{"id":"https://openalex.org/W2164539618","doi":"https://doi.org/10.1093/bib/bbm022","title":"Bayesian Inference for Gene Expression and Proteomics.","display_name":"Bayesian Inference for Gene Expression and Proteomics.","publication_year":2007,"publication_date":"2007-06-20","ids":{"openalex":"https://openalex.org/W2164539618","doi":"https://doi.org/10.1093/bib/bbm022","mag":"2164539618"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbm022","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbm022","pdf_url":"https://academic.oup.com/bib/article-pdf/8/5/376/578311/bbm022.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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":"Briefings in Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bib/article-pdf/8/5/376/578311/bbm022.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100664656","display_name":"Ping Ma","orcid":"https://orcid.org/0000-0002-5728-3596"},"institutions":[{"id":"https://openalex.org/I157725225","display_name":"University of Illinois Urbana-Champaign","ror":"https://ror.org/047426m28","country_code":"US","type":"education","lineage":["https://openalex.org/I157725225"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"P. Ma","raw_affiliation_strings":["Department of Statistics and Institute for Genomic Biology University of Illinois at Urbana-Champaign, USA","Department of Statistics andInstitute for Genomic BiologyUniversity of Illinois at Urbana-Champaign, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Statistics and Institute for Genomic Biology University of Illinois at Urbana-Champaign, USA","institution_ids":["https://openalex.org/I157725225"]},{"raw_affiliation_string":"Department of Statistics andInstitute for Genomic BiologyUniversity of Illinois at Urbana-Champaign, USA","institution_ids":["https://openalex.org/I157725225"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5100664656"],"corresponding_institution_ids":["https://openalex.org/I157725225"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":null,"fwci":1.7614,"has_fulltext":true,"cited_by_count":50,"citation_normalized_percentile":{"value":0.84408179,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"8","issue":"5","first_page":"376","last_page":"377"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10885","display_name":"Gene expression and cancer classification","score":0.8906999826431274,"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/T10885","display_name":"Gene expression and cancer classification","score":0.8906999826431274,"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/T12535","display_name":"Machine Learning and Data Classification","score":0.7675999999046326,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/inference","display_name":"Inference","score":0.7040951251983643},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.6607831716537476},{"id":"https://openalex.org/keywords/proteomics","display_name":"Proteomics","score":0.5847806930541992},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5120354294776917},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.4916730523109436},{"id":"https://openalex.org/keywords/bayesian-probability","display_name":"Bayesian probability","score":0.4849379360675812},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.44471877813339233},{"id":"https://openalex.org/keywords/expression","display_name":"Expression (computer science)","score":0.4385233521461487},{"id":"https://openalex.org/keywords/bayesian-inference","display_name":"Bayesian inference","score":0.41221195459365845},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.39149045944213867},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.35144472122192383},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.3218868374824524},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.2645568549633026}],"concepts":[{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.7040951251983643},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6607831716537476},{"id":"https://openalex.org/C46111723","wikidata":"https://www.wikidata.org/wiki/Q471857","display_name":"Proteomics","level":3,"score":0.5847806930541992},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5120354294776917},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.4916730523109436},{"id":"https://openalex.org/C107673813","wikidata":"https://www.wikidata.org/wiki/Q812534","display_name":"Bayesian probability","level":2,"score":0.4849379360675812},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.44471877813339233},{"id":"https://openalex.org/C90559484","wikidata":"https://www.wikidata.org/wiki/Q778379","display_name":"Expression (computer science)","level":2,"score":0.4385233521461487},{"id":"https://openalex.org/C160234255","wikidata":"https://www.wikidata.org/wiki/Q812535","display_name":"Bayesian inference","level":3,"score":0.41221195459365845},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.39149045944213867},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.35144472122192383},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.3218868374824524},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.2645568549633026},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1093/bib/bbm022","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbm022","pdf_url":"https://academic.oup.com/bib/article-pdf/8/5/376/578311/bbm022.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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":"Briefings in Bioinformatics","raw_type":"journal-article"}],"best_oa_location":{"id":"doi:10.1093/bib/bbm022","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbm022","pdf_url":"https://academic.oup.com/bib/article-pdf/8/5/376/578311/bbm022.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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":"Briefings in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2164539618.pdf","grobid_xml":"https://content.openalex.org/works/W2164539618.grobid-xml"},"referenced_works_count":0,"referenced_works":[],"related_works":["https://openalex.org/W2381031055","https://openalex.org/W2366070815","https://openalex.org/W2372267530","https://openalex.org/W2969189870","https://openalex.org/W3015855446","https://openalex.org/W4303857162","https://openalex.org/W2965643117","https://openalex.org/W2407375987","https://openalex.org/W2505726097","https://openalex.org/W2950975704"],"abstract_inverted_index":{"A":[0,661],"text":[1],"that":[2,82,247,311,509,563,627,667,772,779],"has":[3,13,466],"a":[4,17,23,89,223,281,351,407,435,522,558,601,632,647,719,721,742,760],"systematic":[5],"account":[6],"of":[7,39,92,100,125,141,154,176,208,219,235,256,284,289,296,302,330,337,420,424,438,449,458,478,488,555,557,574,585,655,664,683,692,744,751,764],"Bayesian":[8,30,61,145,159,312,331,425,511,519,524,560,591,684,716,725,752],"analysis":[9,99,121,237,255,685],"in":[10,32,45,59,63,185,226,232,357,388,402,413,427,440,463,504,514,589,593,600,703,715,734,754,769,789],"computational":[11],"biology":[12],"been":[14,468],"needed":[15],"for":[16,54,72,161,286,495,534,572,786,792],"long":[18],"time.":[19],"This":[20],"book":[21,70,86,127,221,366,418,516,740],"is":[22,49,128,299,308,373,508,562,624,650,666,686,727],"timely":[24],"publication":[25],"entirely":[26],"devoted":[27],"to":[28,78,111,134,333,470,500,528,566,635,651,671,673,794],"cutting-edge":[29],"methods":[31,285,313,332,426,451,503,726,732,753],"genomics":[33,428],"and":[34,37,75,104,211,216,242,259,265,318,346,376,405,429,482,748,762],"proteomics":[35],"research":[36,77,400,412,439],"many":[38,370,389,421,510,594],"its":[40],"contributors":[41],"are":[42,57,188,268,498,517,677],"leading":[43],"authorities":[44],"the":[46,69,126,151,155,174,220,269,287,300,324,328,361,365,377,382,386,398,417,441,444,447,459,475,479,489,544,548,582,586,637,641,653,656,687,690,693,709,731,790],"field.":[47,442],"It":[48,108,307],"thus":[50],"an":[51,783],"indispensable":[52],"reference":[53,761],"researchers":[55,788],"who":[56,497],"interested":[58],"applying":[60],"techniques":[62],"their":[64,113,119,505],"own":[65,506],"biological":[66],"research.":[67],"Moreover,":[68,581],"calls":[71],"more":[73],"methodological":[74],"theoretical":[76],"surmount":[79],"challenging":[80],"issues":[81,688],"still":[83],"remain.":[84],"The":[85,123,214,272,294,706],"starts":[87],"with":[88,191,276,539],"brief":[90],"review":[91,283],"three":[93,131,136],"key":[94],"high-throughput":[95],"biotechnologies,":[96],"microarray,":[97],"serial":[98],"gene":[101,177,209,340,460],"expression":[102,178,210,341,461],"(SAGE)":[103],"mass":[105,239],"spectrometry":[106,240,258],"experiments.":[107],"then":[109],"continues":[110],"discuss":[112],"data":[114,241],"structures":[115],"as":[116,118,203,205,474,615,759],"well":[117,204,309,374,625],"statistical":[120,606],"strategy.":[122],"rest":[124],"divided":[129],"into":[130],"sections":[132,218],"corresponding":[133],"these":[135,502],"high":[137,192],"throughput":[138],"technologies,":[139],"each":[140,535],"which":[142,279,576,696],"focuses":[143,168],"on":[144,158,169,238,254,353,410,610,724],"analysis.":[146,717],"Chapters":[147,249,303],"2":[148],"through":[149,251,305,547],"11,":[150],"first":[152],"section":[153,187,274],"book,":[156],"concentrate":[157],"inference":[160,607],"microarray":[162,358],"data.":[163,182],"Among":[164],"them,":[165],"Chapter":[166,277,395,464],"4":[167],"low":[170],"level":[171,193],"analysis,":[172,194],"including":[173,195,339],"estimation":[175,457],"index":[179,462],"from":[180],"image":[181],"Other":[183],"chapters":[184,390],"this":[186,319,414,515,704,735,739],"primarily":[189],"concerned":[190],"identifying":[196],"differentially":[197],"expressed":[198,599],"genes,":[199],"clustering,":[200],"marker":[201],"identification":[202,288],"joint":[206],"modeling":[207],"disease":[212],"status.":[213],"second":[215],"third":[217,273],"fill":[222],"critical":[224],"gap":[225],"existing":[227],"bioinformatics":[228],"books":[229],"by":[230,323,326,369],"providing":[231],"depth":[233],"coverage":[234,750],"rigorous":[236],"DNA":[243],"motif":[244,403],"identification.":[245],"To":[246],"end,":[248],"12":[250],"15":[252],"focus":[253,301],"protein":[257],"SAGE":[260],"data,":[261,338,342,345,540],"where":[262],"mixture":[263],"models":[264,267,512],"mixed":[266],"basic":[270],"ingredients.":[271],"begins":[275],"16,":[278],"gives":[280],"wonderful":[282],"transcription":[290],"factor":[291],"binding":[292,344],"motifs.":[293],"elucidation":[295],"regulatory":[297],"networks":[298],"17":[304],"21.":[306],"known":[310,626],"can":[314,379,542,596,629],"effectively":[315],"extract":[316],"information,":[317],"was":[320,367],"nicely":[321],"illustrated":[322],"authors":[325,707],"showing":[327],"power":[329],"integrate":[334],"multiple":[335],"types":[336],"protein\u2013DNA":[343],"Gene":[347],"Ontology":[348],"annotations.":[349],"Finally,":[350],"chapter":[352],"sample":[354,636],"size":[355],"calculation":[356],"experiments":[359],"concludes":[360],"book.":[362,705,736],"Even":[363],"though":[364],"contributed":[368],"authors,":[371],"it":[372,431,623,758,765,780],"structured":[375],"reader":[378],"easily":[380],"follow":[381],"presentation.":[383],"I":[384,756,773,775],"found":[385],"discussion":[387],"very":[391,579],"useful.":[392],"For":[393,455,718],"example,":[394,456],"16":[396],"provides":[397,741],"current":[399],"trends":[401],"discovery":[404],"sheds":[406],"fresh":[408],"light":[409],"future":[411],"area.":[415],"Since":[416],"consists":[419],"novel":[422],"applications":[423],"proteomics,":[430],"may":[432],"help":[433],"guide":[434],"new":[436],"wave":[437],"On":[443],"other":[445],"hand,":[446],"effectiveness":[448],"some":[450,530],"needs":[452,527,670],"further":[453],"investigation.":[454],"3,":[465],"not":[467,597,644,698],"compared":[469],"similar":[471],"methods,":[472],"such":[473,614],"Li\u2013Wong":[476],"model":[477,549,561,659],"Wong":[480],"group":[481],"robust":[483],"multi-array":[484],"average":[485],"(RMA)":[486],"method":[487,634],"Speed":[490],"group.":[491],"One":[492,680],"cautionary":[493],"note":[494],"practitioners":[496],"eager":[499],"adapt":[501],"research,":[507],"presented":[513,733],"hierarchical":[518,559,590],"models.":[520],"In":[521,737],"typical":[523],"paradigm,":[525],"one":[526,541,564,628],"specify":[529,567],"prior":[531],"(probability":[532],"distribution)":[533],"parameter.":[536],"Then":[537],"combining":[538],"get":[543,699],"posterior":[545,583,638,642,657,668],"distribution":[546,584,669],"using":[550],"Bayes":[551],"theorem.":[552],"Another":[553],"layer":[554],"complexity":[556],"need":[565],"probability":[568],"distributions":[569],"(hierarchical":[570],"prior)":[571],"priors":[573],"parameters,":[575],"could":[577],"be":[578,598,767,782],"tricky.":[580],"parameters":[587,676],"obtained":[588],"model,":[592],"circumstances,":[595],"closed":[602],"analytic":[603],"form.":[604],"Thus,":[605],"heavily":[608],"relies":[609],"iterative":[611,694],"sampling":[612],"techniques,":[613],"Markov":[616],"chain":[617],"Monte":[618],"Carlo":[619],"(MCMC)":[620],"methods.":[621],"However,":[622],"blindly":[630],"design":[631],"MCMC":[633],"even":[639],"if":[640,675],"does":[643],"exist.":[645],"Therefore,":[646],"good":[648],"practice":[649],"check":[652],"existence":[654,665],"after":[658],"setup.":[660],"necessary":[662],"condition":[663],"approach":[672],"zero":[674],"approaching":[678],"infinity.":[679],"related":[681],"aspect":[682],"concerning":[689],"convergence":[691],"samples,":[695],"do":[697],"too":[700],"much":[701],"attention":[702],"assume":[708],"readers":[710],"already":[711],"have":[712,776],"hands-on":[713],"experience":[714],"novice,":[720],"standard":[722],"textbook":[723],"essential":[728],"before":[729],"attempting":[730],"conclusion,":[738],"wealth":[743],"material,":[745],"deep":[746],"insight,":[747],"up-to-date":[749],"bioinformatics.":[755],"use":[757],"parts":[763],"will":[766,781],"used":[768],"graduate":[770],"classes":[771],"teach.":[774],"no":[777],"doubt":[778],"invaluable":[784],"source":[785],"all":[787],"field":[791],"years":[793],"come.":[795]},"counts_by_year":[{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":3},{"year":2019,"cited_by_count":3},{"year":2018,"cited_by_count":2},{"year":2017,"cited_by_count":2},{"year":2016,"cited_by_count":2},{"year":2015,"cited_by_count":3},{"year":2014,"cited_by_count":5},{"year":2013,"cited_by_count":3},{"year":2012,"cited_by_count":4}],"updated_date":"2026-07-30T17:31:21.811387","created_date":"2025-10-10T00:00:00"}