{"id":"https://openalex.org/W3042865765","doi":"https://doi.org/10.1093/bioinformatics/btaa633","title":"Machine Boss: rapid prototyping of bioinformatic automata","display_name":"Machine Boss: rapid prototyping of bioinformatic automata","publication_year":2020,"publication_date":"2020-07-13","ids":{"openalex":"https://openalex.org/W3042865765","doi":"https://doi.org/10.1093/bioinformatics/btaa633","mag":"3042865765","pmid":"https://pubmed.ncbi.nlm.nih.gov/32683444"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btaa633","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaa633","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"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":"hybrid","oa_url":"https://doi.org/10.1093/bioinformatics/btaa633","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5055007356","display_name":"Jordi Silvestre-Ryan","orcid":"https://orcid.org/0000-0002-6520-5790"},"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":"Jordi Silvestre-Ryan","raw_affiliation_strings":["Department of Bioengineering, University of California , Berkeley, CA 94720, USA"],"affiliations":[{"raw_affiliation_string":"Department of Bioengineering, University of California , Berkeley, CA 94720, USA","institution_ids":["https://openalex.org/I95457486"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5035542752","display_name":"Yujie Wang","orcid":"https://orcid.org/0000-0001-5722-2673"},"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":"Yujie Wang","raw_affiliation_strings":["Department of Bioengineering, University of California , Berkeley, CA 94720, USA"],"affiliations":[{"raw_affiliation_string":"Department of Bioengineering, University of California , Berkeley, CA 94720, USA","institution_ids":["https://openalex.org/I95457486"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5114107959","display_name":"Mehak Sharma","orcid":"https://orcid.org/0000-0002-2134-5660"},"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":"Mehak Sharma","raw_affiliation_strings":["Department of Bioengineering, University of California , Berkeley, CA 94720, USA"],"affiliations":[{"raw_affiliation_string":"Department of Bioengineering, University of California , Berkeley, CA 94720, USA","institution_ids":["https://openalex.org/I95457486"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5025114648","display_name":"Stephen Lin","orcid":"https://orcid.org/0000-0002-5616-558X"},"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":"Stephen Lin","raw_affiliation_strings":["Department of Bioengineering, University of California , Berkeley, CA 94720, USA"],"affiliations":[{"raw_affiliation_string":"Department of Bioengineering, University of California , Berkeley, CA 94720, USA","institution_ids":["https://openalex.org/I95457486"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5103916531","display_name":"Yolanda Shen","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":"Yolanda Shen","raw_affiliation_strings":["Department of Bioengineering, University of California , Berkeley, CA 94720, USA"],"affiliations":[{"raw_affiliation_string":"Department of Bioengineering, University of California , Berkeley, CA 94720, USA","institution_ids":["https://openalex.org/I95457486"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5084133222","display_name":"Shihab Dider","orcid":"https://orcid.org/0000-0001-9647-3643"},"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":"Shihab Dider","raw_affiliation_strings":["Department of Bioengineering, University of California , Berkeley, CA 94720, USA"],"affiliations":[{"raw_affiliation_string":"Department of Bioengineering, University of California , Berkeley, CA 94720, USA","institution_ids":["https://openalex.org/I95457486"]}]},{"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":true,"raw_author_name":"Ian Holmes","raw_affiliation_strings":["Department of Bioengineering, University of California , Berkeley, CA 94720, USA"],"affiliations":[{"raw_affiliation_string":"Department of Bioengineering, University of California , Berkeley, CA 94720, USA","institution_ids":["https://openalex.org/I95457486"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5054625887"],"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":0.1672,"has_fulltext":false,"cited_by_count":3,"citation_normalized_percentile":{"value":0.50097906,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":"37","issue":"1","first_page":"29","last_page":"35"},"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/T11269","display_name":"Algorithms and Data Compression","score":0.9997000098228455,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T12029","display_name":"DNA and Biological Computing","score":0.9991000294685364,"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":0.7800114154815674},{"id":"https://openalex.org/keywords/boss","display_name":"Boss","score":0.7152587175369263},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.5765417218208313},{"id":"https://openalex.org/keywords/hidden-markov-model","display_name":"Hidden Markov model","score":0.535308837890625},{"id":"https://openalex.org/keywords/automaton","display_name":"Automaton","score":0.5291728377342224},{"id":"https://openalex.org/keywords/regular-expression","display_name":"Regular expression","score":0.4873989224433899},{"id":"https://openalex.org/keywords/finite-state-machine","display_name":"Finite-state machine","score":0.4811181426048279},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.4748116731643677},{"id":"https://openalex.org/keywords/inference","display_name":"Inference","score":0.4589780867099762},{"id":"https://openalex.org/keywords/rapid-prototyping","display_name":"Rapid prototyping","score":0.4520612955093384},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.41644686460494995},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.4126679301261902},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3938974142074585},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.35642850399017334},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.32884591817855835}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7800114154815674},{"id":"https://openalex.org/C2777020290","wikidata":"https://www.wikidata.org/wiki/Q4947493","display_name":"Boss","level":2,"score":0.7152587175369263},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.5765417218208313},{"id":"https://openalex.org/C23224414","wikidata":"https://www.wikidata.org/wiki/Q176769","display_name":"Hidden Markov model","level":2,"score":0.535308837890625},{"id":"https://openalex.org/C112505250","wikidata":"https://www.wikidata.org/wiki/Q787116","display_name":"Automaton","level":2,"score":0.5291728377342224},{"id":"https://openalex.org/C121329065","wikidata":"https://www.wikidata.org/wiki/Q185612","display_name":"Regular expression","level":2,"score":0.4873989224433899},{"id":"https://openalex.org/C167822520","wikidata":"https://www.wikidata.org/wiki/Q176452","display_name":"Finite-state machine","level":2,"score":0.4811181426048279},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.4748116731643677},{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.4589780867099762},{"id":"https://openalex.org/C2780395129","wikidata":"https://www.wikidata.org/wiki/Q1128971","display_name":"Rapid prototyping","level":2,"score":0.4520612955093384},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.41644686460494995},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.4126679301261902},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3938974142074585},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.35642850399017334},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.32884591817855835},{"id":"https://openalex.org/C78519656","wikidata":"https://www.wikidata.org/wiki/Q101333","display_name":"Mechanical engineering","level":1,"score":0.0},{"id":"https://openalex.org/C192562407","wikidata":"https://www.wikidata.org/wiki/Q228736","display_name":"Materials science","level":0,"score":0.0},{"id":"https://openalex.org/C191897082","wikidata":"https://www.wikidata.org/wiki/Q11467","display_name":"Metallurgy","level":1,"score":0.0},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","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":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017421","descriptor_name":"Sequence Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017421","descriptor_name":"Sequence Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017421","descriptor_name":"Sequence Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btaa633","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaa633","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"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:32683444","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/32683444","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:8034524","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8034524","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":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btaa633","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaa633","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"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":[{"score":0.6499999761581421,"display_name":"Decent work and economic growth","id":"https://metadata.un.org/sdg/8"}],"awards":[{"id":"https://openalex.org/G5338109553","display_name":null,"funder_award_id":"R01-HG004483","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G7714557983","display_name":null,"funder_award_id":"U24-CA220441","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G888126619","display_name":null,"funder_award_id":"R01-GM080203","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320312414","display_name":"Oxford Nanopore Technologies","ror":"https://ror.org/04hyfx005"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":48,"referenced_works":["https://openalex.org/W1525734744","https://openalex.org/W1529209937","https://openalex.org/W1574109141","https://openalex.org/W1579352620","https://openalex.org/W1646393397","https://openalex.org/W1767772592","https://openalex.org/W1802312377","https://openalex.org/W1829137581","https://openalex.org/W1969051510","https://openalex.org/W1973693416","https://openalex.org/W2007772656","https://openalex.org/W2009570821","https://openalex.org/W2046932483","https://openalex.org/W2047405351","https://openalex.org/W2059917021","https://openalex.org/W2062345582","https://openalex.org/W2068448872","https://openalex.org/W2074231493","https://openalex.org/W2087064593","https://openalex.org/W2091851394","https://openalex.org/W2092979861","https://openalex.org/W2102684747","https://openalex.org/W2103074382","https://openalex.org/W2107511706","https://openalex.org/W2108787198","https://openalex.org/W2114122189","https://openalex.org/W2136792657","https://openalex.org/W2137597742","https://openalex.org/W2140872496","https://openalex.org/W2146974293","https://openalex.org/W2157451851","https://openalex.org/W2162980030","https://openalex.org/W2166187656","https://openalex.org/W2226299262","https://openalex.org/W2317495605","https://openalex.org/W2341150241","https://openalex.org/W2514454343","https://openalex.org/W2607669908","https://openalex.org/W2789843538","https://openalex.org/W2898402099","https://openalex.org/W2949279762","https://openalex.org/W2950993016","https://openalex.org/W2952890625","https://openalex.org/W2963464696","https://openalex.org/W3124466221","https://openalex.org/W3145289798","https://openalex.org/W4245668478","https://openalex.org/W6680215730"],"related_works":["https://openalex.org/W3210524396","https://openalex.org/W2136244850","https://openalex.org/W1496945489","https://openalex.org/W1996775904","https://openalex.org/W2092774949","https://openalex.org/W3007787046","https://openalex.org/W4240792019","https://openalex.org/W2146605784","https://openalex.org/W2075637111","https://openalex.org/W4388152937"],"abstract_inverted_index":{"Supplementary":[0],"data":[1],"are":[2],"available":[3],"at":[4],"Bioinformatics":[5],"online.":[6]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":1},{"year":2020,"cited_by_count":1}],"updated_date":"2026-04-21T08:09:41.155169","created_date":"2025-10-10T00:00:00"}
