yujiangwang's Top Recommendations

These recommendations were last updated 29 minutes ago.

	Plasticity of genetic interactions in metabolic networks of yeast [My Copy] PNAS, Vol. 104, No. 7. (13 February 2007), pp. 2307-2312. by Richard Harrison, Balazs Papp, Csaba Pal, Stephen G. Oliver, Daniela Delneri posted by 5 people schwartzjmc benjaminsb michaelbarton edwardmorrissey jiny
	Integrated analysis of regulatory and metabolic networks reveals novel regulatory mechanisms in Saccharomyces cerevisiae. [My Copy] Genome Res, Vol. 16, No. 5. (May 2006), pp. 627-635. by M. J. Herrgård, B. S. Lee, V. Portnoy, B. Ø. Palsson posted by 12 people michaelbarton JeremyZucker nickluscombe aswin kengg koller raiyar cjeans edwardmorrissey EBI-regulation steinmetzlab Plantandetc
	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 by 7 people michaelbarton tmmurali bjorns edwardmorrissey stefanoallesina hryk Takayuki
	Genome-Scale Reconstruction of the Saccharomyces cerevisiae Metabolic Network [My Copy] Genome Research, Vol. 13, No. 2. (1 February 2003), pp. 244-253. by Jochen FÃ¶rster, Iman Famili, Patrick Fu, Bernhard Palsson, Jens Nielsen posted by 15 people sergiun schwartzjmc michaelbarton csanford opheliav wnpx nirfriedman JeremyZucker bsmagic gcalda jpoyatos edwardmorrissey Bioinformatics bioinplant MetabolicModeling
	Reconstruction and validation of Saccharomyces cerevisiae iND750, a fully compartmentalized genome-scale metabolic model. [My Copy] Genome Res, Vol. 14, No. 7. (July 2004), pp. 1298-1309. by N. C. Duarte, M. J. Herrgård, B. Ø. Palsson posted by 4 people michaelbarton RMGraze edwardmorrissey westoll
	A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information. [My Copy] Molecular systems biology, Vol. 3 (26 June 2007) by Adam M. Feist, Christopher S. Henry, Jennifer L. Reed, et al.Markus Krummenacker, Andrew R. Joyce, Peter D. Karp, Linda J. Broadbelt, Vassily Hatzimanikatis, Bernhard Ø. Palsson posted by 8 people winterstream aheilbut schwartzjmc alexg cjeans hryk michaelbarton JeremyZucker
	Advances in flux balance analysis. [My Copy] Curr Opin Biotechnol, Vol. 14, No. 5. (October 2003), pp. 491-496. by K. J. Kauffman, P. Prakash, J. S. Edwards posted by 11 people winterstream beapen wnpx nirfriedman bsmagic edwardmorrissey Bioinformatics Atopic_and_Seborrhoeic_Dermatitis Skin_Deep Applied_Bimatics bioinplant
	Can yeast glycolysis be understood in terms of in vitro kinetics of the constituent enzymes? Testing biochemistry. [My Copy] European journal of biochemistry / FEBS, Vol. 267, No. 17. (September 2000), pp. 5313-5329. by B. Teusink, J. Passarge, C. A. Reijenga, et al.E. Esgalhado, C. C. van der Weijden, M. Schepper, M. C. Walsh, B. M. Bakker, K. van Dam, H. V. Westerhoff, J. L. Snoep posted by 7 people dadiamah schwartzjmc peterli dullhunk pmendes marcio michaelbarton
	Global reconstruction of the human metabolic network based on genomic and bibliomic data. [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 104, No. 6. (6 February 2007), pp. 1777-1782. by N. C. Duarte, S. A. Becker, N. Jamshidi, et al.I. Thiele, M. L. Mo, T. D. Vo, R. Srivas, B. Ø. Palsson posted by 11 people vpenelle peterli schwartzjmc michaelbarton dullhunk guhjy balajis alexg raiyar noby steinmetzlab
	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, and the rest of the SBML Forum:, 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 Novere, 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 by 23 people jporternj daforerog Jiang Research Group whitead antonkratz michaelbarton allysonlister rh020 shikin subhacom irenas husain easr balajis wnpx jbchang lenov dbk-lab nicholasflann pmendes csanford AlexanderPico dullhunk
	Schemes of flux control in a model of Saccharomyces cerevisiae glycolysis. [My Copy] Eur J Biochem, Vol. 269, No. 16. (August 2002), pp. 3894-3904. by L. Pritchard, D. B. Kell posted by 9 people pmendes schwartzjmc peterli michaelbarton dbk LeightonP streptomyces dbk-lab dullhunk
	Modeling methanogenesis with a genome-scale metabolic reconstruction of Methanosarcina barkeri [My Copy] Mol Syst Biol, Vol. 2 (31 January 2006) by Adam M. Feist, Johannes C. Scholten, Bernhard O. Palsson, Fred J. Brockman, Trey Ideker posted by 3 people JeremyZucker michaelbarton lylu
	Analysis of optimality in natural and perturbed metabolic networks. [My Copy] Proc Natl Acad Sci U S A, Vol. 99, No. 23. (12 November 2002), pp. 15112-15117. by D. Segrè, D. Vitkup, G. M. Church posted by 10 people winterstream michaelbarton rklancer nirfriedman koller gcalda kdang roys carlk JeremyZucker
	A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology [My Copy] Nat Biotech, Vol. 26, No. 10. (09 October 2008), pp. 1155-1160. by Markus J. Herrgard, Neil Swainston, Paul Dobson, et al.Warwick B. Dunn, K. Yalcin Arga, Mikko Arvas, Nils Buthgen, Simon Borger, Roeland Costenoble, Matthias Heinemann, Michael Hucka, Nicolas Le Novere, Peter Li, Wolfram Liebermeister, Monica L. Mo, Ana P. Oliveira, Dina Petranovic, Stephen Pettifer, Evangelos Simeonidis, Kieran Smallbone, Irena Spasie, Dieter Weichart, Roger Brent, David S. Broomhead, Hans V. Westerhoff, Betul Kurdar, Merja Penttila, Edda Klipp, Bernhard O. Palsson, Uwe Sauer, Stephen G. Oliver, Pedro Mendes, Jens Nielsen, Douglas B. Kell posted by 25 people m_j pmendes windman83 jfr raiyar neilswainston irenas MetabolicModeling JeremyZucker chasmand schwartzjmc pinney pauldobson alaninmcr allysonlister zwang guhjy dbk BergmanLab michaelbarton ptrobajo neils dullhunk pengchy tmmurali
	Large-scale reconstruction and phylogenetic analysis of metabolic environments. [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 105, No. 38. (23 September 2008), pp. 14482-14487. by E. Borenstein, M. Kupiec, M. W. Feldman, E. Ruppin posted by 4 people michaelbarton schwartzjmc skembel stringertheory
	The growing scope of applications of genome-scale metabolic reconstructions using Escherichia coli [My Copy] Nature Biotechnology, Vol. 26, No. 6. (06 June 2008), pp. 659-667. by Adam M. Feist, Bernhard posted by 9 people eline_koers schwartzjmc lflorez fishtank ptrobajo BergmanLab michaelbarton TNT AlexanderPico
	Unraveling the complexity of flux regulation: A new method demonstrated for nutrient starvation in Saccharomyces cerevisiae [My Copy] Proceedings of the National Academy of Sciences, Vol. 103, No. 7. (14 February 2006), pp. 2166-2171. by Sergio Rossell, Coen C. van der Weijden, Alexander Lindenbergh, et al.Arjen van Tuijl, Christof Francke, Barbara M. Bakker, Hans V. Westerhoff posted by 5 people schwartzjmc michaelbarton JJJ athleem westoll
	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. Cross, Bharat Rash, Leo Zeef, Hui-Sun S. Leong, Hazel M. Davey, Andrew Hayes, Douglas B. Kell, Gareth W. Griffith, Stephen G. Oliver posted by 5 people schwartzjmc Annab michaelbarton dbk dbk-lab
	Post-transcriptional Expression Regulation in the Yeast Saccharomyces cerevisiae on a Genomic Scale [My Copy] Mol Cell Proteomics, Vol. 3, No. 11. (1 November 2004), pp. 1083-1092. by Andreas Beyer, Jens Hollunder, Heinz-Peter Nasheuer, Thomas Wilhelm posted by 4 people cgaugain schwartzjmc roys michaelbarton
	Genome-scale Reconstruction of Metabolic Network in Bacillus subtilis Based on High-throughput Phenotyping and Gene Essentiality Data. [My Copy] J Biol Chem, Vol. 282, No. 39. (28 September 2007), pp. 28791-28799. by Y. K. Oh, B. O. Palsson, S. M. Park, C. H. Schilling, R. Mahadevan posted by 10 people JeremyZucker coela schwartzjmc aschmeis MetabolicModeling jholder michaelbarton lflorez alexg hryk
	Flux balance analysis of a genome-scale yeast model constrained by exometabolomic data allows metabolic system identification of genetically different strains. [My Copy] Biotechnol Prog, Vol. 23, No. 2. (r 2007), pp. 320-326. by T. Cakir, C. Efe, D. Dikicioglu, A. Hortaçsu, B. Kirdar, S. G. Oliver posted by 4 people schwartzjmc cgaugain michaelbarton alexg
	Growth control of the eukaryote cell: a systems biology study in yeast. [My Copy] Journal of biology, Vol. 6, No. 2. (30 April 2007), 4. by Juan I. Castrillo, Leo A. Zeef, David C. Hoyle, et al.Nianshu Zhang, Andrew Hayes, David C. Gardner, Michael J. Cornell, June Petty, Luke Hakes, Leanne Wardleworth, Bharat Rash, Marie Brown, Warwick B. Dunn, David Broadhurst, Kerry O'Donoghue, Svenja S. Hester, Tom P. Dunkley, Sarah R. Hart, Neil Swainston, Peter Li, Simon J. Gaskell, Norman W. Paton, Kathryn S. Lilley, Douglas B. Kell, Stephen G. Oliver posted by 15 people cgaugain mqbphcw3 schwartzjmc neilswainston michaelbarton aalibes alexg dullhunk balabu dylan77 cabbagezs Stew EisenLab roys alanrw
	Minimum information requested in the annotation of biochemical models (MIRIAM) [My Copy] Nature Biotechnology, Vol. 23, No. 12. (06 December 2005), pp. 1509-1515. by Nicolas L. Novere, Andrew Finney, Michael Hucka, et al.Upinder S. Bhalla, Fabien Campagne, Julio Collado-Vides, Edmund J. Crampin, Matt Halstead, Edda Klipp, Pedro Mendes, Poul Nielsen, Herbert Sauro, Bruce Shapiro, Jacky L. Snoep, Hugh D. Spence, Barry L. Wanner posted by 19 people mtaschuk perkeo irenas jmuhlich bertelsen moonhouse schwartzjmc tjtaylor Vincent_Rouilly allysonlister michaelbarton subhacom dullhunk dagmar lenov dIEMoSIRIS compneur pmendes leilaperie
	An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR) [My Copy] Genome Biology, Vol. 4, No. 9. (2003), R54. by Jennifer Reed, Thuy Vo, Christophe Schilling, Bernhard Palsson posted by 8 people schwartzjmc csanford michaelbarton cate bjorns JeremyZucker biospec MetabolicModeling
	Out-of-equilibrium dynamics of gene expression and the Jarzynski equality. [My Copy] Physical review letters, Vol. 100, No. 18. (9 May 2008) by J. Berg posted by 1 person edwardmorrissey
	A predictive model for transcriptional control of physiology in a free living cell. [My Copy] Cell, Vol. 131, No. 7. (28 December 2007), pp. 1354-1365. by Richard Bonneau, Marc T. Facciotti, David J. Reiss, et al.Amy K. Schmid, Min Pan, Amardeep Kaur, Vesteinn Thorsson, Paul Shannon, Michael H. Johnson, J. Christopher Bare, William Longabaugh, Madhavi Vuthoori, Kenia Whitehead, Aviv Madar, Lena Suzuki, Tetsuya Mori, Dong-Eun E. Chang, Jocelyne Diruggiero, Carl H. Johnson, Leroy Hood, Nitin S. Baliga posted by 12 people ptrobajo adampah lawraga edwardmorrissey guhjy tmmurali raiyar oelemento emptyhb megraw roys Borelli
	Inferring genetic regulatory logic from expression data. [My Copy] Bioinformatics, Vol. 21, No. 11. (1 June 2005), pp. 2706-2713. by S. Bulashevska, R. Eils posted by 1 person edwardmorrissey
	Reconstructing gene regulatory networks with bayesian networks by combining expression data with multiple sources of prior knowledge. [My Copy] Statistical applications in genetics and molecular biology, Vol. 6 (2007) by Adriano V. Werhli, Dirk Husmeier posted by 3 people rdiaz edwardmorrissey roys
	Inferring cellular networks - a review [My Copy] BMC Bioinformatics, Vol. 8, No. Suppl 6. (2007), S5. by Florian Markowetz, Rainer Spang posted by 16 people jaspervoskuilen antonkratz daforerog chica ocs roys cswinburne ndiaz edwardmorrissey guhjy tmmurali shigepong dejori heliopais bertelsen czeller
	Gaussian processes for ordinal regression [My Copy] (2004) by W. Chu, Z. Ghahramani posted by 2 people ecome edwardmorrissey
	Adipose Tissue as an Endocrine Organ [My Copy] J Clin Endocrinol Metab, Vol. 89, No. 6. (1 June 2004), pp. 2548-2556. by Erin E. Kershaw, Jeffrey S. Flier posted by 2 people brian edwardmorrissey
	Genome-scale models of microbial cells: evaluating the consequences of constraints. [My Copy] Nat Rev Microbiol, Vol. 2, No. 11. (November 2004), pp. 886-897. by N. D. Price, J. L. Reed, B. Ø. Palsson posted by 1 person edwardmorrissey
	Reconstructing gene-regulatory networks from time series, knock-out data, and prior knowledge [My Copy] BMC Systems Biology, Vol. 1, No. 1. (2007), 11. by Florian Geier, Jens Timmer, Christian Fleck posted by 7 people mjoach edwardmorrissey guhjy tuck wnpx Ao_Li2007 ptrobajo
	Conservation of Expression and Sequence of Metabolic Genes Is Reflected by Activity Across Metabolic States. [My Copy] PLoS Comput Biol, Vol. 2, No. 8. (18 August 2006) by Yonatan Bilu, Tomer Shlomi, Naama Barkai, Eytan Ruppin posted by 6 people ptrobajo JeremyZucker nickluscombe edwardmorrissey EBI-regulation MetabolicModeling
	Multiple knockout analysis of genetic robustness in the yeast metabolic network [My Copy] Nature Genetics, Vol. 38, No. 9. (29 August 2006), pp. 993-998. by David Deutscher, Isaac Meilijson, Martin Kupiec, Eytan Ruppin posted by 11 people shung nzm tmmurali koller raiyar cjeans patrycja_missiuro edwardmorrissey steinmetzlab hryk jiny
	Sensitivity and specificity of inferring genetic regulatory interactions from microarray experiments with dynamic Bayesian networks. [My Copy] Bioinformatics, Vol. 19, No. 17. (22 November 2003), pp. 2271-2282. by D. Husmeier posted by 4 people Borelli wnpx frohike edwardmorrissey
	Comparative evaluation of reverse engineering gene regulatory networks with relevance networks, graphical Gaussian models and Bayesian networks. [My Copy] Bioinformatics (14 July 2006) by Adriano V V. Werhli, Marco Grzegorczyk, Dirk Husmeier posted by 4 people wnpx frohike edwardmorrissey roys
	Discovering molecular pathways from protein interaction and gene expression data [My Copy] Bioinformatics, Vol. 19, No. suppl_1. (3 July 2003), pp. i264-272. by E. Segal, H. Wang, D. Koller posted by 9 people yaredo jfr lfriedl wnpx noano bhaddow edwardmorrissey kdl jiny
	Bayesian sparse hidden components analysis for transcription regulation networks. [My Copy] Bioinformatics (Oxford, England), Vol. 22, No. 6. (15 March 2006), pp. 739-746. by Chiara Sabatti, Gareth M. James posted by 5 people bertelsen engelhardt lp2 hms edwardmorrissey
	Dynamic Bayesian network and nonparametric regression for nonlinear modeling of gene networks from time series gene expression data [My Copy] Biosystems, Vol. 75, No. 1-3. (July 2004), pp. 57-65. by S. Kim, S. Imoto, S. Miyano posted by 6 people tmarstrand ggallone ryang scotts_43035 wnpx edwardmorrissey
	Inferring Genetic Networks and Identifying Compound Mode of Action via Expression Profiling [My Copy] Science, Vol. 301, No. 5629. (4 July 2003), pp. 102-105. by Timothy S. Gardner, Diego di Bernardo, David Lorenz, James J. Collins posted by 24 people Borelli edwardmorrissey myzhang mmcclean BTS-PT-AS-CS vertikalist rklancer kentsis dragonrez rhem1224 rubendrr adepace neveaire jayster4 Biostatistics Computational-Genomics Bioinformatics EisenLab Neuroscience TCR_Signaling cytoskeleton-and-afm SysbioMPI-TCells heliopais roys
	Biomarker discovery in microarray gene expression data with Gaussian processes [My Copy] Bioinformatics, Vol. 21, No. 16. (15 August 2005), pp. 3385-3393. by Wei Chu, Zoubin Ghahramani, Francesco Falciani, David L. Wild posted by 4 people bertelsen Borelli edwardmorrissey cswinburne
	Chemogenomic profiling on a genome-wide scale using reverse-engineered gene networks [My Copy] Nature Biotechnology, Vol. 23, No. 3. (04 March 2005), pp. 377-383. by Diego di Bernardo, Michael J. Thompson, Timothy S. Gardner, et al.Sarah E. Chobot, Erin L. Eastwood, Andrew P. Wojtovich, Sean J. Elliott, Scott E. Schaus, James J. Collins posted by 14 people edwardmorrissey mingzhi VGreiff provero ptrobajo rklancer snuppepuppan kentsis mjt rhem1224 balajis jayster4 TCR_Signaling SysbioMPI-TCells
	Inferring Cellular Networks Using Probabilistic Graphical Models [My Copy] Science, Vol. 303, No. 5659. (6 February 2004), pp. 799-805. by Nir Friedman posted by 27 people antonkratz jxl phoenixzxl abhishek_tiwari richardbickerton ruichu Jarman Lab ggallone bertelsen ldfu ujh lfriedl opheliav ryang wnpx nirfriedman neveaire koller helsley dimatura edwardmorrissey kdl vietanh0 Yumyai srp33 saman_vp jo_davies
	A Bayesian approach to reconstructing genetic regulatory networks with hidden factors [My Copy] Bioinformatics, Vol. 21, No. 3. (01 February 2005), 349. by Matthew J. Beal, Francesco Falciani, Zoubin Ghahramani, Claudia Rangel, David L. Wild posted by 6 people bertelsen Borelli edwardmorrissey helsley frohike cswinburne
	Modular epistasis in yeast metabolism [My Copy] Nat Genet, Vol. 37, No. 1. (12 December 2004), pp. 77-83. by Daniel Segre, Alexander DeLuna, George M. Church, Roy Kishony posted by 12 people colmryan dakelley nzm chasmand ajbattle tmmurali RMGraze balajis i41m nirfriedman koller edwardmorrissey
	Metabolic functions of duplicate genes in Saccharomyces cerevisiae. [My Copy] Genome Res, Vol. 15, No. 10. (October 2005), pp. 1421-1430. by L. Kuepfer, U. Sauer, L. M. Blank posted by 2 people schwartzjmc edwardmorrissey
	Genome-scale thermodynamic analysis of Escherichia coli metabolism. [My Copy] Biophysical journal, Vol. 90, No. 4. (15 February 2006), pp. 1453-1461. by Christopher S. Henry, Matthew D. Jankowski, Linda J. Broadbelt, Vassily Hatzimanikatis posted by 5 people winterstream schwartzjmc csanford lylu JeremyZucker
	Thermodynamics-Based Metabolic Flux Analysis [My Copy] Biophysical Journal, Vol. 92, No. 5. (01 March 2007), pp. 1792-1805. by C. Henry, L. Broadbelt, V. Hatzimanikatis posted by 6 people winterstream schwartzjmc vpenelle BjornJohansson lylu JeremyZucker
	KEGG for linking genomes to life and the environment [My Copy] Nucl. Acids Res., Vol. 36, No. suppl_1. (11 January 2008), pp. D480-484. by Minoru Kanehisa, Michihiro Araki, Susumu Goto, et al.Masahiro Hattori, Mika Hirakawa, Masumi Itoh, Toshiaki Katayama, Shuichi Kawashima, Shujiro Okuda, Toshiaki Tokimatsu, Yoshihiro Yamanishi posted by 32 people ajsferreira Thaverkamp sjcockell JeremyZucker jperkins vkwn pablocarb VGreiff mqbphcw3 karinlag robert85 peterli jjray schwartzjmc ubcg08l allysonlister YukaH Cortel coela daforerog reyez namunet irenas guhjy raiyar barriot renatomilani shung hpaces massivemayhem natstreet TheresaNiederberger
	ChEBI: a database and ontology for chemical entities of biological interest [My Copy] Nucl. Acids Res., Vol. 36, No. suppl_1. (11 January 2008), pp. D344-350. by Kirill Degtyarenko, Paula de Matos, Marcus Ennis, et al.Janna Hastings, Martin Zbinden, Alan McNaught, Rafael Alcantara, Michael Darsow, Mickael Guedj, Michael Ashburner posted by 13 people pauladza guhjy peterli NaCTeM Effie schwartzjmc pauldobson richardbickerton anthropomorphism irenas dullhunk massivemayhem grottenolm
	Something from nothing: bridging the gap between constraint-based and kinetic modelling. [My Copy] The FEBS journal, Vol. 274, No. 21. (November 2007), pp. 5576-5585. by Kieran Smallbone, Evangelos Simeonidis, David S. Broomhead, Douglas B. Kell posted by 6 people dadiamah schwartzjmc dbk dbk-lab peterli pmendes
	The Edinburgh human metabolic network reconstruction and its functional analysis. [My Copy] Molecular systems biology, Vol. 3 (2007) by H. Ma, A. Sorokin, A. Mazein, et al.A. Selkov, E. Selkov, O. Demin, I. Goryanin posted by 11 people JeremyZucker vpenelle peterli schwartzjmc Garamonfok dullhunk grahamc fishtank cjeans shung mdstobbe
	Computational systems biology in drug discovery and development: methods and applications. [My Copy] Drug Discov Today, Vol. 12, No. 7-8. (April 2007), pp. 295-303. by W. Materi, D. S. Wishart posted by 6 people flbarroso schwartzjmc nicklynch guhjy maburkitt csanford
	Systems biology, metabolic modelling and metabolomics in drug discovery and development. [My Copy] Drug discovery today, Vol. 11, No. 23-24. (December 2006), pp. 1085-1092. by Douglas B. Kell posted by 16 people peterli flbarroso schwartzjmc egonw irenas nicklynch alexg dullhunk mhucka raiyar fishtank steinmetzlab shikin GeneGo alanrw gemmalholliday
	Inferring branching pathways in genome-scale metabolic networks [My Copy] BMC Systems Biology, Vol. 3, No. 1. (2009), 103. by Esa Pitkanen, Paula Jouhten, Juho Rousu posted by 1 person michaelbarton
	Shifts in growth strategies reflect tradeoffs in cellular economics. [My Copy] Molecular systems biology, Vol. 5 (03 November 2009) by Douwe Molenaar, Rogier van Berlo, Dick de Ridder, Bas Teusink posted by 2 people karthikraman michaelbarton
	Applications of genome-scale metabolic reconstructions [My Copy] Molecular Systems Biology, Vol. 5 (03 November 2009) by Matthew A. Oberhardt, Bernhard O. Palsson, Jason A. Papin posted by 4 people pjmaybank michaelbarton arne pablocarb
	Computational methods for discovering structural variation with next-generation sequencing [My Copy] Nature Methods, Vol. 6, No. 11s. (15 October 2009), pp. S13-S20. by Paul Medvedev, Monica Stanciu, Michael Brudno posted by 20 people seb1 pst owenlancaster Orengo Group Journal Picks robertrentzsch oannes74 toszko kiekyon michaelbarton jasontsai sameersoi heliopais druvus GeeSharpMinor Peiyong n00c gdv desany Journal picks qayub
	Genome evolution and adaptation in a long-term experiment with Escherichia coli. [My Copy] Nature, Vol. 461, No. 7268. (29 October 2009), pp. 1243-1247. by Jeffrey E. Barrick, Dong Su S. Yu, Sung Ho H. Yoon, et al.Haeyoung Jeong, Tae Kwang K. Oh, Dominique Schneider, Richard E. Lenski, Jihyun F. Kim posted by 36 people pmalkus ronbun_2009au dokky samubernard ilyashl biomcgary kintoki zwang jasontsai Pedro Martinez EvoDevo lab Barcelona aaltenburger sawasthi nurban josepe tjandra venancio maren qayub Garamonfok yyfwuhan Asclepius dbikard nzm jjray iSEEM djkt treangen Journal picks lp2 operon diamantis BergmanLab michaelbarton druvus DrRichardBadge richardfranzese
	Explaining microbial population genomics through phage predation [My Copy] Nature Reviews Microbiology, Vol. 7, No. 11. (01 November 2009), pp. 828-836. by Francisco Rodriguez-Valera, Ana-Belen Martin-Cuadrado, Beltran Rodriguez-Brito, et al.Lejla Pasic, T. Frede Thingstad, Forest Rohwer, Alex Mira posted by 4 people michaelbarton Katje kinestetika maren
	Viral adaptation to host: a proteome-based analysis of codon usage and amino acid preferences [My Copy] Molecular Systems Biology, Vol. 5 (13 October 2009) by Iris Bahir, Menachem Fromer, Yosef Prat, Michal Linial posted by 2 people michaelbarton phoenixzxl
	Reactome Array: Forging a Link Between Metabolome and Genome [My Copy] Science, Vol. 326, No. 5950. (9 October 2009), pp. 252-257. by A. Beloqui, M. E. Guazzaroni, F. Pazos, et al.J. M. Vieites, M. Godoy, O. V. Golyshina, T. N. Chernikova, A. Waliczek, R. Silva-Rocha, Y. Al-ramahi, V. La Cono, C. Mendez, J. A. Salas, R. Solano, M. M. Yakimov, K. N. Timmis, P. N. Golyshin, M. Ferrer posted by 11 people ajsferreira Shared Literature Resource of the Microbial Fitness Group - MPI Bremen kinestetika renatomilani leliavski michaelbarton brianb abhishek_tiwari TRHvidsten ptrobajo gbloeb
	Automated design of synthetic ribosome binding sites to control protein expression. [My Copy] Nature biotechnology, Vol. 27, No. 10. (04 October 2009), pp. 946-950. by Howard M. Salis, Ethan A. Mirsky, Christopher A. Voigt posted by 6 people pmalkus johntheap mhamidi dbikard BergmanLab michaelbarton
	How To Choose a Good Scientific Problem [My Copy] Molecular Cell, Vol. 35, No. 6. (24 September 2009), pp. 726-728. by Uri Alon posted by 133 people janderz8 sdaehne artaban421 cefa gvdh penneyft welliegirl bertelsen thegoose Brain-like research group xawen chriswillmott nellapower ishiken andreff claudiushauptmann cermak bmoores karthikraman applebyb mordiano Gorzomagnificent Horduna ajaymalik mmwoodman dbikard toszko mthomure timflutre cyounkin marsl0am jmzhuo dmorti renatomilani ibre kevinemamy Sergey_gerbek huberse ddbb12 seneca mattbiehl mmborges GeeSharpMinor jjjpppfff zhangfh andreacapocci melo_mcr aaltenburger iannis jichok josephjose TorstenWaldminghaus kshameer rudalert kvalyi UWA Science Communication duel_jetty allaves milab@yzu rabit fercosber hax123 iskanbasal livingthingdan poojamaj gonzalez amynmoore ramalldf pvdg sfalsharif dill2009 singhsh rogermug aha jarekadam Jansen04 cgravlee lkakinami anuragsethi flips robfree kaliczp yyfwuhan luciensamary elsantosneto mgaldino daveGerrard sandfire tnhh lesandrop munzmarci pdpcosta Information Integration Architecture mxro wangngu myriasofo OliverHarriman AnthonySoprano robertlischke R_C_Cordeiro daforerog operon nandipati wenhaosparty jeffcrow leocmcheung fgibson snakehsu cisevol BergmanLab michaelbarton dna dullhunk danilov m_lew abellogin cxshang grahamc SantoshKalwar Xusheng leonardo roys benoitvalley zchen75 darshan druvus Asclepius Roswell Cancer Crosstalk Zephyrus songpku aalibes flieder pedromts
	Empirical Study of Data Sharing by Authors Publishing in PLoS Journals [My Copy] PLoS ONE, Vol. 4, No. 9. (18 September 2009), e7078. by Caroline J. Savage, Andrew J. Vickers posted by 8 people BergmanLab michaelbarton daforerog AlexandraSar scmelton druvus dullhunk CameronNeylon
	Three-Dimensional Structural View of the Central Metabolic Network of Thermotoga maritima [My Copy] Science, Vol. 325, No. 5947. (18 September 2009), pp. 1544-1549. by Ying Zhang, Ines Thiele, Dana Weekes, et al.Zhanwen Li, Lukasz Jaroszewski, Krzysztof Ginalski, Ashley M. Deacon, John Wooley, Scott A. Lesley, Ian A. Wilson, Bernhard Palsson, Andrei Osterman, Adam Godzik posted by 14 people michaelbarton venancio schwartzjmc apocapoc eehsanipour riffraff reyez TRHvidsten flbarroso daveGerrard zwang pablocarb phoenixzxl roys
	Design Parameters to Control Synthetic Gene Expression in Escherichia coli [My Copy] PLoS ONE, Vol. 4, No. 9. (14 September 2009), e7002. by Mark Welch, Sridhar Govindarajan, Jon E. Ness, et al.Alan Villalobos, Austin Gurney, Jeremy Minshull, Claes Gustafsson posted by 8 people dbikard RasmusJensen pala0088 Synthetic Biology jjray Vincent_Rouilly michaelbarton bmduggan
	Comparative genomic analyses of Streptococcus mutans provide insights into chromosomal shuffling and species-specific content [My Copy] BMC Genomics, Vol. 10, No. 1. (2009), 358. by Fumito Maruyama, Mitsuhiko Kobata, Ken Kurokawa, et al.Keishin Nishida, Atsuo Sakurai, Kazuhiko Nakano, Ryota Nomura, Shigetada Kawabata, Takashi Ooshima, Kenta Nakai, Masahira Hattori, Shigeyuki Hamada, Ichiro Nakagawa posted by 1 person michaelbarton
	Googling Food Webs: Can an Eigenvector Measure Species' Importance for Coextinctions? [My Copy] PLoS Comput Biol, Vol. 5, No. 9. (4 September 2009), e1000494. by Stefano Allesina, Mercedes Pascual posted by 8 people jaia peterso maren phig MCB michaelbarton neils thomaskelder
	A Parsimony Approach to Biological Pathway Reconstruction/Inference for Genomes and Metagenomes [My Copy] PLoS Comput Biol, Vol. 5, No. 8. (14 August 2009), e1000465. by Yuzhen Ye, Thomas G. Doak posted by 8 people mstumpf ptrobajo barriot rdiaz michaelbarton kshameer iSEEM djkt
	Local Adaptation of Bacteriophages to Their Bacterial Hosts in Soil [My Copy] Science, Vol. 325, No. 5942. (14 August 2009), 833. by Michiel Vos, Philip J. Birkett, Elizabeth Birch, Robert I. Griffiths, Angus Buckling posted by 5 people maren timothee-poisot michaelbarton iSEEM djkt
	Phylogenetic detection of horizontal gene transfer during the step-wise genesis of Mycobacterium tuberculosis [My Copy] BMC Evolutionary Biology, Vol. 9, No. 1. (2009), 196. by Frederic Veyrier, Daniel Pletzer, Christine Turenne, Marcel Behr posted by 2 people michaelbarton druvus
	Global discovery of adaptive mutations. [My Copy] Nature methods (13 July 2009) by Hani Goodarzi, Alison K. Hottes, Saeed Tavazoie posted by 1 person michaelbarton
	Fifteen years of microbial genomics: meeting the challenges and fulfilling the dream [My Copy] Nat Biotech, Vol. 27, No. 7. (July 2009), pp. 627-632. by Nikos C. Kyrpides posted by 6 people pmalkus seanyuan sharpton BergmanLab michaelbarton neils
	How to stop blogging [My Copy] Nature, Vol. 460, No. 7252. (9 July 2009), pp. 152-152. posted by 13 people Sergey_gerbek thegoose jennifermjones beanformer BergmanLab michaelbarton Science 2.0 / Open Science eLearning in Leicester AJCann MarioPaolucci dullhunk Journal picks ppgardne
	Managing and Analyzing Next-Generation Sequence Data [My Copy] PLoS Comput Biol, Vol. 5, No. 6. (26 June 2009), e1000369. by Brent G. Richter, David P. Sexton posted by 46 people idoerg Geknitics cthachuk hzoltan chvlyl sameersoi hpaces gdv GeeSharpMinor idonaldson darian daveGerrard tharris Yanno inesdesantiago jcaddy agbiotec humburg Zephyrus daforerog stubrown GustavoLacerda torfinnnome natstreet BergmanLab polivares orzenil kongl guhjy druvus n00c leemond31 nuin operon jasontsai jmeppley rdiaz michaelbarton Bioinformatics dswan reyez kshameer TRHvidsten djkt Journal picks ppgardne
	Adaptive prediction of environmental changes by microorganisms [My Copy] Nature, Vol. 460, No. 7252. (17 June 2009), pp. 220-224. by Amir Mitchell, Gal H. Romano, Bella Groisman, et al.Avihu Yona, Erez Dekel, Martin Kupiec, Orna Dahan, Yitzhak Pilpel posted by 10 people yyfwuhan kinestetika biomcgary sriesenfeld timotay izuleta iSEEM djkt jjray michaelbarton
	Avoiding dangerous missense: thermophiles display especially low mutation rates. [My Copy] PLoS genetics, Vol. 5, No. 6. (19 June 2009), e1000520. by John W. Drake posted by 5 people jasontsai operon michaelbarton jjray bpcusack
	Rapid and Accurate Large-Scale Coestimation of Sequence Alignments and Phylogenetic Trees [My Copy] Science, Vol. 324, No. 5934. (19 June 2009), pp. 1561-1564. by Kevin Liu, Sindhu Raghavan, Serita Nelesen, C. Randal Linder, Tandy Warnow posted by 31 people gjuggler parnell kinestetika Orengo Group Journal Picks robertrentzsch xianjun gdb jbhiatt Mycology stajich operon biomcgary kieran101 zwang michaelbarton vingron tatman303 hryk lizbiogen pkonings Journal picks ppgardne dokky aprasad timflutre inquil TRHvidsten iSEEM djkt fenghezi phoenixzxl
	The conservation and evolutionary modularity of metabolism [My Copy] Genome Biology, Vol. 10, No. 6. (12 June 2009), R63. by Jose P. Alvarez, Chris Sanford, John Parkinson posted by 11 people venancio carlk adampah Orengo Group Journal Picks bdessailly barriot biomcgary michaelbarton Winzer tomhebbron grahamc
	Using in silico models to simulate dual perturbation experiments: procedure development and interpretation of outcomes. [My Copy] BMC systems biology, Vol. 3 (2009) by N. Jamshidi, B. O. Palsson posted by 1 person michaelbarton
	Understanding the Adaptive Growth Strategy of <italic>Lactobacillus plantarum</italic> by <italic>In Silico</italic> Optimisation [My Copy] PLoS Comput Biol, Vol. 5, No. 6. (12 June 2009), e1000410. by Bas Teusink, Anne Wiersma, Leo Jacobs, Richard A. Notebaart, Eddy J. Smid posted by 1 person michaelbarton
	Heterotachy, an important process of protein evolution. [My Copy] Molecular biology and evolution, Vol. 19, No. 1. (January 2002), pp. 1-7. by P. Lopez, D. Casane, H. Philippe posted by 3 people BergmanLab michaelbarton ramiro2k
	Integrated Assessment of Genomic Correlates of Protein Evolutionary Rate [My Copy] PLoS Comput Biol, Vol. 5, No. 6. (12 June 2009), e1000413. by Yu Xia, Eric A. Franzosa, Mark B. Gerstein posted by 10 people aprasad chica biomcgary gjuggler Journal picks kiekyon michaelbarton djkt RamuAnandakrishnan bpcusack
	This revolution will be digitized: online tools for radical collaboration [My Copy] Disease Models & Mechanisms, Vol. 2, No. 5-6. (May 2009), pp. 201-205. by Chris Patil, Vivian Siegel posted by 12 people aalves Zephyrus dullhunk leemond31 natstreet druvus ianturton BergmanLab michaelbarton brianb neils psique
	Metabolic-network-driven analysis of bacterial ecological strategies [My Copy] Genome Biology, Vol. 10, No. 6. (05 June 2009), R61. by Shiri Freilich, Anat Kreimer, Elhanan Borenstein, et al.Nir Yosef, Roded Sharan, Uri Gophna, Eytan Ruppin posted by 10 people bovee michaelbarton seamudbug Winzer tomhebbron Microbial-Ecology Thaverkamp druvus iSEEM jlgreen
	Measure of synonymous codon usage diversity among genes in bacteria [My Copy] BMC Bioinformatics, Vol. 10, No. 1. (2009), 167. by Haruo Suzuki, Rintaro Saito, Masaru Tomita posted by 4 people codonusage michaelbarton dokky jmeppley
	Genome assembly reborn: recent computational challenges [My Copy] Brief Bioinform, Vol. 10, No. 4. (1 July 2009), pp. 354-366. by Mihai Pop posted by 32 people jfr hzoltan cthachuk GustavoLacerda n00c agbiotec shabhonam pachorip APRegier jmcq stevebs jonilaserson michaelbarton inesdesantiago GeeSharpMinor bertelsen aprasad ananta_samudra sandfire jmeppley mlangill fgibson Journal picks ppgardne TRHvidsten pengchy robsyme nuin kiekyon natstreet druvus idoerg
	Fast and accurate short read alignment with Burrows-Wheeler transform. [My Copy] Bioinformatics (Oxford, England), Vol. 25, No. 14. (15 July 2009), pp. 1754-1760. by Heng Li, Richard Durbin posted by 38 people lianping hzoltan cthachuk maren bozdagd adijr heliopais jmanning2k GustavoLacerda stubrown jessopher guhjy katholt mkiyer jmcq idonaldson michaelbarton BergmanLab polivares darian orzenil cassj inesdesantiago TRHvidsten djkt operon SIMR bioinformatics ghattem n00c Bioinformatics danmaclean Journal picks ppgardne nuin rschulz natstreet druvus humburg
	Gene expression: Structure versus codon bias [My Copy] Nature Reviews Genetics, Vol. 10, No. 6., pp. 348-349. by Elizabeth Neame posted by 1 person michaelbarton
	Metatranscriptomics reveals unique microbial small RNAs in the ocean\|[rsquo]\|s water column [My Copy] Nature, Vol. 459, No. 7244. (14 May 2009), pp. 266-269. by Yanmei Shi, Gene W. Tyson, Edward F. DeLong posted by 18 people tonamswish kinestetika gdb michaelbarton samgj Papers recommended by the Roscoff Plankton Group Microbial-Ecology vaulot microbiology_nijmegen Katje absterga jmeppley Thaverkamp pengchy iSEEM djkt skembel jbhiatt
	Co-evolutionary networks of genes and cellular processes across fungal species [My Copy] Genome Biology, Vol. 10, No. 5. (2009), R48. by Tamir Tuller, Martin Kupiec, Eytan Ruppin posted by 6 people kiekyon roys inesdesantiago grahamc dokky michaelbarton
	Genome Informatics 14: 629--630 (2003) 629 BioRuby: Open-Source Bioinformatics Library [My Copy] by Naohisa G. Mitsuteru, Naohisa Goto, Mitsuteru C. Nakao, Shiuichi Kawashima, Toshiaki Katayama, Minoru Kanehisa posted by 2 people cmzmasek michaelbarton
	How selection affects phenotypic fluctuation [My Copy] Mol Syst Biol, Vol. 5 (28 April 2009) by Yoichiro Ito, Hitoshi Toyota, Kunihiko Kaneko, Tetsuya Yomo posted by 3 people jjray michaelbarton biomcgary
	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 by 1 person michaelbarton
	Partitioning clustering algorithms for protein sequence data sets. [My Copy] BioData mining, Vol. 2, No. 1. (2 April 2009) by Sondes Fayech, Nadia Essoussi, Mohamed Limam posted by 1 person michaelbarton
	Connecting extracellular metabolomic measurements to intracellular flux states in yeast [My Copy] BMC Systems Biology, Vol. 3, No. 1. (2009), 37. by Monica Mo, Bernhard Palsson, Markus Herrgard posted by 2 people schwartzjmc michaelbarton
	Reconstruction of metabolic pathways for the cattle genome. [My Copy] BMC systems biology, Vol. 3, No. 1. (2009), 33. by Seongwon Seo, Harris A. Lewin posted by 2 people irenas michaelbarton
	Constraint-based analysis of metabolic capacity of Salmonella typhimurium during hostpathogen interaction [My Copy] BMC Systems Biology, Vol. 3, No. 1. (2009), 38. by Anu Raghunathan, Jennifer Reed, Sookil Shin, Bernhard Palsson, Simon Daefler posted by 1 person michaelbarton