bjorns's refs_jme05 [84 articles] Export

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	Mammalian housekeeping genes evolve more slowly than tissue-specific genes. [My Copy] Mol Biol Evol, Vol. 21, No. 2. (February 2004), pp. 236-239. by L. Zhang, W. H. Li posted to refs_jme05 by bjorns on 2005-11-25 12:58:15 as along with 3 people dragonrez gpalidwor skumagai
	Estimating synonymous and nonsynonymous substitution rates under realistic evolutionary models. [My Copy] Mol Biol Evol, Vol. 17, No. 1. (January 2000), pp. 32-43. by Z. Yang, R. Nielsen posted to refs_jme05 by bjorns on 2005-11-25 12:57:04 as along with 9 people and 1 group katholt fernan hdopazo BioNica timflutre Garamonfok ankur_iitg RamuAnandakrishnan Ema BioinfoCIPF
	PAML: a program package for phylogenetic analysis by maximum likelihood. [My Copy] Computer applications in the biosciences : CABIOS, Vol. 13, No. 5. (October 1997), pp. 555-556. by Z. Yang posted to refs_jme05 by bjorns on 2005-11-25 12:56:10 as along with 15 people and 3 groups seb1 thegoose2 alexeid druvus jmjimenez chrn chad_davis indigoviolet penka BioNica stajich pv usagi-kirin tharris skumagai EisenLab Nie Mycology
	Rate of protein evolution versus fitness effect of gene deletion. [My Copy] Mol Biol Evol, Vol. 20, No. 5. (May 2003), pp. 772-774. by J. Yang, Z. Gu, W. H. Li posted to refs_jme05 by bjorns on 2005-11-25 12:55:48 as along with 2 people and 1 group diamantis penka Nie
	The proteins of linked genes evolve at similar rates. [My Copy] Nature, Vol. 407, No. 6806. (19 October 2000), pp. 900-903. by E. J. Williams, L. D. Hurst posted to refs_jme05 by bjorns on 2005-11-25 12:55:07 as along with 3 people and 2 groups stevanspringer penka bpcusack Nie FAB-lab
	Consequences of reductive evolution for gene expression in an obligate endosymbiont. [My Copy] Mol Microbiol, Vol. 48, No. 6. (June 2003), pp. 1491-1500. by J. L. Wilcox, H. E. Dunbar, R. D. Wolfinger, N. A. Moran posted to refs_jme05 by bjorns on 2005-11-25 12:54:38 as
	Functional genomic analysis of the rates of protein evolution. [My Copy] Proc Natl Acad Sci U S A, Vol. 102, No. 15. (12 April 2005), pp. 5483-5488. by D. P. Wall, A. E. Hirsh, H. B. Fraser, et al.J. Kumm, G. Giaever, M. B. Eisen, M. W. Feldman posted to refs_jme05 by bjorns on 2005-11-25 12:53:21 as along with 7 people and 1 group mgomes phoenixzxl balajis opheliav penka RamuAnandakrishnan michaelbarton Nie
	The complete genome sequence of the gastric pathogen Helicobacter pylori. [My Copy] Nature, Vol. 388, No. 6642. (7 August 1997), pp. 539-547. by J. F. Tomb, O. White, A. R. Kerlavage, et al.R. A. Clayton, G. G. Sutton, R. D. Fleischmann, K. A. Ketchum, H. P. Klenk, S. Gill, B. A. Dougherty, K. Nelson, J. Quackenbush, L. Zhou, E. F. Kirkness, S. Peterson, B. Loftus, D. Richardson, R. Dodson, H. G. Khalak, A. Glodek, K. McKenney, L. M. Fitzegerald, N. Lee, M. D. Adams, J. C. Venter posted to refs_jme05 by bjorns on 2005-11-25 12:52:54 as along with 2 people evaf xingxu
	CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. [My Copy] Nucleic acids research, Vol. 22, No. 22. (11 November 1994), pp. 4673-4680. by J. D. Thompson, D. G. Higgins, T. J. Gibson posted to refs_jme05 by bjorns on 2005-11-25 12:52:12 as along with 34 people and 1 group biomcgary vprieto tomjad oceanwind Blackbeard db344 udivi daforerog Md_2007 sebk cen4ik usagi-kirin jmw greger_halltorp jshapiro mercaptan evaf caldavis miguel onlyrey aprasad RMGraze moborg arcticrasta dullhunk caporaso ahanora Haggan BioNica timflutre adijr xingxu newton1234 Lombardo_7 biomedical-nlp
	Helicobacter pylori infection. [My Copy] The New England journal of medicine, Vol. 347, No. 15. (10 October 2002), pp. 1175-1186. by Sebastian Suerbaum, Pierre Michetti posted to refs_jme05 by bjorns on 2005-11-25 12:50:09 as along with 1 person djmonstermo
	The codon Adaptation Index--a measure of directional synonymous codon usage bias, and its potential applications. [My Copy] Nucleic acids research, Vol. 15, No. 3. (11 February 1987), pp. 1281-1295. by P. M. Sharp, W. H. Li posted to refs_jme05 by bjorns on 2005-11-25 12:49:42 as along with 8 people mgomes qluo saunders antonkratz dswan operon gpalidwor aaronsmith
	Variation in the strength of selected codon usage bias among bacteria. [My Copy] Nucleic Acids Res, Vol. 33, No. 4. (2005), pp. 1141-1153. by P. M. Sharp, E. Bailes, R. J. Grocock, J. F. Peden, R. E. Sockett posted to refs_jme05 by bjorns on 2005-11-25 12:49:08 as
	Determinants of DNA sequence divergence between Escherichia coli and Salmonella typhimurium: codon usage, map position, and concerted evolution. [My Copy] J Mol Evol, Vol. 33, No. 1. (July 1991), pp. 23-33. by P. M. Sharp posted to refs_jme05 by bjorns on 2005-11-25 12:48:39 as along with 2 people katholt karfunkel
	Homology, pathway distance and chromosomal localization of the small molecule metabolism enzymes in Escherichia coli. [My Copy] J Mol Biol, Vol. 318, No. 3. (3 May 2002), pp. 911-932. by S. C. Rison, S. A. Teichmann, J. M. Thornton posted to refs_jme05 by bjorns on 2005-11-25 12:43:52 as along with 1 person tjimenez
	Helicobacter pylori and gastrointestinal tract adenocarcinomas. [My Copy] Nat Rev Cancer, Vol. 2, No. 1. (January 2002), pp. 28-37. by R. M. Peek, M. J. Blaser posted to refs_jme05 by bjorns on 2005-11-25 12:42:08 as
	Metabolic network analysis of the causes and evolution of enzyme dispensability in yeast. [My Copy] Nature, Vol. 429, No. 6992. (10 June 2004), pp. 661-664. by B. Papp, C. Pál, L. D. Hurst posted to refs_jme05 by bjorns on 2005-11-25 12:40:10 as along with 6 people michaelbarton tmmurali edwardmorrissey stefanoallesina hryk Takayuki
	Common Pattern of Evolution of Gene Expression Level and Protein Sequence in Drosophila [My Copy] Mol Biol Evol, Vol. 21, No. 7. (1 July 2004), pp. 1308-1317. by Sergey V. Nuzhdin, Marta L. Wayne, Kristy L. Harmon, Lauren M. McIntyre posted to refs_jme05 by bjorns on 2005-11-25 12:37:08 as along with 6 people and 3 groups daveGerrard cisevol jbsaltz RMGraze penka emptyhb BergmanLab cis-regulatory-evolution Nie
	Scientific collaboration networks. II. Shortest paths, weighted networks, and centrality. [My Copy] Phys Rev E Stat Nonlin Soft Matter Phys, Vol. 64, No. 1 Pt 2. (July 2001) by M. E. Newman posted to refs_jme05 by bjorns on 2005-11-25 12:36:25 as along with 6 people and 3 groups korakot PatrickD mrm rasca shivaram ltabourier Philosophy_of_Information Blog_and_Wiki_Research Wikipedia
	A minimal gene set for cellular life derived by comparison of complete bacterial genomes. [My Copy] Proc Natl Acad Sci U S A, Vol. 93, No. 19. (17 September 1996), pp. 10268-10273. by A. R. Mushegian, E. V. Koonin posted to refs_jme05 by bjorns on 2005-11-25 12:35:39 as along with 9 people and 2 groups tomhebbron antonkratz balicea treangen operon ana jwm gbart westoll structural_bioinformatics Bioinformatics
	Frequencies of synonymous substitutions in mammals are gene-specific and correlated with frequencies of nonsynonymous substitutions. [My Copy] J Mol Evol, Vol. 40, No. 1. (January 1995), pp. 107-113. by D. Mouchiroud, C. Gautier, G. Bernardi posted to refs_jme05 by bjorns on 2005-11-25 12:35:05 as
	Regulation of Transcription in a Reduced Bacterial Genome: Nutrient-Provisioning Genes of the Obligate Symbiont Buchnera aphidicola [My Copy] J. Bacteriol., Vol. 187, No. 12. (15 June 2005), pp. 4229-4237. by Nancy A. Moran, Helen E. Dunbar, Jennifer L. Wilcox posted to refs_jme05 by bjorns on 2005-11-25 12:34:31 as along with 1 person kmachemer
	How clonal are bacteria? [My Copy] Proc Natl Acad Sci U S A, Vol. 90, No. 10. (15 May 1993), pp. 4384-4388. by J. M. Smith, N. H. Smith, M. O'Rourke, B. G. Spratt posted to refs_jme05 by bjorns on 2005-11-25 12:32:10 as along with 2 people pkm Xavier
	The minimal cell genome: "on being the right size". [My Copy] Proc Natl Acad Sci U S A, Vol. 93, No. 19. (17 September 1996), pp. 10004-10006. by J. Maniloff posted to refs_jme05 by bjorns on 2005-11-25 12:28:42 as along with 1 person operon
	Analysis of synonymous codon usage bias in Chlamydia. [My Copy] Acta Biochim Biophys Sin (Shanghai), Vol. 37, No. 1. (January 2005), pp. 1-10. by H. Lü, W. M. Zhao, Y. Zheng, H. Wang, M. Qi, X. P. Yu posted to refs_jme05 by bjorns on 2005-11-25 12:28:12 as
	Hydrophobicity, expressivity and aromaticity are the major trends of amino-acid usage in 999 Escherichia coli chromosome-encoded genes. [My Copy] Nucleic Acids Res, Vol. 22, No. 15. (11 August 1994), pp. 3174-3180. by J. R. Lobry, C. Gautier posted to refs_jme05 by bjorns on 2005-11-25 12:27:22 as along with 2 people operon michaelbarton
	A new method for estimating synonymous and nonsynonymous rates of nucleotide substitution considering the relative likelihood of nucleotide and codon changes. [My Copy] Mol Biol Evol, Vol. 2, No. 2. (March 1985), pp. 150-174. by W. H. Li, C. I. Wu, C. C. Luo posted to refs_jme05 by bjorns on 2005-11-25 12:26:56 as along with 1 person and 1 group hdopazo BioinfoCIPF
	Gene loss, protein sequence divergence, gene dispensability, expression level, and interactivity are correlated in eukaryotic evolution. [My Copy] Genome Res, Vol. 13, No. 10. (October 2003), pp. 2229-2235. by D. M. Krylov, Y. I. Wolf, I. B. Rogozin, E. V. Koonin posted to refs_jme05 by bjorns on 2005-11-25 12:23:42 as
	Predicting transmembrane protein topology with a hidden markov model: application to complete genomes1 [My Copy] Journal of Molecular Biology, Vol. 305, No. 3. (19 January 2001), pp. 567-580. by Anders Krogh, Björn Larsson, Gunnar von Heijne, Erik L. L. Sonnhammer posted to refs_jme05 by bjorns on 2005-11-25 12:22:55 as along with 11 people azazello tfuji niallhaslam katholt thaliana andreasauerwein j3xucite happy_manatee massivemayhem twenta sebk
	How many genes can make a cell: the minimal-gene-set concept. [My Copy] Annu Rev Genomics Hum Genet, Vol. 1 (2000), pp. 99-116. by E. V. Koonin posted to refs_jme05 by bjorns on 2005-11-25 12:22:22 as along with 1 person and 2 groups ana structural_bioinformatics Bioinformatics
	Evolution of minimal-gene-sets in host-dependent bacteria. [My Copy] Trends Microbiol, Vol. 12, No. 1. (January 2004), pp. 37-43. by L. Klasson, S. G. Andersson posted to molev refs_jme05 by bjorns on 2005-11-25 12:21:52 as along with 1 person and 2 groups ana structural_bioinformatics Bioinformatics
	Identification and characterization of Helicobacter pylori genes essential for gastric colonization. [My Copy] J Exp Med, Vol. 197, No. 7. (7 April 2003), pp. 813-822. by H. Kavermann, B. P. Burns, K. Angermuller, et al.S. Odenbreit, W. Fischer, K. Melchers, R. Haas posted to refs_jme05 by bjorns on 2005-11-25 12:21:05 as
	Studies of codon usage and tRNA genes of 18 unicellular organisms and quantification of Bacillus subtilis tRNAs: gene expression level and species-specific diversity of codon usage based on multivariate analysis. [My Copy] Gene, Vol. 238, No. 1. (30 September 1999), pp. 143-155. by S. Kanaya, Y. Yamada, Y. Kudo, T. Ikemura posted to refs_jme05 by bjorns on 2005-11-25 12:20:32 as along with 2 people codonusage michaelbarton
	Conservation and Coevolution in the Scale-Free Human Gene Coexpression Network [My Copy] Mol Biol Evol, Vol. 21, No. 11. (1 November 2004), pp. 2058-2070. by I. King Jordan, Leonardo Marino-Ramirez, Yuri I. Wolf, Eugene V. Koonin posted to refs_jme05 by bjorns on 2005-11-25 12:19:49 as along with 4 people daveGerrard pengchy dragonrez Garamonfok
	Essential Genes Are More Evolutionarily Conserved Than Are Nonessential Genes in Bacteria [My Copy] Genome Res., Vol. 12, No. 6. (1 June 2002), pp. 962-968. by King I. Jordan, Igor B. Rogozin, Yuri I. Wolf, Eugene V. Koonin posted to refs_jme05 by bjorns on 2005-11-25 12:18:26 as along with 4 people and 1 group BarrosH penka ankur_iitg tfogal Nie
	Codon usage and tRNA content in unicellular and multicellular organisms. [My Copy] Mol Biol Evol, Vol. 2, No. 1. (January 1985), pp. 13-34. by T. Ikemura posted to refs_jme05 by bjorns on 2005-11-25 12:16:30 as along with 2 people codonusage karfunkel
	Correlation between the abundance of yeast transfer RNAs and the occurrence of the respective codons in protein genes. Differences in synonymous codon choice patterns of yeast and Escherichia coli with reference to the abundance of isoaccepting transfer RNAs. [My Copy] Journal of molecular biology, Vol. 158, No. 4. (15 July 1982), pp. 573-597. by T. Ikemura posted to refs_jme05 by bjorns on 2005-11-25 12:16:06 as along with 3 people and 1 group danatcaret michaelbarton cisevol BergmanLab
	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. [My Copy] J Mol Biol, Vol. 151, No. 3. (25 September 1981), pp. 389-409. by T. Ikemura posted to refs_jme05 by bjorns on 2005-11-25 12:15:40 as
	Converging on a general model of protein evolution. [My Copy] Trends Biotechnol, Vol. 23, No. 10. (October 2005), pp. 485-487. by J. T. Herbeck, D. P. Wall posted to refs_jme05 by bjorns on 2005-11-25 12:11:31 as along with 2 people and 1 group penka i41m Nie
	LIGAND: chemical database for enzyme reactions. [My Copy] Bioinformatics, Vol. 14, No. 7. (1998), pp. 591-599. by S. Goto, T. Nishioka, M. Kanehisa posted to refs_jme05 by bjorns on 2005-11-25 12:10:22 as
	Evolutionary Rate in the Protein Interaction Network [My Copy] Science, Vol. 296, No. 5568. (26 April 2002), pp. 750-752. by Hunter B. Fraser, Aaron E. Hirsh, Lars M. Steinmetz, Curt Scharfe, Marcus W. Feldman posted to refs_jme05 by bjorns on 2005-11-25 12:06:43 as along with 10 people pablocarb mgomes qluo renewang marcio raiyar dragonrez timflutre tale friendpine
	Common themes in microbial pathogenicity revisited. [My Copy] Microbiol Mol Biol Rev, Vol. 61, No. 2. (June 1997), pp. 136-169. by B. B. Finlay, S. Falkow posted to refs_jme05 by bjorns on 2005-11-25 12:04:26 as along with 1 person iskanbasal
	Expression pattern and, surprisingly, gene length shape codon usage in Caenorhabditis, Drosophila, and Arabidopsis [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 96, No. 8. (13 April 1999), pp. 4482-4487. by Laurent Duret, Dominique Mouchiroud posted to refs_jme05 by bjorns on 2005-11-25 12:02:03 as along with 4 people and 1 group saunders robfsouza thegoose2 tharris C. elegans / WormBase
	Co-variation of tRNA abundance and codon usage in Escherichia coli at different growth rates. [My Copy] J Mol Biol, Vol. 260, No. 5. (2 August 1996), pp. 649-663. by H. Dong, L. Nilsson, C. G. Kurland posted to refs_jme05 by bjorns on 2005-11-25 11:59:32 as along with 2 people and 1 group codonusage penka Nie
	Relationship of codon bias to mRNA concentration and protein length in Saccharomyces cerevisiae. [My Copy] Yeast, Vol. 16, No. 12. (15 September 2000), pp. 1131-1145. by A. Coghlan, K. H. Wolfe posted to refs_jme05 by bjorns on 2005-11-25 11:58:41 as along with 1 person michaelbarton
	Evolutionary rate depends on number of protein-protein interactions independently of gene expression level: response. [My Copy] BMC Evol Biol, Vol. 4 (1 June 2004) by J. D. Bloom, C. Adami posted to refs_jme05 by bjorns on 2005-11-25 10:19:34 as along with 1 person diamantis
	The Complete Genome Sequence of Escherichia coli K-12 [My Copy] Science, Vol. 277, No. 5331. (5 September 1997), pp. 1453-1462. by Frederick R. Blattner, Guy Plunkett, Craig A. Bloch, et al.Nicole T. Perna, Valerie Burland, Monica Riley, Julio Collado-Vides, Jeremy D. Glasner, Christopher K. Rode, George Mayhew, F., Jason Gregor, Nelson W. Davis, Heather A. Kirkpatrick, Michael A. Goeden, Debra J. Rose, Bob Mau, Ying Shao posted to refs_jme05 by bjorns on 2005-11-25 10:17:54 as along with 8 people tomd66 katholt YukaH sgoetz Cortel arcticrasta treangen Xavier
	The focusing positions of polypeptides in immobilized pH gradients can be predicted from their amino acid sequences. [My Copy] Electrophoresis, Vol. 14, No. 10. (October 1993), pp. 1023-1031. by B. Bjellqvist, G. J. Hughes, C. Pasquali, et al.N. Paquet, F. Ravier, J. C. Sanchez, S. Frutiger, D. Hochstrasser posted to refs_jme05 by bjorns on 2005-11-25 10:16:45 as
	Evolutionary forces in shaping the codon and amino acid usages in Blochmannia floridanus. [My Copy] J Biomol Struct Dyn, Vol. 22, No. 1. (August 2004), pp. 13-23. by T. Banerjee, S. Basak, S. K. Gupta, T. C. Ghosh posted to refs_jme05 by bjorns on 2005-11-25 10:12:52 as
	The Stanford Microarray Database accommodates additional microarray platforms and data formats. [My Copy] Nucleic Acids Res, Vol. 33, No. Database issue. (1 January 2005) by C. A. Ball, I. A. Awad, J. Demeter, et al.J. Gollub, J. M. Hebert, T. Hernandez-Boussard, H. Jin, J. C. Matese, M. Nitzberg, F. Wymore, Z. K. Zachariah, P. O. Brown, G. Sherlock posted to refs_jme05 by bjorns on 2005-11-25 10:11:19 as along with 1 person nuin
	Codon usage and base composition in Rickettsia prowazekii. [My Copy] J Mol Evol, Vol. 42, No. 5. (May 1996), pp. 525-536. by S. G. Andersson, P. M. Sharp posted to refs_jme05 by bjorns on 2005-11-25 10:10:43 as

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refs_jme05	84
kaks	24
expression	23
typeiv	19
helicobacter	18
networks	17
alpha	16
review	14
duplications	13
typeiii	13
bartonella	12
genome	12
recombination	12
molev	11
rocha	10
codon	9
essentialgenes	9
strain	9
ecoli	8
egs	7
geneconversion	7
gene_organization	7
rate	7
sino	7
theory	7
yeast	7
erythrocytes	6
phylogeny	6
az	5
jc	5
pseudo	5
repeats	5
autotransporter	4
endosymbiotic	4
my	4
simulation	4
adaptive	3
duplication	3
fast	3
pkpd	3
surface	3
454	2
4sis	2
bovis	2
buchnera	2
diversifying	2
flagella	2
lgt	2
metabolic	2
ochrobactrum	2
sequencing	2
trw	2
typeii	2
bada	1
brpa	1
circadian	1
clinical	1
cog	1
drosophila	1
ftsk	1
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gamma	1
gene_content	1
immunesystem	1
lic	1
mito	1
mrna	1
operons	1
opinion	1
preview	1
promoter	1
puf	1
reduction	1
ringoflife	1
salmonella	1
sar11	1
system	1
transporter	1
typev	1

bjorns's refs_jme05 [84 articles] Export

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