A hidden Markov random field-based Bayesian method for the detection of long-range chromosomal interactions in Hi-C data

Statistical confidence estimation for Hi-C data reveals regulatory chromatin contacts

(2014) F. Ay et al.   GENOME RESEARCH

Obesity-associated variants within FTO form long-range functional connections with IRX3

(2014) Scott Smemo et al.   NATURE

Large-scale reconstruction of 3D structures of human chromosomes from chromosomal contact data

(2014) Tuan Trieu et al.   NUCLEIC ACIDS RESEARCH

Statistical Models for Detecting Differential Chromatin Interactions Mediated by a Protein

(2014) Liang Niu et al.   PLoS One

Genome organization and long-range regulation of gene expression by enhancers

(2013) Andrea Smallwood et al.   CURRENT OPINION IN CELL BIOLOGY

Patterns of regulatory activity across diverse human cell types predict tissue identity, transcription factor binding, and long-range interactions

(2013) N. C. Sheffield et al.   GENOME RESEARCH

Chromatin connectivity maps reveal dynamic promoter–enhancer long-range associations

(2013) Yubo Zhang et al.   NATURE

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

(2013) Fulai Jin et al.   NATURE

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

(2013) Job Dekker et al.   NATURE REVIEWS GENETICS

Bayesian Inference of Spatial Organizations of Chromosomes

(2013) Ming Hu et al.   PLoS Computational Biology

Methods for Identifying Higher-Order Chromatin Structure

(2012) Samin A. Sajan et al.   Annual Review of Genomics and Human Genetics

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

(2012) Tom Sexton et al.   CELL

Extensive Promoter-Centered Chromatin Interactions Provide a Topological Basis for Transcription Regulation

(2012) Guoliang Li et al.   CELL

Gene Density, Transcription, and Insulators Contribute to the Partition of the Drosophila Genome into Physical Domains

(2012) Chunhui Hou et al.   MOLECULAR CELL

The long-range interaction landscape of gene promoters

(2012) Amartya Sanyal et al.   NATURE

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

The accessible chromatin landscape of the human genome

(2012) Robert E. Thurman 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

Architecture of the human regulatory network derived from ENCODE data

(2012) Mark B. Gerstein et al.   NATURE

Interpreting noncoding genetic variation in complex traits and human disease

(2012) Lucas D Ward et al.   NATURE BIOTECHNOLOGY

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

(2012) Maxim Imakaev et al.   NATURE METHODS

Factorbook.org: a Wiki-based database for transcription factor-binding data generated by the ENCODE consortium

(2012) J. Wang et al.   NUCLEIC ACIDS RESEARCH

Systematic Localization of Common Disease-Associated Variation in Regulatory DNA

(2012) M. T. Maurano et al.   SCIENCE

From genome-wide association studies to disease mechanisms: celiac disease as a model for autoimmune diseases

(2012) Vinod Kumar et al.   Seminars in Immunopathology

Putting the Pieces Together: Integrative Modeling Platform Software for Structure Determination of Macromolecular Assemblies

(2012) Daniel Russel et al.   PLOS BIOLOGY

Genome-wide association study of rheumatoid arthritis in Koreans: Population-specific loci as well as overlap with European susceptibility loci

(2011) Jan Freudenberg et al.   ARTHRITIS AND RHEUMATISM

A fully Bayesian hidden Ising model for ChIP-seq data analysis

(2011) Q. Mo   BIOSTATISTICS

Disease Risk Links to Gene Regulation

(2011) E. Pennisi   SCIENCE

Bridging the Resolution Gap in Structural Modeling of 3D Genome Organization

(2011) Marc A. Marti-Renom et al.   PLoS Computational Biology

Variable selection for discriminant analysis with Markov random field priors for the analysis of microarray data

(2010) F. C. Stingo et al.   BIOINFORMATICS

HPeak: an HMM-based algorithm for defining read-enriched regions in ChIP-Seq data

(2010) Zhaohui S Qin et al.   BMC BIOINFORMATICS

A Double-Layered Mixture Model for the Joint Analysis of DNA Copy Number and Gene Expression Data

(2010) Hyungwon Choi et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

A three-dimensional model of the yeast genome

(2010) Zhijun Duan et al.   NATURE

The three-dimensional folding of the α-globin gene domain reveals formation of chromatin globules

(2010) Davide Baù et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

A hidden Markov random field model for genome-wide association studies

(2009) H. Li et al.   BIOSTATISTICS

Network-based genomic discovery: application and comparison of Markov random-field models

(2009) Peng Wei et al.   JOURNAL OF THE ROYAL STATISTICAL SOCIETY SERIES C-APPLIED STATISTICS

Potential etiologic and functional implications of genome-wide association loci for human diseases and traits

(2009) L. A. Hindorff 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

The 3D Structure of the Immunoglobulin Heavy-Chain Locus: Implications for Long-Range Genomic Interactions

(2008) Suchit Jhunjhunwala et al.   CELL