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

Scale-space measures for graph topology link protein network architecture to function

(2014) Marc Hulsman et al.   BIOINFORMATICS

Cell-type-based model explaining coexpression patterns of genes in the brain

(2014) P. Grange et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Detecting recurrent gene mutation in interaction network context using multi-scale graph diffusion

(2013) Sepideh Babaei et al.   BMC BIOINFORMATICS

Topology of molecular interaction networks

(2013) Wynand Winterbach et al.   BMC Systems Biology

Transcription Factories: Genome Organization and Gene Regulation

(2013) Argyris Papantonis et al.   CHEMICAL REVIEWS

Using networks to measure similarity between genes: association index selection

(2013) Juan I Fuxman Bass et al.   NATURE METHODS

From neural development to cognition: unexpected roles for chromatin

(2013) Jehnna L. Ronan et al.   NATURE REVIEWS GENETICS

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

(2013) Job Dekker et al.   NATURE REVIEWS GENETICS

Integrative analysis of the connectivity and gene expression atlases in the mouse brain

(2013) Shuiwang Ji et al.   NEUROIMAGE

Dissecting the chromatin interactome of microRNA genes

(2013) D. Chen et al.   NUCLEIC ACIDS RESEARCH

Revealing Long-Range Interconnected Hubs in Human Chromatin Interaction Data Using Graph Theory

(2013) R. E. Boulos et al.   PHYSICAL REVIEW LETTERS

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

(2013) Dirar Homouz et al.   PLoS One

Co-expression Profiling of Autism Genes in the Mouse Brain

(2013) Idan Menashe et al.   PLoS Computational Biology

A decade of 3C technologies: insights into nuclear organization

(2012) E. de Wit et al.   GENES & DEVELOPMENT

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

Architecture of the human regulatory network derived from ENCODE data

(2012) Mark B. Gerstein et al.   NATURE

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

(2012) Maxim Imakaev 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

Large-Scale Functional Organization of Long-Range Chromatin Interaction Networks

(2012) Kuljeet Singh Sandhu et al.   Cell Reports

Transcription factories

(2012) Dietmar Rieder et al.   Frontiers in Genetics

Human transcriptional interactome of chromatin contribute to gene co-expression

(2011) Xiao Dong et al.   BMC GENOMICS

Genome architectures revealed by tethered chromosome conformation capture and population-based modeling

(2011) Reza Kalhor et al.   NATURE BIOTECHNOLOGY

Probabilistic modeling of Hi-C contact maps eliminates systematic biases to characterize global chromosomal architecture

(2011) Eitan Yaffe et al.   NATURE GENETICS

Relationships between Gene Expression and Brain Wiring in the Adult Rodent Brain

(2011) Leon French et al.   PLoS Computational Biology

Gene Expression in the Rodent Brain is Associated with Its Regional Connectivity

(2011) Lior Wolf et al.   PLoS Computational Biology

Generalized walks-based centrality measures for complex biological networks

(2010) Ernesto Estrada   JOURNAL OF THEORETICAL BIOLOGY

Intra- and inter-chromosomal interactions correlate with CTCF binding genome wide

(2010) Marco Botta et al.   Molecular Systems Biology

A three-dimensional model of the yeast genome

(2010) Zhijun Duan et al.   NATURE

Finding distal regulatory elements in the human genome

(2009) Nathaniel D Heintzman et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

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

(2009) Stefan Schoenfelder et al.   NATURE GENETICS

Genomic–anatomic evidence for distinct functional domains in hippocampal field CA1

(2009) Hong-Wei Dong et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

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