{"id":"https://openalex.org/W4229080788","doi":"https://doi.org/10.3390/e24050622","title":"A Family of Fitness Landscapes Modeled through Gene Regulatory Networks","display_name":"A Family of Fitness Landscapes Modeled through Gene Regulatory Networks","publication_year":2022,"publication_date":"2022-04-29","ids":{"openalex":"https://openalex.org/W4229080788","doi":"https://doi.org/10.3390/e24050622","pmid":"https://pubmed.ncbi.nlm.nih.gov/35626507"},"language":"en","primary_location":{"id":"doi:10.3390/e24050622","is_oa":true,"landing_page_url":"https://doi.org/10.3390/e24050622","pdf_url":"https://www.mdpi.com/1099-4300/24/5/622/pdf?version=1651223629","source":{"id":"https://openalex.org/S195231649","display_name":"Entropy","issn_l":"1099-4300","issn":["1099-4300"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310310987","host_organization_name":"Multidisciplinary Digital Publishing Institute","host_organization_lineage":["https://openalex.org/P4310310987"],"host_organization_lineage_names":["Multidisciplinary Digital Publishing Institute"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Entropy","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://www.mdpi.com/1099-4300/24/5/622/pdf?version=1651223629","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5042265400","display_name":"Chia-Hung Yang","orcid":null},"institutions":[{"id":"https://openalex.org/I12912129","display_name":"Northeastern University","ror":"https://ror.org/04t5xt781","country_code":"US","type":"education","lineage":["https://openalex.org/I12912129"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Chia-Hung Yang","raw_affiliation_strings":["Network Science Institute, Northeastern University, Boston, MA 02115, USA"],"raw_orcid":"https://orcid.org/0000-0002-4936-808X","affiliations":[{"raw_affiliation_string":"Network Science Institute, Northeastern University, Boston, MA 02115, USA","institution_ids":["https://openalex.org/I12912129"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5026230453","display_name":"Samuel V. Scarpino","orcid":"https://orcid.org/0000-0001-5716-2770"},"institutions":[{"id":"https://openalex.org/I111236770","display_name":"University of Vermont","ror":"https://ror.org/0155zta11","country_code":"US","type":"education","lineage":["https://openalex.org/I111236770"]},{"id":"https://openalex.org/I12912129","display_name":"Northeastern University","ror":"https://ror.org/04t5xt781","country_code":"US","type":"education","lineage":["https://openalex.org/I12912129"]},{"id":"https://openalex.org/I1308548392","display_name":"Santa Fe Institute","ror":"https://ror.org/01arysc35","country_code":"US","type":"funder","lineage":["https://openalex.org/I1308548392"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Samuel V. Scarpino","raw_affiliation_strings":["Institute for Experiential AI, Northeastern University, Boston, MA 02115, USA","Network Science Institute, Northeastern University, Boston, MA 02115, USA","Physics Department, Northeastern University, Boston, MA 02115, USA","Roux Institute, Northeastern University, Boston, MA 02115, USA","Santa Fe Institute, Santa Fe, NM 87501, USA","Vermont Complex Systems Center, University of Vermont, Burlington, VT 05405, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute for Experiential AI, Northeastern University, Boston, MA 02115, USA","institution_ids":["https://openalex.org/I12912129"]},{"raw_affiliation_string":"Network Science Institute, Northeastern University, Boston, MA 02115, USA","institution_ids":["https://openalex.org/I12912129"]},{"raw_affiliation_string":"Physics Department, Northeastern University, Boston, MA 02115, USA","institution_ids":["https://openalex.org/I12912129"]},{"raw_affiliation_string":"Roux Institute, Northeastern University, Boston, MA 02115, USA","institution_ids":["https://openalex.org/I12912129"]},{"raw_affiliation_string":"Santa Fe Institute, Santa Fe, NM 87501, USA","institution_ids":["https://openalex.org/I1308548392"]},{"raw_affiliation_string":"Vermont Complex Systems Center, University of Vermont, Burlington, VT 05405, USA","institution_ids":["https://openalex.org/I111236770"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5026230453","https://openalex.org/A5042265400"],"corresponding_institution_ids":["https://openalex.org/I111236770","https://openalex.org/I12912129","https://openalex.org/I1308548392"],"apc_list":{"value":2000,"currency":"CHF","value_usd":2165},"apc_paid":{"value":2000,"currency":"CHF","value_usd":2165},"fwci":0.3728,"has_fulltext":false,"cited_by_count":2,"citation_normalized_percentile":{"value":0.66273588,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":96},"biblio":{"volume":"24","issue":"5","first_page":"622","last_page":"622"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11764","display_name":"Evolution and Genetic Dynamics","score":1.0,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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/T11764","display_name":"Evolution and Genetic Dynamics","score":1.0,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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":0.998199999332428,"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/T11252","display_name":"Evolutionary Game Theory and Cooperation","score":0.996999979019165,"subfield":{"id":"https://openalex.org/subfields/3312","display_name":"Sociology and Political Science"},"field":{"id":"https://openalex.org/fields/33","display_name":"Social Sciences"},"domain":{"id":"https://openalex.org/domains/2","display_name":"Social Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/fitness-landscape","display_name":"Fitness landscape","score":0.8009235262870789},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4980957508087158},{"id":"https://openalex.org/keywords/fitness-function","display_name":"Fitness function","score":0.4643094539642334},{"id":"https://openalex.org/keywords/population","display_name":"Population","score":0.4330160915851593},{"id":"https://openalex.org/keywords/fitness-approximation","display_name":"Fitness approximation","score":0.42597153782844543},{"id":"https://openalex.org/keywords/neutral-network","display_name":"Neutral network","score":0.41890770196914673},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.35572943091392517},{"id":"https://openalex.org/keywords/evolutionary-biology","display_name":"Evolutionary biology","score":0.32444483041763306},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3092648983001709},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.29044482111930847},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.19446724653244019},{"id":"https://openalex.org/keywords/genetic-algorithm","display_name":"Genetic algorithm","score":0.11591723561286926}],"concepts":[{"id":"https://openalex.org/C91852762","wikidata":"https://www.wikidata.org/wiki/Q3307742","display_name":"Fitness landscape","level":3,"score":0.8009235262870789},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4980957508087158},{"id":"https://openalex.org/C176066374","wikidata":"https://www.wikidata.org/wiki/Q629118","display_name":"Fitness function","level":3,"score":0.4643094539642334},{"id":"https://openalex.org/C2908647359","wikidata":"https://www.wikidata.org/wiki/Q2625603","display_name":"Population","level":2,"score":0.4330160915851593},{"id":"https://openalex.org/C148392497","wikidata":"https://www.wikidata.org/wiki/Q16250539","display_name":"Fitness approximation","level":4,"score":0.42597153782844543},{"id":"https://openalex.org/C198125213","wikidata":"https://www.wikidata.org/wiki/Q17155419","display_name":"Neutral network","level":3,"score":0.41890770196914673},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.35572943091392517},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.32444483041763306},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3092648983001709},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.29044482111930847},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.19446724653244019},{"id":"https://openalex.org/C8880873","wikidata":"https://www.wikidata.org/wiki/Q187787","display_name":"Genetic algorithm","level":2,"score":0.11591723561286926},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.0},{"id":"https://openalex.org/C149923435","wikidata":"https://www.wikidata.org/wiki/Q37732","display_name":"Demography","level":1,"score":0.0},{"id":"https://openalex.org/C144024400","wikidata":"https://www.wikidata.org/wiki/Q21201","display_name":"Sociology","level":0,"score":0.0}],"mesh":[],"locations_count":5,"locations":[{"id":"doi:10.3390/e24050622","is_oa":true,"landing_page_url":"https://doi.org/10.3390/e24050622","pdf_url":"https://www.mdpi.com/1099-4300/24/5/622/pdf?version=1651223629","source":{"id":"https://openalex.org/S195231649","display_name":"Entropy","issn_l":"1099-4300","issn":["1099-4300"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310310987","host_organization_name":"Multidisciplinary Digital Publishing Institute","host_organization_lineage":["https://openalex.org/P4310310987"],"host_organization_lineage_names":["Multidisciplinary Digital Publishing Institute"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Entropy","raw_type":"journal-article"},{"id":"pmid:35626507","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/35626507","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":"Entropy (Basel, Switzerland)","raw_type":null},{"id":"pmh:oai:doaj.org/article:902c7d9559744b8ea885d172a969cc44","is_oa":true,"landing_page_url":"https://doaj.org/article/902c7d9559744b8ea885d172a969cc44","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":"Entropy, Vol 24, Iss 5, p 622 (2022)","raw_type":"article"},{"id":"pmh:oai:mdpi.com:/1099-4300/24/5/622/","is_oa":true,"landing_page_url":"https://dx.doi.org/10.3390/e24050622","pdf_url":null,"source":{"id":"https://openalex.org/S4306400947","display_name":"MDPI (MDPI AG)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4210097602","host_organization_name":"Multidisciplinary Digital Publishing Institute (Switzerland)","host_organization_lineage":["https://openalex.org/I4210097602"],"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":"Entropy; Volume 24; Issue 5; Pages: 622","raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:9141513","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/9141513","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":"Entropy (Basel)","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.3390/e24050622","is_oa":true,"landing_page_url":"https://doi.org/10.3390/e24050622","pdf_url":"https://www.mdpi.com/1099-4300/24/5/622/pdf?version=1651223629","source":{"id":"https://openalex.org/S195231649","display_name":"Entropy","issn_l":"1099-4300","issn":["1099-4300"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310310987","host_organization_name":"Multidisciplinary Digital Publishing Institute","host_organization_lineage":["https://openalex.org/P4310310987"],"host_organization_lineage_names":["Multidisciplinary Digital Publishing Institute"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Entropy","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/15","score":0.47999998927116394,"display_name":"Life in Land"}],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4229080788.pdf","grobid_xml":"https://content.openalex.org/works/W4229080788.grobid-xml"},"referenced_works_count":106,"referenced_works":["https://openalex.org/W1834385478","https://openalex.org/W1842146513","https://openalex.org/W1967902778","https://openalex.org/W1969857637","https://openalex.org/W1970111538","https://openalex.org/W1970185413","https://openalex.org/W1982583288","https://openalex.org/W1995865334","https://openalex.org/W2004778468","https://openalex.org/W2005356799","https://openalex.org/W2005990191","https://openalex.org/W2011759634","https://openalex.org/W2012404898","https://openalex.org/W2012457691","https://openalex.org/W2013503668","https://openalex.org/W2016666153","https://openalex.org/W2018853124","https://openalex.org/W2021252825","https://openalex.org/W2024655862","https://openalex.org/W2028599082","https://openalex.org/W2032433599","https://openalex.org/W2033142425","https://openalex.org/W2035654977","https://openalex.org/W2037212291","https://openalex.org/W2039227019","https://openalex.org/W2043973090","https://openalex.org/W2051453551","https://openalex.org/W2051853521","https://openalex.org/W2062348064","https://openalex.org/W2064164319","https://openalex.org/W2065709249","https://openalex.org/W2066008754","https://openalex.org/W2074849196","https://openalex.org/W2079052324","https://openalex.org/W2081531630","https://openalex.org/W2088791835","https://openalex.org/W2096704006","https://openalex.org/W2097955805","https://openalex.org/W2098920163","https://openalex.org/W2102795115","https://openalex.org/W2105488715","https://openalex.org/W2107897198","https://openalex.org/W2108386097","https://openalex.org/W2112559518","https://openalex.org/W2114173579","https://openalex.org/W2117428236","https://openalex.org/W2119054472","https://openalex.org/W2121105996","https://openalex.org/W2123653059","https://openalex.org/W2126643167","https://openalex.org/W2129628672","https://openalex.org/W2130289825","https://openalex.org/W2131645382","https://openalex.org/W2151969214","https://openalex.org/W2156477417","https://openalex.org/W2157019229","https://openalex.org/W2161975081","https://openalex.org/W2165327448","https://openalex.org/W2165754843","https://openalex.org/W2339766289","https://openalex.org/W2344715649","https://openalex.org/W2379594833","https://openalex.org/W2399031292","https://openalex.org/W2415886010","https://openalex.org/W2483469645","https://openalex.org/W2531753895","https://openalex.org/W2547075996","https://openalex.org/W2548139648","https://openalex.org/W2560097163","https://openalex.org/W2572573235","https://openalex.org/W2593111110","https://openalex.org/W2765775880","https://openalex.org/W2767891244","https://openalex.org/W2772324587","https://openalex.org/W2786241182","https://openalex.org/W2795842108","https://openalex.org/W2796625107","https://openalex.org/W2800231751","https://openalex.org/W2902394141","https://openalex.org/W2905701416","https://openalex.org/W2950268122","https://openalex.org/W2953058007","https://openalex.org/W2971738761","https://openalex.org/W2992478931","https://openalex.org/W3003432383","https://openalex.org/W3003620317","https://openalex.org/W3013784317","https://openalex.org/W3027041747","https://openalex.org/W3033513666","https://openalex.org/W3034732281","https://openalex.org/W3035258118","https://openalex.org/W3097858317","https://openalex.org/W3098077827","https://openalex.org/W3098712249","https://openalex.org/W3101687092","https://openalex.org/W3155561032","https://openalex.org/W3164125452","https://openalex.org/W3205810214","https://openalex.org/W3215012703","https://openalex.org/W4240357895","https://openalex.org/W4251042002","https://openalex.org/W4254837461","https://openalex.org/W4297977436","https://openalex.org/W6656448762","https://openalex.org/W6684007315","https://openalex.org/W6712446276"],"related_works":["https://openalex.org/W2036107212","https://openalex.org/W2164084664","https://openalex.org/W2159937791","https://openalex.org/W2138958036","https://openalex.org/W192154461","https://openalex.org/W1591022951","https://openalex.org/W1634842376","https://openalex.org/W1974337071","https://openalex.org/W4250294025","https://openalex.org/W3009038870"],"abstract_inverted_index":{"Fitness":[0],"landscapes":[1,14,33,64,80,164,219],"are":[2,18,55,93],"a":[3,51,74,109,139,153,158,171,185,221],"powerful":[4],"metaphor":[5],"for":[6],"understanding":[7],"the":[8,44,82,90,104,114,166,198],"evolution":[9,60,77],"of":[10,31,46,76,84,116,216],"biological":[11],"systems.":[12],"These":[13],"describe":[15],"how":[16,59],"genotypes":[17,47],"connected":[19],"to":[20,57,169,188,226],"each":[21],"other":[22],"through":[23,27],"mutation":[24],"and":[25,48,72,98,124,137,143,152,201,220],"related":[26],"fitness.":[28],"Empirical":[29],"studies":[30,54],"fitness":[32,63,79,135,163,218],"have":[34],"increasingly":[35],"revealed":[36],"conserved":[37,67],"topographical":[38,119],"features":[39,120],"across":[40,133],"diverse":[41],"taxa,":[42],"e.g.,":[43],"accessibility":[45,123,142],"\"ruggedness\".":[49],"As":[50],"result,":[52],"theoretical":[53],"needed":[56],"investigate":[58],"proceeds":[61],"on":[62,78],"with":[65,177],"such":[66,121,190],"features.":[68],"Here,":[69],"we":[70,112,156,183],"develop":[71,184],"study":[73],"model":[75],"using":[81,149],"lens":[83],"Gene":[85],"Regulatory":[86],"Networks":[87],"(GRNs),":[88],"where":[89,165],"regulatory":[91],"products":[92],"computed":[94],"from":[95],"multiple":[96],"genes":[97],"collectively":[99],"treated":[100],"as":[101,122],"phenotypes.":[102],"With":[103],"assumption":[105],"that":[106,129,138],"regulation":[107],"is":[108,175,202],"binary":[110],"process,":[111],"prove":[113],"existence":[115],"empirically":[117],"observed,":[118],"connectivity.":[125],"We":[126],"further":[127],"show":[128],"these":[130],"results":[131,215],"hold":[132],"arbitrary":[134],"functions":[136],"trade-off":[140],"between":[141],"ruggedness":[144],"need":[145],"not":[146,195],"exist.":[147],"Then,":[148],"graph":[150],"theory":[151,225],"coarse-graining":[154],"approach,":[155],"deduce":[157],"mesoscopic":[159,191],"structure":[160],"underlying":[161],"GRN":[162],"information":[167],"necessary":[168],"predict":[170],"population's":[172],"evolutionary":[173],"trajectory":[174],"retained":[176],"minimal":[178],"complexity.":[179],"Using":[180],"this":[181,211],"coarse-graining,":[182],"bottom-up":[186],"algorithm":[187],"construct":[189],"backbones,":[192],"which":[193],"does":[194],"require":[196],"computing":[197],"genotype":[199],"network":[200],"therefore":[203],"far":[204],"more":[205],"efficient":[206],"than":[207],"brute-force":[208],"approaches.":[209],"Altogether,":[210],"work":[212],"provides":[213],"mathematical":[214],"high-dimensional":[217],"path":[222],"toward":[223],"connecting":[224],"empirical":[227],"studies.":[228]},"counts_by_year":[{"year":2023,"cited_by_count":2}],"updated_date":"2026-05-06T08:25:59.206177","created_date":"2025-10-10T00:00:00"}
