{"id":"https://openalex.org/W2152353895","doi":"https://doi.org/10.1093/bioinformatics/btl134","title":"Integrated analysis of transcriptomic and proteomic data of <i>Desulfovibrio vulgaris</i>: zero-inflated Poisson regression models to predict abundance of undetected proteins","display_name":"Integrated analysis of transcriptomic and proteomic data of <i>Desulfovibrio vulgaris</i>: zero-inflated Poisson regression models to predict abundance of undetected proteins","publication_year":2006,"publication_date":"2006-05-04","ids":{"openalex":"https://openalex.org/W2152353895","doi":"https://doi.org/10.1093/bioinformatics/btl134","mag":"2152353895","pmid":"https://pubmed.ncbi.nlm.nih.gov/16675466"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btl134","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btl134","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/22/13/1641/48838194/bioinformatics_22_13_1641.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/22/13/1641/48838194/bioinformatics_22_13_1641.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100642160","display_name":"Lei Nie","orcid":"https://orcid.org/0000-0002-2919-5337"},"institutions":[{"id":"https://openalex.org/I184565670","display_name":"Georgetown University","ror":"https://ror.org/05vzafd60","country_code":"US","type":"education","lineage":["https://openalex.org/I184565670"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Lei Nie","raw_affiliation_strings":["Department of Biostatistics, Bioinformatics and Biomathematics, Georgetown University 1 \u00a0 1 \u00a0 \u00a0 Washington DC 20057, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biostatistics, Bioinformatics and Biomathematics, Georgetown University 1 \u00a0 1 \u00a0 \u00a0 Washington DC 20057, USA","institution_ids":["https://openalex.org/I184565670"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5030319840","display_name":"Gang Wu","orcid":"https://orcid.org/0000-0002-1678-5864"},"institutions":[{"id":"https://openalex.org/I79272384","display_name":"University of Maryland, Baltimore County","ror":"https://ror.org/02qskvh78","country_code":"US","type":"education","lineage":["https://openalex.org/I79272384"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Gang Wu","raw_affiliation_strings":["Department of Biological Sciences, University of Maryland at Baltimore County 2 \u00a0 2 \u00a0 \u00a0 Baltimore, MD 21250, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biological Sciences, University of Maryland at Baltimore County 2 \u00a0 2 \u00a0 \u00a0 Baltimore, MD 21250, USA","institution_ids":["https://openalex.org/I79272384"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5028134583","display_name":"Fred J. Brockman","orcid":null},"institutions":[{"id":"https://openalex.org/I142606810","display_name":"Pacific Northwest National Laboratory","ror":"https://ror.org/05h992307","country_code":"US","type":"facility","lineage":["https://openalex.org/I1325736334","https://openalex.org/I1330989302","https://openalex.org/I142606810","https://openalex.org/I39565521"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Fred J. Brockman","raw_affiliation_strings":["Microbiology Department, Pacific Northwest National Laboratory 3 \u00a0 3 \u00a0 \u00a0 PO Box 999, Mail Stop P7-50, Richland, WA 99352, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Microbiology Department, Pacific Northwest National Laboratory 3 \u00a0 3 \u00a0 \u00a0 PO Box 999, Mail Stop P7-50, Richland, WA 99352, USA","institution_ids":["https://openalex.org/I142606810"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5035916673","display_name":"Weiwen Zhang","orcid":"https://orcid.org/0000-0001-8305-5653"},"institutions":[{"id":"https://openalex.org/I142606810","display_name":"Pacific Northwest National Laboratory","ror":"https://ror.org/05h992307","country_code":"US","type":"facility","lineage":["https://openalex.org/I1325736334","https://openalex.org/I1330989302","https://openalex.org/I142606810","https://openalex.org/I39565521"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Weiwen Zhang","raw_affiliation_strings":["Microbiology Department, Pacific Northwest National Laboratory 3 \u00a0 3 \u00a0 \u00a0 PO Box 999, Mail Stop P7-50, Richland, WA 99352, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Microbiology Department, Pacific Northwest National Laboratory 3 \u00a0 3 \u00a0 \u00a0 PO Box 999, Mail Stop P7-50, Richland, WA 99352, USA","institution_ids":["https://openalex.org/I142606810"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5035916673"],"corresponding_institution_ids":["https://openalex.org/I142606810"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":3.723,"has_fulltext":false,"cited_by_count":58,"citation_normalized_percentile":{"value":0.93596868,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"22","issue":"13","first_page":"1641","last_page":"1647"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10519","display_name":"Advanced Proteomics Techniques and Applications","score":0.9994999766349792,"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"}},"topics":[{"id":"https://openalex.org/T10519","display_name":"Advanced Proteomics Techniques and Applications","score":0.9994999766349792,"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/T10885","display_name":"Gene expression and cancer classification","score":0.9979000091552734,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9940000176429749,"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/desulfovibrio-vulgaris","display_name":"Desulfovibrio vulgaris","score":0.8115682601928711},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.6637436747550964},{"id":"https://openalex.org/keywords/proteomics","display_name":"Proteomics","score":0.5947905778884888},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.565878689289093},{"id":"https://openalex.org/keywords/poisson-distribution","display_name":"Poisson distribution","score":0.5416600704193115},{"id":"https://openalex.org/keywords/dna-microarray","display_name":"DNA microarray","score":0.4961434304714203},{"id":"https://openalex.org/keywords/count-data","display_name":"Count data","score":0.4334403872489929},{"id":"https://openalex.org/keywords/transcriptome","display_name":"Transcriptome","score":0.4286271333694458},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.3393402099609375},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.30083221197128296},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.23245015740394592},{"id":"https://openalex.org/keywords/statistics","display_name":"Statistics","score":0.20305702090263367},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.16223326325416565}],"concepts":[{"id":"https://openalex.org/C2781243026","wikidata":"https://www.wikidata.org/wiki/Q593811","display_name":"Desulfovibrio vulgaris","level":3,"score":0.8115682601928711},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6637436747550964},{"id":"https://openalex.org/C46111723","wikidata":"https://www.wikidata.org/wiki/Q471857","display_name":"Proteomics","level":3,"score":0.5947905778884888},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.565878689289093},{"id":"https://openalex.org/C100906024","wikidata":"https://www.wikidata.org/wiki/Q205692","display_name":"Poisson distribution","level":2,"score":0.5416600704193115},{"id":"https://openalex.org/C95371953","wikidata":"https://www.wikidata.org/wiki/Q591745","display_name":"DNA microarray","level":4,"score":0.4961434304714203},{"id":"https://openalex.org/C33643355","wikidata":"https://www.wikidata.org/wiki/Q5176731","display_name":"Count data","level":3,"score":0.4334403872489929},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.4286271333694458},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.3393402099609375},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.30083221197128296},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.23245015740394592},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.20305702090263367},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.16223326325416565},{"id":"https://openalex.org/C523546767","wikidata":"https://www.wikidata.org/wiki/Q10876","display_name":"Bacteria","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D000255","descriptor_name":"Adenosine Triphosphate","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D000255","descriptor_name":"Adenosine Triphosphate","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D000255","descriptor_name":"Adenosine Triphosphate","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D002138","descriptor_name":"Calibration","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002138","descriptor_name":"Calibration","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002138","descriptor_name":"Calibration","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002853","descriptor_name":"Chromatography, Liquid","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D002853","descriptor_name":"Chromatography, Liquid","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D002853","descriptor_name":"Chromatography, Liquid","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D011336","descriptor_name":"Probability","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011336","descriptor_name":"Probability","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011336","descriptor_name":"Probability","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D012044","descriptor_name":"Regression Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012044","descriptor_name":"Regression Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012044","descriptor_name":"Regression Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012333","descriptor_name":"RNA, Messenger","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012333","descriptor_name":"RNA, Messenger","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012333","descriptor_name":"RNA, Messenger","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D013058","descriptor_name":"Mass Spectrometry","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013058","descriptor_name":"Mass Spectrometry","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013058","descriptor_name":"Mass Spectrometry","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":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016012","descriptor_name":"Poisson Distribution","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016012","descriptor_name":"Poisson Distribution","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016012","descriptor_name":"Poisson Distribution","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016969","descriptor_name":"Desulfovibrio vulgaris","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D016969","descriptor_name":"Desulfovibrio vulgaris","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D016969","descriptor_name":"Desulfovibrio vulgaris","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D016969","descriptor_name":"Desulfovibrio vulgaris","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D016969","descriptor_name":"Desulfovibrio vulgaris","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D016969","descriptor_name":"Desulfovibrio vulgaris","qualifier_ui":"Q000378","qualifier_name":"metabolism","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},{"descriptor_ui":"D020411","descriptor_name":"Oligonucleotide Array Sequence Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020411","descriptor_name":"Oligonucleotide Array Sequence Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020411","descriptor_name":"Oligonucleotide Array Sequence Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D040901","descriptor_name":"Proteomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D040901","descriptor_name":"Proteomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D040901","descriptor_name":"Proteomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/btl134","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btl134","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/22/13/1641/48838194/bioinformatics_22_13_1641.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:16675466","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/16675466","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}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btl134","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btl134","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/22/13/1641/48838194/bioinformatics_22_13_1641.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":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320306084","display_name":"U.S. Department of Energy","ror":"https://ror.org/01bj3aw27"},{"id":"https://openalex.org/F4320306250","display_name":"Battelle","ror":"https://ror.org/01h5tnr73"},{"id":"https://openalex.org/F4320337547","display_name":"Laboratory Directed Research and Development","ror":"https://ror.org/01e41cf67"},{"id":"https://openalex.org/F4320338354","display_name":"Pacific Northwest National Laboratory","ror":"https://ror.org/05h992307"}],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2152353895.pdf"},"referenced_works_count":35,"referenced_works":["https://openalex.org/W1519199376","https://openalex.org/W1528905581","https://openalex.org/W1597678601","https://openalex.org/W1976317980","https://openalex.org/W1994662308","https://openalex.org/W2003172223","https://openalex.org/W2008883486","https://openalex.org/W2014481298","https://openalex.org/W2023848951","https://openalex.org/W2026465178","https://openalex.org/W2045718560","https://openalex.org/W2055412302","https://openalex.org/W2059315009","https://openalex.org/W2059572899","https://openalex.org/W2067642105","https://openalex.org/W2076016052","https://openalex.org/W2082516237","https://openalex.org/W2089492568","https://openalex.org/W2093772131","https://openalex.org/W2101345690","https://openalex.org/W2107363136","https://openalex.org/W2117212863","https://openalex.org/W2119634512","https://openalex.org/W2124681451","https://openalex.org/W2147256329","https://openalex.org/W2150758965","https://openalex.org/W2161723277","https://openalex.org/W2164954378","https://openalex.org/W2168297851","https://openalex.org/W2168846334","https://openalex.org/W2170076251","https://openalex.org/W2170949754","https://openalex.org/W2499163029","https://openalex.org/W3015463134","https://openalex.org/W4301861531"],"related_works":["https://openalex.org/W2060931646","https://openalex.org/W2148216078","https://openalex.org/W4319841362","https://openalex.org/W3134844154","https://openalex.org/W1970711679","https://openalex.org/W2901798679","https://openalex.org/W4388295412","https://openalex.org/W2503331259","https://openalex.org/W3120214361","https://openalex.org/W2116405300"],"abstract_inverted_index":{"MOTIVATION:":[0],"Integrated":[1],"analysis":[2],"of":[3,85,95,188,193,208,233,239],"global":[4],"scale":[5],"transcriptomic":[6],"and":[7,29,38,67,88,114,132,174,216,236],"proteomic":[8,68,86,215],"data":[9,69,87],"can":[10,179],"provide":[11],"important":[12],"insights":[13],"into":[14],"the":[15,24,81,89,109,157,186,194,197,206],"metabolic":[16],"mechanisms":[17],"underlying":[18],"complex":[19],"biological":[20,202],"systems.":[21],"However,":[22],"because":[23],"relationship":[25],"between":[26,112],"protein":[27,115,159,176],"abundance":[28,160,177],"mRNA":[30,113,172],"expression":[31,232,238],"level":[32,161],"is":[33,123],"complicated":[34],"by":[35,119,152,169,212],"many":[36],"cellular":[37],"physical":[39],"processes,":[40],"sophisticated":[41],"statistical":[42,61,210],"models":[43,104,211,228],"need":[44],"to":[45,48,63,107,139],"be":[46,180],"developed":[47],"capture":[49],"their":[50,171],"relationship.":[51],"RESULTS:":[52],"In":[53,117],"this":[54,153,189],"study,":[55,190],"we":[56],"describe":[57],"a":[58,92,124,142],"novel":[59],"data-driven":[60],"model":[62,145],"integrate":[64],"whole-genome":[65],"microarray":[66,217],"collected":[70],"from":[71,219],"Desulfovibrio":[72],"vulgaris":[73],"grown":[74,221,244],"under":[75],"three":[76],"different":[77],"conditions.":[78],"Based":[79],"on":[80,222,245],"Poisson":[82,102],"distribution":[83],"pattern":[84,111],"fact":[90],"that":[91,121,135],"large":[93],"number":[94],"proteins":[96,134,166,184,195],"were":[97,105,136],"undetected":[98,137,183],"(excess":[99],"zeros),":[100],"zero-inflated":[101],"(ZIP)-based":[103],"proposed":[106],"define":[108],"correlation":[110],"abundance.":[116],"addition,":[118],"assuming":[120],"there":[122],"probability":[125],"mass":[126],"at":[127],"zero":[128],"representing":[129],"unexpressed":[130],"genes":[131],"expressed":[133],"owing":[138],"technical":[140],"limitations,":[141],"Potential":[143],"ZIP":[144],"was":[146],"established.":[147],"Two":[148],"significant":[149],"improvements":[150],"introduced":[151],"approach":[154],"are":[155,167],"(1)":[156],"predicted":[158,181,230],"values":[162,178],"for":[163,182,200,242],"experimentally":[164],"detected":[165],"corrected":[168],"considering":[170],"levels":[173],"(2)":[175],"(in":[185],"case":[187],"approximately":[191],"83%":[192],"in":[196],"D.vulgaris":[198,220,243],"genome)":[199],"better":[201],"interpretation.":[203],"We":[204],"demonstrated":[205],"use":[207],"these":[209],"comparatively":[213],"analyzing":[214],"results":[218],"lactate-based":[223],"versus":[224],"formate-based":[225],"media.":[226],"These":[227],"correctly":[229],"increased":[231],"Ech":[234],"hydrogenase":[235,241],"decreased":[237],"Coo":[240],"formate.":[246]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":4},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":3},{"year":2019,"cited_by_count":4},{"year":2018,"cited_by_count":1},{"year":2016,"cited_by_count":7},{"year":2015,"cited_by_count":3},{"year":2014,"cited_by_count":2},{"year":2013,"cited_by_count":5},{"year":2012,"cited_by_count":1}],"updated_date":"2026-06-16T07:32:37.131356","created_date":"2016-06-24T00:00:00"}
