Research graph
References from Mapping nucleosome and chromatin architectures: A survey of computational methods. Local targets link to admitted publications; unresolved targets remain external evidence.
10.1038/38444
10.1038/38444 · External reference
10.1101/gad.399506
10.1101/gad.399506 · External reference
10.1016/j.cell.2009.06.001
10.1016/j.cell.2009.06.001 · External reference
10.1016/j.cell.2017.11.008
10.1016/j.cell.2017.11.008 · External reference
10.1039/b803580f
10.1039/b803580f · External reference
10.1126/science.1152850
10.1126/science.1152850 · External reference
10.1038/s41580-019-0132-4
10.1038/s41580-019-0132-4 · External reference
10.1038/s41594-018-0110-0
10.1038/s41594-018-0110-0 · External reference
Single-molecule and population probing of chromatin structure using DNA methyltransferases
10.1016/j.ymeth.2006.08.008 · 2007 · External reference
10.1038/nature11142
10.1038/nature11142 · External reference
10.1101/gr.192294.115
10.1101/gr.192294.115 · External reference
10.1073/pnas.1424804112
10.1073/pnas.1424804112 · External reference
10.1126/science.1067799
10.1126/science.1067799 · External reference
10.1038/ng1896
10.1038/ng1896 · External reference
10.1101/gr.5571506
10.1101/gr.5571506 · External reference
10.1038/ng.2871
10.1038/ng.2871 · External reference
10.1126/science.1181369
10.1126/science.1181369 · External reference
10.1038/nbt.2057
10.1038/nbt.2057 · External reference
10.1016/j.cell.2015.05.048
10.1016/j.cell.2015.05.048 · External reference
Sequence specific cleavage of DNA by micrococcal nuclease
10.1093/nar/9.12.2643 · 1981 · External reference
10.1186/s13059-019-1815-z
10.1186/s13059-019-1815-z · External reference
Subtracting the sequence bias from partially digested MNase-seq data reveals a general contribution of TFIIS to nucleosome positioning
10.1186/s13072-017-0165-x · 2017 · External reference
10.1038/ng.947
10.1038/ng.947 · External reference
Improved nucleosome-positioning algorithm iNPS for accurate nucleosome positioning from sequencing data
10.1038/ncomms5909 · 2014 · External reference
Identifying positioned nucleosomes with epigenetic marks in human from ChIP-Seq
10.1186/1471-2164-9-537 · 2008 · External reference
10.1038/nmeth.2148
10.1038/nmeth.2148 · External reference
NucHMM: a method for quantitative modeling of nucleosome organization identifying functional nucleosome states distinctly associated with splicing potentiality
10.1186/s13059-021-02465-1 · 2021 · External reference
10.1016/j.cels.2018.01.001
10.1016/j.cels.2018.01.001 · External reference
Modeling and analysis of Hi-C data by HiSIF identifies characteristic promoter-distal loops
10.1186/s13073-020-00769-8 · 2020 · External reference
10.1186/s13059-015-0831-x
10.1186/s13059-015-0831-x · External reference
10.1038/nmeth.1923
10.1038/nmeth.1923 · External reference
10.1080/15366367.2019.1565254
10.1080/15366367.2019.1565254 · External reference
10.1016/j.cell.2008.02.022
10.1016/j.cell.2008.02.022 · External reference
10.1038/nsmb.2506
10.1038/nsmb.2506 · External reference
10.1186/gb-2008-9-9-r137
10.1186/gb-2008-9-9-r137 · External reference
10.1038/nbt.1508
10.1038/nbt.1508 · External reference
ChIPseqR: analysis of ChIP-seq experiments
10.1186/1471-2105-12-39 · 2011 · External reference
10.1093/bioinformatics/bts206
10.1093/bioinformatics/bts206 · External reference
NSeq: a multithreaded Java application for finding positioned nucleosomes from sequencing data
2012 · External reference
A non-homogeneous hidden-state model on first order differences for automatic detection of nucleosome positions
2009 · External reference
10.1093/bioinformatics/btt449
10.1093/bioinformatics/btt449 · External reference
NucleoFinder: a statistical approach for the detection of nucleosome positions
10.1093/bioinformatics/bts719 · 2013 · External reference
10.1093/bioinformatics/btr345
10.1093/bioinformatics/btr345 · External reference
2.0: an R/Bioconductor package for nucleosome positioning using next-generation sequencing data
10.1093/bioinformatics/btt348 · 2013 · External reference
PuFFIN–a parameter-free method to build nucleosome maps from paired-end reads
10.1186/1471-2105-15-s9-s11 · 2014 · External reference
BINOCh: binding inference from nucleosome occupancy changes
10.1093/bioinformatics/btr279 · 2011 · External reference
10.1101/gr.142067.112
10.1101/gr.142067.112 · External reference
DiNuP: a systematic approach to identify regions of differential nucleosome positioning
10.1093/bioinformatics/bts329 · 2012 · External reference
An approach of identifying differential nucleosome regions in multiple samples
10.1186/s12864-017-3541-9 · 2017 · External reference
10.1093/nar/gkz759
10.1093/nar/gkz759 · External reference
10.1093/bioinformatics/btt404
10.1093/bioinformatics/btt404 · External reference
A computational approach to map nucleosome positions and alternative chromatin states with base pair resolution
10.7554/elife.16970 · 2016 · External reference
10.1371/journal.pone.0032095
10.1371/journal.pone.0032095 · External reference
DeNOPA: decoding nucleosome positions sensitively with sparse ATAC-seq data
2021 · External reference
10.1093/bib/bbu037
10.1093/bib/bbu037 · External reference
10.1016/j.cels.2015.07.012
10.1016/j.cels.2015.07.012 · External reference
10.1016/j.molcel.2010.05.004
10.1016/j.molcel.2010.05.004 · External reference
10.1186/s13059-020-02215-9
10.1186/s13059-020-02215-9 · External reference
10.1016/j.cell.2014.11.021
10.1016/j.cell.2014.11.021 · External reference
10.1038/s41467-019-12954-4
10.1038/s41467-019-12954-4 · External reference
10.1038/s41467-021-22666-3
10.1038/s41467-021-22666-3 · External reference
10.1016/j.molcel.2016.05.018
10.1016/j.molcel.2016.05.018 · External reference
10.1038/nature11082
10.1038/nature11082 · External reference
10.1016/j.cell.2012.01.010
10.1016/j.cell.2012.01.010 · External reference
Identification of alternative topological domains in chromatin
10.1186/1748-7188-9-14 · 2014 · External reference
Comparison of computational methods for the identification of topologically associating domains
10.1186/s13059-018-1596-9 · 2018 · External reference
10.1093/nar/gkv1505
10.1093/nar/gkv1505 · External reference
10.1093/nar/gkz201
10.1093/nar/gkz201 · External reference
TAD boundary and strength prediction by integrating sequence and epigenetic profile information
10.1093/bib/bbab139 · 2021 · External reference
10.1093/bioinformatics/btu443
10.1093/bioinformatics/btu443 · 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/gkx735
10.1093/nar/gkx735 · External reference
10.1016/j.cels.2016.07.002
10.1016/j.cels.2016.07.002 · External reference
10.1093/bioinformatics/btv485
10.1093/bioinformatics/btv485 · External reference
10.1186/s13059-019-1893-y
10.1186/s13059-019-1893-y · External reference
10.1038/nature12716
10.1038/nature12716 · External reference
10.1016/j.cell.2016.09.037
10.1016/j.cell.2016.09.037 · External reference
10.1038/nmeth.3999
10.1038/nmeth.3999 · External reference
10.1016/j.cell.2018.05.024
10.1016/j.cell.2018.05.024 · External reference
GRiNCH: simultaneous smoothing and detection of topological units of genome organization from sparse chromatin contact count matrices with matrix factorization
10.1186/s13059-021-02378-z · 2021 · External reference
The 3D genomic landscape of differential response to EGFR/HER2 inhibition in endocrine-resistant breast cancer cells
10.1016/j.bbagrm.2020.194631 · 2020 · External reference
Systematic assessment of gene co-regulation within chromatin domains determines differentially active domains across human cancers
10.1186/s13059-021-02436-6 · 2021 · 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
HIFI: estimating DNA-DNA interaction frequency from Hi-C data at restriction-fragment resolution
10.1186/s13059-019-1913-y · 2020 · External reference
10.1016/j.molcel.2020.06.007
10.1016/j.molcel.2020.06.007 · External reference
10.1101/gr.160374.113
10.1101/gr.160374.113 · External reference
10.1038/s41596-019-0273-0
10.1038/s41596-019-0273-0 · External reference
10.1038/s41467-019-11950-y
10.1038/s41467-019-11950-y · External reference
10.1186/s13059-020-02167-0
10.1186/s13059-020-02167-0 · External reference
10.1038/nmeth.4325
10.1038/nmeth.4325 · External reference
10.2144/btn-2019-0105
10.2144/btn-2019-0105 · External reference
10.1038/nature23884
10.1038/nature23884 · External reference
Genomics: ENCODE explained
10.1038/489052a · 2012 · External reference
10.1093/nar/gks501
10.1093/nar/gks501 · External reference
10.1038/ng.3539
10.1038/ng.3539 · External reference
Integrating epigenomic data and 3D genomic structure with a new measure of chromatin assortativity
10.1186/s13059-016-1003-3 · 2016 · External reference
10.1186/s13059-020-02253-3
10.1186/s13059-020-02253-3 · External reference
10.1016/j.febslet.2015.09.004
10.1016/j.febslet.2015.09.004 · External reference
10.1038/nature12593
10.1038/nature12593 · External reference
10.1038/nmeth.4155
10.1038/nmeth.4155 · External reference
10.1038/nature21429
10.1038/nature21429 · External reference
10.1038/nature23001
10.1038/nature23001 · External reference
10.1038/nature21711
10.1038/nature21711 · External reference
Single-cell landscape of nuclear configuration and gene expression during stem cell differentiation and X inactivation
10.1186/s13059-021-02432-w · 2021 · External reference
10.1038/s41588-018-0161-5
10.1038/s41588-018-0161-5 · External reference
10.1038/s41588-018-0253-2
10.1038/s41588-018-0253-2 · External reference
10.1089/cmb.2019.0100
10.1089/cmb.2019.0100 · External reference
10.1093/bioinformatics/btz181
10.1093/bioinformatics/btz181 · External reference
Si-C is a method for inferring super-resolution intact genome structure from single-cell Hi-C data
10.1038/s41467-021-24662-z · 2021 · External reference
10.1093/bioinformatics/bty285
10.1093/bioinformatics/bty285 · External reference
10.1073/pnas.1901423116
10.1073/pnas.1901423116 · External reference
10.1038/s41587-021-01034-y
10.1038/s41587-021-01034-y · External reference
DeTOKI identifies and characterizes the dynamics of chromatin TAD-like domains in a single cell
10.1186/s13059-021-02435-7 · 2021 · External reference
scHiCStackL: a stacking ensemble learning-based method for single-cell Hi-C classification using cell embedding
2022 · External reference
10.1038/s41592-021-01231-2
10.1038/s41592-021-01231-2 · External reference
scHiCTools: A computational toolbox for analyzing single-cell Hi-C data
10.1371/journal.pcbi.1008978 · 2021 · External reference
10.1259/bjr.20140065
10.1259/bjr.20140065 · External reference
10.1038/s41586-021-04081-2
10.1038/s41586-021-04081-2 · External reference