{"id":"https://openalex.org/W1953491655","doi":"https://doi.org/10.1093/bioinformatics/btv337","title":"Assembling short reads from jumping libraries with large insert sizes","display_name":"Assembling short reads from jumping libraries with large insert sizes","publication_year":2015,"publication_date":"2015-06-03","ids":{"openalex":"https://openalex.org/W1953491655","doi":"https://doi.org/10.1093/bioinformatics/btv337","mag":"1953491655","pmid":"https://pubmed.ncbi.nlm.nih.gov/26040456"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btv337","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btv337","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/31/20/3262/49035885/bioinformatics_31_20_3262.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/31/20/3262/49035885/bioinformatics_31_20_3262.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5018788966","display_name":"Irina Vasilinetc","orcid":"https://orcid.org/0009-0004-3430-1263"},"institutions":[{"id":"https://openalex.org/I1328943360","display_name":"Saint Petersburg Academic University","ror":"https://ror.org/05ne3s142","country_code":"RU","type":"education","lineage":["https://openalex.org/I1313323035","https://openalex.org/I1328943360","https://openalex.org/I4210096333"]}],"countries":["RU"],"is_corresponding":true,"raw_author_name":"Irina Vasilinetc","raw_affiliation_strings":["1 Algorithmic Biology Lab, St. Petersburg Academic University 194021,"],"affiliations":[{"raw_affiliation_string":"1 Algorithmic Biology Lab, St. Petersburg Academic University 194021,","institution_ids":["https://openalex.org/I1328943360"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5020845045","display_name":"Andrey D. Prjibelski","orcid":"https://orcid.org/0000-0003-2816-4608"},"institutions":[{"id":"https://openalex.org/I172901346","display_name":"St Petersburg University","ror":"https://ror.org/023znxa73","country_code":"RU","type":"education","lineage":["https://openalex.org/I172901346"]},{"id":"https://openalex.org/I1328943360","display_name":"Saint Petersburg Academic University","ror":"https://ror.org/05ne3s142","country_code":"RU","type":"education","lineage":["https://openalex.org/I1313323035","https://openalex.org/I1328943360","https://openalex.org/I4210096333"]}],"countries":["RU"],"is_corresponding":false,"raw_author_name":"Andrey D. Prjibelski","raw_affiliation_strings":["1 Algorithmic Biology Lab, St. Petersburg Academic University 194021,","2 Center for Algorithmic Biotechnology, Institute of Translational Biomedicine, St.Petersburg State University, 199004,"],"affiliations":[{"raw_affiliation_string":"1 Algorithmic Biology Lab, St. Petersburg Academic University 194021,","institution_ids":["https://openalex.org/I1328943360"]},{"raw_affiliation_string":"2 Center for Algorithmic Biotechnology, Institute of Translational Biomedicine, St.Petersburg State University, 199004,","institution_ids":["https://openalex.org/I172901346"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5030895995","display_name":"Alexey Gurevich","orcid":"https://orcid.org/0000-0002-5855-3519"},"institutions":[{"id":"https://openalex.org/I172901346","display_name":"St Petersburg University","ror":"https://ror.org/023znxa73","country_code":"RU","type":"education","lineage":["https://openalex.org/I172901346"]},{"id":"https://openalex.org/I1328943360","display_name":"Saint Petersburg Academic University","ror":"https://ror.org/05ne3s142","country_code":"RU","type":"education","lineage":["https://openalex.org/I1313323035","https://openalex.org/I1328943360","https://openalex.org/I4210096333"]}],"countries":["RU"],"is_corresponding":false,"raw_author_name":"Alexey Gurevich","raw_affiliation_strings":["1 Algorithmic Biology Lab, St. Petersburg Academic University 194021,","2 Center for Algorithmic Biotechnology, Institute of Translational Biomedicine, St.Petersburg State University, 199004,"],"affiliations":[{"raw_affiliation_string":"1 Algorithmic Biology Lab, St. Petersburg Academic University 194021,","institution_ids":["https://openalex.org/I1328943360"]},{"raw_affiliation_string":"2 Center for Algorithmic Biotechnology, Institute of Translational Biomedicine, St.Petersburg State University, 199004,","institution_ids":["https://openalex.org/I172901346"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5082993256","display_name":"Anton Korobeynikov","orcid":"https://orcid.org/0000-0002-2937-9259"},"institutions":[{"id":"https://openalex.org/I1328943360","display_name":"Saint Petersburg Academic University","ror":"https://ror.org/05ne3s142","country_code":"RU","type":"education","lineage":["https://openalex.org/I1313323035","https://openalex.org/I1328943360","https://openalex.org/I4210096333"]},{"id":"https://openalex.org/I172901346","display_name":"St Petersburg University","ror":"https://ror.org/023znxa73","country_code":"RU","type":"education","lineage":["https://openalex.org/I172901346"]}],"countries":["RU"],"is_corresponding":false,"raw_author_name":"Anton Korobeynikov","raw_affiliation_strings":["1 Algorithmic Biology Lab, St. Petersburg Academic University 194021,","2 Center for Algorithmic Biotechnology, Institute of Translational Biomedicine, St.Petersburg State University, 199004,","3 Department of Mathematics and Mechanics, St. Petersburg State University, St. Petersburg, 198504, Russia and"],"affiliations":[{"raw_affiliation_string":"1 Algorithmic Biology Lab, St. Petersburg Academic University 194021,","institution_ids":["https://openalex.org/I1328943360"]},{"raw_affiliation_string":"2 Center for Algorithmic Biotechnology, Institute of Translational Biomedicine, St.Petersburg State University, 199004,","institution_ids":["https://openalex.org/I172901346"]},{"raw_affiliation_string":"3 Department of Mathematics and Mechanics, St. Petersburg State University, St. Petersburg, 198504, Russia and","institution_ids":["https://openalex.org/I172901346"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5027480961","display_name":"Pavel A. Pevzner","orcid":"https://orcid.org/0000-0002-0418-165X"},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California, San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]},{"id":"https://openalex.org/I172901346","display_name":"St Petersburg University","ror":"https://ror.org/023znxa73","country_code":"RU","type":"education","lineage":["https://openalex.org/I172901346"]}],"countries":["RU","US"],"is_corresponding":false,"raw_author_name":"Pavel A. Pevzner","raw_affiliation_strings":["2 Center for Algorithmic Biotechnology, Institute of Translational Biomedicine, St.Petersburg State University, 199004,","4 Department of Computer Science and Engineering, University of California, San Diego, CA 92093-0404, USA"],"affiliations":[{"raw_affiliation_string":"2 Center for Algorithmic Biotechnology, Institute of Translational Biomedicine, St.Petersburg State University, 199004,","institution_ids":["https://openalex.org/I172901346"]},{"raw_affiliation_string":"4 Department of Computer Science and Engineering, University of California, San Diego, CA 92093-0404, USA","institution_ids":["https://openalex.org/I36258959"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5018788966"],"corresponding_institution_ids":["https://openalex.org/I1328943360"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":1.9618,"has_fulltext":true,"cited_by_count":76,"citation_normalized_percentile":{"value":0.85941605,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":100},"biblio":{"volume":"31","issue":"20","first_page":"3262","last_page":"3268"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9998999834060669,"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":0.9998999834060669,"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/T11791","display_name":"Microbial Community Ecology and Physiology","score":0.9969000220298767,"subfield":{"id":"https://openalex.org/subfields/2303","display_name":"Ecology"},"field":{"id":"https://openalex.org/fields/23","display_name":"Environmental Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9918000102043152,"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/contig","display_name":"Contig","score":0.8301870822906494},{"id":"https://openalex.org/keywords/insert","display_name":"Insert (composites)","score":0.689551055431366},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6786544322967529},{"id":"https://openalex.org/keywords/sequence-assembly","display_name":"Sequence assembly","score":0.5354825258255005},{"id":"https://openalex.org/keywords/protocol","display_name":"Protocol (science)","score":0.48529452085494995},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.41743218898773193},{"id":"https://openalex.org/keywords/workflow","display_name":"Workflow","score":0.41643598675727844},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.21345144510269165},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.15240365266799927},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.12884452939033508},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.1104663610458374},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.08627817034721375}],"concepts":[{"id":"https://openalex.org/C59582021","wikidata":"https://www.wikidata.org/wiki/Q1128751","display_name":"Contig","level":4,"score":0.8301870822906494},{"id":"https://openalex.org/C2780098074","wikidata":"https://www.wikidata.org/wiki/Q6037362","display_name":"Insert (composites)","level":2,"score":0.689551055431366},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6786544322967529},{"id":"https://openalex.org/C18949551","wikidata":"https://www.wikidata.org/wiki/Q740578","display_name":"Sequence assembly","level":5,"score":0.5354825258255005},{"id":"https://openalex.org/C2780385302","wikidata":"https://www.wikidata.org/wiki/Q367158","display_name":"Protocol (science)","level":3,"score":0.48529452085494995},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.41743218898773193},{"id":"https://openalex.org/C177212765","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Workflow","level":2,"score":0.41643598675727844},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.21345144510269165},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.15240365266799927},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.12884452939033508},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.1104663610458374},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.08627817034721375},{"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/C142724271","wikidata":"https://www.wikidata.org/wiki/Q7208","display_name":"Pathology","level":1,"score":0.0},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.0},{"id":"https://openalex.org/C78519656","wikidata":"https://www.wikidata.org/wiki/Q101333","display_name":"Mechanical engineering","level":1,"score":0.0},{"id":"https://openalex.org/C204787440","wikidata":"https://www.wikidata.org/wiki/Q188504","display_name":"Alternative medicine","level":2,"score":0.0},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"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":"D015723","descriptor_name":"Gene Library","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":true},{"descriptor_ui":"D015723","descriptor_name":"Gene Library","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016680","descriptor_name":"Genome, Bacterial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016680","descriptor_name":"Genome, Bacterial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016680","descriptor_name":"Genome, Bacterial","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":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","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":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btv337","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btv337","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/31/20/3262/49035885/bioinformatics_31_20_3262.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:26040456","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/26040456","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:open-archive.highwire.org:bioinfo:31/20/3262","is_oa":false,"landing_page_url":"http://bioinformatics.oxfordjournals.org/cgi/content/short/31/20/3262","pdf_url":null,"source":{"id":"https://openalex.org/S4406923041","display_name":"HighWire Press Open Archive","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"TEXT"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btv337","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btv337","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/31/20/3262/49035885/bioinformatics_31_20_3262.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":[{"score":0.6000000238418579,"id":"https://metadata.un.org/sdg/9","display_name":"Industry, innovation and infrastructure"}],"awards":[{"id":"https://openalex.org/G2381697726","display_name":null,"funder_award_id":"4-50-00069","funder_id":"https://openalex.org/F4320324099","funder_display_name":"Russian Science Foundation"},{"id":"https://openalex.org/G2548059618","display_name":null,"funder_award_id":"14-50-00069","funder_id":"https://openalex.org/F4320324099","funder_display_name":"Russian Science Foundation"},{"id":"https://openalex.org/G7131804313","display_name":null,"funder_award_id":"14-50-","funder_id":"https://openalex.org/F4320324099","funder_display_name":"Russian Science Foundation"}],"funders":[{"id":"https://openalex.org/F4320324099","display_name":"Russian Science Foundation","ror":"https://ror.org/03y2gwe85"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W1953491655.pdf","grobid_xml":"https://content.openalex.org/works/W1953491655.grobid-xml"},"referenced_works_count":25,"referenced_works":["https://openalex.org/W129849869","https://openalex.org/W1966822396","https://openalex.org/W1970995855","https://openalex.org/W1983403167","https://openalex.org/W2004416209","https://openalex.org/W2022986961","https://openalex.org/W2033292629","https://openalex.org/W2097529842","https://openalex.org/W2107772251","https://openalex.org/W2113287691","https://openalex.org/W2120902911","https://openalex.org/W2127067063","https://openalex.org/W2129744420","https://openalex.org/W2130381109","https://openalex.org/W2134153749","https://openalex.org/W2136651963","https://openalex.org/W2141920662","https://openalex.org/W2142027180","https://openalex.org/W2151794156","https://openalex.org/W2160756584","https://openalex.org/W2160969485","https://openalex.org/W2161546116","https://openalex.org/W2171531867","https://openalex.org/W2171970660","https://openalex.org/W2905576637"],"related_works":["https://openalex.org/W2089480001","https://openalex.org/W3167837387","https://openalex.org/W2885619582","https://openalex.org/W2154683413","https://openalex.org/W54719527","https://openalex.org/W4250462852","https://openalex.org/W2944010518","https://openalex.org/W2993223466","https://openalex.org/W2105191441","https://openalex.org/W2763602215"],"abstract_inverted_index":{"Supplementary":[0],"data":[1],"are":[2],"available":[3],"at":[4],"Bioinformatics":[5],"online.":[6]},"counts_by_year":[{"year":2026,"cited_by_count":6},{"year":2025,"cited_by_count":11},{"year":2024,"cited_by_count":14},{"year":2023,"cited_by_count":5},{"year":2022,"cited_by_count":5},{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":16},{"year":2019,"cited_by_count":4},{"year":2018,"cited_by_count":4},{"year":2017,"cited_by_count":3},{"year":2016,"cited_by_count":4},{"year":2015,"cited_by_count":2}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2025-10-10T00:00:00"}
