Inherent genomic properties underlie the epigenomic heterogeneity of human induced pluripotent stem cells

The Dfam community resource of transposable element families, sequence models, and genome annotations

(2021) Jessica Storer et al.   Mobile DNA

Erosion of human X chromosome inactivation causes major remodeling of the iPSC proteome

(2021) Alejandro J. Brenes et al.   Cell Reports

Contiguous erosion of the inactive X in human pluripotency concludes with global DNA hypomethylation

(2021) Prakhar Bansal et al.   Cell Reports

X chromosome inactivation in human development

(2020) Catherine Patrat et al.   DEVELOPMENT

Mapping the Effects of Genetic Variation on Chromatin State and Gene Expression Reveals Loci That Control Ground State Pluripotency

(2020) Daniel A. Skelly et al.   Cell Stem Cell

Naive Pluripotent Stem Cells Exhibit Phenotypic Variability that Is Driven by Genetic Variation

(2020) Daniel Ortmann et al.   Cell Stem Cell

Pluripotent Stem Cell-Based Cell Therapy—Promise and Challenges

(2020) Shinya Yamanaka   Cell Stem Cell

Cell cycle dynamics of lamina‐associated DNA

(2020) Tom van Schaik et al.   EMBO REPORTS

X-Chromosome Dosage Modulates Multiple Molecular and Cellular Properties of Mouse Pluripotent Stem Cells Independently of Global DNA Methylation Levels

(2019) Juan Song et al.   Stem Cell Reports

epic2 efficiently finds diffuse domains in ChIP-seq data

(2019) Endre Bakken Stovner et al.   BIOINFORMATICS

Transcriptionally active HERV-H retrotransposons demarcate topologically associating domains in human pluripotent stem cells

(2019) Yanxiao Zhang et al.   NATURE GENETICS

X Chromosome Dosage Influences DNA Methylation Dynamics during Reprogramming to Mouse iPSCs

(2018) Vincent Pasque et al.   Stem Cell Reports

Generation of human oogonia from induced pluripotent stem cells in vitro

(2018) Chika Yamashiro et al.   SCIENCE

X-Chromosome Inactivation: A Crossroads Between Chromosome Architecture and Gene Regulation

(2018) Rafael Galupa et al.   Annual Review of Genetics

Phase separation drives heterochromatin domain formation

(2017) Amy R. Strom et al.   NATURE

The 4D nucleome project

(2017) Job Dekker et al.   NATURE

Liquid droplet formation by HP1α suggests a role for phase separation in heterochromatin

(2017) Adam G. Larson et al.   NATURE

Chromatin-state discovery and genome annotation with ChromHMM

(2017) Jason Ernst et al.   Nature Protocols

DNA methylation and transcriptional trajectories during human development and reprogramming of isogenic pluripotent stem cells

(2017) Matthias S. Roost et al.   Nature Communications

GeneHancer: genome-wide integration of enhancers and target genes in GeneCards

(2017) Simon Fishilevich et al.   Database-The Journal of Biological Databases and Curation

Large-Scale Analysis of Loss of Imprinting in Human Pluripotent Stem Cells

(2017) Shiran Bar et al.   Cell Reports

Human Embryonic Stem Cells Do Not Change Their X Inactivation Status during Differentiation

(2017) Sanjeet Patel et al.   Cell Reports

Gender Differences in Global but Not Targeted Demethylation in iPSC Reprogramming

(2017) Inês Milagre et al.   Cell Reports

Epigenetic Variation between Human Induced Pluripotent Stem Cell Lines Is an Indicator of Differentiation Capacity

(2016) Masatoshi Nishizawa et al.   Cell Stem Cell

Global Landscape and Regulatory Principles of DNA Methylation Reprogramming for Germ Cell Specification by Mouse Pluripotent Stem Cells

(2016) Kenjiro Shirane et al.   DEVELOPMENTAL CELL

The mitochondrial protein CHCHD2 primes the differentiation potential of human induced pluripotent stem cells to neuroectodermal lineages

(2016) Lili Zhu et al.   JOURNAL OF CELL BIOLOGY

Genome-wide mapping of autonomous promoter activity in human cells

(2016) Joris van Arensbergen et al.   NATURE BIOTECHNOLOGY

deepTools2: a next generation web server for deep-sequencing data analysis

(2016) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

Deletion ofDXZ4on the human inactive X chromosome alters higher-order genome architecture

(2016) Emily M. Darrow et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Integrated Genomic Analysis of Diverse Induced Pluripotent Stem Cells from the Progenitor Cell Biology Consortium

(2016) Nathan Salomonis et al.   Stem Cell Reports

Erosion of X Chromosome Inactivation in Human Pluripotent Cells Initiates with XACT Coating and Depends on a Specific Heterochromatin Landscape

(2015) Céline Vallot et al.   Cell Stem Cell

Robust In Vitro Induction of Human Germ Cell Fate from Pluripotent Stem Cells

(2015) Kotaro Sasaki et al.   Cell Stem Cell

The inactive X chromosome is epigenetically unstable and transcriptionally labile in breast cancer

(2015) Ronan Chaligné et al.   GENOME RESEARCH

Transcription factor binding dynamics during human ES cell differentiation

(2015) Alexander M. Tsankov et al.   NATURE

A comparison of genetically matched cell lines reveals the equivalence of human iPSCs and ESCs

(2015) Jiho Choi et al.   NATURE BIOTECHNOLOGY

ENCODE data at the ENCODE portal

(2015) Cricket A. Sloan et al.   NUCLEIC ACIDS RESEARCH

Derivation of consensus inactivation status for X-linked genes from genome-wide studies

(2015) Bradley P. Balaton et al.   Biology of Sex Differences

A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping

(2014) Suhas S.P. Rao et al.   CELL

The Two Active X Chromosomes in Female ESCs Block Exit from the Pluripotent State by Modulating the ESC Signaling Network

(2014) Edda G. Schulz et al.   Cell Stem Cell

Genome-wide parent-of-origin DNA methylation analysis reveals the intricacies of human imprinting and suggests a germline methylation-independent mechanism of establishment

(2014) F. Court et al.   GENOME RESEARCH

Abnormalities in human pluripotent cells due to reprogramming mechanisms

(2014) Hong Ma et al.   NATURE

A novel efficient feeder-free culture system for the derivation of human induced pluripotent stem cells

(2014) Masato Nakagawa et al.   Scientific Reports

Genome-Wide Analysis of DNA Methylation Dynamics during Early Human Development

(2014) Hiroaki Okae et al.   PLoS Genetics

A double take on bivalent promoters

(2013) P. Voigt et al.   GENES & DEVELOPMENT

Human inactive X chromosome is compacted through a PRC2-independent SMCHD1-HBiX1 pathway

(2013) Ryu-Suke Nozawa et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Differentiation-defective phenotypes revealed by large-scale analyses of human pluripotent stem cells

(2013) M. Koyanagi-Aoi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Software for Computing and Annotating Genomic Ranges

(2013) Michael Lawrence et al.   PLoS Computational Biology

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

(2013) Daehwan Kim et al.   GENOME BIOLOGY

Derivation Conditions Impact X-Inactivation Status in Female Human Induced Pluripotent Stem Cells

(2012) Kiichiro Tomoda et al.   Cell Stem Cell

Recurrent Variations in DNA Methylation in Human Pluripotent Stem Cells and Their Differentiated Derivatives

(2012) Kristopher L. Nazor et al.   Cell Stem Cell

Erosion of Dosage Compensation Impacts Human iPSC Disease Modeling

(2012) Shila Mekhoubad et al.   Cell Stem Cell

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Amplification-free whole-genome bisulfite sequencing by post-bisulfite adaptor tagging

(2012) Fumihito Miura et al.   NUCLEIC ACIDS RESEARCH

Donor-dependent variations in hepatic differentiation from human-induced pluripotent stem cells

(2012) M. Kajiwara et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Identification of a specific reprogramming-associated epigenetic signature in human induced pluripotent stem cells

(2012) S. Ruiz et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

An Efficient Nonviral Method to Generate Integration-Free Human-Induced Pluripotent Stem Cells from Cord Blood and Peripheral Blood Cells

(2012) Keisuke Okita et al.   STEM CELLS

ggbio: an R package for extending the grammar of graphics for genomic data

(2012) Tengfei Yin et al.   GENOME BIOLOGY

Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications

(2011) Felix Krueger et al.   BIOINFORMATICS

Control-FREEC: a tool for assessing copy number and allelic content using next-generation sequencing data

(2011) Valentina Boeva et al.   BIOINFORMATICS

Reference Maps of Human ES and iPS Cell Variation Enable High-Throughput Characterization of Pluripotent Cell Lines

(2011) Christoph Bock et al.   CELL

Hotspots of aberrant epigenomic reprogramming in human induced pluripotent stem cells

(2011) Ryan Lister et al.   NATURE

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

Incomplete DNA methylation underlies a transcriptional memory of somatic cells in human iPS cells

(2011) Yuki Ohi et al.   NATURE CELL BIOLOGY

Tracking epigenetic histone modifications in single cells using Fab-based live endogenous modification labeling

(2011) Yoko Hayashi-Takanaka et al.   NUCLEIC ACIDS RESEARCH

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

(2010) Heng Li et al.   BIOINFORMATICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Chromatin Structure and Gene Expression Programs of Human Embryonic and Induced Pluripotent Stem Cells

(2010) Matthew G. Guenther et al.   Cell Stem Cell

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

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Targets and dynamics of promoter DNA methylation during early mouse development

(2010) Julie Borgel et al.   NATURE GENETICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources

(2009) Da Wei Huang et al.   Nature Protocols

The Organization of Histone H3 Modifications as Revealed by a Panel of Specific Monoclonal Antibodies

(2008) Hiroshi Kimura et al.   CELL STRUCTURE AND FUNCTION

Polycomb Group Proteins Ezh2 and Rnf2 Direct Genomic Contraction and Imprinted Repression in Early Mouse Embryos

(2008) Rémi Terranova et al.   DEVELOPMENTAL CELL

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY