Research Topics
| Martha BulykSummaryAffiliation: Harvard University Country: USA Publications
Research Grants
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Detail Information
Publications
Approaching a complete repository of sequence-verified protein-encoding clones for Saccharomyces cerevisiaeYanhui 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...- High-resolution DNA-binding specificity analysis of yeast transcription factorsCong 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... - Curated collection of yeast transcription factor DNA binding specificity data reveals novel structural and gene regulatory insightsRaluca 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... - Extensive characterization of NF-κB binding uncovers non-canonical motifs and advances the interpretation of genetic functional traitsDaniel Wong
Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX37BN, UK
Genome Biol 12:R70. 2011.... 
Meta-analysis discovery of tissue-specific DNA sequence motifs from mammalian gene expression dataBertrand 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....- Protein binding microarrays for the characterization of DNA-protein interactionsMartha 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.... - DNA microarray technologies for measuring protein-DNA interactionsMartha 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.... - Integrative functional genomicsMartha 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 - Rapid analysis of the DNA-binding specificities of transcription factors with DNA microarraysSonali 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... - Conservation and regulatory associations of a wide affinity range of mouse transcription factor binding sitesSavina 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.... - Universal protein-binding microarrays for the comprehensive characterization of the DNA-binding specificities of transcription factorsMichael 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... - A motif co-occurrence approach for genome-wide prediction of transcription-factor-binding sites in Escherichia coliMartha 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... - Protein binding microarrays (PBMs) for rapid, high-throughput characterization of the sequence specificities of DNA binding proteinsMichael F Berger
Biophysics Program, Harvard University, Boston, MA, USA
Methods Mol Biol 338:245-60. 2006.... - UniPROBE: an online database of protein binding microarray data on protein-DNA interactionsDaniel 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/... - Variation in homeodomain DNA binding revealed by high-resolution analysis of sequence preferencesMichael 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... - Systematic identification of mammalian regulatory motifs' target genes and functionsJason 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... - Short-term calorie restriction in male mice feminizes gene expression and alters key regulators of conserved aging regulatory pathwaysPreston Wayne Estep
Longenity Inc, Lincoln, MA, USA
PLoS ONE 4:e5242. 2009.... - Nucleotides of transcription factor binding sites exert interdependent effects on the binding affinities of transcription factorsMartha L Bulyk
Harvard University Graduate Biophysics Program, Harvard Medical School, Boston, MA 02115, USA
Nucleic Acids Res 30:1255-61. 2002.... 
A statistical model for investigating binding probabilities of DNA nucleotide sequences using microarraysMei 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...- Computational prediction of transcription-factor binding site locationsMartha 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... - Inferring condition-specific transcription factor function from DNA binding and gene expression dataRachel 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... - Compact, universal DNA microarrays to comprehensively determine transcription-factor binding site specificitiesMichael 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... - Design of compact, universal DNA microarrays for protein binding microarray experimentsAnthony 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... - STAT3 activation of miR-21 and miR-181b-1 via PTEN and CYLD are part of the epigenetic switch linking inflammation to cancerDimitrios 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... - Expression-guided in silico evaluation of candidate cis regulatory codes for Drosophila muscle founder cellsAnthony 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... - Analysis of sequence specificities of DNA-binding proteins with protein binding microarraysMartha 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.... - Precise temporal control of the eye regulatory gene Pax6 via enhancer-binding site affinitySheldon 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... - Biological code breaking in the 21st centuryAlan M Michelson
Mol Syst Biol 2:2006.0018. 2006 - 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 promotersAudra 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... - Discovering DNA regulatory elements with bacteriaMartha L Bulyk
Nat Biotechnol 23:942-4. 2005 - 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... - Specific DNA-binding by apicomplexan AP2 transcription factorsErandi 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... - Microarray analyses of newborn mouse ovaries lacking NoboxYoungsok 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 Grants
- High-Resolution DNA-binding specificity analysis of transcription factorsMartha L Bulyk; Fiscal Year: 2010..The findings from this project will provide data on the potential effects of transcription factor polymorphisms on gene regulation. ..
- Transcriptional control of Drosophila heart developmentMartha Bulyk; Fiscal Year: 2007..Collectively, these studies will provide a detailed understanding of the transcriptional regulatory mechanisms underlying cardiac development. ..
- Universal, Compact Combinatorial Microarrays for DNA Binding Site DiscoveryMartha Bulyk; Fiscal Year: 2009..Such data may also increase the accuracy with which cis regulatory modules can be predicted in higher eukaryotic genomes. ..
- High-Throughput Identification of Tissue/Cell-Type-Specific Cis Regulatory ModuleMartha 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. ..
- Eukaryotic Transcription Factor Binding Site LocationsMartha 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. ..
- Yeast Transcription Factor Binding SpecificitiesMartha 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. ..
- Integrated Genomic Analysis of a Drosophila Transcriptional Regulatory NetworkMartha Bulyk; Fiscal Year: 2007..abstract_text> ..
- High-Resolution DNA-binding specificity analysis of transcription factorsMartha L Bulyk; Fiscal Year: 2010..The findings from this project will provide data on the potential effects of transcription factor polymorphisms on gene regulation. ..