{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,6,19]],"date-time":"2025-06-19T04:18:51Z","timestamp":1750306731179,"version":"3.41.0"},"publisher-location":"New York, NY, USA","reference-count":24,"publisher":"ACM","license":[{"start":{"date-parts":[[2014,9,20]],"date-time":"2014-09-20T00:00:00Z","timestamp":1411171200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/www.acm.org\/publications\/policies\/copyright_policy#Background"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["R01HG006703, P50 GM076468-08"],"award-info":[{"award-number":["R01HG006703, P50 GM076468-08"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000145","name":"Division of Information and Intelligent Systems","doi-asserted-by":"publisher","award":["IIS-1313606"],"award-info":[{"award-number":["IIS-1313606"]}],"id":[{"id":"10.13039\/100000145","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["dl.acm.org"],"crossmark-restriction":true},"short-container-title":[],"published-print":{"date-parts":[[2014,9,20]]},"DOI":"10.1145\/2649387.2649447","type":"proceedings-article","created":{"date-parts":[[2014,10,24]],"date-time":"2014-10-24T15:29:22Z","timestamp":1414164562000},"page":"569-578","update-policy":"https:\/\/doi.org\/10.1145\/crossmark-policy","source":"Crossref","is-referenced-by-count":0,"title":["PseudoLasso"],"prefix":"10.1145","author":[{"given":"Chelsea J.-T.","family":"Ju","sequence":"first","affiliation":[{"name":"University of California, Los Angeles, California"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Zhuangtian","family":"Zhao","sequence":"additional","affiliation":[{"name":"University of California, Los Angeles, California"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Wei","family":"Wang","sequence":"additional","affiliation":[{"name":"University of California, Los Angeles, California"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"320","published-online":{"date-parts":[[2014,9,20]]},"reference":[{"doi-asserted-by":"crossref","unstructured":"S. F. Altschul W. Gish W. Miller E. W. Myers and D. J. Lipman. Basic local alignment search tool. Journal of molecular biology 215(3):403--10 Oct. 1990.  S. F. Altschul W. Gish W. Miller E. W. Myers and D. J. Lipman. Basic local alignment search tool. Journal of molecular biology 215(3):403--10 Oct. 1990.","key":"e_1_3_2_1_1_1","DOI":"10.1016\/S0022-2836(05)80360-2"},{"year":"2014","author":"Flicek P.","journal-title":"J. Searle. Ensembl","key":"e_1_3_2_1_2_1"},{"doi-asserted-by":"crossref","unstructured":"J. Friedman T. Hastie and R. Tibshirani. Regularization Paths for Generalized Linear Models via Coordinate Descent. Journal of statistical software 33(1):1--22 Jan. 2010.  J. Friedman T. Hastie and R. Tibshirani. Regularization Paths for Generalized Linear Models via Coordinate Descent. Journal of statistical software 33(1):1--22 Jan. 2010.","key":"e_1_3_2_1_3_1","DOI":"10.18637\/jss.v033.i01"},{"doi-asserted-by":"publisher","key":"e_1_3_2_1_4_1","DOI":"10.1038\/nmeth.1613"},{"doi-asserted-by":"crossref","unstructured":"Y. J. Han S. F. Ma G. Yourek Y.-D. Park and J. G. N. Garcia. A transcribed pseudogene of MYLK promotes cell proliferation. FASEB journal: official publication of the Federation of American Societies for Experimental Biology 25(7):2305--12 July 2011.  Y. J. Han S. F. Ma G. Yourek Y.-D. Park and J. G. N. Garcia. A transcribed pseudogene of MYLK promotes cell proliferation. FASEB journal: official publication of the Federation of American Societies for Experimental Biology 25(7):2305--12 July 2011.","key":"e_1_3_2_1_5_1","DOI":"10.1096\/fj.10-177808"},{"doi-asserted-by":"publisher","key":"e_1_3_2_1_6_1","DOI":"10.4161\/trns.1.3.13332"},{"doi-asserted-by":"crossref","unstructured":"J. E. Karro Y. Yan D. Zheng Z. Zhang N. Carriero P. Cayting P. Harrrison and M. Gerstein. Pseudogene.org: a comprehensive database and comparison platform for pseudogene annotation. Nucleic acids research 35(Database issue):D55--D60 Jan. 2007.  J. E. Karro Y. Yan D. Zheng Z. Zhang N. Carriero P. Cayting P. Harrrison and M. Gerstein. Pseudogene.org: a comprehensive database and comparison platform for pseudogene annotation. Nucleic acids research 35(Database issue):D55--D60 Jan. 2007.","key":"e_1_3_2_1_7_1","DOI":"10.1093\/nar\/gkl851"},{"doi-asserted-by":"publisher","key":"e_1_3_2_1_8_1","DOI":"10.1186\/gb-2013-14-4-r36"},{"doi-asserted-by":"publisher","key":"e_1_3_2_1_9_1","DOI":"10.1137\/1.9781611971217"},{"doi-asserted-by":"publisher","key":"e_1_3_2_1_10_1","DOI":"10.1186\/1471-2105-12-323"},{"doi-asserted-by":"publisher","key":"e_1_3_2_1_11_1","DOI":"10.1093\/bioinformatics\/btp352"},{"doi-asserted-by":"crossref","unstructured":"H. Lin A. Shabbir M. Molnar and T. Lee. Stem cell regulatory function mediated by expression of a novel mouse Oct4 pseudogene. Biochemical and biophysical research communications 355(1):111--6 Mar. 2007.  H. Lin A. Shabbir M. Molnar and T. Lee. Stem cell regulatory function mediated by expression of a novel mouse Oct4 pseudogene. Biochemical and biophysical research communications 355(1):111--6 Mar. 2007.","key":"e_1_3_2_1_12_1","DOI":"10.1016\/j.bbrc.2007.01.106"},{"doi-asserted-by":"crossref","unstructured":"A. Mortazavi B. A. Williams K. Mccue L. Schaeffer and B. Wold. Mapping and quantifying mammalian transcriptomes by RNA-Seq. 5(7):1--8 2008.  A. Mortazavi B. A. Williams K. Mccue L. Schaeffer and B. Wold. Mapping and quantifying mammalian transcriptomes by RNA-Seq. 5(7):1--8 2008.","key":"e_1_3_2_1_13_1","DOI":"10.1038\/nmeth.1226"},{"doi-asserted-by":"crossref","unstructured":"B. Pa\u00c5§aniuc N. Zaitlen and E. Halperin. Accurate estimation of expression levels of homologous genes in RNA-seq experiments. Journal of computational biology: a journal of computational molecular cell biology 18(3):459--68 Mar. 2011.  B. Pa\u00c5§aniuc N. Zaitlen and E. Halperin. Accurate estimation of expression levels of homologous genes in RNA-seq experiments. Journal of computational biology: a journal of computational molecular cell biology 18(3):459--68 Mar. 2011.","key":"e_1_3_2_1_14_1","DOI":"10.1089\/cmb.2010.0259"},{"doi-asserted-by":"publisher","key":"e_1_3_2_1_15_1","DOI":"10.1186\/gb-2012-13-9-r51"},{"issue":"5","key":"e_1_3_2_1_16_1","first-page":"792","article-title":"pseudo-functional or key regulators in health and disease? RNA (New York","volume":"17","author":"Pink R. C.","year":"2011","journal-title":"N.Y.)"},{"doi-asserted-by":"crossref","unstructured":"Z. Redshaw and A. J. Strain. Human haematopoietic stem cells express Oct4 pseudogenes and lack the ability to initiate Oct4 promoter-driven gene expression. Journal of negative results in biomedicine 9(1):2 Jan. 2010.  Z. Redshaw and A. J. Strain. Human haematopoietic stem cells express Oct4 pseudogenes and lack the ability to initiate Oct4 promoter-driven gene expression. Journal of negative results in biomedicine 9(1):2 Jan. 2010.","key":"e_1_3_2_1_17_1","DOI":"10.1186\/1477-5751-9-2"},{"doi-asserted-by":"publisher","key":"e_1_3_2_1_18_1","DOI":"10.1186\/1471-2164-13-412"},{"doi-asserted-by":"publisher","key":"e_1_3_2_1_19_1","DOI":"10.1038\/nprot.2012.016"},{"doi-asserted-by":"publisher","key":"e_1_3_2_1_20_1","DOI":"10.1038\/nbt.1621"},{"doi-asserted-by":"crossref","unstructured":"Y. Tutar. Pseudogenes. Comparative and functional genomics 2012:424526 Jan. 2012.  Y. Tutar. Pseudogenes. Comparative and functional genomics 2012:424526 Jan. 2012.","key":"e_1_3_2_1_21_1","DOI":"10.1155\/2012\/424526"},{"issue":"13","key":"e_1_3_2_1_22_1","first-page":"i291","article-title":"Pardo Manuel de Villena, L. McMillan, and W. Wang. GeneScissors: a comprehensive approach to detecting and correcting spurious transcriptome inference owing to RNA-seq reads misalignment. Bioinformatics (Oxford","volume":"29","author":"Zhang Z.","year":"2013","journal-title":"England)"},{"doi-asserted-by":"publisher","key":"e_1_3_2_1_23_1","DOI":"10.1101\/gr.5586307"},{"issue":"1","key":"e_1_3_2_1_24_1","first-page":"57","article-title":"Oncogenic Activation of MAP Kinase by BRAF Pseudogene","volume":"11","author":"Zou M.","year":"2009","journal-title":"Thyroid Tumors 1."}],"event":{"sponsor":["SIGBio ACM Special Interest Group on Bioinformatics"],"acronym":"BCB '14","name":"BCB '14: ACM-BCB '14","location":"Newport Beach California"},"container-title":["Proceedings of the 5th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics"],"original-title":[],"link":[{"URL":"https:\/\/dl.acm.org\/doi\/10.1145\/2649387.2649447","content-type":"unspecified","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/dl.acm.org\/doi\/pdf\/10.1145\/2649387.2649447","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,6,18]],"date-time":"2025-06-18T07:19:43Z","timestamp":1750231183000},"score":1,"resource":{"primary":{"URL":"https:\/\/dl.acm.org\/doi\/10.1145\/2649387.2649447"}},"subtitle":["leveraging read alignment in homologous regions to correct pseudogene expression estimates via RNASeq"],"short-title":[],"issued":{"date-parts":[[2014,9,20]]},"references-count":24,"alternative-id":["10.1145\/2649387.2649447","10.1145\/2649387"],"URL":"https:\/\/doi.org\/10.1145\/2649387.2649447","relation":{},"subject":[],"published":{"date-parts":[[2014,9,20]]},"assertion":[{"value":"2014-09-20","order":2,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}]}}