Orchestrating chromosome conformation capture analysis with Bioconductor

[1]  B. Stecher,et al.  Chromosome folding and prophage activation reveal specific genomic architecture for intestinal bacteria , 2023, Microbiome.

[2]  A. Lun.  basilisk: a Bioconductor package for managing Python environments , 2022, J. Open Source Softw..

[3]  P. Park,et al.  The 4D Nucleome Data Portal as a resource for searching and visualizing curated nucleomics data , 2022, Nature Communications.

[4]  Brian D. O’Connor,et al.  Inverting the model of genomics data sharing with the NHGRI Genomic Data Science Analysis, Visualization, and Informatics Lab-space , 2022, Cell genomics.

[5]  L. Mirny,et al.  Mechanisms of Chromosome Folding and Nuclear Organization: Their Interplay and Open Questions. , 2021, Cold Spring Harbor perspectives in biology.

[6]  S. Ceri,et al.  Systematic inference and comparison of multi-scale chromatin sub-compartments connects spatial organization to cell phenotypes , 2021, Nature Communications.

[7]  Elzo de Wit,et al.  Hi-C analyses with GENOVA: a case study with cohesin variants , 2021, bioRxiv.

[8]  L. Mirny,et al.  Systematic evaluation of chromosome conformation capture assays , 2020, Nature Methods.

[9]  Juan M. Vaquerizas,et al.  FAN-C: a feature-rich framework for the analysis and visualisation of chromosome conformation capture data , 2020, Genome Biology.

[10]  T. Misteli.  The Self-Organizing Genome: Principles of Genome Architecture and Function , 2020, Cell.

[11]  Yann Loe Mie,et al.  instaGRAAL: chromosome-level quality scaffolding of genomes using a proximity ligation-based scaffolder , 2020, Genome Biology.

[12]  Martin Vingron,et al.  Hi-C Identifies Complex Genomic Rearrangements and TAD-Shuffling in Developmental Diseases. , 2020, American journal of human genetics.

[13]  Cyril Matthey-Doret,et al.  Computer vision for pattern detection in chromosome contact maps , 2020, Nature Communications.

[14]  Sven Nahnsen,et al.  The nf-core framework for community-curated bioinformatics pipelines , 2020, Nature Biotechnology.

[15]  A. Thierry,et al.  Regulation of Cohesin-Mediated Chromosome Folding by Eco1 and Other Partners. , 2020, Molecular cell.

[16]  Leonid A. Mirny,et al.  Ultrastructural details of mammalian chromosome architecture , 2019, bioRxiv.

[17]  Giacomo Cavalli,et al.  Principles of genome folding into topologically associating domains , 2019, Science Advances.

[18]  Raphael Gottardo,et al.  Orchestrating single-cell analysis with Bioconductor , 2019, Nature Methods.

[19]  Ilya M. Flyamer,et al.  Coolpup.py: versatile pile-up analysis of Hi-C data , 2019, bioRxiv.

[20]  Nezar Abdennur,et al.  Cooler: scalable storage for Hi-C data and other genomically-labeled arrays , 2019, bioRxiv.

[21]  John C Stansfield,et al.  multiHiCcompare: joint normalization and comparative analysis of complex Hi-C experiments , 2019, Bioinform..

[22]  Bing Ren,et al.  Coordinated histone modifications and chromatin reorganization in a single cell revealed by FRET biosensors , 2018, Proceedings of the National Academy of Sciences.

[23]  V. Corces,et al.  Organizational principles of 3D genome architecture , 2018, Nature Reviews Genetics.

[24]  Mikhail G. Dozmorov,et al.  HiCcompare: an R-package for joint normalization and comparison of HI-C datasets , 2018, BMC Bioinformatics.

[25]  J. Ahringer,et al.  Genome organization at different scales: nature, formation and function. , 2018, Current opinion in cell biology.

[26]  J. R. Paulson,et al.  A pathway for mitotic chromosome formation , 2018, Science.

[27]  A. Cournac,et al.  Multiscale Structuring of the E. coli Chromosome by Nucleoid-Associated and Condensin Proteins , 2018, Cell.

[28]  William Stafford Noble,et al.  HiCRep: assessing the reproducibility of Hi-C data using a stratum-adjusted correlation coefficient , 2017, bioRxiv.

[29]  Jonathan Baxter,et al.  SMC complexes differentially compact mitotic chromosomes according to genomic context , 2017, Nature Cell Biology.

[30]  David J Barry,et al.  Condensin-mediated remodeling of the mitotic chromatin landscape in fission yeast , 2017, Nature Genetics.

[31]  A. Thierry,et al.  Cohesins and condensins orchestrate the 4D dynamics of yeast chromosomes during the cell cycle , 2017, The EMBO journal.

[32]  Jacob M. Luber,et al.  HiGlass: web-based visual exploration and analysis of genome interaction maps , 2017, Genome Biology.

[33]  Kin Chung Lam,et al.  High-resolution TADs reveal DNA sequences underlying genome organization in flies , 2017, Nature Communications.

[34]  Lyam Baudry,et al.  Scaffolding bacterial genomes and probing host-virus interactions in gut microbiome by proximity ligation (chromosome capture) assay , 2017, Science Advances.

[35]  William Stafford Noble,et al.  Mapping 3D genome architecture through in situ DNase Hi-C , 2016, Nature Protocols.

[36]  James T. Robinson,et al.  Juicebox Provides a Visualization System for Hi-C Contact Maps with Unlimited Zoom. , 2016, Cell systems.

[37]  Neva C. Durand,et al.  Juicer Provides a One-Click System for Analyzing Loop-Resolution Hi-C Experiments. , 2016, Cell systems.

[38]  Elizabeth Ing-Simmons,et al.  Infrastructure for genomic interactions: Bioconductor classes for Hi-C, ChIA-PET and related experiments , 2016, F1000Research.

[39]  Neva C. Durand,et al.  De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds , 2016, Science.

[40]  Jean-Philippe Vert,et al.  HiC-Pro: an optimized and flexible pipeline for Hi-C data processing , 2015, Genome Biology.

[41]  Philip A. Ewels,et al.  HiCUP: pipeline for mapping and processing Hi-C data , 2015, F1000Research.

[42]  Nir Friedman,et al.  Mapping Nucleosome Resolution Chromosome Folding in Yeast by Micro-C , 2015, Cell.

[43]  A. Visel,et al.  Disruptions of Topological Chromatin Domains Cause Pathogenic Rewiring of Gene-Enhancer Interactions , 2015, Cell.

[44]  J. Dekker,et al.  Condensin-Driven Remodeling of X-Chromosome Topology during Dosage Compensation , 2015, Nature.

[45]  Raphael Gottardo,et al.  Orchestrating high-throughput genomic analysis with Bioconductor , 2015, Nature Methods.

[46]  Neva C. Durand,et al.  A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping , 2014, Cell.

[47]  Antoine Margeot,et al.  High-quality genome (re)assembly using chromosomal contact data , 2014, Nature Communications.

[48]  J. Dekker,et al.  High-throughput genome scaffolding from in-vivo DNA interaction frequency , 2013, Nature Biotechnology.

[49]  Robert Gentleman,et al.  Software for Computing and Annotating Genomic Ranges , 2013, PLoS Comput. Biol..

[50]  L. Mirny,et al.  Iterative Correction of Hi-C Data Reveals Hallmarks of Chromosome Organization , 2012, Nature Methods.

[51]  A. Cournac,et al.  Normalization of a chromosomal contact map , 2012, BMC Genomics.

[52]  Jesse R. Dixon,et al.  Topological Domains in Mammalian Genomes Identified by Analysis of Chromatin Interactions , 2012, Nature.

[53]  Benjamin A. Garcia,et al.  Regulation of HP1–chromatin binding by histone H3 methylation and phosphorylation , 2005, Nature.

[54]  C. Allis,et al.  Mitosis-specific phosphorylation of histone H3 initiates primarily within pericentromeric heterochromatin during G2 and spreads in an ordered fashion coincident with mitotic chromosome condensation , 1997, Chromosoma.

[55]  OUP accepted manuscript , 2021, Bioinformatics.

[56]  Emmanuel Barillot,et al.  HiTC - Exploration of High Throughput ’C’ experiments , 2013 .

[57]  C. Cremer.  NUCLEAR ARCHITECTURE AND GENE REGULATION IN MAMMALIAN CELLS , 2001 .

[58]  I. Amit,et al.  Supporting Online Material Materials and Methods Som Text Comprehensive Mapping of Long-range Interactions Reveals Folding Principles of the Human Genome , 2022 .

[59]  I. Korf,et al.  Distributed under Creative Commons Cc-by 4.0 Strain-and Plasmid-level Deconvolution of a Synthetic Metagenome by Sequencing Proximity Ligation Products , 2022 .