{"id":"https://openalex.org/W4410161661","doi":"https://doi.org/10.1186/s12859-025-06142-z","title":"py_ped_sim: a flexible forward pedigree and genetic simulator for complex family pedigree analysis","display_name":"py_ped_sim: a flexible forward pedigree and genetic simulator for complex family pedigree analysis","publication_year":2025,"publication_date":"2025-05-07","ids":{"openalex":"https://openalex.org/W4410161661","doi":"https://doi.org/10.1186/s12859-025-06142-z","pmid":"https://pubmed.ncbi.nlm.nih.gov/40335952"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-025-06142-z","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-025-06142-z","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-025-06142-z","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/s12859-025-06142-z","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5029491673","display_name":"Miguel Guardado","orcid":"https://orcid.org/0000-0002-1748-3956"},"institutions":[{"id":"https://openalex.org/I180670191","display_name":"University of California, San Francisco","ror":"https://ror.org/043mz5j54","country_code":"US","type":"education","lineage":["https://openalex.org/I180670191"]},{"id":"https://openalex.org/I181233156","display_name":"University of Oregon","ror":"https://ror.org/0293rh119","country_code":"US","type":"education","lineage":["https://openalex.org/I181233156"]},{"id":"https://openalex.org/I4210110664","display_name":"University of California San Francisco Medical Center","ror":"https://ror.org/01t8svj65","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I4210110664"]},{"id":"https://openalex.org/I71838634","display_name":"San Francisco State University","ror":"https://ror.org/05ykr0121","country_code":"US","type":"education","lineage":["https://openalex.org/I71838634"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Miguel Guardado","raw_affiliation_strings":["Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, 94134, USA. Miguel.Guardado@ucsf.edu","Biological and Medical Informatics Graduate Program, University of California San Francisco, San Francisco, CA, 94158, USA. Miguel.Guardado@ucsf.edu","Department of Data Science, University of Oregon, Eugene, OR, 97403, USA. Miguel.Guardado@ucsf.edu","Department of Mathematics, San Francisco State University, San Francisco, CA, 94132, USA. Miguel.Guardado@ucsf.edu"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, 94134, USA. Miguel.Guardado@ucsf.edu","institution_ids":["https://openalex.org/I180670191"]},{"raw_affiliation_string":"Biological and Medical Informatics Graduate Program, University of California San Francisco, San Francisco, CA, 94158, USA. Miguel.Guardado@ucsf.edu","institution_ids":["https://openalex.org/I4210110664"]},{"raw_affiliation_string":"Department of Data Science, University of Oregon, Eugene, OR, 97403, USA. Miguel.Guardado@ucsf.edu","institution_ids":["https://openalex.org/I181233156"]},{"raw_affiliation_string":"Department of Mathematics, San Francisco State University, San Francisco, CA, 94132, USA. Miguel.Guardado@ucsf.edu","institution_ids":["https://openalex.org/I71838634"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5109654499","display_name":"Cynthia P\u00e9rez","orcid":null},"institutions":[{"id":"https://openalex.org/I71838634","display_name":"San Francisco State University","ror":"https://ror.org/05ykr0121","country_code":"US","type":"education","lineage":["https://openalex.org/I71838634"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Cynthia Perez","raw_affiliation_strings":["Department of Biology, San Francisco State University, San Francisco, CA, 94132, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biology, San Francisco State University, San Francisco, CA, 94132, USA","institution_ids":["https://openalex.org/I71838634"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5104266513","display_name":"Sthen Campana","orcid":null},"institutions":[{"id":"https://openalex.org/I181233156","display_name":"University of Oregon","ror":"https://ror.org/0293rh119","country_code":"US","type":"education","lineage":["https://openalex.org/I181233156"]},{"id":"https://openalex.org/I71838634","display_name":"San Francisco State University","ror":"https://ror.org/05ykr0121","country_code":"US","type":"education","lineage":["https://openalex.org/I71838634"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Sthen Campana","raw_affiliation_strings":["Department of Biology, San Francisco State University, San Francisco, CA, 94132, USA","Department of Data Science, University of Oregon, Eugene, OR, 97403, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biology, San Francisco State University, San Francisco, CA, 94132, USA","institution_ids":["https://openalex.org/I71838634"]},{"raw_affiliation_string":"Department of Data Science, University of Oregon, Eugene, OR, 97403, USA","institution_ids":["https://openalex.org/I181233156"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5080789428","display_name":"Berenice Chavez Rojas","orcid":"https://orcid.org/0000-0001-6831-1479"},"institutions":[{"id":"https://openalex.org/I71838634","display_name":"San Francisco State University","ror":"https://ror.org/05ykr0121","country_code":"US","type":"education","lineage":["https://openalex.org/I71838634"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Berenice Chavez Rojas","raw_affiliation_strings":["Department of Biology, San Francisco State University, San Francisco, CA, 94132, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biology, San Francisco State University, San Francisco, CA, 94132, USA","institution_ids":["https://openalex.org/I71838634"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5094275926","display_name":"Joaqu\u00edn Maga\u00f1a","orcid":null},"institutions":[{"id":"https://openalex.org/I71838634","display_name":"San Francisco State University","ror":"https://ror.org/05ykr0121","country_code":"US","type":"education","lineage":["https://openalex.org/I71838634"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Joaqu\u00edn Maga\u00f1a","raw_affiliation_strings":["Department of Biology, San Francisco State University, San Francisco, CA, 94132, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biology, San Francisco State University, San Francisco, CA, 94132, USA","institution_ids":["https://openalex.org/I71838634"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5032460259","display_name":"Shalom Jackson","orcid":null},"institutions":[{"id":"https://openalex.org/I71838634","display_name":"San Francisco State University","ror":"https://ror.org/05ykr0121","country_code":"US","type":"education","lineage":["https://openalex.org/I71838634"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Shalom Jackson","raw_affiliation_strings":["Department of Biology, San Francisco State University, San Francisco, CA, 94132, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biology, San Francisco State University, San Francisco, CA, 94132, USA","institution_ids":["https://openalex.org/I71838634"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5094275927","display_name":"Emily Samperio","orcid":null},"institutions":[{"id":"https://openalex.org/I71838634","display_name":"San Francisco State University","ror":"https://ror.org/05ykr0121","country_code":"US","type":"education","lineage":["https://openalex.org/I71838634"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Emily Samperio","raw_affiliation_strings":["Department of Biology, San Francisco State University, San Francisco, CA, 94132, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biology, San Francisco State University, San Francisco, CA, 94132, USA","institution_ids":["https://openalex.org/I71838634"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5048416703","display_name":"Selena Hernandez","orcid":"https://orcid.org/0000-0003-3641-3811"},"institutions":[{"id":"https://openalex.org/I71838634","display_name":"San Francisco State University","ror":"https://ror.org/05ykr0121","country_code":"US","type":"education","lineage":["https://openalex.org/I71838634"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Selena Hernandez","raw_affiliation_strings":["Department of Biology, San Francisco State University, San Francisco, CA, 94132, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biology, San Francisco State University, San Francisco, CA, 94132, USA","institution_ids":["https://openalex.org/I71838634"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5094275928","display_name":"Kaela Syas","orcid":null},"institutions":[{"id":"https://openalex.org/I71838634","display_name":"San Francisco State University","ror":"https://ror.org/05ykr0121","country_code":"US","type":"education","lineage":["https://openalex.org/I71838634"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Kaela Syas","raw_affiliation_strings":["Department of Mathematics, San Francisco State University, San Francisco, CA, 94132, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Mathematics, San Francisco State University, San Francisco, CA, 94132, USA","institution_ids":["https://openalex.org/I71838634"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5005352234","display_name":"Ryan D. Hernandez","orcid":"https://orcid.org/0000-0001-5249-504X"},"institutions":[{"id":"https://openalex.org/I180670191","display_name":"University of California, San Francisco","ror":"https://ror.org/043mz5j54","country_code":"US","type":"education","lineage":["https://openalex.org/I180670191"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ryan D. Hernandez","raw_affiliation_strings":["Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, 94134, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, 94134, USA","institution_ids":["https://openalex.org/I180670191"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5029594049","display_name":"Elena I. Zavala","orcid":"https://orcid.org/0000-0001-7687-5370"},"institutions":[{"id":"https://openalex.org/I71838634","display_name":"San Francisco State University","ror":"https://ror.org/05ykr0121","country_code":"US","type":"education","lineage":["https://openalex.org/I71838634"]},{"id":"https://openalex.org/I95457486","display_name":"University of California, Berkeley","ror":"https://ror.org/01an7q238","country_code":"US","type":"education","lineage":["https://openalex.org/I95457486"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Elena I. Zavala","raw_affiliation_strings":["Department of Biology, San Francisco State University, San Francisco, CA, 94132, USA","Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, 94720, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biology, San Francisco State University, San Francisco, CA, 94132, USA","institution_ids":["https://openalex.org/I71838634"]},{"raw_affiliation_string":"Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, 94720, USA","institution_ids":["https://openalex.org/I95457486"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5033337198","display_name":"Rori V. Rohlfs","orcid":"https://orcid.org/0000-0002-2625-192X"},"institutions":[{"id":"https://openalex.org/I181233156","display_name":"University of Oregon","ror":"https://ror.org/0293rh119","country_code":"US","type":"education","lineage":["https://openalex.org/I181233156"]},{"id":"https://openalex.org/I71838634","display_name":"San Francisco State University","ror":"https://ror.org/05ykr0121","country_code":"US","type":"education","lineage":["https://openalex.org/I71838634"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Rori V. Rohlfs","raw_affiliation_strings":["Department of Biology, San Francisco State University, San Francisco, CA, 94132, USA. rori@uoregon.edu","Department of Data Science, University of Oregon, Eugene, OR, 97403, USA. rori@uoregon.edu"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biology, San Francisco State University, San Francisco, CA, 94132, USA. rori@uoregon.edu","institution_ids":["https://openalex.org/I71838634"]},{"raw_affiliation_string":"Department of Data Science, University of Oregon, Eugene, OR, 97403, USA. rori@uoregon.edu","institution_ids":["https://openalex.org/I181233156"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":0.0,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":{"value":0.10333604,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"26","issue":"1","first_page":"122","last_page":"122"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10261","display_name":"Genetic Associations and Epidemiology","score":0.43059998750686646,"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/T10261","display_name":"Genetic Associations and Epidemiology","score":0.43059998750686646,"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/T12749","display_name":"Race, Genetics, and Society","score":0.13930000364780426,"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/T11642","display_name":"Genomics and Rare Diseases","score":0.11580000072717667,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/pedigree-chart","display_name":"Pedigree chart","score":0.8952041268348694},{"id":"https://openalex.org/keywords/python","display_name":"Python (programming language)","score":0.6518592834472656},{"id":"https://openalex.org/keywords/inheritance","display_name":"Inheritance (genetic algorithm)","score":0.5186828374862671},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.49815845489501953},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.47747302055358887},{"id":"https://openalex.org/keywords/population","display_name":"Population","score":0.44183269143104553},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.43801528215408325},{"id":"https://openalex.org/keywords/kinship","display_name":"Kinship","score":0.41298532485961914},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.37877321243286133},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.09134158492088318},{"id":"https://openalex.org/keywords/medicine","display_name":"Medicine","score":0.09059178829193115}],"concepts":[{"id":"https://openalex.org/C22593422","wikidata":"https://www.wikidata.org/wiki/Q3242583","display_name":"Pedigree chart","level":3,"score":0.8952041268348694},{"id":"https://openalex.org/C519991488","wikidata":"https://www.wikidata.org/wiki/Q28865","display_name":"Python (programming language)","level":2,"score":0.6518592834472656},{"id":"https://openalex.org/C2780902518","wikidata":"https://www.wikidata.org/wiki/Q6033780","display_name":"Inheritance (genetic algorithm)","level":3,"score":0.5186828374862671},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.49815845489501953},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.47747302055358887},{"id":"https://openalex.org/C2908647359","wikidata":"https://www.wikidata.org/wiki/Q2625603","display_name":"Population","level":2,"score":0.44183269143104553},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.43801528215408325},{"id":"https://openalex.org/C144348335","wikidata":"https://www.wikidata.org/wiki/Q171318","display_name":"Kinship","level":2,"score":0.41298532485961914},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.37877321243286133},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.09134158492088318},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.09059178829193115},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0},{"id":"https://openalex.org/C17744445","wikidata":"https://www.wikidata.org/wiki/Q36442","display_name":"Political science","level":0,"score":0.0},{"id":"https://openalex.org/C99454951","wikidata":"https://www.wikidata.org/wiki/Q932068","display_name":"Environmental health","level":1,"score":0.0},{"id":"https://openalex.org/C199539241","wikidata":"https://www.wikidata.org/wiki/Q7748","display_name":"Law","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","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":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","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":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","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":"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":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010375","descriptor_name":"Pedigree","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010375","descriptor_name":"Pedigree","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010375","descriptor_name":"Pedigree","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010375","descriptor_name":"Pedigree","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010375","descriptor_name":"Pedigree","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":"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}],"locations_count":4,"locations":[{"id":"doi:10.1186/s12859-025-06142-z","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-025-06142-z","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-025-06142-z","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:40335952","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40335952","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":null},{"id":"pmh:oai:doaj.org/article:c70cb113351145d09bbced60fa4e8d7c","is_oa":true,"landing_page_url":"https://doaj.org/article/c70cb113351145d09bbced60fa4e8d7c","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":"BMC Bioinformatics, Vol 26, Iss 1, Pp 1-18 (2025)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:12060417","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12060417","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":"BMC Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/s12859-025-06142-z","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-025-06142-z","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-025-06142-z","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":[],"awards":[{"id":"https://openalex.org/G1338262402","display_name":null,"funder_award_id":"GM008574","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G1818320835","display_name":null,"funder_award_id":"LSAMP HRD-1826490","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G2271575094","display_name":null,"funder_award_id":"R25 GM059298","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G3033686525","display_name":null,"funder_award_id":"2019-DU-BX-0028","funder_id":"https://openalex.org/F4320337430","funder_display_name":"National Institute of Justice"},{"id":"https://openalex.org/G3298864666","display_name":null,"funder_award_id":"T34 GM008574","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G469402298","display_name":null,"funder_award_id":"T34 GM145400","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G5024804595","display_name":null,"funder_award_id":"HRD-1826490","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G5171189338","display_name":null,"funder_award_id":"T34-GM008574","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G5454388386","display_name":null,"funder_award_id":"GM059298","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G6021982713","display_name":null,"funder_award_id":"MBRS-RISE R25-GM059298","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G6756774909","display_name":null,"funder_award_id":"R25-GM059298","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G6988387625","display_name":null,"funder_award_id":"15PNIJ-23-AG-04262-DNAX","funder_id":"https://openalex.org/F4320337430","funder_display_name":"National Institute of Justice"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320309634","display_name":"Adolph C. and Mary Sprague Miller Institute for Basic Research in Science, University of California Berkeley","ror":null},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320332193","display_name":"Genentech","ror":"https://ror.org/04gndp242"},{"id":"https://openalex.org/F4320332622","display_name":"University of California, San Francisco","ror":"https://ror.org/043mz5j54"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"},{"id":"https://openalex.org/F4320337430","display_name":"National Institute of Justice","ror":"https://ror.org/00v8p7w89"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4410161661.pdf","grobid_xml":"https://content.openalex.org/works/W4410161661.grobid-xml"},"referenced_works_count":42,"referenced_works":["https://openalex.org/W1551558112","https://openalex.org/W1580638504","https://openalex.org/W1978150238","https://openalex.org/W2028900796","https://openalex.org/W2071327804","https://openalex.org/W2102213696","https://openalex.org/W2104549677","https://openalex.org/W2105306382","https://openalex.org/W2110450140","https://openalex.org/W2114381854","https://openalex.org/W2120443264","https://openalex.org/W2129494556","https://openalex.org/W2143992683","https://openalex.org/W2147476659","https://openalex.org/W2183589234","https://openalex.org/W2811343296","https://openalex.org/W2882975421","https://openalex.org/W2885647429","https://openalex.org/W2914488418","https://openalex.org/W2915041973","https://openalex.org/W2915686791","https://openalex.org/W2951621382","https://openalex.org/W2951742207","https://openalex.org/W2952952507","https://openalex.org/W2953283624","https://openalex.org/W2991026871","https://openalex.org/W2992571387","https://openalex.org/W2994799276","https://openalex.org/W2994938434","https://openalex.org/W3012452819","https://openalex.org/W3015440270","https://openalex.org/W3033380172","https://openalex.org/W3095467272","https://openalex.org/W3126160703","https://openalex.org/W3128712871","https://openalex.org/W4221069327","https://openalex.org/W4280590417","https://openalex.org/W4310110536","https://openalex.org/W4327682542","https://openalex.org/W4378195027","https://openalex.org/W4395690561","https://openalex.org/W6944244240"],"related_works":["https://openalex.org/W1579373186","https://openalex.org/W4312685612","https://openalex.org/W2046291598","https://openalex.org/W4317827232","https://openalex.org/W4250910493","https://openalex.org/W4237901667","https://openalex.org/W4244444997","https://openalex.org/W4256428044","https://openalex.org/W2601323023","https://openalex.org/W4232070506"],"abstract_inverted_index":{"BACKGROUND:":[0],"Large-scale":[1],"family":[2,54,164,186],"pedigrees":[3,14,92,187],"are":[4,15],"commonly":[5],"used":[6],"across":[7],"medical,":[8,212],"evolutionary,":[9],"and":[10,24,82,103,156,175,198,205,214,228],"forensic":[11,29],"genetics.":[12],"These":[13],"tools":[16],"for":[17,122,143,201],"identifying":[18],"genetic":[19,30,109,226],"disorders,":[20],"tracking":[21],"evolutionary":[22,215],"patterns,":[23],"establishing":[25],"familial":[26],"relationships":[27],"via":[28],"identification.":[31],"However,":[32],"there":[33],"is":[34,195],"a":[35,53,69,88,123,150,163,196],"lack":[36],"of":[37,60,79,85,117,120,125,134,145,162,170,190,225],"software":[38],"to":[39,49,130,152,158,218],"accurately":[40],"simulate":[41,153,183],"different":[42],"pedigree":[43,80,101,176,203,207],"structures":[44,81,204],"along":[45],"with":[46,105,127,188],"genomes":[47,84,184],"corresponding":[48],"those":[50],"individuals":[51,86],"in":[52,87],"pedigree.":[55,89,165],"This":[56],"limits":[57],"simulation-based":[58],"evaluations":[59],"methods":[61],"that":[62,75,180],"use":[63],"pedigrees.":[64],"RESULTS:":[65],"We":[66,139,166,178],"have":[67],"developed":[68],"python":[70],"command-line-based":[71],"tool":[72],"called":[73],"py_ped_sim":[74,90,113,194],"facilitates":[76],"the":[77,83,106,115,128,132,160,168,223],"simulation":[78,116],"represents":[91],"as":[93],"directed":[94],"acyclic":[95],"graphs,":[96],"enabling":[97],"conversion":[98],"between":[99],"standard":[100],"formats":[102],"integration":[104],"forward":[107],"population":[108],"simulator,":[110],"SLiM.":[111],"Notably,":[112],"allows":[114],"varying":[118],"numbers":[119],"offspring":[121],"set":[124],"parents,":[126],"capacity":[129],"shift":[131],"distribution":[133],"sibship":[135],"sizes":[136],"over":[137],"generations.":[138],"additionally":[140],"add":[141],"simulations":[142,157],"events":[144],"misattributed":[146],"paternity,":[147],"which":[148],"offers":[149],"way":[151],"half-sibling":[154],"relationships,":[155],"extend":[159],"breadth":[161],"validated":[167],"accuracy":[169],"both":[171],"our":[172],"genome":[173,208],"simulator":[174],"simulator.":[177],"show":[179],"we":[181],"can":[182],"onto":[185],"levels":[189],"expected":[191],"kinship.":[192],"CONCLUSIONS:":[193],"user-friendly":[197],"open-source":[199],"solution":[200],"simulating":[202],"conducting":[206],"simulations.":[209],"It":[210],"empowers":[211],"forensic,":[213],"genetics":[216],"researchers":[217],"gain":[219],"deeper":[220],"insights":[221],"into":[222],"dynamics":[224],"inheritance":[227],"relatedness":[229],"within":[230],"families.":[231]},"counts_by_year":[],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}
