{"id":"https://openalex.org/W2549951352","doi":"https://doi.org/10.1039/9781782626732-00365","title":"Proteogenomics: Proteomics for Genome Annotation","display_name":"Proteogenomics: Proteomics for Genome Annotation","publication_year":2016,"publication_date":"2016-11-15","ids":{"openalex":"https://openalex.org/W2549951352","doi":"https://doi.org/10.1039/9781782626732-00365","mag":"2549951352"},"language":"en","primary_location":{"id":"doi:10.1039/9781782626732-00365","is_oa":false,"landing_page_url":"https://doi.org/10.1039/9781782626732-00365","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proteome Informatics","raw_type":"book-chapter"},"type":"book-chapter","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/A5052461667","display_name":"Fawaz Ghali","orcid":"https://orcid.org/0000-0002-2628-8562"},"institutions":[{"id":"https://openalex.org/I11983389","display_name":"Manchester Metropolitan University","ror":"https://ror.org/02hstj355","country_code":"GB","type":"education","lineage":["https://openalex.org/I11983389"]},{"id":"https://openalex.org/I146655781","display_name":"University of Liverpool","ror":"https://ror.org/04xs57h96","country_code":"GB","type":"education","lineage":["https://openalex.org/I146655781"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Fawaz Ghali","raw_affiliation_strings":["Institute of Integrative Biology, University of Liverpool, Biosciences Building Crown Street Liverpool L69 7ZB UK andrew.jones@liverpool.ac.uk","School of Computing, Mathematics and Digital Technology, Manchester Metropolitan University, Chester Street Manchester M1 5GD UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Integrative Biology, University of Liverpool, Biosciences Building Crown Street Liverpool L69 7ZB UK andrew.jones@liverpool.ac.uk","institution_ids":["https://openalex.org/I146655781"]},{"raw_affiliation_string":"School of Computing, Mathematics and Digital Technology, Manchester Metropolitan University, Chester Street Manchester M1 5GD UK","institution_ids":["https://openalex.org/I11983389"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5073268875","display_name":"Andrew R. Jones","orcid":"https://orcid.org/0000-0001-6118-9327"},"institutions":[{"id":"https://openalex.org/I146655781","display_name":"University of Liverpool","ror":"https://ror.org/04xs57h96","country_code":"GB","type":"education","lineage":["https://openalex.org/I146655781"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Andrew R. Jones","raw_affiliation_strings":["Institute of Integrative Biology, University of Liverpool, Biosciences Building Crown Street Liverpool L69 7ZB UK andrew.jones@liverpool.ac.uk"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Integrative Biology, University of Liverpool, Biosciences Building Crown Street Liverpool L69 7ZB UK andrew.jones@liverpool.ac.uk","institution_ids":["https://openalex.org/I146655781"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.1964452,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":"365","last_page":"384"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","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"}},"topics":[{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","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/T10519","display_name":"Advanced Proteomics Techniques and Applications","score":0.9980999827384949,"subfield":{"id":"https://openalex.org/subfields/1607","display_name":"Spectroscopy"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T13937","display_name":"Genetics, Bioinformatics, and Biomedical Research","score":0.9921000003814697,"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/proteogenomics","display_name":"Proteogenomics","score":0.9844908118247986},{"id":"https://openalex.org/keywords/annotation","display_name":"Annotation","score":0.6402963399887085},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.6280510425567627},{"id":"https://openalex.org/keywords/proteomics","display_name":"Proteomics","score":0.6226551532745361},{"id":"https://openalex.org/keywords/genome-project","display_name":"Genome project","score":0.6146912574768066},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5982298851013184},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.561907947063446},{"id":"https://openalex.org/keywords/gene-annotation","display_name":"Gene Annotation","score":0.5370781421661377},{"id":"https://openalex.org/keywords/genomics","display_name":"Genomics","score":0.5130833387374878},{"id":"https://openalex.org/keywords/gene-prediction","display_name":"Gene prediction","score":0.5090691447257996},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.481246680021286},{"id":"https://openalex.org/keywords/dna-sequencing","display_name":"DNA sequencing","score":0.4785393178462982},{"id":"https://openalex.org/keywords/rna-splicing","display_name":"RNA splicing","score":0.43107447028160095},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.3731681704521179},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.16390705108642578}],"concepts":[{"id":"https://openalex.org/C145741570","wikidata":"https://www.wikidata.org/wiki/Q7251534","display_name":"Proteogenomics","level":5,"score":0.9844908118247986},{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.6402963399887085},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.6280510425567627},{"id":"https://openalex.org/C46111723","wikidata":"https://www.wikidata.org/wiki/Q471857","display_name":"Proteomics","level":3,"score":0.6226551532745361},{"id":"https://openalex.org/C89566754","wikidata":"https://www.wikidata.org/wiki/Q2273828","display_name":"Genome project","level":4,"score":0.6146912574768066},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5982298851013184},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.561907947063446},{"id":"https://openalex.org/C2908923196","wikidata":"https://www.wikidata.org/wiki/Q5205742","display_name":"Gene Annotation","level":4,"score":0.5370781421661377},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.5130833387374878},{"id":"https://openalex.org/C105565629","wikidata":"https://www.wikidata.org/wiki/Q1248292","display_name":"Gene prediction","level":4,"score":0.5090691447257996},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.481246680021286},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.4785393178462982},{"id":"https://openalex.org/C54458228","wikidata":"https://www.wikidata.org/wiki/Q237218","display_name":"RNA splicing","level":4,"score":0.43107447028160095},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.3731681704521179},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.16390705108642578}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1039/9781782626732-00365","is_oa":false,"landing_page_url":"https://doi.org/10.1039/9781782626732-00365","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proteome Informatics","raw_type":"book-chapter"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G8988616008","display_name":null,"funder_award_id":"BB/L024462/1","funder_id":"https://openalex.org/F4320334629","funder_display_name":"Biotechnology and Biological Sciences Research Council"}],"funders":[{"id":"https://openalex.org/F4320334629","display_name":"Biotechnology and Biological Sciences Research Council","ror":"https://ror.org/00cwqg982"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":40,"referenced_works":["https://openalex.org/W381649575","https://openalex.org/W776868819","https://openalex.org/W1852508338","https://openalex.org/W1903350925","https://openalex.org/W1977790981","https://openalex.org/W1988810589","https://openalex.org/W1999751815","https://openalex.org/W2006886495","https://openalex.org/W2012159778","https://openalex.org/W2014344192","https://openalex.org/W2017867429","https://openalex.org/W2019158910","https://openalex.org/W2023270843","https://openalex.org/W2026433130","https://openalex.org/W2031095666","https://openalex.org/W2035291731","https://openalex.org/W2042415836","https://openalex.org/W2057761395","https://openalex.org/W2062288489","https://openalex.org/W2077631134","https://openalex.org/W2111797812","https://openalex.org/W2111846704","https://openalex.org/W2113620105","https://openalex.org/W2122982012","https://openalex.org/W2126419817","https://openalex.org/W2129272652","https://openalex.org/W2136482257","https://openalex.org/W2141572089","https://openalex.org/W2143110620","https://openalex.org/W2148889933","https://openalex.org/W2156052197","https://openalex.org/W2161811833","https://openalex.org/W2168292723","https://openalex.org/W2174838639","https://openalex.org/W2207888390","https://openalex.org/W2272660092","https://openalex.org/W6639918549","https://openalex.org/W6683149533","https://openalex.org/W6687982328","https://openalex.org/W6694173315"],"related_works":["https://openalex.org/W2294108133","https://openalex.org/W2955310315","https://openalex.org/W2131807022","https://openalex.org/W2117510233","https://openalex.org/W1872959741","https://openalex.org/W1975798613","https://openalex.org/W2754860811","https://openalex.org/W2916192076","https://openalex.org/W2592432365","https://openalex.org/W4251119835"],"abstract_inverted_index":{"One":[0],"of":[1,10,17,22,26,72,84,119,141],"major":[2],"bottlenecks":[3],"in":[4,66,182],"omics":[5],"biology":[6],"is":[7,136,147],"the":[8,18,30,67,70,82,116,125,152,159,175],"generation":[9],"accurate":[11],"gene":[12,56,107],"models,":[13],"including":[14],"correct":[15],"calling":[16],"start":[19],"codon,":[20],"splicing":[21],"introns":[23],"(taking":[24],"account":[25],"alternative":[27],"splicing),":[28],"and":[29,81,105,150,177,186],"stop":[31],"codon":[32],"\u2013":[33],"collectively":[34],"called":[35,148],"genome":[36,39,145],"annotation.":[37],"Current":[38],"annotation":[40,146],"approaches":[41,111,172],"for":[42,61,103,144,154,169,173,179],"newly":[43],"sequenced":[44],"genomes":[45],"are":[46],"generally":[47],"based":[48],"on":[49],"automated":[50],"or":[51],"semi-automated":[52],"methods,":[53],"usually":[54],"involving":[55],"finding":[57],"software":[58,163],"to":[59,114],"look":[60],"intrinsic":[62],"gene-like":[63],"signatures":[64],"(motifs)":[65],"DNA":[68],"sequence,":[69],"propagation":[71],"annotations":[73],"from":[74,89],"other":[75],"(more":[76],"well":[77],"annotated)":[78],"related":[79],"species,":[80],"mapping":[83],"experimental":[85],"data":[86,96,143,181],"sets,":[87],"particularly":[88],"RNA":[90],"Sequencing":[91],"(RNA-Seq).":[92],"Large":[93],"scale":[94],"proteomics":[95,110,142],"can":[97,129],"also":[98],"play":[99],"an":[100],"important":[101],"role":[102],"confirming":[104],"correcting":[106],"models.":[108],"While":[109],"tend":[112],"not":[113],"have":[115,124,166],"same":[117],"level":[118],"sensitivity":[120],"as":[121],"RNA-Seq,":[122],"they":[123,128],"advantage":[126],"that":[127,132,165],"provide":[130],"evidence":[131],"a":[133],"predicted":[134],"gene/transcript":[135],"indeed":[137],"protein-coding.":[138],"The":[139],"use":[140],"proteogenomics,":[149,170],"forms":[151],"basis":[153],"this":[155],"chapter.":[156],"We":[157],"describe":[158],"theoretical":[160],"underpinnings,":[161],"different":[162],"packages":[164],"been":[167],"developed":[168],"statistical":[171],"validating":[174],"evidence,":[176],"support":[178],"proteogenomics":[180],"file":[183],"formats,":[184],"standards":[185],"databases.":[187]},"counts_by_year":[],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}