{"id":"https://openalex.org/W2607673600","doi":"https://doi.org/10.5075/epfl-thesis-7618","title":"Models and Algorithms in Biological Network Evolution with Modularity","display_name":"Models and Algorithms in Biological Network Evolution with Modularity","publication_year":2017,"publication_date":"2017-01-01","ids":{"openalex":"https://openalex.org/W2607673600","doi":"https://doi.org/10.5075/epfl-thesis-7618","mag":"2607673600"},"language":"en","primary_location":{"id":"pmh:oai:infoscience.epfl.ch:227481","is_oa":true,"landing_page_url":"http://infoscience.epfl.ch/record/227481","pdf_url":null,"source":{"id":"https://openalex.org/S4306400487","display_name":"Infoscience (Ecole Polytechnique F\u00e9d\u00e9rale de Lausanne)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Text"},"type":"article","indexed_in":["datacite"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"http://infoscience.epfl.ch/record/227481","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100725242","display_name":"Min Ye","orcid":"https://orcid.org/0000-0002-9952-2380"},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Ye, Min","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":0,"corresponding_author_ids":["https://openalex.org/A5100725242"],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":{"value":0.03087733,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9965999722480774,"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":0.9965999722480774,"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/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9944000244140625,"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/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.9771000146865845,"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/modularity","display_name":"Modularity (biology)","score":0.7201657295227051},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.667664647102356},{"id":"https://openalex.org/keywords/biological-network","display_name":"Biological network","score":0.5681198239326477},{"id":"https://openalex.org/keywords/generative-model","display_name":"Generative model","score":0.501481294631958},{"id":"https://openalex.org/keywords/node","display_name":"Node (physics)","score":0.48748135566711426},{"id":"https://openalex.org/keywords/modular-design","display_name":"Modular design","score":0.4841959774494171},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.4787918031215668},{"id":"https://openalex.org/keywords/inference","display_name":"Inference","score":0.4716845154762268},{"id":"https://openalex.org/keywords/generative-grammar","display_name":"Generative grammar","score":0.4372588098049164},{"id":"https://openalex.org/keywords/merge","display_name":"Merge (version control)","score":0.42779073119163513},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.33157891035079956},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.20706060528755188},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.14863139390945435}],"concepts":[{"id":"https://openalex.org/C2779478453","wikidata":"https://www.wikidata.org/wiki/Q6889748","display_name":"Modularity (biology)","level":2,"score":0.7201657295227051},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.667664647102356},{"id":"https://openalex.org/C28225019","wikidata":"https://www.wikidata.org/wiki/Q4915005","display_name":"Biological network","level":2,"score":0.5681198239326477},{"id":"https://openalex.org/C167966045","wikidata":"https://www.wikidata.org/wiki/Q5532625","display_name":"Generative model","level":3,"score":0.501481294631958},{"id":"https://openalex.org/C62611344","wikidata":"https://www.wikidata.org/wiki/Q1062658","display_name":"Node (physics)","level":2,"score":0.48748135566711426},{"id":"https://openalex.org/C101468663","wikidata":"https://www.wikidata.org/wiki/Q1620158","display_name":"Modular design","level":2,"score":0.4841959774494171},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.4787918031215668},{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.4716845154762268},{"id":"https://openalex.org/C39890363","wikidata":"https://www.wikidata.org/wiki/Q36108","display_name":"Generative grammar","level":2,"score":0.4372588098049164},{"id":"https://openalex.org/C197129107","wikidata":"https://www.wikidata.org/wiki/Q1921621","display_name":"Merge (version control)","level":2,"score":0.42779073119163513},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.33157891035079956},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.20706060528755188},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.14863139390945435},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.0},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.0},{"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/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.0},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0}],"mesh":[],"locations_count":3,"locations":[{"id":"pmh:oai:infoscience.epfl.ch:227481","is_oa":true,"landing_page_url":"http://infoscience.epfl.ch/record/227481","pdf_url":null,"source":{"id":"https://openalex.org/S4306400487","display_name":"Infoscience (Ecole Polytechnique F\u00e9d\u00e9rale de Lausanne)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Text"},{"id":"doi:10.5075/epfl-thesis-7618","is_oa":true,"landing_page_url":"https://doi.org/10.5075/epfl-thesis-7618","pdf_url":null,"source":null,"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":"Dissertation"},{"id":"mag:2607673600","is_oa":false,"landing_page_url":"https://infoscience.epfl.ch/record/227481","pdf_url":null,"source":null,"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":null}],"best_oa_location":{"id":"pmh:oai:infoscience.epfl.ch:227481","is_oa":true,"landing_page_url":"http://infoscience.epfl.ch/record/227481","pdf_url":null,"source":{"id":"https://openalex.org/S4306400487","display_name":"Infoscience (Ecole Polytechnique F\u00e9d\u00e9rale de Lausanne)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Text"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/15","score":0.4000000059604645,"display_name":"Life in Land"}],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":["https://openalex.org/W2471010299","https://openalex.org/W2884075830","https://openalex.org/W2246049295","https://openalex.org/W142301544","https://openalex.org/W2023889921","https://openalex.org/W2183996473","https://openalex.org/W2127874029","https://openalex.org/W60288630","https://openalex.org/W2287803059","https://openalex.org/W2003333003","https://openalex.org/W2951066103","https://openalex.org/W2028793292","https://openalex.org/W2482145710","https://openalex.org/W2214945370","https://openalex.org/W2102707013","https://openalex.org/W2133628070","https://openalex.org/W2308950173","https://openalex.org/W2063639254","https://openalex.org/W2604305619","https://openalex.org/W2238690406"],"abstract_inverted_index":{"Networks":[0],"are":[1,45,113,136],"commonly":[2],"used":[3],"to":[4,90,117,183,187,190,207,246,267,318],"represent":[5],"key":[6],"processes":[7],"in":[8,109,211,234,332],"biology;":[9],"examples":[10],"include":[11],"transcriptional":[12],"regulatory":[13],"networks,":[14,18,20,26,42],"protein-protein":[15],"interaction":[16],"(PPI)":[17],"metabolic":[19],"etc.":[21],"Databases":[22],"store":[23],"many":[24],"such":[25,92],"as":[27,242,374],"graphs,":[28],"observed":[29],"or":[30],"inferred.":[31],"Generative":[32],"models":[33,44,96,115,127,135,253,299],"for":[34,359],"these":[35,103,240,288],"networks":[36,73,210,249,295,309,323,334],"have":[37,102],"been":[38,105],"proposed.":[39],"For":[40],"PPI":[41,322,333],"current":[43,352],"based":[46,129,138],"on":[47,130,139],"duplication":[48],"and":[49,57,119,185,189,254,283,300],"divergence":[50],"(D&D):":[51],"a":[52,76,150,165,200,270,336,360,379],"node":[53],"(gene)":[54],"is":[55,74,79,164,178,341],"duplicated":[56],"inherits":[58],"some":[59],"subset":[60],"of":[61,64,82,158,167,213,222,272,320,324,370],"the":[62,65,110,124,132,140,161,168,175,195,248,280,294,308,321,325,345,357,375],"connections":[63],"original":[66],"node.":[67],"An":[68],"early":[69],"finding":[70],"about":[71],"biological":[72,209],"modularity:":[75],"higher-level":[77],"structure":[78],"prevalent":[80],"consisting":[81],"well":[83],"connected":[84],"subgraphs":[85],"with":[86,107,148,290],"less":[87],"substantial":[88],"connectivity":[89],"other":[91,351],"subgraphs.":[93],"While":[94],"D&D":[95,114,169,252,298],"spontaneously":[97],"generate":[98],"modular":[99,215],"structures,":[100],"neither":[101],"structures":[104],"compared":[106],"those":[108,291,319],"databases":[111,229],"nor":[112],"known":[116],"maintain":[118],"evolve":[120],"them.":[121],"Given":[122],"that":[123,153,307,330,340,365],"preferred":[125],"generative":[126],"being":[128],"D&D,":[131],"network":[133,235,362],"inference":[134,363],"also":[137,204],"same":[141],"principle.":[142],"We":[143,203,217,237,260,328],"describe":[144],"NEMo":[145,180,302,312,347,373],"(Network":[146],"Evolution":[147],"Modularity),":[149],"new":[151],"model":[152,224,258,326,348,364],"embodies":[154],"modularity.":[155],"It":[156],"consists":[157],"two":[159],"layers:":[160],"lower":[162],"layer":[163,177],"derivation":[166],"process":[170],"thus":[171],"node-and-edge":[172],"based,":[173],"while":[174],"upper":[176],"module-aware.":[179],"allows":[181],"modules":[182],"appear":[184],"disappear,":[186],"fission":[188],"merge,":[191],"all":[192],"driven":[193],"by":[194,251,255,263,297,311,344,350],"underlying":[196],"edge-level":[197],"events":[198],"using":[199],"duplication-based":[201],"process.":[202],"introduce":[205],"measures":[206],"compare":[208,247],"terms":[212],"their":[214],"structure.":[216,236],"present":[218],"an":[219,367],"extensive":[220],"study":[221],"six":[223,227,281,284],"organisms":[225],"across":[226],"public":[228],"aimed":[230],"at":[231],"uncovering":[232],"commonalities":[233,241],"then":[238],"use":[239],"reference":[243],"against":[244],"which":[245],"generated":[250,310],"our":[256,265,301,371],"module-aware":[257,346,361,372],"NEMo.":[259],"find":[261,306],"that,":[262],"restricting":[264],"data":[266],"high-confidence":[268],"interactions,":[269],"number":[271],"shared":[273],"structural":[274,314],"features":[275],"can":[276],"be":[277],"identified":[278],"among":[279],"species":[282],"databases.":[285],"When":[286],"comparing":[287],"characteristics":[289,315],"extracted":[292],"from":[293,378],"produced":[296],"model,":[303],"we":[304,355],"further":[305],"exhibit":[313],"much":[316],"closer":[317],"organisms.":[327],"conclude":[329],"modularity":[331],"takes":[335],"particular":[337],"form,":[338],"one":[339],"better":[342],"approximated":[343],"than":[349],"models.":[353],"Finally,":[354],"draft":[356],"ideas":[358],"uses":[366],"altered":[368],"form":[369],"core":[376],"component,":[377],"parsimony":[380],"perspective.":[381]},"counts_by_year":[],"updated_date":"2026-08-01T09:00:35.917206","created_date":"2025-10-10T00:00:00"}