{"id":"https://openalex.org/W1994152349","doi":"https://doi.org/10.1186/s12859-015-0525-0","title":"SimBA: simulation algorithm to fit extant-population distributions","display_name":"SimBA: simulation algorithm to fit extant-population distributions","publication_year":2015,"publication_date":"2015-03-13","ids":{"openalex":"https://openalex.org/W1994152349","doi":"https://doi.org/10.1186/s12859-015-0525-0","mag":"1994152349","pmid":"https://pubmed.ncbi.nlm.nih.gov/25886895"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-015-0525-0","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-015-0525-0","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-015-0525-0","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-015-0525-0","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5025497346","display_name":"Laxmi Parida","orcid":"https://orcid.org/0000-0002-7872-5074"},"institutions":[{"id":"https://openalex.org/I1341412227","display_name":"IBM (United States)","ror":"https://ror.org/05hh8d621","country_code":"US","type":"company","lineage":["https://openalex.org/I1341412227"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Laxmi Parida","raw_affiliation_strings":["Computational Biology Center, IBM T. J. Watson Research, Yorktown Heights, NY, USA. parida@us.ibm.com"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computational Biology Center, IBM T. J. Watson Research, Yorktown Heights, NY, USA. parida@us.ibm.com","institution_ids":["https://openalex.org/I1341412227"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5054652878","display_name":"Niina Haiminen","orcid":"https://orcid.org/0000-0002-8663-1019"},"institutions":[{"id":"https://openalex.org/I1341412227","display_name":"IBM (United States)","ror":"https://ror.org/05hh8d621","country_code":"US","type":"company","lineage":["https://openalex.org/I1341412227"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Niina Haiminen","raw_affiliation_strings":["Computational Biology Center, IBM T. J. Watson Research, Yorktown Heights, NY, USA. nshaimin@us.ibm.com"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computational Biology Center, IBM T. J. Watson Research, Yorktown Heights, NY, USA. nshaimin@us.ibm.com","institution_ids":["https://openalex.org/I1341412227"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5025497346"],"corresponding_institution_ids":["https://openalex.org/I1341412227"],"apc_list":{"value":2990,"currency":"USD","value_usd":2990},"apc_paid":{"value":2990,"currency":"USD","value_usd":2990},"fwci":0.6787,"has_fulltext":true,"cited_by_count":4,"citation_normalized_percentile":{"value":0.74868453,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":96},"biblio":{"volume":"16","issue":"1","first_page":"82","last_page":"82"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10594","display_name":"Genetic and phenotypic traits in livestock","score":0.26269999146461487,"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/T10594","display_name":"Genetic and phenotypic traits in livestock","score":0.26269999146461487,"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/T10100","display_name":"Metaheuristic Optimization Algorithms Research","score":0.147599995136261,"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"}},{"id":"https://openalex.org/T11195","display_name":"Simulation Techniques and Applications","score":0.11900000274181366,"subfield":{"id":"https://openalex.org/subfields/1803","display_name":"Management Science and Operations Research"},"field":{"id":"https://openalex.org/fields/18","display_name":"Decision Sciences"},"domain":{"id":"https://openalex.org/domains/2","display_name":"Social Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/extant-taxon","display_name":"Extant taxon","score":0.8414032459259033},{"id":"https://openalex.org/keywords/population","display_name":"Population","score":0.4931330382823944},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.46595579385757446},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.4145703613758087},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2329966127872467},{"id":"https://openalex.org/keywords/evolutionary-biology","display_name":"Evolutionary biology","score":0.22916153073310852},{"id":"https://openalex.org/keywords/demography","display_name":"Demography","score":0.11232265830039978},{"id":"https://openalex.org/keywords/sociology","display_name":"Sociology","score":0.07447513937950134}],"concepts":[{"id":"https://openalex.org/C178300618","wikidata":"https://www.wikidata.org/wiki/Q1898509","display_name":"Extant taxon","level":2,"score":0.8414032459259033},{"id":"https://openalex.org/C2908647359","wikidata":"https://www.wikidata.org/wiki/Q2625603","display_name":"Population","level":2,"score":0.4931330382823944},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.46595579385757446},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.4145703613758087},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2329966127872467},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.22916153073310852},{"id":"https://openalex.org/C149923435","wikidata":"https://www.wikidata.org/wiki/Q37732","display_name":"Demography","level":1,"score":0.11232265830039978},{"id":"https://openalex.org/C144024400","wikidata":"https://www.wikidata.org/wiki/Q21201","display_name":"Sociology","level":0,"score":0.07447513937950134}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","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":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003247","descriptor_name":"Conservation of Natural Resources","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003247","descriptor_name":"Conservation of Natural Resources","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003247","descriptor_name":"Conservation of Natural Resources","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005787","descriptor_name":"Gene Frequency","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005787","descriptor_name":"Gene Frequency","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005787","descriptor_name":"Gene Frequency","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005828","descriptor_name":"Genetics, Population","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D005828","descriptor_name":"Genetics, Population","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D005828","descriptor_name":"Genetics, Population","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":"D008962","descriptor_name":"Models, Theoretical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008962","descriptor_name":"Models, Theoretical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008962","descriptor_name":"Models, Theoretical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011157","descriptor_name":"Population Dynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011157","descriptor_name":"Population Dynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011157","descriptor_name":"Population Dynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015810","descriptor_name":"Linkage Disequilibrium","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015810","descriptor_name":"Linkage Disequilibrium","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015810","descriptor_name":"Linkage Disequilibrium","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1186/s12859-015-0525-0","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-015-0525-0","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-015-0525-0","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:25886895","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/25886895","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":"BMC bioinformatics","raw_type":"Journal Article"},{"id":"pmh:oai:europepmc.org:3334439","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4372275","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"}],"best_oa_location":{"id":"doi:10.1186/s12859-015-0525-0","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-015-0525-0","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-015-0525-0","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/15","display_name":"Life in Land","score":0.44999998807907104}],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W1994152349.pdf","grobid_xml":"https://content.openalex.org/works/W1994152349.grobid-xml"},"referenced_works_count":18,"referenced_works":["https://openalex.org/W232716440","https://openalex.org/W1502341912","https://openalex.org/W1577941315","https://openalex.org/W1585006589","https://openalex.org/W2015867362","https://openalex.org/W2046956642","https://openalex.org/W2058401000","https://openalex.org/W2059206901","https://openalex.org/W2112285107","https://openalex.org/W2114044285","https://openalex.org/W2136195349","https://openalex.org/W2152200681","https://openalex.org/W2159959024","https://openalex.org/W2160160618","https://openalex.org/W2160184568","https://openalex.org/W2782633006","https://openalex.org/W3151658902","https://openalex.org/W4285719527"],"related_works":["https://openalex.org/W2748952813","https://openalex.org/W3016239368","https://openalex.org/W2402755139","https://openalex.org/W4290948148","https://openalex.org/W4249944690","https://openalex.org/W2353808877","https://openalex.org/W414826439","https://openalex.org/W1530876234","https://openalex.org/W2807827247","https://openalex.org/W2903896635"],"abstract_inverted_index":{"BACKGROUND:":[0],"Simulation":[1],"of":[2,18,30,38,41,80,133,159],"populations":[3,170],"with":[4,124,201],"specified":[5,129,203],"characteristics":[6,119],"such":[7],"as":[8,161,163,204,212],"allele":[9],"frequencies,":[10],"linkage":[11],"disequilibrium":[12],"etc.,":[13],"is":[14,33,106,136,183,218],"an":[15,207],"integral":[16],"component":[17],"many":[19],"studies,":[20],"including":[21],"in-silico":[22],"breeding":[23],"optimization.":[24],"Since":[25],"the":[26,36,39,42,57,94,110,128,134,151,173],"accuracy":[27,160],"and":[28,83,92],"sensitivity":[29],"population":[31,153,211],"simulation":[32,135,154],"critical":[34],"to":[35,51,56,96,109,127,186],"quality":[37],"output":[40],"applications":[43],"that":[44,104,148,171],"use":[45],"them,":[46],"accurate":[47],"algorithms":[48],"are":[49],"required":[50,213],"provide":[52],"a":[53,73,78,88],"strong":[54],"foundation":[55],"methods":[58],"in":[59,121,157],"these":[60],"studies.":[61],"RESULTS:":[62],"In":[63],"this":[64],"paper":[65],"we":[66,102],"present":[67],"SimBA":[68,105,149,182,217],"(Simulation":[69],"using":[70],"Best-fit":[71],"Algorithm)":[72],"non-generative":[74],"approach,":[75],"based":[76],"on":[77],"combination":[79],"stochastic":[81],"techniques":[82],"discrete":[84],"methods.":[85,144,216],"We":[86,146],"optimize":[87],"hill":[89],"climbing":[90],"algorithm":[91],"extend":[93],"framework":[95],"include":[97],"multiple":[98],"subpopulation":[99],"structures.":[100],"Additionally,":[101],"show":[103,147],"very":[107,114],"sensitive":[108],"input":[111,118,174,202],"specifications,":[112],"i.e.,":[113],"similar":[115],"but":[116],"distinct":[117,122],"result":[120],"outputs":[123],"high":[125],"fidelity":[126],"distributions.":[130],"This":[131],"property":[132],"not":[137,190],"explicitly":[138],"modeled":[139],"or":[140,195,210],"studied":[141],"by":[142,214],"previous":[143],"CONCLUSIONS:":[145],"outperforms":[150],"existing":[152],"methods,":[155,181],"both":[156],"terms":[158],"well":[162],"time-efficiency.":[164],"Not":[165],"only":[166],"does":[167,189],"it":[168,198],"construct":[169],"meet":[172],"specifications":[175],"more":[176],"stringently":[177],"than":[178],"other":[179],"published":[180],"also":[184],"easy":[185],"use.":[187],"It":[188],"require":[191],"explicit":[192],"parameter":[193],"adaptations":[194],"calibrations.":[196],"Also,":[197],"can":[199],"work":[200],"distributions,":[205],"without":[206],"exemplar":[208],"matrix":[209],"some":[215],"available":[219],"at":[220],"http://researcher.ibm.com/project/5669":[221],".":[222]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":2}],"updated_date":"2026-08-21T09:56:20.448147","created_date":"2025-10-10T00:00:00"}
