{"id":"https://openalex.org/W1856600885","doi":"https://doi.org/10.1186/1471-2105-7-428","title":"XRate: a fast prototyping, training and annotation tool for phylo-grammars","display_name":"XRate: a fast prototyping, training and annotation tool for phylo-grammars","publication_year":2006,"publication_date":"2006-10-03","ids":{"openalex":"https://openalex.org/W1856600885","doi":"https://doi.org/10.1186/1471-2105-7-428","mag":"1856600885","pmid":"https://pubmed.ncbi.nlm.nih.gov/17018148"},"language":"en","primary_location":{"id":"doi:10.1186/1471-2105-7-428","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-7-428","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-7-428","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/10.1186/1471-2105-7-428","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5041918210","display_name":"Peter S. Klosterman","orcid":null},"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":"Peter S Klosterman","raw_affiliation_strings":["Department of Bioengineering, University of California, Berkeley CA, USA. petek@accesscom.com","Department of Bioengineering, University of California,Berkeley,USA"],"affiliations":[{"raw_affiliation_string":"Department of Bioengineering, University of California, Berkeley CA, USA. petek@accesscom.com","institution_ids":["https://openalex.org/I95457486"]},{"raw_affiliation_string":"Department of Bioengineering, University of California,Berkeley,USA","institution_ids":["https://openalex.org/I95457486"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5029416625","display_name":"Andrew Uzilov","orcid":"https://orcid.org/0000-0002-5411-9280"},"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":"Andrew V Uzilov","raw_affiliation_strings":["Department of Bioengineering, University of California, Berkeley, CA, USA","Department of Bioengineering, University of California,Berkeley,USA"],"affiliations":[{"raw_affiliation_string":"Department of Bioengineering, University of California, Berkeley, CA, USA","institution_ids":["https://openalex.org/I95457486"]},{"raw_affiliation_string":"Department of Bioengineering, University of California,Berkeley,USA","institution_ids":["https://openalex.org/I95457486"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5001496158","display_name":"Yuri R. Benda\u00f1a","orcid":null},"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":"Yuri R Benda\u00f1a","raw_affiliation_strings":["Department of Bioengineering, University of California, Berkeley, CA, USA","Department of Bioengineering, University of California,Berkeley,USA"],"affiliations":[{"raw_affiliation_string":"Department of Bioengineering, University of California, Berkeley, CA, USA","institution_ids":["https://openalex.org/I95457486"]},{"raw_affiliation_string":"Department of Bioengineering, University of California,Berkeley,USA","institution_ids":["https://openalex.org/I95457486"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5032741707","display_name":"Robert K. Bradley","orcid":"https://orcid.org/0000-0002-8046-1063"},"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":"Robert K Bradley","raw_affiliation_strings":["Department of Bioengineering, University of California, Berkeley, CA, USA","Department of Bioengineering, University of California,Berkeley,USA"],"affiliations":[{"raw_affiliation_string":"Department of Bioengineering, University of California, Berkeley, CA, USA","institution_ids":["https://openalex.org/I95457486"]},{"raw_affiliation_string":"Department of Bioengineering, University of California,Berkeley,USA","institution_ids":["https://openalex.org/I95457486"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5013209726","display_name":"Sharon Chao","orcid":null},"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":"Sharon Chao","raw_affiliation_strings":["Department of Bioengineering, University of California, Berkeley, CA, USA","Department of Bioengineering, University of California,Berkeley,USA"],"affiliations":[{"raw_affiliation_string":"Department of Bioengineering, University of California, Berkeley, CA, USA","institution_ids":["https://openalex.org/I95457486"]},{"raw_affiliation_string":"Department of Bioengineering, University of California,Berkeley,USA","institution_ids":["https://openalex.org/I95457486"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5006598290","display_name":"Carolin Kosiol","orcid":"https://orcid.org/0000-0002-3219-6648"},"institutions":[{"id":"https://openalex.org/I205783295","display_name":"Cornell University","ror":"https://ror.org/05bnh6r87","country_code":"US","type":"education","lineage":["https://openalex.org/I205783295"]},{"id":"https://openalex.org/I1303153112","display_name":"European Bioinformatics Institute","ror":"https://ror.org/02catss52","country_code":"GB","type":"facility","lineage":["https://openalex.org/I1303153112","https://openalex.org/I4210138560"]}],"countries":["GB","US"],"is_corresponding":false,"raw_author_name":"Carolin Kosiol","raw_affiliation_strings":["Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY, USA","European Bioinformatics Institute, Hinxton, Cambridgeshire, UK","Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, USA","European Bioinformatics Institute, Hinxton, UK"],"affiliations":[{"raw_affiliation_string":"Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY, USA","institution_ids":["https://openalex.org/I205783295"]},{"raw_affiliation_string":"European Bioinformatics Institute, Hinxton, Cambridgeshire, UK","institution_ids":["https://openalex.org/I1303153112"]},{"raw_affiliation_string":"Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, USA","institution_ids":["https://openalex.org/I205783295"]},{"raw_affiliation_string":"European Bioinformatics Institute, Hinxton, UK","institution_ids":["https://openalex.org/I1303153112"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5020967139","display_name":"Nick Goldman","orcid":"https://orcid.org/0000-0001-8486-2211"},"institutions":[{"id":"https://openalex.org/I1303153112","display_name":"European Bioinformatics Institute","ror":"https://ror.org/02catss52","country_code":"GB","type":"facility","lineage":["https://openalex.org/I1303153112","https://openalex.org/I4210138560"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Nick Goldman","raw_affiliation_strings":["European Bioinformatics Institute, Hinxton, Cambridgeshire, UK","European Bioinformatics Institute, Hinxton, UK"],"affiliations":[{"raw_affiliation_string":"European Bioinformatics Institute, Hinxton, Cambridgeshire, UK","institution_ids":["https://openalex.org/I1303153112"]},{"raw_affiliation_string":"European Bioinformatics Institute, Hinxton, UK","institution_ids":["https://openalex.org/I1303153112"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5054625887","display_name":"Ian Holmes","orcid":"https://orcid.org/0000-0001-7639-5369"},"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":"Ian Holmes","raw_affiliation_strings":["Department of Bioengineering, University of California, Berkeley, CA, USA","Department of Bioengineering, University of California,Berkeley,USA"],"affiliations":[{"raw_affiliation_string":"Department of Bioengineering, University of California, Berkeley, CA, USA","institution_ids":["https://openalex.org/I95457486"]},{"raw_affiliation_string":"Department of Bioengineering, University of California,Berkeley,USA","institution_ids":["https://openalex.org/I95457486"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":8,"corresponding_author_ids":["https://openalex.org/A5041918210"],"corresponding_institution_ids":["https://openalex.org/I95457486"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":2.0433,"has_fulltext":true,"cited_by_count":58,"citation_normalized_percentile":{"value":0.85083482,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"7","issue":"1","first_page":"428","last_page":"428"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9998000264167786,"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":0.9998000264167786,"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/T10012","display_name":"Genetic diversity and population structure","score":0.9908000230789185,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9829000234603882,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7313110828399658},{"id":"https://openalex.org/keywords/rule-based-machine-translation","display_name":"Rule-based machine translation","score":0.6971848011016846},{"id":"https://openalex.org/keywords/context-free-grammar","display_name":"Context-free grammar","score":0.6534936428070068},{"id":"https://openalex.org/keywords/annotation","display_name":"Annotation","score":0.5375179648399353},{"id":"https://openalex.org/keywords/markov-chain","display_name":"Markov chain","score":0.5363214612007141},{"id":"https://openalex.org/keywords/probabilistic-logic","display_name":"Probabilistic logic","score":0.5069406032562256},{"id":"https://openalex.org/keywords/hidden-markov-model","display_name":"Hidden Markov model","score":0.4775068163871765},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.4673609733581543},{"id":"https://openalex.org/keywords/synchronous-context-free-grammar","display_name":"Synchronous context-free grammar","score":0.460538387298584},{"id":"https://openalex.org/keywords/stochastic-context-free-grammar","display_name":"Stochastic context-free grammar","score":0.44157707691192627},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.4077960252761841},{"id":"https://openalex.org/keywords/natural-language-processing","display_name":"Natural language processing","score":0.3903067708015442},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.35935601592063904},{"id":"https://openalex.org/keywords/tree-adjoining-grammar","display_name":"Tree-adjoining grammar","score":0.33502209186553955},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.19981330633163452}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7313110828399658},{"id":"https://openalex.org/C53893814","wikidata":"https://www.wikidata.org/wiki/Q7378909","display_name":"Rule-based machine translation","level":2,"score":0.6971848011016846},{"id":"https://openalex.org/C97212296","wikidata":"https://www.wikidata.org/wiki/Q338047","display_name":"Context-free grammar","level":3,"score":0.6534936428070068},{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.5375179648399353},{"id":"https://openalex.org/C98763669","wikidata":"https://www.wikidata.org/wiki/Q176645","display_name":"Markov chain","level":2,"score":0.5363214612007141},{"id":"https://openalex.org/C49937458","wikidata":"https://www.wikidata.org/wiki/Q2599292","display_name":"Probabilistic logic","level":2,"score":0.5069406032562256},{"id":"https://openalex.org/C23224414","wikidata":"https://www.wikidata.org/wiki/Q176769","display_name":"Hidden Markov model","level":2,"score":0.4775068163871765},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.4673609733581543},{"id":"https://openalex.org/C51802942","wikidata":"https://www.wikidata.org/wiki/Q7662211","display_name":"Synchronous context-free grammar","level":4,"score":0.460538387298584},{"id":"https://openalex.org/C199624470","wikidata":"https://www.wikidata.org/wiki/Q2377216","display_name":"Stochastic context-free grammar","level":5,"score":0.44157707691192627},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4077960252761841},{"id":"https://openalex.org/C204321447","wikidata":"https://www.wikidata.org/wiki/Q30642","display_name":"Natural language processing","level":1,"score":0.3903067708015442},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.35935601592063904},{"id":"https://openalex.org/C134083981","wikidata":"https://www.wikidata.org/wiki/Q1754022","display_name":"Tree-adjoining grammar","level":4,"score":0.33502209186553955},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.19981330633163452},{"id":"https://openalex.org/C24687705","wikidata":"https://www.wikidata.org/wiki/Q3753284","display_name":"Example-based machine translation","level":3,"score":0.0}],"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":"D001185","descriptor_name":"Artificial Intelligence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001185","descriptor_name":"Artificial Intelligence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001185","descriptor_name":"Artificial Intelligence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D002874","descriptor_name":"Chromosome Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D002874","descriptor_name":"Chromosome Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D002874","descriptor_name":"Chromosome Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","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":"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":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017124","descriptor_name":"Conserved Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017124","descriptor_name":"Conserved Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017124","descriptor_name":"Conserved Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":5,"locations":[{"id":"doi:10.1186/1471-2105-7-428","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-7-428","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-7-428","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:17018148","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/17018148","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:88bc39ad8c104100990badac07cda979","is_oa":true,"landing_page_url":"https://doaj.org/article/88bc39ad8c104100990badac07cda979","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"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 7, Iss 1, p 428 (2006)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:1350594","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/1622757","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"},{"id":"pmh:oai:pubmedcentral.nih.gov:1622757","is_oa":true,"landing_page_url":"http://doi.org/10.1186/1471-2105-7-428","pdf_url":null,"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":"BMC Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/1471-2105-7-428","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-7-428","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-7-428","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":[{"score":0.550000011920929,"id":"https://metadata.un.org/sdg/4","display_name":"Quality Education"}],"awards":[{"id":"https://openalex.org/G3611247453","display_name":null,"funder_award_id":"R01GM","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G6894402473","display_name":null,"funder_award_id":"Fellowship","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"},{"id":"https://openalex.org/F4320309411","display_name":"University of California Berkeley","ror":"https://ror.org/01an7q238"},{"id":"https://openalex.org/F4320311904","display_name":"Wellcome Trust","ror":"https://ror.org/029chgv08"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337089","display_name":"Wolfson College, University of Cambridge","ror":null},{"id":"https://openalex.org/F4320337348","display_name":"National Human Genome Research Institute","ror":"https://ror.org/00baak391"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W1856600885.pdf","grobid_xml":"https://content.openalex.org/works/W1856600885.grobid-xml"},"referenced_works_count":107,"referenced_works":["https://openalex.org/W1479758177","https://openalex.org/W1491063910","https://openalex.org/W1525734744","https://openalex.org/W1544729927","https://openalex.org/W1548178570","https://openalex.org/W1574109141","https://openalex.org/W1575431606","https://openalex.org/W1579352620","https://openalex.org/W1822105579","https://openalex.org/W1844951369","https://openalex.org/W1920973730","https://openalex.org/W1963590211","https://openalex.org/W1965399019","https://openalex.org/W1968256798","https://openalex.org/W1969051510","https://openalex.org/W1969620339","https://openalex.org/W1971147414","https://openalex.org/W1971912858","https://openalex.org/W1978470410","https://openalex.org/W1998321956","https://openalex.org/W2003603552","https://openalex.org/W2004178884","https://openalex.org/W2004575181","https://openalex.org/W2009570821","https://openalex.org/W2009596137","https://openalex.org/W2011368877","https://openalex.org/W2022368654","https://openalex.org/W2023206235","https://openalex.org/W2026551295","https://openalex.org/W2026881360","https://openalex.org/W2031206741","https://openalex.org/W2037177386","https://openalex.org/W2037255500","https://openalex.org/W2037683394","https://openalex.org/W2041357436","https://openalex.org/W2045255985","https://openalex.org/W2045895660","https://openalex.org/W2047405351","https://openalex.org/W2048102092","https://openalex.org/W2049633694","https://openalex.org/W2060555982","https://openalex.org/W2061149284","https://openalex.org/W2062018285","https://openalex.org/W2062345582","https://openalex.org/W2063389953","https://openalex.org/W2064345118","https://openalex.org/W2065461553","https://openalex.org/W2066502527","https://openalex.org/W2068011423","https://openalex.org/W2068886104","https://openalex.org/W2081443406","https://openalex.org/W2082853849","https://openalex.org/W2091851394","https://openalex.org/W2092979861","https://openalex.org/W2097706568","https://openalex.org/W2102122585","https://openalex.org/W2102424972","https://openalex.org/W2103074382","https://openalex.org/W2105594594","https://openalex.org/W2107010419","https://openalex.org/W2109314645","https://openalex.org/W2114122189","https://openalex.org/W2116503869","https://openalex.org/W2117853077","https://openalex.org/W2121447534","https://openalex.org/W2123758939","https://openalex.org/W2124790653","https://openalex.org/W2128607924","https://openalex.org/W2130416410","https://openalex.org/W2137640371","https://openalex.org/W2137813581","https://openalex.org/W2137991504","https://openalex.org/W2142664059","https://openalex.org/W2143238378","https://openalex.org/W2145191876","https://openalex.org/W2145436067","https://openalex.org/W2146120203","https://openalex.org/W2148578258","https://openalex.org/W2152454458","https://openalex.org/W2154467419","https://openalex.org/W2154649313","https://openalex.org/W2156521045","https://openalex.org/W2157865313","https://openalex.org/W2158381555","https://openalex.org/W2158826174","https://openalex.org/W2160364329","https://openalex.org/W2160659074","https://openalex.org/W2165001851","https://openalex.org/W2166187656","https://openalex.org/W2166444569","https://openalex.org/W2166480651","https://openalex.org/W2187461225","https://openalex.org/W2257584626","https://openalex.org/W2334003227","https://openalex.org/W2525509737","https://openalex.org/W2600349519","https://openalex.org/W2601913882","https://openalex.org/W2911823491","https://openalex.org/W4205911826","https://openalex.org/W4214695391","https://openalex.org/W4229926969","https://openalex.org/W4233815609","https://openalex.org/W4240021321","https://openalex.org/W4245668478","https://openalex.org/W4245826738","https://openalex.org/W4248373945","https://openalex.org/W4250143236"],"related_works":["https://openalex.org/W2058948626","https://openalex.org/W1656514314","https://openalex.org/W1558874415","https://openalex.org/W4245826738","https://openalex.org/W2413926952","https://openalex.org/W1574721051","https://openalex.org/W1829822087","https://openalex.org/W4385190477","https://openalex.org/W1987502048","https://openalex.org/W2084187640"],"abstract_inverted_index":{"Our":[0],"results":[1],"demonstrate":[2],"that":[3,17],"xrate":[4],"estimates":[5],"biologically":[6],"meaningful":[7],"rates":[8],"and":[9],"makes":[10],"predictions":[11],"whose":[12],"accuracy":[13],"is":[14],"comparable":[15],"to":[16],"of":[18],"more":[19],"specialized":[20],"tools.":[21]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":2},{"year":2020,"cited_by_count":4},{"year":2019,"cited_by_count":2},{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":2},{"year":2016,"cited_by_count":1},{"year":2015,"cited_by_count":1},{"year":2014,"cited_by_count":4},{"year":2013,"cited_by_count":2},{"year":2012,"cited_by_count":6}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2025-10-10T00:00:00"}
