{"id":"https://openalex.org/W4315784200","doi":"https://doi.org/10.3389/fbinf.2023.1121409","title":"Comprehensive genome-scale metabolic model of the human pathogen Cryptococcus neoformans: A platform for understanding pathogen metabolism and identifying new drug targets","display_name":"Comprehensive genome-scale metabolic model of the human pathogen Cryptococcus neoformans: A platform for understanding pathogen metabolism and identifying new drug targets","publication_year":2023,"publication_date":"2023-01-13","ids":{"openalex":"https://openalex.org/W4315784200","doi":"https://doi.org/10.3389/fbinf.2023.1121409","pmid":"https://pubmed.ncbi.nlm.nih.gov/36714093"},"language":"en","primary_location":{"id":"doi:10.3389/fbinf.2023.1121409","is_oa":true,"landing_page_url":"https://doi.org/10.3389/fbinf.2023.1121409","pdf_url":"https://www.frontiersin.org/articles/10.3389/fbinf.2023.1121409/pdf","source":{"id":"https://openalex.org/S4210219554","display_name":"Frontiers in Bioinformatics","issn_l":"2673-7647","issn":["2673-7647"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320527","host_organization_name":"Frontiers Media","host_organization_lineage":["https://openalex.org/P4310320527"],"host_organization_lineage_names":["Frontiers Media"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Frontiers in Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://www.frontiersin.org/articles/10.3389/fbinf.2023.1121409/pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5065217728","display_name":"Enes Fahri Tezcan","orcid":"https://orcid.org/0000-0002-8295-9754"},"institutions":[{"id":"https://openalex.org/I48912391","display_name":"Istanbul Technical University","ror":"https://ror.org/059636586","country_code":"TR","type":"education","lineage":["https://openalex.org/I48912391"]}],"countries":["TR"],"is_corresponding":false,"raw_author_name":"Enes Fahri Tezcan","raw_affiliation_strings":["Department of Molecular Biology and Genetics, Istanbul Technical University, Istanbul, Turkey"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Molecular Biology and Genetics, Istanbul Technical University, Istanbul, Turkey","institution_ids":["https://openalex.org/I48912391"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5031985279","display_name":"Yigit Demirtas","orcid":null},"institutions":[{"id":"https://openalex.org/I4405392","display_name":"Bo\u011fazi\u00e7i University","ror":"https://ror.org/03z9tma90","country_code":"TR","type":"education","lineage":["https://openalex.org/I4405392"]}],"countries":["TR"],"is_corresponding":false,"raw_author_name":"Yigit Demirtas","raw_affiliation_strings":["Department of Chemical Engineering, Bogazici University, Istanbul, Turkey"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemical Engineering, Bogazici University, Istanbul, Turkey","institution_ids":["https://openalex.org/I4405392"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5022136073","display_name":"Zeynep Petek \u00c7akar","orcid":"https://orcid.org/0000-0002-2278-3670"},"institutions":[{"id":"https://openalex.org/I48912391","display_name":"Istanbul Technical University","ror":"https://ror.org/059636586","country_code":"TR","type":"education","lineage":["https://openalex.org/I48912391"]}],"countries":["TR"],"is_corresponding":false,"raw_author_name":"Zeynep Petek Cakar","raw_affiliation_strings":["Department of Molecular Biology and Genetics, Istanbul Technical University, Istanbul, Turkey"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Molecular Biology and Genetics, Istanbul Technical University, Istanbul, Turkey","institution_ids":["https://openalex.org/I48912391"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5055699443","display_name":"Kutlu \u00d6. \u00dclgen","orcid":"https://orcid.org/0000-0003-3668-3467"},"institutions":[{"id":"https://openalex.org/I4405392","display_name":"Bo\u011fazi\u00e7i University","ror":"https://ror.org/03z9tma90","country_code":"TR","type":"education","lineage":["https://openalex.org/I4405392"]}],"countries":["TR"],"is_corresponding":true,"raw_author_name":"Kutlu O. Ulgen","raw_affiliation_strings":["Department of Chemical Engineering, Bogazici University, Istanbul, Turkey"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemical Engineering, Bogazici University, Istanbul, Turkey","institution_ids":["https://openalex.org/I4405392"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5055699443"],"corresponding_institution_ids":["https://openalex.org/I4405392"],"apc_list":{"value":1900,"currency":"USD","value_usd":1900},"apc_paid":{"value":1900,"currency":"USD","value_usd":1900},"fwci":2.1051,"has_fulltext":true,"cited_by_count":11,"citation_normalized_percentile":{"value":0.87452666,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":95,"max":99},"biblio":{"volume":"3","issue":null,"first_page":"1121409","last_page":"1121409"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11037","display_name":"Fungal Infections and Studies","score":0.9998000264167786,"subfield":{"id":"https://openalex.org/subfields/2713","display_name":"Epidemiology"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},"topics":[{"id":"https://openalex.org/T11037","display_name":"Fungal Infections and Studies","score":0.9998000264167786,"subfield":{"id":"https://openalex.org/subfields/2713","display_name":"Epidemiology"},"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/T10150","display_name":"Antifungal resistance and susceptibility","score":0.9957000017166138,"subfield":{"id":"https://openalex.org/subfields/2725","display_name":"Infectious Diseases"},"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/T10076","display_name":"Plant-Microbe Interactions and Immunity","score":0.9641000032424927,"subfield":{"id":"https://openalex.org/subfields/1110","display_name":"Plant Science"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/cryptococcus-neoformans","display_name":"Cryptococcus neoformans","score":0.9540175199508667},{"id":"https://openalex.org/keywords/in-silico","display_name":"In silico","score":0.6600234508514404},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.6326796412467957},{"id":"https://openalex.org/keywords/antifungal-drug","display_name":"Antifungal drug","score":0.5978530049324036},{"id":"https://openalex.org/keywords/fungal-pathogen","display_name":"Fungal pathogen","score":0.5863121151924133},{"id":"https://openalex.org/keywords/cryptococcus","display_name":"Cryptococcus","score":0.5701717138290405},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5456552505493164},{"id":"https://openalex.org/keywords/pathogen","display_name":"Pathogen","score":0.49969029426574707},{"id":"https://openalex.org/keywords/drug-discovery","display_name":"Drug discovery","score":0.47520121932029724},{"id":"https://openalex.org/keywords/antifungal-drugs","display_name":"Antifungal drugs","score":0.43945321440696716},{"id":"https://openalex.org/keywords/human-pathogen","display_name":"Human pathogen","score":0.4381110668182373},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.4373146593570709},{"id":"https://openalex.org/keywords/cryptococcus-gattii","display_name":"Cryptococcus gattii","score":0.4340435564517975},{"id":"https://openalex.org/keywords/antifungal","display_name":"Antifungal","score":0.42972639203071594},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.3730512857437134},{"id":"https://openalex.org/keywords/microbiology","display_name":"Microbiology","score":0.31800615787506104},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.27419745922088623},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.24893230199813843}],"concepts":[{"id":"https://openalex.org/C2777893358","wikidata":"https://www.wikidata.org/wiki/Q131924","display_name":"Cryptococcus neoformans","level":2,"score":0.9540175199508667},{"id":"https://openalex.org/C2775905019","wikidata":"https://www.wikidata.org/wiki/Q192572","display_name":"In silico","level":3,"score":0.6600234508514404},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.6326796412467957},{"id":"https://openalex.org/C2991737395","wikidata":"https://www.wikidata.org/wiki/Q578726","display_name":"Antifungal drug","level":3,"score":0.5978530049324036},{"id":"https://openalex.org/C3019170707","wikidata":"https://www.wikidata.org/wiki/Q6471530","display_name":"Fungal pathogen","level":3,"score":0.5863121151924133},{"id":"https://openalex.org/C2778952914","wikidata":"https://www.wikidata.org/wiki/Q309498","display_name":"Cryptococcus","level":2,"score":0.5701717138290405},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5456552505493164},{"id":"https://openalex.org/C2776460866","wikidata":"https://www.wikidata.org/wiki/Q170065","display_name":"Pathogen","level":2,"score":0.49969029426574707},{"id":"https://openalex.org/C74187038","wikidata":"https://www.wikidata.org/wiki/Q1418791","display_name":"Drug discovery","level":2,"score":0.47520121932029724},{"id":"https://openalex.org/C2909919671","wikidata":"https://www.wikidata.org/wiki/Q578726","display_name":"Antifungal drugs","level":3,"score":0.43945321440696716},{"id":"https://openalex.org/C24527192","wikidata":"https://www.wikidata.org/wiki/Q17149729","display_name":"Human pathogen","level":3,"score":0.4381110668182373},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.4373146593570709},{"id":"https://openalex.org/C2779286289","wikidata":"https://www.wikidata.org/wiki/Q149791","display_name":"Cryptococcus gattii","level":3,"score":0.4340435564517975},{"id":"https://openalex.org/C2779548794","wikidata":"https://www.wikidata.org/wiki/Q578726","display_name":"Antifungal","level":2,"score":0.42972639203071594},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.3730512857437134},{"id":"https://openalex.org/C89423630","wikidata":"https://www.wikidata.org/wiki/Q7193","display_name":"Microbiology","level":1,"score":0.31800615787506104},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.27419745922088623},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.24893230199813843}],"mesh":[],"locations_count":5,"locations":[{"id":"doi:10.3389/fbinf.2023.1121409","is_oa":true,"landing_page_url":"https://doi.org/10.3389/fbinf.2023.1121409","pdf_url":"https://www.frontiersin.org/articles/10.3389/fbinf.2023.1121409/pdf","source":{"id":"https://openalex.org/S4210219554","display_name":"Frontiers in Bioinformatics","issn_l":"2673-7647","issn":["2673-7647"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320527","host_organization_name":"Frontiers Media","host_organization_lineage":["https://openalex.org/P4310320527"],"host_organization_lineage_names":["Frontiers Media"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Frontiers in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:36714093","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/36714093","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":"Frontiers in bioinformatics","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:9880062","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/9880062","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC9880062/pdf/fbinf-03-1121409.pdf","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":"Front Bioinform","raw_type":"Text"},{"id":"pmh:oai:doaj.org/article:15cdcc99509844d2bee7d1cd275df10a","is_oa":true,"landing_page_url":"https://doaj.org/article/15cdcc99509844d2bee7d1cd275df10a","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":"Frontiers in Bioinformatics, Vol 3 (2023)","raw_type":"article"},{"id":"pmh:oai:polen.itu.edu.tr:11527/41821","is_oa":false,"landing_page_url":"https://hdl.handle.net/11527/41821","pdf_url":null,"source":{"id":"https://openalex.org/S4306400460","display_name":"Istanbul Technical University Academic Open Archive (Istanbul Technical University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I48912391","host_organization_name":"Istanbul Technical University","host_organization_lineage":["https://openalex.org/I48912391"],"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":"Article"}],"best_oa_location":{"id":"doi:10.3389/fbinf.2023.1121409","is_oa":true,"landing_page_url":"https://doi.org/10.3389/fbinf.2023.1121409","pdf_url":"https://www.frontiersin.org/articles/10.3389/fbinf.2023.1121409/pdf","source":{"id":"https://openalex.org/S4210219554","display_name":"Frontiers in Bioinformatics","issn_l":"2673-7647","issn":["2673-7647"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320527","host_organization_name":"Frontiers Media","host_organization_lineage":["https://openalex.org/P4310320527"],"host_organization_lineage_names":["Frontiers Media"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Frontiers in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W4315784200.pdf"},"referenced_works_count":91,"referenced_works":["https://openalex.org/W1490724351","https://openalex.org/W1601964432","https://openalex.org/W1969430561","https://openalex.org/W1987640473","https://openalex.org/W2010221734","https://openalex.org/W2024248233","https://openalex.org/W2026089579","https://openalex.org/W2027473247","https://openalex.org/W2030530458","https://openalex.org/W2030776070","https://openalex.org/W2033377040","https://openalex.org/W2038335468","https://openalex.org/W2041216801","https://openalex.org/W2055599095","https://openalex.org/W2075093963","https://openalex.org/W2078355959","https://openalex.org/W2078807571","https://openalex.org/W2079513681","https://openalex.org/W2085993965","https://openalex.org/W2095699986","https://openalex.org/W2096855445","https://openalex.org/W2097170564","https://openalex.org/W2098472248","https://openalex.org/W2100002754","https://openalex.org/W2100765607","https://openalex.org/W2108576174","https://openalex.org/W2109118083","https://openalex.org/W2109483555","https://openalex.org/W2114043874","https://openalex.org/W2124817994","https://openalex.org/W2127257007","https://openalex.org/W2131942193","https://openalex.org/W2133790733","https://openalex.org/W2139472183","https://openalex.org/W2144543496","https://openalex.org/W2145544634","https://openalex.org/W2147472054","https://openalex.org/W2151665495","https://openalex.org/W2152673223","https://openalex.org/W2154139219","https://openalex.org/W2154479185","https://openalex.org/W2156654507","https://openalex.org/W2157589025","https://openalex.org/W2160423401","https://openalex.org/W2161265156","https://openalex.org/W2166862518","https://openalex.org/W2170146596","https://openalex.org/W2202347610","https://openalex.org/W2221356507","https://openalex.org/W2309011052","https://openalex.org/W2358244203","https://openalex.org/W2467318425","https://openalex.org/W2533992176","https://openalex.org/W2562552688","https://openalex.org/W2749916193","https://openalex.org/W2755163126","https://openalex.org/W2762019694","https://openalex.org/W2767088268","https://openalex.org/W2772256670","https://openalex.org/W2791041082","https://openalex.org/W2791963883","https://openalex.org/W2795637773","https://openalex.org/W2796739627","https://openalex.org/W2892176011","https://openalex.org/W2917101543","https://openalex.org/W2951201765","https://openalex.org/W2962391048","https://openalex.org/W2970104886","https://openalex.org/W2977368063","https://openalex.org/W3010629926","https://openalex.org/W3020858351","https://openalex.org/W3042415116","https://openalex.org/W3079721071","https://openalex.org/W3090689814","https://openalex.org/W3096881113","https://openalex.org/W3198110493","https://openalex.org/W4210651685","https://openalex.org/W4211228294","https://openalex.org/W4213025494","https://openalex.org/W4220688018","https://openalex.org/W4223449840","https://openalex.org/W4226306367","https://openalex.org/W4235535738","https://openalex.org/W4238101851","https://openalex.org/W4251916894","https://openalex.org/W4283779735","https://openalex.org/W4294771574","https://openalex.org/W4307581085","https://openalex.org/W4309153107","https://openalex.org/W4311029711","https://openalex.org/W4311720358"],"related_works":["https://openalex.org/W3009675335","https://openalex.org/W4244505027","https://openalex.org/W4251470477","https://openalex.org/W4232433239","https://openalex.org/W3007256597","https://openalex.org/W2168017210","https://openalex.org/W2606931784","https://openalex.org/W2381166911","https://openalex.org/W2056573634","https://openalex.org/W4315784200"],"abstract_inverted_index":{"Introduction:":[0],"The":[1,23,105,133,146],"fungal":[2],"priority":[3],"pathogen":[4,202],"Cryptococcus":[5,139,172],"neoformans":[6,88],"causes":[7],"cryptococcal":[8],"meningoencephalitis":[9],"in":[10,71,125,137,153],"immunocompromised":[11],"individuals":[12],"and":[13,102,119,122,131,148,191,194],"leads":[14],"to":[15,36,50,68,127,160,168,179],"hundreds":[16],"of":[17,19,27,44,75,95,115,135,201],"thousands":[18],"deaths":[20],"per":[21],"year.":[22],"undesirable":[24],"side":[25],"effects":[26],"existing":[28],"treatments,":[29],"the":[30,38,42,56,73,81,113,136,154,158,165],"need":[31],"for":[32,46,58,86,164,183,199],"long":[33],"application":[34],"times":[35],"prevent":[37],"disease":[39],"from":[40],"recurring,":[41],"lack":[43],"resources":[45],"these":[47],"treatment":[48,60],"methods":[49],"spread":[51],"over":[52],"all":[53],"continents":[54],"necessitate":[55],"search":[57],"new":[59,181],"methods.":[61],"Methods:":[62],"Genome-scale":[63],"models":[64],"have":[65,157],"been":[66],"shown":[67],"be":[69,161,169,177],"valuable":[70],"studying":[72],"metabolism":[74,140],"many":[76],"organisms.":[77],"Here":[78],"we":[79],"present":[80],"first":[82],"genome-scale":[83],"metabolic":[84],"model":[85,93,106,175],"C.":[87],",":[89],"iCryptococcus.":[90],"This":[91],"comprehensive":[92],"consists":[94],"1,270":[96],"reactions,":[97],"1,143":[98],"metabolites,":[99],"649":[100],"genes,":[101],"eight":[103],"compartments.":[104],"was":[107,144],"validated,":[108],"proving":[109],"accurate":[110],"when":[111],"predicting":[112],"capability":[114],"utilizing":[116],"different":[117],"carbon":[118],"nitrogen":[120],"sources":[121],"growth":[123],"rate":[124],"comparison":[126],"experimental":[128],"data.":[129],"Results":[130],"Discussion:":[132],"compatibility":[134],"silico":[138],"under":[141],"infection":[142],"conditions":[143],"assessed.":[145],"steroid":[147],"amino":[149],"acid":[150],"metabolisms":[151],"found":[152],"essentiality":[155],"analyses":[156,193],"potential":[159],"drug":[162],"targets":[163,182],"therapeutic":[166],"strategies":[167],"developed":[170],"against":[171],"species.":[173],"iCryptococcus":[174],"can":[176],"applied":[178],"explore":[180],"antifungal":[184],"drugs":[185],"along":[186],"with":[187],"essential":[188],"gene,":[189],"metabolite":[190],"reaction":[192],"provides":[195],"a":[196],"promising":[197],"platform":[198],"elucidation":[200],"metabolism.":[203]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":7}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2023-01-13T00:00:00"}
