Topologically associating domains are disrupted by evolutionary genome rearrangements forming species-specific enhancer connections in mice and humans

Remodeling the chromatin landscape in T lymphocytes by a division of labor among transcription factors

(2021) Golnaz Vahedi   IMMUNOLOGICAL REVIEWS

Genome-wide detection of enhancer-hijacking events from chromatin interaction data in rearranged genomes

(2021) Xiaotao Wang et al.   NATURE METHODS

Nitric oxide controls proliferation of Leishmania major by inhibiting the recruitment of permissive host cells

(2021) Pauline Formaglio et al.   IMMUNITY

Conservation and divergence in gene regulation between mouse and human immune cells deserves equal emphasis

(2021) Sarah E. Gilbertson et al.   TRENDS IN IMMUNOLOGY

Genetic Variation in Type 1 Diabetes Reconfigures the 3D Chromatin Organization of T Cells and Alters Gene Expression

(2020) Maria Fasolino et al.   IMMUNITY

Three-dimensional chromatin landscapes in T cell acute lymphoblastic leukemia

(2020) Andreas Kloetgen et al.   NATURE GENETICS

Mouse transcriptome reveals potential signatures of protection and pathogenesis in human tuberculosis

(2020) Lúcia Moreira-Teixeira et al.   NATURE IMMUNOLOGY

A Roadmap for Understanding the Evolutionary Significance of Structural Genomic Variation

(2020) Claire Mérot et al.   TRENDS IN ECOLOGY & EVOLUTION

Location-specific cell identity rather than exposure to GI microbiota defines many innate immune signalling cascades in the gut epithelium

(2020) Ozge Kayisoglu et al.   GUT

Sensing of ATP via the Purinergic Receptor P2RX7 Promotes CD8+ Trm Cell Generation by Enhancing Their Sensitivity to the Cytokine TGF-β

(2020) Henrique Borges da Silva et al.   IMMUNITY

3DIV update for 2021: a comprehensive resource of 3D genome and 3D cancer genome

(2020) Kyukwang Kim et al.   NUCLEIC ACIDS RESEARCH

A TAD Skeptic: Is 3D Genome Topology Conserved?

(2020) Ittai E. Eres et al.   TRENDS IN GENETICS

Characterizing the Major Structural Variant Alleles of the Human Genome

(2019) Peter A. Audano et al.   CELL

The cis-Regulatory Atlas of the Mouse Immune System

(2019) Hideyuki Yoshida et al.   CELL

Single-Cell Transcriptomics of Human and Mouse Lung Cancers Reveals Conserved Myeloid Populations across Individuals and Species

(2019) Rapolas Zilionis et al.   IMMUNITY

Long-range enhancer–promoter contacts in gene expression control

(2019) Stefan Schoenfelder et al.   NATURE REVIEWS GENETICS

Principles of genome folding into topologically associating domains

(2019) Quentin Szabo et al.   Science Advances

Cooler: scalable storage for Hi-C data and other genomically labeled arrays

(2019) Nezar Abdennur et al.   BIOINFORMATICS

The role of 3D genome organization in development and cell differentiation

(2019) Hui Zheng et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Dynamics of genome reorganization during human cardiogenesis reveal an RBM20-dependent splicing factory

(2019) Alessandro Bertero et al.   Nature Communications

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

(2019) Dafne Campigli Di Giammartino et al.   NATURE CELL BIOLOGY

Extracellular nicotinate phosphoribosyltransferase binds Toll like receptor 4 and mediates inflammation

(2019) Antonella Managò et al.   Nature Communications

Methods for mapping 3D chromosome architecture

(2019) Rieke Kempfer et al.   NATURE REVIEWS GENETICS

Spatial Genome Re-organization between Fetal and Adult Hematopoietic Stem Cells

(2019) Changya Chen et al.   Cell Reports

Analysis of Genetically Diverse Macrophages Reveals Local and Domain-wide Mechanisms that Control Transcription Factor Binding and Function

(2018) Verena M. Link et al.   CELL

Structural variation in the 3D genome

(2018) Malte Spielmann et al.   NATURE REVIEWS GENETICS

The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update

(2018) Enis Afgan et al.   NUCLEIC ACIDS RESEARCH

A modular transcriptional signature identifies phenotypic heterogeneity of human tuberculosis infection

(2018) Akul Singhania et al.   Nature Communications

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

(2018) Fidel Ramírez et al.   Nature Communications

Genome-wide analysis reveals no evidence of trans chromosomal regulation of mammalian immune development

(2018) Timothy M. Johanson et al.   PLoS Genetics

Evolutionary stability of topologically associating domains is associated with conserved gene regulation

(2018) Jan Krefting et al.   BMC BIOLOGY

Transcription Elongation Can Affect Genome 3D Structure

(2018) Sven Heinz et al.   CELL

Control of inducible gene expression links cohesin to hematopoietic progenitor self-renewal and differentiation

(2018) Sergi Cuartero et al.   NATURE IMMUNOLOGY

Salmonella Persist in Activated Macrophages in T Cell-Sparse Granulomas but Are Contained by Surrounding CXCR3 Ligand-Positioned Th1 Cells

(2018) Michael F. Goldberg et al.   IMMUNITY

Organizational principles of 3D genome architecture

(2018) M. Jordan Rowley et al.   NATURE REVIEWS GENETICS

Haemopedia RNA-seq: a database of gene expression during haematopoiesis in mice and humans

(2018) Jarny Choi et al.   NUCLEIC ACIDS RESEARCH

The P2X7 Receptor in Infection and Inflammation

(2017) Francesco Di Virgilio et al.   IMMUNITY

Chromatin states define tumour-specific T cell dysfunction and reprogramming

(2017) Mary Philip et al.   NATURE

3DIV: A 3D-genome Interaction Viewer and database

(2017) Dongchan Yang et al.   NUCLEIC ACIDS RESEARCH

A critical assessment of topologically associating domain prediction tools

(2017) Rola Dali et al.   NUCLEIC ACIDS RESEARCH

Identifying topologically associating domains and subdomains by Gaussian Mixture model And Proportion test

(2017) Wenbao Yu et al.   Nature Communications

Human Tissue-Resident Memory T Cells Are Defined by Core Transcriptional and Functional Signatures in Lymphoid and Mucosal Sites

(2017) Brahma V. Kumar et al.   Cell Reports

Lineage-Specific Genome Architecture Links Enhancers and Non-coding Disease Variants to Target Gene Promoters

(2016) Biola M. Javierre et al.   CELL

Ever-Changing Landscapes: Transcriptional Enhancers in Development and Evolution

(2016) Hannah K. Long et al.   CELL

β-Glucan Reverses the Epigenetic State of LPS-Induced Immunological Tolerance

(2016) Boris Novakovic et al.   CELL

A Stringent Systems Approach Uncovers Gene-Specific Mechanisms Regulating Inflammation

(2016) Ann-Jay Tong et al.   CELL

Multi-tiered Reorganization of the Genome during B Cell Affinity Maturation Anchored by a Germinal Center-Specific Locus Control Region

(2016) Karen L. Bunting et al.   IMMUNITY

Formation of new chromatin domains determines pathogenicity of genomic duplications

(2016) Martin Franke et al.   NATURE

Hobit and Blimp1 instruct a universal transcriptional program of tissue residency in lymphocytes

(2016) L. K. Mackay et al.   SCIENCE

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

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

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

(2015) Darío G. Lupiáñez et al.   CELL

Super-enhancers delineate disease-associated regulatory nodes in T cells

(2015) Golnaz Vahedi et al.   NATURE

Integrative analysis of haplotype-resolved epigenomes across human tissues

(2015) Danny Leung et al.   NATURE

Condensin-driven remodelling of X chromosome topology during dosage compensation

(2015) Emily Crane et al.   NATURE

A global reference for human genetic variation

(2015) Richard A. Gibbs et al.   NATURE

Evolutionary insights into host–pathogen interactions from mammalian sequence data

(2015) Manuela Sironi et al.   NATURE REVIEWS GENETICS

Nitric oxide synthase in innate and adaptive immunity: an update

(2015) Christian Bogdan   TRENDS IN IMMUNOLOGY

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

(2015) Matteo Vietri Rudan et al.   Cell Reports

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

(2014) Suhas S.P. Rao et al.   CELL

Antiviral Activity of Human OASL Protein Is Mediated by Enhancing Signaling of the RIG-I RNA Sensor

(2014) Jianzhong Zhu et al.   IMMUNITY

Epigenetic Silencing of the Human NOS2 Gene: Rethinking the Role of Nitric Oxide in Human Macrophage Inflammatory Responses

(2014) T. J. Gross et al.   JOURNAL OF IMMUNOLOGY

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

(2013) Y. Liao et al.   BIOINFORMATICS

Conservation and divergence in the transcriptional programs of the human and mouse immune systems

(2013) T. Shay et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Topological domains in mammalian genomes identified by analysis of chromatin interactions

(2012) Jesse R. Dixon et al.   NATURE

Conservation and divergence in Toll-like receptor 4-regulated gene expression in primary human versus mouse macrophages

(2012) K. Schroder et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Glioma Stem Cell Proliferation and Tumor Growth Are Promoted by Nitric Oxide Synthase-2

(2011) Christine E. Eyler et al.   CELL

Acquisition of a multifunctional IgA+ plasma cell phenotype in the gut

(2011) Jörg H. Fritz et al.   NATURE

A User's Guide to the Encyclopedia of DNA Elements (ENCODE)

(2011)   PLOS BIOLOGY

GREAT improves functional interpretation of cis-regulatory regions

(2010) Cory Y McLean et al.   NATURE BIOTECHNOLOGY

Breakpoint regions and homologous synteny blocks in chromosomes have different evolutionary histories

(2009) D. M. Larkin et al.   GENOME RESEARCH

The Immunological Genome Project: networks of gene expression in immune cells

(2008) Tracy S P Heng et al.   NATURE IMMUNOLOGY