4.7 Article

Revisiting Assessment of Computational Methods for Hi-C Data Analysis

Related references

Note: Only part of the references are listed.
Article Genetics & Heredity

Comparison of Capture Hi-C Analytical Pipelines

Dina Aljogol et al.

Summary: This article discusses multiple computational pipelines for CHi-C data analysis and compares their efficiency in identifying reproducible interactions and determining biologically significant interactions. The study finds that the optimal pipeline depends on the project-specific tolerance level for false positives and false negatives in chromatin contacts.

FRONTIERS IN GENETICS (2022)

Article Multidisciplinary Sciences

HiC-DC plus enables systematic 3D interaction calls and differential analysis for Hi-C and HiChIP

Merve Sahin et al.

Summary: Recent genome-wide chromosome conformation capture assays have greatly enhanced the resolution of studying 3D genomic architecture and function. HiC-DC+ is a software tool that integrates statistical framework for Hi-C/HiChIP interaction calling and differential analysis, providing a principled statistical analysis tool for genome-wide studies. HiC-DC+ accurately identifies enhancer-promoter interactions and recovers biological findings across conditions, enabling insights into global gene expression control.

NATURE COMMUNICATIONS (2021)

Article Biochemical Research Methods

Cooler: scalable storage for Hi-C data and other genomically labeled arrays

Nezar Abdennur et al.

BIOINFORMATICS (2020)

Article Biochemical Research Methods

Accurate loop calling for 3D genomic data with cLoops

Yaqiang Cao et al.

BIOINFORMATICS (2020)

Article Biochemistry & Molecular Biology

Analysis of Hi-C data using SIP effectively identifies loops in organisms from C. elegans to mammals

M. Jordan Rowley et al.

GENOME RESEARCH (2020)

Article Biochemical Research Methods

Identifying statistically significant chromatin contacts from Hi-C data with FitHiC2

Arya Kaul et al.

NATURE PROTOCOLS (2020)

Article Biotechnology & Applied Microbiology

OnTAD: hierarchical domain structure reveals the divergence of activity among TADs and boundaries

Lin An et al.

GENOME BIOLOGY (2019)

Article Biotechnology & Applied Microbiology

Measuring the reproducibility and quality of Hi-C data

Galip Gurkan Yardimci et al.

GENOME BIOLOGY (2019)

Article Multidisciplinary Sciences

High-resolution TADs reveal DNA sequences underlying genome organization in flies

Fidel Ramirez et al.

NATURE COMMUNICATIONS (2018)

Article Biochemistry & Molecular Biology

HiCDB: a sensitive and robust method for detecting contact domain boundaries

Fengling Chen et al.

NUCLEIC ACIDS RESEARCH (2018)

Article Biotechnology & Applied Microbiology

Comparison of computational methods for the identification of topologically associating domains

Marie Zufferey et al.

GENOME BIOLOGY (2018)

Article Biochemistry & Molecular Biology

HiCRep: assessing the reproducibility of Hi-C data using a stratum-adjusted correlation coefficient

Tao Yang et al.

GENOME RESEARCH (2017)

Article Biochemical Research Methods

Comparison of computational methods for Hi-C data analysis

Mattia Forcato et al.

NATURE METHODS (2017)

Article Biochemistry & Molecular Biology

A critical assessment of topologically associating domain prediction tools

Rola Dali et al.

NUCLEIC ACIDS RESEARCH (2017)

Article Biochemical Research Methods

Automatic analysis and 3D-modelling of Hi-C data using TADbit reveals structural features of the fly chromatin colors

Francois Serra et al.

PLOS COMPUTATIONAL BIOLOGY (2017)

Article Biochemical Research Methods

HiC-spector: a matrix library for spectral and reproducibility analysis of Hi-C contact maps

Koon-Kiu Yan et al.

BIOINFORMATICS (2017)

Article Biochemical Research Methods

Identification of hierarchical chromatin domains

Caleb Weinreb et al.

BIOINFORMATICS (2016)

Article Biochemistry & Molecular Biology

TopDom: an efficient and deterministic method for identifying topological domains in genomes

Hanjun Shin et al.

NUCLEIC ACIDS RESEARCH (2016)

Review Cell Biology

Genome-wide mapping and analysis of chromosome architecture

Anthony D. Schmitt et al.

NATURE REVIEWS MOLECULAR CELL BIOLOGY (2016)

Article Biochemistry & Molecular Biology

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

Neva C. Durand et al.

CELL SYSTEMS (2016)

Article Multidisciplinary Sciences

Condensin-driven remodelling of X chromosome topology during dosage compensation

Emily Crane et al.

NATURE (2015)

Article Genetics & Heredity

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

Borbala Mifsud et al.

NATURE GENETICS (2015)

Article Biotechnology & Applied Microbiology

HiC-Pro: an optimized and flexible pipeline for Hi-C data processing

Nicolas Servant et al.

GENOME BIOLOGY (2015)

Review Biotechnology & Applied Microbiology

Analysis methods for studying the 3D architecture of the genome

Ferhat Ay et al.

GENOME BIOLOGY (2015)

Article Biochemical Research Methods

Identification of alternative topological domains in chromatin

Darya Filippova et al.

ALGORITHMS FOR MOLECULAR BIOLOGY (2014)

Article Biochemical Research Methods

Two-dimensional segmentation for analyzing Hi-C data

Celine Levy-Leduc et al.

BIOINFORMATICS (2014)

Article Biochemistry & Molecular Biology

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

Suhas S. P. Rao et al.

Review Biochemistry & Molecular Biology

Functional implications of genome topology

Giacomo Cavalli et al.

NATURE STRUCTURAL & MOLECULAR BIOLOGY (2013)

Article Multidisciplinary Sciences

The long-range interaction landscape of gene promoters

Amartya Sanyal et al.

NATURE (2012)

Article Multidisciplinary Sciences

Topological domains in mammalian genomes identified by analysis of chromatin interactions

Jesse R. Dixon et al.

NATURE (2012)

Article Biochemical Research Methods

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

Maxim Imakaev et al.

NATURE METHODS (2012)

Article Biochemical Research Methods

The GEM mapper: fast, accurate and versatile alignment by filtration

Santiago Marco-Sola et al.

NATURE METHODS (2012)

Article Biochemical Research Methods

Fast gapped-read alignment with Bowtie 2

Ben Langmead et al.

NATURE METHODS (2012)

Article Biochemical Research Methods

BEDTools: a flexible suite of utilities for comparing genomic features

Aaron R. Quinlan et al.

BIOINFORMATICS (2010)

Article Multidisciplinary Sciences

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

Erez Lieberman-Aiden et al.

SCIENCE (2009)