Research graph
References from Application of Hi-C and other omics data analysis in human cancer and cell differentiation research. Local targets link to admitted publications; unresolved targets remain external evidence.
10.1038/nrg2484
10.1038/nrg2484 · External reference
10.1007/978-1-61779-477-3_24
10.1007/978-1-61779-477-3_24 · External reference
10.1101/pdb.prot5384
10.1101/pdb.prot5384 · External reference
ATAC-seq: a method for assaying chromatin accessibility genome-wide
10.1002/0471142727.mb2129s109 · 2015 · External reference
10.1101/gr.5533506
10.1101/gr.5533506 · External reference
10.1016/j.ymeth.2009.03.003
10.1016/j.ymeth.2009.03.003 · External reference
10.1016/j.ymeth.2009.03.001
10.1016/j.ymeth.2009.03.001 · External reference
10.1126/science.1181369
10.1126/science.1181369 · External reference
Hi-C: a method to study the three-dimensional architecture of genomes
2010 · External reference
10.1242/dev.02239
10.1242/dev.02239 · External reference
10.1093/hmg/ddg180
10.1093/hmg/ddg180 · External reference
Identification of focally amplified lineage-specific super-enhancers in human epithelial cancers
2016 · External reference
10.1016/j.cell.2015.07.038
10.1016/j.cell.2015.07.038 · External reference
10.1126/science.1067799
10.1126/science.1067799 · External reference
10.1038/ng1896
10.1038/ng1896 · External reference
10.1038/nature12593
10.1038/nature12593 · External reference
Fine-scale chromatin interaction maps reveal the cis-regulatory landscape of human lincRNA genes
10.1038/nmeth.3205 · 2014 · External reference
10.1016/j.cell.2014.11.021
10.1016/j.cell.2014.11.021 · External reference
10.1038/nature21411
10.1038/nature21411 · External reference
BL-Hi-C is an efficient and sensitive approach for capturing structural and regulatory chromatin interactions
10.1038/s41467-017-01754-3 · 2017 · External reference
10.1038/nmeth.4155
10.1038/nmeth.4155 · External reference
10.1038/nature21429
10.1038/nature21429 · External reference
10.1101/gad.179804.111
10.1101/gad.179804.111 · External reference
10.1038/nrg3454
10.1038/nrg3454 · External reference
10.1093/bfgp/elaa004
10.1093/bfgp/elaa004 · External reference
Reconstruction of three-dimensional structures of chromatin and its biological implications
2014 · External reference
10.1016/j.csbj.2018.02.003
10.1016/j.csbj.2018.02.003 · External reference
10.1016/j.semcdb.2018.07.008
10.1016/j.semcdb.2018.07.008 · External reference
10.1007/s10565-018-09456-2
10.1007/s10565-018-09456-2 · External reference
An overview of methods for reconstructing 3-D chromosome and genome structures from Hi-C data
10.1186/s12575-019-0094-0 · 2019 · External reference
10.1007/s11427-019-1704-2
10.1007/s11427-019-1704-2 · External reference
10.1080/19491034.2015.1106676
10.1080/19491034.2015.1106676 · External reference
10.1016/j.semcdb.2018.07.022
10.1016/j.semcdb.2018.07.022 · External reference
10.1016/j.semcdb.2018.07.004
10.1016/j.semcdb.2018.07.004 · External reference
Mutational biases drive elevated rates of substitution at regulatory sites across cancer types
2016 · External reference
10.1038/nbt.2030
10.1038/nbt.2030 · External reference
Chromatin organization is a major influence on regional mutation rates in human cancer cells
10.1038/nature11273 · 2012 · External reference
10.1101/178269
10.1101/178269 · External reference
10.1038/nature16490
10.1038/nature16490 · External reference
Pan-cancer analysis of somatic copy-number alterations implicates IRS4 and IGF2 in enhancer hijacking
2016 · External reference
Transcriptionally active HERV-H retrotransposons demarcate topologically associating domains in human pluripotent stem cells
10.1038/s41588-019-0479-7 · 2019 · External reference
Architectural proteins and pluripotency factors cooperate to orchestrate the transcriptional response of hESCs to temperature stress
2018 · External reference
Global reorganisation of $extit{cis}$-regulatory units upon lineage commitment of human embryonic stem cells
2017 · External reference
Enhancer chromatin and 3D genome architecture changes from naive to primed human embryonic stem cell states
10.1016/j.stemcr.2019.04.004 · 2019 · External reference
Dynamics of genome reorganization during human cardiogenesis reveal an RBM20-dependent splicing factory
10.1038/s41467-019-09483-5 · 2019 · External reference
Identifying cis elements for spatiotemporal control of mammalian DNA replication
2018 · External reference
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10.1101/163113
10.1101/163113 · External reference
Dynamic rewiring of promoter-anchored chromatin loops during adipocyte
2017 · External reference
10.1016/j.celrep.2020.108315
10.1016/j.celrep.2020.108315 · External reference
Molecular basis of CTCF binding polarity in genome folding
2020 · External reference
10.1038/s41588-019-0538-0
10.1038/s41588-019-0538-0 · External reference
PRC1 collaborates with SMCHD1 to fold the X-chromosome and spread Xist RNA between chromosome compartments
2019 · External reference
Unresolved reference
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10.1016/j.molcel.2018.11.019
10.1016/j.molcel.2018.11.019 · External reference
Exploration of CTCF post-translation modifications uncovers Serine-224 phosphorylation by PLK1 at pericentric regions during the G2/M transition
2019 · External reference
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Epigenetic silencing of miR-125b is required for normal B-cell development
2018 · External reference
Exonuclease combinations reduce noises in 3D genomics technologies
2020 · External reference
Chromatin architecture reorganization in murine somatic cell nuclear transfer embryos
2020 · External reference
Polycomb group proteins regulate chromatin architecture in mouse oocytes and early embryos
2019 · External reference
An Erg-driven transcriptional program controls B cell lymphopoiesis
2020 · External reference
Promoter-proximal CTCF binding promotes distal enhancer-dependent gene activation
2021 · External reference
10.1016/j.celrep.2019.10.031
10.1016/j.celrep.2019.10.031 · External reference
10.15252/msb.20156492
10.15252/msb.20156492 · External reference
10.1016/j.stem.2015.11.010
10.1016/j.stem.2015.11.010 · External reference
10.1016/j.cell.2018.05.024
10.1016/j.cell.2018.05.024 · External reference
10.1242/dev.188516
10.1242/dev.188516 · External reference
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A fast algorithm for matrix balancing
10.1093/imanum/drs019 · 2013 · External reference
10.1038/nmeth.2148
10.1038/nmeth.2148 · External reference
10.1093/nar/gkr425
10.1093/nar/gkr425 · External reference
10.1093/nar/gkt745
10.1093/nar/gkt745 · External reference
10.1093/bioinformatics/btx747
10.1093/bioinformatics/btx747 · External reference
10.1038/ng.947
10.1038/ng.947 · External reference
10.1186/1471-2164-13-436
10.1186/1471-2164-13-436 · External reference
10.1371/journal.pone.0006700
10.1371/journal.pone.0006700 · External reference
10.1093/bioinformatics/bts570
10.1093/bioinformatics/bts570 · External reference
Effective normalization for copy number variation in Hi-C data
10.1186/s12859-018-2256-5 · 2018 · External reference
10.1038/s41467-018-03113-2
10.1038/s41467-018-03113-2 · External reference
10.1093/bioinformatics/btz251
10.1093/bioinformatics/btz251 · External reference
10.3390/genes10110862
10.3390/genes10110862 · External reference
10.1093/bioinformatics/btz317
10.1093/bioinformatics/btz317 · External reference
DeepHiC: a generative adversarial network for enhancing Hi-C data resolution
10.1371/journal.pcbi.1007287 · 2020 · External reference
10.3389/fgene.2020.00353
10.3389/fgene.2020.00353 · External reference
10.1016/j.ymeth.2014.10.031
10.1016/j.ymeth.2014.10.031 · External reference
10.1016/j.cels.2016.07.002
10.1016/j.cels.2016.07.002 · External reference
A maximum likelihood algorithm for reconstructing 3D structures of human chromosomes from chromosomal contact data
10.1186/s12864-018-4546-8 · 2018 · External reference
10.1093/nar/gkq955
10.1093/nar/gkq955 · External reference
10.1093/bioinformatics/btu268
10.1093/bioinformatics/btu268 · External reference
10.1371/journal.pcbi.1002893
10.1371/journal.pcbi.1002893 · External reference
Impact of data resolution on three-dimensional structure inference methods
10.1186/s12859-016-0894-z · 2016 · External reference
10.1093/nar/gkw437
10.1093/nar/gkw437 · External reference
10.1371/journal.pcbi.1005665
10.1371/journal.pcbi.1005665 · External reference
Chromatin 3D reconstruction from chromosomal contacts using a genetic algorithm
10.1109/tcbb.2018.2814995 · 2018 · External reference
The design space of construction tools for information visualization: a survey
10.1016/j.jvlc.2017.10.001 · 2017 · External reference
Chromosome3D: reconstructing three-dimensional chromosomal structures from Hi-C interaction frequency data using distance geometry simulated annealing
10.1186/s12864-016-3210-4 · 2016 · External reference
Chromatin conformation signatures of cellular differentiation
10.1186/gb-2009-10-4-r37 · 2009 · External reference
10.1101/401513
10.1101/401513 · External reference
10.1093/bioinformatics/btu491
10.1093/bioinformatics/btu491 · External reference
10.1101/415810
10.1101/415810 · External reference
HSA: integrating multi-track Hi-C data for genome-scale reconstruction of 3D chromatin structure
10.1186/s13059-016-0896-1 · 2016 · External reference
10.1007/978-3-642-37195-0_31
10.1007/978-3-642-37195-0_31 · External reference
10.1093/nar/gkv100
10.1093/nar/gkv100 · External reference
An integrated 3-dimensional genome modeling engine for data-driven simulation of spatial genome organization
2016 · External reference
10.1371/journal.pcbi.1005292
10.1371/journal.pcbi.1005292 · External reference
10.1371/journal.pcbi.1004396
10.1371/journal.pcbi.1004396 · External reference
10.1093/bioinformatics/btx271
10.1093/bioinformatics/btx271 · External reference
10.1038/nature08973
10.1038/nature08973 · External reference
EVR: reconstruction of bacterial chromosome 3D structure models using error-vector resultant algorithm
2019 · External reference
3D genome structure modeling by Lorentzian objective function
10.1093/nar/gkw1155 · 2016 · External reference
10.1109/tcbb.2016.2535372
10.1109/tcbb.2016.2535372 · External reference
10.1089/cmb.2013.0076
10.1089/cmb.2013.0076 · External reference
10.1093/nar/gky065
10.1093/nar/gky065 · External reference
Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities
2010 · External reference
10.1038/ng.3286
10.1038/ng.3286 · External reference
Statistical confidence estimation for Hi-C data reveals regulatory chromatin contacts
2014 · External reference
An integrated model for detecting significant chromatin interactions from high-resolution Hi-C data
10.1038/ncomms15454 · 2017 · External reference
10.1101/gr.257832.119
10.1101/gr.257832.119 · External reference
Accurate loop calling for 3D genomic data with cLoops
2019 · External reference
Mustache: multi-scale detection of chromatin loops from Hi-C and micro-C maps using scale-space representation
10.1186/s13059-020-02167-0 · 2020 · External reference
10.1101/gr.193474.115
10.1101/gr.193474.115 · External reference
Promoter-enhancer interactions identified from Hi-C data using probabilistic models and hierarchical topological domains
10.1038/s41467-017-02386-3 · 2017 · External reference
diffHic: a Bioconductor package to detect differential genomic interactions in Hi-C data
2015 · External reference
FIND: difFerential chromatin INteractions Detection using a spatial Poisson process
10.1101/gr.212241.116 · 2018 · External reference
HiCcompare: An R-package for joint normalization and comparison of HI-C datasets
10.1186/s12859-018-2288-x · 2018 · External reference
10.1038/nature11082
10.1038/nature11082 · External reference
Identification of alternative topological domains in chromatin
10.1186/1748-7188-9-14 · 2014 · External reference
10.1093/bioinformatics/btu443
10.1093/bioinformatics/btu443 · External reference
10.1038/nature14450
10.1038/nature14450 · External reference
10.1007/s40484-015-0047-9
10.1007/s40484-015-0047-9 · External reference
TopDom: an efficient and deterministic method for identifying topological domains in genomes
10.1093/nar/gkv1505 · 2015 · External reference
Identification of hierarchical chromatin domains
10.1093/bioinformatics/btv485 · 2015 · External reference
10.1093/bioinformatics/btw221
10.1093/bioinformatics/btw221 · External reference
IC-Finder: inferring robustly the hierarchical organization of chromatin folding
2017 · External reference
10.1371/journal.pcbi.1005647
10.1371/journal.pcbi.1005647 · External reference
Detecting hierarchical genome folding with network modularity
10.1038/nmeth.4560 · 2018 · External reference
10.1093/nar/gkx735
10.1093/nar/gkx735 · External reference
Identifying topologically associating domains and subdomains by Gaussian Mixture model And Proportion test
10.1038/s41467-017-00478-8 · 2017 · External reference
10.1093/nar/gky789
10.1093/nar/gky789 · External reference
Decoding topologically associating domains with ultra-low resolution Hi-C data by graph structural entropy
10.1038/s41467-018-05691-7 · 2018 · External reference
10.1093/nar/gkz315
10.1093/nar/gkz315 · External reference
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TADBD: a sensitive and fast method for detection of typologically associated domain boundaries
2020 · External reference
TADCompare: an R package for differential and temporal analysis of topologically associated domains
10.3389/fgene.2020.00158 · 2020 · External reference
Hierarchical chromatin organization detected by TADpole
10.1093/nar/gkaa087 · 2020 · External reference
SpectralTAD: an R package for defining a hierarchy of topologically associated domains using spectral clustering
2020 · External reference
ClusterTAD: an unsupervised machine learning approach to detecting topologically associated domains of chromosomes from Hi-C data
10.1186/s12859-017-1931-2 · 2017 · External reference
10.1145/3107411.3107448
10.1145/3107411.3107448 · External reference
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10.1186/s13059-015-0831-x
10.1186/s13059-015-0831-x · External reference
Iterative reconstruction of three-dimensional models of human chromosomes from chromosomal contact data
10.1186/s12859-015-0772-0 · 2015 · External reference
MOGEN: a tool for reconstructing 3D models of genomes from chromosomal conformation capturing data
10.1093/bioinformatics/btv754 · 2015 · External reference
Integrating Hi-C and FISH data for modeling of the 3D organization of chromosomes
10.1038/s41467-019-10005-6 · 2019 · External reference
Large-scale 3D chromatin reconstruction from chromosomal contacts
10.1186/s12864-019-5470-2 · 2019 · External reference
10.1038/nmeth.3104
10.1038/nmeth.3104 · External reference
HSA: integrating multi-track Hi-C data for genome-scale reconstruction of 3D chromatin structure
10.1186/s13059-016-0896-1 · 2016 · External reference
Chromatin 3D structure reconstruction with consideration of adjacency relationship among genomic loci
2020 · External reference
10.1038/nprot.2018.008
10.1038/nprot.2018.008 · External reference
10.1101/316265
10.1101/316265 · External reference
10.1109/tcbb.2018.2838669
10.1109/tcbb.2018.2838669 · External reference
The Nucleome Data Bank: web-based resources to simulate and analyze the three-dimensional genome
2020 · External reference
10.1101/499806
10.1101/499806 · External reference
10.1186/s12860-020-00304-y
10.1186/s12860-020-00304-y · External reference
3D-GNOME 2.0: a three-dimensional genome modeling engine for predicting structural variation-driven alterations of chromatin spatial structure in the human genome
10.1093/nar/gkaa388 · 2020 · External reference
10.1093/bioinformatics/btu081
10.1093/bioinformatics/btu081 · External reference
3DIV update for 2021: a comprehensive resource of 3D genome and 3D cancer genome
2020 · External reference
Unresolved reference
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10.1186/gb-2008-9-9-r137
10.1186/gb-2008-9-9-r137 · External reference
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10.1093/bioinformatics/btq033
10.1093/bioinformatics/btq033 · External reference
10.1186/1752-0509-5-s2-s3
10.1186/1752-0509-5-s2-s3 · External reference
10.1093/bioinformatics/btp616
10.1093/bioinformatics/btp616 · External reference
Differential gene expression analysis based on the negative binomial distribution
2009 · External reference
Unresolved reference
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Unresolved reference
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MethGo: a comprehensive tool for analyzing whole-genome bisulfite sequencing data
10.1186/1471-2164-16-s12-s11 · 2015 · External reference
10.1101/gr.107524.110
10.1101/gr.107524.110 · External reference
10.1093/bioinformatics/btp352
10.1093/bioinformatics/btp352 · External reference
10.1089/106652703322756131
10.1089/106652703322756131 · External reference
10.1038/nprot.2012.016
10.1038/nprot.2012.016 · External reference
10.1038/s41467-017-00050-4
10.1038/s41467-017-00050-4 · External reference
Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists
10.1093/nar/gkn923 · 2009 · External reference
10.1038/nprot.2008.211
10.1038/nprot.2008.211 · External reference
10.1093/nar/gkr483
10.1093/nar/gkr483 · External reference
10.1073/pnas.0809501106
10.1073/pnas.0809501106 · External reference
Solid-phase chromosome conformation capture for structural characterization of genome architectures
2012 · External reference
10.1186/s13059-016-1146-2
10.1186/s13059-016-1146-2 · External reference
10.1038/nprot.2018.009
10.1038/nprot.2018.009 · External reference
Three-dimensional modeling of chromatin structure from interaction frequency data using Markov chain Monte Carlo sampling
10.1186/1471-2105-12-414 · 2011 · External reference
10.1038/nsmb.1936
10.1038/nsmb.1936 · External reference
10.1093/nar/gks1029
10.1093/nar/gks1029 · External reference
10.1073/pnas.1512577113
10.1073/pnas.1512577113 · External reference
10.1093/nar/gkt1411
10.1093/nar/gkt1411 · External reference
Large-scale 3D chromatin reconstruction from chromosomal contacts
10.1186/s12864-019-5470-2 · 2019 · External reference
10.1186/s13059-015-0741-y
10.1186/s13059-015-0741-y · External reference
10.1016/j.molp.2017.11.005
10.1016/j.molp.2017.11.005 · External reference
10.1007/978-1-4939-8766-5_16
10.1007/978-1-4939-8766-5_16 · External reference
10.1038/nature11049
10.1038/nature11049 · External reference
TADs as the caller calls them
2019 · External reference
Pancreatic islet chromatin accessibility and conformation reveals distal enhancer networks of type 2 diabetes risk
10.1038/s41467-019-09975-4 · 2019 · External reference
10.1016/j.molcel.2010.05.004
10.1016/j.molcel.2010.05.004 · External reference
10.1038/nbt.1754
10.1038/nbt.1754 · External reference
10.1186/s13059-015-0768-0
10.1186/s13059-015-0768-0 · External reference
Three-dimensional disorganization of the cancer genome occurs coincident with long-range genetic and epigenetic alterations
2016 · External reference
10.1038/s41467-017-01793-w
10.1038/s41467-017-01793-w · External reference
10.1016/j.cell.2017.03.024
10.1016/j.cell.2017.03.024 · External reference
Lineage-specific dynamic and pre-established enhancer–promoter contacts cooperate in terminal differentiation
2017 · External reference
High resolution mapping of chromatin conformation in cardiac myocytes reveals structural remodeling of the epigenome in heart failure
10.1161/circulationaha.117.029430 · 2017 · External reference
10.1038/s41588-018-0218-5
10.1038/s41588-018-0218-5 · External reference
