Prediction and validation of protein–protein interactors from genome-wide DNA-binding data using a knowledge-based machine-learning approach

De novo 9q gain in an infant with tetralogy of Fallot with absent pulmonary valve: Patient report and review of congenital heart disease in 9q duplication syndrome

(2015) Ina E. Amarillo et al.   AMERICAN JOURNAL OF MEDICAL GENETICS PART A

Cardiac transcription factor Nkx2.5 interacts with p53 and modulates its activity

(2015) Snezana Kojic et al.   ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS

CompGO: an R package for comparing and visualizing Gene Ontology enrichment differences between DNA binding experiments

(2015) Ashley J. Waardenberg et al.   BMC BIOINFORMATICS

NKX2-5 mutations causative for congenital heart disease retain functionality and are directed to hundreds of targets

(2015) Romaric Bouveret et al.   eLife

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

(2014) S. M. Ahmad et al.   DEVELOPMENT

Stage-specific control of early B cell development by the transcription factor Ikaros

(2014) Tanja A Schwickert et al.   NATURE IMMUNOLOGY

The BioGRID interaction database: 2015 update

(2014) Andrew Chatr-aryamontri et al.   NUCLEIC ACIDS RESEARCH

STRING v10: protein–protein interaction networks, integrated over the tree of life

(2014) Damian Szklarczyk et al.   NUCLEIC ACIDS RESEARCH

Genetic Networks Governing Heart Development

(2014) A. J. Waardenberg et al.   Cold Spring Harbor Perspectives in Medicine

LEVERAGING BIOLOGICAL REPLICATES TO IMPROVE ANALYSIS IN CHIP-SEQ EXPERIMENTS

(2014) Yajie Yang et al.   Computational and Structural Biotechnology Journal

The MIntAct project—IntAct as a common curation platform for 11 molecular interaction databases

(2013) Sandra Orchard et al.   NUCLEIC ACIDS RESEARCH

JASPAR 2014: an extensively expanded and updated open-access database of transcription factor binding profiles

(2013) Anthony Mathelier et al.   NUCLEIC ACIDS RESEARCH

Genome-Wide Screens for In Vivo Tinman Binding Sites Identify Cardiac Enhancers with Diverse Functional Architectures

(2013) Hong Jin et al.   PLoS Genetics

Scl Represses Cardiomyogenesis in Prospective Hemogenic Endothelium and Endocardium

(2012) Ben Van Handel et al.   CELL

A Temporal Chromatin Signature in Human Embryonic Stem Cells Identifies Regulators of Cardiac Development

(2012) Sharon L. Paige et al.   CELL

Dynamic and Coordinated Epigenetic Regulation of Developmental Transitions in the Cardiac Lineage

(2012) Joseph A. Wamstad et al.   CELL

Transcription factors: from enhancer binding to developmental control

(2012) François Spitz et al.   NATURE REVIEWS GENETICS

A Machine Learning Approach for Identifying Novel Cell Type–Specific Transcriptional Regulators of Myogenesis

(2012) Brian W. Busser et al.   PLoS Genetics

DREME: motif discovery in transcription factor ChIP-seq data

(2011) Timothy L. Bailey   BIOINFORMATICS

Nkx2-5 Represses Gata1 Gene Expression and Modulates the Cellular Fate of Cardiac Progenitors During Embryogenesis

(2011) Arianna Caprioli et al.   CIRCULATION

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

(2011) T. Siggers et al.   Molecular Systems Biology

Cell cycle-specific function of Ikaros in human leukemia

(2011) Zhanjun Li et al.   PEDIATRIC BLOOD & CANCER

E-Cadherin Is Transcriptionally Activated via Suppression of ZEB1 Transcriptional Repressor by Small RNA-Mediated Gene Silencing

(2011) Minami Mazda et al.   PLoS One

Co-occupancy by multiple cardiac transcription factors identifies transcriptional enhancers active in heart

(2011) A. He et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Variance of Gene Expression Identifies Altered Network Constraints in Neurological Disease

(2011) Jessica C. Mar et al.   PLoS Genetics

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

ChIP on Chip: surprising results are often artifacts

(2010) Torsten Waldminghaus et al.   BMC GENOMICS

Zac1 Is an Essential Transcription Factor for Cardiac Morphogenesis

(2010) Shinsuke Yuasa et al.   CIRCULATION RESEARCH

Genome-wide discovery of human heart enhancers

(2010) L. Narlikar et al.   GENOME RESEARCH

Genome-wide identification of TAL1's functional targets: Insights into its mechanisms of action in primary erythroid cells

(2010) M. T. Kassouf et al.   GENOME RESEARCH

Variability in gene expression underlies incomplete penetrance

(2010) Arjun Raj et al.   NATURE

Distinguishing direct versus indirect transcription factor-DNA interactions

(2009) R. Gordan et al.   GENOME RESEARCH

Nkx2–5 transactivates the Ets-related protein 71 gene and specifies an endothelial/endocardial fate in the developing embryo

(2009) Anwarul Ferdous et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Human Protein Reference Database--2009 update

(2008) T. S. Keshava Prasad et al.   NUCLEIC ACIDS RESEARCH

Retinoic acid deficiency alters second heart field formation

(2008) L. Ryckebusch et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Expanding Role for Retinoid Signaling in Heart Development

(2008) Loretta L. Hoover et al.   TheScientificWorldJOURNAL