{"id":"https://openalex.org/W3034605745","doi":"https://doi.org/10.1186/s13040-020-00214-x","title":"Revisiting the use of graph centrality models in biological pathway analysis","display_name":"Revisiting the use of graph centrality models in biological pathway analysis","publication_year":2020,"publication_date":"2020-06-16","ids":{"openalex":"https://openalex.org/W3034605745","doi":"https://doi.org/10.1186/s13040-020-00214-x","mag":"3034605745","pmid":"https://pubmed.ncbi.nlm.nih.gov/32549913"},"language":"en","primary_location":{"id":"doi:10.1186/s13040-020-00214-x","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13040-020-00214-x","pdf_url":"https://biodatamining.biomedcentral.com/track/pdf/10.1186/s13040-020-00214-x","source":{"id":"https://openalex.org/S84409260","display_name":"BioData Mining","issn_l":"1756-0381","issn":["1756-0381"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BioData Mining","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://biodatamining.biomedcentral.com/track/pdf/10.1186/s13040-020-00214-x","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5082256578","display_name":"Pourya Naderi Yeganeh","orcid":"https://orcid.org/0000-0002-4693-8331"},"institutions":[{"id":"https://openalex.org/I102149020","display_name":"University of North Carolina at Charlotte","ror":"https://ror.org/04dawnj30","country_code":"US","type":"education","lineage":["https://openalex.org/I102149020"]},{"id":"https://openalex.org/I1316535847","display_name":"Beth Israel Deaconess Medical Center","ror":"https://ror.org/04drvxt59","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1316535847"]},{"id":"https://openalex.org/I136199984","display_name":"Harvard University","ror":"https://ror.org/03vek6s52","country_code":"US","type":"education","lineage":["https://openalex.org/I136199984"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Pourya Naderi Yeganeh","raw_affiliation_strings":["Beth Israel Deaconess Medical Center, Harvard Medical School, 330 Brookline Ave., Boston, 02215 MA USA","Department of Computer Science, The University of North Carolina at Charlotte, 9201 University City Blvd, Charlotte, 28223 NC USA","Department of Computer Science, The University of North Carolina at Charlotte, 9201 University City Blvd, Charlotte, 28223, NC, USA","Beth Israel Deaconess Medical Center, Harvard Medical School, 330 Brookline Ave., Boston, 02215, MA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Beth Israel Deaconess Medical Center, Harvard Medical School, 330 Brookline Ave., Boston, 02215 MA USA","institution_ids":["https://openalex.org/I1316535847"]},{"raw_affiliation_string":"Department of Computer Science, The University of North Carolina at Charlotte, 9201 University City Blvd, Charlotte, 28223 NC USA","institution_ids":["https://openalex.org/I102149020"]},{"raw_affiliation_string":"Department of Computer Science, The University of North Carolina at Charlotte, 9201 University City Blvd, Charlotte, 28223, NC, USA","institution_ids":["https://openalex.org/I102149020"]},{"raw_affiliation_string":"Beth Israel Deaconess Medical Center, Harvard Medical School, 330 Brookline Ave., Boston, 02215, MA, USA","institution_ids":["https://openalex.org/I1316535847","https://openalex.org/I136199984"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5039568648","display_name":"Chrsitine Richardson","orcid":null},"institutions":[{"id":"https://openalex.org/I102149020","display_name":"University of North Carolina at Charlotte","ror":"https://ror.org/04dawnj30","country_code":"US","type":"education","lineage":["https://openalex.org/I102149020"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Chrsitine Richardson","raw_affiliation_strings":["Department of Biological Sciences, The University of North Carolina at Charlotte, 9201 University City Blvd, Charlotte, 28223 NC USA","Department of Biological Sciences, The University of North Carolina at Charlotte, 9201 University City Blvd, Charlotte, 28223, NC, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biological Sciences, The University of North Carolina at Charlotte, 9201 University City Blvd, Charlotte, 28223 NC USA","institution_ids":["https://openalex.org/I102149020"]},{"raw_affiliation_string":"Department of Biological Sciences, The University of North Carolina at Charlotte, 9201 University City Blvd, Charlotte, 28223, NC, USA","institution_ids":["https://openalex.org/I102149020"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5028427671","display_name":"\u00c9rik Saule","orcid":"https://orcid.org/0000-0003-1634-9234"},"institutions":[{"id":"https://openalex.org/I102149020","display_name":"University of North Carolina at Charlotte","ror":"https://ror.org/04dawnj30","country_code":"US","type":"education","lineage":["https://openalex.org/I102149020"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Erik Saule","raw_affiliation_strings":["Department of Computer Science, The University of North Carolina at Charlotte, 9201 University City Blvd, Charlotte, 28223 NC USA","Department of Computer Science, The University of North Carolina at Charlotte, 9201 University City Blvd, Charlotte, 28223, NC, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, The University of North Carolina at Charlotte, 9201 University City Blvd, Charlotte, 28223 NC USA","institution_ids":["https://openalex.org/I102149020"]},{"raw_affiliation_string":"Department of Computer Science, The University of North Carolina at Charlotte, 9201 University City Blvd, Charlotte, 28223, NC, USA","institution_ids":["https://openalex.org/I102149020"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5074503956","display_name":"Ann E. Loraine","orcid":"https://orcid.org/0000-0002-8365-0177"},"institutions":[{"id":"https://openalex.org/I102149020","display_name":"University of North Carolina at Charlotte","ror":"https://ror.org/04dawnj30","country_code":"US","type":"education","lineage":["https://openalex.org/I102149020"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ann Loraine","raw_affiliation_strings":["Department of Bioinformatics and Genomics, The University of North Carolina at Charlotte, 9201 University City Blvd, Charlotte, 28223 NC USA","Department of Bioinformatics and Genomics, The University of North Carolina at Charlotte, 9201 University City Blvd, Charlotte, 28223, NC, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Bioinformatics and Genomics, The University of North Carolina at Charlotte, 9201 University City Blvd, Charlotte, 28223 NC USA","institution_ids":["https://openalex.org/I102149020"]},{"raw_affiliation_string":"Department of Bioinformatics and Genomics, The University of North Carolina at Charlotte, 9201 University City Blvd, Charlotte, 28223, NC, USA","institution_ids":["https://openalex.org/I102149020"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5021674372","display_name":"M. Mostafavi","orcid":"https://orcid.org/0000-0002-0024-4131"},"institutions":[{"id":"https://openalex.org/I102149020","display_name":"University of North Carolina at Charlotte","ror":"https://ror.org/04dawnj30","country_code":"US","type":"education","lineage":["https://openalex.org/I102149020"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"M. Taghi Mostafavi","raw_affiliation_strings":["Department of Computer Science, The University of North Carolina at Charlotte, 9201 University City Blvd, Charlotte, 28223 NC USA","Department of Computer Science, The University of North Carolina at Charlotte, 9201 University City Blvd, Charlotte, 28223, NC, USA"],"raw_orcid":"https://orcid.org/0000-0002-0024-4131","affiliations":[{"raw_affiliation_string":"Department of Computer Science, The University of North Carolina at Charlotte, 9201 University City Blvd, Charlotte, 28223 NC USA","institution_ids":["https://openalex.org/I102149020"]},{"raw_affiliation_string":"Department of Computer Science, The University of North Carolina at Charlotte, 9201 University City Blvd, Charlotte, 28223, NC, USA","institution_ids":["https://openalex.org/I102149020"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":0.7503,"has_fulltext":true,"cited_by_count":16,"citation_normalized_percentile":{"value":0.69333184,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":99},"biblio":{"volume":"13","issue":"1","first_page":"5","last_page":"5"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9998999834060669,"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"}},"topics":[{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9998999834060669,"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/T10211","display_name":"Computational Drug Discovery Methods","score":0.9993000030517578,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9972000122070312,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/centrality","display_name":"Centrality","score":0.8322871327400208},{"id":"https://openalex.org/keywords/inference","display_name":"Inference","score":0.6936067342758179},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6030858755111694},{"id":"https://openalex.org/keywords/biological-network","display_name":"Biological network","score":0.532986581325531},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.491840124130249},{"id":"https://openalex.org/keywords/upstream","display_name":"Upstream (networking)","score":0.461318701505661},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3918708562850952},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.34796804189682007},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2098313868045807},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.20546692609786987},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.15709921717643738}],"concepts":[{"id":"https://openalex.org/C53811970","wikidata":"https://www.wikidata.org/wiki/Q5062194","display_name":"Centrality","level":2,"score":0.8322871327400208},{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.6936067342758179},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6030858755111694},{"id":"https://openalex.org/C28225019","wikidata":"https://www.wikidata.org/wiki/Q4915005","display_name":"Biological network","level":2,"score":0.532986581325531},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.491840124130249},{"id":"https://openalex.org/C191172861","wikidata":"https://www.wikidata.org/wiki/Q7899321","display_name":"Upstream (networking)","level":2,"score":0.461318701505661},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3918708562850952},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.34796804189682007},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2098313868045807},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.20546692609786987},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.15709921717643738},{"id":"https://openalex.org/C31258907","wikidata":"https://www.wikidata.org/wiki/Q1301371","display_name":"Computer network","level":1,"score":0.0},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.0}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.1186/s13040-020-00214-x","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13040-020-00214-x","pdf_url":"https://biodatamining.biomedcentral.com/track/pdf/10.1186/s13040-020-00214-x","source":{"id":"https://openalex.org/S84409260","display_name":"BioData Mining","issn_l":"1756-0381","issn":["1756-0381"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BioData Mining","raw_type":"journal-article"},{"id":"pmid:32549913","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/32549913","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":"BioData mining","raw_type":null},{"id":"pmh:oai:doaj.org/article:71b400c971534ea3973b631475f113e4","is_oa":true,"landing_page_url":"https://doaj.org/article/71b400c971534ea3973b631475f113e4","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","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":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BioData Mining, Vol 13, Iss 1, Pp 1-23 (2020)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:7296696","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/7296696","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"BioData Min","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/s13040-020-00214-x","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13040-020-00214-x","pdf_url":"https://biodatamining.biomedcentral.com/track/pdf/10.1186/s13040-020-00214-x","source":{"id":"https://openalex.org/S84409260","display_name":"BioData Mining","issn_l":"1756-0381","issn":["1756-0381"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BioData Mining","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Good health and well-being","score":0.46000000834465027,"id":"https://metadata.un.org/sdg/3"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3034605745.pdf","grobid_xml":"https://content.openalex.org/works/W3034605745.grobid-xml"},"referenced_works_count":44,"referenced_works":["https://openalex.org/W1511160855","https://openalex.org/W1875112053","https://openalex.org/W1978486653","https://openalex.org/W1985695385","https://openalex.org/W1988142400","https://openalex.org/W1988319444","https://openalex.org/W1989108446","https://openalex.org/W2006120266","https://openalex.org/W2006683252","https://openalex.org/W2011912935","https://openalex.org/W2054892633","https://openalex.org/W2061425021","https://openalex.org/W2066636486","https://openalex.org/W2069992656","https://openalex.org/W2095319945","https://openalex.org/W2100625056","https://openalex.org/W2100980426","https://openalex.org/W2102140136","https://openalex.org/W2105734437","https://openalex.org/W2109912704","https://openalex.org/W2110065044","https://openalex.org/W2110687686","https://openalex.org/W2117692326","https://openalex.org/W2130410032","https://openalex.org/W2130790725","https://openalex.org/W2132105963","https://openalex.org/W2141224543","https://openalex.org/W2144885342","https://openalex.org/W2147714160","https://openalex.org/W2152285853","https://openalex.org/W2154331071","https://openalex.org/W2155330008","https://openalex.org/W2158293950","https://openalex.org/W2171878761","https://openalex.org/W2558229157","https://openalex.org/W2559588208","https://openalex.org/W2750487367","https://openalex.org/W2912730876","https://openalex.org/W2929796216","https://openalex.org/W2932761314","https://openalex.org/W2963180298","https://openalex.org/W3103786587","https://openalex.org/W4238452917","https://openalex.org/W7067216465"],"related_works":["https://openalex.org/W4229078645","https://openalex.org/W1977345676","https://openalex.org/W4282032776","https://openalex.org/W2047552823","https://openalex.org/W4321606905","https://openalex.org/W3130445735","https://openalex.org/W2322248538","https://openalex.org/W118100147","https://openalex.org/W2135602072","https://openalex.org/W2112534124"],"abstract_inverted_index":{"The":[0,217],"use":[1],"of":[2,21,29,53,107,115,124,133,153,198,227],"graph":[3,42,76,98],"theory":[4],"models":[5],"is":[6,14],"widespread":[7],"in":[8,25,72,118,162,202,222],"biological":[9,31,60,134,233],"pathway":[10,64,205],"analyses":[11],"as":[12,91,127],"it":[13,207],"often":[15],"desired":[16],"to":[17,82,103,182,212],"evaluate":[18,87,149],"the":[19,30,39,49,54,59,83,88,105,113,119,122,138,143,150,183,193,199,203,214],"position":[20,152],"genes":[22,157,161,184],"and":[23,56,70,86,121,130,136,158,168,229],"proteins":[24],"their":[26,163],"interaction":[27],"networks":[28],"systems.":[32],"In":[33],"this":[34],"article,":[35],"we":[36,148],"argue":[37],"that":[38,170],"common":[40,204],"standard":[41,74,108],"centrality":[43],"measures":[44,112],"do":[45],"not":[46],"sufficiently":[47],"capture":[48],"informative":[50,224,232],"topological":[51,80,151,225],"organizations":[52],"pathways,":[55,73,228],"thus,":[57,230],"limit":[58],"inference.":[61,234],"While":[62,192],"key":[63],"elements":[65,85,90],"may":[66],"appear":[67],"both":[68],"upstream":[69,84,120],"downstream":[71,89,123],"directed":[75,97],"centralities":[77,172],"attribute":[78],"significant":[79],"importance":[81,114,181,187],"having":[92],"no":[93],"importance.We":[94],"present":[95],"a":[96,116,125,128,131,189,209],"framework,":[99],"Source/Sink":[100],"Centrality":[101],"(SSC),":[102],"address":[104],"limitations":[106],"models.":[109,216],"SSC":[110,218],"separately":[111],"node":[117],"pathway,":[126],"sender":[129],"receiver":[132],"signals,":[135],"combines":[137],"two":[139],"terms":[140],"for":[141,177],"evaluating":[142],"centrality.":[144],"To":[145],"validate":[146],"SSC,":[147],"known":[154],"human":[155],"cancer":[156],"mouse":[159],"lethal":[160],"respective":[164],"KEGG":[165],"annotated":[166],"pathways":[167],"show":[169],"SSC-derived":[171],"provide":[173],"an":[174],"effective":[175],"framework":[176],"associating":[178],"higher":[179,186],"positional":[180],"with":[185],"from":[188],"priori":[190],"knowledge.":[191],"presented":[194],"work":[195],"challenges":[196],"some":[197],"modeling":[200],"assumptions":[201],"analyses,":[206],"provides":[208],"straight-forward":[210],"methodology":[211],"extend":[213],"existing":[215],"extensions":[219],"can":[220],"result":[221],"more":[223,231],"description":[226]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":3},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":5}],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2020-06-19T00:00:00"}
