Conserved Epigenetic Regulatory Logic Infers Genes Governing Cell Identity

Comorbidity of congenital heart defects and holoprosencephaly is likely genetically driven and gene‐specific

(2020) Cedrik Tekendo‐Ngongang et al.   AMERICAN JOURNAL OF MEDICAL GENETICS PART C-SEMINARS IN MEDICAL GENETICS

Generation and Profiling of 2,135 Human ESC Lines for the Systematic Analyses of Cell States Perturbed by Inducing Single Transcription Factors

(2020) Yuhki Nakatake et al.   Cell Reports

The single-cell transcriptional landscape of mammalian organogenesis

(2019) Junyue Cao et al.   NATURE

Benchmarking single cell RNA-sequencing analysis pipelines using mixture control experiments

(2019) Luyi Tian et al.   NATURE METHODS

A single-cell transcriptional roadmap for cardiopharyngeal fate diversification

(2019) Wei Wang et al.   NATURE CELL BIOLOGY

Molecular architecture of lineage allocation and tissue organization in early mouse embryo

(2019) Guangdun Peng et al.   NATURE

ascend: R package for analysis of single-cell RNA-seq data

(2019) Anne Senabouth et al.   GigaScience

Integrating single-cell transcriptomic data across different conditions, technologies, and species

(2018) Andrew Butler et al.   NATURE BIOTECHNOLOGY

Single-Cell Transcriptomic Analysis of Cardiac Differentiation from Human PSCs Reveals HOPX-Dependent Cardiomyocyte Maturation

(2018) Clayton E. Friedman et al.   Cell Stem Cell

Single-cell transcriptomics of 20 mouse organs creates a Tabula Muris

(2018) et al.   NATURE

SEdb: a comprehensive human super-enhancer database

(2018) Yong Jiang et al.   NUCLEIC ACIDS RESEARCH

SC3: consensus clustering of single-cell RNA-seq data

(2017) Vladimir Yu Kiselev et al.   NATURE METHODS

BET bromodomain inhibition suppresses innate inflammatory and profibrotic transcriptional networks in heart failure

(2017) Qiming Duan et al.   Science Translational Medicine

A transcribed enhancer dictates mesendoderm specification in pluripotency

(2017) Michael Alexanian et al.   Nature Communications

Chromatin and Transcriptional Analysis of Mesoderm Progenitor Cells Identifies HOPX as a Regulator of Primitive Hematopoiesis

(2017) Nathan J. Palpant et al.   Cell Reports

CRISPR Interference Efficiently Induces Specific and Reversible Gene Silencing in Human iPSCs

(2016) Mohammad A. Mandegar et al.   Cell Stem Cell

Spatial Transcriptome for the Molecular Annotation of Lineage Fates and Cell Identity in Mid-gastrula Mouse Embryo

(2016) Guangdun Peng et al.   DEVELOPMENTAL CELL

A predictive computational framework for direct reprogramming between human cell types

(2016) Owen J L Rackham et al.   NATURE GENETICS

Generating high-purity cardiac and endothelial derivatives from patterned mesoderm using human pluripotent stem cells

(2016) Nathan J Palpant et al.   Nature Protocols

Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq

(2016) I. Tirosh et al.   SCIENCE

Epigenomics-Based Identification of Major Cell Identity Regulators within Heterogeneous Cell Populations

(2016) Rizwan Rehimi et al.   Cell Reports

Integrative analysis of 111 reference human epigenomes

(2015) Anshul Kundaje et al.   NATURE

Absence of canonical marks of active chromatin in developmentally regulated genes

(2015) Sílvia Pérez-Lluch et al.   NATURE GENETICS

Decoding the regulatory landscape of melanoma reveals TEADS as regulators of the invasive cell state

(2015) Annelien Verfaillie et al.   Nature Communications

ExAtlas: An interactive online tool for meta-analysis of gene expression data

(2015) Alexei A. Sharov et al.   Journal of Bioinformatics and Computational Biology

A Systematic Approach to Identify Candidate Transcription Factors that Control Cell Identity

(2015) Ana C. D’Alessio et al.   Stem Cell Reports

CellNet: Network Biology Applied to Stem Cell Engineering

(2014) Patrick Cahan et al.   CELL

H3K4me3 Breadth Is Linked to Cell Identity and Transcriptional Consistency

(2014) Bérénice A. Benayoun et al.   CELL

Large hypomethylated domains serve as strong repressive machinery for key developmental genes in vertebrates

(2014) R. Nakamura et al.   DEVELOPMENT

Tissue-specific genome editing in Ciona embryos by CRISPR/Cas9

(2014) A. Stolfi et al.   DEVELOPMENT

The Ubiquitin Ligase RNF220 Enhances Canonical Wnt Signaling through USP7-Mediated Deubiquitination of  -Catenin

(2014) P. Ma et al.   MOLECULAR AND CELLULAR BIOLOGY

An atlas of active enhancers across human cell types and tissues

(2014) Robin Andersson et al.   NATURE

A draft map of the human proteome

(2014) Min-Sik Kim et al.   NATURE

A promoter-level mammalian expression atlas

(2014)   NATURE

Chemically defined generation of human cardiomyocytes

(2014) Paul W Burridge et al.   NATURE METHODS

AnimalTFDB 2.0: a resource for expression, prediction and functional study of animal transcription factors

(2014) Hong-Mei Zhang et al.   NUCLEIC ACIDS RESEARCH

Genetic Networks Governing Heart Development

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

Selective Inhibition of Tumor Oncogenes by Disruption of Super-Enhancers

(2013) Jakob Lovén et al.   CELL

Master Transcription Factors and Mediator Establish Super-Enhancers at Key Cell Identity Genes

(2013) Warren A. Whyte et al.   CELL

Super-Enhancers in the Control of Cell Identity and Disease

(2013) Denes Hnisz et al.   CELL

Developmental Fate and Cellular Maturity Encoded in Human Regulatory DNA Landscapes

(2013) Andrew B. Stergachis et al.   CELL

BET Bromodomains Mediate Transcriptional Pause Release in Heart Failure

(2013) Priti Anand et al.   CELL

A blueprint for engineering cell fate: current technologies to reprogram cell identity

(2013) Samantha A Morris et al.   CELL RESEARCH

The Genotype-Tissue Expression (GTEx) project

(2013) John Lonsdale et al.   NATURE GENETICS

The long non-coding RNAFendrrlinks epigenetic control mechanisms to gene regulatory networks in mammalian embryogenesis

(2013) Phillip Grote et al.   RNA Biology

Human housekeeping genes, revisited

(2013) Eli Eisenberg et al.   TRENDS IN 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

Identifying ChIP-seq enrichment using MACS

(2012) Jianxing Feng et al.   Nature Protocols

Role of the Gut Endoderm in Relaying Left-Right Patterning in Mice

(2012) Manuel Viotti et al.   PLOS BIOLOGY

Tanglegrams for rooted phylogenetic trees and networks

(2011) C. Scornavacca et al.   BIOINFORMATICS

HomeoDB2: functional expansion of a comparative homeobox gene database for evolutionary developmental biology

(2011) Ying-fu Zhong et al.   EVOLUTION & DEVELOPMENT

Genes for embryo development are packaged in blocks of multivalent chromatin in zebrafish sperm

(2011) S.-F. Wu et al.   GENOME RESEARCH

The Polycomb complex PRC2 and its mark in life

(2011) Raphaël Margueron et al.   NATURE

Six3 demarcates the anterior-most developing brain region in bilaterian animals

(2011) Patrick RH Steinmetz et al.   EvoDevo

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

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

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

Directed transdifferentiation of mouse mesoderm to heart tissue by defined factors

(2009) Jun K. Takeuchi et al.   NATURE

BioMart Central Portal—unified access to biological data

(2009) Syed Haider et al.   NUCLEIC ACIDS RESEARCH

Design and analysis of ChIP-seq experiments for DNA-binding proteins

(2008) Peter V Kharchenko et al.   NATURE BIOTECHNOLOGY

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY