Unit 7.8.
Church G (2007) The Personal Exome Project ( Nature Genetics 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?)
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.
Church GM, Shendure J, Porreca G (2006) Sequencing thoroughbreds Nature Biotech 24: 139.
Church, GM (2006) Genomes for all . Scientific American Jan 2006.
Nguyen DH, D'haeseleer P. (2006) Deciphering principles of transcription regulation in eukaryotic genomes . Mol Syst Biol. 2: 2006.0012.
Church GM (2005) Let us go forth and safely multiply. Nature 438: 423.
Church GM (2005) The Personal Genome Project. Nature EMBO Molecular Systems Biology doi:10.1038/msb4100040
Aach J, Church GM. Accommodation or prediction? Science. 2005 Jun 3;308(5727):1409-12; author reply 1409-12.
Pe'er D. Bayesian network analysis of signaling networks: a primer. Sci STKE. 2005 Apr 26;2005(281):pl4.
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.
Church, GM (2005) From systems biology to synthetic biology. Molecular Systems Biology doi: 10.1038/msb4100007 (open access).
Church GM (2004) The Future of Human Nature pp. 41-44
Selinger, D., Wright, M, Church, G.M. (2003) On the complete determination of biological systems . Trends in Biotechnology 21: 251-4.
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
Church, G.M. (2002) Foreword in Scientific American's "Understanding the Genome".
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
Collins FS, Patrinos A, Jordan E, Chakravarti A, Gesteland R, Walters L. (1998) New goals for the U.S. Human Genome Project: 1998-2003. Science 282(5389):682-9.
Church, G.M. (1996) Databases for Gene Expression. Nature Biotechnology 14: 828.
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.
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.
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.
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.
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.
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.
Tempst, P., A. J. Link, Riviere, L.R., 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.
Delehanty J, White RL, Mendelsohn ML. (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
Church, G.M., and Gilbert, W. (1985) The genomic sequencing technique. Prog Clin Biol Res 177:17-21.