{"id":"https://openalex.org/W4399711263","doi":"https://doi.org/10.1093/bioinformatics/btae331","title":"Flexible parsing, interpretation, and editing of technical sequences with <i>splitcode</i>","display_name":"Flexible parsing, interpretation, and editing of technical sequences with <i>splitcode</i>","publication_year":2024,"publication_date":"2024-06-01","ids":{"openalex":"https://openalex.org/W4399711263","doi":"https://doi.org/10.1093/bioinformatics/btae331","pmid":"https://pubmed.ncbi.nlm.nih.gov/38876979"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btae331","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae331","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btae331/58238094/btae331.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/btae331/58238094/btae331.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5060194342","display_name":"Delaney K. Sullivan","orcid":"https://orcid.org/0000-0002-8359-6705"},"institutions":[{"id":"https://openalex.org/I122411786","display_name":"California Institute of Technology","ror":"https://ror.org/05dxps055","country_code":"US","type":"education","lineage":["https://openalex.org/I122411786"]},{"id":"https://openalex.org/I161318765","display_name":"University of California, Los Angeles","ror":"https://ror.org/046rm7j60","country_code":"US","type":"education","lineage":["https://openalex.org/I161318765"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Delaney K Sullivan","raw_affiliation_strings":["Division of Biology and Biological Engineering, California Institute of Technology , Pasadena, CA 91125, United States","UCLA-Caltech Medical Scientist Training Program, David Geffen School of Medicine, University of California, Los Angeles , Los Angeles, CA 90095, United States"],"affiliations":[{"raw_affiliation_string":"Division of Biology and Biological Engineering, California Institute of Technology , Pasadena, CA 91125, United States","institution_ids":["https://openalex.org/I122411786"]},{"raw_affiliation_string":"UCLA-Caltech Medical Scientist Training Program, David Geffen School of Medicine, University of California, Los Angeles , Los Angeles, CA 90095, United States","institution_ids":["https://openalex.org/I122411786","https://openalex.org/I161318765"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5020008219","display_name":"Lior Pachter","orcid":"https://orcid.org/0000-0002-9164-6231"},"institutions":[{"id":"https://openalex.org/I122411786","display_name":"California Institute of Technology","ror":"https://ror.org/05dxps055","country_code":"US","type":"education","lineage":["https://openalex.org/I122411786"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Lior Pachter","raw_affiliation_strings":["Department of Computing and Mathematical Sciences, California Institute of Technology , Pasadena, CA 91125, United States","Division of Biology and Biological Engineering, California Institute of Technology , Pasadena, CA 91125, United States"],"affiliations":[{"raw_affiliation_string":"Department of Computing and Mathematical Sciences, California Institute of Technology , Pasadena, CA 91125, United States","institution_ids":["https://openalex.org/I122411786"]},{"raw_affiliation_string":"Division of Biology and Biological Engineering, California Institute of Technology , Pasadena, CA 91125, United States","institution_ids":["https://openalex.org/I122411786"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5060194342"],"corresponding_institution_ids":["https://openalex.org/I122411786","https://openalex.org/I161318765"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":3.377,"has_fulltext":true,"cited_by_count":9,"citation_normalized_percentile":{"value":0.9345038,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":94,"max":98},"biblio":{"volume":"40","issue":"6","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10904","display_name":"Embedded Systems Design Techniques","score":0.944599986076355,"subfield":{"id":"https://openalex.org/subfields/1708","display_name":"Hardware and Architecture"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T10904","display_name":"Embedded Systems Design Techniques","score":0.944599986076355,"subfield":{"id":"https://openalex.org/subfields/1708","display_name":"Hardware and Architecture"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/parsing","display_name":"Parsing","score":0.8049657344818115},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7353212237358093},{"id":"https://openalex.org/keywords/interpretation","display_name":"Interpretation (philosophy)","score":0.7175679206848145},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.6152689456939697},{"id":"https://openalex.org/keywords/natural-language-processing","display_name":"Natural language processing","score":0.5352993607521057},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.42293494939804077}],"concepts":[{"id":"https://openalex.org/C186644900","wikidata":"https://www.wikidata.org/wiki/Q194152","display_name":"Parsing","level":2,"score":0.8049657344818115},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7353212237358093},{"id":"https://openalex.org/C527412718","wikidata":"https://www.wikidata.org/wiki/Q855395","display_name":"Interpretation (philosophy)","level":2,"score":0.7175679206848145},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.6152689456939697},{"id":"https://openalex.org/C204321447","wikidata":"https://www.wikidata.org/wiki/Q30642","display_name":"Natural language processing","level":1,"score":0.5352993607521057},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.42293494939804077}],"mesh":[{"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},{"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":"D015723","descriptor_name":"Gene Library","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015723","descriptor_name":"Gene Library","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015723","descriptor_name":"Gene Library","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015723","descriptor_name":"Gene Library","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015723","descriptor_name":"Gene Library","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015723","descriptor_name":"Gene Library","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015723","descriptor_name":"Gene Library","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},{"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},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btae331","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae331","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btae331/58238094/btae331.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:38876979","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/38876979","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:11193061","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11193061","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11193061/pdf/btae331.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/btae331","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae331","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btae331/58238094/btae331.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/G1123834119","display_name":null,"funder_award_id":"GM008042","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G1220489096","display_name":null,"funder_award_id":"GM0080","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G3497591915","display_name":null,"funder_award_id":"(NIH)","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G3984687944","display_name":null,"funder_award_id":"T32 GM008042","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G4359693134","display_name":null,"funder_award_id":"NIGMS","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G4667119938","display_name":null,"funder_award_id":"U19MH11483","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G4724093112","display_name":null,"funder_award_id":"T32 GM00804","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G4760074400","display_name":null,"funder_award_id":"U19MH114830","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G5320469269","display_name":null,"funder_award_id":"5UM1HG012077-02","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G6332831770","display_name":null,"funder_award_id":"T32 GM008","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G6345853531","display_name":null,"funder_award_id":"unknown","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G8499101873","display_name":null,"funder_award_id":"GM008042","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G8796907459","display_name":null,"funder_award_id":"T32 GM008042","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320309398","display_name":"California Institute of Technology","ror":"https://ror.org/05dxps055"},{"id":"https://openalex.org/F4320323298","display_name":"H\u00e1sk\u00f3li \u00cdslands","ror":"https://ror.org/01db6h964"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"}],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W4399711263.pdf"},"referenced_works_count":22,"referenced_works":["https://openalex.org/W2036897871","https://openalex.org/W2041677964","https://openalex.org/W2080958324","https://openalex.org/W2131271579","https://openalex.org/W2617452315","https://openalex.org/W2765281411","https://openalex.org/W2794083495","https://openalex.org/W2806123558","https://openalex.org/W2895795340","https://openalex.org/W2950519970","https://openalex.org/W2950856925","https://openalex.org/W2951912016","https://openalex.org/W2952109315","https://openalex.org/W2953170162","https://openalex.org/W3021060601","https://openalex.org/W3202223582","https://openalex.org/W4205374539","https://openalex.org/W4308921004","https://openalex.org/W4313546084","https://openalex.org/W4317360447","https://openalex.org/W4394735445","https://openalex.org/W4394759187"],"related_works":["https://openalex.org/W4313320911","https://openalex.org/W4327743144","https://openalex.org/W4245077728","https://openalex.org/W2607424049","https://openalex.org/W4390922876","https://openalex.org/W6643695","https://openalex.org/W4381248170","https://openalex.org/W3189621521","https://openalex.org/W2173794830","https://openalex.org/W3204019825"],"abstract_inverted_index":{"The":[0],"splitcode":[1],"program":[2],"is":[3],"available":[4],"at":[5],"http://github.com/pachterlab/splitcode.":[6]},"counts_by_year":[{"year":2025,"cited_by_count":3},{"year":2024,"cited_by_count":4},{"year":2023,"cited_by_count":2}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2024-06-16T00:00:00"}