{"id":"https://openalex.org/W2022858350","doi":"https://doi.org/10.1145/2649387.2649447","title":"PseudoLasso","display_name":"PseudoLasso","publication_year":2014,"publication_date":"2014-09-20","ids":{"openalex":"https://openalex.org/W2022858350","doi":"https://doi.org/10.1145/2649387.2649447","mag":"2022858350"},"language":"en","primary_location":{"id":"doi:10.1145/2649387.2649447","is_oa":false,"landing_page_url":"https://doi.org/10.1145/2649387.2649447","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 5th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics","raw_type":"proceedings-article"},"type":"conference-paper","indexed_in":["crossref"],"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/A5073504925","display_name":"Chelsea J.\u2010T. Ju","orcid":"https://orcid.org/0000-0001-8674-5318"},"institutions":[{"id":"https://openalex.org/I161318765","display_name":"University of California, Los Angeles","ror":"https://ror.org/046rm7j60","country_code":"US","type":"education","lineage":["https://openalex.org/I161318765"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Chelsea J.-T. Ju","raw_affiliation_strings":["University of California, Los Angeles, California","University of California , Los Angeles, California"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of California, Los Angeles, California","institution_ids":["https://openalex.org/I161318765"]},{"raw_affiliation_string":"University of California , Los Angeles, California","institution_ids":["https://openalex.org/I161318765"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5028396704","display_name":"Zhuangtian Zhao","orcid":null},"institutions":[{"id":"https://openalex.org/I161318765","display_name":"University of California, Los Angeles","ror":"https://ror.org/046rm7j60","country_code":"US","type":"education","lineage":["https://openalex.org/I161318765"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Zhuangtian Zhao","raw_affiliation_strings":["University of California, Los Angeles, California","University of California , Los Angeles, California"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of California, Los Angeles, California","institution_ids":["https://openalex.org/I161318765"]},{"raw_affiliation_string":"University of California , Los Angeles, California","institution_ids":["https://openalex.org/I161318765"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100392089","display_name":"Wei Wang","orcid":"https://orcid.org/0000-0002-8180-2886"},"institutions":[{"id":"https://openalex.org/I161318765","display_name":"University of California, Los Angeles","ror":"https://ror.org/046rm7j60","country_code":"US","type":"education","lineage":["https://openalex.org/I161318765"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Wei Wang","raw_affiliation_strings":["University of California, Los Angeles, California","University of California , Los Angeles, California"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of California, Los Angeles, California","institution_ids":["https://openalex.org/I161318765"]},{"raw_affiliation_string":"University of California , Los Angeles, California","institution_ids":["https://openalex.org/I161318765"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I161318765"],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":false,"cited_by_count":1,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":"569","last_page":"578"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":1.0,"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":1.0,"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":0.9997000098228455,"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":0.9995999932289124,"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/pseudogene","display_name":"Pseudogene","score":0.9898860454559326},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.621522068977356},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5759220123291016},{"id":"https://openalex.org/keywords/similarity","display_name":"Similarity (geometry)","score":0.533337414264679},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5057220458984375},{"id":"https://openalex.org/keywords/homologous-chromosome","display_name":"Homologous chromosome","score":0.49611005187034607},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.45262807607650757},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.4164756238460541},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.41574737429618835},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.39044201374053955},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3613073229789734}],"concepts":[{"id":"https://openalex.org/C34957205","wikidata":"https://www.wikidata.org/wiki/Q277338","display_name":"Pseudogene","level":4,"score":0.9898860454559326},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.621522068977356},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5759220123291016},{"id":"https://openalex.org/C103278499","wikidata":"https://www.wikidata.org/wiki/Q254465","display_name":"Similarity (geometry)","level":3,"score":0.533337414264679},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5057220458984375},{"id":"https://openalex.org/C64894306","wikidata":"https://www.wikidata.org/wiki/Q849622","display_name":"Homologous chromosome","level":3,"score":0.49611005187034607},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.45262807607650757},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.4164756238460541},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.41574737429618835},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.39044201374053955},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3613073229789734},{"id":"https://openalex.org/C115961682","wikidata":"https://www.wikidata.org/wiki/Q860623","display_name":"Image (mathematics)","level":2,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1145/2649387.2649447","is_oa":false,"landing_page_url":"https://doi.org/10.1145/2649387.2649447","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 5th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[{"score":0.5799999833106995,"display_name":"Quality Education","id":"https://metadata.un.org/sdg/4"}],"awards":[{"id":"https://openalex.org/G5435311862","display_name":null,"funder_award_id":"R01HG006703, P50 GM076468-08","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G949181915","display_name":null,"funder_award_id":"IIS-1313606","funder_id":"https://openalex.org/F4320337389","funder_display_name":"Division of Information and Intelligent Systems"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337389","display_name":"Division of Information and Intelligent Systems","ror":"https://ror.org/053a2cp42"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":24,"referenced_works":["https://openalex.org/W1235517956","https://openalex.org/W1973370476","https://openalex.org/W1974352732","https://openalex.org/W1975073052","https://openalex.org/W1999574084","https://openalex.org/W2022863488","https://openalex.org/W2030914835","https://openalex.org/W2055043387","https://openalex.org/W2055770801","https://openalex.org/W2075665712","https://openalex.org/W2097360283","https://openalex.org/W2100305481","https://openalex.org/W2108234281","https://openalex.org/W2111466507","https://openalex.org/W2116617850","https://openalex.org/W2129524208","https://openalex.org/W2140729960","https://openalex.org/W2141458291","https://openalex.org/W2144882930","https://openalex.org/W2154431984","https://openalex.org/W2159907132","https://openalex.org/W2162558393","https://openalex.org/W4235794973","https://openalex.org/W4294541781"],"related_works":["https://openalex.org/W2769050893","https://openalex.org/W1977805690","https://openalex.org/W2003343781","https://openalex.org/W2367624822","https://openalex.org/W2808331510","https://openalex.org/W2144270675","https://openalex.org/W2059178206","https://openalex.org/W2118397457","https://openalex.org/W1491700128","https://openalex.org/W1922950661"],"abstract_inverted_index":{"Pseudogenes":[0],"have":[1,15],"long":[2],"been":[3],"considered":[4],"to":[5,18,40,77,90,104,126,137],"be":[6,74],"nonfunctional":[7],"segments":[8],"in":[9,24,31,61],"the":[10,28,62,93,127],"genome,":[11],"but":[12],"recent":[13],"studies":[14],"provided":[16],"evidence":[17],"support":[19],"their":[20,69,98,105],"novel":[21],"regulatory":[22],"roles":[23],"biological":[25],"processes.":[26],"With":[27],"growing":[29],"interests":[30],"pseudogene":[32,58],"research,":[33],"scientists":[34],"rely":[35],"on":[36,57,110],"RNA":[37],"sequencing":[38],"technology":[39],"estimate":[41,92],"expression":[42],"level":[43],"of":[44,55,95,145],"pseudogenes":[45,67,96],"at":[46],"different":[47],"tissues":[48],"or":[49],"cell":[50],"lines.":[51],"The":[52],"major":[53],"challenge":[54],"RNASeq":[56],"quantification":[59],"falls":[60],"high":[63],"sequence":[64],"similarity":[65],"between":[66],"and":[68,97,100,115,122],"homologous":[70,79],"parents.":[71],"Reads":[72],"can":[73],"ambiguously":[75],"aligned":[76],"multiple":[78],"regions.":[80],"In":[81],"this":[82,117],"article,":[83],"we":[84],"present":[85],"PseudoLasso,":[86],"a":[87,141],"genome-wide":[88],"approach":[89,108],"accurately":[91],"abundance":[94,120],"parents,":[99],"correctly":[101],"align":[102],"reads":[103],"origins.":[106],"Our":[107],"focuses":[109],"learning":[111],"read":[112,128],"alignment":[113,123],"behaviors,":[114],"leveraging":[116],"knowledge":[118],"for":[119],"estimation":[121],"correction.":[124],"Compared":[125],"count":[129],"estimates":[130,139],"reported":[131],"by":[132],"TopHat2,":[133],"PseudoLasso":[134],"is":[135],"able":[136],"provide":[138],"with":[140],"reduced":[142],"error":[143],"rate":[144],"10-fold.":[146]},"counts_by_year":[{"year":2016,"cited_by_count":1}],"updated_date":"2026-07-14T23:27:15.235271","created_date":"2016-06-24T00:00:00"}
