Martha Bulyk

Summary

Affiliation: Harvard University
Country: USA

Publications

  1. pmc Approaching a complete repository of sequence-verified protein-encoding clones for Saccharomyces cerevisiae
    Yanhui Hu
    Harvard Institute of Proteomics, Harvard Medical School, Cambridge, MA 02141, USA
    Genome Res 17:536-43. 2007
  2. pmc High-resolution DNA-binding specificity analysis of yeast transcription factors
    Cong Zhu
    Division of Genetics, Department of Medicine, Brigham and Women s Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA
    Genome Res 19:556-66. 2009
  3. pmc Inferring condition-specific transcription factor function from DNA binding and gene expression data
    Rachel Patton McCord
    Division of Genetics, Department of Medicine, Brigham and Women s Hospital and Harvard Medical School, Boston, MA 02115, USA
    Mol Syst Biol 3:100. 2007
  4. pmc UniPROBE: an online database of protein binding microarray data on protein-DNA interactions
    Daniel E Newburger
    Division of Genetics, Department of Medicine, Brigham and Women s Hospital, Harvard Medical School and Harvard MIT Division of Health Sciences and Technology, Harvard Medical School, Boston, MA 02115, USA
    Nucleic Acids Res 37:D77-82. 2009
  5. pmc Highly parallel assays of tissue-specific enhancers in whole Drosophila embryos
    Stephen S Gisselbrecht
    Department of Medicine, Division of Genetics, Brigham and Women s Hospital and Harvard Medical School, Boston, Massachusetts, USA
    Nat Methods 10:774-80. 2013
  6. pmc UniPROBE, update 2011: expanded content and search tools in the online database of protein-binding microarray data on protein-DNA interactions
    Kimberly Robasky
    Department of Medicine, Division of Genetics, Brigham and Women s Hospital and Harvard Medical School, Boston, MA 02115, USA
    Nucleic Acids Res 39:D124-8. 2011
  7. pmc Principles of dimer-specific gene regulation revealed by a comprehensive characterization of NF-κB family DNA binding
    Trevor Siggers
    Division of Genetics, Department of Medicine, Brigham and Women s Hospital and Harvard Medical School, Boston, Massachusetts, USA
    Nat Immunol 13:95-102. 2012
  8. pmc Non-DNA-binding cofactors enhance DNA-binding specificity of a transcriptional regulatory complex
    Trevor Siggers
    Division of Genetics, Department of Medicine, Brigham and Women s Hospital and Harvard Medical School, Boston, MA, USA
    Mol Syst Biol 7:555. 2011
  9. pmc Molecular mechanism underlying the regulatory specificity of a Drosophila homeodomain protein that specifies myoblast identity
    Brian W Busser
    Laboratory of Developmental Systems Biology, Genetics and Developmental Biology Center, Division of Intramural Research, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
    Development 139:1164-74. 2012
  10. pmc Curated collection of yeast transcription factor DNA binding specificity data reveals novel structural and gene regulatory insights
    Raluca Gordân
    Division of Genetics, Department of Medicine, Brigham and Women s Hospital and Harvard Medical School, Boston, MA 02115, USA
    Genome Biol 12:R125. 2011

Collaborators

Detail Information

Publications39

  1. pmc Approaching a complete repository of sequence-verified protein-encoding clones for Saccharomyces cerevisiae
    Yanhui Hu
    Harvard Institute of Proteomics, Harvard Medical School, Cambridge, MA 02141, USA
    Genome Res 17:536-43. 2007
    ..Availability of this collection makes possible a wide variety of studies from purified proteins to mutation suppression analysis, which should contribute to a global understanding of yeast protein function...
  2. pmc High-resolution DNA-binding specificity analysis of yeast transcription factors
    Cong Zhu
    Division of Genetics, Department of Medicine, Brigham and Women s Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA
    Genome Res 19:556-66. 2009
    ..These approaches could be adapted to identify TFs and cis regulatory elements in higher eukaryotes...
  3. pmc Inferring condition-specific transcription factor function from DNA binding and gene expression data
    Rachel Patton McCord
    Division of Genetics, Department of Medicine, Brigham and Women s Hospital and Harvard Medical School, Boston, MA 02115, USA
    Mol Syst Biol 3:100. 2007
    ..This approach can be used to suggest conditions for directed in vivo experimentation and to predict TF function...
  4. pmc UniPROBE: an online database of protein binding microarray data on protein-DNA interactions
    Daniel E Newburger
    Division of Genetics, Department of Medicine, Brigham and Women s Hospital, Harvard Medical School and Harvard MIT Division of Health Sciences and Technology, Harvard Medical School, Boston, MA 02115, USA
    Nucleic Acids Res 37:D77-82. 2009
    ..The UniPROBE database is available at http://thebrain.bwh.harvard.edu/uniprobe/...
  5. pmc Highly parallel assays of tissue-specific enhancers in whole Drosophila embryos
    Stephen S Gisselbrecht
    Department of Medicine, Division of Genetics, Brigham and Women s Hospital and Harvard Medical School, Boston, Massachusetts, USA
    Nat Methods 10:774-80. 2013
    ..Application of eFS to other cell types and organisms should accelerate the cataloging of enhancers and understanding how transcriptional regulation is encoded in them. ..
  6. pmc UniPROBE, update 2011: expanded content and search tools in the online database of protein-binding microarray data on protein-DNA interactions
    Kimberly Robasky
    Department of Medicine, Division of Genetics, Brigham and Women s Hospital and Harvard Medical School, Boston, MA 02115, USA
    Nucleic Acids Res 39:D124-8. 2011
    ..The UniPROBE database is available at http://uniprobe.org...
  7. pmc Principles of dimer-specific gene regulation revealed by a comprehensive characterization of NF-κB family DNA binding
    Trevor Siggers
    Division of Genetics, Department of Medicine, Brigham and Women s Hospital and Harvard Medical School, Boston, Massachusetts, USA
    Nat Immunol 13:95-102. 2012
    ..This study provides a database that can be used in efforts to identify NF-κB target sites and uncover gene regulatory circuitry...
  8. pmc Non-DNA-binding cofactors enhance DNA-binding specificity of a transcriptional regulatory complex
    Trevor Siggers
    Division of Genetics, Department of Medicine, Brigham and Women s Hospital and Harvard Medical School, Boston, MA, USA
    Mol Syst Biol 7:555. 2011
    ..Our results highlight the need to examine TF/cofactor complexes, as novel specificity can result from cofactors that lack intrinsic DNA-binding specificity...
  9. pmc Molecular mechanism underlying the regulatory specificity of a Drosophila homeodomain protein that specifies myoblast identity
    Brian W Busser
    Laboratory of Developmental Systems Biology, Genetics and Developmental Biology Center, Division of Intramural Research, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
    Development 139:1164-74. 2012
    ..Collectively, these studies provide new insights into the roles of individual HD TFs in determining cellular identity, and suggest that the diversity of HD binding preferences can confer regulatory specificity...
  10. pmc Curated collection of yeast transcription factor DNA binding specificity data reveals novel structural and gene regulatory insights
    Raluca Gordân
    Division of Genetics, Department of Medicine, Brigham and Women s Hospital and Harvard Medical School, Boston, MA 02115, USA
    Genome Biol 12:R125. 2011
    ..Recent surveys have examined the DNA binding specificities of most Saccharomyces cerevisiae TFs, but a comprehensive evaluation of their data has been lacking...
  11. pmc Extensive characterization of NF-κB binding uncovers non-canonical motifs and advances the interpretation of genetic functional traits
    Daniel Wong
    Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX37BN, UK
    Genome Biol 12:R70. 2011
    ....
  12. pmc Meta-analysis discovery of tissue-specific DNA sequence motifs from mammalian gene expression data
    Bertrand R Huber
    Division of Genetics, Department of Medicine, Brigham and Women s Hospital and Harvard Medical School, Boston, MA 02115, USA
    BMC Bioinformatics 7:229. 2006
    ....
  13. pmc DNA microarray technologies for measuring protein-DNA interactions
    Martha L Bulyk
    Division of Genetics, Department of Medicine, Harvard MIT Division of Health Sciences and Technology HST, Brigham and Women s Hospital and Harvard Medical School, Boston, MA 02115, USA
    Curr Opin Biotechnol 17:422-30. 2006
    ....
  14. pmc Integrative functional genomics
    Martha L Bulyk
    Brigham and Women s Hospital and Harvard Medical School, New Research Building, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
    Genome Biol 5:331. 2004
  15. pmc Rapid analysis of the DNA-binding specificities of transcription factors with DNA microarrays
    Sonali Mukherjee
    Division of Genetics, Department of Medicine, Harvard Medical School Boston Massachusetts 02115, USA
    Nat Genet 36:1331-9. 2004
    ..Similar PBM experiments should be useful in identifying new cis regulatory elements and transcriptional regulatory networks in various genomes...
  16. pmc Protein binding microarrays for the characterization of DNA-protein interactions
    Martha L Bulyk
    Division of Genetics, Department of Medicine, Brigham and Women s Hospital and Harvard Medical School, Harvard Medical School New Research Bldg, Room 466D, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
    Adv Biochem Eng Biotechnol 104:65-85. 2007
    ....
  17. pmc Universal protein-binding microarrays for the comprehensive characterization of the DNA-binding specificities of transcription factors
    Michael F Berger
    Division of Genetics, Department of Medicine, Brigham and Women s Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA
    Nat Protoc 4:393-411. 2009
    ..Multiple proteins can be tested in parallel in separate chambers on a single microarray, enabling the processing of a dozen or more TFs in a single day...
  18. pmc Conservation and regulatory associations of a wide affinity range of mouse transcription factor binding sites
    Savina A Jaeger
    Division of Genetics, Department of Medicine, Brigham and Women s Hospital and Harvard Medical School, Boston, MA 02115, USA
    Genomics 95:185-95. 2010
    ....
  19. pmc Protein binding microarrays (PBMs) for rapid, high-throughput characterization of the sequence specificities of DNA binding proteins
    Michael F Berger
    Biophysics Program, Harvard University, Boston, MA, USA
    Methods Mol Biol 338:245-60. 2006
    ....
  20. 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...
  21. pmc Short-term calorie restriction in male mice feminizes gene expression and alters key regulators of conserved aging regulatory pathways
    Preston Wayne Estep
    Longenity Inc, Lincoln, MA, USA
    PLoS ONE 4:e5242. 2009
    ....
  22. pmc Variation in homeodomain DNA binding revealed by high-resolution analysis of sequence preferences
    Michael F Berger
    Division of Genetics, Department of Medicine, Brigham and Women s Hospital and Harvard Medical School, Boston, MA 02115, USA
    Cell 133:1266-76. 2008
    ..Our results provide an unprecedented level of resolution in the analysis of this simple domain structure and suggest that variation in sequence recognition may be a factor in its functional diversity and evolutionary success...
  23. 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
    ....
  24. 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...
  25. pmc Systematic identification of mammalian regulatory motifs' target genes and functions
    Jason B Warner
    Division of Genetics, Department of Medicine, Harvard Medical School, Harvard Medical School New Research Building, Room 466D, 77 Ave Louis Pasteur, Boston, Massachusetts 02115, USA
    Nat Methods 5:347-53. 2008
    ..This approach is general and can be applied readily to any cell type, gene expression pattern or organism of interest...
  26. pmc Computational prediction of transcription-factor binding site locations
    Martha L Bulyk
    Division of Genetics, Department of Medicine, Brigham and Women s Hospital and Harvard Medical School, New Research Building, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
    Genome Biol 5:201. 2003
    ..Various experimental and computational approaches have been used to detect these sites; methods involving computational comparisons of related genomes have been particularly successful...
  27. pmc Design of compact, universal DNA microarrays for protein binding microarray experiments
    Anthony A Philippakis
    Division of Genetics, Department of Medicine, Brigham and Women s Hospital and Harvard Medical School, Boston, Massachusetts, USA
    J Comput Biol 15:655-65. 2008
    ..This design yields a powerful experimental platform that allows the binding preferences of TFs to be determined with unprecedented resolution...
  28. ncbi request reprint Compact, universal DNA microarrays to comprehensively determine transcription-factor binding site specificities
    Michael F Berger
    Division of Genetics, Department of Medicine, Brigham and Women s Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA
    Nat Biotechnol 24:1429-35. 2006
    ..The unbiased coverage of all k-mers permits high-throughput interrogation of binding site preferences, including nucleotide interdependencies, at unprecedented resolution...
  29. pmc Analysis of sequence specificities of DNA-binding proteins with protein binding microarrays
    Martha L Bulyk
    Division of Genetics, Department of Medicine, Harvard MIT Division of Health Sciences and Technology HST, Brigham and Women s Hospital, Harvard Medical School, Boston, Massachusetts, USA
    Methods Enzymol 410:279-99. 2006
    ....
  30. pmc Expression-guided in silico evaluation of candidate cis regulatory codes for Drosophila muscle founder cells
    Anthony A Philippakis
    Division of Genetics, Department of Medicine, Brigham and Women s Hospital and Harvard Medical School, Boston, Massachusetts, USA
    PLoS Comput Biol 2:e53. 2006
    ..We have confirmed this hypothesis by experimentally discovering six (out of 12 tested) new CRMs driving expression in the embryonic mesoderm, four of which drive expression in founder cells...
  31. pmc STAT3 activation of miR-21 and miR-181b-1 via PTEN and CYLD are part of the epigenetic switch linking inflammation to cancer
    Dimitrios Iliopoulos
    Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
    Mol Cell 39:493-506. 2010
    ..Thus, STAT3 is not only a downstream target of IL-6 but, with miR-21, miR-181b-1, PTEN, and CYLD, is part of the positive feedback loop that underlies the epigenetic switch that links inflammation to cancer...
  32. pmc A transcriptional signature and common gene networks link cancer with lipid metabolism and diverse human diseases
    Heather A Hirsch
    Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
    Cancer Cell 17:348-61. 2010
    ..We suggest that the interplay between this common transcriptional program and cell-type-specific factors gives rise to phenotypically disparate human diseases...
  33. pmc Precise temporal control of the eye regulatory gene Pax6 via enhancer-binding site affinity
    Sheldon Rowan
    Division of Genetics, Department of Medicine, Brigham and Women s Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA
    Genes Dev 24:980-5. 2010
    ..Finally, we describe a mechanism whereby Pax6 levels are determined by transcriptional synergy of Prep1 bound to the two sites, while timing of enhancer activation is determined by binding site affinity...
  34. pmc Biological code breaking in the 21st century
    Alan M Michelson
    Mol Syst Biol 2:2006.0018. 2006
  35. pmc Discovering DNA regulatory elements with bacteria
    Martha L Bulyk
    Nat Biotechnol 23:942-4. 2005
  36. pmc The Vibrio harveyi master quorum-sensing regulator, LuxR, a TetR-type protein is both an activator and a repressor: DNA recognition and binding specificity at target promoters
    Audra J Pompeani
    Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
    Mol Microbiol 70:76-88. 2008
    ..Together, the in silico and biochemical results enabled us to scan the genome and identify novel targets of LuxR in V. harveyi and thus expand the understanding of the quorum-sensing regulon...
  37. pmc Additivity in protein-DNA interactions: how good an approximation is it?
    Panayiotis V Benos
    Department of Genetics, Campus Box 8232, Washington University, School of Medicine, St Louis, MO 63110, USA
    Nucleic Acids Res 30:4442-51. 2002
    ..Therefore, additive models can be very useful for the discovery and prediction of binding sites in genomic DNA...
  38. ncbi request reprint Microarray analyses of newborn mouse ovaries lacking Nobox
    Youngsok Choi
    Department of Obstetrics and Gynecology, Baylor College of Medicine, Houston, Texas 77030, USA
    Biol Reprod 77:312-9. 2007
    ..Our findings indicate that Nobox is likely an activator of oocyte-specific gene expression and suggest that the oocyte plays an important role in suppressing expression of male-determining genes, such as Dmrt1...
  39. pmc Specific DNA-binding by apicomplexan AP2 transcription factors
    Erandi K De Silva
    Department of Molecular Biology and Lewis Sigler Institute for Integrative Genomics, Princeton University, 246 Carl Icahn Laboratory, Princeton, NJ 08544, USA
    Proc Natl Acad Sci U S A 105:8393-8. 2008
    ..Because of their origin in the plant lineage, ApiAP2 proteins have no homologues in the human host and may prove to be ideal antimalarial targets...

Research Grants20

  1. High-Resolution DNA-binding specificity analysis of transcription factors
    Martha L Bulyk; Fiscal Year: 2010
    ..The findings from this project will provide data on the potential effects of transcription factor polymorphisms on gene regulation. ..
  2. Eukaryotic Transcription Factor Binding Site Locations
    Martha Bulyk; Fiscal Year: 2003
    ..In addition, we will make our data publicly available, so that other researchers may focus their efforts on those genomic regions most likely to contain cis regulatory elements. ..
  3. Transcriptional control of Drosophila heart development
    Martha Bulyk; Fiscal Year: 2007
    ..Collectively, these studies will provide a detailed understanding of the transcriptional regulatory mechanisms underlying cardiac development. ..
  4. Universal, Compact Combinatorial Microarrays for DNA Binding Site Discovery
    Martha Bulyk; Fiscal Year: 2009
    ..Such data may also increase the accuracy with which cis regulatory modules can be predicted in higher eukaryotic genomes. ..
  5. High-Throughput Identification of Tissue/Cell-Type-Specific Cis Regulatory Module
    Martha L Bulyk; Fiscal Year: 2010
    ..We anticipate that the technologies, approaches, tools, and data resulting from this project will be generally applicable to other systems and organisms. ..
  6. Universal, Compact Combinatorial Microarrays for DNA Binding Site Discovery
    Martha Bulyk; Fiscal Year: 2007
    ..Such data may also increase the accuracy with which cis regulatory modules can be predicted in higher eukaryotic genomes. ..
  7. Eukaryotic Transcription Factor Binding Site Locations
    Martha Bulyk; Fiscal Year: 2007
    ..In addition, we will make our data publicly available, so that other researchers may focus their efforts on those genomic regions most likely to contain cis regulatory elements. ..
  8. Eukaryotic Transcription Factor Binding Site Locations
    Martha Bulyk; Fiscal Year: 2004
    ..In addition, we will make our data publicly available, so that other researchers may focus their efforts on those genomic regions most likely to contain cis regulatory elements. ..
  9. Yeast Transcription Factor Binding Specificities
    Martha Bulyk; Fiscal Year: 2004
    ..This PBM approach could also be used to study TFs from other genomes. We will make our data publicly available in a web-accessible database. ..
  10. Eukaryotic Transcription Factor Binding Site Locations
    Martha Bulyk; Fiscal Year: 2005
    ..In addition, we will make our data publicly available, so that other researchers may focus their efforts on those genomic regions most likely to contain cis regulatory elements. ..
  11. Yeast Transcription Factor Binding Specificities
    Martha Bulyk; Fiscal Year: 2005
    ..This PBM approach could also be used to study TFs from other genomes. We will make our data publicly available in a web-accessible database. ..
  12. Universal, Compact Combinatorial Microarrays for DNA Binding Site Discovery
    Martha Bulyk; Fiscal Year: 2006
    ..Such data may also increase the accuracy with which cis regulatory modules can be predicted in higher eukaryotic genomes. ..
  13. Eukaryotic Transcription Factor Binding Site Locations
    Martha Bulyk; Fiscal Year: 2006
    ..In addition, we will make our data publicly available, so that other researchers may focus their efforts on those genomic regions most likely to contain cis regulatory elements. ..
  14. Yeast Transcription Factor Binding Specificities
    Martha Bulyk; Fiscal Year: 2006
    ..This PBM approach could also be used to study TFs from other genomes. We will make our data publicly available in a web-accessible database. ..
  15. Integrated Genomic Analysis of a Drosophila Transcriptional Regulatory Network
    Martha Bulyk; Fiscal Year: 2007
    ..abstract_text> ..
  16. High-Resolution DNA-binding specificity analysis of transcription factors
    Martha L Bulyk; Fiscal Year: 2010
    ..The findings from this project will provide data on the potential effects of transcription factor polymorphisms on gene regulation. ..