Research graph
References from Chromatin Hubs: A biological and computational outlook. Local targets link to admitted publications; unresolved targets remain external evidence.
In the loop: promoter-enhancer interactions and bioinformatics
2016 · External reference
10.1126/science.1067799
10.1126/science.1067799 · External reference
10.1126/science.1181369
10.1126/science.1181369 · External reference
10.1002/jcb.22116
10.1002/jcb.22116 · External reference
10.1038/ng.3286
10.1038/ng.3286 · External reference
10.1016/j.cell.2014.11.021
10.1016/j.cell.2014.11.021 · External reference
10.1093/nar/gkaa817
10.1093/nar/gkaa817 · External reference
10.1016/j.tig.2011.05.006
10.1016/j.tig.2011.05.006 · External reference
10.1016/j.cell.2016.04.047
10.1016/j.cell.2016.04.047 · External reference
10.1126/science.aar3958
10.1126/science.aar3958 · External reference
10.1016/j.cell.2017.02.007
10.1016/j.cell.2017.02.007 · External reference
10.1093/nar/gkaa828
10.1093/nar/gkaa828 · External reference
10.1038/nature11082
10.1038/nature11082 · External reference
10.1073/pnas.1317788111
10.1073/pnas.1317788111 · External reference
10.1016/j.cell.2017.05.004
10.1016/j.cell.2017.05.004 · External reference
10.1038/nrg3454
10.1038/nrg3454 · External reference
Comparison of computational methods for the identification of topologically associating domains
10.1186/s13059-018-1596-9 · 2018 · External reference
10.1038/s41587-021-00998-1
10.1038/s41587-021-00998-1 · External reference
10.1038/s41588-020-00716-8
10.1038/s41588-020-00716-8 · External reference
10.1126/science.aau1783
10.1126/science.aau1783 · External reference
10.1126/science.abn6583
10.1126/science.abn6583 · External reference
10.1038/nature22989
10.1038/nature22989 · External reference
10.1038/s41576-019-0135-1
10.1038/s41576-019-0135-1 · External reference
10.1016/j.cell.2017.04.022
10.1016/j.cell.2017.04.022 · External reference
10.1186/s13059-020-02003-5
10.1186/s13059-020-02003-5 · External reference
10.1016/j.cell.2019.03.009
10.1016/j.cell.2019.03.009 · External reference
10.1016/j.cell.2015.08.040
10.1016/j.cell.2015.08.040 · External reference
A-type lamins bind both hetero- and euchromatin, the latter being regulated by lamina-associated polypeptide 2 alpha
10.1101/gr.196220.115 · 2016 · External reference
10.1038/s41586-019-1233-0
10.1038/s41586-019-1233-0 · External reference
Transcription factories
10.3389/fgene.2012.00221 · 2012 · External reference
10.1021/cr300513p
10.1021/cr300513p · External reference
10.1016/j.ceb.2022.01.005
10.1016/j.ceb.2022.01.005 · External reference
10.1016/j.gde.2012.01.010
10.1016/j.gde.2012.01.010 · External reference
10.1101/gad.454008
10.1101/gad.454008 · External reference
10.1371/journal.pone.0001661
10.1371/journal.pone.0001661 · External reference
10.1101/gr.111153.110
10.1101/gr.111153.110 · External reference
Human transcriptional interactome of chromatin contribute to gene co-expression
10.1186/1471-2164-11-704 · 2010 · External reference
10.1038/sj.emboj.7600385
10.1038/sj.emboj.7600385 · External reference
10.1093/nar/gkt1294
10.1093/nar/gkt1294 · External reference
10.1038/emboj.2012.288
10.1038/emboj.2012.288 · External reference
10.1101/gad.289704
10.1101/gad.289704 · External reference
10.1038/ni1115
10.1038/ni1115 · External reference
10.1038/ng1913
10.1038/ng1913 · External reference
10.1371/journal.pbio.0050192
10.1371/journal.pbio.0050192 · External reference
10.1101/gad.1606308
10.1101/gad.1606308 · External reference
10.1038/nature08497
10.1038/nature08497 · External reference
10.1111/j.1471-4159.2010.06956.x
10.1111/j.1471-4159.2010.06956.x · External reference
10.1098/rsob.120176
10.1098/rsob.120176 · External reference
The transcription factor Znf219 regulates chondrocyte differentiation by assembling a transcription factory with Sox9
10.1242/jcs.071373 · 2010 · External reference
10.1016/j.cell.2011.10.023
10.1016/j.cell.2011.10.023 · External reference
10.1126/science.1207194
10.1126/science.1207194 · External reference
10.1126/science.1234167
10.1126/science.1234167 · External reference
10.1016/j.mce.2011.09.006
10.1016/j.mce.2011.09.006 · External reference
10.1073/pnas.1112570109
10.1073/pnas.1112570109 · External reference
10.1016/j.stem.2013.04.013
10.1016/j.stem.2013.04.013 · External reference
High-resolution analysis of cis-acting regulatory networks at the alpha-globin locus
10.1098/rstb.2012.0361 · 2013 · External reference
10.1016/j.celrep.2018.07.091
10.1016/j.celrep.2018.07.091 · External reference
10.1038/nrg2592
10.1038/nrg2592 · External reference
The expanding RNA polymerase III transcriptome
10.1016/j.tig.2007.09.001 · 2007 · External reference
10.1016/j.stemcr.2020.10.011
10.1016/j.stemcr.2020.10.011 · External reference
10.1016/j.tig.2020.12.006
10.1016/j.tig.2020.12.006 · External reference
10.1038/s41580-021-00398-y
10.1038/s41580-021-00398-y · External reference
10.1101/gad.326488.119
10.1101/gad.326488.119 · External reference
10.1074/jbc.ra118.006620
10.1074/jbc.ra118.006620 · External reference
PRC1 components exhibit different binding kinetics in Polycomb bodies
10.1111/boc.201300077 · 2014 · External reference
Theoretical analysis of Polycomb-Trithorax systems predicts that poised chromatin is bistable and not bivalent
10.1038/s41467-019-10130-2 · 2019 · External reference
A theoretical model of Polycomb/Trithorax action unites stable epigenetic memory and dynamic regulation
10.1038/s41467-020-18507-4 · 2020 · External reference
10.1371/journal.pgen.1003436
10.1371/journal.pgen.1003436 · External reference
10.1016/j.molcel.2014.07.012
10.1016/j.molcel.2014.07.012 · External reference
10.1016/j.celrep.2015.07.033
10.1016/j.celrep.2015.07.033 · External reference
GRID-seq reveals the global RNA-chromatin interactome
10.1038/nbt.3968 · 2017 · External reference
10.1016/j.tcb.2018.12.003
10.1016/j.tcb.2018.12.003 · External reference
10.1016/j.cell.2013.04.028
10.1016/j.cell.2013.04.028 · External reference
10.1007/s00418-018-1696-3
10.1007/s00418-018-1696-3 · External reference
10.1101/gad.283838.116
10.1101/gad.283838.116 · External reference
10.1371/journal.pone.0178821
10.1371/journal.pone.0178821 · External reference
10.1093/nar/gkx759
10.1093/nar/gkx759 · External reference
10.1083/jcb.200803174
10.1083/jcb.200803174 · External reference
10.1007/s00018-013-1465-3
10.1007/s00018-013-1465-3 · External reference
10.1016/j.cub.2014.03.053
10.1016/j.cub.2014.03.053 · External reference
10.1016/j.molcel.2018.05.019
10.1016/j.molcel.2018.05.019 · External reference
Cajal bodies are linked to genome conformation
10.1038/ncomms10966 · 2016 · External reference
10.1101/cshperspect.a000653
10.1101/cshperspect.a000653 · External reference
10.1074/jbc.m312580200
10.1074/jbc.m312580200 · External reference
10.1083/jcb.148.2.283
10.1083/jcb.148.2.283 · External reference
Evidence for DNA-mediated nuclear compartmentalization distinct from phase separation
10.7554/elife.47098 · 2019 · External reference
Physiological and Pathological Aging Affects Chromatin Dynamics, Structure and Function at the Nuclear Edge
10.3389/fgene.2016.00153 · 2016 · External reference
10.1128/mcb.02019-06
10.1128/mcb.02019-06 · External reference
10.1093/nar/gkab609
10.1093/nar/gkab609 · External reference
G-quadruplexes are transcription factor binding hubs in human chromatin
10.1186/s13059-021-02324-z · 2021 · External reference
G-quadruplex structures trigger RNA phase separation
2019 · External reference
G-Quadruplex Structures Colocalize with Transcription Factories and Nuclear Speckles Surrounded by Acetylated and Dimethylated Histones H3
10.3390/ijms22041995 · 2021 · External reference
10.1038/nature12593
10.1038/nature12593 · External reference
10.1038/nprot.2015.127
10.1038/nprot.2015.127 · External reference
10.1038/nmeth.4155
10.1038/nmeth.4155 · External reference
10.1038/nature21429
10.1038/nature21429 · External reference
10.1038/nature21711
10.1038/nature21711 · External reference
10.1038/nature23001
10.1038/nature23001 · External reference
10.1371/journal.pcbi.1008173
10.1371/journal.pcbi.1008173 · External reference
A New View of Genome Organization Through RNA Directed Interactions
10.3389/fcell.2020.00517 · 2020 · External reference
Identifying gene locus associations with promyelocytic leukemia nuclear bodies using immuno-TRAP
10.1083/jcb.201211097 · 2013 · External reference
10.1016/j.molcel.2020.04.004
10.1016/j.molcel.2020.04.004 · External reference
10.1016/j.celrep.2019.09.052
10.1016/j.celrep.2019.09.052 · External reference
10.1038/nature20158
10.1038/nature20158 · External reference
10.1038/s41588-018-0253-2
10.1038/s41588-018-0253-2 · External reference
10.1038/s41588-018-0161-5
10.1038/s41588-018-0161-5 · External reference
10.1101/833590
10.1101/833590 · External reference
10.1038/nature21411
10.1038/nature21411 · External reference
10.1016/j.cell.2018.05.024
10.1016/j.cell.2018.05.024 · External reference
10.1038/s41586-019-0949-1
10.1038/s41586-019-0949-1 · External reference
10.1038/nature12787
10.1038/nature12787 · External reference
10.1101/gr.164079.113
10.1101/gr.164079.113 · External reference
10.1073/pnas.1320308111
10.1073/pnas.1320308111 · External reference
10.1093/nar/gkv865
10.1093/nar/gkv865 · External reference
10.1038/ng.3539
10.1038/ng.3539 · External reference
10.1038/ng.3950
10.1038/ng.3950 · External reference
10.1093/bioinformatics/btx257
10.1093/bioinformatics/btx257 · External reference
Prediction of enhancer-promoter interactions via natural language processing
10.1186/s12864-018-4459-6 · 2018 · External reference
10.1007/s40484-019-0154-0
10.1007/s40484-019-0154-0 · External reference
A simple convolutional neural network for prediction of enhancer-promoter interactions with DNA sequence data
10.1093/bioinformatics/bty1050 · 2019 · External reference
Prediction of enhancer-promoter interactions using the cross-cell type information and domain adversarial neural network
10.1186/s12859-020-03844-4 · 2020 · External reference
10.1016/j.celrep.2012.09.022
10.1016/j.celrep.2012.09.022 · External reference
10.1016/j.cell.2011.12.014
10.1016/j.cell.2011.12.014 · External reference
Chromatin interaction networks revealed unique connectivity patterns of broad H3K4me3 domains and super enhancers in 3D chromatin
10.1038/s41598-017-14389-7 · 2017 · External reference
10.1101/gr.185272.114
10.1101/gr.185272.114 · External reference
10.1038/s41588-020-0709-z
10.1038/s41588-020-0709-z · External reference
10.1371/journal.pcbi.1004221
10.1371/journal.pcbi.1004221 · External reference
10.1093/bioinformatics/btaa445
10.1093/bioinformatics/btaa445 · External reference
GREG-studying transcriptional regulation using integrative graph databases
2020 · External reference
10.1093/nar/gkv1505
10.1093/nar/gkv1505 · External reference
10.1093/bioinformatics/btu443
10.1093/bioinformatics/btu443 · External reference
10.1101/gr.212803.116
10.1101/gr.212803.116 · External reference
10.1007/s40484-015-0047-9
10.1007/s40484-015-0047-9 · External reference
IC-Finder: inferring robustly the hierarchical organization of chromatin folding
2017 · External reference
10.1093/nar/gku324
10.1093/nar/gku324 · External reference
Unresolved reference
External reference
R-Loop Tracker: Web Access-Based Tool for R-Loop Detection and Analysis in Genomic DNA Sequences
10.3390/ijms222312857 · 2021 · External reference
10.1093/nar/gki609
10.1093/nar/gki609 · External reference
10.1093/nar/gkl253
10.1093/nar/gkl253 · External reference
10.1093/nar/gkl529
10.1093/nar/gkl529 · External reference
QuadBase: genome-wide database of G4 DNA–occurrence and conservation in human, chimpanzee, mouse and rat promoters and 146 microbes
10.1093/nar/gkm781 · 2008 · External reference
Re-evaluation of G-quadruplex propensity with G4Hunter
10.1093/nar/gkw006 · 2016 · External reference
Computational detection and analysis of sequences with duplex-derived interstrand G-quadruplex forming potential
10.1016/j.ymeth.2012.05.002 · 2012 · External reference
G-quadruplexes involving both strands of genomic DNA are highly abundant and colocalize with functional sites in the human genome
10.1371/journal.pone.0146174 · 2016 · External reference
10.1093/nar/gks1360
10.1093/nar/gks1360 · External reference
10.1016/j.cell.2015.08.001
10.1016/j.cell.2015.08.001 · External reference
Mining 3D genome structure populations identifies major factors governing the stability of regulatory communities
10.1038/ncomms11549 · 2016 · External reference
10.1101/gr.215004.116
10.1101/gr.215004.116 · External reference
10.1093/nar/gkw070
10.1093/nar/gkw070 · External reference
10.1073/pnas.1708028115
10.1073/pnas.1708028115 · External reference
10.1038/ncomms10812
10.1038/ncomms10812 · External reference
MIA-Sig: multiplex chromatin interaction analysis by signal processing and statistical algorithms
10.1186/s13059-019-1868-z · 2019 · External reference
10.1016/j.cels.2020.04.004
10.1016/j.cels.2020.04.004 · External reference
10.1371/journal.pcbi.1009669
10.1371/journal.pcbi.1009669 · External reference
10.1038/nature07829
10.1038/nature07829 · External reference
10.1016/j.devcel.2011.06.008
10.1016/j.devcel.2011.06.008 · External reference
10.1038/nature09906
10.1038/nature09906 · External reference
10.1038/nature11232
10.1038/nature11232 · External reference
10.1093/nar/gkx885
10.1093/nar/gkx885 · External reference
10.1186/s13059-015-0741-y
10.1186/s13059-015-0741-y · External reference
10.1016/j.tibtech.2017.06.012
10.1016/j.tibtech.2017.06.012 · External reference
A toolbox for predicting g-quadruplex formation and stability
2010 · External reference
10.1093/nar/gkaa1209
10.1093/nar/gkaa1209 · External reference
Chromatin network retards nucleoli coalescence
10.1038/s41467-021-27123-9 · 2021 · External reference
10.1016/j.gde.2015.10.007
10.1016/j.gde.2015.10.007 · External reference
10.1016/j.molcel.2015.07.019
10.1016/j.molcel.2015.07.019 · External reference
10.1038/s41588-019-0392-0
10.1038/s41588-019-0392-0 · External reference
Improvements and impacts of GRCh38 human reference on high throughput sequencing data analysis
10.1016/j.ygeno.2017.01.005 · 2017 · External reference
10.1038/s41586-022-04570-y
10.1038/s41586-022-04570-y · External reference
10.1016/j.cell.2015.04.004
10.1016/j.cell.2015.04.004 · External reference
10.1016/j.gde.2016.03.008
10.1016/j.gde.2016.03.008 · External reference
10.1038/nature19800
10.1038/nature19800 · External reference
Role of the nucleolus in human diseases. Preface
10.1016/j.bbadis.2014.03.004 · 2014 · External reference
10.1161/circulationaha.117.029430
10.1161/circulationaha.117.029430 · External reference
3Disease Browser: A Web server for integrating 3D genome and disease-associated chromosome rearrangement data
10.1038/srep34651 · 2016 · External reference
