{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,22]],"date-time":"2026-01-22T20:19:21Z","timestamp":1769113161315,"version":"3.49.0"},"reference-count":6,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2022,11,28]],"date-time":"2022-11-28T00:00:00Z","timestamp":1669593600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["U24HG006620"],"award-info":[{"award-number":["U24HG006620"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["U24CA231877"],"award-info":[{"award-number":["U24CA231877"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,1,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>It has been observed in different kinds of networks, such as social or biological ones, a typical behavior inspired by the general principle \u2018similarity breeds connections\u2019. These networks are defined as homophilic as nodes belonging to the same class preferentially interact with each other. In this work, we present HONTO (HOmophily Network TOol), a user-friendly open-source Python3 package designed to evaluate and analyze homophily in complex networks. The tool takes in input from the network along with a partition of its nodes into classes and yields a matrix whose entries are the homophily\/heterophily z-score values. To complement the analysis, the tool also provides z-score values of nodes that do not interact with any other node of the same class. Homophily\/heterophily z-scores values are presented as a heatmap allowing a visual at-a-glance interpretation of results.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>Tool\u2019s source code is available at https:\/\/github.com\/cumbof\/honto under the MIT license, installable as a package from PyPI (pip install honto) and conda-forge (conda install -c conda-forge honto), and has a wrapper for the Galaxy platform available on the official Galaxy ToolShed (Blankenberg et al., 2014) at https:\/\/toolshed.g2.bx.psu.edu\/view\/fabio\/honto.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btac763","type":"journal-article","created":{"date-parts":[[2022,11,24]],"date-time":"2022-11-24T21:59:02Z","timestamp":1669327142000},"source":"Crossref","is-referenced-by-count":6,"title":["Evaluating homophily in networks via <i>HONTO<\/i> (HOmophily Network TOol): a case study of chromosomal interactions in human PPI networks"],"prefix":"10.1093","volume":"39","author":[{"given":"Nicola","family":"Apollonio","sequence":"first","affiliation":[{"name":"Institute for Applied Mathematics \u201cMauro Picone\u201d, National Research Council of Italy , Rome 00185, Italy"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6833-9049","authenticated-orcid":false,"given":"Daniel","family":"Blankenberg","sequence":"additional","affiliation":[{"name":"Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic , Cleveland, OH 44195, USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2920-5838","authenticated-orcid":false,"given":"Fabio","family":"Cumbo","sequence":"additional","affiliation":[{"name":"Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic , Cleveland, OH 44195, USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5464-4069","authenticated-orcid":false,"given":"Paolo Giulio","family":"Franciosa","sequence":"additional","affiliation":[{"name":"Department of Statistical Science, University of Rome \u201cLa Sapienza\u201d , Rome 00185, Italy"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1898-5285","authenticated-orcid":false,"given":"Daniele","family":"Santoni","sequence":"additional","affiliation":[{"name":"Institute for Systems Analysis and Computer Science \u201cAntonio Ruberti\u201d, National Research Council of Italy , Rome 00185, Italy"}]}],"member":"286","published-online":{"date-parts":[[2022,11,28]]},"reference":[{"key":"2023010107513123700_btac763-B1","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1038\/s41598-022-12710-7","article-title":"A novel method for assessing and measuring homophily in networks through second-order statistics","volume":"12","author":"Apollonio","year":"2022","journal-title":"Sci. Rep"},{"key":"2023010107513123700_btac763-B2","doi-asserted-by":"crossref","first-page":"403","DOI":"10.1186\/gb4161","article-title":"Dissemination of scientific software with Galaxy ToolShed","volume":"15","author":"Blankenberg","year":"2014","journal-title":"Genome Biol"},{"key":"2023010107513123700_btac763-B3","doi-asserted-by":"crossref","first-page":"415","DOI":"10.1146\/annurev.soc.27.1.415","article-title":"Birds of a feather: homophily in social networks","volume":"27","author":"McPherson","year":"2001","journal-title":"Annu. Rev. Sociol"},{"key":"2023010107513123700_btac763-B4","doi-asserted-by":"crossref","first-page":"e57707","DOI":"10.1371\/journal.pone.0057707","article-title":"Identifying correlations between chromosomal proximity of genes and distance of their products in protein-protein interaction networks of yeast","volume":"8","author":"Santoni","year":"2013","journal-title":"PLoS One"},{"key":"2023010107513123700_btac763-B5","doi-asserted-by":"crossref","first-page":"D605","DOI":"10.1093\/nar\/gkaa1074","article-title":"The STRING database in 2021: customizable protein\u2013protein networks, and functional characterization of user-uploaded gene\/measurement sets","volume":"49","author":"Szklarczyk","year":"2021","journal-title":"Nucleic Acids Res"},{"key":"2023010107513123700_btac763-B6","doi-asserted-by":"crossref","first-page":"W345","DOI":"10.1093\/nar\/gkac247","article-title":"The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2022 update","volume":"50","author":"The Galaxy Community","year":"2022","journal-title":"Nucleic Acids Res"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btac763\/47604015\/btac763.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/39\/1\/btac763\/48448664\/btac763.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/39\/1\/btac763\/48448664\/btac763.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,1]],"date-time":"2023-01-01T10:08:09Z","timestamp":1672567689000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/doi\/10.1093\/bioinformatics\/btac763\/6849517"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2022,11,28]]},"references-count":6,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2022,11,28]]},"published-print":{"date-parts":[[2023,1,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btac763","relation":{},"ISSN":["1367-4811"],"issn-type":[{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2023,1,1]]},"published":{"date-parts":[[2022,11,28]]},"article-number":"btac763"}}