{"id":"https://openalex.org/W2890720538","doi":"https://doi.org/10.1093/bioinformatics/bty773","title":"SCOP: a novel scaffolding algorithm based on contig classification and optimization","display_name":"SCOP: a novel scaffolding algorithm based on contig classification and optimization","publication_year":2018,"publication_date":"2018-09-01","ids":{"openalex":"https://openalex.org/W2890720538","doi":"https://doi.org/10.1093/bioinformatics/bty773","mag":"2890720538","pmid":"https://pubmed.ncbi.nlm.nih.gov/30184046"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/bty773","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty773","pdf_url":null,"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":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100719013","display_name":"Min Li","orcid":"https://orcid.org/0000-0002-0188-1394"},"institutions":[{"id":"https://openalex.org/I139660479","display_name":"Central South University","ror":"https://ror.org/00f1zfq44","country_code":"CN","type":"education","lineage":["https://openalex.org/I139660479"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Min Li","raw_affiliation_strings":["Department of computer science, School of Information Science and Engineering, Central South University, Changsha, China"],"affiliations":[{"raw_affiliation_string":"Department of computer science, School of Information Science and Engineering, Central South University, Changsha, China","institution_ids":["https://openalex.org/I139660479"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5103788844","display_name":"Li Tang","orcid":null},"institutions":[{"id":"https://openalex.org/I139660479","display_name":"Central South University","ror":"https://ror.org/00f1zfq44","country_code":"CN","type":"education","lineage":["https://openalex.org/I139660479"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Li Tang","raw_affiliation_strings":["Department of computer science, School of Information Science and Engineering, Central South University, Changsha, China"],"affiliations":[{"raw_affiliation_string":"Department of computer science, School of Information Science and Engineering, Central South University, Changsha, China","institution_ids":["https://openalex.org/I139660479"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5091157395","display_name":"Fang\u2010Xiang Wu","orcid":"https://orcid.org/0000-0002-4593-9332"},"institutions":[{"id":"https://openalex.org/I32625721","display_name":"University of Saskatchewan","ror":"https://ror.org/010x8gc63","country_code":"CA","type":"education","lineage":["https://openalex.org/I32625721"]},{"id":"https://openalex.org/I139660479","display_name":"Central South University","ror":"https://ror.org/00f1zfq44","country_code":"CN","type":"education","lineage":["https://openalex.org/I139660479"]}],"countries":["CA","CN"],"is_corresponding":false,"raw_author_name":"Fang-Xiang Wu","raw_affiliation_strings":["Department of computer science, School of Information Science and Engineering, Central South University, Changsha, China","Division of Biomedical Engineering, University of Saskatchewan, Saskatoon SK, Canada"],"affiliations":[{"raw_affiliation_string":"Department of computer science, School of Information Science and Engineering, Central South University, Changsha, China","institution_ids":["https://openalex.org/I139660479"]},{"raw_affiliation_string":"Division of Biomedical Engineering, University of Saskatchewan, Saskatoon SK, Canada","institution_ids":["https://openalex.org/I32625721"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101465265","display_name":"Yi Pan","orcid":"https://orcid.org/0000-0002-2766-3096"},"institutions":[{"id":"https://openalex.org/I139660479","display_name":"Central South University","ror":"https://ror.org/00f1zfq44","country_code":"CN","type":"education","lineage":["https://openalex.org/I139660479"]},{"id":"https://openalex.org/I181565077","display_name":"Georgia State University","ror":"https://ror.org/03qt6ba18","country_code":"US","type":"education","lineage":["https://openalex.org/I181565077"]}],"countries":["CN","US"],"is_corresponding":false,"raw_author_name":"Yi Pan","raw_affiliation_strings":["Department of Computer Science, Georgia State University, Atlanta, GA, USA","Department of computer science, School of Information Science and Engineering, Central South University, Changsha, China"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Georgia State University, Atlanta, GA, USA","institution_ids":["https://openalex.org/I181565077"]},{"raw_affiliation_string":"Department of computer science, School of Information Science and Engineering, Central South University, Changsha, China","institution_ids":["https://openalex.org/I139660479"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100438360","display_name":"Jianxin Wang","orcid":"https://orcid.org/0000-0003-1516-0480"},"institutions":[{"id":"https://openalex.org/I139660479","display_name":"Central South University","ror":"https://ror.org/00f1zfq44","country_code":"CN","type":"education","lineage":["https://openalex.org/I139660479"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Jianxin Wang","raw_affiliation_strings":["Department of computer science, School of Information Science and Engineering, Central South University, Changsha, China"],"affiliations":[{"raw_affiliation_string":"Department of computer science, School of Information Science and Engineering, Central South University, Changsha, China","institution_ids":["https://openalex.org/I139660479"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5100438360","https://openalex.org/A5100719013"],"corresponding_institution_ids":["https://openalex.org/I139660479"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.9192,"has_fulltext":false,"cited_by_count":16,"citation_normalized_percentile":{"value":0.74255185,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"35","issue":"7","first_page":"1142","last_page":"1150"},"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9983000159263611,"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/T10602","display_name":"Glycosylation and Glycoproteins Research","score":0.9860000014305115,"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":0.9473311901092529},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6399924755096436},{"id":"https://openalex.org/keywords/scaffold","display_name":"Scaffold","score":0.6278231143951416},{"id":"https://openalex.org/keywords/spurious-relationship","display_name":"Spurious relationship","score":0.567128598690033},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.5176480412483215},{"id":"https://openalex.org/keywords/sequence-assembly","display_name":"Sequence assembly","score":0.4826229512691498},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.46032634377479553},{"id":"https://openalex.org/keywords/cuboid","display_name":"Cuboid","score":0.4438796043395996},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.33213526010513306},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3028870224952698},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.26343485713005066},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.21315142512321472},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.18334031105041504},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.17173486948013306},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.16292819380760193},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.13997435569763184},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.08840745687484741}],"concepts":[{"id":"https://openalex.org/C59582021","wikidata":"https://www.wikidata.org/wiki/Q1128751","display_name":"Contig","level":4,"score":0.9473311901092529},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6399924755096436},{"id":"https://openalex.org/C89429830","wikidata":"https://www.wikidata.org/wiki/Q735710","display_name":"Scaffold","level":2,"score":0.6278231143951416},{"id":"https://openalex.org/C97256817","wikidata":"https://www.wikidata.org/wiki/Q1462316","display_name":"Spurious relationship","level":2,"score":0.567128598690033},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.5176480412483215},{"id":"https://openalex.org/C18949551","wikidata":"https://www.wikidata.org/wiki/Q740578","display_name":"Sequence assembly","level":5,"score":0.4826229512691498},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.46032634377479553},{"id":"https://openalex.org/C203527163","wikidata":"https://www.wikidata.org/wiki/Q262959","display_name":"Cuboid","level":2,"score":0.4438796043395996},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.33213526010513306},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3028870224952698},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.26343485713005066},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.21315142512321472},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.18334031105041504},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.17173486948013306},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.16292819380760193},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.13997435569763184},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.08840745687484741},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.0},{"id":"https://openalex.org/C2524010","wikidata":"https://www.wikidata.org/wiki/Q8087","display_name":"Geometry","level":1,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"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":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":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020451","descriptor_name":"Contig Mapping","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020451","descriptor_name":"Contig Mapping","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020451","descriptor_name":"Contig Mapping","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":2,"locations":[{"id":"doi:10.1093/bioinformatics/bty773","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty773","pdf_url":null,"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:30184046","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/30184046","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}],"best_oa_location":null,"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/17","score":0.44999998807907104,"display_name":"Partnerships for the goals"}],"awards":[{"id":"https://openalex.org/G1187543282","display_name":null,"funder_award_id":"61772557","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G1729077721","display_name":null,"funder_award_id":"61732009","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G4066238608","display_name":null,"funder_award_id":"B18059","funder_id":"https://openalex.org/F4320327912","funder_display_name":"Higher Education Discipline Innovation Project"},{"id":"https://openalex.org/G8210156615","display_name":null,"funder_award_id":"61622213","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/F4320327912","display_name":"Higher Education Discipline Innovation Project","ror":null}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":42,"referenced_works":["https://openalex.org/W576031931","https://openalex.org/W1966822396","https://openalex.org/W1970995855","https://openalex.org/W1975398519","https://openalex.org/W1995663053","https://openalex.org/W2018756106","https://openalex.org/W2076151007","https://openalex.org/W2103441770","https://openalex.org/W2107164256","https://openalex.org/W2107772251","https://openalex.org/W2108640362","https://openalex.org/W2114795390","https://openalex.org/W2115501618","https://openalex.org/W2121832832","https://openalex.org/W2124985265","https://openalex.org/W2126552018","https://openalex.org/W2127067063","https://openalex.org/W2127768708","https://openalex.org/W2127781493","https://openalex.org/W2129744420","https://openalex.org/W2129933858","https://openalex.org/W2140059069","https://openalex.org/W2141920662","https://openalex.org/W2142027180","https://openalex.org/W2145186656","https://openalex.org/W2157624015","https://openalex.org/W2165795500","https://openalex.org/W2169002484","https://openalex.org/W2170551349","https://openalex.org/W2171531867","https://openalex.org/W2178309410","https://openalex.org/W2180318265","https://openalex.org/W2330617919","https://openalex.org/W2520464109","https://openalex.org/W2537565528","https://openalex.org/W2610924493","https://openalex.org/W2773089832","https://openalex.org/W2883056464","https://openalex.org/W2905576637","https://openalex.org/W2963010081","https://openalex.org/W6747070096","https://openalex.org/W6752982638"],"related_works":["https://openalex.org/W2089480001","https://openalex.org/W3167837387","https://openalex.org/W2885619582","https://openalex.org/W2949198880","https://openalex.org/W2275256942","https://openalex.org/W3216110456","https://openalex.org/W3129402903","https://openalex.org/W4311302642","https://openalex.org/W2971458848","https://openalex.org/W2890720538"],"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":2},{"year":2022,"cited_by_count":4},{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":6},{"year":2018,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}