George M Church

Summary

Affiliation: Harvard University
Country: USA

Publications

  1. pmc Targeted and genome-scale strategies reveal gene-body methylation signatures in human cells
    Madeleine P Ball
    Department of Genetics, Harvard Medical School, Cambridge, MA, USA
    Nat Biotechnol 27:361-8. 2009
  2. pmc High-fidelity gene synthesis by retrieval of sequence-verified DNA identified using high-throughput pyrosequencing
    Mark Matzas
    Febit group, Heidelberg, Germany
    Nat Biotechnol 28:1291-4. 2010
  3. pmc BRAIN: innovative neurotechnologies for imaging and therapeutics
    George M Church
    Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
    Dialogues Clin Neurosci 15:241-3. 2013
  4. pmc Large-scale identification of genetic design strategies using local search
    Desmond S Lun
    Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
    Mol Syst Biol 5:296. 2009
  5. pmc A BioBrick compatible strategy for genetic modification of plants
    Patrick M Boyle
    Department of Systems Biology, Harvard Medical School, Boston, MA, 02115, USA
    J Biol Eng 6:8. 2012
  6. pmc A new dawn for industrial photosynthesis
    Dan E Robertson
    Biological Sciences, Joule Unlimited, Cambridge, MA 02142, USA
    Photosynth Res 107:269-77. 2011
  7. pmc Model-driven analysis of experimentally determined growth phenotypes for 465 yeast gene deletion mutants under 16 different conditions
    Evan S Snitkin
    Bioinformatics Graduate Program, Boston University, Boston, MA 02215, USA
    Genome Biol 9:R140. 2008
  8. pmc New technologies for integrating genomic, environmental and trait data
    George M Church
    Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
    J Clin Sleep Med 7:S43-4. 2011
  9. 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
  10. 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

Collaborators

Detail Information

Publications90

  1. pmc Targeted and genome-scale strategies reveal gene-body methylation signatures in human cells
    Madeleine P Ball
    Department of Genetics, Harvard Medical School, Cambridge, MA, USA
    Nat Biotechnol 27:361-8. 2009
    ..Our observations highlight the usefulness of techniques that are not inherently or intentionally biased towards particular subsets like CpG islands or promoter regions...
  2. pmc High-fidelity gene synthesis by retrieval of sequence-verified DNA identified using high-throughput pyrosequencing
    Mark Matzas
    Febit group, Heidelberg, Germany
    Nat Biotechnol 28:1291-4. 2010
    ..We use DNA obtained by megacloning to assemble synthetic genes. In principle, millions of DNA fragments can be sequenced, characterized and sorted in a single megacloner run, enabling constructive biology up to the megabase scale...
  3. pmc BRAIN: innovative neurotechnologies for imaging and therapeutics
    George M Church
    Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
    Dialogues Clin Neurosci 15:241-3. 2013
    ..It concentrates on the use of new imaging technologies in conjunction with genomics to inform therapeutic decisions. ..
  4. pmc Large-scale identification of genetic design strategies using local search
    Desmond S Lun
    Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
    Mol Syst Biol 5:296. 2009
    ....
  5. pmc A BioBrick compatible strategy for genetic modification of plants
    Patrick M Boyle
    Department of Systems Biology, Harvard Medical School, Boston, MA, 02115, USA
    J Biol Eng 6:8. 2012
    ..abstract:..
  6. pmc A new dawn for industrial photosynthesis
    Dan E Robertson
    Biological Sciences, Joule Unlimited, Cambridge, MA 02142, USA
    Photosynth Res 107:269-77. 2011
    ..This concept, currently enabled for production of ethanol and alkane diesel fuel molecules, and operating at pilot scale, establishes a new paradigm for high productivity manufacturing of nonfossil-derived fuels and chemicals...
  7. pmc Model-driven analysis of experimentally determined growth phenotypes for 465 yeast gene deletion mutants under 16 different conditions
    Evan S Snitkin
    Bioinformatics Graduate Program, Boston University, Boston, MA 02215, USA
    Genome Biol 9:R140. 2008
    ..Integration of high-throughput experimental assays and genome-scale computational methods is likely to produce insight otherwise unreachable, but specific examples of such integration have only begun to be explored...
  8. pmc New technologies for integrating genomic, environmental and trait data
    George M Church
    Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
    J Clin Sleep Med 7:S43-4. 2011
    ..To expand this further we have established community resources for open access collection, integration and interpretation of diverse personal genomic, environmental and trait data evidence.personalgenomes.org)...
  9. 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...
  10. 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
    ....
  11. 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...
  12. 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...
  13. pmc Using bacteria to determine protein kinase specificity and predict target substrates
    Michael F Chou
    Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
    PLoS ONE 7:e52747. 2012
    ....
  14. 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...
  15. pmc Rational optimization of tolC as a powerful dual selectable marker for genome engineering
    Christopher J Gregg
    Department of Genetics and Wyss Institute for Biologically Inspired Engineering, Harvard Medical School, Boston, MA 02115, USA, Program in Chemical Biology, Harvard University, Cambridge, MA 02138, USA, Biological and Biomedical Sciences, Harvard Medical School, Boston, MA 02115, USA and Molecular, Cellular, Developmental and Systems Biology Institute, Yale University, New Haven, CT 06516, USA
    Nucleic Acids Res 42:4779-90. 2014
    ..Finally, we combined these advances to create an optimized E. coli strain for genome engineering that is ∼10-fold more efficient at achieving allelic diversity than previous best practices. ..
  16. 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...
  17. 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...
  18. 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...
  19. 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...
  20. pmc Proteome-wide systems analysis of a cellulosic biofuel-producing microbe
    Andrew C Tolonen
    Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
    Mol Syst Biol 7:461. 2011
    ..This study gives a systems-level understanding of how this microbe ferments biomass and provides a rational, empirical basis to identify engineering targets for industrial cellulosic fermentation...
  21. pmc An integrated strategy for analyzing the unique developmental programs of different myoblast subtypes
    Beatriz Estrada
    Division of Genetics, Department of Medicine, Brigham and Women s Hospital and Harvard Medical School, Boston, Massachusetts, USA
    PLoS Genet 2:e16. 2006
    ..This integrated strategy for examining embryonic gene expression and function provides a substantially expanded framework for further studies of this model developmental system...
  22. 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...
  23. pmc Composability of regulatory sequences controlling transcription and translation in Escherichia coli
    Sriram Kosuri
    Wyss Institute for Biologically Inspired Engineering, Boston, MA 02115, USA
    Proc Natl Acad Sci U S A 110:14024-9. 2013
    ..The ease and scale this of approach indicates that rather than relying on prediction or standardization, we can screen synthetic libraries for desired behavior. ..
  24. 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...
  25. 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...
  26. pmc Extensive phosphorylation with overlapping specificity by Mycobacterium tuberculosis serine/threonine protein kinases
    Sladjana Prisic
    Division of Infectious Diseases, Children s Hospital Boston, Harvard Medical School, Boston, MA 02115, USA
    Proc Natl Acad Sci U S A 107:7521-6. 2010
    ..tuberculosis and create a resource for understanding how specific phosphorylation events modulate protein activity. The results further provide the potential to predict likely cognate STPKs for newly identified phosphoproteins...
  27. ncbi request reprint From annotated genomes to metabolic flux models and kinetic parameter fitting
    Daniel Segrè
    Lipper Center for Computational Genetics, Harvard Medical School, Boston, Massachusetts, USA
    OMICS 7:301-16. 2003
    ..In addition, we propose a framework for the integration of flux modeling results and high throughput proteomic data, which can potentially help in the inference of whole-cell kinetic parameters...
  28. 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...
  29. doi request reprint Genome-wide identification of human RNA editing sites by parallel DNA capturing and sequencing
    Jin Billy Li
    Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
    Science 324:1210-3. 2009
    ..This efficient approach greatly expands the repertoire of RNA editing targets and can be applied to studies involving RNA editing-related human diseases...
  30. pmc Heritable custom genomic modifications in Caenorhabditis elegans via a CRISPR-Cas9 system
    Yonatan B Tzur
    Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115
    Genetics 195:1181-5. 2013
    ..This system can be used to create specific insertions, deletions, and base pair changes in the germline of C. elegans. ..
  31. doi request reprint Genomically recoded organisms expand biological functions
    Marc J Lajoie
    Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
    Science 342:357-60. 2013
    ..The GRO also exhibited increased resistance to T7 bacteriophage, demonstrating that new genetic codes could enable increased viral resistance. ..
  32. 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...
  33. pmc Enhanced multiplex genome engineering through co-operative oligonucleotide co-selection
    Peter A Carr
    The Center for Bits and Atoms, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
    Nucleic Acids Res 40:e132. 2012
    ..We apply this technique to the modification of 80 sites in the E. coli genome...
  34. 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...
  35. 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
    ....
  36. pmc Genome-scale promoter engineering by coselection MAGE
    Harris H Wang
    Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts, USA
    Nat Methods 9:591-3. 2012
    ..Promoter libraries can be quickly generated to study gain-of-function epistatic interactions in gene networks...
  37. 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...
  38. doi request reprint Multiplexed genome engineering and genotyping methods applications for synthetic biology and metabolic engineering
    Harris H Wang
    Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
    Methods Enzymol 498:409-26. 2011
    ..Here, we discuss ways to utilize these multiplexed genome engineering methods, with special emphasis on experimental design and implementation...
  39. doi request reprint Precise manipulation of chromosomes in vivo enables genome-wide codon replacement
    Farren J Isaacs
    Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
    Science 333:348-53. 2011
    ..Our methods treat the chromosome as both an editable and an evolvable template, permitting the exploration of vast genetic landscapes...
  40. 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...
  41. 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...
  42. pmc Genome engineering in Saccharomyces cerevisiae using CRISPR-Cas systems
    James E Dicarlo
    Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA
    Nucleic Acids Res 41:4336-43. 2013
    ..Our approach provides foundations for a simple and powerful genome engineering tool for site-specific mutagenesis and allelic replacement in yeast...
  43. 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...
  44. 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...
  45. 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...
  46. 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...
  47. doi request reprint The most conserved genome segments for life detection on Earth and other planets
    Thomas A Isenbarger
    Department of Molecular Biology, Massachusetts General Hospital, and Microbial Sciences Initiative, Harvard University, Cambridge, MA, USA
    Orig Life Evol Biosph 38:517-33. 2008
    ..This set of sequences defines a core set of DNA regions that have changed the least over billions of years of evolution and provides a means to identify and classify divergent life, including ancestrally related life on other planets...
  48. pmc Autoantigen discovery with a synthetic human peptidome
    H Benjamin Larman
    Harvard MIT Division of Health Sciences and Technology, Cambridge, Massachusetts, USA
    Nat Biotechnol 29:535-41. 2011
    ..We also show how T7-Pep can be used more generally to identify peptide-protein interactions, suggesting the broader utility of our approach for proteomic research...
  49. 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...
  50. doi request reprint Causes and effects of N-terminal codon bias in bacterial genes
    Daniel B Goodman
    Wyss Institute for Biologically Inspired Engineering, 3 Blackfan Circle, Boston, MA 02115, USA
    Science 342:475-9. 2013
    ..Our observations resolve controversies over the roles of N-terminal codon bias and suggest a straightforward method for optimizing heterologous gene expression in bacteria. ..
  51. 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...
  52. 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
    ....
  53. 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...
  54. 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...
  55. 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
    ....
  56. 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...
  57. pmc Orthogonal Cas9 proteins for RNA-guided gene regulation and editing
    Kevin M Esvelt
    1 Wyss Institute for Biologically Inspired Engineering, Harvard Medical School, Boston, Massachusetts, USA 2
    Nat Methods 10:1116-21. 2013
    ..We provide a basal set of orthogonal RNA-guided proteins for controlling biological systems and establish a general methodology for characterizing additional proteins. ..
  58. 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...
  59. 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...
  60. 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
    ....
  61. pmc Efficient construction of sequence-specific TAL effectors for modulating mammalian transcription
    Feng Zhang
    Harvard University, Cambridge, Massachusetts, USA
    Nat Biotechnol 29:149-53. 2011
    ..We synthesized 17 TALEs that are customized to recognize specific DNA-binding sites, and demonstrate that they can specifically modulate transcription of endogenous genes (SOX2 and KLF4) in human cells...
  62. 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...
  63. pmc Identification of many microRNAs that copurify with polyribosomes in mammalian neurons
    John Kim
    Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
    Proc Natl Acad Sci U S A 101:360-5. 2004
    ..Moreover, all of the miRNAs that were tested cofractionate with polyribosomes, the sites of active translation. These findings indicate that a large, diverse population of miRNAs may function to regulate translation in mammalian neurons...
  64. 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...
  65. 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...
  66. 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...
  67. ncbi request reprint Single molecule profiling of alternative pre-mRNA splicing
    Jun Zhu
    Department of Genetics, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115, USA
    Science 301:836-8. 2003
    ..Digital polony exon profiling can be used to investigate the physiological and pathological roles of alternately spliced messenger RNAs, as well as the mechanisms by which these messenger RNAs are produced...
  68. 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
    ....
  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. 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
    ....
  71. 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...
  72. 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...
  73. 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...
  74. 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...
  75. 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...
  76. pmc 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...
  77. 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
    ....
  78. 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...
  79. 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...
  80. ncbi request reprint Genomes for all
    George M Church
    Harvard Medical School, USA
    Sci Am 294:46-54. 2006
  81. 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...
  82. doi request reprint Bacteria subsisting on antibiotics
    Gautam Dantas
    Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
    Science 320:100-3. 2008
    ..This phenomenon suggests that this unappreciated reservoir of antibiotic-resistance determinants can contribute to the increasing levels of multiple antibiotic resistance in pathogenic bacteria...
  83. 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...
  84. 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...
  85. 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'...
  86. 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...
  87. pmc Rapid prototyping of 3D DNA-origami shapes with caDNAno
    Shawn M Douglas
    Department of Cancer Biology, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA
    Nucleic Acids Res 37:5001-6. 2009
    ..The software is available at http://cadnano.org/, along with example designs and video tutorials demonstrating their construction. The source code is released under the MIT license...
  88. pmc Analysis of optimality in natural and perturbed metabolic networks
    Daniel Segrè
    Lipper Center for Computational Genetics and Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
    Proc Natl Acad Sci U S A 99:15112-7. 2002
    ..MOMA and its possible future extensions may be useful in understanding the evolutionary optimization of metabolism...
  89. 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...
  90. doi request reprint Collection and motif-based prediction of phosphorylation sites in human viruses
    Daniel Schwartz
    Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
    Sci Signal 3:rs2. 2010
    ....