{"id":"https://openalex.org/W2133432092","doi":"https://doi.org/10.1186/1471-2105-11-s1-s35","title":"Functional characterization and topological modularity of molecular interaction networks","display_name":"Functional characterization and topological modularity of molecular interaction networks","publication_year":2010,"publication_date":"2010-01-01","ids":{"openalex":"https://openalex.org/W2133432092","doi":"https://doi.org/10.1186/1471-2105-11-s1-s35","mag":"2133432092","pmid":"https://pubmed.ncbi.nlm.nih.gov/20122208"},"language":"en","primary_location":{"id":"doi:10.1186/1471-2105-11-s1-s35","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-11-s1-s35","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-11-S1-S35","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"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":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-11-S1-S35","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5069688744","display_name":"Jayesh Pandey","orcid":"https://orcid.org/0000-0003-4009-9677"},"institutions":[{"id":"https://openalex.org/I219193219","display_name":"Purdue University West Lafayette","ror":"https://ror.org/02dqehb95","country_code":"US","type":"education","lineage":["https://openalex.org/I219193219"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jayesh Pandey","raw_affiliation_strings":["Department of Computer Science, Purdue University, West Lafayette, IN, USA. jpandey@cs.purdue.edu","Department of Computer Science, Purdue University, West Lafayette, IN, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Purdue University, West Lafayette, IN, USA. jpandey@cs.purdue.edu","institution_ids":["https://openalex.org/I219193219"]},{"raw_affiliation_string":"Department of Computer Science, Purdue University, West Lafayette, IN, USA","institution_ids":["https://openalex.org/I219193219"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5035558591","display_name":"Mehmet Koyut\u00fcrk","orcid":"https://orcid.org/0000-0002-3434-5512"},"institutions":[{"id":"https://openalex.org/I58956616","display_name":"Case Western Reserve University","ror":"https://ror.org/051fd9666","country_code":"US","type":"education","lineage":["https://openalex.org/I58956616"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Mehmet Koyut\u00fcrk","raw_affiliation_strings":["Center for Proteomics & Bioinformatics, Case Western Reserve University, Cleveland, OH, USA","Department of Electrical Engineering & Computer Science, Case Western Reserve University, Cleveland, OH, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Proteomics & Bioinformatics, Case Western Reserve University, Cleveland, OH, USA","institution_ids":["https://openalex.org/I58956616"]},{"raw_affiliation_string":"Department of Electrical Engineering & Computer Science, Case Western Reserve University, Cleveland, OH, USA","institution_ids":["https://openalex.org/I58956616"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5019202832","display_name":"Ananth Grama","orcid":"https://orcid.org/0000-0002-9378-9244"},"institutions":[{"id":"https://openalex.org/I219193219","display_name":"Purdue University West Lafayette","ror":"https://ror.org/02dqehb95","country_code":"US","type":"education","lineage":["https://openalex.org/I219193219"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ananth Grama","raw_affiliation_strings":["Department of Computer Science, Purdue University, West Lafayette, IN, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Purdue University, West Lafayette, IN, USA","institution_ids":["https://openalex.org/I219193219"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"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":2.0421,"has_fulltext":true,"cited_by_count":21,"citation_normalized_percentile":{"value":0.8656474,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"11","issue":"S1","first_page":"S35","last_page":"S35"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.8719000220298767,"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":0.8719000220298767,"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":0.049400001764297485,"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/T12536","display_name":"Topological and Geometric Data Analysis","score":0.027899999171495438,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6284701824188232},{"id":"https://openalex.org/keywords/modularity","display_name":"Modularity (biology)","score":0.5744926929473877},{"id":"https://openalex.org/keywords/interaction-network","display_name":"Interaction network","score":0.5637645125389099},{"id":"https://openalex.org/keywords/topology","display_name":"Topology (electrical circuits)","score":0.5063034296035767},{"id":"https://openalex.org/keywords/coherence","display_name":"Coherence (philosophical gambling strategy)","score":0.48381274938583374},{"id":"https://openalex.org/keywords/similarity","display_name":"Similarity (geometry)","score":0.4789198637008667},{"id":"https://openalex.org/keywords/interaction-information","display_name":"Interaction information","score":0.4733597934246063},{"id":"https://openalex.org/keywords/domain","display_name":"Domain (mathematical analysis)","score":0.4367046356201172},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.4349586069583893},{"id":"https://openalex.org/keywords/characterization","display_name":"Characterization (materials science)","score":0.4220200181007385},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3612670302391052},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.21373146772384644},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.1383390724658966},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.10039958357810974}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6284701824188232},{"id":"https://openalex.org/C2779478453","wikidata":"https://www.wikidata.org/wiki/Q6889748","display_name":"Modularity (biology)","level":2,"score":0.5744926929473877},{"id":"https://openalex.org/C55105296","wikidata":"https://www.wikidata.org/wiki/Q841382","display_name":"Interaction network","level":3,"score":0.5637645125389099},{"id":"https://openalex.org/C184720557","wikidata":"https://www.wikidata.org/wiki/Q7825049","display_name":"Topology (electrical circuits)","level":2,"score":0.5063034296035767},{"id":"https://openalex.org/C2781181686","wikidata":"https://www.wikidata.org/wiki/Q4226068","display_name":"Coherence (philosophical gambling strategy)","level":2,"score":0.48381274938583374},{"id":"https://openalex.org/C103278499","wikidata":"https://www.wikidata.org/wiki/Q254465","display_name":"Similarity (geometry)","level":3,"score":0.4789198637008667},{"id":"https://openalex.org/C38764148","wikidata":"https://www.wikidata.org/wiki/Q17098245","display_name":"Interaction information","level":2,"score":0.4733597934246063},{"id":"https://openalex.org/C36503486","wikidata":"https://www.wikidata.org/wiki/Q11235244","display_name":"Domain (mathematical analysis)","level":2,"score":0.4367046356201172},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.4349586069583893},{"id":"https://openalex.org/C2780841128","wikidata":"https://www.wikidata.org/wiki/Q5073781","display_name":"Characterization (materials science)","level":2,"score":0.4220200181007385},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3612670302391052},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.21373146772384644},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.1383390724658966},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.10039958357810974},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","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},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.0},{"id":"https://openalex.org/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","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/C120665830","wikidata":"https://www.wikidata.org/wiki/Q14620","display_name":"Optics","level":1,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D020543","descriptor_name":"Proteome","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D020543","descriptor_name":"Proteome","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D020543","descriptor_name":"Proteome","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D040901","descriptor_name":"Proteomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D040901","descriptor_name":"Proteomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D040901","descriptor_name":"Proteomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1186/1471-2105-11-s1-s35","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-11-s1-s35","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-11-S1-S35","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"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":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:20122208","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/20122208","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":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:doaj.org/article:026aeecf27a34b1e9c7fe1e2d578c9b9","is_oa":true,"landing_page_url":"https://doaj.org/article/026aeecf27a34b1e9c7fe1e2d578c9b9","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":"BMC Bioinformatics, Vol 11, Iss Suppl 1, p S35 (2010)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:3009507","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3009507","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":"BMC Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/1471-2105-11-s1-s35","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-11-s1-s35","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-11-S1-S35","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"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":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G2955839788","display_name":"Biochemical Pathways Workbench","funder_award_id":"0641037","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G5436631784","display_name":"CDI-Type II: Hierarchiacal Modularity in Evolution and Function","funder_award_id":"0835541","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2133432092.pdf","grobid_xml":"https://content.openalex.org/works/W2133432092.grobid-xml"},"referenced_works_count":34,"referenced_works":["https://openalex.org/W1493403933","https://openalex.org/W1513501940","https://openalex.org/W1972636593","https://openalex.org/W1973110501","https://openalex.org/W1975414584","https://openalex.org/W1980948656","https://openalex.org/W1986269714","https://openalex.org/W1986512768","https://openalex.org/W1988572854","https://openalex.org/W1994745117","https://openalex.org/W2013520054","https://openalex.org/W2047693963","https://openalex.org/W2096939566","https://openalex.org/W2099047355","https://openalex.org/W2100935296","https://openalex.org/W2103017472","https://openalex.org/W2104261859","https://openalex.org/W2106202847","https://openalex.org/W2114921810","https://openalex.org/W2117805756","https://openalex.org/W2118446779","https://openalex.org/W2123501554","https://openalex.org/W2126225210","https://openalex.org/W2127563440","https://openalex.org/W2134962976","https://openalex.org/W2135230352","https://openalex.org/W2137623997","https://openalex.org/W2151296292","https://openalex.org/W2152495216","https://openalex.org/W2160521949","https://openalex.org/W2166468869","https://openalex.org/W2168108570","https://openalex.org/W2170241526","https://openalex.org/W2917431650"],"related_works":["https://openalex.org/W2952813980","https://openalex.org/W1996087298","https://openalex.org/W1511491607","https://openalex.org/W2020286660","https://openalex.org/W3087302704","https://openalex.org/W2184981123","https://openalex.org/W2137238644","https://openalex.org/W2104919487","https://openalex.org/W2321384651","https://openalex.org/W2131347449"],"abstract_inverted_index":{"BACKGROUND:":[0],"Analyzing":[1],"interaction":[2,21,115,143,151,185],"networks":[3,144,152],"for":[4],"functional":[5,26,45,61,86,94,132],"characterization":[6],"poses":[7],"significant":[8],"challenges":[9],"arising":[10],"from":[11],"the":[12,20,58,70,74,91,120],"noisy,":[13],"incomplete,":[14],"and":[15,63,113,134,172,196,200],"generic":[16],"nature":[17],"of":[18,28,57,72,76,78,93,104,162,168,177,207,212],"both":[19],"data":[22],"as":[23,25,88,90,202,204],"well":[24,89,203],"annotation":[27],"molecules.":[29,213],"Network-based":[30],"methods":[31,190],"focus":[32],"on":[33,191,205],"interacting":[34],"molecules":[35],"(pairs":[36],"or":[37],"sets)":[38],"occurring":[39],"in":[40,66,123,137],"close":[41],"proximity":[42,65,106,136,179],"to":[43,111,166,183],"infer":[44],"associations.":[46],"RESULTS:":[47],"In":[48],"this":[49,124],"paper":[50],"we":[51],"perform":[52],"a":[53],"formal":[54],"comparative":[55],"investigation":[56],"relationship":[59],"between":[60,131],"coherence":[62,75,158],"topological":[64,105,135,178],"networks.":[67],"We":[68,99,118,187],"investigate":[69],"problem":[71],"assessing":[73],"sets":[77,161,206],"biomolecules":[79],"(or":[80],"segments":[81],"thereof)":[82],"taking":[83],"into":[84],"account":[85],"specificity":[87],"distribution":[92],"attributes":[95],"across":[96],"entity":[97],"groups.":[98],"also":[100],"propose":[101],"novel":[102],"measures":[103,155,176],"that":[107,156],"are":[108,164,180],"more":[109],"robust":[110],"noisy":[112],"incomplete":[114],"data.":[116,186],"CONCLUSION:":[117],"derive":[119],"following":[121],"results":[122],"paper:":[125],"(i)":[126],"there":[127],"exists":[128],"strong":[129],"correlation":[130,148],"similarity":[133],"various":[138],"network":[139],"abstractions,":[140],"with":[141],"domain":[142],"(DDIs)":[145],"demonstrating":[146],"higher":[147],"than":[149],"protein":[150],"(PPIs);":[153],"(ii)":[154],"quantify":[157],"among":[159],"entire":[160],"proteins":[163],"superior":[165],"aggregates":[167],"known":[169,208],"pair-wise":[170],"measures;":[171],"(iii)":[173],"random-walk":[174],"based":[175],"better":[181],"suited":[182],"existing":[184],"validate":[188],"our":[189],"diverse":[192],"data,":[193],"including":[194],"experimentally":[195],"computationally":[197],"derived":[198],"PPIs":[199],"DDIs,":[201],"biologically":[209],"related":[210],"groups":[211]},"counts_by_year":[{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":2},{"year":2015,"cited_by_count":2},{"year":2013,"cited_by_count":1},{"year":2012,"cited_by_count":6}],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2025-10-10T00:00:00"}