TY - JOUR AU - Sharp, P. M. AU - Li, W. H. PY - 1987 DA - 1987// TI - The codon adaptation index: a measure of directional synonymous codon usage bias, and its potential applications JO - Nucleic Acids Res VL - 15 UR - https://doi.org/10.1093/nar/15.3.1281 DO - 10.1093/nar/15.3.1281 ID - Sharp1987 ER - TY - JOUR AU - Ikemura, T. PY - 1981 DA - 1981// TI - Correlation between the abundance of Escherichia coli transfer RNAs and the occurrence of the respective codons in its protein genes: a proposal for a synonymous codon choice that is optimal for the E. coli translational system JO - J Mol Biol VL - 151 UR - https://doi.org/10.1016/0022-2836(81)90003-6 DO - 10.1016/0022-2836(81)90003-6 ID - Ikemura1981 ER - TY - JOUR AU - Gribskov, M. AU - Devereux, J. AU - Burgess, R. R. PY - 1984 DA - 1984// TI - The codon preference plot: graphic analysis of protein coding sequences and prediction of gene expression JO - Nucleic Acids Res VL - 12 UR - https://doi.org/10.1093/nar/12.1Part2.539 DO - 10.1093/nar/12.1Part2.539 ID - Gribskov1984 ER - TY - JOUR AU - Wright, F. PY - 1990 DA - 1990// TI - The 'effective number of codons' used in a gene JO - Gene VL - 87 UR - https://doi.org/10.1016/0378-1119(90)90491-9 DO - 10.1016/0378-1119(90)90491-9 ID - Wright1990 ER - TY - JOUR AU - Karlin, S. AU - Barnett, M. J. AU - Campbell, A. M. AU - Fisher, R. F. AU - Mrazek, J. PY - 2003 DA - 2003// TI - Predicting gene expression levels from codon biases in alpha-proteobacterial genomes JO - Proc Natl Acad Sci USA VL - 100 UR - https://doi.org/10.1073/pnas.1232298100 DO - 10.1073/pnas.1232298100 ID - Karlin2003 ER - TY - JOUR AU - Sharp, P. M. AU - Li, W. H. PY - 1986 DA - 1986// TI - Codon usage in regulatory genes in Escherichia coli does not reflect selection for 'rare' codons JO - Nucleic Acids Res VL - 14 UR - https://doi.org/10.1093/nar/14.19.7737 DO - 10.1093/nar/14.19.7737 ID - Sharp1986 ER - TY - JOUR AU - Carbone, A. AU - Kepes, F. AU - Zinovyev, A. PY - 2005 DA - 2005// TI - Codon bias signatures, organization of microorganisms in codon space, and lifestyle JO - Mol Biol Evol VL - 22 UR - https://doi.org/10.1093/molbev/msi040 DO - 10.1093/molbev/msi040 ID - Carbone2005 ER - TY - JOUR AU - Carbone, A. AU - Zinovyev, A. AU - Kepes, F. PY - 2003 DA - 2003// TI - Codon adaptation index as a measure of dominating codon bias JO - Bioinformatics VL - 19 UR - https://doi.org/10.1093/bioinformatics/btg272 DO - 10.1093/bioinformatics/btg272 ID - Carbone2003 ER - TY - JOUR AU - Gygi, S. P. AU - Rochon, Y. AU - Franza, B. R. AU - Aebersold, R. PY - 1999 DA - 1999// TI - Correlation between protein and mRNA abundance in yeast JO - Mol Cell Biol VL - 19 UR - https://doi.org/10.1128/MCB.19.3.1720 DO - 10.1128/MCB.19.3.1720 ID - Gygi1999 ER - TY - JOUR AU - Ghaemmaghami, S. AU - Huh, W. K. AU - Bower, K. AU - Howson, R. W. AU - Belle, A. AU - Dephoure, N. AU - O'Shea, E. K. AU - Weissman, J. S. PY - 2003 DA - 2003// TI - Global analysis of protein expression in yeast JO - Nature VL - 425 UR - https://doi.org/10.1038/nature02046 DO - 10.1038/nature02046 ID - Ghaemmaghami2003 ER - TY - JOUR AU - Hallin, P. F. AU - Ussery, D. W. PY - 2004 DA - 2004// TI - CBS Genome Atlas Database: a dynamic storage for bioinformatic results and sequence data JO - Bioinformatics VL - 20 UR - https://doi.org/10.1093/bioinformatics/bth423 DO - 10.1093/bioinformatics/bth423 ID - Hallin2004 ER - TY - JOUR AU - Rocha, E. P. PY - 2004 DA - 2004// TI - Codon usage bias from tRNA's point of view: redundancy, specialization, and efficient decoding for translation optimization JO - Genome Res VL - 14 UR - https://doi.org/10.1101/gr.2896904 DO - 10.1101/gr.2896904 ID - Rocha2004 ER - TY - JOUR AU - Sharp, P. M. AU - Bailes, E. AU - Grocock, R. J. AU - Peden, J. F. AU - Sockett, R. E. PY - 2005 DA - 2005// TI - Variation in the strength of selected codon usage bias among bacteria JO - Nucleic Acids Res VL - 33 UR - https://doi.org/10.1093/nar/gki242 DO - 10.1093/nar/gki242 ID - Sharp2005 ER - TY - JOUR AU - Ussery, D. W. AU - Hallin, P. F. AU - Lagesen, K. AU - Coenye, T. PY - 2004 DA - 2004// TI - Genome update: rRNAs in sequenced microbial genomes JO - Microbiology VL - 150 UR - https://doi.org/10.1099/mic.0.27173-0 DO - 10.1099/mic.0.27173-0 ID - Ussery2004 ER - TY - STD TI - Supplementary material: an environmental signature for 323 microbial genomes based on codon adaptation indices. [http://www.cbs.dtu.dk/services/GenomeAtlas/suppl/CAI/] UR - http://www.cbs.dtu.dk/services/GenomeAtlas/suppl/CAI/ ID - ref15 ER - TY - JOUR AU - Rocap, G. AU - Larimer, F. W. AU - Lamerdin, J. AU - Malfatti, S. AU - Chain, P. AU - Ahlgren, N. A. AU - Arellano, A. AU - Coleman, M. AU - Hauser, L. AU - Hess, W. R. PY - 2003 DA - 2003// TI - Genome divergence in two Prochlorococcus ecotypes reflects oceanic niche differentiation JO - Nature VL - 424 UR - https://doi.org/10.1038/nature01947 DO - 10.1038/nature01947 ID - Rocap2003 ER - TY - JOUR AU - Giovannoni, S. J. AU - Tripp, H. J. AU - Givan, S. AU - Podar, M. AU - Vergin, K. L. AU - Baptista, D. AU - Bibbs, L. AU - Eads, J. AU - Richardson, T. H. AU - Noordewier, M. PY - 2005 DA - 2005// TI - Genome streamlining in a cosmopolitan oceanic bacterium JO - Science VL - 309 UR - https://doi.org/10.1126/science.1114057 DO - 10.1126/science.1114057 ID - Giovannoni2005 ER - TY - JOUR AU - Paulsen, I. T. AU - Seshadri, R. AU - Nelson, K. E. AU - Eisen, J. A. AU - Heidelberg, J. F. AU - Read, T. D. AU - Dodson, R. J. AU - Umayam, L. AU - Brinkac, L. M. AU - Beanan, M. J. PY - 2002 DA - 2002// TI - The Brucella suis genome reveals fundamental similarities between animal and plant pathogens and symbionts JO - Proc Natl Acad Sci USA VL - 99 UR - https://doi.org/10.1073/pnas.192319099 DO - 10.1073/pnas.192319099 ID - Paulsen2002 ER - TY - JOUR AU - Baar, C. AU - Eppinger, M. AU - Raddatz, G. AU - Simon, J. AU - Lanz, C. AU - Klimmek, O. AU - Nandakumar, R. AU - Gross, R. AU - Rosinus, A. AU - Keller, H. PY - 2003 DA - 2003// TI - Complete genome sequence and analysis of Wolinella succinogenes JO - Proc Natl Acad Sci USA VL - 100 UR - https://doi.org/10.1073/pnas.1932838100 DO - 10.1073/pnas.1932838100 ID - Baar2003 ER - TY - JOUR AU - Tekaia, F. AU - Yeramian, E. AU - Dujon, B. PY - 2002 DA - 2002// TI - Amino acid composition of genomes, lifestyles of organisms, and evolutionary trends: a global picture with correspondence analysis JO - Gene VL - 297 UR - https://doi.org/10.1016/S0378-1119(02)00871-5 DO - 10.1016/S0378-1119(02)00871-5 ID - Tekaia2002 ER - TY - JOUR AU - Kreil, D. P. AU - Ouzounis, C. A. PY - 2001 DA - 2001// TI - Identification of thermophilic species by the amino acid compositions deduced from their genomes JO - Nucleic Acids Res VL - 29 UR - https://doi.org/10.1093/nar/29.7.1608 DO - 10.1093/nar/29.7.1608 ID - Kreil2001 ER - TY - JOUR AU - Foerstner, K. U. AU - von Mering, C. AU - Hooper, S. D. AU - Bork, P. PY - 2005 DA - 2005// TI - Environments shape the nucleotide composition of genomes JO - EMBO Rep VL - 6 UR - https://doi.org/10.1038/sj.embor.7400538 DO - 10.1038/sj.embor.7400538 ID - Foerstner2005 ER - TY - JOUR AU - Barrett, T. AU - Edgar, R. PY - 2006 DA - 2006// TI - Gene expression omnibus: microarray data storage, submission, retrieval, and analysis JO - Methods Enzymol VL - 411 UR - https://doi.org/10.1016/S0076-6879(06)11019-8 DO - 10.1016/S0076-6879(06)11019-8 ID - Barrett2006 ER - TY - JOUR AU - Covert, M. W. AU - Knight, E. M. AU - Reed, J. L. AU - Herrgard, M. J. AU - Palsson, B. O. PY - 2004 DA - 2004// TI - Integrating high-throughput and computational data elucidates bacterial networks JO - Nature VL - 429 UR - https://doi.org/10.1038/nature02456 DO - 10.1038/nature02456 ID - Covert2004 ER - TY - JOUR AU - Stintzi, A. AU - Whitworth, L. PY - 2003 DA - 2003// TI - Investigation of the Campylobacter jejuni Cold Shock response by global gene expression analysis JO - J Genome Sci Technol VL - 2 ID - Stintzi2003 ER - TY - JOUR AU - Salunkhe, P. AU - Topfer, T. AU - Buer, J. AU - Tummler, B. PY - 2005 DA - 2005// TI - Genome-wide transcriptional profiling of the steady-state response of Pseudomonas aeruginosa to hydrogen peroxide JO - J Bacteriol VL - 187 UR - https://doi.org/10.1128/JB.187.8.2565-2572.2005 DO - 10.1128/JB.187.8.2565-2572.2005 ID - Salunkhe2005 ER - TY - JOUR AU - Bulik, D. A. AU - Olczak, M. AU - Lucero, H. A. AU - Osmond, B. C. AU - Robbins, P. W. AU - Specht, C. A. PY - 2003 DA - 2003// TI - Chitin synthesis in Saccharomyces cerevisiae in response to supplementation of growth medium with glucosamine and cell wall stress JO - Eukaryot Cell VL - 2 UR - https://doi.org/10.1128/EC.2.5.886-900.2003 DO - 10.1128/EC.2.5.886-900.2003 ID - Bulik2003 ER - TY - JOUR AU - Ronald, J. AU - Akey, J. M. AU - Whittle, J. AU - Smith, E. N. AU - Yvert, G. AU - Kruglyak, L. PY - 2005 DA - 2005// TI - Simultaneous genotyping, gene-expression measurement, and detection of allele-specific expression with oligonucleotide arrays JO - Genome Res VL - 15 UR - https://doi.org/10.1101/gr.2850605 DO - 10.1101/gr.2850605 ID - Ronald2005 ER - TY - JOUR AU - Workman, C. AU - Jensen, L. J. AU - Jarmer, H. AU - Berka, R. AU - Gautier, L. AU - Nielser, H. B. AU - Saxild, H. H. AU - Nielsen, C. AU - Brunak, S. AU - Knudsen, S. PY - 2002 DA - 2002// TI - A new non-linear normalization method for reducing variability in DNA microarray experiments JO - Genome Biol VL - 3 UR - https://doi.org/10.1186/gb-2002-3-9-research0048 DO - 10.1186/gb-2002-3-9-research0048 ID - Workman2002 ER - TY - JOUR AU - Li, C. AU - Wong, W. PY - 2001 DA - 2001// TI - Model-based analysis of oligonucleotide arrays: model validation, design issues and standard error application JO - Genome Biol VL - 2 ID - Li2001 ER - TY - JOUR AU - Methe, B. A. AU - Webster, J. AU - Nevin, K. AU - Butler, J. AU - Lovley, D. R. PY - 2005 DA - 2005// TI - DNA microarray analysis of nitrogen fixation and Fe(III) reduction in Geobacter sulfurreducens JO - Appl Environ Microbiol VL - 71 UR - https://doi.org/10.1128/AEM.71.5.2530-2538.2005 DO - 10.1128/AEM.71.5.2530-2538.2005 ID - Methe2005 ER - TY - JOUR AU - Helmann, J. D. AU - Wu, M. F. AU - Gaballa, A. AU - Kobel, P. A. AU - Morshedi, M. M. AU - Fawcett, P. AU - Paddon, C. PY - 2003 DA - 2003// TI - The global transcriptional response of Bacillus subtilis to peroxide stress is coordinated by three transcription factors JO - J Bacteriol VL - 185 UR - https://doi.org/10.1128/JB.185.1.243-253.2003 DO - 10.1128/JB.185.1.243-253.2003 ID - Helmann2003 ER - TY - JOUR AU - Altschul, S. F. AU - Madden, T. L. AU - Schaffer, A. A. AU - Zhang, J. AU - Zhang, Z. AU - Miller, W. AU - Lipman, D. J. PY - 1997 DA - 1997// TI - Gapped BLAST and PSI-BLAST: a new generation of protein database search programs JO - Nucleic Acids Res VL - 25 UR - https://doi.org/10.1093/nar/25.17.3389 DO - 10.1093/nar/25.17.3389 ID - Altschul1997 ER - TY - JOUR AU - Sharp, P. M. AU - Tuohy, T. M. AU - Mosurski, K. R. PY - 1986 DA - 1986// TI - Codon usage in yeast: cluster analysis clearly differentiates highly and lowly expressed genes JO - Nucleic Acids Res VL - 14 UR - https://doi.org/10.1093/nar/14.13.5125 DO - 10.1093/nar/14.13.5125 ID - Sharp1986 ER - TY - STD TI - Pfam. [http://www.sanger.ac.uk/Software/Pfam/] UR - http://www.sanger.ac.uk/Software/Pfam/ ID - ref35 ER - TY - JOUR AU - Best, D. J. AU - Roberts, D. E. PY - 1975 DA - 1975// TI - Algorithm AS 89: the upper tail probabilities of Spearman's rho JO - Appl Stat VL - 24 UR - https://doi.org/10.2307/2347111 DO - 10.2307/2347111 ID - Best1975 ER -