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Your search keyword '"Bulyk, Martha L"' showing total 6 results
Start Over Author "Bulyk, Martha L" Journal genome biology
6 results on '"Bulyk, Martha L"'

2. CellMapper: rapid and accurate inference of gene expression in difficult-to-isolate cell types

Author

Nelms, Bradlee D., primary, Waldron, Levi, additional, Barrera, Luis A., additional, Weflen, Andrew W., additional, Goettel, Jeremy A., additional, Guo, Guoji, additional, Montgomery, Robert K., additional, Neutra, Marian R., additional, Breault, David T., additional, Snapper, Scott B., additional, Orkin, Stuart H., additional, Bulyk, Martha L., additional, Huttenhower, Curtis, additional, and Lencer, Wayne I., additional

Published
2016
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4. Integrative functional genomics

Author

Bulyk, Martha L

Subjects
Meeting Report
Abstract

A report on the Keystone Symposium 'Biological Discovery Using Diverse High-Throughput Data', Steamboat Springs, USA, 30 March-4 April 2004.

Published
2004

5. Curated collection of yeast transcription factor DNA binding specificity data reveals novel structural and gene regulatory insights

Author

Kevin F. Murphy, Cong Zhu, Raluca Gordân, Rachel Patton McCord, Anastasia Vedenko, Martha L. Bulyk, Harvard University--MIT Division of Health Sciences and Technology, and Bulyk, Martha L.

Subjects
Chromatin Immunoprecipitation, Saccharomyces cerevisiae Proteins, Response element, genetic processes, Molecular Sequence Data, Protein Array Analysis, Saccharomyces cerevisiae, Biology, 03 medical and health sciences, chemistry.chemical_compound, 0302 clinical medicine, Gene Expression Regulation, Fungal, Genes, Regulator, Amino Acid Sequence, Binding site, Nucleotide Motifs, Gene, Transcription factor, 030304 developmental biology, Genetics, 0303 health sciences, Binding Sites, Research, DNA, 3. Good health, DNA binding site, chemistry, DNA microarray, Chromatin immunoprecipitation, 030217 neurology & neurosurgery, Protein Binding, Transcription Factors
Abstract

Background: Transcription factors (TFs) play a central role in regulating gene expression by interacting with cis-regulatory DNA elements associated with their target genes. Recent surveys have examined the DNA binding specificities of most Saccharomyces cerevisiae TFs, but a comprehensive evaluation of their data has been lacking. Results: We analyzed in vitro and in vivo TF-DNA binding data reported in previous large-scale studies to generate a comprehensive, curated resource of DNA binding specificity data for all characterized S. cerevisiae TFs. Our collection comprises DNA binding site motifs and comprehensive in vitro DNA binding specificity data for all possible 8-bp sequences. Investigation of the DNA binding specificities within the basic leucine zipper (bZIP) and VHT1 regulator (VHR) TF families revealed unexpected plasticity in TF-DNA recognition: intriguingly, the VHR TFs, newly characterized by protein binding microarrays in this study, recognize bZIP-like DNA motifs, while the bZIP TF Hac1 recognizes a motif highly similar to the canonical E-box motif of basic helix-loop-helix (bHLH) TFs. We identified several TFs with distinct primary and secondary motifs, which might be associated with different regulatory functions. Finally, integrated analysis of in vivo TF binding data with protein binding microarray data lends further support for indirect DNA binding in vivo by sequence-specific TFs. Conclusions: The comprehensive data in this curated collection allow for more accurate analyses of regulatory TF-DNA interactions, in-depth structural studies of TF-DNA specificity determinants, and future experimental investigations of the TFs' predicted target genes and regulatory roles., National Human Genome Research Institute (U.S.) (grant R01 HG003420), National Human Genome Research Institute (U.S.) (grant R01 HG003985), American Heart Association (postdoctoral fellowship 10POST3650060)

Published
2011

6. Computational prediction of transcription-factor binding site locations.

Author

Bulyk ML

Subjects
Animals, Base Sequence, Binding Sites genetics, Computational Biology statistics & numerical data, DNA, Fungal genetics, Humans, Molecular Sequence Data, Predictive Value of Tests, Chromosome Mapping methods, Computational Biology methods, Transcription Factors genetics
Abstract

Identifying genomic locations of transcription-factor binding sites, particularly in higher eukaryotic genomes, has been an enormous challenge. Various experimental and computational approaches have been used to detect these sites; methods involving computational comparisons of related genomes have been particularly successful.

Published
2003
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