{"id":"https://openalex.org/W4310167591","doi":"https://doi.org/10.1093/bioinformatics/btac763","title":"Evaluating homophily in networks via <i>HONTO</i> (HOmophily Network TOol): a case study of chromosomal interactions in human PPI networks","display_name":"Evaluating homophily in networks via <i>HONTO</i> (HOmophily Network TOol): a case study of chromosomal interactions in human PPI networks","publication_year":2022,"publication_date":"2022-11-24","ids":{"openalex":"https://openalex.org/W4310167591","doi":"https://doi.org/10.1093/bioinformatics/btac763","pmid":"https://pubmed.ncbi.nlm.nih.gov/36440918"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btac763","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac763","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/39/1/btac763/48448664/btac763.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/39/1/btac763/48448664/btac763.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5068548647","display_name":"Nicola Apollonio","orcid":"https://orcid.org/0000-0001-6089-1333"},"institutions":[{"id":"https://openalex.org/I4210106125","display_name":"Istituto per le Applicazioni del Calcolo Mauro Picone","ror":"https://ror.org/00ygy3d85","country_code":"IT","type":"facility","lineage":["https://openalex.org/I4210106125","https://openalex.org/I4210155236"]},{"id":"https://openalex.org/I4210155236","display_name":"National Research Council","ror":"https://ror.org/04zaypm56","country_code":"IT","type":"nonprofit","lineage":["https://openalex.org/I4210155236"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Nicola Apollonio","raw_affiliation_strings":["Institute for Applied Mathematics \u201cMauro Picone\u201d, National Research Council of Italy , Rome 00185, Italy"],"affiliations":[{"raw_affiliation_string":"Institute for Applied Mathematics \u201cMauro Picone\u201d, National Research Council of Italy , Rome 00185, Italy","institution_ids":["https://openalex.org/I4210106125","https://openalex.org/I4210155236"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5075101770","display_name":"Daniel Blankenberg","orcid":"https://orcid.org/0000-0002-6833-9049"},"institutions":[{"id":"https://openalex.org/I36373038","display_name":"Cleveland Clinic Lerner College of Medicine","ror":"https://ror.org/02x4b0932","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1316902750","https://openalex.org/I36373038"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Daniel Blankenberg","raw_affiliation_strings":["Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic , Cleveland, OH 44195, USA"],"affiliations":[{"raw_affiliation_string":"Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic , Cleveland, OH 44195, USA","institution_ids":["https://openalex.org/I36373038"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5010164802","display_name":"Fabio Cumbo","orcid":"https://orcid.org/0000-0003-2920-5838"},"institutions":[{"id":"https://openalex.org/I36373038","display_name":"Cleveland Clinic Lerner College of Medicine","ror":"https://ror.org/02x4b0932","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1316902750","https://openalex.org/I36373038"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Fabio Cumbo","raw_affiliation_strings":["Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic , Cleveland, OH 44195, USA"],"affiliations":[{"raw_affiliation_string":"Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic , Cleveland, OH 44195, USA","institution_ids":["https://openalex.org/I36373038"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5045218419","display_name":"Paolo Giulio Franciosa","orcid":"https://orcid.org/0000-0002-5464-4069"},"institutions":[{"id":"https://openalex.org/I861853513","display_name":"Sapienza University of Rome","ror":"https://ror.org/02be6w209","country_code":"IT","type":"education","lineage":["https://openalex.org/I861853513"]}],"countries":["IT"],"is_corresponding":true,"raw_author_name":"Paolo Giulio Franciosa","raw_affiliation_strings":["Department of Statistical Science, University of Rome \u201cLa Sapienza\u201d , Rome 00185, Italy"],"affiliations":[{"raw_affiliation_string":"Department of Statistical Science, University of Rome \u201cLa Sapienza\u201d , Rome 00185, Italy","institution_ids":["https://openalex.org/I861853513"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5015205454","display_name":"Daniele Santoni","orcid":"https://orcid.org/0000-0003-1898-5285"},"institutions":[{"id":"https://openalex.org/I4210155236","display_name":"National Research Council","ror":"https://ror.org/04zaypm56","country_code":"IT","type":"nonprofit","lineage":["https://openalex.org/I4210155236"]},{"id":"https://openalex.org/I4210162062","display_name":"Istituto di Analisi dei Sistemi ed Informatica Antonio Ruberti","ror":"https://ror.org/054ye0e45","country_code":"IT","type":"facility","lineage":["https://openalex.org/I4210155236","https://openalex.org/I4210162062"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Daniele Santoni","raw_affiliation_strings":["Institute for Systems Analysis and Computer Science \u201cAntonio Ruberti\u201d, National Research Council of Italy , Rome 00185, Italy"],"affiliations":[{"raw_affiliation_string":"Institute for Systems Analysis and Computer Science \u201cAntonio Ruberti\u201d, National Research Council of Italy , Rome 00185, Italy","institution_ids":["https://openalex.org/I4210162062","https://openalex.org/I4210155236"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5045218419"],"corresponding_institution_ids":["https://openalex.org/I861853513"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.626,"has_fulltext":true,"cited_by_count":6,"citation_normalized_percentile":{"value":0.67067072,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":95,"max":98},"biblio":{"volume":"39","issue":"1","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10064","display_name":"Complex Network Analysis Techniques","score":0.9997000098228455,"subfield":{"id":"https://openalex.org/subfields/3109","display_name":"Statistical and Nonlinear Physics"},"field":{"id":"https://openalex.org/fields/31","display_name":"Physics and Astronomy"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T10064","display_name":"Complex Network Analysis Techniques","score":0.9997000098228455,"subfield":{"id":"https://openalex.org/subfields/3109","display_name":"Statistical and Nonlinear Physics"},"field":{"id":"https://openalex.org/fields/31","display_name":"Physics and Astronomy"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9984999895095825,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T12592","display_name":"Opinion Dynamics and Social Influence","score":0.9559000134468079,"subfield":{"id":"https://openalex.org/subfields/3109","display_name":"Statistical and Nonlinear Physics"},"field":{"id":"https://openalex.org/fields/31","display_name":"Physics and Astronomy"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/homophily","display_name":"Homophily","score":0.9818457961082458},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7418267130851746},{"id":"https://openalex.org/keywords/class","display_name":"Class (philosophy)","score":0.5089848041534424},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.5083939433097839},{"id":"https://openalex.org/keywords/node","display_name":"Node (physics)","score":0.5070490837097168},{"id":"https://openalex.org/keywords/similarity","display_name":"Similarity (geometry)","score":0.4897046387195587},{"id":"https://openalex.org/keywords/code","display_name":"Code (set theory)","score":0.4391419589519501},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.4203365445137024},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.23393258452415466},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.11699587106704712},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.10652536153793335}],"concepts":[{"id":"https://openalex.org/C2779812341","wikidata":"https://www.wikidata.org/wiki/Q5891525","display_name":"Homophily","level":2,"score":0.9818457961082458},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7418267130851746},{"id":"https://openalex.org/C2777212361","wikidata":"https://www.wikidata.org/wiki/Q5127848","display_name":"Class (philosophy)","level":2,"score":0.5089848041534424},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.5083939433097839},{"id":"https://openalex.org/C62611344","wikidata":"https://www.wikidata.org/wiki/Q1062658","display_name":"Node (physics)","level":2,"score":0.5070490837097168},{"id":"https://openalex.org/C103278499","wikidata":"https://www.wikidata.org/wiki/Q254465","display_name":"Similarity (geometry)","level":3,"score":0.4897046387195587},{"id":"https://openalex.org/C2776760102","wikidata":"https://www.wikidata.org/wiki/Q5139990","display_name":"Code (set theory)","level":3,"score":0.4391419589519501},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.4203365445137024},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.23393258452415466},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.11699587106704712},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.10652536153793335},{"id":"https://openalex.org/C66938386","wikidata":"https://www.wikidata.org/wiki/Q633538","display_name":"Structural engineering","level":1,"score":0.0},{"id":"https://openalex.org/C115961682","wikidata":"https://www.wikidata.org/wiki/Q860623","display_name":"Image (mathematics)","level":2,"score":0.0},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.0},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.0},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/btac763","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac763","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/39/1/btac763/48448664/btac763.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:36440918","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/36440918","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:iris.uniroma1.it:11573/1665277","is_oa":true,"landing_page_url":"https://hdl.handle.net/11573/1665277","pdf_url":"https://iris.uniroma1.it/bitstream/11573/1665277/1/Apollonio_Evaluating-homophily_2022.pdf","source":{"id":"https://openalex.org/S4377196107","display_name":"IRIS Research product catalog (Sapienza University of Rome)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:pubmedcentral.nih.gov:9805585","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/9805585","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btac763","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac763","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/39/1/btac763/48448664/btac763.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1600747626","display_name":null,"funder_award_id":"U24CA231877","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G3472427780","display_name":null,"funder_award_id":"CA231877","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G5502778774","display_name":null,"funder_award_id":"U24HG006620","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G7895748443","display_name":null,"funder_award_id":"HG006620","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4310167591.pdf","grobid_xml":"https://content.openalex.org/works/W4310167591.grobid-xml"},"referenced_works_count":6,"referenced_works":["https://openalex.org/W1998522428","https://openalex.org/W2097464861","https://openalex.org/W2130354913","https://openalex.org/W3107527779","https://openalex.org/W4226051960","https://openalex.org/W4282573367"],"related_works":["https://openalex.org/W3185373886","https://openalex.org/W3010567961","https://openalex.org/W4200127153","https://openalex.org/W4385338594","https://openalex.org/W2588006872","https://openalex.org/W3119171992","https://openalex.org/W2560747187","https://openalex.org/W2902086760","https://openalex.org/W2098964748","https://openalex.org/W3081644756"],"abstract_inverted_index":{"Tool's":[0],"source":[1],"code":[2],"is":[3],"available":[4,35],"at":[5,45],"https://github.com/cumbof/honto":[6],"under":[7],"the":[8,32,37],"MIT":[9],"license,":[10],"installable":[11],"as":[12],"a":[13,29],"package":[14],"from":[15],"PyPI":[16],"(pip":[17],"install":[18,23],"honto)":[19],"and":[20,27],"conda-forge":[21,25],"(conda":[22],"-c":[24],"honto),":[26],"has":[28],"wrapper":[30],"for":[31],"Galaxy":[33,39],"platform":[34],"on":[36],"official":[38],"ToolShed":[40],"(Blankenberg":[41],"et":[42],"al.,":[43],"2014)":[44],"https://toolshed.g2.bx.psu.edu/view/fabio/honto.":[46]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":3}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2022-11-30T00:00:00"}