Brahma safeguards canalization of cardiac mesoderm differentiation

mSWI/SNF promotes Polycomb repression both directly and through genome-wide redistribution

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Dynamic BAF chromatin remodeling complex subunit inclusion promotes temporally distinct gene expression programs in cardiogenesis

(2019) Swetansu K. Hota et al.   DEVELOPMENT

DoubletFinder: Doublet Detection in Single-Cell RNA Sequencing Data Using Artificial Nearest Neighbors

(2019) Christopher S. McGinnis et al.   Cell Systems

Diverse compositions and functions of chromatin remodeling machines in cancer

(2019) Cigall Kadoch   Science Translational Medicine

The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update

(2018) Enis Afgan et al.   NUCLEIC ACIDS RESEARCH

Single-cell reconstruction of developmental trajectories during zebrafish embryogenesis

(2018) Jeffrey A. Farrell et al.   SCIENCE

Correcting the Mean-Variance Dependency for Differential Variability Testing Using Single-Cell RNA Sequencing Data

(2018) Nils Eling et al.   Cell Systems

The PRIDE database and related tools and resources in 2019: improving support for quantification data

(2018) Yasset Perez-Riverol et al.   NUCLEIC ACIDS RESEARCH

An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues

(2017) M Ryan Corces et al.   NATURE METHODS

Single-cell entropy for accurate estimation of differentiation potency from a cell’s transcriptome

(2017) Andrew E. Teschendorff et al.   Nature Communications

BRG1 and BRM SWI/SNF ATPases redundantly maintain cardiomyocyte homeostasis by regulating cardiomyocyte mitophagy and mitochondrial dynamics in vivo

(2016) Scott J. Bultman et al.   CARDIOVASCULAR PATHOLOGY

Dissecting direct reprogramming from fibroblast to neuron using single-cell RNA-seq

(2016) Barbara Treutlein et al.   NATURE

Expression of Terminal Effector Genes in Mammalian Neurons Is Maintained by a Dynamic Relay of Transient Enhancers

(2016) Ho Sung Rhee et al.   NEURON

Spatial reconstruction of single-cell gene expression data

(2015) Rahul Satija et al.   NATURE BIOTECHNOLOGY

limma powers differential expression analyses for RNA-sequencing and microarray studies

(2015) Matthew E. Ritchie et al.   NUCLEIC ACIDS RESEARCH

BMP gradients: A paradigm for morphogen-mediated developmental patterning

(2015) E. Bier et al.   SCIENCE

Knockdown ofBrmandBaf170, Components of Chromatin Remodeling Complex, Facilitates Reprogramming of Somatic Cells

(2015) Zongliang Jiang et al.   STEM CELLS AND DEVELOPMENT

MSstats: an R package for statistical analysis of quantitative mass spectrometry-based proteomic experiments

(2014) Meena Choi et al.   BIOINFORMATICS

Functional epigenetics approach identifies BRM/SMARCA2 as a critical synthetic lethal target in BRG1-deficient cancers

(2014) G. R. Hoffman et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Sequential histone-modifying activities determine the robustness of transdifferentiation

(2014) S. Zuryn et al.   SCIENCE

The transcription factor Pou3f1 promotes neural fate commitment via activation of neural lineage genes and inhibition of external signaling pathways

(2014) Qingqing Zhu et al.   eLife

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

(2013) Y. Liao et al.   BIOINFORMATICS

Multiplex Genome Engineering Using CRISPR/Cas Systems

(2013) L. Cong et al.   SCIENCE

BEDOPS: high-performance genomic feature operations

(2012) Shane Neph et al.   BIOINFORMATICS

GO-Elite: a flexible solution for pathway and ontology over-representation

(2012) Alexander C. Zambon et al.   BIOINFORMATICS

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

(2012) Joseph A. Wamstad et al.   CELL

Bistability, Bifurcations, and Waddington's Epigenetic Landscape

(2012) James E. Ferrell   CURRENT BIOLOGY

Combined gene dosage requirement for SWI/SNF catalytic subunits during early mammalian development

(2012) Stephanie L. Smith-Roe et al.   MAMMALIAN GENOME

Heterozygous missense mutations in SMARCA2 cause Nicolaides-Baraitser syndrome

(2012) Jeroen K J Van Houdt et al.   NATURE GENETICS

Mutations affecting components of the SWI/SNF complex cause Coffin-Siris syndrome

(2012) Yoshinori Tsurusaki et al.   NATURE GENETICS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation

(2012) Davis J. McCarthy et al.   NUCLEIC ACIDS RESEARCH

Genome-Wide Localization of Protein-DNA Binding and Histone Modification by a Bayesian Change-Point Method with ChIP-seq Data

(2012) Haipeng Xing et al.   PLoS Computational Biology

A deterministic map of Waddington's epigenetic landscape for cell fate specification

(2011) Sudin Bhattacharya et al.   BMC Systems Biology

Pluripotency Factors in Embryonic Stem Cells Regulate Differentiation into Germ Layers

(2011) Matt Thomson et al.   CELL

Stage-Specific Optimization of Activin/Nodal and BMP Signaling Promotes Cardiac Differentiation of Mouse and Human Pluripotent Stem Cell Lines

(2011) Steven J. Kattman et al.   Cell Stem Cell

Negative feedback in the bone morphogenetic protein 4 (BMP4) synexpression group governs its dynamic signaling range and canalizes development

(2011) M. Paulsen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Quantifying the Waddington landscape and biological paths for development and differentiation

(2011) J. Wang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Chromatin remodelling complex dosage modulates transcription factor function in heart development

(2011) Jun K. Takeuchi et al.   Nature Communications

Modeling cardiac β-adrenergic signaling with normalized-Hill differential equations: comparison with a biochemical model

(2010) Matthew J Kraeutler et al.   BMC Systems Biology

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

GREAT improves functional interpretation of cis-regulatory regions

(2010) Cory Y McLean et al.   NATURE BIOTECHNOLOGY

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

An embryonic stem cell chromatin remodeling complex, esBAF, is essential for embryonic stem cell self-renewal and pluripotency

(2009) L. Ho et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Baf60c is a component of the neural progenitor-specific BAF complex in developing retina

(2008) Deepak A. Lamba et al.   DEVELOPMENTAL DYNAMICS

MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification

(2008) Jürgen Cox et al.   NATURE BIOTECHNOLOGY

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY