{"id":"https://openalex.org/W3032942021","doi":"https://doi.org/10.1371/journal.pcbi.1007889","title":"Disease evolution in reaction networks: Implications for a diagnostic problem","display_name":"Disease evolution in reaction networks: Implications for a diagnostic problem","publication_year":2020,"publication_date":"2020-06-04","ids":{"openalex":"https://openalex.org/W3032942021","doi":"https://doi.org/10.1371/journal.pcbi.1007889","mag":"3032942021","pmid":"https://pubmed.ncbi.nlm.nih.gov/32497038"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1007889","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1007889","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1007889&type=printable","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://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1007889&type=printable","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5026698378","display_name":"Abolfazl Ramezanpour","orcid":"https://orcid.org/0000-0002-3650-7722"},"institutions":[{"id":"https://openalex.org/I121797337","display_name":"Leiden University","ror":"https://ror.org/027bh9e22","country_code":"NL","type":"education","lineage":["https://openalex.org/I121797337"]},{"id":"https://openalex.org/I166459259","display_name":"Shiraz University","ror":"https://ror.org/028qtbk54","country_code":"IR","type":"education","lineage":["https://openalex.org/I166459259"]},{"id":"https://openalex.org/I4210133171","display_name":"Centre for Human Drug Research","ror":"https://ror.org/044hshx49","country_code":"NL","type":"facility","lineage":["https://openalex.org/I4210133171"]}],"countries":["IR","NL"],"is_corresponding":false,"raw_author_name":"Abolfazl Ramezanpour","raw_affiliation_strings":["Medical Systems Biophysics and Bioengineering, Leiden Academic Centre for Drug Research, Faculty of Science, Leiden University, Leiden, The Netherlands","Physics Department, College of Sciences, Shiraz University, Shiraz, Iran"],"raw_orcid":"https://orcid.org/0000-0002-3650-7722","affiliations":[{"raw_affiliation_string":"Medical Systems Biophysics and Bioengineering, Leiden Academic Centre for Drug Research, Faculty of Science, Leiden University, Leiden, The Netherlands","institution_ids":["https://openalex.org/I4210133171","https://openalex.org/I121797337"]},{"raw_affiliation_string":"Physics Department, College of Sciences, Shiraz University, Shiraz, Iran","institution_ids":["https://openalex.org/I166459259"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5029816593","display_name":"Alireza Mashaghi","orcid":"https://orcid.org/0000-0002-2157-1211"},"institutions":[{"id":"https://openalex.org/I121797337","display_name":"Leiden University","ror":"https://ror.org/027bh9e22","country_code":"NL","type":"education","lineage":["https://openalex.org/I121797337"]},{"id":"https://openalex.org/I4210133171","display_name":"Centre for Human Drug Research","ror":"https://ror.org/044hshx49","country_code":"NL","type":"facility","lineage":["https://openalex.org/I4210133171"]}],"countries":["NL"],"is_corresponding":true,"raw_author_name":"Alireza Mashaghi","raw_affiliation_strings":["Medical Systems Biophysics and Bioengineering, Leiden Academic Centre for Drug Research, Faculty of Science, Leiden University, Leiden, The Netherlands"],"raw_orcid":"https://orcid.org/0000-0002-2157-1211","affiliations":[{"raw_affiliation_string":"Medical Systems Biophysics and Bioengineering, Leiden Academic Centre for Drug Research, Faculty of Science, Leiden University, Leiden, The Netherlands","institution_ids":["https://openalex.org/I4210133171","https://openalex.org/I121797337"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5029816593"],"corresponding_institution_ids":["https://openalex.org/I121797337","https://openalex.org/I4210133171"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":0.1672,"has_fulltext":true,"cited_by_count":2,"citation_normalized_percentile":{"value":0.49674094,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":"16","issue":"6","first_page":"e1007889","last_page":"e1007889"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9998000264167786,"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/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9998000264167786,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9986000061035156,"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":0.9970999956130981,"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/disease","display_name":"Disease","score":0.6318148374557495},{"id":"https://openalex.org/keywords/probabilistic-logic","display_name":"Probabilistic logic","score":0.5579257607460022},{"id":"https://openalex.org/keywords/population","display_name":"Population","score":0.5222612023353577},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4602597653865814},{"id":"https://openalex.org/keywords/function","display_name":"Function (biology)","score":0.45585522055625916},{"id":"https://openalex.org/keywords/statistics","display_name":"Statistics","score":0.36541467905044556},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.33279091119766235},{"id":"https://openalex.org/keywords/medicine","display_name":"Medicine","score":0.26989316940307617},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.2686145603656769},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.254645437002182},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.17408379912376404},{"id":"https://openalex.org/keywords/pathology","display_name":"Pathology","score":0.1293751299381256}],"concepts":[{"id":"https://openalex.org/C2779134260","wikidata":"https://www.wikidata.org/wiki/Q12136","display_name":"Disease","level":2,"score":0.6318148374557495},{"id":"https://openalex.org/C49937458","wikidata":"https://www.wikidata.org/wiki/Q2599292","display_name":"Probabilistic logic","level":2,"score":0.5579257607460022},{"id":"https://openalex.org/C2908647359","wikidata":"https://www.wikidata.org/wiki/Q2625603","display_name":"Population","level":2,"score":0.5222612023353577},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4602597653865814},{"id":"https://openalex.org/C14036430","wikidata":"https://www.wikidata.org/wiki/Q3736076","display_name":"Function (biology)","level":2,"score":0.45585522055625916},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.36541467905044556},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.33279091119766235},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.26989316940307617},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.2686145603656769},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.254645437002182},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.17408379912376404},{"id":"https://openalex.org/C142724271","wikidata":"https://www.wikidata.org/wiki/Q7208","display_name":"Pathology","level":1,"score":0.1293751299381256},{"id":"https://openalex.org/C99454951","wikidata":"https://www.wikidata.org/wiki/Q932068","display_name":"Environmental health","level":1,"score":0.0}],"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":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D004194","descriptor_name":"Disease","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D004194","descriptor_name":"Disease","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D004194","descriptor_name":"Disease","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D005075","descriptor_name":"Biological Evolution","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D005075","descriptor_name":"Biological Evolution","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D005075","descriptor_name":"Biological Evolution","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"D010641","descriptor_name":"Phenotype","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010641","descriptor_name":"Phenotype","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010641","descriptor_name":"Phenotype","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011336","descriptor_name":"Probability","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011336","descriptor_name":"Probability","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011336","descriptor_name":"Probability","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":5,"locations":[{"id":"doi:10.1371/journal.pcbi.1007889","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1007889","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1007889&type=printable","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:32497038","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/32497038","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:RePEc:plo:pcbi00:1007889","is_oa":false,"landing_page_url":"https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1007889","pdf_url":null,"source":{"id":"https://openalex.org/S4306401271","display_name":"RePEc: Research Papers in Economics","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I77793887","host_organization_name":"Federal Reserve Bank of St. Louis","host_organization_lineage":["https://openalex.org/I77793887"],"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"},{"id":"pmh:oai:doaj.org/article:14236b32faf94f118dd2b7368c54c0a6","is_oa":true,"landing_page_url":"https://doaj.org/article/14236b32faf94f118dd2b7368c54c0a6","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"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 16, Iss 6, p e1007889 (2020)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:7272006","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/7272006","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.1007889","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1007889","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1007889&type=printable","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":[{"id":"https://openalex.org/F4320309036","display_name":"Purdue University","ror":"https://ror.org/02dqehb95"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3032942021.pdf","grobid_xml":"https://content.openalex.org/works/W3032942021.grobid-xml"},"referenced_works_count":47,"referenced_works":["https://openalex.org/W32516901","https://openalex.org/W868534065","https://openalex.org/W1492040047","https://openalex.org/W1503398984","https://openalex.org/W1519068578","https://openalex.org/W1834893312","https://openalex.org/W1902630711","https://openalex.org/W1946143552","https://openalex.org/W1974631391","https://openalex.org/W1980717706","https://openalex.org/W1995732126","https://openalex.org/W2000258229","https://openalex.org/W2024060531","https://openalex.org/W2029202173","https://openalex.org/W2034927155","https://openalex.org/W2041303826","https://openalex.org/W2044651471","https://openalex.org/W2056782561","https://openalex.org/W2066580949","https://openalex.org/W2080739873","https://openalex.org/W2085360136","https://openalex.org/W2099308902","https://openalex.org/W2102787760","https://openalex.org/W2104108767","https://openalex.org/W2133667940","https://openalex.org/W2140368114","https://openalex.org/W2166132142","https://openalex.org/W2167154952","https://openalex.org/W2169288958","https://openalex.org/W2409439195","https://openalex.org/W2414588418","https://openalex.org/W2566505556","https://openalex.org/W2584002887","https://openalex.org/W2737000379","https://openalex.org/W2790268968","https://openalex.org/W2805388541","https://openalex.org/W2891593617","https://openalex.org/W2949499968","https://openalex.org/W2955098217","https://openalex.org/W3008437073","https://openalex.org/W3099488856","https://openalex.org/W3101812839","https://openalex.org/W3104859924","https://openalex.org/W3144895209","https://openalex.org/W4213182854","https://openalex.org/W4246232459","https://openalex.org/W4302036486"],"related_works":["https://openalex.org/W2494523064","https://openalex.org/W2943623134","https://openalex.org/W2215759665","https://openalex.org/W2960358116","https://openalex.org/W2030292806","https://openalex.org/W3041172967","https://openalex.org/W2749065928","https://openalex.org/W2147155098","https://openalex.org/W4287727129","https://openalex.org/W2938171715"],"abstract_inverted_index":{"We":[0,63],"study":[1],"the":[2,12,23,41,45,50,55,59,70,81,106,118,133,140,147,154,158,170,191,198,230,237,241],"time":[3,155,178,211],"evolution":[4,239],"of":[5,14,25,36,44,52,58,83,99,108,114,120,135,142,157,172,177,184,232,240],"symptoms":[6],"(signs)":[7],"with":[8,76,129],"some":[9,66],"defects":[10,53],"in":[11,137,195,202,220],"dynamics":[13,43],"a":[15,19,33,77,86,97,112,162,175,181,223,233],"reaction":[16,37],"network":[17],"as":[18,96,174],"(microscopic)":[20],"model":[21,79,151,183,216],"for":[22,69,80,212,222],"progress":[24],"disease":[26,73,125,163,234],"phenotypes.":[27],"To":[28],"this":[29],"end,":[30],"we":[31],"take":[32],"large":[34],"population":[35],"networks":[38],"and":[39,72,117,139,186,197],"follow":[40],"stochastic":[42],"system":[46],"to":[47,168,207,228],"see":[48],"how":[49],"development":[51],"affects":[54],"macroscopic":[56],"states":[57,74],"signs":[60,185],"probability":[61],"distribution.":[62],"start":[64],"from":[65],"plausible":[67],"definitions":[68],"healthy":[71,92],"along":[75],"dynamical":[78,224],"emergence":[82],"diseases":[84],"by":[85,179],"reverse":[87],"simulated":[88],"annealing":[89],"algorithm.":[90],"The":[91,150,188],"state":[93,98],"is":[94,105,127],"defined":[95,128],"maximum":[100],"objective":[101,148,199],"function,":[102],"which":[103],"here":[104],"sum":[107],"mutual":[109],"information":[110],"between":[111,190],"subset":[113,119],"signal":[115],"variables":[116],"assigned":[121],"response":[122],"variables.":[123],"A":[124],"phenotype":[126],"two":[130],"parameters":[131],"controlling":[132],"rate":[134,141],"mutations":[136,144],"reactions":[138],"accepting":[143],"that":[145],"reduce":[146],"function.":[149],"can":[152,204],"provide":[153],"dependence":[156],"sign":[159],"probabilities":[160],"given":[161,236],"phenotype.":[164],"This":[165],"allows":[166],"us":[167],"obtain":[169],"accuracy":[171,193],"diagnosis":[173,192],"function":[176,200],"using":[180],"probabilistic":[182],"diseases.":[187],"trade-off":[189],"(increasing":[194],"time)":[196,203],"(decreasing":[201],"be":[205,218],"used":[206],"suggest":[208],"an":[209],"optimal":[210],"medical":[213],"intervention.":[214],"Our":[215],"would":[217],"useful":[219],"particular":[221],"(history-based)":[225],"diagnostic":[226],"problem,":[227],"estimate":[229],"likelihood":[231],"hypothesis":[235],"temporal":[238],"signs.":[242]},"counts_by_year":[{"year":2023,"cited_by_count":1},{"year":2020,"cited_by_count":1}],"updated_date":"2026-01-13T01:12:25.745995","created_date":"2025-10-10T00:00:00"}
