George Church

Summary

Affiliation: Harvard University
Country: USA

Publications

  1. pmc Expression dynamics of a cellular metabolic network
    Peter Kharchenko
    Department of Genetics, Harvard Medical School, Boston, MA, USA
    Mol Syst Biol 1:2005.0016. 2005
  2. pmc A global view of pleiotropy and phenotypically derived gene function in yeast
    Aimée Marie Dudley
    Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
    Mol Syst Biol 1:2005.0001. 2005
  3. pmc The amino-acid mutational spectrum of human genetic disease
    Dennis Vitkup
    Lipper Center for Computational Genetics and Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
    Genome Biol 4:R72. 2003
  4. ncbi request reprint Gene synthesis by circular assembly amplification
    Duhee Bang
    Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, Massachusetts 02115, USA
    Nat Methods 5:37-9. 2008
  5. ncbi request reprint Preferred in vivo ubiquitination sites
    Andre Catic
    Department of Pathology, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
    Bioinformatics 20:3302-7. 2004
  6. pmc Multiplex padlock targeted sequencing reveals human hypermutable CpG variations
    Jin Billy Li
    Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
    Genome Res 19:1606-15. 2009
  7. ncbi request reprint Sequencing genomes from single cells by polymerase cloning
    Kun Zhang
    Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, Massachusetts 02115, USA
    Nat Biotechnol 24:680-6. 2006
  8. ncbi request reprint A sequence-oriented comparison of gene expression measurements across different hybridization-based technologies
    Winston Patrick Kuo
    Department of Developmental Biology, Harvard School of Dental Medicine, 188 Longwood Ave, Boston, Massachusetts 02115, USA
    Nat Biotechnol 24:832-40. 2006
  9. pmc Identifying metabolic enzymes with multiple types of association evidence
    Peter Kharchenko
    Department of Genetics, New Research Building NRB Room 238, 77 Ave, Louis Pasteur, Harvard Medical School, Boston, MA 02115, USA
    BMC Bioinformatics 7:177. 2006
  10. ncbi request reprint Long-range polony haplotyping of individual human chromosome molecules
    Kun Zhang
    Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
    Nat Genet 38:382-7. 2006

Collaborators

Detail Information

Publications82

  1. pmc Expression dynamics of a cellular metabolic network
    Peter Kharchenko
    Department of Genetics, Harvard Medical School, Boston, MA, USA
    Mol Syst Biol 1:2005.0016. 2005
    ..We show that basic topological motifs of the metabolic network exhibit statistically significant differences in coexpression behavior...
  2. pmc A global view of pleiotropy and phenotypically derived gene function in yeast
    Aimée Marie Dudley
    Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
    Mol Syst Biol 1:2005.0001. 2005
    ..Applying these functional classifications to pleiotropic genes, we are able to dissect phenotypes into groups associated with specific gene functions...
  3. pmc The amino-acid mutational spectrum of human genetic disease
    Dennis Vitkup
    Lipper Center for Computational Genetics and Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
    Genome Biol 4:R72. 2003
    ..We compare the disease spectrum to the spectra of mutual amino-acid mutation frequencies, non-disease polymorphisms in human genes, and substitutions fixed between species...
  4. ncbi request reprint Gene synthesis by circular assembly amplification
    Duhee Bang
    Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, Massachusetts 02115, USA
    Nat Methods 5:37-9. 2008
    ..We used this method to construct genes encoding a small thermostable DNA polymerase, a highly repetitive DNA sequence and large (>4 kb) constructs...
  5. ncbi request reprint Preferred in vivo ubiquitination sites
    Andre Catic
    Department of Pathology, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
    Bioinformatics 20:3302-7. 2004
    ..However, a better understanding of acceptor site selection could help to predict ubiquitination sites and clarify yet unsolved structure-function relationships of the transfer reaction...
  6. pmc Multiplex padlock targeted sequencing reveals human hypermutable CpG variations
    Jin Billy Li
    Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
    Genome Res 19:1606-15. 2009
    ..In addition, the significantly improved padlock capture technology can be readily applied to other projects that require multiplex sample preparation...
  7. ncbi request reprint Sequencing genomes from single cells by polymerase cloning
    Kun Zhang
    Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, Massachusetts 02115, USA
    Nat Biotechnol 24:680-6. 2006
    ..Polymerase cloning should provide a critical tool for systematic characterization of genome diversity in the biosphere...
  8. ncbi request reprint A sequence-oriented comparison of gene expression measurements across different hybridization-based technologies
    Winston Patrick Kuo
    Department of Developmental Biology, Harvard School of Dental Medicine, 188 Longwood Ave, Boston, Massachusetts 02115, USA
    Nat Biotechnol 24:832-40. 2006
    ..We demonstrate that, after stringent preprocessing, commercial arrays were more consistent than in-house arrays, and by most measures, one-dye platforms were more consistent than two-dye platforms...
  9. pmc Identifying metabolic enzymes with multiple types of association evidence
    Peter Kharchenko
    Department of Genetics, New Research Building NRB Room 238, 77 Ave, Louis Pasteur, Harvard Medical School, Boston, MA 02115, USA
    BMC Bioinformatics 7:177. 2006
    ..Existing computational strategies for identifying such missing genes rely primarily on sequence homology to known enzyme-encoding genes...
  10. ncbi request reprint Long-range polony haplotyping of individual human chromosome molecules
    Kun Zhang
    Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
    Nat Genet 38:382-7. 2006
    ..This haplotyping method is well suited for candidate gene-based association studies as well as for investigating the pattern of recombination in mammalian cells...
  11. ncbi request reprint MapQuant: open-source software for large-scale protein quantification
    Kyriacos C Leptos
    Harvard Medical School, Department of Genetics, Boston, MA 02115, USA
    Proteomics 6:1770-82. 2006
    ....
  12. pmc Preferred analysis methods for Affymetrix GeneChips revealed by a wholly defined control dataset
    Sung E Choe
    Department of Genetics, Harvard Medical School, New Research Building, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
    Genome Biol 6:R16. 2005
    ..As more methods are developed to analyze RNA-profiling data, assessing their performance using control datasets becomes increasingly important...
  13. pmc Predicting protein post-translational modifications using meta-analysis of proteome scale data sets
    Daniel Schwartz
    Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
    Mol Cell Proteomics 8:365-79. 2009
    ..New motif discovery is a byproduct of this approach, and the phosphorylation motif analyses provide strong evidence of evolutionary conservation of both known and novel kinase motifs...
  14. ncbi request reprint A statistical model for investigating binding probabilities of DNA nucleotide sequences using microarrays
    Mei Ling Ting Lee
    Channing Laboratory, Brigham and Women s Hospital, 181 Longwood Avenue, Boston, Massachusetts 02115, USA
    Biometrics 58:981-8. 2002
    ..This model is convenient because it employs familiar statistical concepts and procedures and also because it is effective for investigating the probability structure of the binding mechanism...
  15. doi request reprint The human microbiome harbors a diverse reservoir of antibiotic resistance genes
    Morten O A Sommer
    Department of Genetics, Harvard Medical School, Boston, MA, USA
    Virulence 1:299-303. 2010
    ....
  16. pmc Scalable gene synthesis by selective amplification of DNA pools from high-fidelity microchips
    Sriram Kosuri
    Wyss Institute for Biologically Inspired Engineering, Boston, Massachusetts, USA
    Nat Biotechnol 28:1295-9. 2010
    ..These assemblies were performed from a complex background containing 13,000 oligonucleotides encoding ∼2.5 megabases of DNA, which is at least 50 times larger than in previously published attempts...
  17. pmc A survey of genomic traces reveals a common sequencing error, RNA editing, and DNA editing
    Alexander Wait Zaranek
    Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
    PLoS Genet 6:e1000954. 2010
    ..We show that the NCBI Trace Archive provides a valuable resource for the investigation of the phenomena of DNA and RNA editing, as well as setting the stage for a comprehensive mapping of editing events in large-scale genomic datasets...
  18. pmc A functional metagenomic approach for expanding the synthetic biology toolbox for biomass conversion
    Morten O A Sommer
    Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
    Mol Syst Biol 6:360. 2010
    ..This platform presents a route for expanding the repertoire of genetic elements available to synthetic biology and provides a starting point for efforts to engineer robust strains for biofuel generation...
  19. pmc A robust approach to identifying tissue-specific gene expression regulatory variants using personalized human induced pluripotent stem cells
    Je Hyuk Lee
    Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
    PLoS Genet 5:e1000718. 2009
    ..We show that our approach to mapping cis-regulatory variants reduces in vitro experimental noise and reveals additional tissue-specific variants using skin-derived human iPS cells...
  20. doi request reprint Functional characterization of the antibiotic resistance reservoir in the human microflora
    Morten O A Sommer
    Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
    Science 325:1128-31. 2009
    ..The immense diversity of resistance genes in the human microbiome could contribute to future emergence of antibiotic resistance in human pathogens...
  21. ncbi request reprint Programming cells by multiplex genome engineering and accelerated evolution
    Harris H Wang
    Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
    Nature 460:894-8. 2009
    ..Our multiplex approach embraces engineering in the context of evolution by expediting the design and evolution of organisms with new and improved properties...
  22. pmc A network of transcriptionally coordinated functional modules in Saccharomyces cerevisiae
    Allegra A Petti
    Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
    Genome Res 15:1298-306. 2005
    ....
  23. doi request reprint Efficient microRNA capture and bar-coding via enzymatic oligonucleotide adenylation
    Francois Vigneault
    Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, Massachusetts 02115, USA
    Nat Methods 5:777-9. 2008
    ..As a case study, we used these oligonucleotides in an ATP-independent ligation to miRNAs, suggesting the utility of our method in end-capture protocols and high-throughput sequencing applications...
  24. pmc Discovering functional transcription-factor combinations in the human cell cycle
    Zhou Zhu
    Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
    Genome Res 15:848-55. 2005
    ..We also detected many homotypic combinations, supporting the importance of binding-site density in transcriptional regulation of higher eukaryotes...
  25. pmc Synthetic gene networks that count
    Ari E Friedland
    Howard Hughes Medical Institute, Department of Biomedical Engineering, Center for BioDynamics and Center for Advanced Biotechnology, Boston University, Boston, MA 02215, USA
    Science 324:1199-202. 2009
    ..These modular devices permit counting of varied user-defined inputs over a range of frequencies and can be expanded to count higher numbers...
  26. pmc Modified bases enable high-efficiency oligonucleotide-mediated allelic replacement via mismatch repair evasion
    Harris H Wang
    Wyss Institute for Biologically Inspired Engineering, Harvard University, Department of Genetics, Harvard Medical School, Harvard University, Boston, MA 02115, USA
    Nucleic Acids Res 39:7336-47. 2011
    ..These results further elucidate the mechanism of oligo-mediated allelic replacement (OMAR) and enable improved methodologies for efficient, large-scale engineering of genomes...
  27. ncbi request reprint Quantitative morphological signatures define local signaling networks regulating cell morphology
    Chris Bakal
    Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
    Science 316:1753-6. 2007
    ..We analyzed a compendium of quantitative morphological signatures and described the existence of local signaling networks that act to regulate cell protrusion, adhesion, and tension...
  28. pmc Automated modelling of signal transduction networks
    Martin Steffen
    Dept of Genetics, Harvard Medical School, 200 Longwood Avenue, Boston, Massachusetts, 02115, USA
    BMC Bioinformatics 3:34. 2002
    ..Understanding the mechanisms cells use to accomplish this important process requires a detailed molecular description of the networks involved...
  29. doi request reprint Protein interaction discovery using parallel analysis of translated ORFs (PLATO)
    Jian Zhu
    Department of Medicine, Division of Genetics, Brigham and Women s Hospital, Boston, Massachusetts, USA
    Nat Biotechnol 31:331-4. 2013
    ..We demonstrate the broad utility of the method for human proteins by identifying known and previously unidentified interacting partners of LYN kinase, patient autoantibodies, and the small-molecules gefitinib and dasatinib...
  30. ncbi request reprint Improving molecular cancer class discovery through sparse non-negative matrix factorization
    Yuan Gao
    Department of Genetics, Harvard Medical School Boston, MA 02115, USA
    Bioinformatics 21:3970-5. 2005
    ..In this paper, we investigate the benefit of explicitly enforcing sparseness in the factorization process...
  31. ncbi request reprint Accurate multiplex gene synthesis from programmable DNA microchips
    Jingdong Tian
    Harvard Medical School, 77 Ave Louis Pasteur, Boston, Massachusetts 02115, USA
    Nature 432:1050-4. 2004
    ..This is a significant step towards the synthesis of ribosomes in vitro and should have utility for synthetic biology in general...
  32. pmc Transcriptional profiling of CD4 T cells identifies distinct subgroups of HIV-1 elite controllers
    Francois Vigneault
    Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
    J Virol 85:3015-9. 2011
    ..Thus, these data identify a specific subgroup of elite controllers whose immunological and gene expression characteristics approximate those of HIV-1-negative persons...
  33. pmc A microarray-based antibiotic screen identifies a regulatory role for supercoiling in the osmotic stress response of Escherichia coli
    Kevin J Cheung
    Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
    Genome Res 13:206-15. 2003
    ..In addition, these studies implicate 60 uncharacterized genes in the osmotic stress regulon, and offer evidence for a broader role for supercoiling in the control of stress-induced transcription...
  34. ncbi request reprint Multiplex amplification of large sets of human exons
    Gregory J Porreca
    Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, Massachusetts 02115, USA
    Nat Methods 4:931-6. 2007
    ..We anticipate that highly multiplexed methods for targeted amplification will enable the comprehensive resequencing of human exons at a fraction of the cost of whole-genome resequencing...
  35. ncbi request reprint Genome-wide expression dynamics of a marine virus and host reveal features of co-evolution
    Debbie Lindell
    Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
    Nature 449:83-6. 2007
    ..Thus activation of host genes during infection may be directing the co-evolution of gene content in both host and phage genomes...
  36. pmc Global RNA half-life analysis in Escherichia coli reveals positional patterns of transcript degradation
    Douglas W Selinger
    Harvard Medical School, Department of Genetics, Boston, Massachusetts 02115, USA
    Genome Res 13:216-23. 2003
    ..We discuss the application of subgenic resolution DNA microarray analysis to study global mechanisms of RNA transcription and processing...
  37. ncbi request reprint Regulatory network of acid resistance genes in Escherichia coli
    Nobuhisa Masuda
    Department of Genetics, Warren Alpert Building, Room 513, Harvard Medical School, 200 Longwood Ave, Boston, MA 02115, USA
    Mol Microbiol 48:699-712. 2003
    ..We propose a model of the regulatory network of the acid resistance genes...
  38. ncbi request reprint Polony multiplex analysis of gene expression (PMAGE) in mouse hypertrophic cardiomyopathy
    Jae Bum Kim
    Cardiovascular Division, Brigham and Women s Hospital, Boston, MA 02115, USA
    Science 316:1481-4. 2007
    ..PMAGE provided a comprehensive profile of cardiac mRNAs, including low-abundance mRNAs encoding signaling molecules and transcription factors that are likely to participate in disease pathogenesis...
  39. ncbi request reprint Relationships between p63 binding, DNA sequence, transcription activity, and biological function in human cells
    Annie Yang
    Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA
    Mol Cell 24:593-602. 2006
    ..Many p63 binding regions are evolutionarily conserved and/or associated with sequence motifs for other transcription factors, suggesting that a substantial portion of p63 sites is biologically relevant...
  40. ncbi request reprint The transition between transcriptional initiation and elongation in E. coli is highly variable and often rate limiting
    Nikos B Reppas
    Harvard University Biophysics Program, Harvard Medical School, Boston, Massachusetts 02115, USA
    Mol Cell 24:747-57. 2006
    ..The genomic pattern of RNAP density in E. coli differs from that in yeast and mammalian cells...
  41. ncbi request reprint Synthetic biology projects in vitro
    Anthony C Forster
    Department of Pharmacology and Vanderbilt Institute of Chemical Biology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
    Genome Res 17:1-6. 2007
    ..Known functions are being integrated and debugged with the aim of synthesizing life-like systems. The goals are knowledge, tools, smart materials, and therapies...
  42. ncbi request reprint Identification of a novel set of genes regulated by a unique liver X receptor-alpha -mediated transcription mechanism
    Leonard M Anderson
    Department of Medicine, Division of Cardiovascular Research, Laboratory of Genetic Physiology, Pain Research Center, Brigham and Women s Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA
    J Biol Chem 278:15252-60. 2003
    ....
  43. pmc Chromosomal periodicity of evolutionarily conserved gene pairs
    Matthew A Wright
    Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
    Proc Natl Acad Sci U S A 104:10559-64. 2007
    ..Our approach indicates an evolutionarily maintained preference in the spacing of genes along the chromosome and offers a general comparative genomics framework for studying chromosome structure, broadly applicable to other organisms...
  44. ncbi request reprint An open-source oligomicroarray standard for human and mouse
    Matthew A Wright
    Nat Biotechnol 20:1082-3. 2002
  45. pmc Nucleotides of transcription factor binding sites exert interdependent effects on the binding affinities of transcription factors
    Martha L Bulyk
    Harvard University Graduate Biophysics Program, Harvard Medical School, Boston, MA 02115, USA
    Nucleic Acids Res 30:1255-61. 2002
    ....
  46. pmc Discrimination between paralogs using microarray analysis: application to the Yap1p and Yap2p transcriptional networks
    Barak A Cohen
    Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
    Mol Biol Cell 13:1608-14. 2002
    ....
  47. pmc Measuring absolute expression with microarrays with a calibrated reference sample and an extended signal intensity range
    AIMEE M DUDLEY
    Department of Genetics, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115, USA
    Proc Natl Acad Sci U S A 99:7554-9. 2002
    ..We discuss future applications of our method to measure RNA expression on the absolute scale of number of transcripts per cell from any organism for which oligo-based spotted-glass microarrays are available...
  48. ncbi request reprint Computational identification of transcription factor binding sites via a transcription-factor-centric clustering (TFCC) algorithm
    Zhou Zhu
    Department of Genetics and Lippar Center for Computing and Genetics, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115, USA
    J Mol Biol 318:71-81. 2002
    ..In addition, we also made de novo predictions for some unknown TF binding sites...
  49. pmc Computation-based discovery of related transcriptional regulatory modules and motifs using an experimentally validated combinatorial model
    Marc S Halfon
    Howard Hughes Medical Institute and Department of Medicine, Brigham and Women s Hospital, Boston, Massachusetts 02115, USA
    Genome Res 12:1019-28. 2002
    ....
  50. pmc Genome-scale metabolic model of Helicobacter pylori 26695
    Christophe H Schilling
    Genomatica, Inc, San Diego, California 92121, USA
    J Bacteriol 184:4582-93. 2002
    ..Collectively, the results presented herein suggest an effective strategy of combining in silico modeling with experimental technologies to enhance biological discovery for less characterized organisms and their genomes...
  51. pmc Computational discovery of sense-antisense transcription in the human and mouse genomes
    Jay Shendure
    Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
    Genome Biol 3:RESEARCH0044. 2002
    ..We computationally mined public mouse and human expressed sequence tag (EST) databases to search for additional examples of bidirectionally transcribed genomic regions...
  52. pmc Escherichia coli gene expression responsive to levels of the response regulator EvgA
    Nobuhisa Masuda
    Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
    J Bacteriol 184:6225-34. 2002
    ..In addition, EvgA overexpression did not confer resistance in a tolC-deficient strain. These results suggest that YhiUV induced by EvgA overexpression is functionally associated with TolC and contributes to multidrug resistance...
  53. ncbi request reprint Predicting phenotype from patterns of annotation
    Oliver D King
    Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 250 Longwood Avenue, Boston, Massachusetts, 02115, USA
    Bioinformatics 19:i183-9. 2003
    ..Predicting the outcome of specific experiments (such as the growth of a particular mutant strain in a particular medium) has the potential to allow researchers to devote resources to experiments with higher expected numbers of 'hits'...
  54. pmc Global gene expression of Prochlorococcus ecotypes in response to changes in nitrogen availability
    Andrew C Tolonen
    Department of Biology, MIT WHOI Joint Program in Oceanography, Cambridge, MA, USA
    Mol Syst Biol 2:53. 2006
    ..There were also important differences between the strains such as in the expression patterns of carbon metabolism genes, suggesting that the two strains integrate N and C metabolism in fundamentally different ways...
  55. pmc Genomic analysis of LexA binding reveals the permissive nature of the Escherichia coli genome and identifies unconventional target sites
    Joseph T Wade
    Department of Biological Chemistry and Molecular Pharmacology, Harvard University, Boston, Massachusetts 02115, USA
    Genes Dev 19:2619-30. 2005
    ..coli genome is permissive to transcription factor binding. The permissive nature of the E. coli genome has important consequences for the nature of transcriptional regulatory proteins, biological specificity, and evolution...
  56. ncbi request reprint Genomes for all
    George M Church
    Harvard Medical School, USA
    Sci Am 294:46-54. 2006
  57. pmc The complete genome and proteome of Mycoplasma mobile
    Jacob D Jaffe
    Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02138, USA
    Genome Res 14:1447-61. 2004
    ..The results of these analyses leave open the possibility that gliding motility might have arisen independently more than once in the mycoplasma lineage...
  58. ncbi request reprint Advanced sequencing technologies: methods and goals
    Jay Shendure
    Harvard Medical School, 77 Avenue Louis Pasteur, Boston, Massachusetts 02115, USA
    Nat Rev Genet 5:335-44. 2004
  59. pmc yMGV: a cross-species expression data mining tool
    Gaelle Lelandais
    Laboratoire de Genetique Moleculaire, CNRS UMR8541, Ecole Normale Superieure, Paris, France
    Nucleic Acids Res 32:D323-5. 2004
    ..This should enable the fission yeast community to take advantage of the large amount of available information on budding yeast transcriptome. New tools and ongoing developments are also presented here...
  60. ncbi request reprint Proteogenomic mapping as a complementary method to perform genome annotation
    Jacob D Jaffe
    Harvard Medical School Department of Genetics, Boston, MA 02115, USA
    Proteomics 4:59-77. 2004
    ..This technique is a cost-effective means to add value to genome annotation, and a prerequisite for proteome quantitation and in vivo interaction measures...
  61. ncbi request reprint Accurate multiplex polony sequencing of an evolved bacterial genome
    Jay Shendure
    Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
    Science 309:1728-32. 2005
    ..Cost per base was roughly one-ninth as much as that of conventional sequencing. Our protocols were implemented with off-the-shelf instrumentation and reagents...
  62. pmc A motif co-occurrence approach for genome-wide prediction of transcription-factor-binding sites in Escherichia coli
    Martha L Bulyk
    Harvard University Graduate Biophysics Program, Harvard Medical School, Boston, Massachusetts 02115, USA
    Genome Res 14:201-8. 2004
    ..This approach may be useful in analyzing binding sites in a variety of organisms...
  63. ncbi request reprint Localization to the proteasome is sufficient for degradation
    Daniel M Janse
    Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
    J Biol Chem 279:21415-20. 2004
    ..We conclude that localization to the proteasome is sufficient for degradation and, therefore, any added functions polyubiquitin chains possess beyond tethering substrates to the proteasome are not strictly necessary for proteolysis...
  64. ncbi request reprint Filling gaps in a metabolic network using expression information
    Peter Kharchenko
    Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
    Bioinformatics 20:i178-85. 2004
    ..We present a computational approach for identifying genes encoding such missing metabolic enzymes in a partially reconstructed metabolic network...
  65. pmc Parallel competition analysis of Saccharomyces cerevisiae strains differing by a single base using polymerase colonies
    Joshua Merritt
    Department of Chemical Engineering, University of Delaware, Newark, DE 19716, USA
    Nucleic Acids Res 31:e84. 2003
    ..By functional complementation of yeast deletions with human homologs, our technique could be readily applied to the functional analysis of single nucleotide polymorphisms in human genes of medical interest...
  66. pmc Identifying regulatory mechanisms using individual variation reveals key role for chromatin modification
    Su In Lee
    Department of Computer Science, Stanford University, Stanford, CA 94305 9010, USA
    Proc Natl Acad Sci U S A 103:14062-7. 2006
    ..Overall, our results suggest that a significant part of individual expression variation in yeast arises from evolution of a small number of chromatin structure modifiers...
  67. pmc PEPPeR, a platform for experimental proteomic pattern recognition
    Jacob D Jaffe
    The Broad Institute of Harvard and the Massachusetts Institute of Technology, Cambridge, 02142, USA
    Mol Cell Proteomics 5:1927-41. 2006
    ..These results have provided a real world validation of the platform for marker discovery...
  68. ncbi request reprint Prediction of similarly acting cis-regulatory modules by subsequence profiling and comparative genomics in Drosophila melanogaster and D.pseudoobscura
    Yonatan H Grad
    The Lipper Center for Computational Genetics, Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, Massachusetts, 02115, USA
    Bioinformatics 20:2738-50. 2004
    ....
  69. pmc Digital genotyping and haplotyping with polymerase colonies
    Robi D Mitra
    Lipper Center for Computational Genetics and Department of Genetics, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115, USA
    Proc Natl Acad Sci U S A 100:5926-31. 2003
    ..The results indicate that polony genotyping and haplotyping may play an important role in understanding the structure of genetic variation...
  70. ncbi request reprint Mathematical models of diffusion-constrained polymerase chain reactions: basis of high-throughput nucleic acid assays and simple self-organizing systems
    John Aach
    Department of Genetics and Lipper Center for Computational Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, New Research Building, Rm 238, Boston, MA 02115, USA
    J Theor Biol 228:31-46. 2004
    ..Our polony modeling software is available at our web site...
  71. ncbi request reprint Computational and experimental identification of C. elegans microRNAs
    Yonatan Grad
    The Lipper Center for Computational Genetics and Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
    Mol Cell 11:1253-63. 2003
    ..Based on hypotheses underlying our computational methods, we estimate that the C. elegans genome may encode between 140 and 300 miRNAs and potentially many more...
  72. ncbi request reprint On the complete determination of biological systems
    Douglas W Selinger
    Harvard Medical School, Department of Genetics, 200 Longwood Ave, Boston, MA 02115, USA
    Trends Biotechnol 21:251-4. 2003
    ..Based on these estimates, we suggest that the complete determination of a biological system is a concrete, achievable goal...
  73. ncbi request reprint Digital quantitative measurements of gene expression
    Venugopal Mikkilineni
    Department of Chemical Engineering, University of Delaware, Newark, Delaware 19716, USA
    Biotechnol Bioeng 86:117-24. 2004
    ..DAGE is likely to have profound implications in the field of functional genomics because the gene expression measurements are digital in nature and therefore more accurate than any other technologies...
  74. ncbi request reprint Assessing computational tools for the discovery of transcription factor binding sites
    Martin Tompa
    Department of Computer Science and Engineering, Box 352350, University of Washington, Seattle, Washington 98195 2350, USA
    Nat Biotechnol 23:137-44. 2005
    ..The purpose of the current assessment is twofold: to provide some guidance to users regarding the accuracy of currently available tools in various settings, and to provide a benchmark of data sets for assessing future tools...
  75. ncbi request reprint Modular epistasis in yeast metabolism
    Daniel Segrè
    Lipper Center for Computational Genetics and Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
    Nat Genet 37:77-83. 2005
    ..Our approach can be used to infer functional gene modules from purely phenotypic epistasis measurements...
  76. ncbi request reprint Mammalian ultraconserved elements are strongly depleted among segmental duplications and copy number variants
    Adnan Derti
    Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA
    Nat Genet 38:1216-20. 2006
    ..Notably, of the UCEs that are found in segmental duplications or copy number variants, the majority overlap exons, indicating, along with other findings presented, that UCEs overlapping exons represent a distinct subset...
  77. doi request reprint From genetic privacy to open consent
    Jeantine E Lunshof
    Department of Molecular Cell Physiology, c o room M236, Faculty of Earth and Life Sciences, VU University Amsterdam, De Boelelaan 1085, 1081 HV Amsterdam, The Netherlands
    Nat Rev Genet 9:406-11. 2008
    ..Here, we show the feasibility of the co-development of scientific innovation and ethics, using the open-consent framework that was implemented in the Personal Genome Project as an example...
  78. pmc Patterns and implications of gene gain and loss in the evolution of Prochlorococcus
    Gregory C Kettler
    Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
    PLoS Genet 3:e231. 2007
    ....
  79. ncbi request reprint Fluorescent in situ sequencing on polymerase colonies
    Robi D Mitra
    Lipper Center for Computational Genetics, Harvard Medical School, 200 Longwood Ave, Boston, MA 02115, USA
    Anal Biochem 320:55-65. 2003
    ..Finally, we have developed software for automated image alignment and sequence calling...
  80. ncbi request reprint Identification of foreign gene sequences by transcript filtering against the human genome
    Griffin Weber
    Department of Adult Oncology, Dana Farber Cancer Institute, 44 Binney Street, Boston, Massachusetts 02115, USA
    Nat Genet 30:141-2. 2002
    ..We demonstrate the potential of this method by identifying sequences from known pathogens in established expressed-sequence tag libraries...
  81. pmc An analysis of the relationship between metabolism, developmental schedules, and longevity using phylogenetic independent contrasts
    João Pedro de Magalhães
    Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
    J Gerontol A Biol Sci Med Sci 62:149-60. 2007
    ..Our work provides a detailed view of factors related to species longevity with implications for how comparative studies of aging are interpreted...
  82. pmc Genome-wide co-occurrence of promoter elements reveals a cis-regulatory cassette of rRNA transcription motifs in Saccharomyces cerevisiae
    Priya Sudarsanam
    Department of Genetics and Lipper Center for Computational Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
    Genome Res 12:1723-31. 2002
    ..The methodology introduced here should prove particularly useful for analyzing transcriptional regulation in more complex genomes...

Research Grants5

  1. Molecular and Genomic Imaging Center
    George Church; Fiscal Year: 2007
    ..6) An ELSI component focuses on issues of translation of technology to clinical applications and challenges to the concepts of anonymity. ..
  2. Targeted 2nd generation sequencing in phenotyped Framingham & PGP populations.
    George Church; Fiscal Year: 2009
    ..It will eventually also enable health providers to learn the genetic variations of their patients very inexpensively and thus help refine and improve their medical care. ..
  3. Targeted 2nd generation sequencing in phenotyped Framingham & PGP populations.
    George M Church; Fiscal Year: 2010
    ..It will eventually also enable health providers to learn the genetic variations of their patients very inexpensively and thus help refine and improve their medical care. ..