{"id":"https://openalex.org/W2276982311","doi":"https://doi.org/10.1371/journal.pcbi.1004772","title":"BinPacker: Packing-Based De Novo Transcriptome Assembly from RNA-seq Data","display_name":"BinPacker: Packing-Based De Novo Transcriptome Assembly from RNA-seq Data","publication_year":2016,"publication_date":"2016-02-19","ids":{"openalex":"https://openalex.org/W2276982311","doi":"https://doi.org/10.1371/journal.pcbi.1004772","mag":"2276982311","pmid":"https://pubmed.ncbi.nlm.nih.gov/26894997"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1004772","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1004772","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1004772&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1004772&type=printable","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","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, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Mathematics, Shandong University, Jinan, China","institution_ids":["https://openalex.org/I154099455"]}]},{"author_position":"middle","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":["School of Mathematics, Shandong University, Jinan, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Mathematics, Shandong University, Jinan, China","institution_ids":["https://openalex.org/I154099455"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5042441651","display_name":"Zheng Chang","orcid":"https://orcid.org/0000-0003-3766-820X"},"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":"Zheng Chang","raw_affiliation_strings":["School of Mathematics, Shandong University, Jinan, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Mathematics, Shandong University, Jinan, China","institution_ids":["https://openalex.org/I154099455"]}]},{"author_position":"middle","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, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Mathematics, Shandong University, Jinan, China","institution_ids":["https://openalex.org/I154099455"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5017344694","display_name":"Bingqiang Liu","orcid":"https://orcid.org/0000-0002-5734-1135"},"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":"Bingqiang Liu","raw_affiliation_strings":["School of Mathematics, Shandong University, Jinan, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Mathematics, Shandong University, Jinan, China","institution_ids":["https://openalex.org/I154099455"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5068277957","display_name":"Rick McMullen","orcid":null},"institutions":[{"id":"https://openalex.org/I78715868","display_name":"University of Arkansas at Fayetteville","ror":"https://ror.org/05jbt9m15","country_code":"US","type":"education","lineage":["https://openalex.org/I78715868"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Rick McMullen","raw_affiliation_strings":["High Performance Computing Center, University of Arkansas, Fayetteville, Arkansas, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"High Performance Computing Center, University of Arkansas, Fayetteville, Arkansas, United States of America","institution_ids":["https://openalex.org/I78715868"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5032446100","display_name":"Pengyin Chen","orcid":"https://orcid.org/0000-0002-2663-7734"},"institutions":[{"id":"https://openalex.org/I78715868","display_name":"University of Arkansas at Fayetteville","ror":"https://ror.org/05jbt9m15","country_code":"US","type":"education","lineage":["https://openalex.org/I78715868"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Pengyin Chen","raw_affiliation_strings":["Crop, Soil, and Environmental Sciences, University of Arkansas, Fayetteville, Arkansas, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Crop, Soil, and Environmental Sciences, University of Arkansas, Fayetteville, Arkansas, United States of America","institution_ids":["https://openalex.org/I78715868"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5021456840","display_name":"Xiuzhen Huang","orcid":"https://orcid.org/0000-0003-0498-3131"},"institutions":[{"id":"https://openalex.org/I125956826","display_name":"Arkansas State University","ror":"https://ror.org/006pyvd89","country_code":"US","type":"education","lineage":["https://openalex.org/I125956826"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Xiuzhen Huang","raw_affiliation_strings":["Department of Computer Science, Arkansas State University, Jonesboro, Arkansas, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Arkansas State University, Jonesboro, Arkansas, United States of America","institution_ids":["https://openalex.org/I125956826"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5021456840","https://openalex.org/A5100696687"],"corresponding_institution_ids":["https://openalex.org/I125956826","https://openalex.org/I154099455"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":13.1562,"has_fulltext":true,"cited_by_count":140,"citation_normalized_percentile":{"value":0.99092474,"is_in_top_1_percent":true,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":94,"max":100},"biblio":{"volume":"12","issue":"2","first_page":"e1004772","last_page":"e1004772"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10604","display_name":"RNA Research and Splicing","score":0.9994999766349792,"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/T10604","display_name":"RNA Research and Splicing","score":0.9994999766349792,"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":0.9994000196456909,"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":0.9993000030517578,"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":0.6134536862373352},{"id":"https://openalex.org/keywords/rna-splicing","display_name":"RNA splicing","score":0.5658285617828369},{"id":"https://openalex.org/keywords/rna-seq","display_name":"RNA-Seq","score":0.5351788401603699},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5223259329795837},{"id":"https://openalex.org/keywords/transcriptome","display_name":"Transcriptome","score":0.5155789256095886},{"id":"https://openalex.org/keywords/mit-license","display_name":"MIT License","score":0.4997141361236572},{"id":"https://openalex.org/keywords/de-novo-transcriptome-assembly","display_name":"De novo transcriptome assembly","score":0.4977457821369171},{"id":"https://openalex.org/keywords/download","display_name":"Download","score":0.4328421354293823},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.4223422408103943},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.4173658788204193},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.373513787984848},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.3566770553588867},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.3491969704627991},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.32586362957954407},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.26154786348342896},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.23532336950302124},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.21350285410881042},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.2009533941745758},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.12391003966331482},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.09169286489486694}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6134536862373352},{"id":"https://openalex.org/C54458228","wikidata":"https://www.wikidata.org/wiki/Q237218","display_name":"RNA splicing","level":4,"score":0.5658285617828369},{"id":"https://openalex.org/C107397762","wikidata":"https://www.wikidata.org/wiki/Q2542347","display_name":"RNA-Seq","level":5,"score":0.5351788401603699},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5223259329795837},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.5155789256095886},{"id":"https://openalex.org/C174183944","wikidata":"https://www.wikidata.org/wiki/Q334661","display_name":"MIT License","level":3,"score":0.4997141361236572},{"id":"https://openalex.org/C50489715","wikidata":"https://www.wikidata.org/wiki/Q5244960","display_name":"De novo transcriptome assembly","level":5,"score":0.4977457821369171},{"id":"https://openalex.org/C2780154274","wikidata":"https://www.wikidata.org/wiki/Q7126717","display_name":"Download","level":2,"score":0.4328421354293823},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.4223422408103943},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.4173658788204193},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.373513787984848},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.3566770553588867},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.3491969704627991},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.32586362957954407},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.26154786348342896},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.23532336950302124},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.21350285410881042},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.2009533941745758},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.12391003966331482},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.09169286489486694},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"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":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004285","descriptor_name":"Dogs","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004285","descriptor_name":"Dogs","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004285","descriptor_name":"Dogs","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012333","descriptor_name":"RNA, Messenger","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012333","descriptor_name":"RNA, Messenger","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012333","descriptor_name":"RNA, Messenger","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012333","descriptor_name":"RNA, Messenger","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D012333","descriptor_name":"RNA, Messenger","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D012333","descriptor_name":"RNA, Messenger","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","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":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","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":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1371/journal.pcbi.1004772","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1004772","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1004772&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},{"id":"pmid:26894997","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/26894997","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":"PLoS computational biology","raw_type":null},{"id":"pmh:oai:europepmc.org:3752587","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4760927","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":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":null,"raw_type":"Text"},{"id":"pmh:oai:doaj.org/article:c409da98974e446fb1b062bd88e829f0","is_oa":true,"landing_page_url":"https://doaj.org/article/c409da98974e446fb1b062bd88e829f0","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Computational Biology, Vol 12, Iss 2, p e1004772 (2016)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1004772","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1004772","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1004772&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/17","display_name":"Partnerships for the goals","score":0.46000000834465027}],"awards":[{"id":"https://openalex.org/G1300799131","display_name":null,"funder_award_id":"P20RR016460","funder_id":"https://openalex.org/F4320337375","funder_display_name":"National Center for Research Resources"},{"id":"https://openalex.org/G2683385012","display_name":null,"funder_award_id":"P20GM103429","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G2940576611","display_name":"\u4ec5\u57fa\u4e8eRNA-Seq\u6570\u636e\u62fc\u88c5\u53ef\u53d8\u526a\u63a5\u8f6c\u5f55\u7ec4\u7684\u8ba1\u7b97\u65b9\u6cd5\u7814\u7a76","funder_award_id":"61272016","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G3040862546","display_name":"\u57fa\u4e8e\u9ad8\u901a\u91cfRNA-seq\u6570\u636e\u8f6c\u5f55\u7ec4\u62fc\u63a5\u7684\u5173\u952e\u6280\u672f\u4e0e\u7b97\u6cd5\u7814\u7a76","funder_award_id":"61432010","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G3877602480","display_name":"III: EAGER: Novel algorithms for de novo transcriptome assembly using RNA-seq data and for metagenome assembly","funder_award_id":"1553680","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G7302575904","display_name":null,"funder_award_id":"P20 GM103429","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"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/G8415158154","display_name":null,"funder_award_id":"P20 RR016460","funder_id":"https://openalex.org/F4320337375","funder_display_name":"National Center for Research Resources"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"},{"id":"https://openalex.org/F4320337375","display_name":"National Center for Research Resources","ror":"https://ror.org/04pw6fb54"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2276982311.pdf","grobid_xml":"https://content.openalex.org/works/W2276982311.grobid-xml"},"referenced_works_count":25,"referenced_works":["https://openalex.org/W1966822396","https://openalex.org/W1971899779","https://openalex.org/W2000875411","https://openalex.org/W2003605043","https://openalex.org/W2048120844","https://openalex.org/W2053057991","https://openalex.org/W2063123613","https://openalex.org/W2104005232","https://openalex.org/W2105371278","https://openalex.org/W2109936378","https://openalex.org/W2110392562","https://openalex.org/W2112888168","https://openalex.org/W2118526609","https://openalex.org/W2126419817","https://openalex.org/W2127963635","https://openalex.org/W2136145671","https://openalex.org/W2141458291","https://openalex.org/W2143447881","https://openalex.org/W2151081606","https://openalex.org/W2155804510","https://openalex.org/W2155839887","https://openalex.org/W2156841387","https://openalex.org/W2165064122","https://openalex.org/W2166558929","https://openalex.org/W4230266413"],"related_works":["https://openalex.org/W4317780692","https://openalex.org/W4394359997","https://openalex.org/W4252248862","https://openalex.org/W1021674602","https://openalex.org/W4362511652","https://openalex.org/W4362511917","https://openalex.org/W4244502392","https://openalex.org/W4246813243","https://openalex.org/W4362511922","https://openalex.org/W2268123450"],"abstract_inverted_index":{"High-throughput":[0],"RNA-seq":[1,31,129],"technology":[2],"has":[3,90],"provided":[4],"an":[5,19],"unprecedented":[6],"opportunity":[7],"to":[8,25],"reveal":[9],"the":[10,52,88,101,135,142,153,171,182],"very":[11],"complex":[12],"structures":[13],"of":[14,29,60,62,69,77,170],"transcriptomes.":[15],"However,":[16],"it":[17,131,159],"is":[18,174,184,191],"important":[20],"and":[21,127,145,163,181],"highly":[22],"challenging":[23],"task":[24],"assemble":[26],"vast":[27],"amounts":[28],"short":[30],"reads":[32,107],"into":[33,87],"transcriptomes":[34],"with":[35,64],"alternative":[36],"splicing":[37,96,120],"isoforms.":[38],"In":[39,157],"this":[40],"study,":[41],"we":[42],"present":[43],"a":[44,58,75,113,119],"novel":[45],"de":[46,137],"novo":[47,138],"assembler,":[48],"BinPacker,":[49],"by":[50,73,111],"modeling":[51],"transcriptome":[53],"assembly":[54],"problem":[55],"as":[56],"tracking":[57],"set":[59],"trajectories":[61],"items":[63],"their":[65,70],"sizes":[66],"representing":[67],"coverage":[68,85],"corresponding":[71],"isoforms":[72],"solving":[74],"series":[76],"bin-packing":[78],"problems.":[79],"This":[80],"approach,":[81],"which":[82],"subtly":[83],"integrates":[84],"information":[86],"procedure,":[89],"two":[91],"exclusive":[92],"features:":[93],"1)":[94],"only":[95],"junctions":[97],"are":[98,108],"involved":[99],"in":[100],"assembling":[102],"procedure;":[103],"2)":[104],"massive":[105],"pell-mell":[106],"assembled":[109],"seemingly":[110],"moving":[112],"comb":[114],"along":[115],"junction":[116],"edges":[117],"on":[118,124,140,152],"graph.":[121],"Being":[122],"tested":[123,143],"both":[125],"real":[126,154],"simulated":[128],"datasets,":[130,144],"outperforms":[132,147],"almost":[133],"all":[134,141],"existing":[136],"assemblers":[139,151],"even":[146],"those":[148],"ab":[149],"initio":[150],"dog":[155],"dataset.":[156],"addition,":[158],"runs":[160],"substantially":[161],"faster":[162],"requires":[164],"less":[165],"memory":[166],"space":[167],"than":[168],"most":[169],"assemblers.":[172],"BinPacker":[173],"published":[175],"under":[176],"GNU":[177],"GENERAL":[178],"PUBLIC":[179],"LICENSE":[180],"source":[183],"available":[185,192],"from:":[186,193],"http://sourceforge.net/projects/transcriptomeassembly/files/BinPacker_1.0.tar.gz/download.":[187],"Quick":[188],"installation":[189],"version":[190],"http://sourceforge.net/projects/transcriptomeassembly/files/BinPacker_binary.tar.gz/download.":[194]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":3},{"year":2024,"cited_by_count":9},{"year":2023,"cited_by_count":5},{"year":2022,"cited_by_count":14},{"year":2021,"cited_by_count":12},{"year":2020,"cited_by_count":19},{"year":2019,"cited_by_count":24},{"year":2018,"cited_by_count":25},{"year":2017,"cited_by_count":21},{"year":2016,"cited_by_count":7}],"updated_date":"2026-01-13T01:12:25.745995","created_date":"2025-10-10T00:00:00"}
