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 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
  4. 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
  5. 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
  6. 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
  7. 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
  8. 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
  9. 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
  10. 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

Collaborators

  • Esther T Chan
  • T R Hughes
  • Michael Snyder
  • Wen Zhang
  • Bertrand R Huber
  • Joshua Labaer
  • Abigail Manson McGuire
  • Beatriz Estrada
  • Preston Wayne Estep
  • Philip L F Johnson
  • Kevin Struhl
  • R Maas
  • RICHARD A contact YOUNG
  • Panayiotis V Benos
  • Manuel Llinas
  • Richard Kolodner
  • G D Stormo
  • Alan M Michelson
  • Michael F Berger
  • Anthony A Philippakis
  • Savina A Jaeger
  • Cong Zhu
  • Daniel E Newburger
  • Rachel Patton McCord
  • Yanhui Hu
  • Daniel Wong
  • Raluca Gordân
  • Trevor Siggers
  • Sheldon Rowan
  • Dimitrios Iliopoulos
  • Andrew R Gehrke
  • Andreas Rolfs
  • Jason B Warner
  • Audra J Pompeani
  • Erandi K De Silva
  • Youngsok Choi
  • Aaron M Qureshi
  • Fangxue Sherry He
  • Sonali Mukherjee
  • Mei Ling Ting Lee
  • Stefan Dimitrov
  • Dimitar Angelov
  • Irina A Udalova
  • Rachel P McCord
  • Peter Humburg
  • Ana Teixeira
  • Anastasia Vedenko
  • David Saliba
  • Imtiaz Nisar Lone
  • Spyros Oikonomopoulos
  • Jiannis Ragoussis
  • Kevin F Murphy
  • Rolf Stottmann
  • Yingzi Yue
  • Salil A Lachke
  • Heather A Hirsch
  • Federico De Masi
  • Marcin Pacek
  • Tal Murthy
  • Zhenwei Shi
  • Katrina Saulrieta
  • Zachary Smith
  • Kelsey J R P Byers
  • Mita V Shah
  • Mathangi Radhakrishnan
  • Lourdes Pena-Castillo
  • Olga B Botvinnik
  • Gwenael Badis
  • Kellen Olszewski
  • Faiqua Khalid
  • Ilsa León
  • Ned S Wingreen
  • Jolinta Lin
  • Shaheynoor Talukder
  • Quaid D Morris
  • Trevis M Alleyne
  • Daniel Newburger
  • Joseph J Irgon
  • Bonnie L Bassler
  • Sanie Mnaimneh
  • Jasdave S Chahal
  • Daniel J Ballow
  • Aleksandar Rajkovic
  • Daniel Jepson
  • Dongmei Zuo
  • Donna Moreira
  • Tellamraju V S Murthy
  • Seamus McCarron
  • Bhupinder Bhullar
  • Andrew Simpson

Detail Information

Publications33

  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 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...
  4. 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
    ....
  5. 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
    ....
  6. 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
    ....
  7. 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
    ....
  8. 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
  9. 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...
  10. 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
    ....
  11. 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...
  12. 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...
  13. 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
    ....
  14. 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/...
  15. 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...
  16. 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...
  17. 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
    ....
  18. 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
    ....
  19. 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...
  20. 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...
  21. 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...
  22. 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...
  23. 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...
  24. 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...
  25. 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...
  26. 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
    ....
  27. 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...
  28. pmc Biological code breaking in the 21st century
    Alan M Michelson
    Mol Syst Biol 2:2006.0018. 2006
  29. 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...
  30. pmc Discovering DNA regulatory elements with bacteria
    Martha L Bulyk
    Nat Biotechnol 23:942-4. 2005
  31. 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...
  32. 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...
  33. 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...

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. 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. ..
  3. 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. ..
  4. 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. ..
  5. 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. ..
  6. 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. ..
  7. Integrated Genomic Analysis of a Drosophila Transcriptional Regulatory Network
    Martha Bulyk; Fiscal Year: 2007
    ..abstract_text> ..
  8. 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. ..