{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,27]],"date-time":"2025-10-27T04:52:51Z","timestamp":1761540771633},"publisher-location":"Berlin, Heidelberg","reference-count":32,"publisher":"Springer Berlin Heidelberg","isbn-type":[{"type":"print","value":"9783540482932"},{"type":"electronic","value":"9783540485407"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"DOI":"10.1007\/978-3-540-48540-7_10","type":"book-chapter","created":{"date-parts":[[2007,5,15]],"date-time":"2007-05-15T20:28:49Z","timestamp":1179260929000},"page":"107-118","source":"Crossref","is-referenced-by-count":1,"title":["Examination of the tRNA Adaptation Index as a Predictor of Protein Expression Levels"],"prefix":"10.1007","author":[{"given":"Orna","family":"Man","sequence":"first","affiliation":[]},{"given":"Joel L.","family":"Sussman","sequence":"additional","affiliation":[]},{"given":"Yitzhak","family":"Pilpel","sequence":"additional","affiliation":[]}],"member":"297","reference":[{"key":"10_CR1","doi-asserted-by":"publisher","first-page":"5036","DOI":"10.1093\/nar\/gkh834","volume":"32","author":"M. Reis dos","year":"2004","unstructured":"dos Reis, M., Savva, R., Wernisch, L.: Solving the riddle of codon usage preferences: a test for translational selection. Nucleic Acids Res.\u00a032, 5036\u20135044 (2004)","journal-title":"Nucleic Acids Res."},{"key":"10_CR2","doi-asserted-by":"publisher","first-page":"4285","DOI":"10.1073\/pnas.96.8.4285","volume":"96","author":"M. Pellegrini","year":"1999","unstructured":"Pellegrini, M., Marcotte, E.M., Thompson, M.J., Eisenberg, D., Yeates, T.O.: Assigning protein functions by comparative genome analysis: protein phylogenetic profiles. Proc. Natl. Acad. Sci. U S A\u00a096, 4285\u20134288 (1999)","journal-title":"Proc. Natl. Acad. Sci. U S A"},{"key":"10_CR3","doi-asserted-by":"publisher","first-page":"527","DOI":"10.1016\/S0092-8674(04)00412-X","volume":"117","author":"T. Avidor-Reiss","year":"2004","unstructured":"Avidor-Reiss, T., Maer, A.M., Koundakjian, E., Polyanovsky, A., Keil, T., Subramaniam, S., Zuker, C.S.: Decoding cilia function: defining specialized genes required for compartmentalized cilia biogenesis. Cell\u00a0117, 527\u2013539 (2004)","journal-title":"Cell"},{"key":"10_CR4","doi-asserted-by":"publisher","first-page":"991","DOI":"10.1101\/gr.678303","volume":"13","author":"M.J. Martin","year":"2003","unstructured":"Martin, M.J., Herrero, J., Mateos, A., Dopazo, J.: Comparing bacterial genomes through conservation profiles. Genome Res.\u00a013, 991\u2013998 (2003)","journal-title":"Genome Res."},{"key":"10_CR5","doi-asserted-by":"publisher","first-page":"9033","DOI":"10.1073\/pnas.0402591101","volume":"101","author":"H.B. Fraser","year":"2004","unstructured":"Fraser, H.B., Hirsh, A.E., Wall, D.P., Eisen, M.B.: Coevolution of gene expression among interacting proteins. Proc. Natl. Acad. Sci. U S A\u00a0101, 9033\u20139038 (2004)","journal-title":"Proc. Natl. Acad. Sci. U S A"},{"key":"10_CR6","doi-asserted-by":"publisher","first-page":"1051","DOI":"10.1093\/nar\/gki261","volume":"33","author":"G. Lithwick","year":"2005","unstructured":"Lithwick, G., Margalit, H.: Relative predicted protein levels of functionally associated proteins are conserved across organisms. Nucleic Acids Res.\u00a033, 1051\u20131057 (2005)","journal-title":"Nucleic Acids Res."},{"key":"10_CR7","doi-asserted-by":"publisher","first-page":"1281","DOI":"10.1093\/nar\/15.3.1281","volume":"15","author":"P.M. Sharp","year":"1987","unstructured":"Sharp, P.M., Li, W.H.: The codon Adaptation Index\u2013a measure of directional synonymous codon usage bias, and its potential applications. Nucleic Acids Res.\u00a015, 1281\u20131295 (1987)","journal-title":"Nucleic Acids Res."},{"key":"10_CR8","doi-asserted-by":"publisher","first-page":"322","DOI":"10.1006\/jmbi.1997.0942","volume":"268","author":"R. Percudani","year":"1997","unstructured":"Percudani, R., Pavesi, A., Ottonello, S.: Transfer RNA gene redundancy and translational selection in Saccharomyces cerevisiae. J. Mol. Biol.\u00a0268, 322\u2013330 (1997)","journal-title":"J. Mol. Biol."},{"key":"10_CR9","doi-asserted-by":"publisher","first-page":"737","DOI":"10.1038\/nature02046","volume":"425","author":"S. Ghaemmaghami","year":"2003","unstructured":"Ghaemmaghami, S., Huh, W.K., Bower, K., Howson, R.W., Belle, A., Dephoure, N., O\u2019Shea, E.K., Weissman, J.S.: Global analysis of protein expression in yeast. Nature\u00a0425, 737\u2013741 (2003)","journal-title":"Nature"},{"key":"10_CR10","doi-asserted-by":"publisher","first-page":"585","DOI":"10.1093\/bioinformatics\/18.4.585","volume":"18","author":"D. Greenbaum","year":"2002","unstructured":"Greenbaum, D., Jansen, R., Gerstein, M.: Analysis of mRNA expression and protein abundance data: an approach for the comparison of the enrichment of features in the cellular population of proteins and transcripts. Bioinformatics\u00a018, 585\u2013596 (2002)","journal-title":"Bioinformatics"},{"key":"10_CR11","doi-asserted-by":"publisher","first-page":"127","DOI":"10.1016\/j.gene.2004.11.035","volume":"345","author":"Y. Lavner","year":"2005","unstructured":"Lavner, Y., Kotlar, D.: Codon bias as a factor in regulating expression via translation rate in the human genome. Gene\u00a0345, 127\u2013138 (2005)","journal-title":"Gene"},{"key":"10_CR12","doi-asserted-by":"publisher","first-page":"1083","DOI":"10.1002\/yea.1150","volume":"21","author":"M. Friberg","year":"2004","unstructured":"Friberg, M., von Rohr, P., Gonnet, G.: Limitations of codon adaptation index and other coding DNA-based features for prediction of protein expression in Saccharomyces cerevisiae. Yeast\u00a021, 1083\u20131093 (2004)","journal-title":"Yeast"},{"key":"10_CR13","doi-asserted-by":"publisher","first-page":"717","DOI":"10.1016\/S0092-8674(00)81641-4","volume":"95","author":"F.C. Holstege","year":"1998","unstructured":"Holstege, F.C., Jennings, E.G., Wyrick, J.J., Lee, T.I., Hengartner, C.J., Green, M.R., Golub, T.R., Lander, E.S., Young, R.A.: Dissecting the regulatory circuitry of a eukaryotic genome. Cell\u00a095, 717\u2013728 (1998)","journal-title":"Cell"},{"key":"10_CR14","doi-asserted-by":"crossref","first-page":"1720","DOI":"10.1128\/MCB.19.3.1720","volume":"19","author":"S.P. Gygi","year":"1999","unstructured":"Gygi, S.P., Rochon, Y., Franza, B.R., Aebersold, R.: Correlation between protein and mRNA abundance in yeast. Mol. Cell. Biol.\u00a019, 1720\u20131730 (1999)","journal-title":"Mol. Cell. Biol."},{"key":"10_CR15","doi-asserted-by":"publisher","first-page":"249","DOI":"10.1016\/S0092-8674(00)80835-1","volume":"101","author":"K.J. Travers","year":"2000","unstructured":"Travers, K.J., Patil, C.K., Wodicka, L., Lockhart, D.J., Weissman, J.S., Walter, P.: Functional and genomic analyses reveal an essential coordination between the unfolded protein response and ER-associated degradation. Cell\u00a0101, 249\u2013258 (2000)","journal-title":"Cell"},{"key":"10_CR16","doi-asserted-by":"crossref","first-page":"4241","DOI":"10.1091\/mbc.11.12.4241","volume":"11","author":"A.P. Gasch","year":"2000","unstructured":"Gasch, A.P., Spellman, P.T., Kao, C.M., Carmel-Harel, O., Eisen, M.B., Storz, G., Botstein, D., Brown, P.O.: Genomic expression programs in the response of yeast cells to environmental changes. Mol. Biol. Cell\u00a011, 4241\u20134257 (2000)","journal-title":"Mol. Biol. Cell"},{"key":"10_CR17","doi-asserted-by":"publisher","first-page":"23","DOI":"10.1016\/0378-1119(90)90491-9","volume":"87","author":"F. Wright","year":"1990","unstructured":"Wright, F.: The \u2019effective number of codons\u2019 used in a gene. Gene\u00a087, 23\u201329 (1990)","journal-title":"Gene"},{"key":"10_CR18","doi-asserted-by":"publisher","first-page":"399","DOI":"10.1038\/nature750","volume":"417","author":"C. Mering von","year":"2002","unstructured":"von Mering, C., Krause, R., Snel, B., Cornell, M., Oliver, S.G., Fields, S., Bork, P.: Comparative assessment of large-scale data sets of protein-protein interactions. Nature\u00a0417, 399\u2013403 (2002)","journal-title":"Nature"},{"key":"10_CR19","unstructured":"Arnaud, M.B., Costanzo, M.C., Skrzypek, M.S., Binkley, G., Lane, C., Miyasato, S.R., Sherlock, G.: Candida Genome Database (14 August 2005), \n                  \n                    http:\/\/www.candidagenome.org\/"},{"key":"10_CR20","unstructured":"Balakrishnan, R., Christie, K.R., Costanzo, M.C., Dolinski, K., Dwight, S.S., Engel, S.R., Fisk, D.G., Hirschman, J.E., Hong, E.L., Nash, R., Oughtred, R., Skrzypek, M., Theesfeld, C.L., Binkley, G., Dong, Q., Lane, C., Sethuraman, A., Weng, S., Botstein, D., Cherry, J.M.: Saccharomyces Genome Database (16 June 2005), \n                  \n                    ftp:\/\/ftp.yeastgenome.org\/yeast\/"},{"key":"10_CR21","doi-asserted-by":"publisher","first-page":"617","DOI":"10.1038\/nature02424","volume":"428","author":"M. Kellis","year":"2004","unstructured":"Kellis, M., Birren, B.W., Lander, E.S.: Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisiae. Nature\u00a0428, 617\u2013624 (2004)","journal-title":"Nature"},{"key":"10_CR22","doi-asserted-by":"publisher","first-page":"179","DOI":"10.1007\/3-540-28904-6_8","volume":"5","author":"M. Pruess","year":"2005","unstructured":"Pruess, M., Kersey, P., Apweiler, R.: The Integr8 project\u2013a resource for genomic and proteomic data. In Silico Biol.\u00a05, 179\u2013185 (2005)","journal-title":"In Silico Biol."},{"key":"10_CR23","doi-asserted-by":"publisher","first-page":"29","DOI":"10.1093\/nar\/gki098","volume":"33","author":"C. Kanz","year":"2005","unstructured":"Kanz, C., Aldebert, P., Althorpe, N., Baker, W., Baldwin, A., Bates, K., Browne, P., van den Broek, A., Castro, M., Cochrane, G., Duggan, K., Eberhardt, R., Faruque, N., Gamble, J., Diez, F.G., Harte, N., Kulikova, T., Lin, Q., Lombard, V., Lopez, R., Mancuso, R., McHale, M., Nardone, F., Silventoinen, V., Sobhany, S., Stoehr, P., Tuli, M.A., Tzouvara, K., Vaughan, R., Wu, D., Zhu, W., Apweiler, R.: The EMBL Nucleotide Sequence Database. Nucleic Acids Res.\u00a033, D29\u201333 (2005)","journal-title":"Nucleic Acids Res."},{"key":"10_CR24","doi-asserted-by":"publisher","first-page":"1611","DOI":"10.1101\/gr.361602","volume":"12","author":"J.E. Stajich","year":"2002","unstructured":"Stajich, J.E., Block, D., Boulez, K., Brenner, S.E., Chervitz, S.A., Dagdigian, C., Fuellen, G., Gilbert, J.G., Korf, I., Lapp, H., Lehvaslaiho, H., Matsalla, C., Mungall, C.J., Osborne, B.I., Pocock, M.R., Schattner, P., Senger, M., Stein, L.D., Stupka, E., Wilkinson, M.D., Birney, E.: The Bioperl toolkit: Perl modules for the life sciences. Genome Res.\u00a012, 1611\u20131618 (2002)","journal-title":"Genome Res."},{"key":"10_CR25","doi-asserted-by":"publisher","first-page":"955","DOI":"10.1093\/nar\/25.5.955","volume":"25","author":"T.M. Lowe","year":"1997","unstructured":"Lowe, T.M., Eddy, S.R.: tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res.\u00a025, 955\u2013964 (1997)","journal-title":"Nucleic Acids Res."},{"key":"10_CR26","doi-asserted-by":"publisher","first-page":"17","DOI":"10.1016\/S0014-5793(00)02274-2","volume":"487","author":"F. Tekaia","year":"2000","unstructured":"Tekaia, F., Blandin, G., Malpertuy, A., Llorente, B., Durrens, P., Toffano-Nioche, C., Ozier-Kalogeropoulos, O., Bon, E., Gaillardin, C., Aigle, M., Bolotin-Fukuhara, M., Casaregola, S., de Montigny, J., Lepingle, A., Neuveglise, C., Potier, S., Souciet, J., Wesolowski-Louvel, M., Dujon, B.: Genomic exploration of the hemiascomycetous yeasts: 3. Methods and strategies used for sequence analysis and annotation. FEBS Lett.\u00a0487, 17\u201330 (2000)","journal-title":"FEBS Lett."},{"key":"10_CR27","doi-asserted-by":"crossref","first-page":"79","DOI":"10.1016\/S0723-2020(99)80030-7","volume":"22","author":"T. Sugita","year":"1999","unstructured":"Sugita, T., Nakase, T.: Non-universal usage of the leucine CUG codon and the molecular phylogeny of the genus Candida. Syst. Appl. Microbiol.\u00a022, 79\u201386 (1999)","journal-title":"Syst. Appl. Microbiol."},{"key":"10_CR28","doi-asserted-by":"publisher","first-page":"1041","DOI":"10.1006\/jmbi.2000.5197","volume":"314","author":"M. Remm","year":"2001","unstructured":"Remm, M., Storm, C.E., Sonnhammer, E.L.: Automatic clustering of orthologs and in-paralogs from pairwise species comparisons. J. Mol. Biol.\u00a0314, 1041\u20131052 (2001)","journal-title":"J. Mol. Biol."},{"key":"10_CR29","doi-asserted-by":"publisher","first-page":"3461","DOI":"10.1093\/nar\/gkg591","volume":"31","author":"J. Herrero","year":"2003","unstructured":"Herrero, J., Al-Shahrour, F., Diaz-Uriarte, R., Mateos, A., Vaquerizas, J.M., Santoyo, J., Dopazo, J.: GEPAS: A web-based resource for microarray gene expression data analysis. Nucleic Acids Res.\u00a031, 3461\u20133467 (2003)","journal-title":"Nucleic Acids Res."},{"key":"10_CR30","doi-asserted-by":"publisher","first-page":"886","DOI":"10.1128\/EC.2.5.886-900.2003","volume":"2","author":"D.A. Bulik","year":"2003","unstructured":"Bulik, D.A., Olczak, M., Lucero, H.A., Osmond, B.C., Robbins, P.W., Specht, C.A.: Chitin synthesis in Saccharomyces cerevisiae in response to supplementation of growth medium with glucosamine and cell wall stress. Eukaryot Cell\u00a02, 886\u2013900 (2003)","journal-title":"Eukaryot Cell"},{"key":"10_CR31","doi-asserted-by":"publisher","first-page":"562","DOI":"10.1093\/nar\/gki022","volume":"33","author":"T. Barrett","year":"2005","unstructured":"Barrett, T., Suzek, T.O., Troup, D.B., Wilhite, S.E., Ngau, W.C., Ledoux, P., Rudnev, D., Lash, A.E., Fujibuchi, W., Edgar, R.: NCBI GEO: mining millions of expression profiles\u2013database and tools. Nucleic Acids Res.\u00a033, D562\u2013566 (2005)","journal-title":"Nucleic Acids Res."},{"key":"10_CR32","unstructured":"Balakrishnan, R., Christie, K.R., Costanzo, M.C., Dolinski, K., Dwight, S.S., Engel, S.R., Fisk, D.G., Hirschman, J.E., Hong, E.L., Nash, R., Oughtred, R., Skrzypek, M., Theesfeld, C.L., Binkley, G., Dong, Q., Lane, C., Sethuraman, A., Weng, S., Botstein, D., Cherry, J.M.: Saccharomyces Genome Database (1 February 2006), \n                  \n                    http:\/\/www.yeastgenome.org\/"}],"container-title":["Lecture Notes in Computer Science","Systems Biology and Regulatory Genomics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1007\/978-3-540-48540-7_10.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,11,19]],"date-time":"2020-11-19T04:47:21Z","timestamp":1605761241000},"score":1,"resource":{"primary":{"URL":"http:\/\/link.springer.com\/10.1007\/978-3-540-48540-7_10"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[null]]},"ISBN":["9783540482932","9783540485407"],"references-count":32,"URL":"https:\/\/doi.org\/10.1007\/978-3-540-48540-7_10","relation":{},"subject":[]}}