{"id":"https://openalex.org/W3004333847","doi":"https://doi.org/10.1093/bioinformatics/btaa052","title":"iPAC: a genome-guided assembler of isoforms via phasing and combing paths","display_name":"iPAC: a genome-guided assembler of isoforms via phasing and combing paths","publication_year":2020,"publication_date":"2020-01-20","ids":{"openalex":"https://openalex.org/W3004333847","doi":"https://doi.org/10.1093/bioinformatics/btaa052","mag":"3004333847","pmid":"https://pubmed.ncbi.nlm.nih.gov/31985799"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btaa052","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaa052","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/36/9/2712/33181163/btaa052.pdf","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":null,"license_id":null,"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":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/36/9/2712/33181163/btaa052.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5101933930","display_name":"Ting Yu","orcid":"https://orcid.org/0000-0002-0073-9644"},"institutions":[{"id":"https://openalex.org/I154099455","display_name":"Shandong University","ror":"https://ror.org/0207yh398","country_code":"CN","type":"education","lineage":["https://openalex.org/I154099455"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Ting Yu","raw_affiliation_strings":["School of Mathematics , Shandong University, Jinan 250100, China"],"affiliations":[{"raw_affiliation_string":"School of Mathematics , Shandong University, Jinan 250100, China","institution_ids":["https://openalex.org/I154099455"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100621526","display_name":"Juntao Liu","orcid":"https://orcid.org/0000-0002-7296-906X"},"institutions":[{"id":"https://openalex.org/I154099455","display_name":"Shandong University","ror":"https://ror.org/0207yh398","country_code":"CN","type":"education","lineage":["https://openalex.org/I154099455"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Juntao Liu","raw_affiliation_strings":["School of Mathematics , Shandong University, Jinan 250100, China"],"affiliations":[{"raw_affiliation_string":"School of Mathematics , Shandong University, Jinan 250100, China","institution_ids":["https://openalex.org/I154099455"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100618900","display_name":"Xin Gao","orcid":"https://orcid.org/0000-0002-7108-3574"},"institutions":[{"id":"https://openalex.org/I71920554","display_name":"King Abdullah University of Science and Technology","ror":"https://ror.org/01q3tbs38","country_code":"SA","type":"education","lineage":["https://openalex.org/I71920554"]}],"countries":["SA"],"is_corresponding":true,"raw_author_name":"Xin Gao","raw_affiliation_strings":["Computer , Electrical and Mathematical Sciences and Engineering (CEMSE) Division, Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal 23955, Saudi Arabia"],"affiliations":[{"raw_affiliation_string":"Computer , Electrical and Mathematical Sciences and Engineering (CEMSE) Division, Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal 23955, Saudi Arabia","institution_ids":["https://openalex.org/I71920554"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100696687","display_name":"Guojun Li","orcid":"https://orcid.org/0000-0003-1581-5897"},"institutions":[{"id":"https://openalex.org/I154099455","display_name":"Shandong University","ror":"https://ror.org/0207yh398","country_code":"CN","type":"education","lineage":["https://openalex.org/I154099455"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Guojun Li","raw_affiliation_strings":["Research Center for Mathematics and Interdisciplinary Sciences , Shandong University, Qingdao 266237, China","School of Mathematics , Shandong University, Jinan 250100, China"],"affiliations":[{"raw_affiliation_string":"Research Center for Mathematics and Interdisciplinary Sciences , Shandong University, Qingdao 266237, China","institution_ids":["https://openalex.org/I154099455"]},{"raw_affiliation_string":"School of Mathematics , Shandong University, Jinan 250100, China","institution_ids":["https://openalex.org/I154099455"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5100618900","https://openalex.org/A5100696687"],"corresponding_institution_ids":["https://openalex.org/I154099455","https://openalex.org/I71920554"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.4143,"has_fulltext":false,"cited_by_count":5,"citation_normalized_percentile":{"value":0.58423096,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":96},"biblio":{"volume":"36","issue":"9","first_page":"2712","last_page":"2717"},"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/T11482","display_name":"RNA modifications and cancer","score":0.9990000128746033,"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":0.9983999729156494,"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/combing","display_name":"Combing","score":0.8709810972213745},{"id":"https://openalex.org/keywords/phaser","display_name":"Phaser","score":0.720396876335144},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6047577857971191},{"id":"https://openalex.org/keywords/focus","display_name":"Focus (optics)","score":0.5821020603179932},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.5468092560768127},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.4975931942462921},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.49339476227760315},{"id":"https://openalex.org/keywords/sequence-assembly","display_name":"Sequence assembly","score":0.4432210326194763},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.3203412890434265},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.2851716876029968},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2462981641292572},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.24614045023918152},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.135567307472229},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.11270681023597717},{"id":"https://openalex.org/keywords/materials-science","display_name":"Materials science","score":0.0792161226272583},{"id":"https://openalex.org/keywords/transcriptome","display_name":"Transcriptome","score":0.07038533687591553}],"concepts":[{"id":"https://openalex.org/C2778952367","wikidata":"https://www.wikidata.org/wiki/Q3491532","display_name":"Combing","level":2,"score":0.8709810972213745},{"id":"https://openalex.org/C135393689","wikidata":"https://www.wikidata.org/wiki/Q1551588","display_name":"Phaser","level":2,"score":0.720396876335144},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6047577857971191},{"id":"https://openalex.org/C192209626","wikidata":"https://www.wikidata.org/wiki/Q190909","display_name":"Focus (optics)","level":2,"score":0.5821020603179932},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.5468092560768127},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.4975931942462921},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.49339476227760315},{"id":"https://openalex.org/C18949551","wikidata":"https://www.wikidata.org/wiki/Q740578","display_name":"Sequence assembly","level":5,"score":0.4432210326194763},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.3203412890434265},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.2851716876029968},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2462981641292572},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.24614045023918152},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.135567307472229},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.11270681023597717},{"id":"https://openalex.org/C192562407","wikidata":"https://www.wikidata.org/wiki/Q228736","display_name":"Materials science","level":0,"score":0.0792161226272583},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.07038533687591553},{"id":"https://openalex.org/C120665830","wikidata":"https://www.wikidata.org/wiki/Q14620","display_name":"Optics","level":1,"score":0.0},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.0},{"id":"https://openalex.org/C159985019","wikidata":"https://www.wikidata.org/wiki/Q181790","display_name":"Composite material","level":1,"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":"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":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020033","descriptor_name":"Protein Isoforms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020033","descriptor_name":"Protein Isoforms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020033","descriptor_name":"Protein Isoforms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btaa052","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaa052","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/36/9/2712/33181163/btaa052.pdf","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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:31985799","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/31985799","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:repository.kaust.edu.sa:10754/661333","is_oa":false,"landing_page_url":"http://hdl.handle.net/10754/661333","pdf_url":null,"source":{"id":"https://openalex.org/S4306401596","display_name":"King Abdullah University of Science and Technology Repository (King Abdullah University of Science and Technology)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I71920554","host_organization_name":"King Abdullah University of Science and Technology","host_organization_lineage":["https://openalex.org/I71920554"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Article"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btaa052","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaa052","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/36/9/2712/33181163/btaa052.pdf","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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G2185879301","display_name":null,"funder_award_id":"FCC/1/1976-26-01","funder_id":"https://openalex.org/F4320322320","funder_display_name":"King Abdullah University of Science and Technology"},{"id":"https://openalex.org/G2702908835","display_name":null,"funder_award_id":"FCC/1/1976-23-01","funder_id":"https://openalex.org/F4320322320","funder_display_name":"King Abdullah University of Science and Technology"},{"id":"https://openalex.org/G3220252743","display_name":null,"funder_award_id":"11931008","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G3847064998","display_name":null,"funder_award_id":"FCS/1/4102-02-01","funder_id":"https://openalex.org/F4320322320","funder_display_name":"King Abdullah University of Science and Technology"},{"id":"https://openalex.org/G3956605221","display_name":null,"funder_award_id":"61877064","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G6225982113","display_name":null,"funder_award_id":"61801265","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G7695499337","display_name":null,"funder_award_id":"ZR2018PA001","funder_id":"https://openalex.org/F4320324174","funder_display_name":"Natural Science Foundation of Shandong Province"},{"id":"https://openalex.org/G7739191700","display_name":null,"funder_award_id":"FCC/1/1976-25-01","funder_id":"https://openalex.org/F4320322320","funder_display_name":"King Abdullah University of Science and Technology"},{"id":"https://openalex.org/G7877521841","display_name":null,"funder_award_id":"31571354","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G8069041701","display_name":null,"funder_award_id":"FCC/1/1976-18-01","funder_id":"https://openalex.org/F4320322320","funder_display_name":"King Abdullah University of Science and Technology"},{"id":"https://openalex.org/G8450993626","display_name":null,"funder_award_id":"URF/1/4098-01-01","funder_id":"https://openalex.org/F4320322320","funder_display_name":"King Abdullah University of Science and Technology"},{"id":"https://openalex.org/G8467640970","display_name":null,"funder_award_id":"61771009","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320322320","display_name":"King Abdullah University of Science and Technology","ror":"https://ror.org/01q3tbs38"},{"id":"https://openalex.org/F4320324174","display_name":"Natural Science Foundation of Shandong Province","ror":null}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3004333847.pdf","grobid_xml":"https://content.openalex.org/works/W3004333847.grobid-xml"},"referenced_works_count":38,"referenced_works":["https://openalex.org/W1973996769","https://openalex.org/W1981509058","https://openalex.org/W1988245212","https://openalex.org/W2000875411","https://openalex.org/W2003605043","https://openalex.org/W2004419591","https://openalex.org/W2038230536","https://openalex.org/W2048120844","https://openalex.org/W2053057991","https://openalex.org/W2096441981","https://openalex.org/W2097065948","https://openalex.org/W2102278945","https://openalex.org/W2102813686","https://openalex.org/W2104005232","https://openalex.org/W2105371278","https://openalex.org/W2109936378","https://openalex.org/W2110392562","https://openalex.org/W2112491476","https://openalex.org/W2117688129","https://openalex.org/W2118526609","https://openalex.org/W2121211805","https://openalex.org/W2122789575","https://openalex.org/W2126419817","https://openalex.org/W2126766730","https://openalex.org/W2135592053","https://openalex.org/W2136132915","https://openalex.org/W2140729960","https://openalex.org/W2141458291","https://openalex.org/W2155804510","https://openalex.org/W2166558929","https://openalex.org/W2169456326","https://openalex.org/W2255292617","https://openalex.org/W2276982311","https://openalex.org/W2298558585","https://openalex.org/W2323326409","https://openalex.org/W2519019984","https://openalex.org/W2768985026","https://openalex.org/W2947275858"],"related_works":["https://openalex.org/W2382950503","https://openalex.org/W2374316087","https://openalex.org/W2351264995","https://openalex.org/W2359486762","https://openalex.org/W2374605473","https://openalex.org/W2366644843","https://openalex.org/W2010977033","https://openalex.org/W2794386548","https://openalex.org/W4381279187","https://openalex.org/W1841715584"],"abstract_inverted_index":{"Supplementary":[0],"data":[1],"are":[2],"available":[3],"at":[4],"Bioinformatics":[5],"online.":[6]},"counts_by_year":[{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":2}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
