{"id":"https://openalex.org/W2127143129","doi":"https://doi.org/10.1093/bioinformatics/btl116","title":"PseudoPipe: an automated pseudogene identification pipeline","display_name":"PseudoPipe: an automated pseudogene identification pipeline","publication_year":2006,"publication_date":"2006-03-30","ids":{"openalex":"https://openalex.org/W2127143129","doi":"https://doi.org/10.1093/bioinformatics/btl116","mag":"2127143129","pmid":"https://pubmed.ncbi.nlm.nih.gov/16574694"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btl116","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btl116","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/22/12/1437/48838169/bioinformatics_22_12_1437.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/22/12/1437/48838169/bioinformatics_22_12_1437.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5009847434","display_name":"Zhaolei Zhang","orcid":"https://orcid.org/0000-0002-7303-6472"},"institutions":[{"id":"https://openalex.org/I185261750","display_name":"University of Toronto","ror":"https://ror.org/03dbr7087","country_code":"CA","type":"education","lineage":["https://openalex.org/I185261750"]}],"countries":["CA"],"is_corresponding":true,"raw_author_name":"Zhaolei Zhang","raw_affiliation_strings":["Banting and Best Department of Medical Research, Donnelly CCBR, University of Toronto 1 \u00a0 1 \u00a0 \u00a0 160 College Street, Toronto, ON M5S 3E1, Canada"],"affiliations":[{"raw_affiliation_string":"Banting and Best Department of Medical Research, Donnelly CCBR, University of Toronto 1 \u00a0 1 \u00a0 \u00a0 160 College Street, Toronto, ON M5S 3E1, Canada","institution_ids":["https://openalex.org/I185261750"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5008524932","display_name":"Nicholas Carriero","orcid":null},"institutions":[{"id":"https://openalex.org/I32971472","display_name":"Yale University","ror":"https://ror.org/03v76x132","country_code":"US","type":"education","lineage":["https://openalex.org/I32971472"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Nicholas Carriero","raw_affiliation_strings":["Department of Computer Science, Yale University 2 \u00a0 2 \u00a0 \u00a0 New Haven, CT 06520, USA"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Yale University 2 \u00a0 2 \u00a0 \u00a0 New Haven, CT 06520, USA","institution_ids":["https://openalex.org/I32971472"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5053246999","display_name":"Deyou Zheng","orcid":"https://orcid.org/0000-0003-4354-5337"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Deyou Zheng","raw_affiliation_strings":["Department of Molecular Biophysics and Biochemistry 3 \u00a0 3 \u00a0 \u00a0 New Haven, CT 06520, USA"],"affiliations":[{"raw_affiliation_string":"Department of Molecular Biophysics and Biochemistry 3 \u00a0 3 \u00a0 \u00a0 New Haven, CT 06520, USA","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5027197880","display_name":"John Karro","orcid":null},"institutions":[{"id":"https://openalex.org/I130769515","display_name":"Pennsylvania State University","ror":"https://ror.org/04p491231","country_code":"US","type":"education","lineage":["https://openalex.org/I130769515"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"John Karro","raw_affiliation_strings":["Department of Biology 4 \u00a0 4 \u00a0 \u00a0 506 Wartik \u00a0 \u00a0 PA 16802, USA","Pennsylvania State University, University Park 4 \u00a0 4 \u00a0 \u00a0 506 Wartik \u00a0 \u00a0 PA 16802, USA","Department of Biology 506 Wartik Pennsylvania State University, University Park PA 16802, USA"],"affiliations":[{"raw_affiliation_string":"Department of Biology 4 \u00a0 4 \u00a0 \u00a0 506 Wartik \u00a0 \u00a0 PA 16802, USA","institution_ids":[]},{"raw_affiliation_string":"Pennsylvania State University, University Park 4 \u00a0 4 \u00a0 \u00a0 506 Wartik \u00a0 \u00a0 PA 16802, USA","institution_ids":["https://openalex.org/I130769515"]},{"raw_affiliation_string":"Department of Biology 506 Wartik Pennsylvania State University, University Park PA 16802, USA","institution_ids":["https://openalex.org/I130769515"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5051233756","display_name":"Paul M. Harrison","orcid":"https://orcid.org/0000-0002-7477-1014"},"institutions":[{"id":"https://openalex.org/I5023651","display_name":"McGill University","ror":"https://ror.org/01pxwe438","country_code":"CA","type":"education","lineage":["https://openalex.org/I5023651"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Paul M. Harrison","raw_affiliation_strings":["Department of Biology, McGill University 5 \u00a0 5 \u00a0 \u00a0 Stewart Biology Building, 1205 Dr Penfield Avenue, Montreal, QC, H3A 1B1, Canada"],"affiliations":[{"raw_affiliation_string":"Department of Biology, McGill University 5 \u00a0 5 \u00a0 \u00a0 Stewart Biology Building, 1205 Dr Penfield Avenue, Montreal, QC, H3A 1B1, Canada","institution_ids":["https://openalex.org/I5023651"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5042321575","display_name":"Mark Gerstein","orcid":"https://orcid.org/0000-0002-9746-3719"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Mark Gerstein","raw_affiliation_strings":["Department of Molecular Biophysics and Biochemistry 3 \u00a0 3 \u00a0 \u00a0 New Haven, CT 06520, USA"],"affiliations":[{"raw_affiliation_string":"Department of Molecular Biophysics and Biochemistry 3 \u00a0 3 \u00a0 \u00a0 New Haven, CT 06520, USA","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5009847434"],"corresponding_institution_ids":["https://openalex.org/I185261750"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":3.8143,"has_fulltext":false,"cited_by_count":211,"citation_normalized_percentile":{"value":0.93826744,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":97,"max":100},"biblio":{"volume":"22","issue":"12","first_page":"1437","last_page":"1439"},"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":0.9993000030517578,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9993000030517578,"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":0.9170396327972412},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.744366466999054},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.5972332954406738},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.5517895221710205},{"id":"https://openalex.org/keywords/homology","display_name":"Homology (biology)","score":0.5476131439208984},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5439853072166443},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.5225110054016113},{"id":"https://openalex.org/keywords/retrotransposon","display_name":"Retrotransposon","score":0.4580904245376587},{"id":"https://openalex.org/keywords/intergenic-region","display_name":"Intergenic region","score":0.4301387071609497},{"id":"https://openalex.org/keywords/transposable-element","display_name":"Transposable element","score":0.33866554498672485}],"concepts":[{"id":"https://openalex.org/C34957205","wikidata":"https://www.wikidata.org/wiki/Q277338","display_name":"Pseudogene","level":4,"score":0.9170396327972412},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.744366466999054},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5972332954406738},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.5517895221710205},{"id":"https://openalex.org/C165525559","wikidata":"https://www.wikidata.org/wiki/Q224180","display_name":"Homology (biology)","level":3,"score":0.5476131439208984},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5439853072166443},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.5225110054016113},{"id":"https://openalex.org/C7029365","wikidata":"https://www.wikidata.org/wiki/Q413988","display_name":"Retrotransposon","level":5,"score":0.4580904245376587},{"id":"https://openalex.org/C195139083","wikidata":"https://www.wikidata.org/wiki/Q3463539","display_name":"Intergenic region","level":4,"score":0.4301387071609497},{"id":"https://openalex.org/C4918238","wikidata":"https://www.wikidata.org/wiki/Q121438","display_name":"Transposable element","level":4,"score":0.33866554498672485}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001331","descriptor_name":"Automation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001331","descriptor_name":"Automation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001331","descriptor_name":"Automation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011544","descriptor_name":"Pseudogenes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011544","descriptor_name":"Pseudogenes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011544","descriptor_name":"Pseudogenes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","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":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019143","descriptor_name":"Evolution, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019143","descriptor_name":"Evolution, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019143","descriptor_name":"Evolution, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btl116","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btl116","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/22/12/1437/48838169/bioinformatics_22_12_1437.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:16574694","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/16574694","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:CiteSeerX.psu:10.1.1.109.3137","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.109.3137","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"http://bioinformatics.oxfordjournals.org/cgi/reprint/btl116v1.pdf","raw_type":"text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btl116","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btl116","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/22/12/1437/48838169/bioinformatics_22_12_1437.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":[{"id":"https://metadata.un.org/sdg/15","score":0.4000000059604645,"display_name":"Life in Land"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320322015","display_name":"University of Toronto","ror":"https://ror.org/03dbr7087"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2127143129.pdf","grobid_xml":"https://content.openalex.org/works/W2127143129.grobid-xml"},"referenced_works_count":8,"referenced_works":["https://openalex.org/W2045742821","https://openalex.org/W2050341877","https://openalex.org/W2110182011","https://openalex.org/W2113394593","https://openalex.org/W2138008048","https://openalex.org/W2138731801","https://openalex.org/W2158714788","https://openalex.org/W4242105792"],"related_works":["https://openalex.org/W1977805690","https://openalex.org/W2769050893","https://openalex.org/W2003343781","https://openalex.org/W2947397308","https://openalex.org/W2033277669","https://openalex.org/W2955897131","https://openalex.org/W2089350008","https://openalex.org/W2121859226","https://openalex.org/W1940341482","https://openalex.org/W3013628298"],"abstract_inverted_index":{"We":[0],"have":[1],"developed":[2],"a":[3,11,19,67,76],"homology-based":[4],"computational":[5],"pipeline":[6,29],"('PseudoPipe')":[7],"that":[8],"can":[9],"search":[10],"mammalian":[12],"genome":[13,45],"and":[14,21,46,61,63,84,89],"identify":[15],"pseudogene":[16],"sequences":[17],"in":[18,27],"comprehensive":[20],"consistent":[22],"manner.":[23],"The":[24],"key":[25],"steps":[26],"the":[28,40,44,49],"involve":[30],"using":[31],"BLAST":[32],"to":[33],"rapidly":[34],"cross-reference":[35],"potential":[36],"\"parent\"":[37],"proteins":[38],"against":[39],"intergenic":[41],"regions":[42],"of":[43,78,86],"then":[47],"processing":[48],"resulting":[50],"\"raw":[51],"hits\"":[52],"--":[53],"i.e.":[54],"eliminating":[55],"redundant":[56],"ones,":[57],"clustering":[58],"together":[59],"neighbors,":[60],"associating":[62],"aligning":[64],"clusters":[65],"with":[66],"unique":[68],"parent.":[69],"Finally,":[70],"pseudogenes":[71],"are":[72],"classified":[73],"based":[74],"on":[75],"combination":[77],"criteria":[79],"including":[80],"homology,":[81],"intron-exon":[82],"structure,":[83],"existence":[85],"stop":[87],"codons":[88],"frameshifts.":[90]},"counts_by_year":[{"year":2026,"cited_by_count":7},{"year":2025,"cited_by_count":12},{"year":2024,"cited_by_count":15},{"year":2023,"cited_by_count":8},{"year":2022,"cited_by_count":10},{"year":2021,"cited_by_count":29},{"year":2020,"cited_by_count":14},{"year":2019,"cited_by_count":10},{"year":2018,"cited_by_count":9},{"year":2017,"cited_by_count":9},{"year":2016,"cited_by_count":9},{"year":2015,"cited_by_count":6},{"year":2014,"cited_by_count":17},{"year":2013,"cited_by_count":4},{"year":2012,"cited_by_count":7}],"updated_date":"2026-04-19T08:26:33.389920","created_date":"2025-10-10T00:00:00"}
