{"id":"https://openalex.org/W4220754011","doi":"https://doi.org/10.1038/s43588-022-00216-1","title":"Accurate assembly of multi-end RNA-seq data with Scallop2","display_name":"Accurate assembly of multi-end RNA-seq data with Scallop2","publication_year":2022,"publication_date":"2022-03-28","ids":{"openalex":"https://openalex.org/W4220754011","doi":"https://doi.org/10.1038/s43588-022-00216-1","pmid":"https://pubmed.ncbi.nlm.nih.gov/36713932"},"language":"en","primary_location":{"id":"doi:10.1038/s43588-022-00216-1","is_oa":false,"landing_page_url":"https://doi.org/10.1038/s43588-022-00216-1","pdf_url":null,"source":{"id":"https://openalex.org/S4210228084","display_name":"Nature Computational Science","issn_l":"2662-8457","issn":["2662-8457"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319908","host_organization_name":"Nature Portfolio","host_organization_lineage":["https://openalex.org/P4310319908","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Nature Portfolio","Springer Nature"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nature Computational Science","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/9879047","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5101815502","display_name":"Qimin Zhang","orcid":"https://orcid.org/0000-0002-5990-1765"},"institutions":[{"id":"https://openalex.org/I130769515","display_name":"Pennsylvania State University","ror":"https://ror.org/04p491231","country_code":"US","type":"education","lineage":["https://openalex.org/I130769515"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Qimin Zhang","raw_affiliation_strings":["Department of Computer Science and Engineering, School of Electrical Engineering and Computer Science, The Pennsylvania State University","Department of Computer Science and Engineering, School of Electrical Engineering and Computer Science, The Pennsylvania State University, Pennsylvania, PA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering, School of Electrical Engineering and Computer Science, The Pennsylvania State University","institution_ids":["https://openalex.org/I130769515"]},{"raw_affiliation_string":"Department of Computer Science and Engineering, School of Electrical Engineering and Computer Science, The Pennsylvania State University, Pennsylvania, PA, USA","institution_ids":["https://openalex.org/I130769515"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101883296","display_name":"Qian Shi","orcid":"https://orcid.org/0009-0004-2925-0481"},"institutions":[{"id":"https://openalex.org/I130769515","display_name":"Pennsylvania State University","ror":"https://ror.org/04p491231","country_code":"US","type":"education","lineage":["https://openalex.org/I130769515"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Qian Shi","raw_affiliation_strings":["Department of Computer Science and Engineering, School of Electrical Engineering and Computer Science, The Pennsylvania State University","Department of Computer Science and Engineering, School of Electrical Engineering and Computer Science, The Pennsylvania State University, Pennsylvania, PA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering, School of Electrical Engineering and Computer Science, The Pennsylvania State University","institution_ids":["https://openalex.org/I130769515"]},{"raw_affiliation_string":"Department of Computer Science and Engineering, School of Electrical Engineering and Computer Science, The Pennsylvania State University, Pennsylvania, PA, USA","institution_ids":["https://openalex.org/I130769515"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5052979637","display_name":"Mingfu Shao","orcid":"https://orcid.org/0000-0001-6112-5139"},"institutions":[{"id":"https://openalex.org/I130769515","display_name":"Pennsylvania State University","ror":"https://ror.org/04p491231","country_code":"US","type":"education","lineage":["https://openalex.org/I130769515"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Mingfu Shao","raw_affiliation_strings":["Department of Computer Science and Engineering, School of Electrical Engineering and Computer Science, The Pennsylvania State University","Huck Institutes of the Life Sciences, The Pennsylvania State University","Department of Computer Science and Engineering, School of Electrical Engineering and Computer Science, The Pennsylvania State University, Pennsylvania, PA, USA"],"raw_orcid":"https://orcid.org/0000-0001-6112-5139","affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering, School of Electrical Engineering and Computer Science, The Pennsylvania State University","institution_ids":["https://openalex.org/I130769515"]},{"raw_affiliation_string":"Huck Institutes of the Life Sciences, The Pennsylvania State University","institution_ids":["https://openalex.org/I130769515"]},{"raw_affiliation_string":"Department of Computer Science and Engineering, School of Electrical Engineering and Computer Science, The Pennsylvania State University, Pennsylvania, PA, USA","institution_ids":["https://openalex.org/I130769515"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5052979637"],"corresponding_institution_ids":["https://openalex.org/I130769515"],"apc_list":{"value":12690,"currency":"USD","value_usd":12690},"apc_paid":null,"fwci":2.2017,"has_fulltext":false,"cited_by_count":32,"citation_normalized_percentile":{"value":0.88612392,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"2","issue":"3","first_page":"148","last_page":"152"},"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/T11970","display_name":"Molecular Biology Techniques and Applications","score":0.9980999827384949,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9980000257492065,"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/splice","display_name":"splice","score":0.7404548525810242},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6201843023300171},{"id":"https://openalex.org/keywords/de-bruijn-graph","display_name":"De Bruijn graph","score":0.5600712299346924},{"id":"https://openalex.org/keywords/barcode","display_name":"Barcode","score":0.5153836011886597},{"id":"https://openalex.org/keywords/leverage","display_name":"Leverage (statistics)","score":0.4918225109577179},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.43469563126564026},{"id":"https://openalex.org/keywords/end-to-end-principle","display_name":"End-to-end principle","score":0.4325101971626282},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.4139770269393921},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.39982354640960693},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.37430232763290405},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3441433310508728},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.28781571984291077},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.20873519778251648},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.16161590814590454},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.15099379420280457},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.13037827610969543}],"concepts":[{"id":"https://openalex.org/C2780989783","wikidata":"https://www.wikidata.org/wiki/Q7578557","display_name":"splice","level":3,"score":0.7404548525810242},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6201843023300171},{"id":"https://openalex.org/C20218877","wikidata":"https://www.wikidata.org/wiki/Q3066095","display_name":"De Bruijn graph","level":3,"score":0.5600712299346924},{"id":"https://openalex.org/C2776841711","wikidata":"https://www.wikidata.org/wiki/Q856","display_name":"Barcode","level":2,"score":0.5153836011886597},{"id":"https://openalex.org/C153083717","wikidata":"https://www.wikidata.org/wiki/Q6535263","display_name":"Leverage (statistics)","level":2,"score":0.4918225109577179},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.43469563126564026},{"id":"https://openalex.org/C74296488","wikidata":"https://www.wikidata.org/wiki/Q2527392","display_name":"End-to-end principle","level":2,"score":0.4325101971626282},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.4139770269393921},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.39982354640960693},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.37430232763290405},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3441433310508728},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.28781571984291077},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.20873519778251648},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.16161590814590454},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.15099379420280457},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.13037827610969543},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.1038/s43588-022-00216-1","is_oa":false,"landing_page_url":"https://doi.org/10.1038/s43588-022-00216-1","pdf_url":null,"source":{"id":"https://openalex.org/S4210228084","display_name":"Nature Computational Science","issn_l":"2662-8457","issn":["2662-8457"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319908","host_organization_name":"Nature Portfolio","host_organization_lineage":["https://openalex.org/P4310319908","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Nature Portfolio","Springer Nature"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nature Computational Science","raw_type":"journal-article"},{"id":"pmid:36713932","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/36713932","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":"Nature computational science","raw_type":"Journal Article"},{"id":"pmh:oai:pubmedcentral.nih.gov:9879047","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/9879047","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Nat Comput Sci","raw_type":"Text"}],"best_oa_location":{"id":"pmh:oai:pubmedcentral.nih.gov:9879047","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/9879047","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Nat Comput Sci","raw_type":"Text"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1219243184","display_name":"Computational Methods for Assembling Multiple RNA-seq Samples","funder_award_id":"5r01hg011065-03","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G3280907188","display_name":null,"funder_award_id":"R01HG011065","funder_id":"https://openalex.org/F4320337348","funder_display_name":"National Human Genome Research Institute"},{"id":"https://openalex.org/G5836720286","display_name":null,"funder_award_id":"R01 GM122935","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G6827177365","display_name":"BBSRC-NSF/BIO: IIBR Informatics: Collaborative Research: Inference of isoform-level regulatory infrastructures with studies in steroid-producing cells","funder_award_id":"2019797","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G8882735600","display_name":"Computational Methods for Assembling Multiple RNA-seq Samples","funder_award_id":"5r01hg011065-04","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G8957502139","display_name":null,"funder_award_id":"R01HG011065","funder_id":"https://openalex.org/F4320306085","funder_display_name":"U.S. Department of Health and Human Services"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320306085","display_name":"U.S. Department of Health and Human Services","ror":"https://ror.org/033jnv181"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337348","display_name":"National Human Genome Research Institute","ror":"https://ror.org/00baak391"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":24,"referenced_works":["https://openalex.org/W2000875411","https://openalex.org/W2068767807","https://openalex.org/W2102278945","https://openalex.org/W2104005232","https://openalex.org/W2126766730","https://openalex.org/W2140729960","https://openalex.org/W2141458291","https://openalex.org/W2169456326","https://openalex.org/W2259938310","https://openalex.org/W2298558585","https://openalex.org/W2519019984","https://openalex.org/W2768985026","https://openalex.org/W2773298966","https://openalex.org/W2995527562","https://openalex.org/W2995642161","https://openalex.org/W3004548325","https://openalex.org/W3007172120","https://openalex.org/W3021060601","https://openalex.org/W3022572641","https://openalex.org/W3029935300","https://openalex.org/W4233582454","https://openalex.org/W6927131790","https://openalex.org/W6968973568","https://openalex.org/W6969071160"],"related_works":["https://openalex.org/W2256570403","https://openalex.org/W2074156223","https://openalex.org/W2103246366","https://openalex.org/W2901653204","https://openalex.org/W2102526470","https://openalex.org/W4378447789","https://openalex.org/W2613659923","https://openalex.org/W3207557903","https://openalex.org/W2612311319","https://openalex.org/W2951065104"],"abstract_inverted_index":null,"counts_by_year":[{"year":2026,"cited_by_count":4},{"year":2025,"cited_by_count":13},{"year":2024,"cited_by_count":10},{"year":2023,"cited_by_count":4},{"year":2022,"cited_by_count":1}],"updated_date":"2026-08-21T09:56:20.448147","created_date":"2025-10-10T00:00:00"}
