Discovering hotspots in functional genomic data superposed on 3D chromatin configuration reconstructions

Single-cell Hi-C for genome-wide detection of chromatin interactions that occur simultaneously in a single cell

(2015) Takashi Nagano et al.   Nature Protocols

Spatiotemporal control of estrogen-responsive transcription in ERα-positive breast cancer cells

(2015) P-Y Hsu et al.   ONCOGENE

FisHiCal: an R package for iterative FISH-based calibration of Hi-C data

(2014) Yoli Shavit et al.   BIOINFORMATICS

A statistical approach for inferring the 3D structure of the genome

(2014) N. Varoquaux et al.   BIOINFORMATICS

Hi-Corrector: a fast, scalable and memory-efficient package for normalizing large-scale Hi-C data

(2014) Wenyuan Li et al.   BIOINFORMATICS

Reproducibility of 3D chromatin configuration reconstructions

(2014) M. R. Segal et al.   BIOSTATISTICS

Distance-based assessment of the localization of functional annotations in 3D genome reconstructions

(2014) Daniel Capurso et al.   BMC GENOMICS

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

(2014) Suhas S.P. Rao et al.   CELL

Three-dimensional modeling of the P. falciparum genome during the erythrocytic cycle reveals a strong connection between genome architecture and gene expression

(2014) F. Ay et al.   GENOME RESEARCH

3D genome reconstruction from chromosomal contacts

(2014) Annick Lesne et al.   NATURE METHODS

Building silent compartments at the nuclear periphery: a recurrent theme

(2013) Peter Meister et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

3D Chromosome Modeling with Semi-Definite Programming and Hi-C Data

(2013) ZhiZhuo Zhang et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Single-cell Hi-C reveals cell-to-cell variability in chromosome structure

(2013) Takashi Nagano et al.   NATURE

Spatial localization of co-regulated genes exceeds genomic gene clustering in the Saccharomyces cerevisiae genome

(2013) Shay Ben-Elazar et al.   NUCLEIC ACIDS RESEARCH

Widespread Misinterpretable ChIP-seq Bias in Yeast

(2013) Daechan Park et al.   PLoS One

Nuclear Organization and Genome Function

(2012) Kevin Van Bortle et al.   Annual Review of Cell and Developmental Biology

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

(2012) Ming Hu et al.   BIOINFORMATICS

Structure and Function in the Budding Yeast Nucleus

(2012) A. Taddei et al.   GENETICS

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

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

On the assessment of statistical significance of three-dimensional colocalization of sets of genomic elements

(2012) Daniela M. Witten et al.   NUCLEIC ACIDS RESEARCH

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

(2012) Xun Lan et al.   NUCLEIC ACIDS RESEARCH

Classification of human genomic regions based on experimentally determined binding sites of more than 100 transcription-related factors

(2012) Kevin Y Yip et al.   GENOME BIOLOGY

Processing and analyzing ChIP-seq data: from short reads to regulatory interactions

(2011) M. Leleu et al.   Briefings in Functional Genomics

A Comprehensive Genomic Binding Map of Gene and Chromatin Regulatory Proteins in Saccharomyces

(2011) Bryan J. Venters et al.   MOLECULAR CELL

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

(2011) Eitan Yaffe et al.   NATURE GENETICS

Saccharomyces Genome Database: the genomics resource of budding yeast

(2011) J. M. Cherry et al.   NUCLEIC ACIDS RESEARCH

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

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

Genome3D: a viewer-model framework for integrating and visualizing multi-scale epigenomic information within a three-dimensional genome

(2010) Thomas M Asbury et al.   BMC BIOINFORMATICS

A three-dimensional model of the yeast genome

(2010) Zhijun Duan et al.   NATURE

The Sequence Read Archive

(2010) R. Leinonen et al.   NUCLEIC ACIDS RESEARCH

ShortRead: a bioconductor package for input, quality assessment and exploration of high-throughput sequence data

(2009) M. Morgan et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Computation for ChIP-seq and RNA-seq studies

(2009) Shirley Pepke et al.   NATURE METHODS

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

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

Cleavage of the signaling mucin Msb2 by the aspartyl protease Yps1 is required for MAPK activation in yeast

(2008) Nadia Vadaie et al.   JOURNAL OF CELL BIOLOGY

Design and analysis of ChIP-seq experiments for DNA-binding proteins

(2008) Peter V Kharchenko et al.   NATURE BIOTECHNOLOGY