Conserved Epigenetic Regulatory Logic Infers Genes Governing Cell Identity
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Title
Conserved Epigenetic Regulatory Logic Infers Genes Governing Cell Identity
Authors
Keywords
H3K27me3, epigenetic, single cell RNA-seq, TRIAGE, EpiMap, pluripotent stem cell, predictions, cell differentiation, computational method
Journal
Cell Systems
Volume 11, Issue 6, Pages 625-639.e13
Publisher
Elsevier BV
Online
2020-12-04
DOI
10.1016/j.cels.2020.11.001
References
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Note: Only part of the references are listed.- 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
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- (2020) Yuhki Nakatake et al. Cell Reports
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- (2019) Junyue Cao et al. NATURE
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- (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
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