Inferring dynamic gene regulatory networks in cardiac differentiation through the integration of multi-dimensional data

FIREWACh: high-throughput functional detection of transcriptional regulatory modules in mammalian cells

(2014) Matthew Murtha et al.   NATURE METHODS

Inferring microRNA and transcription factor regulatory networks in heterogeneous data

(2013) Thuc D Le et al.   BMC BIOINFORMATICS

Super-Enhancers in the Control of Cell Identity and Disease

(2013) Denes Hnisz et al.   CELL

DNA-Binding Specificities of Human Transcription Factors

(2013) Arttu Jolma et al.   CELL

Braveheart, a Long Noncoding RNA Required for Cardiovascular Lineage Commitment

(2013) Carla A. Klattenhoff et al.   CELL

Essential and Unexpected Role of Yin Yang 1 to Promote Mesodermal Cardiac Differentiation

(2013) Serge Gregoire et al.   CIRCULATION RESEARCH

Hippo signaling impedes adult heart regeneration

(2013) T. Heallen et al.   DEVELOPMENT

Network deconvolution as a general method to distinguish direct dependencies in networks

(2013) Soheil Feizi et al.   NATURE BIOTECHNOLOGY

RNA in unexpected places: long non-coding RNA functions in diverse cellular contexts

(2013) Sarah Geisler et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Models incorporating chromatin modification data identify functionally important p53 binding sites

(2013) Ji-Hyun Lim 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

BMP4 Promotes EMT and Mesodermal Commitment in Human Embryonic Stem Cells via SLUG and MSX2

(2013) Anne Richter et al.   STEM CELLS

Systematic repression of transcription factors reveals limited patterns of gene expression changes in ES cells

(2013) Akira Nishiyama et al.   Scientific Reports

Integrated Module and Gene-Specific Regulatory Inference Implicates Upstream Signaling Networks

(2013) Sushmita Roy et al.   PLoS Computational Biology

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

Epigenomic Annotation of Enhancers Predicts Transcriptional Regulators of Human Neural Crest

(2012) Alvaro Rada-Iglesias et al.   Cell Stem Cell

Spatiotemporal clustering of the epigenome reveals rules of dynamic gene regulation

(2012) P. Yu et al.   GENOME RESEARCH

SWI/SNF Protein Component BAF250a Regulates Cardiac Progenitor Cell Differentiation by Modulating Chromatin Accessibility during Second Heart Field Development

(2012) Ienglam Lei et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Wisdom of crowds for robust gene network inference

(2012) Daniel Marbach et al.   NATURE METHODS

Unsupervised pattern discovery in human chromatin structure through genomic segmentation

(2012) Michael M Hoffman et al.   NATURE METHODS

ChIPBase: a database for decoding the transcriptional regulation of long non-coding RNA and microRNA genes from ChIP-Seq data

(2012) Jian-Hua Yang et al.   NUCLEIC ACIDS RESEARCH

Reverse-engineering the genetic circuitry of a cancer cell with predicted intervention in chronic lymphocytic leukemia

(2012) L. Vallat et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Epigenetic signatures distinguish multiple classes of enhancers with distinct cellular functions

(2011) Gabriel E. Zentner et al.   GENOME RESEARCH

A gene regulatory network controlling the embryonic specification of endoderm

(2011) Isabelle S. Peter et al.   NATURE

Mapping and analysis of chromatin state dynamics in nine human cell types

(2011) Jason Ernst et al.   NATURE

Quantitative analysis demonstrates most transcription factors require only simple models of specificity

(2011) Yue Zhao et al.   NATURE BIOTECHNOLOGY

Large-scale discovery of enhancers from human heart tissue

(2011) Dalit May et al.   NATURE GENETICS

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

Generation of mouse ES cell lines engineered for the forced induction of transcription factors

(2011) Lina S. Correa-Cerro et al.   Scientific Reports

The Cardiac Transcription Network Modulated by Gata4, Mef2a, Nkx2.5, Srf, Histone Modifications, and MicroRNAs

(2011) Jenny Schlesinger et al.   PLoS Genetics

Fast and accurate long-read alignment with Burrows–Wheeler transform

(2010) Heng Li et al.   BIOINFORMATICS

TimeDelay-ARACNE: Reverse engineering of gene networks from time-course data by an information theoretic approach

(2010) Pietro Zoppoli et al.   BMC BIOINFORMATICS

Statistical inference of the time-varying structure of gene-regulation networks

(2010) Sophie Lèbre et al.   BMC Systems Biology

The Nuclear Receptor Nr5a2 Can Replace Oct4 in the Reprogramming of Murine Somatic Cells to Pluripotent Cells

(2010) Jian-Chien Dominic Heng et al.   Cell Stem Cell

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

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

Genome-wide discovery of human heart enhancers

(2010) L. Narlikar et al.   GENOME RESEARCH

Integrating multiple evidence sources to predict transcription factor binding in the human genome

(2010) J. Ernst et al.   GENOME RESEARCH

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

(2010) A. Jolma et al.   GENOME RESEARCH

Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data

(2010) R. Pique-Regi et al.   GENOME RESEARCH

Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities

(2010) Sven Heinz et al.   MOLECULAR CELL

A unique chromatin signature uncovers early developmental enhancers in humans

(2010) Alvaro Rada-Iglesias et al.   NATURE

ChIP-Seq identification of weakly conserved heart enhancers

(2010) Matthew J Blow et al.   NATURE GENETICS

Histone H3K27ac separates active from poised enhancers and predicts developmental state

(2010) M. P. Creyghton et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Community Structure in Time-Dependent, Multiscale, and Multiplex Networks

(2010) P. J. Mucha et al.   SCIENCE

Genome-wide prediction of transcription factor binding sites using an integrated model

(2010) Kyoung-Jae Won et al.   GENOME BIOLOGY

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

Uncovering Early Response of Gene Regulatory Networks in ESCs by Systematic Induction of Transcription Factors

(2009) Akira Nishiyama et al.   Cell Stem Cell

Downstream of FGF during mesoderm formation in Xenopus: The roles of Elk-1 and Egr-1

(2009) Oliver Nentwich et al.   DEVELOPMENTAL BIOLOGY

Histone modifications at human enhancers reflect global cell-type-specific gene expression

(2009) Nathaniel D. Heintzman et al.   NATURE

ChIP-seq accurately predicts tissue-specific activity of enhancers

(2009) Axel Visel et al.   NATURE

Incorporating Existing Network Information into Gene Network Inference

(2009) Scott Christley et al.   PLoS One

Recovering time-varying networks of dependencies in social and biological studies

(2009) A. Ahmed et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

SIRENE: supervised inference of regulatory networks

(2008) F. Mordelet et al.   BIOINFORMATICS

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

(2008) Michael F. Berger et al.   CELL

Integration of External Signaling Pathways with the Core Transcriptional Network in Embryonic Stem Cells

(2008) Xi Chen et al.   CELL

BAF250B-Associated SWI/SNF Chromatin-Remodeling Complex Is Required to Maintain Undifferentiated Mouse Embryonic Stem Cells

(2008) Zhijiang Yan et al.   STEM CELLS