Comparison of computational methods for Hi-C data analysis

A critical assessment of topologically associating domain prediction tools

(2017) Rola Dali et al.   NUCLEIC ACIDS RESEARCH

Genome-wide mapping and analysis of chromosome architecture

(2016) Anthony D. Schmitt et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Juicer Provides a One-Click System for Analyzing Loop-Resolution Hi-C Experiments

(2016) Neva C. Durand et al.   Cell Systems

Identification of hierarchical chromatin domains

(2015) Caleb Weinreb et al.   BIOINFORMATICS

diffHic: a Bioconductor package to detect differential genomic interactions in Hi-C data

(2015) Aaron T.L. Lun et al.   BMC BIOINFORMATICS

How computer science can help in understanding the 3D genome architecture

(2015) Yoli Shavit et al.   BRIEFINGS IN BIOINFORMATICS

Modeling chromosomes: Beyond pretty pictures

(2015) Maxim V. Imakaev et al.   FEBS LETTERS

The pluripotent regulatory circuitry connecting promoters to their long-range interacting elements

(2015) Stefan Schoenfelder et al.   GENOME RESEARCH

Chromatin architecture reorganization during stem cell differentiation

(2015) Jesse R. Dixon et al.   NATURE

Integrative analysis of 111 reference human epigenomes

(2015) Anshul Kundaje et al.   NATURE

Condensin-driven remodelling of X chromosome topology during dosage compensation

(2015) Emily Crane et al.   NATURE

Mapping long-range promoter contacts in human cells with high-resolution capture Hi-C

(2015) Borbala Mifsud et al.   NATURE GENETICS

Three-dimensional genome architecture: players and mechanisms

(2015) Ana Pombo et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Identification of alternative topological domains in chromatin

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

HIPPIE: a high-throughput identification pipeline for promoter interacting enhancer elements

(2014) Yih-Chii Hwang et al.   BIOINFORMATICS

Two-dimensional segmentation for analyzing Hi-C data

(2014) C. Levy-Leduc et al.   BIOINFORMATICS

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

(2014) Suhas S.P. Rao et al.   CELL

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

(2014) F. Ay et al.   GENOME RESEARCH

Comparative analysis of metazoan chromatin organization

(2014) Joshua W. K. Ho et al.   NATURE

Functional implications of genome topology

(2013) Giacomo Cavalli et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

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

(2012) Tom Sexton et al.   CELL

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

Spatial partitioning of the regulatory landscape of the X-inactivation centre

(2012) Elphège P. Nora 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

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

(2011) Eitan Yaffe et al.   NATURE GENETICS

Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities

(2010) Sven Heinz et al.   MOLECULAR CELL

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

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

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

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY