George Church

Personal Home Page

http://arep.med.harvard.edu/gmc/

Articles in Scholarly Journals [Incomplete List]

  1. The Most Conserved Genome Segments for Life Detection on Earth and Other Planets
    Origins of Life and Evolution of Biospheres, vol. 38, no. 6, pp. 517–533, 2008
  2. Hippocrates revisited? Old ideals and new realities
    Genomic Medicine, 2008
  3. Efficient microRNA capture and bar-coding via enzymatic oligonucleotide adenylation
    Nature Methods, vol. 5, no. 9, Article ID nmeth.1244, 2 pages, 2008
  4. From genetic privacy to open consent
    Nature Reviews Genetics, vol. 9, no. 5, Article ID nrg2360, 5 pages, 2008
  5. Bacteria Subsisting on Antibiotics
    Science, vol. 320, no. 5872, pp. 100–103, 2008
  6. Model-driven analysis of experimentally determined growth phenotypes for 465 yeast gene deletion mutants under 16 different conditions
    Genome Biology, vol. 9, no. 9, p. R140, 2008
  7. Patterns and Implications of Gene Gain and Loss in the Evolution of Prochlorococcus
    PLoS Genetics, vol. 3, no. 12, p. e231, 2007
  8. Single molecule profiling of tau gene expression in Alzheimer’s disease
    Journal of Neurochemistry, vol. 103, no. 3, pp. 1228–1236, 2007
  9. Polony Multiplex Analysis of Gene Expression (PMAGE) in Mouse Hypertrophic Cardiomyopathy
    Science, vol. 316, no. 5830, pp. 1481–1484, 2007
  10. Quantitative Morphological Signatures Define Local Signaling Networks Regulating Cell Morphology
    Science, vol. 316, no. 5832, pp. 1753–1756, 2007
  11. Multiplex amplification of large sets of human exons
    Nature Methods, vol. 4, no. 11, Article ID nmeth1110, 5 pages, 2007
  12. Gene synthesis by circular assembly amplification
    Nature Methods, vol. 5, no. 1, Article ID nmeth1136, 2 pages, 2007
  13. Chromosomal periodicity of evolutionarily conserved gene pairs
    Proceedings of the National Academy of Sciences, vol. 104, no. 25, pp. 10559–10564, 2007
  14. Genome-wide expression dynamics of a marine virus and host reveal features of co-evolution
    Nature, vol. 449, no. 7158, Article ID nature06130, 3 pages, 2007
  15. Analyses of human–chimpanzee orthologous gene pairs to explore evolutionary hypotheses of aging
    Mechanisms of Ageing and Development, vol. 128, no. 5-6, pp. 355–364, 2007
  16. Relationships between p63 Binding, DNA Sequence, Transcription Activity, and Biological Function in Human Cells
    Molecular Cell, vol. 24, no. 4, pp. 593–602, 2006
  17. MapQuant: Open-source software for large-scale protein quantification
    PROTEOMICS, vol. 6, no. 6, pp. 1770–1782, 2006
  18. Cells discover fire: Employing reactive oxygen species in developmentand consequences for aging
    Experimental Gerontology, vol. 41, no. 1, pp. 1–10, 2006
  19. Global gene expression of Prochlorococcus ecotypes in response to changes in nitrogen availability
    Molecular Systems Biology, vol. 2, Article ID msb4100087, 2006
  20. Towards synthesis of a minimal cell
    Molecular Systems Biology, vol. 2, Article ID msb4100090, 2006
  21. Sequencing thoroughbreds
    Nature Biotechnology, vol. 24, no. 2, Article ID nbt0206-139b, 1 pages, 2006
  22. Sequencing genomes from single cells by polymerase cloning
    Nature Biotechnology, vol. 24, no. 6, Article ID nbt1214, 6 pages, 2006
  23. A sequence-oriented comparison of gene expression measurements across different hybridization-based technologies
    Nature Biotechnology, vol. 24, no. 7, Article ID nbt1217, 8 pages, 2006
  24. Long-range polony haplotyping of individual human chromosome molecules
    Nature Genetics, vol. 38, no. 3, Article ID ng1741, 5 pages, 2006
  25. Mammalian ultraconserved elements are strongly depleted among segmental duplications and copy number variants
    Nature Genetics, vol. 38, no. 10, Article ID ng1888, 4 pages, 2006
  26. Identifying regulatory mechanisms using individual variation reveals key role for chromatin modification
    Proceedings of the National Academy of Sciences, vol. 103, no. 38, pp. 14062–14067, 2006
  27. Assaying chromosomal inversions by single-molecule haplotyping
    Nature Methods, vol. 3, no. 6, Article ID nmeth881, 6 pages, 2006
  28. Synthetic biology projects in vitro
    Genome Research, vol. 17, no. 1, pp. 1–6, 2006
  29. PEPPeR, a Platform for Experimental Proteomic Pattern Recognition
    Molecular & Cellular Proteomics, vol. 5, no. 10, pp. 1927–1941, 2006
  30. An Integrated Strategy for Analyzing the Unique Developmental Programs of Different Myoblast Subtypes
    PLoS Genetics, vol. 2, no. 2, p. e16, 2006
  31. BMC Bioinformatics, vol. 7, no. 1, p. 177, 2006
  32. Proteome Science, vol. 3, no. 1, p. 6, 2005
  33. Accurate Multiplex Polony Sequencing of an Evolved Bacterial Genome
    Science, vol. 309, no. 5741, pp. 1728–1732, 2005
  34. Improving molecular cancer class discovery through sparse non-negative matrix factorization
    Bioinformatics, vol. 21, no. 21, pp. 3970–3975, 2005
  35. Discovering functional transcription-factor combinations in the human cell cycle
    Genome Research, vol. 15, no. 6, pp. 848–855, 2005
  36. A network of transcriptionally coordinated functional modules in Saccharomyces cerevisiae
    Genome Research, vol. 15, no. 9, pp. 1298–1306, 2005
  37. Genomic analysis of LexA binding reveals the permissive nature of the Escherichia coli genome and identifies unconventional target sites
    Genes & Development, vol. 19, no. 21, pp. 2619–2630, 2005
  38. Photosynthesis genes in marine viruses yield proteins during host infection
    Nature, vol. 438, no. 7064, Article ID nature04111, 3 pages, 2005
  39. Assessing computational tools for the discovery of transcription factor binding sites
    Nature Biotechnology, vol. 23, no. 1, Article ID nbt1053, 7 pages, 2005
  40. Let us go forth and safely multiply
    Nature, vol. 438, no. 7067, Article ID 438423a, 1 pages, 2005
  41. Accurate multiplex gene synthesis from programmable DNA microchips
    Nature, vol. 432, no. 7020, Article ID nature03151, 4 pages, 2004
  42. Mathematical models of diffusion-constrained polymerase chain reactions: basis of high-throughput nucleic acid assays and simple self-organizing systems
    Journal of Theoretical Biology, vol. 228, no. 1, pp. 31–46, 2004
  43. Digital quantitative measurements of gene expression
    Biotechnology and Bioengineering, vol. 86, no. 2, pp. 117–124, 2004
  44. Proteogenomic mapping as a complementary method to perform genome annotation
    PROTEOMICS, vol. 4, no. 1, pp. 59–77, 2004
  45. Erratum to “Fluorescent in situ sequencing on polymerase colonies” [Anal. Biochem. 320 (2003) 55–65]
    Analytical Biochemistry, vol. 328, no. 2, p. 245, 2004
  46. Advanced sequencing technologies: methods and goals
    Nature Reviews Genetics, vol. 5, no. 5, Article ID nrg1325, 9 pages, 2004
  47. Modular epistasis in yeast metabolism
    Nature Genetics, Article ID ng1489, 2004
  48. A Motif Co-Occurrence Approach for Genome-Wide Prediction of Transcription-Factor-Binding Sites in Escherichia coli
    Genome Research, vol. 14, no. 2, pp. 201–208, 2004
  49. The Complete Genome and Proteome of Mycoplasma mobile
    Genome Research, vol. 14, no. 8, pp. 1447–1461, 2004
  50. Prediction of similarly acting cis-regulatory modules by subsequence profiling and comparative genomics in Drosophila melanogaster and D.pseudoobscura
    Bioinformatics, vol. 20, no. 16, pp. 2738–2750, 2004
  51. Preferred in vivo ubiquitination sites
    Bioinformatics, vol. 20, no. 18, pp. 3302–3307, 2004
  52. Filling gaps in a metabolic network using expression information
    Bioinformatics, vol. 20, no. suppl_1, pp. i178–i185, 2004
  53. Localization to the Proteasome Is Sufficient for Degradation
    Journal of Biological Chemistry, vol. 279, no. 20, pp. 21415–21420, 2004
  54. Genomic Studies with Escherichia coli MelR Protein: Applications of Chromatin Immunoprecipitation and Microarrays
    Journal of Bacteriology, vol. 186, no. 20, pp. 6938–6943, 2004
  55. Gene Expression Profiling Reveals Progesterone-Mediated Cell Cycle and Immunoregulatory Roles of Hoxa-10 in the Preimplantation Uterus
    Molecular Endocrinology, vol. 17, no. 4, pp. 610–627, 2003
  56. Identification of a Novel Set of Genes Regulated by a Unique Liver X Receptor-alpha -mediated Transcription Mechanism
    Journal of Biological Chemistry, vol. 278, no. 17, pp. 15252–15260, 2003
  57. Identification of many microRNAs that copurify with polyribosomes in mammalian neurons
    Proceedings of the National Academy of Sciences, vol. 101, no. 1, pp. 360–365, 2003
  58. Predicting phenotype from patterns of annotation
    Bioinformatics, vol. 19, no. 90001, pp. 183i–189, 2003
  59. A Microarray-Based Antibiotic Screen Identifies a Regulatory Role for Supercoiling in the Osmotic Stress Response of Escherichia coli
    Genome Research, vol. 13, no. 2, pp. 206–215, 2003
  60. Global RNA Half-Life Analysis in Escherichia coli Reveals Positional Patterns of Transcript Degradation
    Genome Research, vol. 13, no. 2, pp. 216–223, 2003
  61. Single Molecule Profiling of Alternative Pre-mRNA Splicing
    Science, vol. 301, no. 5634, pp. 836–838, 2003
  62. Regulatory network of acid resistance genes in Escherichia coli
    Molecular Microbiology, vol. 48, no. 3, pp. 699–712, 2003
  63. Digital genotyping and haplotyping with polymerase colonies
    Proceedings of the National Academy of Sciences, vol. 100, no. 10, pp. 5926–5931, 2003
  64. Does mapping reveal correlation between gene expression and protein–protein interaction?
    Nature Genetics, vol. 33, no. 1, Article ID ng0103-15, 1 pages, 2003
  65. Fluorescent in situ sequencing on polymerase colonies
    Analytical Biochemistry, vol. 320, no. 1, pp. 55–65, 2003
  66. On the complete determination of biological systems
    Trends in Biotechnology, vol. 21, no. 6, pp. 251–254, 2003
  67. Computational and Experimental Identification of C. elegans microRNAs
    Molecular Cell, vol. 11, no. 5, pp. 1253–1263, 2003
  68. Computational Identification of Transcription Factor Binding Sites via a Transcription-factor-centric Clustering (TFCC) Algorithm
    Journal of Molecular Biology, vol. 318, no. 1, pp. 71–81, 2002
  69. Measuring absolute expression with microarrays with a calibrated reference sample and an extended signal intensity range
    Proceedings of the National Academy of Sciences, vol. 99, no. 11, pp. 7554–7559, 2002
  70. Analysis of optimality in natural and perturbed metabolic networks
    Proceedings of the National Academy of Sciences, vol. 99, no. 23, pp. 15112–15117, 2002
  71. An open-source oligomicroarray standard for human and mouse
    Nature Biotechnology, vol. 20, no. 11, Article ID nbt1102-1082, 1 pages, 2002
  72. Nucleotides of transcription factor binding sites exert interdependent effects on the binding affinities of transcription factors
    Nucleic Acids Research, vol. 30, no. 5, pp. 1255–1261, 2002
  73. Genome-wide Co-occurrence of Promoter Elements Reveals a cis-Regulatory Cassette of rRNA Transcription Motifs in Saccharomyces cerevisiae
    Genome Research, vol. 12, no. 11, pp. 1723–1731, 2002
  74. Identification of a Novel cis-Regulatory Element Involved in the Heat Shock Response in Caenorhabditis elegans Using Microarray Gene Expression and Computational Methods
    Genome Research, vol. 12, no. 5, pp. 701–712, 2002
  75. Discrimination between Paralogs using Microarray Analysis: Application to the Yap1p and Yap2p Transcriptional Networks
    Molecular Biology of the Cell, vol. 13, no. 5, pp. 1608–1614, 2002
  76. Genome-Scale Metabolic Model of Helicobacter pylori 26695
    Journal of Bacteriology, vol. 184, no. 16, pp. 4582–4593, 2002
  77. Escherichia coli Gene Expression Responsive to Levels of the Response Regulator EvgA
    Journal of Bacteriology, vol. 184, no. 22, pp. 6225–6234, 2002
  78. Dynamic simulation of the human red blood cell metabolic network
    Bioinformatics, vol. 17, no. 3, pp. 286–287, 2001
  79. Aligning gene expression time series with time warping algorithms
    Bioinformatics, vol. 17, no. 6, pp. 495–508, 2001
  80. A Dynamic Programming Approach to De Novo Peptide Sequencing via Tandem Mass Spectrometry
    Journal of Computational Biology, vol. 8, no. 3, pp. 325–337, 2001
  81. Algorithms for Identifying Protein Cross-Links via Tandem Mass Spectrometry
    Journal of Computational Biology, vol. 8, no. 6, pp. 571–583, 2001
  82. Nature Biotechnology, vol. 19, no. 11, pp. 1060–1065, 2001
  83. Exploring the DNA-binding specificities of zinc fingers with DNA microarrays
    Proceedings of the National Academy of Sciences, vol. 98, no. 13, pp. 7158–7163, 2001
  84. Nature Genetics, vol. 29, no. 2, pp. 153–159, 2001
  85. Nature Genetics, vol. 29, no. 4, pp. 482–486, 2001
  86. Computational comparison of two draft sequences of the human genome
    Nature, vol. 409, no. 6822, Article ID 35057055, 3 pages, 2001
  87. Nature Genetics, vol. 26, no. 2, pp. 183–186, 2000
  88. Nature Biotechnology, vol. 18, no. 12, pp. 1262–1268, 2000
  89. Microarray analysis of the transcriptional network controlled by the photoreceptor homeobox gene Crx
    Current Biology, vol. 10, no. 6, pp. 301–310, 2000
  90. The Isw2 Chromatin Remodeling Complex Represses Early Meiotic Genes upon Recruitment by Ume6p
    Cell, vol. 103, no. 3, pp. 423–433, 2000
  91. Computational identification of Cis-regulatory elements associated with groups of functionally related genes in Saccharomyces cerevisiae
    Journal of Molecular Biology, vol. 296, no. 5, pp. 1205–1214, 2000
  92. Predicting ligand-binding function in families of bacterial receptors
    Proceedings of the National Academy of Sciences, vol. 97, no. 8, pp. 3965–3970, 2000
  93. Fast assignment of protein structures to sequences using the Intermediate Sequence Library PDB-ISL
    Bioinformatics, vol. 16, no. 2, pp. 117–124, 2000
  94. Sequence variability and candidate gene analysis in complex disease: association of micro opioid receptor gene variation with substance dependence
    Human Molecular Genetics, vol. 9, no. 19, pp. 2895–2908, 2000
  95. Predicting regulons and their cis-regulatory motifs by comparative genomics
    Nucleic Acids Research, vol. 28, no. 22, pp. 4523–4530, 2000
  96. Systematic Management and Analysis of Yeast Gene Expression Data
    Genome Research, vol. 10, no. 4, pp. 431–445, 2000
  97. Conservation of DNA Regulatory Motifs and Discovery of New Motifs in Microbial Genomes
    Genome Research, vol. 10, no. 6, pp. 744–757, 2000
  98. Regulatory Networks Revealed by Transcriptional Profiling of Damaged Saccharomyces cerevisiae Cells: Rpn4 Links Base Excision Repair with Proteasomes
    Molecular and Cellular Biology, vol. 20, no. 21, pp. 8157–8167, 2000
  99. A weight matrix for binding recognition by the redox-response regulator ArcA-P of Escherichia coli
    Molecular Microbiology, vol. 32, no. 1, pp. 219–221, 1999
  100. Alignment and structure prediction of divergent protein families: periplasmic and outer membrane proteins of bacterial efflux pumps1
    Journal of Molecular Biology, vol. 287, no. 3, pp. 695–715, 1999
  101. Nature Genetics, vol. 22, no. 3, pp. 281–285, 1999
  102. Nature Biotechnology, vol. 17, no. 6, pp. 573–577, 1999
  103. A comprehensive library of DNA-binding site matrices for 55 proteins applied to the complete Escherichia coli K-12 genome
    Journal of Molecular Biology, vol. 284, no. 2, pp. 241–254, 1998
  104. Finding DNA regulatory motifs within unaligned noncoding sequences clustered by whole-genome mRNA quantitation
    Nature Biotechnology, vol. 16, no. 10, Article ID nbt1098-939, 6 pages, 1998
  105. Quantitative whole-genome analysis of DNA-protein interactions by in vivo methylase protection in E. coli
    Nature Biotechnology, vol. 16, no. 6, Article ID nbt0698-566, 5 pages, 1998
  106. Detection via laser desorption and mass spectrometry of multiplex electrophore-labeled albumin
    Rapid Communications in Mass Spectrometry, vol. 11, no. 16, pp. 1781–1784, 1997
  107. Comparing the predicted and observed properties of proteins encoded in the genome ofEscherichia coli K-12
    Electrophoresis, vol. 18, no. 8, pp. 1259–1313, 1997
  108. Analytical Chemistry, vol. 69, no. 17, pp. 3595–3602, 1997
  109. Databases for gene expression
    Nature Biotechnology, vol. 14, no. 7, Article ID nbt0796-828a, 1 pages, 1996
  110. Large scale bacterial gene discovery by similarity search
    Nature Genetics, vol. 7, no. 2, Article ID ng0694-205, 9 pages, 1994
  111. Cloning and Sequencing of Thiol-Specific Antioxidant from Mammalian Brain: Alkyl Hydroperoxide Reductase and Thiol-Specific Antioxidant Define a Large Family of Antioxidant Enzymes
    Proceedings of the National Academy of Sciences, vol. 91, no. 15, pp. 7017–7021, 1994
  112. A whole genome approach to in vivo DNA-protein interactions in E. coli
    Nature, vol. 360, no. 6404, Article ID 360606a0, 4 pages, 1992
  113. Complementary recognition in condensed DNA: Accelerated DNA renaturation*1
    Journal of Molecular Biology, vol. 222, no. 4, pp. 1085–1108, 1991
  114. Cell-type-specific contacts to immunoglobulin enhancers in nuclei
    Nature, vol. 313, no. 6005, Article ID 313798a0, 3 pages, 1985
  115. Genomic Sequencing
    Proceedings of the National Academy of Sciences, vol. 81, no. 7, pp. 1991–1995, 1984
  116. Pleiotropic mutations within two yeast mitochondrial cytochrome genes block mRNA processing
    Cell, vol. 18, no. 4, pp. 1209–1215, 1979
  117. Secondary Structural Complementarity between DNA and Proteins
    Proceedings of the National Academy of Sciences, vol. 74, no. 4, pp. 1458–1462, 1977