KLF4 is involved in the organization and regulation of pluripotency-associated three-dimensional enhancer networks

Epigenetic regulation of REX1 expression and chromatin binding specificity by HMGNs

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Multiplex chromatin interactions with single-molecule precision

(2019) Meizhen Zheng et al.   NATURE

Resolving Cell Fate Decisions during Somatic Cell Reprogramming by Single-Cell RNA-Seq

(2019) Lin Guo et al.   MOLECULAR CELL

Optimal-Transport Analysis of Single-Cell Gene Expression Identifies Developmental Trajectories in Reprogramming

(2019) Geoffrey Schiebinger et al.   CELL

Transcription factors and 3D genome conformation in cell-fate decisions

(2019) Ralph Stadhouders et al.   NATURE

Cellular trajectories and molecular mechanisms of iPSC reprogramming

(2018) Effie Apostolou et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Transcription factors orchestrate dynamic interplay between genome topology and gene regulation during cell reprogramming

(2018) Ralph Stadhouders et al.   NATURE GENETICS

Enhancer hubs and loop collisions identified from single-allele topologies

(2018) Amin Allahyar et al.   NATURE GENETICS

Mediator and RNA polymerase II clusters associate in transcription-dependent condensates

(2018) Won-Ki Cho et al.   SCIENCE

Dissecting super-enhancer hierarchy based on chromatin interactions

(2018) Jialiang Huang et al.   Nature Communications

Stratification of TAD boundaries reveals preferential insulation of super-enhancers by strong boundaries

(2018) Yixiao Gong et al.   Nature Communications

High-resolution TADs reveal DNA sequences underlying genome organization in flies

(2018) Fidel Ramírez et al.   Nature Communications

Long-Range Enhancer Interactions Are Prevalent in Mouse Embryonic Stem Cells and Are Reorganized upon Pluripotent State Transition

(2018) Clara Lopes Novo et al.   Cell Reports

Identification and Single-Cell Functional Characterization of an Endodermally Biased Pluripotent Substate in Human Embryonic Stem Cells

(2018) Thomas F. Allison et al.   Stem Cell Reports

Transcription Factors Drive Tet2-Mediated Enhancer Demethylation to Reprogram Cell Fate

(2018) Jose Luis Sardina et al.   Cell Stem Cell

Transcription Factors Activate Genes through the Phase-Separation Capacity of Their Activation Domains

(2018) Ann Boija et al.   CELL

Single-allele chromatin interactions identify regulatory hubs in dynamic compartmentalized domains

(2018) A. Marieke Oudelaar et al.   NATURE GENETICS

YY1 and CTCF orchestrate a 3D chromatin looping switch during early neural lineage commitment

(2017) Jonathan A. Beagan et al.   GENOME RESEARCH

Lineage-specific dynamic and pre-established enhancer–promoter contacts cooperate in terminal differentiation

(2017) Adam J Rubin et al.   NATURE GENETICS

Enhancer connectome in primary human cells identifies target genes of disease-associated DNA elements

(2017) Maxwell R Mumbach et al.   NATURE GENETICS

Salmon provides fast and bias-aware quantification of transcript expression

(2017) Rob Patro et al.   NATURE METHODS

Widespread Mitotic Bookmarking by Histone Marks and Transcription Factors in Pluripotent Stem Cells

(2017) Yiyuan Liu et al.   Cell Reports

Enhancer Control of Transcriptional Bursting

(2016) Takashi Fukaya et al.   CELL

Local Genome Topology Can Exhibit an Incompletely Rewired 3D-Folding State during Somatic Cell Reprogramming

(2016) Jonathan A. Beagan et al.   Cell Stem Cell

Cell-of-Origin-Specific 3D Genome Structure Acquired during Somatic Cell Reprogramming

(2016) Peter Hugo Lodewijk Krijger et al.   Cell Stem Cell

The role of Polycomb in stem cell genome architecture

(2016) Gloria Mas et al.   CURRENT OPINION IN CELL BIOLOGY

Capturing pairwise and multi-way chromosomal conformations using chromosomal walks

(2016) Pedro Olivares-Chauvet et al.   NATURE

HiChIP: efficient and sensitive analysis of protein-directed genome architecture

(2016) Maxwell R Mumbach et al.   NATURE METHODS

Rapid immunoprecipitation mass spectrometry of endogenous proteins (RIME) for analysis of chromatin complexes

(2016) Hisham Mohammed et al.   Nature Protocols

Identification of multi-loci hubs from 4C-seq demonstrates the functional importance of simultaneous interactions

(2016) Tingting Jiang et al.   NUCLEIC ACIDS RESEARCH

Hierarchical Oct4 Binding in Concert with Primed Epigenetic Rearrangements during Somatic Cell Reprogramming

(2016) Jun Chen et al.   Cell Reports

A Compendium of Chromatin Contact Maps Reveals Spatially Active Regions in the Human Genome

(2016) Anthony D. Schmitt et al.   Cell Reports

4C-ker: A Method to Reproducibly Identify Genome-Wide Interactions Captured by 4C-Seq Experiments

(2016) Ramya Raviram et al.   PLoS Computational Biology

Mango: a bias-correcting ChIA-PET analysis pipeline

(2015) Douglas H. Phanstiel et al.   BIOINFORMATICS

LOLA: enrichment analysis for genomic region sets and regulatory elements in R and Bioconductor

(2015) Nathan C. Sheffield et al.   BIOINFORMATICS

Pioneer Transcription Factors Target Partial DNA Motifs on Nucleosomes to Initiate Reprogramming

(2015) Abdenour Soufi et al.   CELL

A Continuous Molecular Roadmap to iPSC Reprogramming through Progression Analysis of Single-Cell Mass Cytometry

(2015) Eli R. Zunder et al.   Cell Stem Cell

Polycomb repressive complex PRC1 spatially constrains the mouse embryonic stem cell genome

(2015) Stefan Schoenfelder et al.   NATURE GENETICS

Functional annotation of native enhancers with a Cas9–histone demethylase fusion

(2015) Nicola A Kearns et al.   NATURE METHODS

Control of Cell Identity Genes Occurs in Insulated Neighborhoods in Mammalian Chromosomes

(2014) Jill M. Dowen et al.   CELL

Architectural proteins: regulators of 3D genome organization in cell fate

(2014) Elena Gómez-Díaz et al.   TRENDS IN CELL BIOLOGY

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

(2013) Warren A. Whyte et al.   CELL

Klf4 Organizes Long-Range Chromosomal Interactions with the Oct4 Locus in Reprogramming and Pluripotency

(2013) Zong Wei et al.   Cell Stem Cell

Long-Range Chromatin Contacts in Embryonic Stem Cells Reveal a Role for Pluripotency Factors and Polycomb Proteins in Genome Organization

(2013) Matthew Denholtz et al.   Cell Stem Cell

Genome-wide Chromatin Interactions of the Nanog Locus in Pluripotency, Differentiation, and Reprogramming

(2013) Effie Apostolou et al.   Cell Stem Cell

Chromatin dynamics during cellular reprogramming

(2013) Effie Apostolou et al.   NATURE

The pluripotent genome in three dimensions is shaped around pluripotency factors

(2013) Elzo de Wit et al.   NATURE

CRISPR interference (CRISPRi) for sequence-specific control of gene expression

(2013) Matthew H Larson et al.   Nature Protocols

Facilitators and Impediments of the Pluripotency Reprogramming Factors' Initial Engagement with the Genome

(2012) Abdenour Soufi et al.   CELL

A Molecular Roadmap of Reprogramming Somatic Cells into iPS Cells

(2012) Jose M. Polo et al.   CELL

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Topological domains in mammalian genomes identified by analysis of chromatin interactions

(2012) Jesse R. Dixon et al.   NATURE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Control of the Embryonic Stem Cell State

(2011) Richard A. Young   CELL

Historical Origins of Transdifferentiation and Reprogramming

(2011) Thomas Graf   Cell Stem Cell

Maintaining Cell Identity through Global Control of Genomic Organization

(2010) Gioacchino Natoli   IMMUNITY

Aberrant silencing of imprinted genes on chromosome 12qF1 in mouse induced pluripotent stem cells

(2010) Matthias Stadtfeld et al.   NATURE

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

Role of the Murine Reprogramming Factors in the Induction of Pluripotency

(2009) Rupa Sridharan et al.   CELL

Preferential associations between co-regulated genes reveal a transcriptional interactome in erythroid cells

(2009) Stefan Schoenfelder et al.   NATURE GENETICS

A reprogrammable mouse strain from gene-targeted embryonic stem cells

(2009) Matthias Stadtfeld et al.   NATURE METHODS

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

(2009) Da Wei Huang et al.   Nature Protocols

Defining Molecular Cornerstones during Fibroblast to iPS Cell Reprogramming in Mouse

(2008) Matthias Stadtfeld et al.   Cell Stem Cell

A core Klf circuitry regulates self-renewal of embryonic stem cells

(2008) Jianming Jiang et al.   NATURE CELL BIOLOGY