Reorganization of 3D genome structure may contribute to gene regulatory evolution in primates

Quantifying the similarity of topological domains across normal and cancer human cell types

(2018) Natalie Sauerwald et al.   BIOINFORMATICS

Inversion variants in human and primate genomes

(2018) Claudia Rita Catacchio et al.   GENOME RESEARCH

Epigenetic maintenance of topological domains in the highly rearranged gibbon genome

(2018) Nathan H. Lazar et al.   GENOME RESEARCH

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

(2018) Fidel Ramírez et al.   Nature Communications

A Comparative Assessment of Human and Chimpanzee iPSC-derived Cardiomyocytes with Primary Heart Tissues

(2018) Bryan J. Pavlovic et al.   Scientific Reports

Comparative analysis of three-dimensional chromosomal architecture identifies a novel fetal hemoglobin regulatory element

(2017) Peng Huang et al.   GENES & DEVELOPMENT

Transposable elements are the primary source of novelty in primate gene regulation

(2017) Marco Trizzino et al.   GENOME RESEARCH

Dynamic Rewiring of Promoter-Anchored Chromatin Loops during Adipocyte Differentiation

(2017) Rasmus Siersbæk et al.   MOLECULAR CELL

Evolutionarily Conserved Principles Predict 3D Chromatin Organization

(2017) M. Jordan Rowley et al.   MOLECULAR CELL

3D Chromatin Architecture of Large Plant Genomes Determined by Local A/B Compartments

(2017) Pengfei Dong et al.   Molecular Plant

Comparison of computational methods for Hi-C data analysis

(2017) Mattia Forcato et al.   NATURE METHODS

Endothelial cell differentiation is encompassed by changes in long range interactions between inactive chromatin regions

(2017) Henri Niskanen et al.   NUCLEIC ACIDS RESEARCH

A critical assessment of topologically associating domain prediction tools

(2017) Rola Dali et al.   NUCLEIC ACIDS RESEARCH

De novo prediction of human chromosome structures: Epigenetic marking patterns encode genome architecture

(2017) Michele Di Pierro et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Modeling gene regulation from paired expression and chromatin accessibility data

(2017) Zhana Duren et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Topologically associating domains are ancient features that coincide with Metazoan clusters of extreme noncoding conservation

(2017) Nathan Harmston et al.   Nature Communications

Promoter-enhancer interactions identified from Hi-C data using probabilistic models and hierarchical topological domains

(2017) Gil Ron et al.   Nature Communications

MrTADFinder: A network modularity based approach to identify topologically associating domains in multiple resolutions

(2017) Koon-Kiu Yan et al.   PLoS Computational Biology

Chromosome conformation and gene expression patterns differ profoundly in human fibroblasts grown in spheroids versus monolayers

(2017) Haiming Chen et al.   Nucleus

Chromosome conformation and gene expression patterns differ profoundly in human fibroblasts grown in spheroids versus monolayers

(2017) Haiming Chen et al.   Nucleus

Enhancer Control of Transcriptional Bursting

(2016) Takashi Fukaya et al.   CELL

The molecular hallmarks of epigenetic control

(2016) C. David Allis et al.   NATURE REVIEWS GENETICS

Synteny Portal: a web-based application portal for synteny block analysis

(2016) Jongin Lee 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

Constructing 3D interaction maps from 1D epigenomes

(2016) Yun Zhu et al.   Nature Communications

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

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

Juicer Provides a One-Click System for Analyzing Loop-Resolution Hi-C Experiments

(2016) Neva C. Durand et al.   Cell Systems

Enhancer Divergence and cis-Regulatory Evolution in the Human and Chimp Neural Crest

(2015) Sara L. Prescott et al.   CELL

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

(2015) Darío G. Lupiáñez et al.   CELL

Widespread Rearrangement of 3D Chromatin Organization Underlies Polycomb-Mediated Stress-Induced Silencing

(2015) Li Li et al.   MOLECULAR CELL

A predictive modeling approach for cell line-specific long-range regulatory interactions

(2015) Sushmita Roy et al.   NUCLEIC ACIDS RESEARCH

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

(2015) Hanjun Shin et al.   NUCLEIC ACIDS RESEARCH

Evolutionary comparison reveals that diverging CTCF sites are signatures of ancestral topological associating domains borders

(2015) Carlos Gómez-Marín et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Comparative Hi-C Reveals that CTCF Underlies Evolution of Chromosomal Domain Architecture

(2015) Matteo Vietri Rudan et al.   Cell Reports

Hi-C Chromatin Interaction Networks Predict Co-expression in the Mouse Cortex

(2015) Sepideh Babaei et al.   PLoS Computational Biology

A panel of induced pluripotent stem cells from chimpanzees: a resource for comparative functional genomics

(2015) Irene Gallego Romero et al.   eLife

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

(2014) Suhas S.P. Rao et al.   CELL

Distinct structural transitions of chromatin topological domains correlate with coordinated hormone-induced gene regulation

(2014) François Le Dily et al.   GENES & DEVELOPMENT

Quickly Finding Orthologs as Reciprocal Best Hits with BLAT, LAST, and UBLAST: How Much Do We Miss?

(2014) Natalie Ward et al.   PLoS One

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

(2014) Masato Nakagawa et al.   Scientific Reports

voom: precision weights unlock linear model analysis tools for RNA-seq read counts

(2014) Charity W Law et al.   GENOME BIOLOGY

Analysis of the Human Tissue-specific Expression by Genome-wide Integration of Transcriptomics and Antibody-based Proteomics

(2013) Linn Fagerberg et al.   MOLECULAR & CELLULAR PROTEOMICS

A high-resolution map of the three-dimensional chromatin interactome in human cells

(2013) Fulai Jin et al.   NATURE

Enhancers: five essential questions

(2013) Len A. Pennacchio et al.   NATURE REVIEWS GENETICS

The 3D Organization of the Yeast Genome Correlates with Co-Expression and Reflects Functional Relations between Genes

(2013) Dirar Homouz et al.   PLoS One

Physical tethering and volume exclusion determine higher-order genome organization in budding yeast

(2012) H. Tjong et al.   GENOME RESEARCH

Insights into hominid evolution from the gorilla genome sequence

(2012) Aylwyn Scally et al.   NATURE

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

(2012) Yin Shen et al.   NATURE

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

Architecture of the human regulatory network derived from ENCODE data

(2012) Mark B. Gerstein et al.   NATURE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Integration of Hi-C and ChIP-seq data reveals distinct types of chromatin linkages

(2012) Xun Lan et al.   NUCLEIC ACIDS RESEARCH

Human-Specific Histone Methylation Signatures at Transcription Start Sites in Prefrontal Neurons

(2012) Hennady P. Shulha et al.   PLOS BIOLOGY

Identification of novel phosphorylation modification sites in human proteins that originated after the human–chimpanzee divergence

(2011) Dong Seon Kim et al.   BIOINFORMATICS

Human transcriptional interactome of chromatin contribute to gene co-expression

(2011) Xiao Dong et al.   BMC GENOMICS

Gene Expression Differences Among Primates Are Associated With Changes in a Histone Epigenetic Modification

(2011) C. E. Cain et al.   GENETICS

A bioinformatic assay for pluripotency in human cells

(2011) Franz-Josef Müller et al.   NATURE METHODS

Enhancer function: new insights into the regulation of tissue-specific gene expression

(2011) Chin-Tong Ong et al.   NATURE REVIEWS GENETICS

A Genome-Wide Study of DNA Methylation Patterns and Gene Expression Levels in Multiple Human and Chimpanzee Tissues

(2011) Athma A. Pai et al.   PLoS Genetics

The similarity of gene expression between human and mouse tissues

(2011) Robin D Dowell   GENOME BIOLOGY

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Transcriptional Enhancers in Animal Development and Evolution

(2010) Mike Levine   CURRENT BIOLOGY

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

Mediator and cohesin connect gene expression and chromatin architecture

(2010) Michael H. Kagey et al.   NATURE

Functional consequences of genetic variation in primates on tyrosine hydroxylase (TH) expression in vitro

(2009) Lisa R. Warner et al.   BRAIN RESEARCH

Evolution of transcriptional control in mammals

(2009) Michael D Wilson et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Segmental Duplications Contribute to Gene Expression Differences Between Humans and Chimpanzees

(2009) R. Blekhman et al.   GENETICS

Multiple Functional Variants in cis Modulate PDYN Expression

(2009) C. C. Babbitt et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

(2009) Stefan Schoenfelder et al.   NATURE GENETICS

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

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

Prediction of regulatory elements in mammalian genomes using chromatin signatures

(2008) Kyoung-Jae Won et al.   BMC BIOINFORMATICS

Gene Regulation in the Third Dimension

(2008) J. Dekker   SCIENCE

Human-Specific Gain of Function in a Developmental Enhancer

(2008) S. Prabhakar et al.   SCIENCE

Gene Regulation in Primates Evolves under Tissue-Specific Selection Pressures

(2008) Ran Blekhman et al.   PLoS Genetics