Combinatorial bZIP dimers display complex DNA-binding specificity landscapes

DNA-dependent formation of transcription factor pairs alters their binding specificity

(2015) Arttu Jolma et al.   NATURE

The transcription factor GABP selectively binds and activates the mutant TERT promoter in cancer

(2015) R. J. A. Bell et al.   SCIENCE

Mapping and analysis of Caenorhabditis elegans transcription factor sequence specificities

(2015) Kamesh Narasimhan et al.   eLife

ATF4 licenses C/EBPβ activity in human mesenchymal stem cells primed for adipogenesis

(2015) Daniel M Cohen et al.   eLife

Conservation of transcription factor binding specificities across 600 million years of bilateria evolution

(2015) Kazuhiro R Nitta et al.   eLife

Determination and Inference of Eukaryotic Transcription Factor Sequence Specificity

(2014) Matthew T. Weirauch et al.   CELL

DNA-binding specificities of plant transcription factors and their potential to define target genes

(2014) José M. Franco-Zorrilla et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

C/EBPα is an essential collaborator in Hoxa9/Meis1-mediated leukemogenesis

(2014) Cailin Collins et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

An oncogenic super-enhancer formed through somatic mutation of a noncoding intergenic element

(2014) M. R. Mansour et al.   SCIENCE

In Vivo RNAi Screen for BMI1 Targets Identifies TGF-β/BMP-ER Stress Pathways as Key Regulators of Neural- and Malignant Glioma-Stem Cell Homeostasis

(2013) Gaetano Gargiulo et al.   CANCER CELL

Transcriptional Regulation and Its Misregulation in Disease

(2013) Tong Ihn Lee et al.   CELL

DNA-Binding Specificities of Human Transcription Factors

(2013) Arttu Jolma et al.   CELL

Dynamic trans-Acting Factor Colocalization in Human Cells

(2013) Dan Xie et al.   CELL

CG methylated microarrays identify a novel methylated sequence bound by the CEBPB ATF4 heterodimer that is active in vivo

(2013) I. K. Mann et al.   GENOME RESEARCH

Networks of bZIP Protein-Protein Interactions Diversified Over a Billion Years of Evolution

(2013) A. W. Reinke et al.   SCIENCE

A Comprehensive Nuclear Receptor Network for Breast Cancer Cells

(2013) Ralf Kittler et al.   Cell Reports

BEDOPS: high-performance genomic feature operations

(2012) Shane Neph et al.   BIOINFORMATICS

A Validated Regulatory Network for Th17 Cell Specification

(2012) Maria Ciofani et al.   CELL

Annotation of functional variation in personal genomes using RegulomeDB

(2012) A. P. Boyle et al.   GENOME RESEARCH

A High-Throughput Chromatin Immunoprecipitation Approach Reveals Principles of Dynamic Gene Regulation in Mammals

(2012) Manuel Garber et al.   MOLECULAR CELL

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Systematic Localization of Common Disease-Associated Variation in Regulatory DNA

(2012) M. T. Maurano et al.   SCIENCE

Cooperativity in RNA-Protein Interactions: Global Analysis of RNA Binding Specificity

(2012) Zachary T. Campbell et al.   Cell Reports

MEME-ChIP: motif analysis of large DNA datasets

(2011) Philip Machanick et al.   BIOINFORMATICS

A Partner Evokes Latent Differences between Hox Proteins

(2011) Aseem Z. Ansari et al.   CELL

Cofactor Binding Evokes Latent Differences in DNA Binding Specificity between Hox Proteins

(2011) Matthew Slattery et al.   CELL

The CCAAT/enhancer (C/EBP) family of basic-leucine zipper (bZIP) transcription factors is a multifaceted highly-regulated system for gene regulation

(2011) Junichi Tsukada et al.   CYTOKINE

Transcription Factor AP1 Potentiates Chromatin Accessibility and Glucocorticoid Receptor Binding

(2011) Simon C. Biddie et al.   MOLECULAR CELL

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

(2011) Trevor Siggers et al.   NATURE IMMUNOLOGY

Systems Analysis of ATF3 in Stress Response and Cancer Reveals Opposing Effects on Pro-Apoptotic Genes in p53 Pathway

(2011) Yujiro Tanaka et al.   PLoS One

E4BP4: an unexpected player in the immune response

(2011) Victoria Male et al.   TRENDS IN IMMUNOLOGY

A User's Guide to the Encyclopedia of DNA Elements (ENCODE)

(2011)   PLOS BIOLOGY

Cross-Disorder Genomewide Analysis of Schizophrenia, Bipolar Disorder, and Depression

(2010) Jie Huang et al.   AMERICAN JOURNAL OF PSYCHIATRY

ChIPpeakAnno: a Bioconductor package to annotate ChIP-seq and ChIP-chip data

(2010) Lihua J Zhu et al.   BMC BIOINFORMATICS

Genome-wide association reveals genetic effects on human Aβ 42 and τ protein levels in cerebrospinal fluids: a case control study

(2010) Mi-Ryung Han et al.   BMC Neurology

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

(2010) Gong-Hong Wei et al.   EMBO JOURNAL

ATF3, a Hub of the Cellular Adaptive-Response Network, in the Pathogenesis of Diseases: Is Modulation of Inflammation a Unifying Component?

(2010) TSONWIN HAI et al.   GENE EXPRESSION

Multiplexed massively parallel SELEX for characterization of human transcription factor binding specificities

(2010) A. Jolma et al.   GENOME RESEARCH

Activating Transcription Factor 3 Is a Positive Regulator of Human IFNG Gene Expression

(2010) S. Filen et al.   JOURNAL OF IMMUNOLOGY

The Nrf2 System as a Potential Target for the Development of Indirect Antioxidants

(2010) Kyeong-Ah Jung et al.   MOLECULES

From noncoding variant to phenotype via SORT1 at the 1p13 cholesterol locus

(2010) Kiran Musunuru et al.   NATURE

De novo identification and biophysical characterization of transcription-factor binding sites with microfluidic affinity analysis

(2010) Polly M Fordyce et al.   NATURE BIOTECHNOLOGY

GREAT improves functional interpretation of cis-regulatory regions

(2010) Cory Y McLean et al.   NATURE BIOTECHNOLOGY

Genome-wide meta-analysis increases to 71 the number of confirmed Crohn's disease susceptibility loci

(2010) Andre Franke et al.   NATURE GENETICS

Determining the specificity of protein–DNA interactions

(2010) Gary D. Stormo et al.   NATURE REVIEWS GENETICS

Specificity landscapes of DNA binding molecules elucidate biological function

(2010) C. D. Carlson et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences

(2010) Jeremy Goecks et al.   GENOME BIOLOGY

CSI–FID: High throughput label-free detection of DNA binding molecules

(2009) Karl E. Hauschild et al.   BIOORGANIC & MEDICINAL CHEMISTRY LETTERS

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

(2009) Christian A. Grove et al.   CELL

The Importance of Being Flexible: The Case of Basic Region Leucine Zipper Transcriptional Regulators

(2009) Maria Miller   CURRENT PROTEIN & PEPTIDE SCIENCE

ATF3 transcription factor and its emerging roles in immunity and cancer

(2009) Matthew R. Thompson et al.   JOURNAL OF MOLECULAR MEDICINE-JMM

Bind-n-Seq: high-throughput analysis of in vitro protein–DNA interactions using massively parallel sequencing

(2009) Artem Zykovich et al.   NUCLEIC ACIDS RESEARCH

Fine mapping and functional analysis of a common variant in MSMB on chromosome 10q11.2 associated with prostate cancer susceptibility

(2009) H. Lou et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Diversity and Complexity in DNA Recognition by Transcription Factors

(2009) G. Badis et al.   SCIENCE

Inferring Binding Energies from Selected Binding Sites

(2009) Yue Zhao et al.   PLoS Computational Biology

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

(2008) Michael F. Berger et al.   CELL

Analysis of Homeodomain Specificities Allows the Family-wide Prediction of Preferred Recognition Sites

(2008) Marcus B. Noyes et al.   CELL

A Library of Yeast Transcription Factor Motifs Reveals a Widespread Function for Rsc3 in Targeting Nucleosome Exclusion at Promoters

(2008) Gwenael Badis et al.   MOLECULAR CELL

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY