{"id":"https://openalex.org/W4414228986","doi":"https://doi.org/10.1371/journal.pcbi.1013300","title":"NeKo: A tool for automatic network construction from prior knowledge","display_name":"NeKo: A tool for automatic network construction from prior knowledge","publication_year":2025,"publication_date":"2025-09-16","ids":{"openalex":"https://openalex.org/W4414228986","doi":"https://doi.org/10.1371/journal.pcbi.1013300","pmid":"https://pubmed.ncbi.nlm.nih.gov/40956863"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1013300","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1013300","pdf_url":null,"source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.1371/journal.pcbi.1013300","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5068648735","display_name":"Marco Ruscone","orcid":"https://orcid.org/0000-0002-7607-0203"},"institutions":[{"id":"https://openalex.org/I154526488","display_name":"Inserm","ror":"https://ror.org/02vjkv261","country_code":"FR","type":"government","lineage":["https://openalex.org/I154526488"]},{"id":"https://openalex.org/I2746051580","display_name":"Universit\u00e9 Paris Sciences et Lettres","ror":"https://ror.org/013cjyk83","country_code":"FR","type":"education","lineage":["https://openalex.org/I2746051580"]},{"id":"https://openalex.org/I2799803557","display_name":"Barcelona Supercomputing Center","ror":"https://ror.org/05sd8tv96","country_code":"ES","type":"facility","lineage":["https://openalex.org/I2799803557","https://openalex.org/I9617848"]},{"id":"https://openalex.org/I70768539","display_name":"\u00c9cole Nationale Sup\u00e9rieure des Mines de Paris","ror":"https://ror.org/04y8cs423","country_code":"FR","type":"education","lineage":["https://openalex.org/I190752583","https://openalex.org/I2746051580","https://openalex.org/I70768539"]},{"id":"https://openalex.org/I80043","display_name":"Institut Curie","ror":"https://ror.org/04t0gwh46","country_code":"FR","type":"nonprofit","lineage":["https://openalex.org/I80043"]},{"id":"https://openalex.org/I9617848","display_name":"Universitat Polit\u00e8cnica de Catalunya","ror":"https://ror.org/03mb6wj31","country_code":"ES","type":"education","lineage":["https://openalex.org/I9617848"]}],"countries":["ES","FR"],"is_corresponding":true,"raw_author_name":"Marco Ruscone","raw_affiliation_strings":["Barcelona Supercomputing Center (BSC), Barcelona, Spain","INSERM, U900, Paris, France","Institut Curie, Universit\u00e9 PSL, Paris, France","Mines ParisTech, Universit\u00e9 PSL, Paris, France"],"raw_orcid":"https://orcid.org/0000-0002-7607-0203","affiliations":[{"raw_affiliation_string":"Barcelona Supercomputing Center (BSC), Barcelona, Spain","institution_ids":["https://openalex.org/I9617848","https://openalex.org/I2799803557"]},{"raw_affiliation_string":"INSERM, U900, Paris, France","institution_ids":["https://openalex.org/I154526488"]},{"raw_affiliation_string":"Institut Curie, Universit\u00e9 PSL, Paris, France","institution_ids":["https://openalex.org/I2746051580","https://openalex.org/I80043"]},{"raw_affiliation_string":"Mines ParisTech, Universit\u00e9 PSL, Paris, France","institution_ids":["https://openalex.org/I70768539","https://openalex.org/I2746051580"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5077473333","display_name":"Eirini Tsirvouli","orcid":"https://orcid.org/0000-0002-6456-6463"},"institutions":[{"id":"https://openalex.org/I204778367","display_name":"Norwegian University of Science and Technology","ror":"https://ror.org/05xg72x27","country_code":"NO","type":"education","lineage":["https://openalex.org/I204778367"]}],"countries":["NO"],"is_corresponding":true,"raw_author_name":"Eirini Tsirvouli","raw_affiliation_strings":["Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway"],"raw_orcid":"https://orcid.org/0000-0002-6456-6463","affiliations":[{"raw_affiliation_string":"Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway","institution_ids":["https://openalex.org/I204778367"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5080251805","display_name":"Andrea Checcoli","orcid":"https://orcid.org/0000-0002-8290-6310"},"institutions":[{"id":"https://openalex.org/I154526488","display_name":"Inserm","ror":"https://ror.org/02vjkv261","country_code":"FR","type":"government","lineage":["https://openalex.org/I154526488"]},{"id":"https://openalex.org/I2746051580","display_name":"Universit\u00e9 Paris Sciences et Lettres","ror":"https://ror.org/013cjyk83","country_code":"FR","type":"education","lineage":["https://openalex.org/I2746051580"]},{"id":"https://openalex.org/I39804081","display_name":"Sorbonne Universit\u00e9","ror":"https://ror.org/02en5vm52","country_code":"FR","type":"education","lineage":["https://openalex.org/I39804081"]},{"id":"https://openalex.org/I4210092322","display_name":"Centre de Recherche des Cordeliers","ror":"https://ror.org/00dmms154","country_code":"FR","type":"facility","lineage":["https://openalex.org/I154526488","https://openalex.org/I204730241","https://openalex.org/I39804081","https://openalex.org/I4210092322"]},{"id":"https://openalex.org/I70768539","display_name":"\u00c9cole Nationale Sup\u00e9rieure des Mines de Paris","ror":"https://ror.org/04y8cs423","country_code":"FR","type":"education","lineage":["https://openalex.org/I190752583","https://openalex.org/I2746051580","https://openalex.org/I70768539"]},{"id":"https://openalex.org/I80043","display_name":"Institut Curie","ror":"https://ror.org/04t0gwh46","country_code":"FR","type":"nonprofit","lineage":["https://openalex.org/I80043"]}],"countries":["FR"],"is_corresponding":true,"raw_author_name":"Andrea Checcoli","raw_affiliation_strings":["Centre de Recherche des Cordeliers, Sorbonne Universit\u00e9, Paris, France","INSERM, U900, Paris, France","Institut Curie, Universit\u00e9 PSL, Paris, France","Mines ParisTech, Universit\u00e9 PSL, Paris, France"],"raw_orcid":"https://orcid.org/0000-0002-8290-6310","affiliations":[{"raw_affiliation_string":"Centre de Recherche des Cordeliers, Sorbonne Universit\u00e9, Paris, France","institution_ids":["https://openalex.org/I4210092322","https://openalex.org/I39804081"]},{"raw_affiliation_string":"INSERM, U900, Paris, France","institution_ids":["https://openalex.org/I154526488"]},{"raw_affiliation_string":"Institut Curie, Universit\u00e9 PSL, Paris, France","institution_ids":["https://openalex.org/I2746051580","https://openalex.org/I80043"]},{"raw_affiliation_string":"Mines ParisTech, Universit\u00e9 PSL, Paris, France","institution_ids":["https://openalex.org/I70768539","https://openalex.org/I2746051580"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5028302173","display_name":"D\u00e9nes T\u00fcrei","orcid":"https://orcid.org/0000-0002-7249-9379"},"institutions":[{"id":"https://openalex.org/I223822909","display_name":"Heidelberg University","ror":"https://ror.org/038t36y30","country_code":"DE","type":"education","lineage":["https://openalex.org/I223822909"]},{"id":"https://openalex.org/I2802164966","display_name":"University Hospital Heidelberg","ror":"https://ror.org/013czdx64","country_code":"DE","type":"healthcare","lineage":["https://openalex.org/I2802164966"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Denes Turei","raw_affiliation_strings":["Faculty of Medicine and Heidelberg University Hospital, Institute for Computational Biomedicine, Heidelberg University, Heidelberg, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Faculty of Medicine and Heidelberg University Hospital, Institute for Computational Biomedicine, Heidelberg University, Heidelberg, Germany","institution_ids":["https://openalex.org/I2802164966","https://openalex.org/I223822909"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5062067186","display_name":"Emmanuel Barillot","orcid":"https://orcid.org/0000-0003-2724-2002"},"institutions":[{"id":"https://openalex.org/I154526488","display_name":"Inserm","ror":"https://ror.org/02vjkv261","country_code":"FR","type":"government","lineage":["https://openalex.org/I154526488"]},{"id":"https://openalex.org/I2746051580","display_name":"Universit\u00e9 Paris Sciences et Lettres","ror":"https://ror.org/013cjyk83","country_code":"FR","type":"education","lineage":["https://openalex.org/I2746051580"]},{"id":"https://openalex.org/I70768539","display_name":"\u00c9cole Nationale Sup\u00e9rieure des Mines de Paris","ror":"https://ror.org/04y8cs423","country_code":"FR","type":"education","lineage":["https://openalex.org/I190752583","https://openalex.org/I2746051580","https://openalex.org/I70768539"]},{"id":"https://openalex.org/I80043","display_name":"Institut Curie","ror":"https://ror.org/04t0gwh46","country_code":"FR","type":"nonprofit","lineage":["https://openalex.org/I80043"]}],"countries":["FR"],"is_corresponding":true,"raw_author_name":"Emmanuel Barillot","raw_affiliation_strings":["INSERM, U900, Paris, France","Institut Curie, Universit\u00e9 PSL, Paris, France","Mines ParisTech, Universit\u00e9 PSL, Paris, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"INSERM, U900, Paris, France","institution_ids":["https://openalex.org/I154526488"]},{"raw_affiliation_string":"Institut Curie, Universit\u00e9 PSL, Paris, France","institution_ids":["https://openalex.org/I2746051580","https://openalex.org/I80043"]},{"raw_affiliation_string":"Mines ParisTech, Universit\u00e9 PSL, Paris, France","institution_ids":["https://openalex.org/I70768539","https://openalex.org/I2746051580"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5005499510","display_name":"Julio S\u00e1ez-Rodr\u00edguez","orcid":"https://orcid.org/0000-0002-8552-8976"},"institutions":[{"id":"https://openalex.org/I1303153112","display_name":"European Bioinformatics Institute","ror":"https://ror.org/02catss52","country_code":"GB","type":"facility","lineage":["https://openalex.org/I1303153112","https://openalex.org/I4210138560"]},{"id":"https://openalex.org/I223822909","display_name":"Heidelberg University","ror":"https://ror.org/038t36y30","country_code":"DE","type":"education","lineage":["https://openalex.org/I223822909"]},{"id":"https://openalex.org/I2802164966","display_name":"University Hospital Heidelberg","ror":"https://ror.org/013czdx64","country_code":"DE","type":"healthcare","lineage":["https://openalex.org/I2802164966"]}],"countries":["DE","GB"],"is_corresponding":true,"raw_author_name":"Julio Saez-Rodriguez","raw_affiliation_strings":["European Bioinformatics Institute, European Molecular Biology Laboratory, Hinxton, United Kingdom","Faculty of Medicine and Heidelberg University Hospital, Institute for Computational Biomedicine, Heidelberg University, Heidelberg, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"European Bioinformatics Institute, European Molecular Biology Laboratory, Hinxton, United Kingdom","institution_ids":["https://openalex.org/I1303153112"]},{"raw_affiliation_string":"Faculty of Medicine and Heidelberg University Hospital, Institute for Computational Biomedicine, Heidelberg University, Heidelberg, Germany","institution_ids":["https://openalex.org/I2802164966","https://openalex.org/I223822909"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5063905929","display_name":"Loredana Martignetti","orcid":"https://orcid.org/0000-0003-1535-7515"},"institutions":[{"id":"https://openalex.org/I154526488","display_name":"Inserm","ror":"https://ror.org/02vjkv261","country_code":"FR","type":"government","lineage":["https://openalex.org/I154526488"]},{"id":"https://openalex.org/I2746051580","display_name":"Universit\u00e9 Paris Sciences et Lettres","ror":"https://ror.org/013cjyk83","country_code":"FR","type":"education","lineage":["https://openalex.org/I2746051580"]},{"id":"https://openalex.org/I70768539","display_name":"\u00c9cole Nationale Sup\u00e9rieure des Mines de Paris","ror":"https://ror.org/04y8cs423","country_code":"FR","type":"education","lineage":["https://openalex.org/I190752583","https://openalex.org/I2746051580","https://openalex.org/I70768539"]},{"id":"https://openalex.org/I80043","display_name":"Institut Curie","ror":"https://ror.org/04t0gwh46","country_code":"FR","type":"nonprofit","lineage":["https://openalex.org/I80043"]}],"countries":["FR"],"is_corresponding":true,"raw_author_name":"Loredana Martignetti","raw_affiliation_strings":["INSERM, U900, Paris, France","Institut Curie, Universit\u00e9 PSL, Paris, France","Mines ParisTech, Universit\u00e9 PSL, Paris, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"INSERM, U900, Paris, France","institution_ids":["https://openalex.org/I154526488"]},{"raw_affiliation_string":"Institut Curie, Universit\u00e9 PSL, Paris, France","institution_ids":["https://openalex.org/I2746051580","https://openalex.org/I80043"]},{"raw_affiliation_string":"Mines ParisTech, Universit\u00e9 PSL, Paris, France","institution_ids":["https://openalex.org/I70768539","https://openalex.org/I2746051580"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5011858469","display_name":"\u00c5smund Flobak","orcid":"https://orcid.org/0000-0002-3357-425X"},"institutions":[{"id":"https://openalex.org/I204778367","display_name":"Norwegian University of Science and Technology","ror":"https://ror.org/05xg72x27","country_code":"NO","type":"education","lineage":["https://openalex.org/I204778367"]}],"countries":["NO"],"is_corresponding":true,"raw_author_name":"\u00c5smund Flobak","raw_affiliation_strings":["Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway"],"raw_orcid":"https://orcid.org/0000-0002-3357-425X","affiliations":[{"raw_affiliation_string":"Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway","institution_ids":["https://openalex.org/I204778367"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5061154457","display_name":"Laurence Calzone","orcid":"https://orcid.org/0000-0002-7835-1148"},"institutions":[{"id":"https://openalex.org/I154526488","display_name":"Inserm","ror":"https://ror.org/02vjkv261","country_code":"FR","type":"government","lineage":["https://openalex.org/I154526488"]},{"id":"https://openalex.org/I2746051580","display_name":"Universit\u00e9 Paris Sciences et Lettres","ror":"https://ror.org/013cjyk83","country_code":"FR","type":"education","lineage":["https://openalex.org/I2746051580"]},{"id":"https://openalex.org/I70768539","display_name":"\u00c9cole Nationale Sup\u00e9rieure des Mines de Paris","ror":"https://ror.org/04y8cs423","country_code":"FR","type":"education","lineage":["https://openalex.org/I190752583","https://openalex.org/I2746051580","https://openalex.org/I70768539"]},{"id":"https://openalex.org/I80043","display_name":"Institut Curie","ror":"https://ror.org/04t0gwh46","country_code":"FR","type":"nonprofit","lineage":["https://openalex.org/I80043"]}],"countries":["FR"],"is_corresponding":true,"raw_author_name":"Laurence Calzone","raw_affiliation_strings":["INSERM, U900, Paris, France","Institut Curie, Universit\u00e9 PSL, Paris, France","Mines ParisTech, Universit\u00e9 PSL, Paris, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"INSERM, U900, Paris, France","institution_ids":["https://openalex.org/I154526488"]},{"raw_affiliation_string":"Institut Curie, Universit\u00e9 PSL, Paris, France","institution_ids":["https://openalex.org/I2746051580","https://openalex.org/I80043"]},{"raw_affiliation_string":"Mines ParisTech, Universit\u00e9 PSL, Paris, France","institution_ids":["https://openalex.org/I70768539","https://openalex.org/I2746051580"]}]}],"institutions":[],"countries_distinct_count":5,"institutions_distinct_count":9,"corresponding_author_ids":["https://openalex.org/A5005499510","https://openalex.org/A5011858469","https://openalex.org/A5028302173","https://openalex.org/A5061154457","https://openalex.org/A5062067186","https://openalex.org/A5063905929","https://openalex.org/A5068648735","https://openalex.org/A5077473333","https://openalex.org/A5080251805"],"corresponding_institution_ids":["https://openalex.org/I1303153112","https://openalex.org/I154526488","https://openalex.org/I204778367","https://openalex.org/I223822909","https://openalex.org/I2746051580","https://openalex.org/I2799803557","https://openalex.org/I2802164966","https://openalex.org/I39804081","https://openalex.org/I4210092322","https://openalex.org/I70768539","https://openalex.org/I80043","https://openalex.org/I9617848"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":3.7528,"has_fulltext":false,"cited_by_count":6,"citation_normalized_percentile":{"value":0.93674829,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":96,"max":99},"biblio":{"volume":"21","issue":"9","first_page":"e1013300","last_page":"e1013300"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9962999820709229,"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":0.9962999820709229,"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/T11986","display_name":"Scientific Computing and Data Management","score":0.9925000071525574,"subfield":{"id":"https://openalex.org/subfields/1802","display_name":"Information Systems and Management"},"field":{"id":"https://openalex.org/fields/18","display_name":"Decision Sciences"},"domain":{"id":"https://openalex.org/domains/2","display_name":"Social Sciences"}},{"id":"https://openalex.org/T11273","display_name":"Advanced Graph Neural Networks","score":0.980400025844574,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"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/python","display_name":"Python (programming language)","score":0.6941999793052673},{"id":"https://openalex.org/keywords/construct","display_name":"Construct (python library)","score":0.5928999781608582},{"id":"https://openalex.org/keywords/biological-network","display_name":"Biological network","score":0.5640000104904175},{"id":"https://openalex.org/keywords/codebase","display_name":"Codebase","score":0.43700000643730164},{"id":"https://openalex.org/keywords/network-analysis","display_name":"Network analysis","score":0.38029998540878296},{"id":"https://openalex.org/keywords/gene-regulatory-network","display_name":"Gene regulatory network","score":0.32910001277923584},{"id":"https://openalex.org/keywords/filter","display_name":"Filter (signal processing)","score":0.3230000138282776},{"id":"https://openalex.org/keywords/downstream","display_name":"Downstream (manufacturing)","score":0.30889999866485596}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8048999905586243},{"id":"https://openalex.org/C519991488","wikidata":"https://www.wikidata.org/wiki/Q28865","display_name":"Python (programming language)","level":2,"score":0.6941999793052673},{"id":"https://openalex.org/C2780801425","wikidata":"https://www.wikidata.org/wiki/Q5164392","display_name":"Construct (python library)","level":2,"score":0.5928999781608582},{"id":"https://openalex.org/C28225019","wikidata":"https://www.wikidata.org/wiki/Q4915005","display_name":"Biological network","level":2,"score":0.5640000104904175},{"id":"https://openalex.org/C51929080","wikidata":"https://www.wikidata.org/wiki/Q2425187","display_name":"Codebase","level":3,"score":0.43700000643730164},{"id":"https://openalex.org/C32946077","wikidata":"https://www.wikidata.org/wiki/Q618079","display_name":"Network analysis","level":2,"score":0.38029998540878296},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.33340001106262207},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.33169999718666077},{"id":"https://openalex.org/C67339327","wikidata":"https://www.wikidata.org/wiki/Q1502576","display_name":"Gene regulatory network","level":4,"score":0.32910001277923584},{"id":"https://openalex.org/C106131492","wikidata":"https://www.wikidata.org/wiki/Q3072260","display_name":"Filter (signal processing)","level":2,"score":0.3230000138282776},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.31709998846054077},{"id":"https://openalex.org/C2776207758","wikidata":"https://www.wikidata.org/wiki/Q5303302","display_name":"Downstream (manufacturing)","level":2,"score":0.30889999866485596},{"id":"https://openalex.org/C55105296","wikidata":"https://www.wikidata.org/wiki/Q841382","display_name":"Interaction network","level":3,"score":0.30630001425743103},{"id":"https://openalex.org/C2781067378","wikidata":"https://www.wikidata.org/wiki/Q17027399","display_name":"Interpretability","level":2,"score":0.27619999647140503},{"id":"https://openalex.org/C13540734","wikidata":"https://www.wikidata.org/wiki/Q5318996","display_name":"Dynamic network analysis","level":2,"score":0.2759999930858612},{"id":"https://openalex.org/C2984074130","wikidata":"https://www.wikidata.org/wiki/Q73539779","display_name":"R package","level":2,"score":0.27320000529289246},{"id":"https://openalex.org/C37789001","wikidata":"https://www.wikidata.org/wiki/Q782543","display_name":"Graphical user interface","level":2,"score":0.2720000147819519},{"id":"https://openalex.org/C137753397","wikidata":"https://www.wikidata.org/wiki/Q2434424","display_name":"Network science","level":3,"score":0.2702000141143799},{"id":"https://openalex.org/C115903868","wikidata":"https://www.wikidata.org/wiki/Q80993","display_name":"Software engineering","level":1,"score":0.26759999990463257},{"id":"https://openalex.org/C123757187","wikidata":"https://www.wikidata.org/wiki/Q9195957","display_name":"Network dynamics","level":2,"score":0.26579999923706055},{"id":"https://openalex.org/C34947359","wikidata":"https://www.wikidata.org/wiki/Q665189","display_name":"Complex network","level":2,"score":0.26260000467300415},{"id":"https://openalex.org/C107457646","wikidata":"https://www.wikidata.org/wiki/Q207434","display_name":"Human\u2013computer interaction","level":1,"score":0.2623000144958496},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.258899986743927}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","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":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","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":false},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":5,"locations":[{"id":"doi:10.1371/journal.pcbi.1013300","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1013300","pdf_url":null,"source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},{"id":"pmid:40956863","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40956863","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":"PLoS computational biology","raw_type":null},{"id":"pmh:oai:doaj.org/article:47cc647ea7574c0dafc79e1513a8fe8a","is_oa":true,"landing_page_url":"https://doaj.org/article/47cc647ea7574c0dafc79e1513a8fe8a","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":"PLoS Computational Biology, Vol 21, Iss 9, p e1013300 (2025)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:11265063","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12456767","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:12456767","is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC12456767/","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":"PLoS Comput Biol","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1013300","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1013300","pdf_url":null,"source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":29,"referenced_works":["https://openalex.org/W12154863","https://openalex.org/W22095172","https://openalex.org/W1270845237","https://openalex.org/W2003003919","https://openalex.org/W2012034410","https://openalex.org/W2059917368","https://openalex.org/W2062533676","https://openalex.org/W2109384743","https://openalex.org/W2153398041","https://openalex.org/W2157658519","https://openalex.org/W2159675211","https://openalex.org/W2169589032","https://openalex.org/W2269026928","https://openalex.org/W2557833574","https://openalex.org/W2616437816","https://openalex.org/W2737542366","https://openalex.org/W2892282588","https://openalex.org/W2981350712","https://openalex.org/W2986455832","https://openalex.org/W2997831639","https://openalex.org/W3000150252","https://openalex.org/W4226317251","https://openalex.org/W4237335579","https://openalex.org/W4288045534","https://openalex.org/W4306353209","https://openalex.org/W4318670429","https://openalex.org/W4388832953","https://openalex.org/W4391060036","https://openalex.org/W4401798061"],"related_works":[],"abstract_inverted_index":{"Biological":[0],"networks":[1,60,93],"provide":[2,74],"a":[3,39,51,139],"structured":[4],"framework":[5],"for":[6,164],"analyzing":[7],"the":[8,56,118,147,155],"dynamic":[9],"interplay":[10],"and":[11,22,36,41,63,87,111,123,162],"interactions":[12,66,101],"between":[13],"molecular":[14,65],"entities,":[15],"facilitating":[16],"deeper":[17],"insights":[18],"into":[19],"cellular":[20],"functions":[21],"biological":[23,59],"processes.":[24],"Network":[25],"construction":[26,57],"often":[27],"requires":[28],"extensive":[29],"manual":[30],"curation":[31],"based":[32,94,141],"on":[33,95,142],"scientific":[34],"literature":[35],"public":[37],"databases,":[38],"time-consuming":[40],"laborious":[42],"task.":[43],"To":[44],"address":[45],"this":[46],"challenge,":[47],"we":[48,137,149],"introduce":[49],"NeKo,":[50],"Python":[52],"package":[53],"to":[54,73,91,116,120],"automate":[55],"of":[58,77,129],"by":[61,102],"integrating":[62],"prioritizing":[64],"from":[67,144],"various":[68,103],"databases.":[69],"NeKo":[70,153],"allows":[71],"users":[72],"their":[75,121],"molecules":[76],"interest":[78],"(e.g.,":[79],"genes,":[80],"proteins":[81],"or":[82,108,113],"phosphosites),":[83],"select":[84],"interaction":[85],"resources":[86],"apply":[88],"flexible":[89],"strategies":[90],"build":[92],"prior":[96],"knowledge.":[97],"Users":[98],"can":[99],"filter":[100],"criteria,":[104],"such":[105],"as":[106],"direct":[107],"indirect":[109],"links":[110],"signed":[112],"unsigned":[114],"interactions,":[115],"tailor":[117],"network":[119,140],"needs":[122],"downstream":[124],"analysis.":[125],"We":[126],"demonstrate":[127],"some":[128],"NeKo's":[130],"capabilities":[131],"in":[132,146],"two":[133],"use":[134],"cases:":[135],"first":[136],"construct":[138],"transcriptomics":[143],"medulloblastoma;":[145],"second,":[148],"model":[150],"drug":[151],"synergies.":[152],"streamlines":[154],"network-building":[156],"process,":[157],"making":[158],"it":[159],"more":[160],"accessible":[161],"efficient":[163],"researchers.":[165]},"counts_by_year":[{"year":2026,"cited_by_count":3},{"year":2025,"cited_by_count":3}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}