{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,28]],"date-time":"2026-03-28T03:14:49Z","timestamp":1774667689195,"version":"3.50.1"},"reference-count":24,"publisher":"Oxford University Press (OUP)","license":[{"start":{"date-parts":[[2016,10,3]],"date-time":"2016-10-03T00:00:00Z","timestamp":1475452800000},"content-version":"vor","delay-in-days":1737,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/2.5"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2012,1,1]]},"DOI":"10.1093\/database\/bas002","type":"journal-article","created":{"date-parts":[[2012,2,9]],"date-time":"2012-02-09T20:40:14Z","timestamp":1328820014000},"source":"Crossref","is-referenced-by-count":25,"title":["The gene-specific codon counting database: a genome-based catalog of one-, two-, three-, four- and five-codon combinations present in Saccharomyces cerevisiae genes"],"prefix":"10.1093","volume":"2012","author":[{"given":"Sudheer","family":"Tumu","sequence":"first","affiliation":[{"name":"Department of Computer Science, 2Cancer Research Center, University at Albany, 3RNA Institute and 4College of Nanoscale Science and Engineering, University at Albany, State University of New York, Albany, NY 12222, USA"}]},{"given":"Ashish","family":"Patil","sequence":"additional","affiliation":[{"name":"Department of Computer Science, 2Cancer Research Center, University at Albany, 3RNA Institute and 4College of Nanoscale Science and Engineering, University at Albany, State University of New York, Albany, NY 12222, USA"},{"name":"Department of Computer Science, 2Cancer Research Center, University at Albany, 3RNA Institute and 4College of Nanoscale Science and Engineering, University at Albany, State University of New York, Albany, NY 12222, USA"}]},{"given":"William","family":"Towns","sequence":"additional","affiliation":[{"name":"Department of Computer Science, 2Cancer Research Center, University at Albany, 3RNA Institute and 4College of Nanoscale Science and Engineering, University at Albany, State University of New York, Albany, NY 12222, USA"},{"name":"Department of Computer Science, 2Cancer Research Center, University at Albany, 3RNA Institute and 4College of Nanoscale Science and Engineering, University at Albany, State University of New York, Albany, NY 12222, USA"},{"name":"Department of Computer Science, 2Cancer Research Center, University at Albany, 3RNA Institute and 4College of Nanoscale Science and Engineering, University at Albany, State University of New York, Albany, NY 12222, USA"}]},{"given":"Madhu","family":"Dyavaiah","sequence":"additional","affiliation":[{"name":"Department of Computer Science, 2Cancer Research Center, University at Albany, 3RNA Institute and 4College of Nanoscale Science and Engineering, University at Albany, State University of New York, Albany, NY 12222, USA"},{"name":"Department of Computer Science, 2Cancer Research Center, University at Albany, 3RNA Institute and 4College of Nanoscale Science and Engineering, University at Albany, State University of New York, Albany, NY 12222, USA"},{"name":"Department of Computer Science, 2Cancer Research Center, University at Albany, 3RNA Institute and 4College of Nanoscale Science and Engineering, University at Albany, State University of New York, Albany, NY 12222, USA"}]},{"given":"Thomas J.","family":"Begley","sequence":"additional","affiliation":[{"name":"Department of Computer Science, 2Cancer Research Center, University at Albany, 3RNA Institute and 4College of Nanoscale Science and Engineering, University at Albany, State University of New York, Albany, NY 12222, USA"},{"name":"Department of Computer Science, 2Cancer Research Center, University at Albany, 3RNA Institute and 4College of Nanoscale Science and Engineering, University at Albany, State University of New York, Albany, NY 12222, USA"},{"name":"Department of Computer Science, 2Cancer Research Center, University at Albany, 3RNA Institute and 4College of Nanoscale Science and Engineering, University at Albany, State University of New York, Albany, NY 12222, USA"}]}],"member":"286","published-online":{"date-parts":[[2012,2,8]]},"reference":[{"key":"key\n\t\t\t\t20180618190234_bas002-B1","doi-asserted-by":"crossref","first-page":"e104","DOI":"10.1093\/nar\/gkq024","article-title":"Translational control analysis by translationally active RNA capture\/microarray analysis (TrIP-Chip)","volume":"38","author":"Kudo","year":"2010","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20180618190234_bas002-B2","doi-asserted-by":"crossref","first-page":"1051","DOI":"10.1146\/annurev.bi.58.070189.005155","article-title":"Molecular mechanisms of transcriptional regulation in yeast","volume":"58","author":"Struhl","year":"1989","journal-title":"Annu. Rev. Biochem."},{"key":"key\n\t\t\t\t20180618190234_bas002-B3","doi-asserted-by":"crossref","first-page":"399","DOI":"10.1146\/annurev.cellbio.14.1.399","article-title":"Control of translation initiation in animals","volume":"14","author":"Gray","year":"1998","journal-title":"Annu. Rev. Cell Dev. Biol."},{"key":"key\n\t\t\t\t20180618190234_bas002-B4","doi-asserted-by":"crossref","first-page":"355","DOI":"10.1146\/annurev.ge.19.120185.002035","article-title":"The regulation of transcription initiation in bacteria","volume":"19","author":"Reznikoff","year":"1985","journal-title":"Annu. Rev. Genet."},{"key":"key\n\t\t\t\t20180618190234_bas002-B5","doi-asserted-by":"crossref","first-page":"31","DOI":"10.3109\/10799890903517921","article-title":"Promoter-proximal pausing of RNA polymerase II: an opportunity to regulate gene transcription","volume":"30","author":"Fujita","year":"2010","journal-title":"J. Recept. Signal Transduct. Res."},{"key":"key\n\t\t\t\t20180618190234_bas002-B6","doi-asserted-by":"crossref","first-page":"8763","DOI":"10.1073\/pnas.90.19.8763","article-title":"An operational RNA code for amino acids and possible relationship to genetic code","volume":"90","author":"Schimmel","year":"1993","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"key\n\t\t\t\t20180618190234_bas002-B7","doi-asserted-by":"crossref","first-page":"860","DOI":"10.1016\/j.molcel.2007.09.021","article-title":"Trm9-catalyzed tRNA modifications link translation to the DNA damage response","volume":"28","author":"Begley","year":"2007","journal-title":"Mol. Cell"},{"key":"key\n\t\t\t\t20180618190234_bas002-B8","doi-asserted-by":"crossref","first-page":"1281","DOI":"10.1093\/nar\/15.3.1281","article-title":"The codon Adaptation Index\u2013a measure of directional synonymous codon usage bias, and its potential applications","volume":"15","author":"Sharp","year":"1987","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20180618190234_bas002-B9","doi-asserted-by":"crossref","first-page":"800","DOI":"10.1093\/molbev\/msp281","article-title":"Modal codon usage: assessing the typical codon usage of a genome","volume":"27","author":"Davis","year":"2010","journal-title":"Mol. Biol. Evol."},{"key":"key\n\t\t\t\t20180618190234_bas002-B10","doi-asserted-by":"crossref","first-page":"6016","DOI":"10.1093\/nar\/gkr169","article-title":"Specialization versus adaptation: two strategies employed by cyanophages to enhance their translation efficiencies","volume":"14","author":"Limor-Waisberg","year":"2011","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20180618190234_bas002-B11","doi-asserted-by":"crossref","first-page":"2279","DOI":"10.1101\/gr.2896904","article-title":"Codon usage bias from tRNA's point of view: redundancy, specialization, and efficient decoding for translation optimization","volume":"14","author":"Rocha","year":"2004","journal-title":"Genome Res."},{"key":"key\n\t\t\t\t20180618190234_bas002-B12","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/j.biosystems.2009.06.005","article-title":"Di-codon usage for classification of genes","volume":"98","author":"Nguyen","year":"2009","journal-title":"Biosystems"},{"key":"key\n\t\t\t\t20180618190234_bas002-B13","doi-asserted-by":"crossref","first-page":"134","DOI":"10.1109\/TCBB.2007.70240","article-title":"Gene classification using codon usage and support vector machines","volume":"6","author":"Ma","year":"2009","journal-title":"IEEE\/ACM Trans. Comput. Biol. Bioinform."},{"key":"key\n\t\t\t\t20180618190234_bas002-B14","doi-asserted-by":"crossref","first-page":"5623","DOI":"10.1093\/nar\/gkl723","article-title":"MetaGene: prokaryotic gene finding from environmental genome shotgun sequences","volume":"34","author":"Noguchi","year":"2006","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20180618190234_bas002-B15","doi-asserted-by":"crossref","first-page":"218","DOI":"10.1186\/1471-2105-12-218","article-title":"OntoCAT - simple ontology search and integration in Java, R and REST\/JavaScript","volume":"12","author":"Adamusiak","year":"2011","journal-title":"BMC Bioinformatics"},{"key":"key\n\t\t\t\t20180618190234_bas002-B16","doi-asserted-by":"crossref","first-page":"1871","DOI":"10.1093\/bioinformatics\/btr301","article-title":"Genome-wide Association Studies Pipeline (GWASpi): a desktop application for genome-wide SNP analysis and management","volume":"13","author":"Muniz-Fernandez","year":"2011","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t20180618190234_bas002-B17","first-page":"83","article-title":"Cluster analysis and its applications to gene expression data","volume":"38","author":"Sharan","year":"2002","journal-title":"Ernst Schering Res Found Workshop"},{"key":"key\n\t\t\t\t20180618190234_bas002-B18","first-page":"357","article-title":"TreeView: an application to display phylogenetic trees on personal computers","volume":"12","author":"Page","year":"1996","journal-title":"Comput. Appl. Biosci."},{"key":"key\n\t\t\t\t20180618190234_bas002-B19","doi-asserted-by":"crossref","first-page":"35","DOI":"10.1186\/1471-2105-3-35","article-title":"FunSpec: a web-based cluster interpreter for yeast","volume":"3","author":"Robinson","year":"2002","journal-title":"BMC Bioinformatics"},{"key":"key\n\t\t\t\t20180618190234_bas002-B20","first-page":"797","article-title":"An ontology-neutral framework for enrichment analysis","volume":"80","author":"Tirrell","year":"2010","journal-title":"AMIA Annu. Symp. Proc."},{"key":"key\n\t\t\t\t20180618190234_bas002-B21","doi-asserted-by":"crossref","first-page":"185","DOI":"10.1007\/BF00312608","article-title":"Yeast ribosomal proteins: XI. Molecular analysis of two genes encoding YL41, an extremely small and basic ribosomal protein, from Saccharomyces cerevisiae","volume":"17","author":"Suzuki","year":"1990","journal-title":"Curr. Genet."},{"key":"key\n\t\t\t\t20180618190234_bas002-B22","doi-asserted-by":"crossref","first-page":"3045","DOI":"10.1093\/bioinformatics\/btp536","article-title":"QuickGO: a web-based tool for Gene Ontology searching","volume":"25","author":"Binns","year":"2009","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t20180618190234_bas002-B23","doi-asserted-by":"crossref","first-page":"71","DOI":"10.1038\/sj.embor.7400036","article-title":"Reconsidering the evolution of eukaryotic selenoproteins: a novel nonmammalian family with scattered phylogenetic distribution","volume":"5","author":"Castellano","year":"2004","journal-title":"EMBO Rep."},{"key":"key\n\t\t\t\t20180618190234_bas002-B24","doi-asserted-by":"crossref","first-page":"1974","DOI":"10.1074\/jbc.M008892200","article-title":"Reproducing tna operon regulation in vitro in an S-30 system. Tryptophan induction inhibits cleavage of TnaC peptidyl-tRNA","volume":"276","author":"Gong","year":"2001","journal-title":"J. Biol. Chem."}],"container-title":["Database"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/database\/article-pdf\/doi\/10.1093\/database\/bas002\/16728577\/bas002.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,6,23]],"date-time":"2019-06-23T08:14:19Z","timestamp":1561277659000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/database\/article\/doi\/10.1093\/database\/bas002\/431327"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2012,1,1]]},"references-count":24,"URL":"https:\/\/doi.org\/10.1093\/database\/bas002","relation":{},"ISSN":["1758-0463"],"issn-type":[{"value":"1758-0463","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2012]]},"published":{"date-parts":[[2012,1,1]]}}}