Uncovering direct and indirect molecular determinants of chromatin loops using a computational integrative approach

Nanometer resolved single-molecule colocalization of nuclear factors by two-color super resolution microscopy imaging

(2016) Mariya Georgieva et al.   METHODS

MEF2C protects bone marrow B-lymphoid progenitors during stress haematopoiesis

(2016) Wenyuan Wang et al.   Nature Communications

Chromatin topology is coupled to Polycomb group protein subnuclear organization

(2016) Ajazul H. Wani et al.   Nature Communications

Computational Identification of Genomic Features That Influence 3D Chromatin Domain Formation

(2016) Raphaël Mourad et al.   PLoS Computational Biology

Insulator speckles associated with long-distance chromatin contacts

(2016) Melanie K. Buxa et al.   Biology Open

CTCF-Mediated Human 3D Genome Architecture Reveals Chromatin Topology for Transcription

(2015) Zhonghui Tang et al.   CELL

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

(2015) Darío G. Lupiáñez et al.   CELL

Architectural proteins, transcription, and the three-dimensional organization of the genome

(2015) Caelin Cubeñas-Potts et al.   FEBS LETTERS

Parallel Selective Algorithms for Nonconvex Big Data Optimization

(2015) Francisco Facchinei et al.   IEEE TRANSACTIONS ON SIGNAL PROCESSING

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

Chromatin extrusion explains key features of loop and domain formation in wild-type and engineered genomes

(2015) Adrian L. Sanborn 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

Regularization Paths for Generalized Linear Models via Coordinate Descent

(2015) Jerome Friedman et al.   Journal of Statistical Software

ZNF143 provides sequence specificity to secure chromatin interactions at gene promoters

(2015) Swneke D. Bailey et al.   Nature Communications

Identification of alternative topological domains in chromatin

(2014) Darya Filippova et al.   Algorithms for Molecular Biology

Chromatin Immunoprecipitation Indirect Peaks Highlight Long-Range Interactions of Insulator Proteins and Pol II Pausing

(2014) Jun Liang et al.   MOLECULAR CELL

Enhancer–core-promoter specificity separates developmental and housekeeping gene regulation

(2014) Muhammad A. Zabidi et al.   NATURE

An atlas of active enhancers across human cell types and tissues

(2014) Robin Andersson et al.   NATURE

Topologically associating domains are stable units of replication-timing regulation

(2014) Benjamin D. Pope et al.   NATURE

Modeling epigenome folding: formation and dynamics of topologically associated chromatin domains

(2014) Daniel Jost et al.   NUCLEIC ACIDS RESEARCH

From a melt of rings to chromosome territories: the role of topological constraints in genome folding

(2014) Jonathan D Halverson et al.   REPORTS ON PROGRESS IN PHYSICS

Chromatin Loops as Allosteric Modulators of Enhancer-Promoter Interactions

(2014) Boryana Doyle et al.   PLoS Computational Biology

Chromatin Insulator Factors Involved in Long-Range DNA Interactions and Their Role in the Folding of the Drosophila Genome

(2014) Jutta Vogelmann et al.   PLoS Genetics

Insulator function and topological domain border strength scale with architectural protein occupancy

(2014) Kevin Van Bortle et al.   GENOME BIOLOGY

Architectural Protein Subclasses Shape 3D Organization of Genomes during Lineage Commitment

(2013) Jennifer E. Phillips-Cremins et al.   CELL

Transcriptional/epigenetic regulator CBP/p300 in tumorigenesis: structural and functional versatility in target recognition

(2013) Feng Wang et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

Distinct mechanisms of transcriptional pausing orchestrated by GAGA factor and M1BP, a novel transcription factor

(2013) Jian Li et al.   EMBO JOURNAL

The Hierarchy of the 3D Genome

(2013) Johan H. Gibcus et al.   MOLECULAR CELL

Chromatin Insulators: Linking Genome Organization to Cellular Function

(2013) Jennifer E. Phillips-Cremins et al.   MOLECULAR CELL

Exploring the three-dimensional organization of genomes: interpreting chromatin interaction data

(2013) Job Dekker et al.   NATURE REVIEWS GENETICS

Distinct isoforms of the Drosophila Brd4 homologue are present at enhancers, promoters and insulator sites

(2013) Wendy A. Kellner et al.   NUCLEIC ACIDS RESEARCH

Cohesin and CTCF differentially affect chromatin architecture and gene expression in human cells

(2013) J. Zuin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Long distance relationships: Enhancer–promoter communication and dynamic gene transcription

(2012) Judith Marsman et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

HiCNorm: removing biases in Hi-C data via Poisson regression

(2012) Ming Hu et al.   BIOINFORMATICS

Three-Dimensional Folding and Functional Organization Principles of the Drosophila Genome

(2012) Tom Sexton et al.   CELL

Drosophila CTCF tandemly aligns with other insulator proteins at the borders of H3K27me3 domains

(2012) K. Van Bortle et al.   GENOME RESEARCH

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

Iterative correction of Hi-C data reveals hallmarks of chromosome organization

(2012) Maxim Imakaev et al.   NATURE METHODS

Regulation of Chromatin Organization and Inducible Gene Expression by a Drosophila Insulator

(2011) Ashley M. Wood et al.   MOLECULAR CELL

The Ikaros gene family: Transcriptional regulators of hematopoiesis and immunity

(2011) Liza B. John et al.   MOLECULAR IMMUNOLOGY

Genomic binding profiles of functionally distinct RNA polymerase III transcription complexes in human cells

(2010) Zarmik Moqtaderi et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

A Comprehensive Map of Insulator Elements for the Drosophila Genome

(2010) Nicolas Nègre et al.   PLoS Genetics

Genome-Wide Mapping of Boundary Element-Associated Factor (BEAF) Binding Sites in Drosophila melanogaster Links BEAF to Transcription

(2009) N. Jiang et al.   MOLECULAR AND CELLULAR BIOLOGY

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

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