{"id":"https://openalex.org/W7121555575","doi":"https://doi.org/10.1093/bioinformatics/btag004","title":"<i>sedimix</i> : a workflow for the analysis of hominin nuclear DNA sequences from sediments","display_name":"<i>sedimix</i> : a workflow for the analysis of hominin nuclear DNA sequences from sediments","publication_year":2026,"publication_date":"2026-01-03","ids":{"openalex":"https://openalex.org/W7121555575","doi":"https://doi.org/10.1093/bioinformatics/btag004","pmid":"https://pubmed.ncbi.nlm.nih.gov/41512286"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btag004","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btag004","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.1093/bioinformatics/btag004","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":null,"display_name":"Jierui Xu","orcid":"https://orcid.org/0000-0003-1146-3775"},"institutions":[{"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":true,"raw_author_name":"Jierui Xu","raw_affiliation_strings":["University of California, Berkeley Department of Molecular and Cell Biology, , Berkeley, CA, 94720,"],"affiliations":[{"raw_affiliation_string":"University of California, Berkeley Department of Molecular and Cell Biology, , Berkeley, CA, 94720,","institution_ids":["https://openalex.org/I95457486"]}]},{"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/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":["University of California, Berkeley Department of Molecular and Cell Biology, , Berkeley, CA, 94720,"],"affiliations":[{"raw_affiliation_string":"University of California, Berkeley Department of Molecular and Cell Biology, , Berkeley, CA, 94720,","institution_ids":["https://openalex.org/I95457486"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5056611778","display_name":"Priya Moorjani","orcid":"https://orcid.org/0000-0002-0947-5673"},"institutions":[{"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":"Priya Moorjani","raw_affiliation_strings":["University of California, Berkeley Center for Computational Biology, , Berkeley, CA, 94720,","University of California, Berkeley Department of Molecular and Cell Biology, , Berkeley, CA, 94720,"],"affiliations":[{"raw_affiliation_string":"University of California, Berkeley Center for Computational Biology, , Berkeley, CA, 94720,","institution_ids":["https://openalex.org/I95457486"]},{"raw_affiliation_string":"University of California, Berkeley Department of Molecular and Cell Biology, , Berkeley, CA, 94720,","institution_ids":["https://openalex.org/I95457486"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I95457486"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.0,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":{"value":0.07210166,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"42","issue":"2","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10751","display_name":"Forensic and Genetic Research","score":0.5521000027656555,"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/T10751","display_name":"Forensic and Genetic Research","score":0.5521000027656555,"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/T10421","display_name":"Pleistocene-Era Hominins and Archaeology","score":0.38339999318122864,"subfield":{"id":"https://openalex.org/subfields/3314","display_name":"Anthropology"},"field":{"id":"https://openalex.org/fields/33","display_name":"Social Sciences"},"domain":{"id":"https://openalex.org/domains/2","display_name":"Social Sciences"}},{"id":"https://openalex.org/T12640","display_name":"Environmental DNA in Biodiversity Studies","score":0.013299999758601189,"subfield":{"id":"https://openalex.org/subfields/2303","display_name":"Ecology"},"field":{"id":"https://openalex.org/fields/23","display_name":"Environmental Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/workflow","display_name":"Workflow","score":0.8342999815940857},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.6442999839782715},{"id":"https://openalex.org/keywords/software-tool","display_name":"Software tool","score":0.3772999942302704},{"id":"https://openalex.org/keywords/dna-sequencing","display_name":"DNA sequencing","score":0.3197999894618988},{"id":"https://openalex.org/keywords/hominidae","display_name":"Hominidae","score":0.3075999915599823}],"concepts":[{"id":"https://openalex.org/C177212765","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Workflow","level":2,"score":0.8342999815940857},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.6442999839782715},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5758000016212463},{"id":"https://openalex.org/C2984968299","wikidata":"https://www.wikidata.org/wiki/Q1077784","display_name":"Software tool","level":3,"score":0.3772999942302704},{"id":"https://openalex.org/C127313418","wikidata":"https://www.wikidata.org/wiki/Q1069","display_name":"Geology","level":0,"score":0.3206999897956848},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.3197999894618988},{"id":"https://openalex.org/C2779987252","wikidata":"https://www.wikidata.org/wiki/Q635162","display_name":"Hominidae","level":3,"score":0.3075999915599823},{"id":"https://openalex.org/C115903868","wikidata":"https://www.wikidata.org/wiki/Q80993","display_name":"Software engineering","level":1,"score":0.304500013589859},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.2815999984741211},{"id":"https://openalex.org/C98045186","wikidata":"https://www.wikidata.org/wiki/Q205663","display_name":"Process (computing)","level":2,"score":0.2802000045776367},{"id":"https://openalex.org/C2984499602","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Computer software","level":2,"score":0.2793999910354614}],"mesh":[{"descriptor_ui":"D000072441","descriptor_name":"DNA, Ancient","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":true},{"descriptor_ui":"D000072441","descriptor_name":"DNA, Ancient","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":true},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000235","qualifier_name":"genetics","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":"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":"D015186","descriptor_name":"Hominidae","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D015186","descriptor_name":"Hominidae","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019015","descriptor_name":"Geologic Sediments","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D019015","descriptor_name":"Geologic Sediments","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D057188","descriptor_name":"Workflow","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057188","descriptor_name":"Workflow","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/btag004","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btag004","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:41512286","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/41512286","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":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:pure.atira.dk:publications/ca87deb4-5432-4fb6-8a5d-dee0e72a4e88","is_oa":true,"landing_page_url":"https://researchprofiles.ku.dk/da/publications/ca87deb4-5432-4fb6-8a5d-dee0e72a4e88","pdf_url":null,"source":{"id":"https://openalex.org/S4306401983","display_name":"Research at the University of Copenhagen (University of Copenhagen)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I124055696","host_organization_name":"University of Copenhagen","host_organization_lineage":["https://openalex.org/I124055696"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Xu , J , Zavala , E & Moorjani , P 2026 , ' sedimix : a workflow for the analysis of hominin nuclear DNA sequences from sediments ' , Bioinformatics , vol. 42 , no. 2 , btag004 . https://doi.org/10.1093/bioinformatics/btag004","raw_type":"article"},{"id":"pmh:oai:europepmc.org:11673996","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12866666","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:10.1093/bioinformatics/btag004","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btag004","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320306133","display_name":"Burroughs Wellcome Fund","ror":"https://ror.org/01d35cw23"},{"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/F4320322436","display_name":"Novo Nordisk","ror":"https://ror.org/0435rc536"},{"id":"https://openalex.org/F4320322596","display_name":"Tel Aviv University","ror":"https://ror.org/04mhzgx49"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":23,"referenced_works":["https://openalex.org/W1997927740","https://openalex.org/W2022327489","https://openalex.org/W2034552366","https://openalex.org/W2047998066","https://openalex.org/W2050254973","https://openalex.org/W2102619694","https://openalex.org/W2103441770","https://openalex.org/W2104549677","https://openalex.org/W2150163641","https://openalex.org/W2156330112","https://openalex.org/W2170551349","https://openalex.org/W2343039634","https://openalex.org/W2544029679","https://openalex.org/W2608083544","https://openalex.org/W2951160681","https://openalex.org/W2964989753","https://openalex.org/W2990618091","https://openalex.org/W3131055609","https://openalex.org/W3131443014","https://openalex.org/W3152826503","https://openalex.org/W3175387722","https://openalex.org/W3179308956","https://openalex.org/W4367856465"],"related_works":[],"abstract_inverted_index":{"sedimix":[0],"is":[1,29],"available":[2,19,30],"as":[3],"an":[4],"open-source":[5],"software":[6],"with":[7,16],"the":[8],"associated":[9],"code,":[10],"example":[11],"data,":[12],"and":[13],"user":[14],"manual":[15],"installation":[17],"instructions":[18],"at":[20],"https://github.com/jierui-cell/sedimix.":[21],"A":[22],"permanent":[23],"archived":[24],"version":[25],"of":[26],"this":[27],"release":[28],"via":[31],"Zenodo:":[32],"https://doi.org/10.5281/zenodo.17244854.":[33]},"counts_by_year":[],"updated_date":"2026-04-09T08:11:56.329763","created_date":"2026-01-11T00:00:00"}
