{"id":"https://openalex.org/W2104680847","doi":"https://doi.org/10.1093/bioinformatics/bti092","title":"A novel means of using gene clusters in a two-step empirical Bayes method for predicting classes of samples","display_name":"A novel means of using gene clusters in a two-step empirical Bayes method for predicting classes of samples","publication_year":2004,"publication_date":"2004-10-28","ids":{"openalex":"https://openalex.org/W2104680847","doi":"https://doi.org/10.1093/bioinformatics/bti092","mag":"2104680847","pmid":"https://pubmed.ncbi.nlm.nih.gov/15514000"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/bti092","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bti092","pdf_url":null,"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":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5080090747","display_name":"Yuan Ji","orcid":"https://orcid.org/0000-0003-4712-5567"},"institutions":[{"id":"https://openalex.org/I1343551460","display_name":"The University of Texas MD Anderson Cancer Center","ror":"https://ror.org/04twxam07","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1343551460"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yuan Ji","raw_affiliation_strings":["Department of Biostatistics and Applied Mathematics, The University of Texas M.D. Anderson Cancer Center Houston, TX 77030, USA. yuanji@mdanderson.org","Department of Biostatistics and Applied Mathematics , The University of Texas, M.D. Anderson Cancer Center , Houston, TX, 77030, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biostatistics and Applied Mathematics, The University of Texas M.D. Anderson Cancer Center Houston, TX 77030, USA. yuanji@mdanderson.org","institution_ids":["https://openalex.org/I1343551460"]},{"raw_affiliation_string":"Department of Biostatistics and Applied Mathematics , The University of Texas, M.D. Anderson Cancer Center , Houston, TX, 77030, USA","institution_ids":["https://openalex.org/I1343551460"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5012231058","display_name":"Kam\u2010Wah Tsui","orcid":null},"institutions":[{"id":"https://openalex.org/I135310074","display_name":"University of Wisconsin\u2013Madison","ror":"https://ror.org/01y2jtd41","country_code":"US","type":"education","lineage":["https://openalex.org/I135310074"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Kam-Wah Tsui","raw_affiliation_strings":["Department of Statistics, The University of Wisconsin-Madison Madison, WI 53706, USA#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Statistics, The University of Wisconsin-Madison Madison, WI 53706, USA#TAB#","institution_ids":["https://openalex.org/I135310074"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5001986524","display_name":"KyungMann Kim","orcid":"https://orcid.org/0000-0002-6726-003X"},"institutions":[{"id":"https://openalex.org/I135310074","display_name":"University of Wisconsin\u2013Madison","ror":"https://ror.org/01y2jtd41","country_code":"US","type":"education","lineage":["https://openalex.org/I135310074"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"KyungMann Kim","raw_affiliation_strings":["Department of Biostatistics and Medical Informatics, The University of Wisconsin-Madison Madison, WI 53792, USA#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biostatistics and Medical Informatics, The University of Wisconsin-Madison Madison, WI 53792, USA#TAB#","institution_ids":["https://openalex.org/I135310074"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":3989,"currency":"USD","value_usd":3989},"apc_paid":null,"fwci":0.2263,"has_fulltext":false,"cited_by_count":7,"citation_normalized_percentile":{"value":0.52610939,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":96},"biblio":{"volume":"21","issue":"7","first_page":"1055","last_page":"1061"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10885","display_name":"Gene expression and cancer classification","score":0.9399999976158142,"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":0.9399999976158142,"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/T11901","display_name":"Bayesian Methods and Mixture Models","score":0.0203000009059906,"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"}},{"id":"https://openalex.org/T10136","display_name":"Statistical Methods and Inference","score":0.006500000134110451,"subfield":{"id":"https://openalex.org/subfields/2613","display_name":"Statistics and Probability"},"field":{"id":"https://openalex.org/fields/26","display_name":"Mathematics"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/bayes-theorem","display_name":"Bayes' theorem","score":0.8081797361373901},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5834845304489136},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.49622660875320435},{"id":"https://openalex.org/keywords/bayesian-probability","display_name":"Bayesian probability","score":0.32766157388687134},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3221876621246338},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2840576767921448}],"concepts":[{"id":"https://openalex.org/C207201462","wikidata":"https://www.wikidata.org/wiki/Q182505","display_name":"Bayes' theorem","level":3,"score":0.8081797361373901},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5834845304489136},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.49622660875320435},{"id":"https://openalex.org/C107673813","wikidata":"https://www.wikidata.org/wiki/Q812534","display_name":"Bayesian probability","level":2,"score":0.32766157388687134},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3221876621246338},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2840576767921448}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005786","descriptor_name":"Gene Expression Regulation","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D005786","descriptor_name":"Gene Expression Regulation","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D005786","descriptor_name":"Gene Expression Regulation","qualifier_ui":"Q000502","qualifier_name":"physiology","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":"D007938","descriptor_name":"Leukemia","qualifier_ui":"Q000175","qualifier_name":"diagnosis","is_major_topic":false},{"descriptor_ui":"D007938","descriptor_name":"Leukemia","qualifier_ui":"Q000175","qualifier_name":"diagnosis","is_major_topic":false},{"descriptor_ui":"D007938","descriptor_name":"Leukemia","qualifier_ui":"Q000175","qualifier_name":"diagnosis","is_major_topic":false},{"descriptor_ui":"D007938","descriptor_name":"Leukemia","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D007938","descriptor_name":"Leukemia","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D007938","descriptor_name":"Leukemia","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009363","descriptor_name":"Neoplasm Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D009363","descriptor_name":"Neoplasm Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D009363","descriptor_name":"Neoplasm Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D010363","descriptor_name":"Pattern Recognition, Automated","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D010363","descriptor_name":"Pattern Recognition, Automated","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D010363","descriptor_name":"Pattern Recognition, Automated","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D014408","descriptor_name":"Biomarkers, Tumor","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D014408","descriptor_name":"Biomarkers, Tumor","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D014408","descriptor_name":"Biomarkers, Tumor","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020411","descriptor_name":"Oligonucleotide Array Sequence Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020411","descriptor_name":"Oligonucleotide Array Sequence Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020411","descriptor_name":"Oligonucleotide Array Sequence Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/bti092","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bti092","pdf_url":null,"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:15514000","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/15514000","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":"Comparative Study"}],"best_oa_location":null,"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/15","display_name":"Life in Land","score":0.47999998927116394}],"awards":[{"id":"https://openalex.org/G3792621242","display_name":null,"funder_award_id":"CA 90270","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"},{"id":"https://openalex.org/G937877068","display_name":null,"funder_award_id":"CA-52733","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"}],"funders":[{"id":"https://openalex.org/F4320337351","display_name":"National Cancer Institute","ror":"https://ror.org/040gcmg81"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":12,"referenced_works":["https://openalex.org/W1579271636","https://openalex.org/W1966701961","https://openalex.org/W2016728733","https://openalex.org/W2107956883","https://openalex.org/W2109363337","https://openalex.org/W2135187880","https://openalex.org/W2146646206","https://openalex.org/W2149720473","https://openalex.org/W2150926065","https://openalex.org/W2168561598","https://openalex.org/W2309277749","https://openalex.org/W2488678869"],"related_works":["https://openalex.org/W2748952813","https://openalex.org/W2390279801","https://openalex.org/W2358668433","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W2382290278","https://openalex.org/W2478288626","https://openalex.org/W2350741829","https://openalex.org/W2530322880","https://openalex.org/W1596801655"],"abstract_inverted_index":{"Abstract":[0],"Motivation:":[1],"The":[2,160],"classification":[3,26,99,190],"of":[4,34,43,45,64,67,121,152,200],"samples":[5],"using":[6,185],"gene":[7,46,58,123],"expression":[8,47,59,124],"profiles":[9],"is":[10,27,39,61,163,222],"an":[11,172],"important":[12,50],"application":[13],"in":[14,52,70,143,155],"areas":[15],"such":[16],"as":[17,101],"cancer":[18],"research":[19],"and":[20,36,182],"environmental":[21],"health":[22],"studies.":[23],"However,":[24],"the":[25,62,65,71,108,113,131,136,141,144,150],"usually":[28],"based":[29],"on":[30],"a":[31,40,95,102,118,197],"small":[32,84],"number":[33,66,151,199],"samples,":[35],"each":[37],"sample":[38],"long":[41],"vector":[42],"thousands":[44],"levels.":[48],"An":[49,217],"issue":[51],"parametric":[53],"modeling":[54],"for":[55,89,139,204,220],"so":[56],"many":[57],"levels":[60,125],"control":[63],"nuisance":[68,153],"parameters":[69,154],"model.":[72,158],"Large":[73],"models":[74,85],"often":[75],"lead":[76],"to":[77,104,126,168,228],"intensive":[78],"or":[79],"even":[80,195],"intractable":[81],"computation,":[82],"while":[83],"may":[86],"be":[87],"inadequate":[88],"complex":[90],"data.":[91],"Methodology:":[92],"We":[93,177],"propose":[94],"two-step":[96],"empirical":[97,173],"Bayes":[98,174],"method":[100],"solution":[103],"this":[105],"issue.":[106],"At":[107,130],"first":[109],"step,":[110,133],"we":[111,147],"use":[112],"model-based":[114],"cluster":[115],"algorithm":[116],"with":[117],"non-traditional":[119],"purpose":[120],"assigning":[122],"form":[127],"abundance":[128],"groups.":[129],"second":[132],"by":[134,226],"assuming":[135],"same":[137,145],"variance":[138],"all":[140],"genes":[142,201],"group,":[146],"substantially":[148],"reduce":[149],"our":[156,186],"statistical":[157],"Results:":[159],"proposed":[161],"model":[162],"more":[164],"parsimonious,":[165],"which":[166],"leads":[167],"efficient":[169],"computation":[170,221],"under":[171],"estimation":[175],"procedure.":[176],"consider":[178],"two":[179],"real":[180],"examples":[181],"simulate":[183],"data":[184],"method.":[187],"Desired":[188],"low":[189],"error":[191],"rates":[192],"are":[193,202,213],"obtained":[194],"when":[196],"large":[198],"pre-selected":[203],"class":[205],"prediction.":[206],"Availability:":[207],"Supplemental":[208],"materials":[209],"including":[210],"technical":[211],"details":[212],"available":[214,223],"at":[215],"\u201chttp://odin.mdacc.tmc.edu/~yuanj/papers/sup.pdf\u201d.":[216],"R":[218],"program":[219],"upon":[224],"request":[225],"email":[227],"Yuan":[229],"Ji":[230],"(yuanji@mdanderson.org)":[231],"Contact:":[232],"yuanji@mdanderson.org":[233]},"counts_by_year":[{"year":2023,"cited_by_count":1},{"year":2013,"cited_by_count":1},{"year":2012,"cited_by_count":2}],"updated_date":"2026-08-21T09:56:20.448147","created_date":"2025-10-10T00:00:00"}