mingzhi's Top Recommendations

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	Accurate molecular classification of cancer using simple rules [My Copy] BMC Medical Genomics, Vol. 2, No. 1. (2009), 64. by Xiaosheng Wang, Osamu Gotoh posted by 2 people ptrobajo phoenixzxl
	Harnessing gene expression to identify the genetic basis of drug resistance [My Copy] Molecular Systems Biology, Vol. 5 (13 October 2009) by Bo-Juen Chen, Helen C. Causton, Denesy Mancenido, Noel L. Goddard, Ethan O. Perlstein, Dana Pe'er posted by 5 people dswan ashishanand phoenixzxl ptrobajo frohike
	How to identify essential genes from molecular networks? [My Copy] BMC Systems Biology, Vol. 3, No. 1. (2009), 102. by Gabriel D. Rio, Dirk Koschutzki, Gerardo Coello posted by 8 people operon tmmurali kshameer phoenixzxl ptrobajo renatomilani druvus daforerog
	Correlating gene and protein expression data using Correlated Factor Analysis [My Copy] BMC Bioinformatics, Vol. 10, No. 1. (01 September 2009), 272. by Chuen S. Tan, Agus Salim, Alexander Ploner, Janne Lehtio, Kee S. Chia, Yudi Pawitan posted by 5 people mayercd rdiaz ptrobajo coffeerv phoenixzxl
	A Quick Guide to Teaching R Programming to Computational Biology Students [My Copy] PLoS Comput Biol, Vol. 5, No. 8. (28 August 2009), e1000482. by Stephen J. Eglen posted by 67 people nuin kaliczp maren sobolevnrm ltitodem zchen75 artaban421 natstreet jasonn tomhebbron psique Bioinformatics - CRUK Stew eshirdel guhjy polivares ajw fishtank diamantis fastjoe23 kshameer daveGerrard hrogers JoeBanks BergmanLab cisevol srijit hwright Ayest VGreiff welliegirl asadrahman rdiaz ptrobajo heliopais coffeerv Vincent_Rouilly marekrud tnhh barry ansobol Zephyrus walshtp bertelsen fgibson pkonings Borelli klauso dlizcano dswan skembel djkt jclau lwaldron phoenixzxl timhubbard eLearning in Leicester AJCann thegoose dullhunk brianb neils silberbauer daforerog Journal picks ppgardne druvus
	R/BHC: fast Bayesian hierarchical clustering for microarray data [My Copy] BMC Bioinformatics, Vol. 10, No. 1. (6 August 2009), 242. by Richard Savage, Katherine Heller, Yang Xu, et al.Zoubin Ghahramani, William Truman, Murray Grant, Katherine Denby, David Wild posted by 12 people ptrobajo meanerelk nuin rdiaz guhjy Bioinformatics lwaldron rschulz phoenixzxl barriot RamuAnandakrishnan erexhepa
	Global networks of functional coupling in eukaryotes from comprehensive data integration. [My Copy] Genome research, Vol. 19, No. 6. (25 June 2009), pp. 1107-1116. by Andrey Alexeyenko, Erik L. Sonnhammer posted by 9 people phoenixzxl ParkinsonLab_at_MaRS ptrobajo kshameer rdiaz guhjy provero roys grahamc
	Dynamic modularity in protein interaction networks predicts breast cancer outcome. [My Copy] Nature biotechnology, Vol. 27, No. 2. (1 February 2009), pp. 199-204. by Ian W. Taylor, Rune Linding, David Warde-Farley, et al.Yongmei Liu, Catia Pesquita, Daniel Faria, Shelley Bull, Tony Pawson, Quaid Morris, Jeffrey L. Wrana posted by 16 people ukhan zufar guhjy jfr frohike fenghezi ptrobajo jaimie nedwards dakelley absterga cube_and_beyond phoenixzxl grahamc provero brianb
	Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists [My Copy] Nucl. Acids Res., Vol. 37, No. 1. (1 January 2009), pp. 1-13. by Da W. Huang, Brad T. Sherman, Richard A. Lempicki posted by 47 people darian chasmand hzoltan ipark-kaist giovenko lwaldron jcaddy antonkratz Zephyrus shikin yaredo tonamswish ddunbar robfsouza Keywan daforerog ptrobajo rdiaz bertelsen Bioinformatics - CRUK Stew inesdesantiago heliopais ConklinLab AlexanderPico aviad_work ekotelnikova frohike aramesh2 jfr zufar ilyashl dolchan paszkows lptolik thomaskelder AbnerCYH neils tmmurali ealloza barriot druvus renatomilani pengchy phoenixzxl guhjy sjcockell
	Network-based prediction of human tissue-specific metabolism. [My Copy] Nature biotechnology, Vol. 26, No. 9. (17 September 2008), pp. 1003-1010. by Tomer Shlomi, Moran N. Cabili, Markus J. Herrgård, Bernhard Ø. Palsson, Eytan Ruppin posted by 13 people phoenixzxl grahamc yaredo Sonix jfr roys mdstobbe klo peterli ptrobajo renatomilani zwang guhjy
	Global alignment of multiple protein interaction networks with application to functional orthology detection [My Copy] Proceedings of the National Academy of Sciences, Vol. 105, No. 35. (2 September 2008), pp. 12763-12768. by Rohit Singh, Jinbo Xu, Bonnie Berger posted by 8 people nliu82 phoenixzxl ptrobajo icq242500260 dakelley renatomilani bpcusack roys
	Improving Subcellular Localization Prediction using Text Classification and the Gene Ontology [My Copy] Bioinformatics (26 August 2008), btn463. by Alona Fyshe, Yifeng Liu, Duane Szafron, Russ Greiner, Paul Lu posted by 4 people guhjy grahamc ptrobajo phoenixzxl
	High-Quality Binary Protein Interaction Map of the Yeast Interactome Network [My Copy] Science, Vol. 322, No. 5898. (3 October 2008), pp. 104-110. by Haiyuan Yu, Pascal Braun, Muhammed A. Yildirim, et al.Irma Lemmens, Kavitha Venkatesan, Julie Sahalie, Tomoko Hirozane-Kishikawa, Fana Gebreab, Na Li, Nicolas Simonis, Tong Hao, Jean-Francois Rual, Amelie Dricot, Alexei Vazquez, Ryan R. Murray, Christophe Simon, Leah Tardivo, Stanley Tam, Nenad Svrzikapa, Changyu Fan, Anne-Sophie de Smet, Adriana Motyl, Michael E. Hudson, Juyong Park, Xiaofeng Xin, Michael E. Cusick, Troy Moore, Charlie Boone, Michael Snyder, Frederick P. Roth, Albert-Laszlo Barabasi, Jan Tavernier, David E. Hill, Marc Vidal posted by 29 people aceol mgomes nzm pauldobson cabbagezs mariap3636 semin roys phoenixzxl kintoki jbhiatt elenaz jfr ocs cerca ptrobajo carlk zwang BenosLab gracio reyez mdperry dullhunk Petersarkies grahamc yeastyboy guhjy maralena neils
	What is the expectation maximization algorithm? [My Copy] Nature biotechnology, Vol. 26, No. 8. (August 2008), pp. 897-899. by Chuong B. Do, Serafim Batzoglou posted by 16 people kimsoohwan daforerog tonamswish Yanno robert85 claudiamichelle Roswell Cancer Crosstalk Zephyrus ptrobajo druvus jfr Tominator GeeSharpMinor guhjy zwang phoenixzxl
	Predicting Pathway Membership via Domain Signatures [My Copy] Bioinformatics (1 August 2008), btn403. by Holger Frohlich, Mark Fellmann, Holger Sultmann, Annemarie Poustka, Tim Beissbarth posted by 10 people le-gal druvus jameswasmuth kshameer jfr barriot ptrobajo mdstobbe phoenixzxl guhjy
	A critical assessment of Mus musculus gene function prediction using integrated genomic evidence [My Copy] Genome Biology, Vol. 9, No. Suppl 1. (2008), S2. by Lourdes P. Castillo, Murat Tasan, Chad Myers, et al.Hyunju Lee, Trupti Joshi, Chao Zhang, Yuanfang Guan, Michele Leone, Andrea Pagnani, Wan Kim, Chase Krumpelman, Weidong Tian, Guillaume Obozinski, Yanjun Qi, Sara Mostafavi, Guan Lin, Gabriel Berriz, Francis Gibbons, Gert Lanckriet, Jian Qiu, Charles Grant, Zafer Barutcuoglu, David Hill, David W. Farley, Chris Grouios, Debajyoti Ray, Judith Blake, Minghua Deng, Michael Jordan, William Noble, Quaid Morris, Judith K. Seetharaman, Ziv B. Joseph, Ting Chen, Fengzhu Sun, Olga Troyanskaya, Edward Marcotte, Dong Xu, Timothy Hughes, Frederick Roth posted by 7 people phoenixzxl saket carlk kgutwin ptrobajo guhjy aconesa
	Seeded Bayesian Networks: Constructing genetic networks from microarray data [My Copy] BMC Systems Biology, Vol. 2, No. 1. (2008), 57. by Amira Djebbari, John Quackenbush posted by 8 people meanerelk ptrobajo jfr frohike renatomilani beete phoenixzxl guhjy
	Use and misuse of the gene ontology annotations [My Copy] Nature Reviews Genetics, Vol. 9, No. 7. (13 May 2008), pp. 509-515. by Seung Yon Rhee, Valerie Wood, Kara Dolinski, Sorin Draghici posted by 44 people singhsh epigenetics davidmam Thaverkamp druvus dullhunk 8_01 suizan dolchan Borelli Zephyrus VGreiff klo thomaskelder ilyashl phoenixzxl MarcoAlvarez isakemal bertelsen daforerog jfr djkt guhjy aheilbut mariakmejia cmzmasek A_Olympia logics of knowledge realzhang carlk roys gjuggler fpattyn RamuAnandakrishnan ptrobajo giovenko cabbagesofdoom tmmurali renatomilani capitall marck rvosa FAB-lab bpcusack
	A map of human protein interactions derived from co-expression of human mRNAs and their orthologs [My Copy] Mol Syst Biol, Vol. 4 (15 April 2008) by Arun K. Ramani, Zhihua Li, G. Traver Hart, Mark W. Carlson, Daniel R. Boutz, Edward M. Marcotte posted by 14 people KeatingJClub kgutwin windman83 druvus jeremymiller tmmurali biomcgary phoenixzxl zwang giovanni grahamc ardalby OPIG ptrobajo
	Protein networks in disease. [My Copy] Genome research, Vol. 18, No. 4. (1 April 2008), pp. 644-652. by Trey Ideker, Roded Sharan posted by 28 people shikin carlk isimpson chica saket zufar kaarsinogen giovenko guhjy balicea tmmurali Borelli jwdietrich frohike bootsy nedwards roys mclarenv phoenixzxl brianb schuylrp jfr paolomarcatili gracio thomaskelder ptrobajo raiyar zwang
	Predicting Gene Expression from Sequence: A Reexamination [My Copy] PLoS Comput Biol, Vol. 3, No. 11. (30 November 2007), e243. by Yuan Yuan, Lei Guo, Lei Shen, Jun S. Liu posted by 5 people roys maximilianh Ema phoenixzxl ptrobajo
	How to infer gene networks from expression profiles [My Copy] Molecular Systems Biology, Vol. 3 (13 February 2007) by Mukesh Bansal, Vincenzo Belcastro, Alberto Ambesi-Impiombato, Diego di Bernardo posted by 42 people Jporci beete tonamswish zufar nicholasflann icq242500260 guhjy Zephyrus antonkratz phoenixzxl bertelsen isimpson daforerog poirel agonzale roys Neeperando APRegier rdiaz klo Borelli Jarman Lab ggallone ptrobajo druvus cswinburne jfr eckart_bindewald wnpx nickluscombe kengg mikaelhuss jrbanga BIBLIOma RockHI lp2 natstreet EBI-regulation Plantandetc heliopais mariakmejia tmmurali
	Genome-wide association studies: progress and potential for drug discovery and development [My Copy] Nature Reviews Drug Discovery, Vol. 7, No. 3. (01 February 2008), pp. 221-230. by Stephen F. Kingsmore, Ingrid E. Lindquist, Joann Mudge, Damian D. Gessler, William D. Beavis posted by 8 people phoenixzxl ubcg08l ajaymalik guhjy massivemayhem psique Petersarkies parkinson's disease references
	Relating Three-Dimensional Structures to Protein Networks Provides Evolutionary Insights [My Copy] Science, Vol. 314, No. 5807. (22 December 2006), pp. 1938-1941. by Philip M. Kim, Long J. Lu, Yu Xia, Mark B. Gerstein posted by 26 people ucbcjbm pablocarb mgomes rsaito MatthiasReimann cerca bicko lfriedl chad_davis Einat tny choonpeng timflutre grahamc ramensky massivemayhem efge lpfernandes structural_bioinformatics kdl cdeane Pao-Yang phoenixzxl carlk paolomarcatili saket
	Pfam: clans, web tools and services. [My Copy] Nucleic Acids Res, Vol. 34, No. Database issue. (1 January 2006) by R. D. Finn, J. Mistry, B. Schuster-Böckler, et al.S. Griffiths-Jones, V. Hollich, T. Lassmann, S. Moxon, M. Marshall, A. Khanna, R. Durbin, S. R. Eddy, E. L. Sonnhammer, A. Bateman posted by 13 people robert85 cerca gbart dullhunk massivemayhem cjeans siebertm lpfernandes pablomendes antonkratz natstreet Lombardo_7 phoenixzxl
	Insights into Protein–Protein Interfaces using a Bayesian Network Prediction Method [My Copy] Journal of Molecular Biology, Vol. 362, No. 2. (15 September 2006), pp. 365-386. by James R. Bradford, Chris J. Needham, Andrew J. Bulpitt, David R. Westhead posted by 11 people dfdong barry conkymacro ameetsoni grahamc massivemayhem structural_bioinformatics Bioinformatics phoenixzxl marti paolomarcatili
	Dynamic complex formation during the yeast cell cycle. [My Copy] Science (New York, N.Y.), Vol. 307, No. 5710. (4 February 2005), pp. 724-727. by U. de Lichtenberg, L. J. Jensen, S. Brunak, P. Bork posted by 14 people chica mdimmic chad_davis balajis wnpx koller massivemayhem cjeans arne dIEMoSIRIS phoenixzxl larsjuhljensen carlk gjuggler
	A Bayesian Networks Approach for Predicting Protein-Protein Interactions from Genomic Data [My Copy] Science, Vol. 302, No. 5644. (17 October 2003), pp. 449-453. by Ronald Jansen, Haiyuan Yu, Dov Greenbaum, et al.Yuval Kluger, Nevan J. Krogan, Sambath Chung, Andrew Emili, Michael Snyder, Jack F. Greenblatt, Mark Gerstein posted by 25 people cerca hagechouchin443 aelef Robinder lfriedl balajis opheliav yuval wnpx nickluscombe ruvido raiyar massivemayhem kdang dbgrant nedwards karfunkel kdl EBI-regulation Evangelia shung phoenixzxl penpen926 carlk frohike
	Coevolution at protein complex interfaces can be detected by the complementarity trace with important impact for predictive docking [My Copy] Proceedings of the National Academy of Sciences, Vol. 105, No. 22. (3 June 2008), pp. 7708-7713. by Hocine Madaoui, RaphaÃ«l Guerois posted by 9 people dfdong qluo robfsouza RebeccaHamer orr cabbagesofdoom phoenixzxl bicko zwang
	Co-evolving residues in membrane proteins [My Copy] Bioinformatics, Vol. 23, No. 24. (15 December 2007), pp. 3312-3319. by Angelika Fuchs, Antonio J. Martin-Galiano, Matan Kalman, Sarel Fleishman, Nir Ben-Tal, Dmitrij Frishman posted by 10 people qluo operon breden cjeans zwang SFUAntibodyResearch signal-duplication blasco_morozzo phoenixzxl Lombardo_7
	Predicting domain-domain interactions using a parsimony approach [My Copy] Genome Biology, Vol. 7, No. 11. (09 November 2006), R104. by Katia Guimaraes, Raja Jothi, Elena Zotenko, Teresa Przytycka posted by 7 people dfdong qluo marti cerca phoenixzxl carlk saket
	Modeling and Simulation of Genetic Regulatory Systems: A Literature Review [My Copy] Journal of Computational Biology, Vol. 9, No. 1. (January 2002), pp. 67-103. by Hidde de Jong posted by 34 people mjoach Borelli qluo antonkratz reyez smac tlse65 wangbo GEB dlobo jago behindtherabbit cswinburne Jarman Lab ggallone softsimu eldan tmmurali bayesian balicea Happybene wnpx kengg noano sstoma josepe dagmar jo_davies VirtualPlants Plantandetc compneur roys maburkitt phoenixzxl
	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
	High-confidence prediction of global interactomes based on genome-wide coevolutionary networks. [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 105, No. 3. (22 January 2008), pp. 934-939. by David Juan, Florencio Pazos, Alfonso Valencia posted by 20 people dfdong ptrobajo biomcgary qluo winterschlaefer marti tmmurali brant balicea sebastien_vigneau bluto cjeans aconesa microbiology_nijmegen Katje roys friendpine huali mdstobbe paolomarcatili
	Identification of functional modules using network topology and high-throughput data. [My Copy] BMC systems biology, Vol. 1, No. 1. (2007), 8. by Igor Ulitsky, Ron Shamir posted by 19 people greg akshayk ptrobajo yaredo isimpson qluo aheilbut zufar roys frohike tmmurali dragonrez jfr wnpx Ao_Li2007 lyndon bertelsen ellakat carlk
	CREDO: A Protein–Ligand Interaction Database for Drug Discovery [My Copy] Chemical Biology & Drug Design, Vol. 73, No. 2. (February 2009), pp. 157-167. by Adrian Schreyer, Tom Blundell posted by 7 people mijam richardbickerton pansapiens bicko nanonan massivemayhem higueruelo
	Ultrafast shape recognition: Evaluating a new ligand-based virtual screening technology [My Copy] Journal of Molecular Graphics and Modelling, Vol. 27, No. 7. (14 April 2009), pp. 836-845. by Pedro J. Ballester, Paul W. Finn, W. Graham Richards posted by 3 people richardbickerton massivemayhem reyez
	The use of protein-ligand interaction fingerprints in docking. [My Copy] Current opinion in drug discovery & development, Vol. 11, No. 3. (May 2008), pp. 356-364. by S. C. Brewerton posted by 4 people flbarroso richardbickerton higueruelo massivemayhem
	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
	Optimizing Fragment and Scaffold Docking by Use of Molecular Interaction Fingerprints [My Copy] Journal of Chemical Information and Modeling, Vol. 47, No. 1. (1 January 2007), pp. 195-207. by Gilles Marcou, Didier Rognan posted by 9 people RebeccaHamer klexa richardbickerton nanonan BragilMassoud peprovy schlauchi massivemayhem sithmein
	Strategies for cellular decision-making. [My Copy] Molecular systems biology, Vol. 5 (17 November 2009) by Theodore J. Perkins, Peter S. Swain posted by 3 people karthikraman pmalkus phoenixzxl
	Genetic Variation and Recent Positive Selection in Worldwide Human Populations: Evidence from Nearly 1 Million SNPs. [My Copy] PloS one, Vol. 4, No. 11. (18 November 2009), e7888. by David López Herráez, Marc Bauchet, Kun Tang, et al.Christoph Theunert, Irina Pugach, Jing Li, Madhusudan R. Nandineni, Arnd Gross, Markus Scholz, Mark Stoneking posted by 2 people gjuggler phoenixzxl
	GExplore: a web server for integrated queries of protein domains, gene expression and mutant phenotypes [My Copy] BMC Genomics, Vol. 10, No. 1. (2009), 529. by Harald Hutter, Man P. Ng, Nansheng Chen posted by 1 person phoenixzxl
	Co-expression Networks: Graph Properties and Topological Comparisons [My Copy] Bioinformatics (12 November 2009), btp632. by Ramon Xulvi-Brunet, Hongzhe Li posted by 3 people kshameer neils phoenixzxl
	Predicting new molecular targets for known drugs [My Copy] Nature, Vol. 462, No. 7270. (01 November 2009), pp. 175-181. by Michael J. Keiser, Vincent Setola, John J. Irwin, et al.Christian Laggner, Atheir I. Abbas, Sandra J. Hufeisen, Niels H. Jensen, Michael B. Kuijer, Roberto C. Matos, Thuy B. Tran, Ryan Whaley, Richard A. Glennon, Jerome Hert, Kelan L. H. Thomas, Douglas D. Edwards, Brian K. Shoichet, Bryan L. Roth posted by 16 people venancio okapi Journal picks ahmetbakan zufar pablocarb zwang TRHvidsten phoenixzxl qshao Yanno mnishimu tmmurali sjcockell seb1 abhishek_tiwari
	Prediction of hot spot residues at protein-protein interfaces by combining machine learning and energy-based methods [My Copy] BMC Bioinformatics, Vol. 10, No. 1. (30 October 2009), 365. by Stefano Lise, Cedric Archambeau, Massimiliano Pontil, David Jones posted by 8 people Orengo Group Journal Picks sillitoe apaydin kshameer zwang phoenixzxl higueruelo neils
	Structure of Protein Interaction Networks and Their Implications on Drug Design [My Copy] PLoS Comput Biol, Vol. 5, No. 10. (30 October 2009), e1000550. by Takeshi Hase, Hiroshi Tanaka, Yasuhiro Suzuki, So Nakagawa, Hiroaki Kitano posted by 11 people kiekyon nickolay kshameer zwang phoenixzxl venancio Orengo Group Journal Picks CorinYeats ess30 poirel jbesnard
	phyloXML: XML for evolutionary biology and comparative genomics [My Copy] BMC Bioinformatics, Vol. 10, No. 1. (2009), 356. by Mira Han, Christian Zmasek posted by 8 people operon BergmanLab cisevol kshameer Geknitics druvus phoenixzxl cmzmasek
	Bayesian Modeling of the Yeast SH3 Domain Interactome Predicts Spatiotemporal Dynamics of Endocytosis Proteins [My Copy] PLoS Biol, Vol. 7, No. 10. (20 October 2009), e1000218. by Raffi Tonikian, Xiaofeng Xin, Christopher P. Toret, et al.David Gfeller, Christiane Landgraf, Simona Panni, Serena Paoluzi, Luisa Castagnoli, Bridget Currell, Somasekar Seshagiri, Haiyuan Yu, Barbara Winsor, Marc Vidal, Mark B. Gerstein, Gary D. Bader, Rudolf Volkmer, Gianni Cesareni, David G. Drubin, Philip M. Kim, Sachdev S. Sidhu, Charles Boone posted by 5 people kiekyon phoenixzxl venancio pedrobeltrao cabbagesofdoom
	Clustering of protein domains for functional and evolutionary studies. [My Copy] BMC bioinformatics, Vol. 10, No. 1. (2009), 335. by Pavle Goldstein, Jurica Zucko, Dusica Vujaklija, et al.Anita Krisko, Daslav Hranueli, Paul F. Long, Catherine Etchebest, Bojan Basrak, John Cullum posted by 8 people Orengo Group Journal Picks sillitoe kshameer druvus Journal picks ppgardne zwang phoenixzxl
	Phylogenetic analysis of modularity in protein interaction networks. [My Copy] BMC bioinformatics, Vol. 10, No. 1. (14 October 2009), 333. by Sinan Erten, Xin Li, Gurkan Bebek, Jing Li, Mehmet Koyutürk posted by 10 people Orengo Group Journal Picks sillitoe biomcgary Journal picks ppgardne grahamc zwang druvus barriot phoenixzxl
	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
	Costly punishment does not always increase cooperation [My Copy] Proceedings of the National Academy of Sciences, Vol. 106, No. 41. (13 October 2009), pp. 17448-17451. by Jia-Jia Wu, Bo-Yu Zhang, Zhen-Xing Zhou, et al.Qiao-Qiao He, Xiu-Deng Zheng, Ross Cressman, Yi Tao posted by 1 person phoenixzxl
	The interwinding nature of protein-protein interfaces and its implication for protein complex formation [My Copy] Bioinformatics, Vol. 25, No. 23. (1 December 2009), pp. 3108-3113. by Kei Yura, Steven Hayward posted by 5 people kshameer dfdong higueruelo tprpip phoenixzxl
	Structural relationships among proteins with different global topologies and their implications for function annotation strategies [My Copy] Proceedings of the National Academy of Sciences, Vol. 106, No. 41. (13 October 2009), pp. 17377-17382. by Donald Petrey, Markus Fischer, Barry Honig posted by 7 people apaydin Orengo Group Journal Picks philcarter carlosjavierna TRHvidsten zwang phoenixzxl
	A coiled-coil motif that sequesters ions to the hydrophobic core [My Copy] Proceedings of the National Academy of Sciences, Vol. 106, No. 40. (6 October 2009), pp. 16950-16955. by Marcus D. Hartmann, Oswin Ridderbusch, Kornelius Zeth, et al.Reinhard Albrecht, Oli Testa, Derek N. Woolfson, Guido Sauer, Stanislaw Dunin-Horkawicz, Andrei N. Lupas, Birte H. Alvarez posted by 3 people phoenixzxl paulschlesinger kevinchannon
	Modeling system states in liver cells: Survival, apoptosis and their modifications in response to viral infection [My Copy] BMC Systems Biology, Vol. 3, No. 1. (2009), 97. by Nicole Philippi, Dorothee Walter, Rebekka Schlatter, et al.Karine Ferreira, Michael Ederer, Oliver Sawodny, Jens Timmer, Christoph Borner, Thomas Dandekar posted by 2 people tmmurali phoenixzxl
	Prediction of antigenic epitopes on protein surfaces by consensus scoring [My Copy] BMC Bioinformatics, Vol. 10, No. 1. (2009), 302. by Shide Liang, Dandan Zheng, Chi Zhang, Martin Zacharias posted by 3 people zwang phoenixzxl niallhaslam
	Understanding hydrogen-bond patterns in proteins using network motifs [My Copy] Bioinformatics, Vol. 25, No. 22. (15 November 2009), pp. 2921-2928. by Ofer Rahat, Uri Alon, Yaakov Levy, Gideon Schreiber posted by 5 people tomhebbron VGreiff zwang scmelton phoenixzxl
	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
	Bioinformatics construction of the human cell surfaceome. [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 106, No. 39. (29 September 2009), pp. 16752-16757. by J. P. da Cunha, P. A. Galante, J. E. de Souza, et al.R. F. de Souza, P. M. Carvalho, D. T. Ohara, R. P. Moura, S. M. Oba-Shinja, S. K. Marie, W. A. Silva, R. O. Perez, B. Stransky, M. Pieprzyk, J. Moore, O. Caballero, J. Gama-Rodrigues, A. Habr-Gama, W. P. Kuo, A. J. Simpson, A. A. Camargo, Lloyd J. Old, S. J. de Souza posted by 4 people frohike tonamswish renatomilani phoenixzxl
	CCHMM_PROF: a HMM-based Coiled-Coil Predictor with Evolutionary Information [My Copy] Bioinformatics (10 September 2009), btp539. by Lisa Bartoli, Piero Fariselli, Anders Krogh, Rita Casadio posted by 1 person phoenixzxl
	Seasonal transmission potential and activity peaks of the new influenza A(H1N1): a Monte Carlo likelihood analysis based on human mobility [My Copy] BMC Medicine, Vol. 7, No. 1. (14 Sep 2009), 45. by Duygu Balcan, Hao Hu, Bruno Goncalves, et al.Paolo Bajardi, Chiara Poletto, Jose J. Ramasco, Daniela Paolotti, Nicola Perra, Michele Tizzoni, Wouter Van den Broeck, Vittoria Colizza, Alessandro Vespignani posted by 3 people marinari phoenixzxl simdoc
	RRW: repeated random walks on genome-scale protein networks for local cluster discovery [My Copy] BMC Bioinformatics, Vol. 10, No. 1. (9 September 2009), 283. by Kathy Macropol, Tolga Can, Ambuj Singh posted by 5 people Orengo Group Journal Picks sillitoe barriot poirel phoenixzxl
	Structural domain-domain interactions: Assessment and comparison with protein-protein interaction data to improve the interactome. [My Copy] Proteins, Vol. 9999, No. 9999. (5 August 2009), NA. by C. Prieto, J. De Las Rivas posted by 3 people higueruelo phoenixzxl zwang
	Chemical approaches to synthetic biology [My Copy] Current Opinion in Biotechnology (03 September 2009) by Cristiano Chiarabelli, Pasquale Stano, Pier L. Luisi posted by 2 people abhishek_tiwari phoenixzxl
	A combinatorial approach to detect coevolved amino acid networks in protein families of variable divergence. [My Copy] PLoS computational biology, Vol. 5, No. 9. (4 September 2009), e1000488. by Julie Baussand, Alessandra Carbone posted by 8 people dfdong anuragsethi sobolevnrm phoenixzxl maren Bioinformatics barry zwang
	The evolution of information suppression in communicating robots with conflicting interests [My Copy] Proceedings of the National Academy of Sciences, Vol. 106, No. 37. (15 September 2009), pp. 15786-15790. by Sara Mitri, Dario Floreano, Laurent Keller posted by 3 people vgauthier rdiaz phoenixzxl
	Analyzing biological network parameters with CentiScaPe [My Copy] Bioinformatics, Vol. 25, No. 21. (1 November 2009), pp. 2857-2859. by Giovanni Scardoni, Michele Petterlini, Carlo Laudanna posted by 6 people ess30 colmryan operon kshameer dolchan phoenixzxl
	Regression Applied to Protein Binding Site Prediction and Comparison with Classification [My Copy] BMC Bioinformatics, Vol. 10, No. 1. (03 September 2009), 276. by Joachim Giard, Jerome Ambroise, Jean L. Gala, Benoit Macq posted by 2 people jinghu_fandm phoenixzxl
	Context-Specific Target Definition in Influenza A Virus Hemagglutinin-Glycan Receptor Interactions [My Copy] Vol. 16, No. 8. (28 August 2009), pp. 803-814. by Zachary Shriver, Rahul Raman, Karthik Viswanathan, Ram Sasisekharan posted by 1 person phoenixzxl
	Comparative analysis and unification of domain-domain interaction networks [My Copy] Bioinformatics, Vol. 25, No. 22. (15 November 2009), pp. 3020-3025. by Patrik Bjorkholm, Erik L. L. Sonnhammer posted by 5 people molnet-mna Orengo Group Journal Picks ilhem zwang phoenixzxl
	Pushing Structural Information into the Yeast Interactome by High-Throughput Protein Docking Experiments [My Copy] PLoS Comput Biol, Vol. 5, No. 8. (28 August 2009), e1000490. by Roberto Mosca, Carles Pons, Juan Fernández-Recio, Patrick Aloy posted by 6 people klexa Orengo Group Journal Picks bdessailly zwang phoenixzxl TRHvidsten
	BigFoot: Bayesian alignment and phylogenetic footprinting with MCMC [My Copy] BMC Evolutionary Biology, Vol. 9, No. 1. (28 August 2009), 217. by Rahul Satija, Adam Novak, Istvan Miklos, Rune Lyngso, Jotun Hein posted by 6 people cmzmasek cis-regulatory-evolution BergmanLab cisevol djkt phoenixzxl
	Using a mutual information-based site transition network to map the genetic evolution of influenza A/H3N2 virus. [My Copy] Bioinformatics (Oxford, England), Vol. 25, No. 18. (15 September 2009), pp. 2309-2317. by Zhen Xia, Gulei Jin, Jun Zhu, Ruhong Zhou posted by 4 people marywaye zwang phoenixzxl druvus
	Assessing the druggability of protein-protein interactions by a supervised machine-learning method [My Copy] BMC Bioinformatics, Vol. 10, No. 1. (25 August 2009), 263. by Nobuyoshi Sugaya, Kazuyoshi Ikeda posted by 3 people iris_2001 higueruelo phoenixzxl
	The human protein coevolution network. [My Copy] Genome research, Vol. 19, No. 10. (20 October 2009), pp. 1861-1871. by Elisabeth R. Tillier, Robert L. Charlebois posted by 8 people dfdong Garamonfok venancio jperkins TRHvidsten djkt phoenixzxl tmmurali
	Two Steps Forward for Synthetic Biology [My Copy] Science, Vol. 325, No. 5943. (21 August 2009), pp. 928-929. by Elizabeth Pennisi posted by 5 people abhishek_tiwari zwang phoenixzxl renatomilani rdiaz
	Evolutionary Interactions between N-Linked Glycosylation Sites in the HIV-1 Envelope [My Copy] PLoS Comput Biol, Vol. 3, No. 1. (19 January 2007), e11. by Art F. Y. Poon, Fraser I. Lewis, Sergei L. Pond, Simon D. W. Frost posted by 1 person phoenixzxl
	Biosynthetic Potentials of Metabolites and Their Hierarchical Organization [My Copy] PLoS Comput Biol, Vol. 4, No. 4. (4 April 2008), e1000049. by Franziska Matthäus, Carlos Salazar, Oliver Ebenhöh posted by 1 person phoenixzxl
	A boosting approach to structure learning of graphs with and without prior knowledge [My Copy] Bioinformatics, Vol. 25, No. 22. (15 November 2009), pp. 2929-2936. by Shahzia Anjum, Arnaud Doucet, Chris C. Holmes posted by 7 people hughitt1 tmmurali fastjoe23 TRHvidsten rdiaz phoenixzxl frohike
	In vitro and in vivo characterization of new swine-origin H1N1 influenza viruses [My Copy] Nature, Vol. 460, No. 7258. (20 August 2009), pp. 1021-1025. by Yasushi Itoh, Kyoko Shinya, Maki Kiso, et al.Tokiko Watanabe, Yoshihiro Sakoda, Masato Hatta, Yukiko Muramoto, Daisuke Tamura, Yuko Sakai-Tagawa, Takeshi Noda, Saori Sakabe, Masaki Imai, Yasuko Hatta, Shinji Watanabe, Chengjun Li, Shinya Yamada, Ken Fujii, Shin Murakami, Hirotaka Imai, Satoshi Kakugawa, Mutsumi Ito, Ryo Takano, Kiyoko Iwatsuki-Horimoto, Masayuki Shimojima, Taisuke Horimoto, Hideo Goto, Kei Takahashi, Akiko Makino, Hirohito Ishigaki, Misako Nakayama, Masatoshi Okamatsu, Kazuo Takahashi, David Warshauer, Peter A. Shult, Reiko Saito, Hiroshi Suzuki, Yousuke Furuta, Makoto Yamashita, Keiko Mitamura, Kunio Nakano, Morio Nakamura, Rebecca Brockman-Schneider, Hiroshi Mitamura, Masahiko Yamazaki, Norio Sugaya, M. Suresh, Makoto Ozawa, Gabriele Neumann, James Gern, Hiroshi Kida, Kazumasa Ogasawara, Yoshihiro Kawaoka posted by 2 people AlexBateman phoenixzxl
	Simultaneous inference of biological networks of multiple species from genome-wide data and evolutionary information: a semi-supervised approach [My Copy] Bioinformatics, Vol. 25, No. 22. (15 November 2009), pp. 2962-2968. by Hisashi Kashima, Yoshihiro Yamanishi, Tsuyoshi Kato, Masashi Sugiyama, Koji Tsuda posted by 5 people Orengo Group Journal Picks jperkins roys phoenixzxl druvus
	A Search for Energy Minimized Sequences of Proteins [My Copy] PLoS ONE, Vol. 4, No. 8. (19 August 2009), e6684. by Anupam N. Jha, G. K. Ananthasuresh, Saraswathi Vishveshwara posted by 2 people zwang phoenixzxl
	A Thermodynamic Model of Microtubule Assembly and Disassembly [My Copy] PLoS ONE, Vol. 4, No. 8. (11 August 2009), e6378. by Bernard M. A. G. Piette, Junli Liu, Kasper Peeters, et al.Andrei Smertenko, Timothy Hawkins, Michael Deeks, Roy Quinlan, Wojciech J. Zakrzewski, Patrick J. Hussey posted by 1 person phoenixzxl
	Optimal drug combinations and minimal hitting sets [My Copy] BMC Systems Biology, Vol. 3, No. 1. (2009), 81. by Alexei Vazquez posted by 3 people ipark-kaist phoenixzxl reyez
	Sequence physical properties encode the global organization of protein structure space [My Copy] Proceedings of the National Academy of Sciences, Vol. 106, No. 34. (25 August 2009), pp. 14345-14348. by S. Rackovsky posted by 4 people zwang phoenixzxl roys kevinchannon
	Knowledge-guided inference of domain-domain interactions from incomplete protein-protein interaction networks [My Copy] Bioinformatics, Vol. 25, No. 19. (1 October 2009), pp. 2492-2499. by Mei Liu, Xue-wen Chen, Raja Jothi posted by 4 people zwang grahamc robfsouza phoenixzxl
	Development of biomarker classifiers from high-dimensional data [My Copy] Brief Bioinform, Vol. 10, No. 5. (1 September 2009), pp. 537-546. by Songjoon Baek, Chen-An Tsai, James J. Chen posted by 9 people zufar Orengo Group Journal Picks jperkins lwaldron brianb druvus nuin neils phoenixzxl
	Correlations between RNA and protein expression profiles in 23 human cell lines [My Copy] BMC Genomics, Vol. 10, No. 1. (07 August 2009), 365. by Marcus Gry, Rebecca Rimini, Sara Stromberg, et al.Anna Asplund, Fredrik Ponten, Mathias Uhlen, Peter Nilsson posted by 3 people rdiaz natstreet phoenixzxl
	Geometric De-noising of Protein-Protein Interaction Networks [My Copy] PLoS Comput Biol, Vol. 5, No. 8. (7 August 2009), e1000454. by Oleksii Kuchaiev, Marija Rašajski, Desmond J. Higham, Nataša Pržulj posted by 10 people Orengo Group Journal Picks CorinYeats klexa tmmurali roys grahamc zwang robfsouza phoenixzxl kiekyon
	Human disease-drug network based on genomic expression profiles. [My Copy] PloS one, Vol. 4, No. 8. (6 August 2009), e6536. by Guanghui Hu, Pankaj Agarwal posted by 5 people ipark-kaist bertelsen installe phoenixzxl frohike
	Folding DNA into Twisted and Curved Nanoscale Shapes [My Copy] Science, Vol. 325, No. 5941. (7 August 2009), pp. 725-730. by Hendrik Dietz, Shawn M. Douglas, William M. Shih posted by 3 people phoenixzxl melting jbhiatt
	Synthetic protein scaffolds provide modular control over metabolic flux [My Copy] Nature Biotechnology, Vol. 27, No. 8. (02 August 2009), pp. 753-759. by John E. Dueber, Gabriel C. Wu, G. Reza Malmirchegini, et al.Tae S. Moon, Christopher J. Petzold, Adeeti V. Ullal, Kristala L. J. Prather, Jay D. Keasling posted by 7 people abhishek_tiwari dbikard grahamc phoenixzxl kevinchannon biomcgary jdoconnell
	Multi-level learning: improving the prediction of protein, domain and residue interactions by allowing information flow between levels [My Copy] BMC Bioinformatics, Vol. 10, No. 1. (2009), 241. by Kevin Yip, Philip Kim, Drew McDermott, Mark Gerstein posted by 10 people flbarroso zwang Simulation of operations and interactions jago gwallau installe barriot kshameer peteruetz phoenixzxl
	A Tool for calculating binding-site residues on proteins from PDB Structures [My Copy] BMC Structural Biology, Vol. 9, No. 1. (2009), 52. by Jing Hu, Changhui Yan posted by 4 people dfdong balewis peteruetz phoenixzxl
	Folding of glycoproteins: toward understanding the biophysics of the glycosylation code [My Copy] Current Opinion in Structural Biology, Vol. 19, No. 5. (03 October 2009), pp. 524-533. by Dalit Shental-Bechor, Yaakov Levy posted by 2 people sobolevnrm phoenixzxl
	The Validation and Assessment of Machine Learning: A Game of Prediction from High-Dimensional Data [My Copy] PLoS ONE, Vol. 4, No. 8. (4 August 2009), e6287. by Tune H. Pers, Anders Albrechtsen, Claus Holst, Thorkild I. A. Sørensen, Thomas A. Gerds posted by 7 people zwang daforerog rdiaz phoenixzxl installe operon frohike
	A phylogenetic and Markov model approach for the reconstruction of mutational pathways of drug resistance. [My Copy] Bioinformatics (Oxford, England) (3 August 2009), btp466. by Patricia Buendia, Brice Cadwallader, Victor Degruttola posted by 2 people nuin phoenixzxl
	Semantic Similarity in Biomedical Ontologies [My Copy] PLoS Comput Biol, Vol. 5, No. 7. (31 July 2009), e1000443. by Catia Pesquita, Daniel Faria, André O. Falcão, Phillip Lord, Francisco M. Couto posted by 11 people sobolevnrm bertelsen MarcoAlvarez Journal picks adamjamesreid fgibson dullhunk guhjy badger_master phoenixzxl druvus