{"id":"https://openalex.org/W4383481209","doi":"https://doi.org/10.1093/bioinformatics/btad425","title":"Tau-typing: a Nextflow pipeline for finding the best phylogenetic markers in the genome for molecular typing of microbial species","display_name":"Tau-typing: a Nextflow pipeline for finding the best phylogenetic markers in the genome for molecular typing of microbial species","publication_year":2023,"publication_date":"2023-07-01","ids":{"openalex":"https://openalex.org/W4383481209","doi":"https://doi.org/10.1093/bioinformatics/btad425","pmid":"https://pubmed.ncbi.nlm.nih.gov/37417952"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btad425","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad425","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btad425/50838244/btad425.pdf","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://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btad425/50838244/btad425.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5072968154","display_name":"Matthew H. Seabolt","orcid":"https://orcid.org/0000-0002-0336-5545"},"institutions":[{"id":"https://openalex.org/I114662689","display_name":"Leidos (United States)","ror":"https://ror.org/012cvds63","country_code":"US","type":"company","lineage":["https://openalex.org/I114662689"]},{"id":"https://openalex.org/I130701444","display_name":"Georgia Institute of Technology","ror":"https://ror.org/01zkghx44","country_code":"US","type":"education","lineage":["https://openalex.org/I130701444"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Matthew H Seabolt","raw_affiliation_strings":["Leidos Inc. , Reston, VA 20190, United States","School of Biological Sciences, Georgia Institute of Technology , Atlanta, GA 30332, United States"],"affiliations":[{"raw_affiliation_string":"Leidos Inc. , Reston, VA 20190, United States","institution_ids":["https://openalex.org/I114662689"]},{"raw_affiliation_string":"School of Biological Sciences, Georgia Institute of Technology , Atlanta, GA 30332, United States","institution_ids":["https://openalex.org/I130701444"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5071631414","display_name":"Arun K. Boddapati","orcid":"https://orcid.org/0000-0002-7661-8443"},"institutions":[{"id":"https://openalex.org/I114662689","display_name":"Leidos (United States)","ror":"https://ror.org/012cvds63","country_code":"US","type":"company","lineage":["https://openalex.org/I114662689"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Arun K Boddapati","raw_affiliation_strings":["Leidos Inc. , Reston, VA 20190, United States"],"affiliations":[{"raw_affiliation_string":"Leidos Inc. , Reston, VA 20190, United States","institution_ids":["https://openalex.org/I114662689"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5015882356","display_name":"Joshua J Forstedt","orcid":null},"institutions":[{"id":"https://openalex.org/I114662689","display_name":"Leidos (United States)","ror":"https://ror.org/012cvds63","country_code":"US","type":"company","lineage":["https://openalex.org/I114662689"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Joshua J Forstedt","raw_affiliation_strings":["Leidos Inc. , Reston, VA 20190, United States"],"affiliations":[{"raw_affiliation_string":"Leidos Inc. , Reston, VA 20190, United States","institution_ids":["https://openalex.org/I114662689"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5087588208","display_name":"Konstantinos T. Konstantinidis","orcid":"https://orcid.org/0000-0002-0954-4755"},"institutions":[{"id":"https://openalex.org/I130701444","display_name":"Georgia Institute of Technology","ror":"https://ror.org/01zkghx44","country_code":"US","type":"education","lineage":["https://openalex.org/I130701444"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Konstantinos T Konstantinidis","raw_affiliation_strings":["School of Biological Sciences, Georgia Institute of Technology , Atlanta, GA 30332, United States","School of Civil and Environmental Engineering, Georgia Institute of Technology , Atlanta, GA 30332, United States"],"affiliations":[{"raw_affiliation_string":"School of Biological Sciences, Georgia Institute of Technology , Atlanta, GA 30332, United States","institution_ids":["https://openalex.org/I130701444"]},{"raw_affiliation_string":"School of Civil and Environmental Engineering, Georgia Institute of Technology , Atlanta, GA 30332, United States","institution_ids":["https://openalex.org/I130701444"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5072968154"],"corresponding_institution_ids":["https://openalex.org/I114662689","https://openalex.org/I130701444"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.1523,"has_fulltext":true,"cited_by_count":1,"citation_normalized_percentile":{"value":0.58328336,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":91,"max":95},"biblio":{"volume":"39","issue":"7","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9997000098228455,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9997000098228455,"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/T10141","display_name":"Probiotics and Fermented Foods","score":0.9994999766349792,"subfield":{"id":"https://openalex.org/subfields/1106","display_name":"Food Science"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T11048","display_name":"Bacteriophages and microbial interactions","score":0.9977999925613403,"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/typing","display_name":"Typing","score":0.8403462767601013},{"id":"https://openalex.org/keywords/phylogenetic-tree","display_name":"Phylogenetic tree","score":0.7144516110420227},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.6043717861175537},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.560877799987793},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5545840263366699},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.5286814570426941},{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.4671610891819},{"id":"https://openalex.org/keywords/phylogenetic-relationship","display_name":"Phylogenetic relationship","score":0.42314326763153076},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.2707936763763428},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.15432843565940857},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.07494613528251648}],"concepts":[{"id":"https://openalex.org/C2781209916","wikidata":"https://www.wikidata.org/wiki/Q3215756","display_name":"Typing","level":2,"score":0.8403462767601013},{"id":"https://openalex.org/C193252679","wikidata":"https://www.wikidata.org/wiki/Q242125","display_name":"Phylogenetic tree","level":3,"score":0.7144516110420227},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.6043717861175537},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.560877799987793},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5545840263366699},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.5286814570426941},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.4671610891819},{"id":"https://openalex.org/C2992072516","wikidata":"https://www.wikidata.org/wiki/Q171184","display_name":"Phylogenetic relationship","level":4,"score":0.42314326763153076},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.2707936763763428},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.15432843565940857},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.07494613528251648}],"mesh":[{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","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":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D058889","descriptor_name":"Molecular Typing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D058889","descriptor_name":"Molecular Typing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D058889","descriptor_name":"Molecular Typing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btad425","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad425","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btad425/50838244/btad425.pdf","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:37417952","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/37417952","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:pubmedcentral.nih.gov:10336021","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10336021","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10336021/pdf/btad425.pdf","source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btad425","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad425","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btad425/50838244/btad425.pdf","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":[{"id":"https://openalex.org/G2537072889","display_name":null,"funder_award_id":"1759831","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G5921281487","display_name":null,"funder_award_id":"number","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G6755165505","display_name":null,"funder_award_id":"award","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G848032724","display_name":null,"funder_award_id":"Science","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"}],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W4383481209.pdf"},"referenced_works_count":27,"referenced_works":["https://openalex.org/W1981946092","https://openalex.org/W2031611770","https://openalex.org/W2053940732","https://openalex.org/W2104253405","https://openalex.org/W2117801354","https://openalex.org/W2142678478","https://openalex.org/W2143559680","https://openalex.org/W2432815617","https://openalex.org/W2587970647","https://openalex.org/W2605897695","https://openalex.org/W2613409207","https://openalex.org/W2765745983","https://openalex.org/W2801467281","https://openalex.org/W2951254987","https://openalex.org/W2969464561","https://openalex.org/W2979549191","https://openalex.org/W2995864131","https://openalex.org/W2997069256","https://openalex.org/W3006653136","https://openalex.org/W3022572641","https://openalex.org/W3035074698","https://openalex.org/W3113162057","https://openalex.org/W3121039364","https://openalex.org/W3132558036","https://openalex.org/W4214676060","https://openalex.org/W4233582454","https://openalex.org/W4291016578"],"related_works":["https://openalex.org/W3150750732","https://openalex.org/W2388579761","https://openalex.org/W2386173511","https://openalex.org/W4254698667","https://openalex.org/W903818084","https://openalex.org/W2982036139","https://openalex.org/W2352802959","https://openalex.org/W3202916294","https://openalex.org/W2375151634","https://openalex.org/W2002719115"],"abstract_inverted_index":{"Tau-typing":[0],"is":[1,8],"freely":[2],"available":[3],"at":[4],"https://github.com/hseabolt/tautyping.":[5],"The":[6],"pipeline":[7],"implemented":[9],"in":[10],"Nextflow":[11],"with":[12],"Singularity":[13],"support.":[14]},"counts_by_year":[{"year":2025,"cited_by_count":1}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2025-10-10T00:00:00"}
