M. Bulyk

发表

Variation in Homeodomain DNA Binding Revealed by High-Resolution Analysis of Sequence Preferences

Daniel E. Newburger, Esther T. Chan, Trevis M. Alleyne, 2008, Cell.

UniPROBE, update 2011: expanded content and search tools in the online database of protein-binding microarray data on protein–DNA interactions

Martha L. Bulyk, Kimberly Robasky, K. Robasky, 2010, Nucleic Acids Res..

Computational prediction of transcription-factor binding site locations

M. Bulyk, 2003, Genome Biology.

Rapid analysis of the DNA-binding specificities of transcription factors with DNA microarrays

R. Young, M. Berger, M. Bulyk, 2004, Nature Genetics.

Specific DNA-binding by Apicomplexan AP2 transcription factors

Andrew R. Gehrke, Kellen L. Olszewski, M. Bulyk, 2008, Proceedings of the National Academy of Sciences.

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

M. Berger, M. Bulyk, N. Wingreen, 2008, Molecular microbiology.

Genome-wide promoter analysis of the SOX4 transcriptional network in prostate cancer cells.

Colleen D. McCabe, M. Berger, M. Bulyk, 2009, Cancer research.

High-resolution DNA-binding specificity analysis of yeast transcription factors.

Daniel E. Newburger, A. Philippakis, M. Berger, 2009, Genome research.

Transcriptional regulation and stabilization of left-right neuronal identity in C. elegans.

Andrew R. Gehrke, Cori Bargmann, M. Bulyk, 2009, Genes & development.

Diversity and Complexity in DNA Recognition by Transcription Factors

Daniel E. Newburger, Esther T. Chan, Andrew R. Gehrke, 2009, Science.

Compact, universal DNA microarrays to comprehensively determine transcription-factor binding site specificities

A. Philippakis, M. Berger, M. Bulyk, 2006, Nature Biotechnology.

Genome-wide analysis of ETS-family DNA-binding in vitro and in vivo

Andrew R. Gehrke, T. Hughes, Shaheynoor Talukder, 2010, The EMBO journal.

Exploring the DNA-binding specificities of zinc fingers with DNA microarrays

G. Church, M. Bulyk, X. Huang, 2001, Proceedings of the National Academy of Sciences of the United States of America.

A Multiparameter Network Reveals Extensive Divergence between C. elegans bHLH Transcription Factors

Daniel E. Newburger, Christian A. Grove, Mark J Alkema, 2009, Cell.

Using protein design algorithms to understand the molecular basis of disease caused by protein–DNA interactions: the Pax6 example

M. Bulyk, L. Serrano, F. De Masi, 2010, Nucleic acids research.

Nucleotides of transcription factor binding sites exert interdependent effects on the binding affinities of transcription factors.

G. Church, M. Bulyk, Philip L. F. Johnson, 2002, Nucleic acids research.

Protein binding microarrays (PBMs) for rapid, high-throughput characterization of the sequence specificities of DNA binding proteins.

M. Berger, M. Bulyk, 2006, Methods in molecular biology.

Survey of variation in human transcription factors reveals prevalent DNA binding changes

Jaie C. Woodard, M. Daly, Manolis Kellis, 2016, Science.

Universal protein-binding microarrays for the comprehensive characterization of the DNA-binding specificities of transcription factors

M. Berger, M. Bulyk, 2009, Nature Protocols.

Evaluation of methods for modeling transcription factor sequence specificity

Atina G. Coté, R. Norel, T. Hughes, 2013, Nature Biotechnology.

The multiple mechanisms that regulate p53 activity and cell fate

M. Bulyk, G. Lahav, Antonina Hafner, 2019, Nature Reviews Molecular Cell Biology.

p53 pulses lead to distinct patterns of gene expression albeit similar DNA-binding dynamics

Jeremy E Purvis, Galit Lahav, Martha L Bulyk, 2017, Nature Structural &Molecular Biology.

Highly parallel assays of tissue-specific enhancers in whole Drosophila embryos

Martha L. Bulyk, Brian W. Busser, Stephen S. Gisselbrecht, 2013, Nature Methods.

Precise temporal control of the eye regulatory gene Pax6 via enhancer-binding site affinity.

Martha L Bulyk, Yingzi Yue, M. Bulyk, 2010, Genes & development.

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

Raluca Gordân, Martha L Bulyk, M. Bulyk, 2011, Genome Biology.

transcription factors High-resolution DNA-binding specificity analysis of yeast Material Supplemental

Anthony A. Philippakis, Martha L. Bulyk, Yanhui Hu, 2009 .

Additivity in protein-DNA interactions: how good an approximation is it?

G. Stormo, M. Bulyk, P. Benos, 2002, Nucleic acids research.

DNA microarray technologies for measuring protein-DNA interactions.

Martha L Bulyk, M. Bulyk, 2006, Current opinion in biotechnology.

A transcriptional signature and common gene networks link cancer with lipid metabolism and diverse human diseases.

K. Struhl, S. Jaeger, M. Bulyk, 2010, Cancer cell.

Principles of dimer-specific gene regulation revealed by a comprehensive characterization of NF-κB family DNA binding

J. Ragoussis, M. Bulyk, Trevor Siggers, 2011, Nature Immunology.

A Comprehensive Drosophila melanogaster Transcription Factor Interactome

Stephen S. Gisselbrecht, M. Bulyk, B. Deplancke, 2019, Cell reports.

Transcriptional Silencers in Drosophila Serve a Dual Role as Transcriptional Enhancers in Alternate Cellular Contexts.

Stephen S. Gisselbrecht, M. Bulyk, J. Dekker, 2019, Molecular cell.

Integrative analysis of the zinc finger transcription factor Lame duck in the Drosophila myogenic gene regulatory network

Ting Ni, Ivan Ovcharenko, Di Huang, 2012, Proceedings of the National Academy of Sciences.

The CLAMP protein links the MSL complex to the X chromosome during Drosophila dosage compensation.

Michael Y Tolstorukov, Peter J Park, Martha L Bulyk, 2013, Genes & development.

MEDEA: analysis of transcription factor binding motifs in accessible chromatin

Stephen S. Gisselbrecht, M. Bulyk, S. Gisselbrecht, 2020, Genome research.

Transcription factor-DNA binding: beyond binding site motifs.

M. Bulyk, K. Kock, S. Inukai, 2017, Current opinion in genetics & development.

A motif co-occurrence approach for genome-wide prediction of transcription-factor-binding sites in Escherichia coli.

G. Church, M. Bulyk, A. McGuire, 2004, Genome research.

Genomic regions flanking E-box binding sites influence DNA binding specificity of bHLH transcription factors through DNA shape.

M. Bulyk, Tianyin Zhou, R. Gordân, 2013, Cell reports.

Jury remains out on simple models of transcription factor specificity

T. Hughes, Q. Morris, M. Bulyk, 2011, Nature Biotechnology.

Identification of Human Lineage-Specific Transcriptional Coregulators Enabled by a Glossary of Binding Modules and Tunable Genomic Backgrounds.

M. Bulyk, Anastasia Vedenko, Luis A. Barrera, 2017, Cell systems.

Dual transcriptional activator and repressor roles of TBX20 regulate adult cardiac structure and function.

M. Bulyk, M. Nóbrega, Soo-young Park, 2012, Human molecular genetics.

DNA Sequence Preferences of Transcriptional Activators Correlate More Strongly than Repressors with Nucleosomes

S. Teichmann, M. Bulyk, M. Babu, 2012, Molecular cell.

Protein binding microarrays for the characterization of DNA-protein interactions.

Martha L Bulyk, M. Bulyk, 2007, Advances in biochemical engineering/biotechnology.

Approaching a complete repository of sequence-verified protein-encoding clones for Saccharomyces cerevisiae.

Yanhui Hu, Bhupinder Bhullar, Joshua LaBaer, 2007, Genome research.

DNA binding site analysis of Burkholderia thailandensis response regulators.

Elizabeth Hong-Geller, Martha L Bulyk, John Dunbar, 2012, Journal of microbiological methods.

Machine learning classification of cell-specific cardiac enhancers uncovers developmental subnetworks regulating progenitor cell division and cell fate specification

Martha L. Bulyk, Ivan Ovcharenko, Neal Jeffries, 2014, Development.

Noncooperative interactions between transcription factors and clustered DNA binding sites enable graded transcriptional responses to environmental inputs.

Guido Tiana, Luca Giorgetti, Paolo Milani, 2010, Molecular cell.

Contribution of Distinct Homeodomain DNA Binding Specificities to Drosophila Embryonic Mesodermal Cell-Specific Gene Expression Programs

A. Michelson, M. Bulyk, Caitlin E. Gamble, 2013, PloS one.

Differential regulation of mesodermal gene expression by Drosophila cell type-specific Forkhead transcription factors

A. Michelson, M. Bulyk, A. Aboukhalil, 2012, Development.

DNA-binding specificity changes in the evolution of forkhead transcription factors

Martha L. Bulyk, So Nakagawa, Stephen S. Gisselbrecht, 2013, Proceedings of the National Academy of Sciences.

DNA-Binding and -Bending Activities of SAP30L and SAP30 Are Mediated by a Zinc-Dependent Module and Monophosphoinositides

M. Bulyk, Trevor Siggers, M. Mäki, 2008, Molecular and Cellular Biology.

Applying whole-genome studies of epigenetic regulation to study human disease

S. Henikoff, M. Bulyk, J. Lieb, 2006, Cytogenetic and Genome Research.

Trans-omics analysis of insulin action reveals a cell growth subnetwork which co-regulates anabolic processes

N. Perrimon, M. Bulyk, Yanhui Hu, 2022, iScience.

Short-Term Calorie Restriction in Male Mice Feminizes Gene Expression and Alters Key Regulators of Conserved Aging Regulatory Pathways

M. Bulyk, Preston W. Estep, J. Warner, 2009, PloS one.

Screening of PCRP transcription factor antibodies in biochemical assays

Bryan J Venters, Bryan J. Venters, William K. M. Lai, 2020 .

Objective sequence-based subfamily classifications of mouse homeodomains reflect their in vitro DNA-binding preferences

Andrei L. Turinsky, Andrew R. Gehrke, T. Hughes, 2010, Nucleic acids research.

interactions Distinguishing direct versus indirect transcription factor-DNA

M. Bulyk, R. Gordân, A. Hartemink, 2009 .

GA-repeats on mammalian X chromosomes support Ohno’s hypothesis of dosage compensation by transcriptional upregulation

Peter W. Markstein, M. Bulyk, Vicky Markstein, 2018, bioRxiv.

Zinc Finger Protein SALL4 Functions through an AT-Rich Motif to Regulate Gene Expression

Kol Jia Yong, Mahmoud A. Bassal, Hong Kee Tan, 2020, bioRxiv.

Toward a systems-level understanding of developmental regulatory networks.

A. Michelson, M. Bulyk, B. Busser, 2008, Current opinion in genetics & development.

Extensive characterization of NF-κB binding uncovers non-canonical motifs and advances the interpretation of genetic functional traits

Martha Bulyk, Jiannis Ragoussis, Peter Humburg, 2011, Genome Biology.

Loss of the p16INK4a and p15INK4b genes, as well as neighboring 9p21 markers, in sporadic melanoma.

M. Bulyk, D. Housman, N. Hayward, 1996, Cancer research.

Conservation and regulatory associations of a wide affinity range of mouse transcription factor binding sites.

Esther T. Chan, T. Hughes, M. Berger, 2010, Genomics.

Precision Medicine: Addressing the Challenges of Sharing, Analysis, and Privacy at Scale.

Alexander A. Morgan, M. Bulyk, S. Brenner, 2019, Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing.

Bispecific Forkhead Transcription Factor FoxN3 Recognizes Two Distinct Motifs with Different DNA Shapes.

M. Bulyk, S. Blacklow, J. Rogers, 2019, Molecular cell.

Diversification of transcription factor–DNA interactions and the evolution of gene regulatory networks

M. Bulyk, J. Rogers, 2018, Wiley interdisciplinary reviews. Systems biology and medicine.

Context and number of noncanonical repeat variable diresidues impede the design of TALE proteins with improved DNA targeting

M. Bulyk, Luis A. Barrera, J. Rogers, 2019, Protein science : a publication of the Protein Society.

Bispecific Forkhead Trans cription Factor FoxN 3 Recognizes Two Distinct Motifs with Different DNA Shapes Graphical

M. Bulyk, S. Blacklow, J. Rogers, 2019 .

Comparative chromatin accessibility upon BDNF stimulation delineates neuronal regulatory elements

Judith B. Zaugg, M. Bulyk, M. Savitski, 2022, Molecular systems biology.

Lineage-specific control of convergent differentiation by a Forkhead repressor

M. Bulyk, J. Murray, J. Rogers, 2019, bioRxiv.

Neural-specific Sox2 input and differential Gli-binding affinity provide context and positional information in Shh-directed neural patterning.

Alexander van Oudenaarden, Wing H Wong, Timothy L Bailey, 2012, Genes & development.

Saccharomyces cerevisiaeprotein-encoding clones for Approaching a complete repository of sequence-verified data

Janice, M. Berger, M. Bulyk, 2007 .

Loss of the pJ 6 INK 4 aand @ 15 INK 4 bGenes , as well as Neighboring 9 p 2 i Markers , in Sporadic Melanoma 1

M. Bulyk, D. Housman, N. Hayward, 2022 .

Podocyte lineage marker expression is preserved across Wilms tumor subtypes and enhanced in tumors harboring the SIX1/2 p.Q177R mutation

Stephen S. Gisselbrecht, M. Bulyk, S. Gisselbrecht, 2022, bioRxiv.

The histone acetyltransferase KAT6A is recruited to unmethylated CpG islands via a DNA binding winged helix domain

Stephen S. Gisselbrecht, M. Bulyk, S. Gisselbrecht, 2022, Nucleic acids research.

Inferring condition‐specific transcription factor function from DNA binding and gene expression data

A. Philippakis, M. Berger, M. Bulyk, 2007 .

EP300 Selectively Controls the Enhancer Landscape of MYCN-Amplified Neuroblastoma

M. Bulyk, A. Look, K. Stegmaier, 2021, Cancer discovery.

LUX ARRHYTHMO Encodes a Nighttime Repressor of Circadian Gene Expression in the Arabidopsis Core Clock

Martha L. Bulyk, Steve A. Kay, Andrew R. Gehrke, 2011, Current Biology.

Interspecies analysis of MYC targets identifies tRNA synthetases as mediators of growth and survival in MYC-overexpressing cells

N. Perrimon, S. Elledge, M. Bulyk, 2019, Proceedings of the National Academy of Sciences.

Non-DNA-binding cofactors enhance DNA-binding specificity of a transcriptional regulatory complex

Martha L Bulyk, M. Bulyk, Trevor Siggers, 2011, Molecular systems biology.

Using a structural and logics systems approach to infer bHLH–DNA binding specificity determinants

Martha L. Bulyk, Andreu Alibés, Christian A. Grove, 2011, Nucleic acids research.

iSyTE: integrated Systems Tool for Eye gene discovery.

Peter J Park, Martha L Bulyk, Anton Aboukhalil, 2012, Investigative ophthalmology & visual science.

Distant cis-regulatory elements in human skeletal muscle differentiation.

M. Bulyk, R. McCord, Vicky W. Zhou, 2011, Genomics.

STAT3 activation of miR-21 and miR-181b-1 via PTEN and CYLD are part of the epigenetic switch linking inflammation to cancer.

Kevin Struhl, Martha L Bulyk, Dimitrios Iliopoulos, 2010, Molecular cell.

Direct Promoter Repression by BCL11A Controls the Fetal to Adult Hemoglobin Switch

Martha L. Bulyk, Guo-Cheng Yuan, Qian Zhu, 2018, Cell.

An Evolutionarily Conserved Enhancer Regulates Bmp4 Expression in Developing Incisor and Limb Bud

Martha L. Bulyk, Joshua W. K. Ho, Bjorn R. Olsen, 2012, PloS one.

Supplemental Information Dna Sequence Preferences of Transcriptional Activators Correlate More Strongly than Repressors with Nucleosomes Supplemental Experimental Procedures

S. Teichmann, M. Bulyk, M. Babu, 2022 .

Gene Regulatory Networks

M. Bulyk, A. J. Walhout, A. Walhout, 2013 .

Molecular mechanism underlying the regulatory specificity of a Drosophila homeodomain protein that specifies myoblast identity

Martha L. Bulyk, Michael F. Berger, Brian W. Busser, 2012, Development.

Quantitative-enhancer-FACS-seq (QeFS) reveals epistatic interactions among motifs within transcriptional enhancers in developing Drosophila tissue

M. Bulyk, S. Gisselbrecht, T. Cafarelli, 2021, Genome Biology.

Quantitative-enhancer-FACS-seq (QeFS) reveals epistatic interactions among motifs within transcriptional enhancers in developing Drosophila tissue

M. Bulyk, S. Gisselbrecht, T. Cafarelli, 2021, Genome biology.

A ChIP-exo screen of 887 Protein Capture Reagents Program transcription factor antibodies in human cells

Bryan J. Venters, William K. M. Lai, A. Shilatifard, 2021, Genome research.

A ChIP-exo screen of 887 PCRP transcription factor antibodies in human cells

Bryan J. Venters, William K. M. Lai, A. Shilatifard, 2020, bioRxiv.

Context influences on TALE–DNA binding revealed by quantitative profiling

Jeffry D. Sander, Manolis Kellis, J. Joung, 2015, Nature Communications.

Diversification of transcription factor paralogs via noncanonical modularity in C2H2 zinc finger DNA binding.

M. Bulyk, Trevor Siggers, J. Reddy, 2014, Molecular cell.

71 Genomic regions flanking E-box binding sites influence DNA binding specificity of bHLH transcription factors through DNA shape

M. Bulyk, Tianyin Zhou, R. Gordân, 2013 .

Bayesian hierarchical model of protein-binding microarray k-mer data reduces noise and identifies transcription factor subclasses and preferred k-mers

Martha L. Bulyk, Bo Jiang, Jun S. Liu, 2013, Bioinform..

Distinguishing Direct versus Indirect Transcription Factor-DNA Interactions

Martha L. Bulyk, Alexander J. Hartemink, Raluca Gordân, 2010, RECOMB.

Distinguishing direct versus indirect transcription factor-DNA interactions.

Raluca Gordân, Martha L Bulyk, Alexander J Hartemink, 2009, Genome research.

Bulyk interactions DNA − Distinguishing direct versus indirect transcription factor Material Supplemental

M. Bulyk, R. Gordân, A. Hartemink, 2009 .

interactionsdirect versus indirect transcription factor-DNA

M. Bulyk, R. Gordân, A. Hartemink, 2009 .

Common variants in signaling transcription-factor-binding sites drive phenotypic variability in red blood cell traits

J. Rinn, R. Young, L. Zon, 2020, Nature Genetics.

A direct fate exclusion mechanism by Sonic hedgehog-regulated transcriptional repressors

M. Bulyk, A. McMahon, Winston A Hide, 2015, Development.

patterning provide context and positional information in Shh-directed neural Neural-specific Sox 2 input and differential Gli-binding affinity

T. Mikkelsen, A. Oudenaarden, W. Wong, 2012 .

UniPROBE, update 2015: new tools and content for the online database of protein-binding microarray data on protein–DNA interactions

Martha L. Bulyk, Stephen S. Gisselbrecht, Maxwell A. Hume, 2014, Nucleic Acids Res..

Expansion of GA Dinucleotide Repeats Increases the Density of CLAMP Binding Sites on the X-Chromosome to Promote Drosophila Dosage Compensation

W. Liu, M. Bulyk, Lin Yang, 2016, PLoS genetics.

LIN28B regulates transcription and potentiates MYCN-induced neuroblastoma through binding to ZNF143 at target gene promotors

John T. Powers, R. Young, K. Ross, 2020, Proceedings of the National Academy of Sciences.

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

Martha L. Bulyk, Levi Waldron, Curtis Huttenhower, 2016, Genome Biology.

Meta-analysis discovery of tissue-specific DNA sequence motifs from mammalian gene expression data

Martha L. Bulyk, Bertrand R. Huber, M. Bulyk, 2006, BMC Bioinformatics.

Systematic identification of mammalian regulatory motifs' target genes and functions

Fangxue Sherry He, Martha L Bulyk, A. Philippakis, 2008, Nature Methods.

ModuleFinder: A Tool for Computational Discovery of Cis Regulatory Modules

Anthony A. Philippakis, Fangxue Sherry He, Martha L. Bulyk, 2004, Pacific Symposium on Biocomputing.

Modular Evolution of DNA-Binding Preference of a Tbrain Transcription Factor Provides a Mechanism for Modifying Gene Regulatory Networks

Martha L. Bulyk, Veronica F. Hinman, M. Bulyk, 2014, Molecular biology and evolution.

5'RNA-Seq identifies Fhl1 as a genetic modifier in cardiomyopathy.

J. Seidman, M. Bulyk, P. D. De Jager, 2014, The Journal of clinical investigation.

Nuclear respiratory factor 2 induces SIRT3 expression

M. Bulyk, F. Satterstrom, M. Haigis, 2015, Aging cell.

A feed-forward relay integrates the regulatory activities of Bicoid and Orthodenticle via sequential binding to suboptimal sites

M. Bulyk, S. Small, Jesse V. Kurland, 2018, Genes & development.

A feed-forward relay between Bicoid and Orthodenticle regulates the timing of embryonic patterning in Drosophila

M. Bulyk, S. Small, Jesse V. Kurland, 2017, bioRxiv.

UniPROBE: an online database of protein binding microarray data on protein–DNA interactions

Martha L. Bulyk, Daniel E. Newburger, M. Bulyk, 2008, Nucleic Acids Res..

Transcriptional Silencers: Driving Gene Expression with the Brakes On.

Stephen S. Gisselbrecht, M. Bulyk, S. Gisselbrecht, 2021, Trends in genetics : TIG.

Differential Occupancy of Two GA-Binding Proteins Promotes Targeting of the Drosophila Dosage Compensation Complex to the Male X Chromosome

Nicolas L. Fawzi, M. Bulyk, M. Tolstorukov, 2018, Cell reports.

Notch and MAML-1 Complexation Do Not Detectably Alter the DNA Binding Specificity of the Transcription Factor CSL

Martha L. Bulyk, Stephen C. Blacklow, Michael F. Berger, 2010, PloS one.

Design of Compact, Universal DNA Microarrays for Protein Binding Microarray Experiments

Anthony A. Philippakis, Martha L. Bulyk, Aaron M. Qureshi, 2007, RECOMB.

Microarray Analyses of Newborn Mouse Ovaries Lacking Nobox1

Martha L Bulyk, Yingying Qin, Michael F Berger, 2007, Biology of reproduction.

The NF-κB genomic landscape in lymphoblastoid B cells.

Manolis Kellis, Elliott Kieff, Bo Zhao, 2014, Cell reports.

Cell Reports Resource The NFk B Genomic Landscape in Lymphoblastoid B Cells

Manolis Kellis, M. Bulyk, E. Kieff, 2014 .

Mutations in the RNA Granule Component TDRD7 Cause Cataract and Glaucoma

Fowzan S Alkuraya, Martha L Bulyk, Anton Aboukhalil, 2011, Science.

Quantifying DNA–protein interactions by double-stranded DNA arrays

Martha L. Bulyk, George M. Church, David J. Lockhart, 1999, Nature Biotechnology.

Comparative chromatin accessibility upon BDNF-induced neuronal activity delineates neuronal regulatory elements

Judith B. Zaugg, M. Bulyk, M. Savitski, 2021, bioRxiv.

Expression-Guided In Silico Evaluation of Candidate Cis Regulatory Codes for Drosophila Muscle Founder Cells

Anthony A. Philippakis, Fangxue Sherry He, Martha L. Bulyk, 2006, PLoS Comput. Biol..

Inferring condition-specific transcription factor function from DNA binding and gene expression data

Rachel Patton McCord, Martha L Bulyk, Michael F Berger, 2007, Molecular systems biology.

Direct Promoter Repression by BCL 11 A Controls the Fetal to Adult Hemoglobin Switch Graphical Abstract Highlights

M. Bulyk, S. Orkin, Qian Zhu, 2018 .

Lineage-specific control of convergent cell identity by a Forkhead repressor

M. Bulyk, J. Rogers, S. Shaham, 2019 .

The SAM domain-containing protein 1 (SAMD1) acts as a repressive chromatin regulator at unmethylated CpG islands

M. Bulyk, Yang Shi, T. Stiewe, 2021, Science Advances.

Ancient mechanisms for the evolution of the bicoid homeodomain's function in fly development

M. Bulyk, S. Small, J. Rogers, 2018, eLife.

Polycomb-like proteins link the PRC2 complex to CpG islands

M. Bulyk, D. Patel, Yang Shi, 2017, Nature.

Computational comparison of two draft sequences of the human genome

Martha L. Bulyk, Jay Shendure, George M. Church, 2001, Nature.

Multi-step control of muscle diversity by Hox proteins in the Drosophila embryo

A. Philippakis, A. Michelson, M. Bulyk, 2010, Development.

Meta-Profiles of Gene Expression during Aging: Limited Similarities between Mouse and Human and an Unexpectedly Decreased Inflammatory Signature

Martha L. Bulyk, Andrew Johnston, William R. Swindell, 2012, PloS one.

MORF and MOZ acetyltransferases target unmethylated CpG islands through the winged helix domain

M. Bulyk, Christopher C. Ebmeier, Yawen Bai, 2023, Nature Communications.

Phosphorylation of the chromatin remodeling factor DPF3a induces cardiac hypertrophy through releasing HEY repressors from DNA

M. Berger, M. Bulyk, S. Sauer, 2015, Nucleic acids research.

Analysis of sequence specificities of DNA-binding proteins with protein binding microarrays.

Martha L Bulyk, M. Bulyk, 2006, Methods in enzymology.

Grhl2 is required in nonneural tissues for neural progenitor survival and forebrain development

M. Bulyk, Trevor Siggers, D. Beier, 2015, Genesis.

Blood cell traits’ GWAS loci colocalization with variation in PU.1 genomic occupancy prioritizes causal noncoding regulatory variants

M. Bulyk, Raehoon Jeong, 2023, Cell genomics.

Colocalization of blood cell traits GWAS associations and variation in PU.1 genomic occupancy prioritizes causal noncoding regulatory variants

M. Bulyk, Raehoon Jeong, 2023, bioRxiv.

as a genetic modifier in cardiomyopathy

M. Bulyk, A. Aboukhalil, C. Seidman, 2014 .

Computational Challenges and Artificial Intelligence in Precision Medicine

Dana C. Crawford, Steven E. Brenner, Joanne Berghout, 2020, PSB.

Faculty Opinions recommendation of Crosstalk between C/EBPbeta phosphorylation, arginine methylation, and SWI/SNF/Mediator implies an indexing transcription factor code.

M. Bulyk, 2010 .

Biological code breaking in the 21st century

A. Michelson, M. Bulyk, 2006, Molecular systems biology.

Intrinsic Disorder Within and Flanking the DNA-Binding Domains of Human Transcription Factors

Xin Guo, Martha L. Bulyk, Alexander J. Hartemink, 2011, Pacific Symposium on Biocomputing.

SYSTEMS BIOLOGY: GLOBAL REGULATION OF GENE EXPRESSION

M. Bulyk, H. Bussemaker, B. Bernstein, 2010 .

Genome-wide analysis of ETS-family DNA-binding in vitro and in vivo

Andrew R. Gehrke, T. Hughes, Shaheynoor Talukder, 2010, The EMBO journal.

DNA binding analysis of rare variants in homeodomains reveals novel homeodomain specificity-determining residues

R. Irizarry, M. Bulyk, S. Blacklow, 2023, bioRxiv.

Inferring Condition-Specific Transcription Factor Function from DNA Binding and Gene Expression Data

A. Philippakis, M. Bulyk, Rachel Patton McCord, 2007 .

Precision Medicine: Using Artificial Intelligence to Improve Diagnostics and Healthcare.

Jonathan H. Chen, M. Bulyk, S. Brenner, 2021, Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing.

A stem cell epigenome is associated with primary nonresponse to CD19 CAR T cells in pediatric acute lymphoblastic leukemia

M. Bulyk, Jun S. Wei, Chaoyu Wang, 2023, Blood advances.

Genome-wide analysis of ETS-family DNA-binding in vitro and in vivo

Andrew R. Gehrke, T. Hughes, Shaheynoor Talukder, 2010, The EMBO journal.

iSyTE: integrated Systems Tool for Eye gene discovery.

Daniel J. O'Connell, P. Park, M. Bulyk, 2012, Investigative ophthalmology & visual science.

Diversity and Complexity in DNA Recognition by Transcription Factors

Daniel E. Newburger, Esther T. Chan, Andrew R. Gehrke, 2009, Science.

Survey of variation in human transcription factors reveals prevalent DNA binding changes

Jaie C. Woodard, Stephen S. Gisselbrecht, M. Daly, 2016, Science.

UniPROBE, update 2011: expanded content and search tools in the online database of protein-binding microarray data on protein–DNA interactions

K. Robasky, M. Bulyk, 2010, Nucleic Acids Res..

A transcriptional signature and common gene networks link cancer with lipid metabolism and diverse human diseases.

K. Struhl, S. Jaeger, M. Bulyk, 2010, Cancer cell.

Universal protein-binding microarrays for the comprehensive characterization of the DNA-binding specificities of transcription factors

M. Berger, M. Bulyk, 2009, Nature Protocols.

UniPROBE: an online database of protein binding microarray data on protein–DNA interactions

Daniel E. Newburger, M. Bulyk, 2008, Nucleic Acids Res..

Variation in Homeodomain DNA Binding Revealed by High-Resolution Analysis of Sequence Preferences

Daniel E. Newburger, Esther T. Chan, Trevis M. Alleyne, 2008, Cell.

A Statistical Model for Investigating Binding Probabilities of DNA Nucleotide Sequences Using Microarrays

G A Whitmore, G. A. Whitmore, Mei-Ling Ting Lee, 2002, Biometrics.

Bioinformatic and molecular investigation of Sirt3 expression

M. Bulyk, F. Satterstrom, M. Haigis, 2012, BMC Proceedings.

Meta-analysis discovery of tissue-specific DNA sequence motifs from mammalian gene expression data

M. Bulyk, B. Huber, 2006, BMC Bioinformatics.

MVB-12, a Fourth Subunit of Metazoan ESCRT-I, Functions in Receptor Downregulation

M. Bulyk, Bertrand R. Huber, 2006, BMC Bioinformatics.

Faculty Opinions recommendation of Telomerase reactivation reverses tissue degeneration in aged telomerase-deficient mice.

M. Bulyk, Preston W. Estep, 2011 .

Monophosphoinositides Zinc-dependent Module and Sap30l and Sap30 Are Mediated by a Dna-binding and -bending Activities of Supplemental Material

M. Bulyk, Trevor Siggers, J. Valjakka, 2008 .

LOESS correction for length variation in gene set-based genomic sequence analysis

Martha L. Bulyk, Anton Aboukhalil, M. Bulyk, 2012, Bioinform..

Genome-wide analysis of ETS-family DNA-binding in vitro and in vivo

Shaheynoor Talukder, E. Ukkonen, Gwenael Badis, 2010, The EMBO journal.

Specific DNA-binding by Apicomplexan AP2 transcription factors

Andrew R. Gehrke, Kellen L. Olszewski, M. Bulyk, 2008, Proceedings of the National Academy of Sciences.

Lineage-specific control of convergent cell identity by a Forkhead repressor

M. Bulyk, J. Rogers, S. Shaham, 2019 .