{"id":"https://openalex.org/W2951702327","doi":"https://doi.org/10.7287/peerj.preprints.1301","title":"Next generation cluster editing","display_name":"Next generation cluster editing","publication_year":2015,"publication_date":"2015-08-13","ids":{"openalex":"https://openalex.org/W2951702327","doi":"https://doi.org/10.7287/peerj.preprints.1301","mag":"2951702327"},"language":"en","primary_location":{"id":"doi:10.7287/peerj.preprints.1301","doi":"https://doi.org/10.7287/peerj.preprints.1301","is_oa":true,"landing_page_url":"https://doi.org/10.7287/peerj.preprints.1301","pdf_url":null,"source":null,"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":null,"raw_type":"posted-content"},"volume":null,"type":"preprint","indexed_in":["arxiv","crossref","datacite"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://doi.org/10.7287/peerj.preprints.1301","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5043348180","display_name":"Thomas Bellitto","orcid":"https://orcid.org/0009-0001-5424-0742","observed_orcids":["https://orcid.org/0009-0001-5424-0742"]},"institutions":[{"id":"https://openalex.org/I4210142254","display_name":"Laboratoire Bordelais de Recherche en Informatique","ror":"https://ror.org/03adqg323","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I15057530","https://openalex.org/I4210142254","https://openalex.org/I4210159245","https://openalex.org/I4210160189"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Thomas Bellitto","raw_affiliation_strings":["Combinatorics and Algorithms Team, Laboratoire Bordelais de Recherche en Informatique, Bordeaux, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Combinatorics and Algorithms Team, Laboratoire Bordelais de Recherche en Informatique, Bordeaux, France","institution_ids":["https://openalex.org/I4210142254"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5067570776","display_name":"Tobias Marschall","orcid":"https://orcid.org/0000-0002-9376-1030","observed_orcids":["https://orcid.org/0000-0002-9376-1030","https://orcid.org/0000-0001-6664-3082"]},"institutions":[{"id":"https://openalex.org/I149899117","display_name":"Max Planck Society","ror":"https://ror.org/01hhn8329","country_code":"DE","type":"nonprofit","lineage":["https://openalex.org/I149899117"]},{"id":"https://openalex.org/I4210109712","display_name":"Max Planck Institute for Informatics","ror":"https://ror.org/01w19ak89","country_code":"DE","type":"facility","lineage":["https://openalex.org/I149899117","https://openalex.org/I4210109712"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Tobias Marschall","raw_affiliation_strings":["Max Planck Institute for Informatics, Saarbr\u00fccken, Germany","Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Max Planck Institute for Informatics, Saarbr\u00fccken, Germany","institution_ids":["https://openalex.org/I4210109712"]},{"raw_affiliation_string":"Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society","institution_ids":["https://openalex.org/I149899117","https://openalex.org/I4210109712"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5001148638","display_name":"Alexander Sch\u00f6nhuth","orcid":"https://orcid.org/0000-0003-3529-0856","observed_orcids":["https://orcid.org/0000-0003-3529-0856"]},"institutions":[{"id":"https://openalex.org/I1341640284","display_name":"Centrum Wiskunde & Informatica","ror":"https://ror.org/00x7ekv49","country_code":"NL","type":"facility","lineage":["https://openalex.org/I1341640284","https://openalex.org/I2800991832","https://openalex.org/I4405262988"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"Alexander Sch\u00f6nhuth","raw_affiliation_strings":["Life Sciences, Centrum Wiskunde & Informatica, Amsterdam, The Netherlands"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Life Sciences, Centrum Wiskunde & Informatica, Amsterdam, The Netherlands","institution_ids":["https://openalex.org/I1341640284"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5029642674","display_name":"Gunnar W. Klau","orcid":"https://orcid.org/0000-0002-6340-0090","observed_orcids":["https://orcid.org/0000-0002-6340-0090"]},"institutions":[{"id":"https://openalex.org/I1341640284","display_name":"Centrum Wiskunde & Informatica","ror":"https://ror.org/00x7ekv49","country_code":"NL","type":"facility","lineage":["https://openalex.org/I1341640284","https://openalex.org/I2800991832","https://openalex.org/I4405262988"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"Gunnar W Klau","raw_affiliation_strings":["Life Sciences, Centrum Wiskunde & Informatica, Amsterdam, The Netherlands"],"raw_orcid":"https://orcid.org/0000-0002-6340-0090","affiliations":[{"raw_affiliation_string":"Life Sciences, Centrum Wiskunde & Informatica, Amsterdam, The Netherlands","institution_ids":["https://openalex.org/I1341640284"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":4,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":true,"cited_by_count":1,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.7128999829292297,"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":0.7128999829292297,"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/T11213","display_name":"Genomic variations and chromosomal abnormalities","score":0.19679999351501465,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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/T13664","display_name":"Genome Rearrangement Algorithms","score":0.06019999831914902,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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/structural-variants","display_name":"structural variants","score":0.5860000252723694},{"id":"https://openalex.org/keywords/polynomial-time-algorithms","display_name":"polynomial-time algorithms","score":0.6320000290870667},{"id":"https://openalex.org/keywords/variant-discovery","display_name":"variant discovery","score":0.5860000252723694}],"concepts":[{"id":"https://openalex.org/C173801870","wikidata":"https://www.wikidata.org/wiki/Q201413","display_name":"Heuristic","level":2,"score":0.7331187129020691},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7167457342147827},{"id":"https://openalex.org/C164866538","wikidata":"https://www.wikidata.org/wiki/Q367351","display_name":"Cluster (spacecraft)","level":2,"score":0.6051285862922668},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.4784281849861145},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3638952374458313},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.3392655849456787},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.08008161187171936}],"mesh":[],"locations_count":10,"locations":[{"id":"doi:10.7287/peerj.preprints.1301","doi":"https://doi.org/10.7287/peerj.preprints.1301","is_oa":true,"landing_page_url":"https://doi.org/10.7287/peerj.preprints.1301","pdf_url":null,"source":null,"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":null,"raw_type":"posted-content"},{"id":"pmh:oai:arXiv.org:1310.3353","doi":null,"is_oa":true,"landing_page_url":"http://arxiv.org/abs/1310.3353","pdf_url":"https://arxiv.org/pdf/1310.3353","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":"2331-8422","issn":["2331-8422"],"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"text"},{"id":"pmh:oai:cwi.nl:22195","doi":null,"is_oa":true,"landing_page_url":"https://ir.cwi.nl/pub/22195","pdf_url":"https://ir.cwi.nl/pub/22195/22195B.pdf","source":{"id":"https://openalex.org/S7407055335","display_name":"Centrum Wiskunde & Informatica (CWI), the national research institute for mathematics and computer science in the Netherlands","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"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":null,"raw_type":"info:eu-repo/semantics/other"},{"id":"pmh:oai:pure.mpg.de:item_2242870","doi":null,"is_oa":true,"landing_page_url":"https://hdl.handle.net/11858/00-001M-0000-0029-5E4D-6","pdf_url":"https://hdl.handle.net/11858/00-001M-0000-002C-1F15-C","source":{"id":"https://openalex.org/S4306400654","display_name":"MPG.PuRe (Max Planck Society)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I149899117","host_organization_name":"Max Planck Society","host_organization_lineage":["https://openalex.org/I149899117"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"German Conference on Bioinformatics","raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.739.9252","doi":null,"is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.739.9252","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://arxiv.org/pdf/1310.3353.pdf","raw_type":"text"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.846.6473","doi":null,"is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.846.6473","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"https://peerj.com/preprints/1301.pdf","raw_type":"text"},{"id":"pmh:cwi:oai:cwi.nl:22195","doi":null,"is_oa":true,"landing_page_url":"https://ir.cwi.nl/pub/22195","pdf_url":null,"source":{"id":"https://openalex.org/S4306401843","display_name":"Data Archiving and Networked Services (DANS)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I1322597698","host_organization_name":"Royal Netherlands Academy of Arts and Sciences","host_organization_lineage":["https://openalex.org/I1322597698"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"info:eu-repo/semantics/other"},{"id":"pmh:cwi:oai:cwi.nl:23764","doi":null,"is_oa":true,"landing_page_url":"https://ir.cwi.nl/pub/23764","pdf_url":null,"source":{"id":"https://openalex.org/S4306401843","display_name":"Data Archiving and Networked Services (DANS)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I1322597698","host_organization_name":"Royal Netherlands Academy of Arts and Sciences","host_organization_lineage":["https://openalex.org/I1322597698"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PeerJ PrePrints, 3","raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:cwi.nl:23764","doi":null,"is_oa":true,"landing_page_url":"https://ir.cwi.nl/pub/23764/Fulltext","pdf_url":null,"source":{"id":"https://openalex.org/S7407055335","display_name":"Centrum Wiskunde & Informatica (CWI), the national research institute for mathematics and computer science in the Netherlands","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PeerJ PrePrints vol. 3","raw_type":"info:eu-repo/semantics/article"},{"id":"doi:10.48550/arxiv.1310.3353","doi":"https://doi.org/10.48550/arxiv.1310.3353","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.1310.3353","pdf_url":null,"source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":"2331-8422","issn":["2331-8422"],"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Preprint"}],"best_oa_location":{"id":"doi:10.7287/peerj.preprints.1301","doi":"https://doi.org/10.7287/peerj.preprints.1301","is_oa":true,"landing_page_url":"https://doi.org/10.7287/peerj.preprints.1301","pdf_url":null,"source":null,"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":null,"raw_type":"posted-content"},"sustainable_development_goals":[],"study_designs":[],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2951702327.pdf","grobid_xml":"https://content.openalex.org/works/W2951702327.grobid-xml"},"referenced_works_count":15,"referenced_works":["https://openalex.org/W1487118672","https://openalex.org/W1566407554","https://openalex.org/W1601278659","https://openalex.org/W2026721694","https://openalex.org/W2052386658","https://openalex.org/W2065183358","https://openalex.org/W2065817684","https://openalex.org/W2103011829","https://openalex.org/W2109174028","https://openalex.org/W2110065044","https://openalex.org/W2133112449","https://openalex.org/W2142642738","https://openalex.org/W2146081992","https://openalex.org/W2154397429","https://openalex.org/W2611831635"],"related_works":["https://openalex.org/W7096992381","https://openalex.org/W2107830007","https://openalex.org/W4253465315","https://openalex.org/W2951113516","https://openalex.org/W4396808924","https://openalex.org/W3048918864","https://openalex.org/W2024528333","https://openalex.org/W2750824798","https://openalex.org/W2545248606","https://openalex.org/W7155465077"],"abstract_inverted_index":{"Genomic":[0],"structural":[1,15],"variations":[2],"play":[3],"key":[4],"roles":[5],"in":[6,14,47,89,140,143,162],"genetic":[7],"diversity":[8],"and":[9,27,55,65,81,111],"disease.":[10],"Despite":[11],"recent":[12,35],"advances":[13],"variation":[16],"discovery,":[17],"many":[18],"variants":[19],"are":[20,52,82,108],"yet":[21],"to":[22,77,87,113,118],"be":[23,78,114],"discovered.":[24],"Midsize":[25],"insertions":[26],"deletions":[28],"pose":[29],"particularly":[30],"involved":[31],"algorithmic":[32],"challenges.":[33],"The":[34,149],"CLEVER":[36],"algorithm":[37,157],"addressed":[38],"these":[39,105],"challenges":[40],"with":[41],"a":[42,48,60,96,130,134],"statistical":[43,61],"model":[44,97,171],"on":[45,63,99,125,153],"cliques":[46],"graph":[49],"whose":[50,56],"nodes":[51],"read":[53,68,73,127],"alignments":[54,128],"edges":[57],"arise":[58],"from":[59],"test":[62],"length":[64,145],"overlap":[66],"of":[67,129,146],"alignments.":[69],"However,":[70],"the":[71,120,144,147,169],"resulting":[72],"alignment":[74],"clusters":[75,107],"tend":[76,112],"too":[79],"small":[80],"heavily":[83],"overlapping,":[84],"which":[85,103,138],"leads":[86],"losses":[88],"recall":[90,173],"performance":[91],"rates.":[92],"Here":[93],"we":[94,132],"present":[95,133],"based":[98,152],"weighted":[100,159],"cluster":[101,160],"editing,":[102],"alleviates":[104],"issues:":[106],"provably":[109],"non-overlapping":[110],"larger.":[115],"In":[116],"order":[117],"render":[119],"inherent":[121],"optimization":[122],"problem":[123],"tractable":[124],"all":[126],"genome,":[131],"novel,":[135],"principled":[136],"heuristic,":[137],"runs":[139],"time":[141],"linear":[142],"genome.":[148],"heuristic":[150],"is":[151],"an":[154],"exact":[155],"polynomial-time":[156],"for":[158],"editing":[161],"one-dimensional":[163],"point":[164],"graphs.":[165],"We":[166],"demonstrate":[167],"that":[168],"new":[170],"improves":[172],"rates":[174],"achieved":[175],"by":[176],"CLEVER.":[177]},"counts_by_year":[{"year":2014,"cited_by_count":1}],"updated_date":"2026-11-05T12:25:35.769452","created_date":"2019-06-27T00:00:00"}