{"id":"https://openalex.org/W2554575351","doi":"https://doi.org/10.1142/s0219720016600027","title":"Is the average shortest path length of gene set a reflection of their biological relatedness?","display_name":"Is the average shortest path length of gene set a reflection of their biological relatedness?","publication_year":2016,"publication_date":"2016-11-09","ids":{"openalex":"https://openalex.org/W2554575351","doi":"https://doi.org/10.1142/s0219720016600027","mag":"2554575351","pmid":"https://pubmed.ncbi.nlm.nih.gov/28073302"},"language":"en","primary_location":{"id":"doi:10.1142/s0219720016600027","is_oa":true,"landing_page_url":"https://doi.org/10.1142/s0219720016600027","pdf_url":"https://www.worldscientific.com/doi/pdf/10.1142/S0219720016600027","source":{"id":"https://openalex.org/S155349577","display_name":"Journal of Bioinformatics and Computational Biology","issn_l":"0219-7200","issn":["0219-7200","1757-6334"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310311754","host_organization_name":"Imperial College Press","host_organization_lineage":["https://openalex.org/P4310311754"],"host_organization_lineage_names":["Imperial College Press"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Bioinformatics and Computational Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://www.worldscientific.com/doi/pdf/10.1142/S0219720016600027","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5020235116","display_name":"Varsha Embar","orcid":null},"institutions":[{"id":"https://openalex.org/I74973139","display_name":"Carnegie Mellon University","ror":"https://ror.org/05x2bcf33","country_code":"US","type":"education","lineage":["https://openalex.org/I74973139"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Varsha Embar","raw_affiliation_strings":["Language Technologies Institute, Carnegie Mellon University, Pittsburgh, PA 15213, USA"],"affiliations":[{"raw_affiliation_string":"Language Technologies Institute, Carnegie Mellon University, Pittsburgh, PA 15213, USA","institution_ids":["https://openalex.org/I74973139"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5077843924","display_name":"Adam Handen","orcid":"https://orcid.org/0000-0002-1371-9466"},"institutions":[{"id":"https://openalex.org/I170201317","display_name":"University of Pittsburgh","ror":"https://ror.org/01an3r305","country_code":"US","type":"education","lineage":["https://openalex.org/I170201317"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Adam Handen","raw_affiliation_strings":["Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh, PA 15213, USA"],"affiliations":[{"raw_affiliation_string":"Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh, PA 15213, USA","institution_ids":["https://openalex.org/I170201317"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5000049528","display_name":"Madhavi K. Ganapathiraju","orcid":"https://orcid.org/0000-0002-3825-0924"},"institutions":[{"id":"https://openalex.org/I170201317","display_name":"University of Pittsburgh","ror":"https://ror.org/01an3r305","country_code":"US","type":"education","lineage":["https://openalex.org/I170201317"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Madhavi K. Ganapathiraju","raw_affiliation_strings":["Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh, PA 15213, USA"],"affiliations":[{"raw_affiliation_string":"Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh, PA 15213, USA","institution_ids":["https://openalex.org/I170201317"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5000049528"],"corresponding_institution_ids":["https://openalex.org/I170201317"],"apc_list":null,"apc_paid":null,"fwci":0.5229,"has_fulltext":true,"cited_by_count":14,"citation_normalized_percentile":{"value":0.72711664,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":98},"biblio":{"volume":"14","issue":"06","first_page":"1660002","last_page":"1660002"},"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/T10086","display_name":"Alzheimer's disease research and treatments","score":0.9912999868392944,"subfield":{"id":"https://openalex.org/subfields/2737","display_name":"Physiology"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},{"id":"https://openalex.org/T10885","display_name":"Gene expression and cancer classification","score":0.9850000143051147,"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/gene","display_name":"Gene","score":0.4909878075122833},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.4554568827152252},{"id":"https://openalex.org/keywords/disease","display_name":"Disease","score":0.4418320059776306},{"id":"https://openalex.org/keywords/context","display_name":"Context (archaeology)","score":0.43751320242881775},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.372843861579895},{"id":"https://openalex.org/keywords/medicine","display_name":"Medicine","score":0.2967855930328369},{"id":"https://openalex.org/keywords/pathology","display_name":"Pathology","score":0.11818498373031616}],"concepts":[{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.4909878075122833},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.4554568827152252},{"id":"https://openalex.org/C2779134260","wikidata":"https://www.wikidata.org/wiki/Q12136","display_name":"Disease","level":2,"score":0.4418320059776306},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.43751320242881775},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.372843861579895},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.2967855930328369},{"id":"https://openalex.org/C142724271","wikidata":"https://www.wikidata.org/wiki/Q7208","display_name":"Pathology","level":1,"score":0.11818498373031616},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","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":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011897","descriptor_name":"Random Allocation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011897","descriptor_name":"Random Allocation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011897","descriptor_name":"Random Allocation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D060066","descriptor_name":"Protein Interaction Maps","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D060066","descriptor_name":"Protein Interaction Maps","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D060066","descriptor_name":"Protein Interaction Maps","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1142/s0219720016600027","is_oa":true,"landing_page_url":"https://doi.org/10.1142/s0219720016600027","pdf_url":"https://www.worldscientific.com/doi/pdf/10.1142/S0219720016600027","source":{"id":"https://openalex.org/S155349577","display_name":"Journal of Bioinformatics and Computational Biology","issn_l":"0219-7200","issn":["0219-7200","1757-6334"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310311754","host_organization_name":"Imperial College Press","host_organization_lineage":["https://openalex.org/P4310311754"],"host_organization_lineage_names":["Imperial College Press"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Bioinformatics and Computational Biology","raw_type":"journal-article"},{"id":"pmid:28073302","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/28073302","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":"Journal of bioinformatics and computational biology","raw_type":null},{"id":"pmh:oai:europepmc.org:4639608","is_oa":false,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/5726383","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1142/s0219720016600027","is_oa":true,"landing_page_url":"https://doi.org/10.1142/s0219720016600027","pdf_url":"https://www.worldscientific.com/doi/pdf/10.1142/S0219720016600027","source":{"id":"https://openalex.org/S155349577","display_name":"Journal of Bioinformatics and Computational Biology","issn_l":"0219-7200","issn":["0219-7200","1757-6334"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310311754","host_organization_name":"Imperial College Press","host_organization_lineage":["https://openalex.org/P4310311754"],"host_organization_lineage_names":["Imperial College Press"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Bioinformatics and Computational Biology","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G5700992986","display_name":null,"funder_award_id":"R01MH094564","funder_id":"https://openalex.org/F4320337346","funder_display_name":"National Institute of Mental Health"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337346","display_name":"National Institute of Mental Health","ror":"https://ror.org/04xeg9z08"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2554575351.pdf","grobid_xml":"https://content.openalex.org/works/W2554575351.grobid-xml"},"referenced_works_count":19,"referenced_works":["https://openalex.org/W598156564","https://openalex.org/W638149299","https://openalex.org/W1508416409","https://openalex.org/W1974944535","https://openalex.org/W2035914845","https://openalex.org/W2043461587","https://openalex.org/W2070412833","https://openalex.org/W2117540545","https://openalex.org/W2119114096","https://openalex.org/W2119220491","https://openalex.org/W2130790725","https://openalex.org/W2146021040","https://openalex.org/W2147714160","https://openalex.org/W2159482845","https://openalex.org/W2163485494","https://openalex.org/W2230524653","https://openalex.org/W2344057082","https://openalex.org/W2410743230","https://openalex.org/W4294216483"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2082860237","https://openalex.org/W2119695867","https://openalex.org/W2130076355","https://openalex.org/W1990804418","https://openalex.org/W1993764875","https://openalex.org/W2046158694","https://openalex.org/W2788277189","https://openalex.org/W2013243191","https://openalex.org/W2034625591"],"abstract_inverted_index":{"When":[0],"a":[1,11,35,52,114,124,130,141,208],"set":[2,125],"of":[3,37,40,81,92,99,106,123,126,133,143,147,154,157,168,171,186,210,213,223],"genes":[4,49,64,83,88,109,127,155,194,199,215],"are":[5,96],"identified":[6],"to":[7,10,21,56,69,86,104,111,166],"be":[8,57,66],"related":[9,63],"disease,":[12],"say":[13],"through":[14],"gene":[15],"expression":[16],"analysis,":[17],"it":[18,138],"is":[19,47,102,128,139,207],"common":[20],"examine":[22],"the":[23,31,73,90,94,121,144,152,187,211,214,217],"average":[24,76],"distance":[25],"among":[26,97],"their":[27,196],"protein":[28],"products":[29],"in":[30,72,89,113],"human":[32],"interactome":[33],"as":[34,87],"measure":[36,132],"biological":[38,134],"relatedness":[39,135],"these":[41,100],"genes.":[42,149],"The":[43],"reasoning":[44],"for":[45],"this":[46],"that,":[48],"associated":[50,193],"with":[51],"disease":[53,82,159,192],"would":[54,65],"tend":[55],"functionally":[58,62],"related,":[59],"and":[60,160,163,183,195,216,220],"that":[61,191,222],"closely":[67],"connected":[68],"each":[70],"other":[71,204],"interactome.":[74],"Typically,":[75],"shortest":[77],"path":[78],"length":[79],"(ASPL)":[80],"(although":[84],"referred":[85],"context":[91],"disease-associations,":[93],"interactions":[95],"protein-products":[98],"genes)":[101],"compared":[103,164],"ASPL":[105,112,122,153,167,206],"randomly":[107,115,172],"selected":[108,173],"or":[110,136],"permuted":[116],"network.":[117,188],"We":[118,150,189],"examined":[119,151],"whether":[120,137],"indeed":[129],"good":[131],"simply":[140],"characteristic":[142,209],"degree":[145,212],"distribution":[146],"those":[148],"sets":[156],"some":[158],"pathway":[161],"associations":[162],"them":[165],"three":[169],"types":[170],"control":[174],"sets:":[175],"uniform":[176],"selection,":[177,182],"from":[178],"entire":[179],"proteome,":[180],"degree-matched":[181,197],"random":[184,198],"permutation":[185],"found":[190],"have":[200],"comparable":[201],"ASPL.":[202],"In":[203],"words,":[205],"network":[218],"topology,":[219],"not":[221],"functional":[224],"coherence.":[225]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":5},{"year":2020,"cited_by_count":4},{"year":2019,"cited_by_count":2},{"year":2016,"cited_by_count":1}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2025-10-10T00:00:00"}