michaelbarton's mdb-thesis [112 articles] Export

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	A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach. [My Copy] Molecular Biology and Evolution, Vol. 18, No. 5. (1 May 2001), pp. 691-699. by S. Whelan, N. Goldman posted to mdb-thesis mdb-manuscript-1 evolutionary-rate amino-acid-substitution by michaelbarton on 2009-08-07 16:36:02 as along with 7 people calderonv BioNica bpb chrn ssgong gjuggler gisle
	Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing [My Copy] Journal of the Royal Statistical Society. Series B (Methodological), Vol. 57, No. 1. (1995), pp. 289-300. by Yoav Benjamini, Yosef Hochberg posted to mdb-thesis statistics by michaelbarton on 2009-08-07 14:22:26 as along with 38 people and 4 groups ctacmo abrentnall jperkins CulCog jlorent zufar bertelsen Zephyrus fisherp dakelley lwaldron polivares brianb ucbcjbm jfr xingxu emptyhb renewang Yanno sdvillal druvus natstreet czeller guhjy RMGraze oannes vplagnol frohike grahamc shigepong ccr axelon ugengma amsantos rschulz dragonrez isimpson vertikalist Biostatistics Bioinformatics Regulomics_UCHSC BTS-PT-AS-CS
	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 codon-usage mdb-thesis yeast by michaelbarton on 2009-07-29 11:35:42 as along with 1 person bjorns
	Revisiting the codon adaptation index from a whole-genome perspective: analyzing the relationship between gene expression and codon occurrence in yeast using a variety of models. [My Copy] Nucleic Acids Research, Vol. 31, No. 8. (15 April 2003), pp. 2242-2251. by R. Jansen, H. J. Bussemaker, M. Gerstein posted to yeast mdb-thesis mdb-manuscript-1 gene-expression codon-usage by michaelbarton on 2009-07-19 19:35:03 as along with 1 person nedwards
	Fundamentals of Enzyme Kinetics [My Copy] (29 February 2004) by Athel Cornish-Bowden posted to enzyme mdb-thesis metabolism by michaelbarton on 2009-07-08 14:06:46 as along with 2 people Rayn fishtank
	A functional genomics strategy that uses metabolome data to reveal the phenotype of silent mutations. [My Copy] Nature Biotechnology, Vol. 19, No. 1. (January 2001), pp. 45-50. by L. M. Raamsdonk, B. Teusink, D. Broadhurst, et al.N. Zhang, A. Hayes, M. C. Walsh, J. A. Berden, K. M. Brindle, D. B. Kell, J. J. Rowland, H. V. Westerhoff, K. van Dam, S. G. Oliver posted to gene-dispensability mdb-thesis yeast by michaelbarton on 2009-07-06 16:35:13 as along with 8 people and 3 groups Garth_9145 czeller dbk irenas dullhunk raiyar katerinakal JeremyZucker streptomyces dbk-lab steinmetzlab
	Co-regulation of metabolic genes is better explained by flux coupling than by network distance [My Copy] PLoS Computational Biology, Vol. 4, No. 1. (25 January 2008), e26. by Richard A. Notebaart, Bas Teusink, Roland J. Siezen, Balázs Papp posted to ecoli flux-balance-analysis genome-scale-model mdb-thesis metabolism yeast by michaelbarton on 2009-07-06 16:28:35 as along with 4 people yujiangwang arne maralena jjray
	Yeast and drug discovery. [My Copy] Functional & Integrative Genomics, Vol. 2, No. 4-5. (September 2002), pp. 199-211. by T. R. Hughes posted to mdb-thesis yeast by michaelbarton on 2009-07-03 12:14:10 as along with 1 person Dualsystems
	Quantitative phenotypic analysis of yeast deletion mutants using a highly parallel molecular bar-coding strategy. [My Copy] Nature Genetics, Vol. 14, No. 4. (December 1996), pp. 450-456. by D. D. Shoemaker, D. A. Lashkari, D. Morris, M. Mittmann, R. W. Davis posted to mdb-thesis by michaelbarton on 2009-07-02 17:28:19 as along with 1 person Kiarostami
	Automated protein function prediction--the genomic challenge. [My Copy] Briefings in Bioinformatics, Vol. 7, No. 3. (23 September 2006), pp. 225-242. by I. Friedberg posted to genome-annotation mdb-thesis by michaelbarton on 2009-07-02 16:23:17 as along with 12 people and 3 groups kiekyon MarcoAlvarez Keywan idoerg shung tjimenez yas marcius j3xucite cdallett sgoetz bootsy T_lab BioinfoCIPF SGU-CIPF
	Population genomics of domestic and wild yeasts. [My Copy] Nature, Vol. 458, No. 7236. (19 March 2009), pp. 337-341. by G. Liti, D. M. Carter, A. M. Moses, et al.J. Warringer, L. Parts, S. A. James, R. P. Davey, I. N. Roberts, A. Burt, V. Koufopanou, I. J. Tsai, C. M. Bergman, D. Bensasson, M. J. O'Kelly, A. van Oudenaarden, D. B. Barton, E. Bailes, A. N. Nguyen, M. Jones, M. A. Quail, I. Goodhead, S. Sims, F. Smith, A. Blomberg, R. Durbin, E. J. Louis posted to mdb-thesis population-genetics srs srs-resequencing yeast by michaelbarton on 2009-07-02 14:19:26 as along with 12 people and 3 groups aprasad emptyhb benjaminsb dpollard fungal absterga anphony druvus stajich jasontsai skoch3 dullhunk RockmanLab Mycology Koch_Lab
	Life with 6000 Genes [My Copy] Science, Vol. 274, No. 5287. (25 October 1996), pp. 546-567. by A. Goffeau, B. G. Barrell, H. Bussey, et al.R. W. Davis, B. Dujon, H. Feldmann, F. Galibert, J. D. Hoheisel, C. Jacq, M. Johnston, E. J. Louis, H. W. Mewes, Y. Murakami, P. Philippsen, H. Tettelin, S. G. Oliver posted to genome-sequencing mdb-thesis yeast by michaelbarton on 2009-07-02 14:13:43 as along with 10 people tomd66 timflutre nzm sdinka Cortel rebeccahainess arcticrasta treangen yulian2108 farhat
	Transposable element annotation of the rice genome. [My Copy] Bioinformatics (Oxford, England), Vol. 20, No. 2. (22 January 2004), pp. 155-160. by Nikoleta Juretic, Thomas E. Bureau, Richard M. Bruskiewich posted to genome-annoation mdb-thesis non-coding-dna transposable-elements by michaelbarton on 2009-07-02 13:47:17 as along with 3 people operon urgi xwbcn
	Genome-scale analysis to the impact of gene deletion on the metabolism of E. coli: constraint-based simulation approach. [My Copy] BMC Bioinformatics, Vol. 10 Suppl 1 (2009) by Z. Xu, X. Sun, S. Yu posted to flux-balance-analysis gene-dispensability mdb-thesis by michaelbarton on 2009-06-30 11:09:57 as along with 1 person Winzer
	Genome sequencing in microfabricated high-density picolitre reactors [My Copy] Nature, Vol. 437, No. 7057. (15 September 2005), pp. 376-380. by Marcel Margulies, Michael Egholm, William E. Altman, et al.Said Attiya, Joel S. Bader, Lisa A. Bemben, Jan Berka, Michael S. Braverman, Yi-Ju Chen, Zhoutao Chen, Scott B. Dewell, Lei Du, Joseph M. Fierro, Xavier V. Gomes, Brian C. Godwin, Wen He, Scott Helgesen, Chun H. Ho, Gerard P. Irzyk, Szilveszter C. Jando, Maria L. I. Alenquer, Thomas P. Jarvie, Kshama B. Jirage, Jong-Bum Kim, James R. Knight, Janna R. Lanza, John H. Leamon, Steven M. Lefkowitz, Ming Lei, Jing Li, Kenton L. Lohman, Hong Lu, Vinod B. Makhijani, Keith E. Mcdade, Michael P. Mckenna, Eugene W. Myers, Elizabeth Nickerson, John R. Nobile, Ramona Plant, Bernard P. Puc, Michael T. Ronan, George T. Roth, Gary J. Sarkis, Jan F. Simons, John W. Simpson, Maithreyan Srinivasan, Karrie R. Tartaro, Alexander Tomasz, Kari A. Vogt, Greg A. Volkmer, Shally H. Wang, Yong Wang, Michael P. Weiner, Pengguang Yu, Richard F. Begley, Jonathan M. Rothberg posted to mdb-thesis srs by michaelbarton on 2009-06-29 11:02:18 as along with 36 people and 5 groups seb1 pachorip katiehumphry jonilaserson sandfire natstreet daforerog idoerg mmartin azazello jbhiatt alessandrobrozzi leechuck bjorns dayjm jmeppley arve RMGraze JAShapiro balajis cdawson AaronDarling treangen usagi-kirin beatrizfernandez wenhan xingxu erbon tpreeprem farhat carpi bpb mcox GustavoLacerda jlgreen kieran101 Microbial-Ecology GIG gatech-compgenomics Green Lab iSEEM
	Next-generation DNA sequencing [My Copy] Nature Biotechnology, Vol. 26, No. 10. (09 October 2008), pp. 1135-1145. by Jay Shendure, Hanlee Ji posted to mdb-thesis srs by michaelbarton on 2009-06-29 11:00:26 as along with 42 people and 3 groups cthachuk giovenko heliopais seb1 installe niallhaslam Vincent_Rouilly rschulz fishtank bluto Annab katholt jmcq n00c jfr dna nzm farhat idoerg mhz mmartin antonkratz jbhiatt yupu behindtherabbit guhjy Pascalichouchou frohike dakelley ptrobajo zwang Zephyrus psique natstreet druvus nuin alexknight reyez dbk wsjames pengchy GeeSharpMinor Bioinformatics Roswell Cancer Crosstalk Oxford Virology
	Gene Ontology annotations at SGD: new data sources and annotation methods. [My Copy] Nucleic Acids Research, Vol. 36, No. Database. (23 December 2008), pp. D577-D581. by E. L. Hong, R. Balakrishnan, Q. Dong, et al.K. R. Christie, J. Park, G. Binkley, M. C. Costanzo, S. S. Dwight, S. R. Engel, D. G. Fisk, J. E. Hirschman, B. C. Hitz, C. J. Krieger, M. S. Livstone, S. R. Miyasato, R. S. Nash, R. Oughtred, M. S. Skrzypek, S. Weng, E. D. Wong, K. K. Zhu, K. Dolinski, D. Botstein, J. M. Cherry posted to yeast mdb-thesis mdb-manuscript-1 database by michaelbarton on 2009-06-24 15:52:35 as along with 5 people fgibson taroleo dullhunk hplatero carlk
	Functional profiling of the Saccharomyces cerevisiae genome. [My Copy] Nature, Vol. 418, No. 6896. (25 July 2002), pp. 387-391. by G. Giaever, A. M. Chu, L. Ni, et al.C. Connelly, L. Riles, S. Véronneau, S. Dow, A. Lucau-Danila, K. Anderson, B. André, A. P. Arkin, A. Astromoff, M. El-Bakkoury, R. Bangham, R. Benito, S. Brachat, S. Campanaro, M. Curtiss, K. Davis, A. Deutschbauer, K. D. Entian, P. Flaherty, F. Foury, D. J. Garfinkel, M. Gerstein, D. Gotte, U. Güldener, J. H. Hegemann, S. Hempel, Z. Herman, D. F. Jaramillo, D. E. Kelly, S. L. Kelly, P. Kötter, D. Labonte, D. C. Lamb, N. Lan, H. Liang, H. Liao, L. Liu, C. Luo, M. Lussier, R. Mao, P. Menard, S. L. Ooi, J. L. Revuelta, C. J. Roberts, M. Rose, P. Ross-Macdonald, B. Scherens, G. Schimmack, B. Shafer, D. D. Shoemaker, S. Sookhai-Mahadeo, R. K. Storms, J. N. Strathern, G. Valle, M. Voet, G. Volckaert, C. Y. Wang, T. R. Ward, J. Wilhelmy, E. A. Winzeler, Y. Yang, G. Yen, E. Youngman, K. Yu, H. Bussey, J. D. Boeke, M. Snyder, P. Philippsen, R. W. Davis, M. Johnston posted to gene-dispensability mdb-thesis yeast by michaelbarton on 2009-06-23 14:29:09 as along with 16 people and 3 groups myzhang thegoose2 mdstobbe tharris pcahan1 lfriedl balajis rebeccahainess nirfriedman koller raiyar cjeans jiny hplatero chasmand dylanwalker C. elegans / WormBase kdl steinmetzlab
	Why highly expressed proteins evolve slowly. [My Copy] Proceedings of the National Academy of Sciences (21 September 2005), pp. 14338-14343. by D. A. A. Drummond, Jesse D. D. Bloom, Christoph Adami, Claus O. O. Wilke, Frances H. H. Arnold posted to evolutionary-rate gene-expression mdb-thesis prote-evolution by michaelbarton on 2009-06-15 11:45:50 as along with 17 people and 5 groups codonusage allmaya rklancer stevanspringer bjorns imouthesmp aprasad dayjm Einat marcius xwbcn penka balabu malcook balicea RamuAnandakrishnan wilbur structural_bioinformatics Nie FAB-lab BioinfoCIPF SGU-CIPF
	Highly Expressed Genes in Yeast Evolve Slowly [My Copy] Genetics, Vol. 158, No. 2. (1 June 2001), pp. 927-931. by Csaba Pal, Balazs Papp, Laurence D. Hurst posted to evolutionary-rate gene-expression mdb-thesis by michaelbarton on 2009-06-15 11:38:37 as along with 6 people and 1 group pablocarb bjorns penka lewbin balicea skumagai Nie
	Genomic profiling of drug sensitivities via induced haploinsufficiency [My Copy] Nature Genetics, Vol. 21, No. 3. (March 1999), pp. 278-283. by G. Giaever, D. D. Shoemaker, T. W. Jones, et al.H. Liang, E. A. Winzeler, A. Astromoff, R. W. Davis posted to haploinsufficiency mdb-thesis yeast by michaelbarton on 2009-06-10 16:26:52 as along with 1 person and 1 group raiyar steinmetzlab
	Identification and characterization of high-flux-control genes of yeast through competition analyses in continuous cultures. [My Copy] Nature Genetics, Vol. 40, No. 1. (23 January 2008), pp. 113-117. by Daniela Delneri, David C. Hoyle, Konstantinos Gkargkas, et al.Emma J. M. Cross, Bharat Rash, Leo Zeef, Hui-Sun Leong, Hazel M. Davey, Andrew Hayes, Douglas B. Kell, Gareth W. Griffith, Stephen G. Oliver posted to haploinsufficiency mdb-thesis metabolic-control-analysis by michaelbarton on 2009-06-10 11:33:52 as along with 2 people and 1 group Annab dbk dbk-lab
	Estimating the frequency of events that cause multiple-nucleotide changes. [My Copy] Genetics, Vol. 167, No. 4. (August 2004), pp. 2027-2043. by S. Whelan, N. Goldman posted to instance-rate-matrix mdb-thesis prote-evolution by michaelbarton on 2009-05-25 11:14:19 as along with 2 people robsyme gjuggler
	An integrated view of protein evolution. [My Copy] Nature reviews. Genetics, Vol. 7, No. 5. (May 2006), pp. 337-348. by C. Pál, B. Papp, M. J. Lercher posted to mdb-thesis prote-evolution by michaelbarton on 2009-05-25 10:40:38 as along with 13 people and 2 groups mgomes chica gurprit_raunu gjuggler biomcgary icases dayjm tny entropy markbothwell BioNica mingzhi phoenixzxl Bothwellab TNT
	BioRuby: open-source bioinformatics library [My Copy] Genome Informatics, Vol. 14 (2003), pp. 629-630. by Naohisa G. Mitsuteru, Naohisa Goto, Mitsuteru C. Nakao, Shiuichi Kawashima, Toshiaki Katayama, Minoru Kanehisa posted to bioruby mdb-thesis ruby by michaelbarton on 2009-05-04 17:23:22 as along with 1 person cmzmasek
	Algorithm AS 136: A k-means clustering algorithm [My Copy] Applied Statistics, Vol. 28, No. 1. (1979), pp. 100-108. by J. A. Hartigan, M. A. Wong posted to classification clustering mdb-thesis statistics by michaelbarton on 2009-04-20 23:29:35 as
	The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models [My Copy] Bioinformatics, Vol. 19, No. 4. (1 March 2003), pp. 524-531. by M. Hucka, A. Finney, H. M. Sauro, et al.H. Bolouri, J. C. Doyle, H. Kitano, A. P. Arkin, B. J. Bornstein, D. Bray, A. Cornish-Bowden, A. A. Cuellar, S. Dronov, E. D. Gilles, M. Ginkel, V. Gor, I. I. Goryanin, W. J. Hedley, T. C. Hodgman, J. H. Hofmeyr, P. J. Hunter, N. S. Juty, J. L. Kasberger, A. Kremling, U. Kummer, N. Le Novère, L. M. Loew, D. Lucio, P. Mendes, E. Minch, E. D. Mjolsness, Y. Nakayama, M. R. Nelson, P. F. Nielsen, T. Sakurada, J. C. Schaff, B. E. Shapiro, T. S. Shimizu, H. D. Spence, J. Stelling, K. Takahashi, M. Tomita, J. Wagner, J. Wang posted to mdb-thesis by michaelbarton on 2009-04-01 12:53:43 as along with 20 people and 2 groups jporternj daforerog whitead antonkratz allysonlister rh020 shikin subhacom irenas husain easr balajis wnpx jbchang lenov nicholasflann pmendes csanford AlexanderPico dullhunk Jiang Research Group dbk-lab
	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 codon-usage mdb-thesis by michaelbarton on 2009-03-04 18:15:07 as along with 2 people codonusage bjorns
	Finding functional features in Saccharomyces genomes by phylogenetic footprinting. [My Copy] Science, Vol. 301, No. 5629. (4 July 2003), pp. 71-76. by P. Cliften, P. Sudarsanam, A. Desikan, et al.L. Fulton, B. Fulton, J. Majors, R. Waterston, B. A. Cohen, M. Johnston posted to comparative-genomics genomics mdb-thesis yeast by michaelbarton on 2009-03-04 18:13:29 as along with 6 people and 1 group wowalz evaf chad_davis dquest Eonwe cisevol cis-regulatory-evolution
	Sequencing and comparison of yeast species to identify genes and regulatory elements. [My Copy] Nature, Vol. 423, No. 6937. (15 May 2003), pp. 241-254. by Manolis Kellis, Nick Patterson, Matthew Endrizzi, Bruce Birren, Eric S. Lander posted to comparative-genomics evolution genomics mdb-thesis yeast by michaelbarton on 2009-03-04 18:09:52 as along with 10 people and 4 groups roys evaf RMGraze balajis opheliav dchughes dquest franklin azazello cisevol G4ID Genetics-of-Gambling MBLAB cis-regulatory-evolution
	Selection on synthesis cost affects interprotein amino acid usage in all three domains of life [My Copy] Journal of Molecular Evolution, Vol. 64, No. 5. (6 May 2007), pp. 558-571. by Jonathan Swire posted to mdb-thesis mdb-manuscript-1 amino-acid-usage amino-acid-cost by michaelbarton on 2009-03-04 18:05:26 as along with 1 person youdon
	A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. [My Copy] Bioinformatics (Oxford, England), Vol. 19, No. 2. (22 January 2003), pp. 185-193. by B. M. Bolstad, R. A. Irizarry, M. Astrand, T. P. Speed posted to statistics normalisation mdb-thesis mdb-manuscript-1 by michaelbarton on 2009-03-04 17:58:38 as along with 22 people jperkins vplagnol brianb neils ipark-kaist shikin emptyhb noushin huiminC cassj Dax42 pcahan1 chad_davis RMGraze gjuggler filmsternchen qmwwallace joepickrell ghattem bertelsen vertikalist GeeSharpMinor
	R: A Language and Environment for Statistical Computing [My Copy] by R Development Core Team posted to statistics software mdb-thesis mdb-manuscript-1 by michaelbarton on 2009-03-04 17:54:52 as along with 5 people asmusolsen bertelsen humburg kohei-h thegoose
	Modeling residue usage in aligned protein sequences via maximum likelihood. [My Copy] Mol Biol Evol, Vol. 13, No. 10. (December 1996), pp. 1368-1374. by W. J. Bruno posted to amino-acid-substitution amino-acid-usage evolutionary-rate mdb-thesis by michaelbarton on 2009-03-02 22:56:59 as
	PAML 4: Phylogenetic analysis by maximum likelihood [My Copy] Molecular Biology and Evolution, Vol. 24, No. 8. (1 August 2007), pp. 1586-1591. by Ziheng Yang posted to mdb-thesis mdb-manuscript-1 evolutionary-rate by michaelbarton on 2009-03-02 22:52:02 as along with 13 people and 1 group ckenaley biomcgary dquest druvus operon akifumi hdopazo BioNica stajich ryanraaum RamuAnandakrishnan CharlesM Ema Mycology
	Identifying protein-coding genes in genomic sequences [My Copy] Genome Biology, Vol. 10, No. 1. (30 January 2009), 201. by Jennifer Harrow, Alinda Nagy, Alexandre Reymond, et al.Tyler Alioto, Laszlo Patthy, Stylianos Antonarakis, Roderic Guigo posted to gene-prediction genome-annotation genome-sequencing mdb-thesis by michaelbarton on 2009-03-02 22:42:01 as along with 14 people and 2 groups jfr antonkratz robfsouza nlapalu renatomilani ArtemPankin hpaces guhjy idoerg jm12 pawelszczesny natstreet barriot druvus Bioinformatics Khavkin's lab
	Protein carbon content evolves in response to carbon availability and may influence the fate of duplicated genes. [My Copy] Proceedings of the Royal Society B, Vol. 274, No. 1613. (22 April 2007), pp. 1063-1070. by J. G. Bragg, A. Wagner posted to atomic-content gene-duplication mdb-thesis by michaelbarton on 2009-03-02 22:38:26 as
	A framework for evolutionary systems biology [My Copy] BMC Systems Biology, Vol. 3, No. 1. (2009), 27. by L. Loewe posted to evolutionary-systems-biology mdb-thesis by michaelbarton on 2009-02-27 09:34:47 as along with 16 people and 1 group tomhebbron pawelsobko leemond31 maren gwenknight Scis0000002 agomez dswan bertelsen JeremyZucker JoeDunckley Zephyrus trfield jjray VGreiff druvus Roswell Cancer Crosstalk
	Genome streamlining in a cosmopolitan oceanic bacterium. [My Copy] Science, Vol. 309, No. 5738. (19 August 2005), pp. 1242-1245. by S. J. Giovannoni, H. J. Tripp, S. Givan, et al.M. Podar, K. L. Vergin, D. Baptista, L. Bibbs, J. Eads, T. H. Richardson, M. Noordewier, M. S. Rappé, J. M. Short, J. C. Carrington, E. J. Mathur posted to amino-acid-usage genomics mdb-thesis by michaelbarton on 2009-02-16 17:34:23 as along with 5 people sanxiyn johanviklund knaseanka bjorns vrich
	Evolution of proteomes: Fundamental signatures and global trends in amino acid compositions [My Copy] BMC Genomics, Vol. 7 (05 December 2006), 307. by Fredj Tekaia, Edouard Yeramian posted to amino-acid-usage mdb-thesis by michaelbarton on 2009-02-07 16:35:03 as along with 1 person and 1 group brant EisenLab
	Quantifying environmental adaptation of metabolic pathways in metagenomics [My Copy] Proceedings of the National Academy of Sciences, Vol. 106, No. 5. (3 February 2009), pp. 1374-1379. by T. A. Gianoulis, J. Raes, P. V. Patel, et al.R. Bjornson, J. O. Korbel, I. Letunic, T. Yamada, A. Paccanaro, L. J. Jensen, M. Snyder, P. Bork, M. B. Gerstein posted to amino-acid-cost amino-acid-usage atomic-content mdb-thesis metagenomics by michaelbarton on 2009-02-07 16:14:17 as along with 16 people and 2 groups paccanarolab vvoorr djkt jjray roys sharpton Lizzy_fun skembel jlgreen Thaverkamp dbensasson anphony idoerg trfield larsjuhljensen jmeppley Paccanaro Lab iSEEM
	Regulatory on/off minimization of metabolic flux changes after genetic perturbations. [My Copy] Proceedings of the National Academy of Sciences, Vol. 102, No. 21. (24 May 2005), pp. 7695-7700. by T. Shlomi, O. Berkman, E. Ruppin posted to suboptimal-solution mdb-thesis mdb-manuscript-1 genome-scale-model flux-balance-analysis by michaelbarton on 2009-02-03 16:12:19 as along with 3 people yujiangwang koller roys
	Why is the correlation between gene importance and gene evolutionary rate so weak? [My Copy] PLoS Genetics, Vol. 5, No. 1. (January 2009), e1000329. by Zhi Wang, Jianzhi Zhang posted to evolutionary-rate evolutionary-systems-biology gene-dispensability gene-knockout mdb-thesis systems-biology by michaelbarton on 2009-02-03 16:05:50 as along with 11 people and 2 groups daveGerrard rdiaz renatomilani dpollard pkonings katholt druvus Zephyrus djkt trfield cabbagesofdoom RockmanLab R.E.A.D
	Exploration of essential gene functions via titratable promoter alleles. [My Copy] Cell, Vol. 118, No. 1. (9 July 2004), pp. 31-44. by S. Mnaimneh, A. P. Davierwala, J. Haynes, et al.J. Moffat, W. T. Peng, W. Zhang, X. Yang, J. Pootoolal, G. Chua, A. Lopez, M. Trochesset, D. Morse, N. J. Krogan, S. L. Hiley, Z. Li, Q. Morris, J. Grigull, N. Mitsakakis, C. J. Roberts, J. F. Greenblatt, C. Boone, C. A. Kaiser, B. J. Andrews, T. R. Hughes posted to haploinsufficiency mdb-thesis yeast by michaelbarton on 2009-02-03 15:48:10 as along with 4 people and 2 groups raiyar irenas chasmand nickluscombe dbk-lab EBI-regulation
	A global view of pleiotropy and phenotypically derived gene function in yeast [My Copy] Molecular Systems Biology, Vol. 1, No. 1. (29 March 2005), pp. msb4100004-E1-msb4100004-E11. by Aimée M. Dudley, Daniel M. Janse, Amos Tanay, Ron Shamir, George M. Church posted to mdb-thesis yeast by michaelbarton on 2009-02-03 15:46:02 as along with 9 people nicholasflann dbensasson chihchun_chen balajis balicea i41m nirfriedman koller jiny
	Variation among species in proteomic sulphur content is related to environmental conditions. [My Copy] Proceedings of the Royal Society B, Vol. 273, No. 1591. (22 May 2006), pp. 1293-1300. by J. G. Bragg, D. Thomas, P. Baudouin-Cornu posted to nutrient-limitation mdb-thesis mdb-manuscript-1 gene-characteristics atomic-content amino-acid-usage by michaelbarton on 2009-02-03 15:35:22 as
	Mechanisms of Haploinsufficiency Revealed by Genome-Wide Profiling in Yeast [My Copy] Genetics, Vol. 169, No. 4. (1 April 2005), pp. 1915-1925. by Adam M. Deutschbauer, Daniel F. Jaramillo, Michael Proctor, et al.Jochen Kumm, Maureen E. Hillenmeyer, Ronald W. Davis, Corey Nislow, Guri Giaever posted to haploinsufficiency mdb-thesis yeast by michaelbarton on 2009-02-03 15:34:37 as along with 3 people yagyav madhadron chasmand
	Computational approaches to the topology, stability and dynamics of metabolic networks. [My Copy] Phytochemistry, Vol. 68, No. 16-18. (p 2007), pp. 2139-2151. by R. Steuer posted to flux-balance-analysis genome-scale-model mdb-thesis systems-biology by michaelbarton on 2009-02-03 15:34:02 as
	Amino acid cost and codon-usage biases in 6 prokaryotic genomes: a whole-genome analysis [My Copy] Molecular Biology and Evolution, Vol. 23, No. 9. (1 September 2006), pp. 1670-1680. by Esley M. Heizer, Douglas W. Raiford, Michael L. Raymer, Travis E. Doom, Robert V. Miller, Dan E. Krane posted to mdb-thesis mdb-manuscript-1 gene-characteristics cost-minimisation amino-acid-usage by michaelbarton on 2009-02-03 15:33:06 as along with 4 people codonusage operon dylan77 bpcusack
	The effects of alternate optimal solutions in constraint-based genome-scale metabolic models. [My Copy] Metabolic Engineering, Vol. 5, No. 4. (October 2003), pp. 264-276. by R. Mahadevan, C. H. Schilling posted to flux-balance-analysis mdb-thesis suboptimal-solution by michaelbarton on 2009-02-03 15:30:42 as along with 1 person yujiangwang

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mdb-thesis	112
yeast	65
amino-acid-usage	50
mdb-manuscript-1	46
gene-expression	38
flux-balance-analysis	34
genome-scale-model	34
evolutionary-rate	29
evolution	25
cost-minimisation	24
codon-usage	23
reviewed	21
ecoli	20
gene-dispensability	20
metabolism	20
srs	17
systems-biology	15
amino-acid-substitution	13
environment	13
gene-characteristics	10
metabolic-control-analysis	10
metagenomics	10
nutrient-limitation	10
translation	10
diauxic-shift	8
genomics	8
gc-content	7
gene-duplication	7
transcription	7
evolutionary-systems-biology	6
phylogenomics	6
srs-resequencing	6
statistics	6
amino-acid-cost	5
atomic-content	5
comparative-genomics	5
fitness	5
gene-length	5
genome-annotation	5
genome-sequencing	5
glycolysis	5
haploinsufficiency	5
mutation	5
prote-evolution	5
srs-assembly	5
translational-selection	5
database	4
energy-production	4
extremophile	4
insertion-deletion	4
proteins	4
sequence-alignment	4
snp	4
thermophile	4
trna	4
cost-benefit-analysis	3
enzyme	3
gene-expression-degradation	3
metabolomics	3
pharmacology	3
phylogeny	3
population-genetics	3
protein-structure	3
sequence-homology	3
trna-copy	3
alignment-concatenation	2
classification	2
clustering	2
data-mining	2
drosophila	2
gene-knockout	2
genetic-code	2
genetic-variation	2
gene-transfer	2
genome-scale-model-construction	2
kinetic-modelling	2
model-fitting	2
moma	2
mrna-degradation	2
multiple-sequence-alignment	2
noise	2
non-synonymous-substitutions	2
proteome	2
regulation	2
software	2
srs-challenges	2
standards	2
suboptimal-solution	2
synonymous-substitutions	2
transcription-factors	2
transcriptome	2
translational-accuracy	2
akaike-information-criterion	1
alignment	1
bibliometrics	1
binding-sites	1
bioruby	1
bloggging	1
blogging	1
buchnera	1
chemicals	1
citation-analysis	1
collaboration	1
density	1
drug	1
endosymbiotic	1
eubacteria	1
functional-constaint	1
functional-constraint	1
gene-prediction	1
genome-annoation	1
genome-duplication	1
hiv	1
insertions-deletions	1
instance-rate-matrix	1
isoenzymes	1
lac-operon	1
lactose	1
linear-optimisation	1
log-likelihood	1
metabolic_efficiency	1
metabolic-engineering	1
metabolite	1
metabolome	1
microarray	1
modelling	1
mrna-stability	1
mrn-degradation	1
multivariate	1
network-analysis	1
non-coding-dna	1
normalisation	1
ontology	1
open-science	1
page-rank	1
paralogs	1
paramter-scanning	1
phenotype-prediction	1
promoters	1
protein-atomic-content	1
protein-degradation	1
protein-production	1
purifying-selection	1
regression	1
research	1
review	1
ribosomal	1
ribosomal-density	1
rna-structure	1
room	1
ruby	1
sequence	1
shadow-prices	1
solexa	1
species-tree	1
srs-deep	1
srs-simulation	1
strain-design	1
structural-constraint	1
sulfur	1
symbiosis	1
tap-tag	1
thermophiles	1
tiling-array	1
trace-metals	1
transcription-network	1
transposable-elements	1
virus	1

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