Phase separation of OCT4 controls TAD reorganization to promote cell fate transitions

Three-dimensional chromatin landscapes in T cell acute lymphoblastic leukemia

(2020) Andreas Kloetgen et al.   NATURE GENETICS

Long-range interactions between topologically associating domains shape the four-dimensional genome during differentiation

(2019) Jonas Paulsen et al.   NATURE GENETICS

Transcription Factor-Directed Re-wiring of Chromatin Architecture for Somatic Cell Nuclear Reprogramming toward trans-Differentiation

(2019) Alessandra Dall’Agnese et al.   MOLECULAR CELL

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

(2019) Yanxiao Zhang et al.   NATURE GENETICS

Organization of Chromatin by Intrinsic and Regulated Phase Separation

(2019) Bryan A. Gibson et al.   CELL

Mitotic Implantation of the Transcription Factor Prospero via Phase Separation Drives Terminal Neuronal Differentiation

(2019) Xiaodan Liu et al.   DEVELOPMENTAL CELL

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

(2018) Ralph Stadhouders et al.   NATURE GENETICS

hichipper: a preprocessing pipeline for calling DNA loops from HiChIP data

(2018) Caleb A Lareau et al.   NATURE METHODS

Coactivator condensation at super-enhancers links phase separation and gene control

(2018) Benjamin R. Sabari et al.   SCIENCE

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

(2018) Ann Boija et al.   CELL

HiCRep: assessing the reproducibility of Hi-C data using a stratum-adjusted correlation coefficient

(2017) Tao Yang et al.   GENOME RESEARCH

Dynamic Rewiring of Promoter-Anchored Chromatin Loops during Adipocyte Differentiation

(2017) Rasmus Siersbæk et al.   MOLECULAR CELL

Corrigendum: The 4D nucleome project

(2017) Job Dekker et al.   NATURE

Manipulation of nuclear architecture through CRISPR-mediated chromosomal looping

(2017) Stefanie L. Morgan et al.   Nature Communications

The pioneer factor OCT4 requires the chromatin remodeller BRG1 to support gene regulatory element function in mouse embryonic stem cells

(2017) Hamish W King et al.   eLife

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

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

(2016) Maxwell R Mumbach et al.   NATURE METHODS

ChIA-PET2: a versatile and flexible pipeline for ChIA-PET data analysis

(2016) Guipeng Li et al.   NUCLEIC ACIDS RESEARCH

Activation of proto-oncogenes by disruption of chromosome neighborhoods

(2016) D. Hnisz et al.   SCIENCE

diffHic: a Bioconductor package to detect differential genomic interactions in Hi-C data

(2015) Aaron T.L. Lun et al.   BMC BIOINFORMATICS

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

(2015) Abdenour Soufi et al.   CELL

Disruptions of Topological Chromatin Domains Cause Pathogenic Rewiring of Gene-Enhancer Interactions

(2015) Darío G. Lupiáñez et al.   CELL

Formation and Maturation of Phase-Separated Liquid Droplets by RNA-Binding Proteins

(2015) Yuan Lin et al.   MOLECULAR CELL

Hierarchical folding and reorganization of chromosomes are linked to transcriptional changes in cellular differentiation

(2015) J. Fraser et al.   Molecular Systems Biology

Chromatin architecture reorganization during stem cell differentiation

(2015) Jesse R. Dixon et al.   NATURE

TopDom: an efficient and deterministic method for identifying topological domains in genomes

(2015) Hanjun Shin et al.   NUCLEIC ACIDS RESEARCH

HTSeq--a Python framework to work with high-throughput sequencing data

(2014) S. Anders et al.   BIOINFORMATICS

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

(2014) Suhas S.P. Rao et al.   CELL

Molecular Control of Induced Pluripotency

(2014) Thorold W. Theunissen et al.   Cell Stem Cell

Selective Inhibition of Tumor Oncogenes by Disruption of Super-Enhancers

(2013) Jakob Lovén et al.   CELL

Hierarchical Mechanisms for Direct Reprogramming of Fibroblasts to Neurons

(2013) Orly L. Wapinski 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

SAINTexpress: Improvements and additional features in Significance Analysis of INTeractome software

(2013) Guoci Teo et al.   Journal of Proteomics

Reprogramming in vivo produces teratomas and iPS cells with totipotency features

(2013) María Abad et al.   NATURE

The pluripotent genome in three dimensions is shaped around pluripotency factors

(2013) Elzo de Wit et al.   NATURE

Proteomic and genomic approaches reveal critical functions of H3K9 methylation and heterochromatin protein-1γ in reprogramming to pluripotency

(2013) Rupa Sridharan et al.   NATURE CELL BIOLOGY

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

(2012) Abdenour Soufi et al.   CELL

A Late Transition in Somatic Cell Reprogramming Requires Regulators Distinct from the Pluripotency Network

(2012) Azadeh Golipour et al.   Cell Stem Cell

A map of the cis-regulatory sequences in the mouse genome

(2012) Yin Shen et al.   NATURE

Topological domains in mammalian genomes identified by analysis of chromatin interactions

(2012) Jesse R. Dixon et al.   NATURE

Spatial partitioning of the regulatory landscape of the X-inactivation centre

(2012) Elphège P. Nora et al.   NATURE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Yin Yang 1 extends the Myc-related transcription factors network in embryonic stem cells

(2012) Pietro Vella et al.   NUCLEIC ACIDS RESEARCH

Oct4 links multiple epigenetic pathways to the pluripotency network

(2011) Junjun Ding et al.   CELL RESEARCH

Sequentially acting Sox transcription factors in neural lineage development

(2011) M. Bergsland et al.   GENES & DEVELOPMENT

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Pax6 Is a Human Neuroectoderm Cell Fate Determinant

(2010) Xiaoqing Zhang et al.   Cell Stem Cell

A genome-wide RNAi screen reveals determinants of human embryonic stem cell identity

(2010) Na-Yu Chia et al.   NATURE

Mediator and cohesin connect gene expression and chromatin architecture

(2010) Michael H. Kagey et al.   NATURE

Direct conversion of fibroblasts to functional neurons by defined factors

(2010) Thomas Vierbuchen et al.   NATURE

SAINT: probabilistic scoring of affinity purification–mass spectrometry data

(2010) Hyungwon Choi et al.   NATURE METHODS

DEGseq: an R package for identifying differentially expressed genes from RNA-seq data

(2009) Likun Wang et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

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

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

A genome-wide RNAi screen identifies a new transcriptional module required for self-renewal

(2009) G. Hu et al.   GENES & DEVELOPMENT

Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome

(2009) E. Lieberman-Aiden et al.   SCIENCE

An RNAi Screen of Chromatin Proteins Identifies Tip60-p400 as a Regulator of Embryonic Stem Cell Identity

(2008) Thomas G. Fazzio et al.   CELL

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY