{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,2,22]],"date-time":"2025-02-22T00:39:16Z","timestamp":1740184756604,"version":"3.37.3"},"reference-count":47,"publisher":"Oxford University Press (OUP)","issue":"15","license":[{"start":{"date-parts":[[2021,2,1]],"date-time":"2021-02-01T00:00:00Z","timestamp":1612137600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"name":"Italian Ministry for University"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,8,9]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Hi-C matrices are cornerstones for qualitative and quantitative studies of genome folding, from its territorial organization to compartments and topological domains. The high dynamic range of genomic distances probed in Hi-C assays reflects in an inherent stochastic background of the interactions matrices, which inevitably convolve the features of interest with largely non-specific ones.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>Here, we introduce and discuss essHi-C, a method to isolate the specific or essential component of Hi-C matrices from the non-specific portion of the spectrum compatible with random matrices. Systematic comparisons show that essHi-C improves the clarity of the interaction patterns, enhances the robustness against sequencing depth of topologically associating domains identification, allows the unsupervised clustering of experiments in different cell lines and recovers the cell-cycle phasing of single-cells based on Hi-C data. Thus, essHi-C provides means for isolating significant biological and physical features from Hi-C matrices.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>The essHi-C software package is available at https:\/\/github.com\/stefanofranzini\/essHIC.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btab062","type":"journal-article","created":{"date-parts":[[2021,1,28]],"date-time":"2021-01-28T21:30:48Z","timestamp":1611869448000},"page":"2088-2094","source":"Crossref","is-referenced-by-count":0,"title":["essHi-C: essential component analysis of Hi-C matrices"],"prefix":"10.1093","volume":"37","author":[{"given":"Stefano","family":"Franzini","sequence":"first","affiliation":[{"name":"SISSA \u2013 Scuola Internazionale Superiore di Studi Avanzati , Trieste I-34077, Italy"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6195-4754","authenticated-orcid":false,"given":"Marco","family":"Di Stefano","sequence":"additional","affiliation":[{"name":"Structural Genomics Group, CNAG-CRG Centre Nacional d\u2019An\u00e1lisi Gen\u00f3mica \u2013 Centre de Regulaci\u00f3 Gen\u00f3mica , Barcelona 08028, Spain"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1022-1638","authenticated-orcid":false,"given":"Cristian","family":"Micheletti","sequence":"additional","affiliation":[{"name":"SISSA \u2013 Scuola Internazionale Superiore di Studi Avanzati , Trieste I-34077, Italy"}]}],"member":"286","published-online":{"date-parts":[[2021,2,1]]},"reference":[{"key":"2023061310294573300_btab062-B1","doi-asserted-by":"crossref","first-page":"412","DOI":"10.1002\/prot.340170408","article-title":"Essential dynamics of proteins","volume":"17","author":"Amadei","year":"1993","journal-title":"Proteins Struct. Funct. Bioinf"},{"key":"2023061310294573300_btab062-B2","doi-asserted-by":"crossref","first-page":"999","DOI":"10.1101\/gr.160374.113","article-title":"Statistical confidence estimation for hi-c data reveals regulatory chromatin contacts","volume":"24","author":"Ay","year":"2014","journal-title":"Genome Res"},{"key":"2023061310294573300_btab062-B3","doi-asserted-by":"crossref","first-page":"557","DOI":"10.1016\/j.cell.2017.09.043","article-title":"Multiscale 3d genome rewiring during mouse neural development","volume":"171","author":"Bonev","year":"2017","journal-title":"Cell"},{"key":"2023061310294573300_btab062-B4","doi-asserted-by":"crossref","first-page":"240","DOI":"10.1038\/nature14450","article-title":"Condensin-driven remodelling of x chromosome topology during dosage compensation","volume":"523","author":"Crane","year":"2015","journal-title":"Nature"},{"key":"2023061310294573300_btab062-B5","doi-asserted-by":"crossref","first-page":"292","DOI":"10.1038\/35066075","article-title":"Chromosome territories, nuclear architecture and gene regulation in mammalian cells","volume":"2","author":"Cremer","year":"2001","journal-title":"Nat. Rev. Genet"},{"key":"2023061310294573300_btab062-B6","doi-asserted-by":"crossref","first-page":"1306","DOI":"10.1126\/science.1067799","article-title":"Capturing chromosome conformation","volume":"295","author":"Dekker","year":"2002","journal-title":"Science"},{"key":"2023061310294573300_btab062-B7","doi-asserted-by":"crossref","first-page":"390","DOI":"10.1038\/nrg3454","article-title":"Exploring the three-dimensional organization of genomes: interpreting chromatin interaction data","volume":"14","author":"Dekker","year":"2013","journal-title":"Nat. Rev. Genet"},{"key":"2023061310294573300_btab062-B8","doi-asserted-by":"crossref","first-page":"376","DOI":"10.1038\/nature11082","article-title":"Topological domains in mammalian genomes identified by analysis of chromatin interactions","volume":"485","author":"Dixon","year":"2012","journal-title":"Nature"},{"key":"2023061310294573300_btab062-B9","doi-asserted-by":"crossref","first-page":"180","DOI":"10.1186\/s13059-015-0741-y","article-title":"Reconstructing A\/B compartments as revealed by Hi-C using long-range correlations in epigenetic data","volume":"16","author":"Fortin","year":"2015","journal-title":"Genome Biol"},{"key":"2023061310294573300_btab062-B10","doi-asserted-by":"crossref","first-page":"852","DOI":"10.15252\/msb.20156492","article-title":"Hierarchical folding and reorganization of chromosomes are linked to transcriptional changes in cellular differentiation","volume":"11","author":"Fraser","year":"2015","journal-title":"Mol. Syst. Biol"},{"key":"2023061310294573300_btab062-B11","doi-asserted-by":"crossref","first-page":"950","DOI":"10.1016\/j.cell.2014.03.025","article-title":"Predictive polymer modeling reveals coupled fluctuations in chromosome conformation and transcription","volume":"157","author":"Giorgetti","year":"2014","journal-title":"Cell"},{"key":"2023061310294573300_btab062-B12","first-page":"233","volume-title":"Methods Mol. Biol","author":"Grob","year":"2018"},{"key":"2023061310294573300_btab062-B13","doi-asserted-by":"crossref","first-page":"999","DOI":"10.1038\/nmeth.2148","article-title":"Iterative correction of hi-c data reveals hallmarks of chromosome organization","volume":"9","author":"Imakaev","year":"2012","journal-title":"Nat. Methods"},{"key":"2023061310294573300_btab062-B14","doi-asserted-by":"crossref","first-page":"1029","DOI":"10.1093\/imanum\/drs019","article-title":"A fast algorithm for matrix balancing","volume":"33","author":"Knight","year":"2013","journal-title":"IMA J. Numer. Anal"},{"key":"2023061310294573300_btab062-B15","doi-asserted-by":"crossref","first-page":"771","DOI":"10.1038\/nrm.2016.138","article-title":"Regulation of disease-associated gene expression in the 3d genome","volume":"17","author":"Krijger","year":"2016","journal-title":"Nat. Rev. Mol. Cell Biol"},{"key":"2023061310294573300_btab062-B16","doi-asserted-by":"crossref","first-page":"289","DOI":"10.1126\/science.1181369","article-title":"Comprehensive mapping of long-range interactions reveals folding principles of the human genome","volume":"326","author":"Lieberman-Aiden","year":"2009","journal-title":"Science"},{"key":"2023061310294573300_btab062-B17","doi-asserted-by":"crossref","DOI":"10.1007\/978-3-319-70885-0","volume-title":"Introduction to Random Matrices","author":"Livan","year":"2018"},{"key":"2023061310294573300_btab062-B18","doi-asserted-by":"crossref","first-page":"1012","DOI":"10.1016\/j.cell.2015.04.004","article-title":"Disruptions of topological chromatin domains cause pathogenic rewiring of gene-enhancer interactions","volume":"161","author":"Lupi\u00e1\u00f1ez","year":"2015","journal-title":"Cell"},{"key":"2023061310294573300_btab062-B19","doi-asserted-by":"crossref","first-page":"11","DOI":"10.1002\/0471250953.bi1113s50","article-title":"efficient alignment of illumina-like high-throughput sequencing reads with the GEnomic Multi-tool (GEM) mapper","volume":"50","author":"Marco-Sola","year":"2015","journal-title":"Curr. Protoc. Bioinf"},{"key":"2023061310294573300_btab062-B20","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/j.plrev.2012.10.009","article-title":"Comparing proteins by their internal dynamics: exploring structure\u2013function relationships beyond static structural alignments","volume":"10","author":"Micheletti","year":"2013","journal-title":"Phys. Life Rev"},{"key":"2023061310294573300_btab062-B21","doi-asserted-by":"crossref","first-page":"61","DOI":"10.1038\/nature23001","article-title":"Cell-cycle dynamics of chromosomal organization at single-cell resolution","volume":"547","author":"Nagano","year":"2017","journal-title":"Nature"},{"key":"2023061310294573300_btab062-B22","doi-asserted-by":"crossref","first-page":"381","DOI":"10.1038\/nature11049","article-title":"Spatial partitioning of the regulatory landscape of the x-inactivation centre","volume":"485","author":"Nora","year":"2012","journal-title":"Nature"},{"key":"2023061310294573300_btab062-B23","doi-asserted-by":"crossref","first-page":"361","DOI":"10.1016\/j.jcta.2016.06.008","article-title":"Eigenvectors of random matrices: a survey","volume":"144","author":"O\u2019Rourke","year":"2016","journal-title":"J. Combin. Theory Ser. A"},{"key":"2023061310294573300_btab062-B24","doi-asserted-by":"crossref","first-page":"835","DOI":"10.1038\/s41588-019-0392-0","article-title":"Long-range interactions between topologically associating domains shape the four-dimensional genome during differentiation","volume":"51","author":"Paulsen","year":"2019","journal-title":"Nat. Genet"},{"key":"2023061310294573300_btab062-B25","doi-asserted-by":"crossref","first-page":"1665","DOI":"10.1016\/j.cell.2014.11.021","article-title":"A 3d map of the human genome at kilobase resolution reveals principles of chromatin looping","volume":"159","author":"Rao","year":"2014","journal-title":"Cell"},{"key":"2023061310294573300_btab062-B26","doi-asserted-by":"crossref","first-page":"8","DOI":"10.1186\/1755-8166-7-8","article-title":"Differences and homologies of chromosomal alterations within and between breast cancer cell lines: a clustering analysis","volume":"7","author":"Rond\u00f3n-Lagos","year":"2014","journal-title":"Mol. Cytogenet"},{"key":"2023061310294573300_btab062-B27","doi-asserted-by":"crossref","first-page":"522","DOI":"10.1016\/j.molcel.2020.03.007","article-title":"4d genome rewiring during oncogene-induced and replicative senescence","volume":"78","author":"Sati","year":"2020","journal-title":"Mol. Cell"},{"key":"2023061310294573300_btab062-B28","doi-asserted-by":"crossref","first-page":"2042","DOI":"10.1016\/j.celrep.2016.10.061","article-title":"A compendium of chromatin contact maps reveals spatially active regions in the human genome","volume":"17","author":"Schmitt","year":"2016","journal-title":"Cell Rep"},{"key":"2023061310294573300_btab062-B29","doi-asserted-by":"crossref","first-page":"2987","DOI":"10.1016\/j.febslet.2015.05.012","article-title":"Restraint-based three-dimensional modeling of genomes and genomic domains","volume":"589","author":"Serra","year":"2015","journal-title":"FEBS Lett"},{"key":"2023061310294573300_btab062-B30","doi-asserted-by":"crossref","first-page":"e1005665","DOI":"10.1371\/journal.pcbi.1005665","article-title":"Automatic analysis and 3d-modelling of hi-c data using TADbit reveals structural features of the fly chromatin colors","volume":"13","author":"Serra","year":"2017","journal-title":"PLoS Comput. Biol"},{"key":"2023061310294573300_btab062-B31","doi-asserted-by":"crossref","first-page":"1049","DOI":"10.1016\/j.cell.2015.02.040","article-title":"The role of chromosome domains in shaping the functional genome","volume":"160","author":"Sexton","year":"2015","journal-title":"Cell"},{"key":"2023061310294573300_btab062-B32","doi-asserted-by":"crossref","first-page":"458","DOI":"10.1016\/j.cell.2012.01.010","article-title":"Three-dimensional folding and functional organization principles of the drosophila genome","volume":"148","author":"Sexton","year":"2012","journal-title":"Cell"},{"key":"2023061310294573300_btab062-B33","doi-asserted-by":"crossref","first-page":"238","DOI":"10.1038\/s41588-017-0030-7","article-title":"Transcription factors orchestrate dynamic interplay between genome topology and gene regulation during cell reprogramming","volume":"50","author":"Stadhouders","year":"2018","journal-title":"Nat. Genet"},{"key":"2023061310294573300_btab062-B34","doi-asserted-by":"crossref","first-page":"279","DOI":"10.1186\/s12859-018-2288-x","article-title":"HiCcompare: an r-package for joint normalization and comparison of HI-c datasets","volume":"19","author":"Stansfield","year":"2018","journal-title":"BMC Bioinformatics"},{"key":"2023061310294573300_btab062-B35","doi-asserted-by":"crossref","first-page":"E1663","DOI":"10.1073\/pnas.1512577113","article-title":"Population-based 3d genome structure analysis reveals driving forces in spatial genome organization","volume":"113","author":"Tjong","year":"2016","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"2023061310294573300_btab062-B36","doi-asserted-by":"crossref","first-page":"3465","DOI":"10.1093\/nar\/gkv221","article-title":"Assessing the limits of restraint-based 3d modeling of genomes and genomic domains","volume":"43","author":"Trussart","year":"2015","journal-title":"Nucleic Acids Res"},{"key":"2023061310294573300_btab062-B37","first-page":"395","article-title":"Technologies to study spatial genome organization: beyond 3c","volume":"18","author":"\u00dcbelmesser","year":"2019","journal-title":"Brief. Funct. Genomics"},{"key":"2023061310294573300_btab062-B38","doi-asserted-by":"crossref","first-page":"2701","DOI":"10.1093\/bioinformatics\/bty164","article-title":"GenomeDISCO: a concordance score for chromosome conformation capture experiments using random walks on contact map graphs","volume":"34","author":"Ursu","year":"2018","journal-title":"Bioinformatics"},{"key":"2023061310294573300_btab062-B39","doi-asserted-by":"crossref","first-page":"e49","DOI":"10.1093\/nar\/gky064","article-title":"Oned: increasing reproducibility of hi-c samples with abnormal karyotypes","volume":"46","author":"Vidal","year":"2018","journal-title":"Nucleic Acids Res"},{"key":"2023061310294573300_btab062-B40","first-page":"1","article-title":"Dynamics of genome architecture and chromatin function during human b cell differentiation and neoplastic transformation","author":"Vilarrasa-Blasi","year":"2021","journal-title":"Nat. Commun"},{"key":"2023061310294573300_btab062-B41","doi-asserted-by":"crossref","first-page":"1059","DOI":"10.1038\/ng.947","article-title":"Probabilistic modeling of hi-c contact maps eliminates systematic biases to characterize global chromosomal architecture","volume":"43","author":"Yaffe","year":"2011","journal-title":"Nat. Genet"},{"key":"2023061310294573300_btab062-B42","doi-asserted-by":"crossref","first-page":"2199","DOI":"10.1093\/bioinformatics\/btx152","article-title":"HiC-spector: a matrix library for spectral and reproducibility analysis of hi-c contact maps","volume":"33","author":"Yan","year":"2017","journal-title":"Bioinformatics"},{"key":"2023061310294573300_btab062-B43","doi-asserted-by":"crossref","first-page":"1939","DOI":"10.1101\/gr.220640.117","article-title":"HiCRep: assessing the reproducibility of hi-c data using a stratum-adjusted correlation coefficient","volume":"27","author":"Yang","year":"2017","journal-title":"Genome Res"},{"key":"2023061310294573300_btab062-B44","doi-asserted-by":"crossref","first-page":"57","DOI":"10.1186\/s13059-019-1658-7","article-title":"Measuring the reproducibility and quality of hi-c data","volume":"20","author":"Yard Imc I","year":"2019","journal-title":"Genome Biol"},{"key":"2023061310294573300_btab062-B45","doi-asserted-by":"crossref","first-page":"535","DOI":"10.1038\/s41580-019-0132-4","article-title":"The role of 3d genome organization in development and cell differentiation","volume":"20","author":"Zheng","year":"2019","journal-title":"Nat. Rev. Mol. Cell Biol"},{"key":"2023061310294573300_btab062-B46","doi-asserted-by":"crossref","first-page":"14011","DOI":"10.1073\/pnas.1901423116","article-title":"Robust single-cell hi-c clustering by convolution- and random-walk-based imputation","volume":"116","author":"Zhou","year":"2019","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"2023061310294573300_btab062-B47","doi-asserted-by":"crossref","first-page":"217","DOI":"10.1186\/s13059-018-1596-9","article-title":"Comparison of computational methods for the identification of topologically associating domains","volume":"19","author":"Zufferey","year":"2018","journal-title":"Genome Biol"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btab062\/36287961\/btab062.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/37\/15\/2088\/50578554\/btab062.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/37\/15\/2088\/50578554\/btab062.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,6,13]],"date-time":"2023-06-13T10:32:11Z","timestamp":1686652331000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/37\/15\/2088\/6125382"}},"subtitle":[],"editor":[{"given":"Pier Luigi","family":"Martelli","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2021,2,1]]},"references-count":47,"journal-issue":{"issue":"15","published-print":{"date-parts":[[2021,8,9]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btab062","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"type":"print","value":"1367-4803"},{"type":"electronic","value":"1367-4811"}],"subject":[],"published-other":{"date-parts":[[2021,8,1]]},"published":{"date-parts":[[2021,2,1]]}}}