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List of works by Martha L Bulyk

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

scientific article published on 10 February 2014

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

scientific article published on 23 August 2021

A Comprehensive Drosophila melanogaster Transcription Factor Interactome

scientific article published on 01 April 2019

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

scientific article

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

scientific article published on 15 May 2018

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

scientific article published on February 2004

A multiparameter network reveals extensive divergence between C. elegans bHLH transcription factors

scientific article

A statistical model for investigating binding probabilities of DNA nucleotide sequences using microarrays

scientific article

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

scientific article

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

scientific article

An evolutionarily conserved enhancer regulates Bmp4 expression in developing incisor and limb bud.

scientific article

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

scientific article published on January 2006

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

article

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

scientific article published on 23 February 2007

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

scientific article

Bioinformatic and molecular investigation of Sirt3 expression.

scientific article published in June 2012

Biological code breaking in the 21st century

scientific article published on 2 May 2006

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

scientific article published on 27 February 2019

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

scientific article published on 29 September 2016

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

scientific article published on 23 November 2020

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

scientific article (publication date: 24 September 2006)

Computational prediction of transcription-factor binding site locations

scientific article

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

scientific article

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

scientific article published on 24 December 2019

Context influences on TALE-DNA binding revealed by quantitative profiling

scientific article published on 11 June 2015

Contribution of distinct homeodomain DNA binding specificities to Drosophila embryonic mesodermal cell-specific gene expression programs

scientific article

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

scientific article

DNA binding site analysis of Burkholderia thailandensis response regulators.

scientific article

DNA microarray technologies for measuring protein-DNA interactions

scientific article published on 12 July 2006

DNA sequence preferences of transcriptional activators correlate more strongly than repressors with nucleosomes

scientific article published on July 2012

DNA-binding and -bending activities of SAP30L and SAP30 are mediated by a zinc-dependent module and monophosphoinositides

scientific article

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

scientific article published on 08 July 2013

Design of compact, universal DNA microarrays for protein binding microarray experiments

scientific article

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

scientific article published in March 2018

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

scientific article published on 29 February 2012

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

scientific article published on 28 March 2018

Discovering DNA regulatory elements with bacteria

scientific article

Distant cis-regulatory elements in human skeletal muscle differentiation.

scientific article published on 23 August 2011

Distinguishing direct versus indirect transcription factor-DNA interactions

scientific article

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

scientific article published on 17 July 2014

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

scientific article published on 25 April 2018

Diversity and complexity in DNA recognition by transcription factors

scientific article (publication date: 26 June 2009)

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

scientific article published on February 10, 2012

EP300 Selectively Controls the Enhancer Landscape of MYCN-Amplified Neuroblastoma

scientific article published on 01 March 2022

Evaluation of methods for modeling transcription factor sequence specificity

scientific article published on 27 January 2013

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

scientific article

Expression-guided in silico evaluation of candidate cis regulatory codes for Drosophila muscle founder cells

scientific article

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

scientific article published on 29 July 2011

Functional trends in structural classes of the DNA binding domains of regulatory transcription factors.

scientific article published on January 2008

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

scientific article

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

scientific article

Genomes and evolution: advances in deciphering the genomics of gene regulation in evolution

scientific article published on 22 November 2009

Genomic Regions Flanking E-Box Binding Sites Influence DNA Binding Specificity of bHLH Transcription Factors through DNA Shape ⬇️

scientific article published on April 4, 2013

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

scientific article

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

scientific article

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

scientific article

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

scientific article published on September 2017

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

scientific article published in December 2017

Identification of cell cycle-regulated, putative hyphal genes in Candida albicans ⬇️

scientific article published on January 1, 2012

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

scientific article published on 17 April 2007

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

scientific article published on 13 April 2010

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

scientific article

Integrative functional genomics

scientific article

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

scientific article published on 01 July 2019

Intrinsic disorder within and flanking the DNA-binding domains of human transcription factors ⬇️

scientific article published on January 1, 2012

Jury remains out on simple models of transcription factor specificity

scientific article published on 7 June 2011

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

scientific article published on 29 June 2020

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

scientific article published on April 5, 2012

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

scientific article published on January 13, 2011

List of Contributors

MEDEA: analysis of transcription factor binding motifs in accessible chromatin

scientific article published on 18 May 2020

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

scientific article published on February 2014

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

scientific article

Meta-profiles of gene expression during aging: limited similarities between mouse and human and an unexpectedly decreased inflammatory signature

scientific article

Microarray analyses of newborn mouse ovaries lacking Nobox

scientific journal article

Modular evolution of DNA-binding preference of a Tbrain transcription factor provides a mechanism for modifying gene regulatory networks

scientific article

Modulefinder: a tool for computational discovery of cis regulatory modules

scientific article published on January 2005

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

scientific article published on February 2012

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

scientific article

Mutations in the RNA granule component TDRD7 cause cataract and glaucoma

scientific article

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

scientific article

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

scientific article published on 06 December 2011

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

scientific article

Notch and MAML-1 complexation do not detectably alter the DNA binding specificity of the transcription factor CSL

scientific article

Nuclear respiratory factor 2 induces SIRT3 expression.

scientific article published on 24 June 2015

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

scientific article

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

scientific article

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

scientific article

Polycomb-like proteins link the PRC2 complex to CpG islands.

scientific article published on 6 September 2017

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

scientific article published on 22 April 2010

Precision Medicine: Improving health through high-resolution analysis of personal data

scientific article published on 01 January 2019

Predicting the binding preference of transcription factors to individual DNA k-mers.

scientific article published on 16 December 2008

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

scientific article published on November 20, 2011

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

scientific article published on January 2006

Protein binding microarrays for the characterization of DNA-protein interactions

scientific article published on January 2007

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

scientific article published on 20 December 2021

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

scientific article

STAT3 Activation of miR-21 and miR-181b-1 via PTEN and CYLD Are Part of the Epigenetic Switch Linking Inflammation to Cancer ⬇️

scientific article published on August 27, 2010

Short-term calorie restriction in male mice feminizes gene expression and alters key regulators of conserved aging regulatory pathways

scientific article published in 2009

Specific DNA-binding by apicomplexan AP2 transcription factors

scientific article (publication date: 17 June 2008)

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

scientific article

Systematic identification of mammalian regulatory motifs' target genes and functions

scientific article published on 02 March 2008

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

scientific article published on July 2013

The NF-κB genomic landscape in lymphoblastoid B cells

scientific article

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

scientific article published on 4 August 2008

The multiple mechanisms that regulate p53 activity and cell fate

scientific article published on 01 April 2019

Toward a systems-level understanding of developmental regulatory networks

scientific article published on 09 October 2008

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

scientific article published on 08 April 2022

Transcription factor-DNA binding: beyond binding site motifs.

scientific article published on 27 March 2017

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

scientific article published on 05 November 2019

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

scientific article published on February 2009

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

scientific article

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

scientific article

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

scientific article

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

scientific article

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

scientific article

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

scientific article

Variation in homeodomain DNA binding revealed by high-resolution analysis of sequence preferences

scientific article published on June 2008

Workshop during the Pacific Symposium of Biocomputing, Jan 3-7, 2019: Reading between the genes: interpreting non-coding DNA in high-throughput

scientific article published on 01 January 2019

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

scientific article published on 01 January 2021

iSyTE: integrated Systems Tool for Eye gene discovery.

scientific article published on 21 March 2012

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

scientific article published on 21 August 2017

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