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tmmuralis library [381 articles]

Senaste artiklarna i tmmuralis bibliotek ordnat efter prioritet.
  • Using the principle of entropy maximization to infer genetic interaction networks from gene expression patterns.
    Proc Natl Acad Sci U S A (30 November 2006)
    by Timothy R R Lezon, Jayanth R R Banavar, Marek Cieplak, Amos Maritan, Nina V V Fedoroff
    posted to reverse_engineering by tmmurali on 2008-09-01 19:49:30 as ***** along with 6 people yaredo jfr aswin hmk iris_2001 macavity1g
  • Integration of relational and hierarchical network information for protein function prediction
    BMC Bioinformatics, Vol. 9, No. 1. (2008)
    by Xiaoyu Jiang, Naoki Nariai, Martin Steffen, Simon Kasif, Eric Kolaczyk
    posted to gene-function-prediction by tmmurali on 2008-09-01 19:02:43 as ***** along with 3 people grahamc barriot dansullivanblk
  • Low duplicability and network fragility of cancer genes
    Trends in Genetics, Vol. 24, No. 9. (September 2008), pp. 427-430.
    by Davide Rambaldi, Federico M Giorgi, Fabrizio Capuani, Andrea Ciliberto, Francesca D Ciccarelli
    posted to network_structure by tmmurali on 2008-08-27 21:34:27 as ***** along with 1 person djkt
  • Identifying functional modules in protein-protein interaction networks: an integrated exact approach
    Bioinformatics, Vol. 24, No. 13. (1 July 2008), pp. i223-231.
    by Marcus T Dittrich, Gunnar W Klau, Andreas Rosenwald, Thomas Dandekar, Tobias Muller
    posted to active-networks by tmmurali on 2008-08-27 19:32:12 as ***** along with 4 people chad_davis marck renatomilani dragonrez
  • Herpesviral Protein Networks and Their Interaction with the Human Proteome
    Science, Vol. 311, No. 5758. (13 January 2006), pp. 239-242.
    by Peter Uetz, Yu-An Dong, Christine Zeretzke, Christine Atzler, Armin Baiker, Bonnie Berger, Seesandra V Rajagopala, Maria Roupelieva, Dietlind Rose, Even Fossum, Jurgen Haas
    posted to host-pathogen host-pathogen-dataset by tmmurali on 2008-08-15 19:34:44 as ***** along with 2 people zukeboy hpaces
  • RNA interference screen for human genes associated with West Nile virus infection
    Nature (06 August 2008)
    by Manoj N Krishnan, Aylwin Ng, Bindu Sukumaran, Felicia D Gilfoy, Pradeep D Uchil, Hameeda Sultana, Abraham L Brass, Rachel Adametz, Melody Tsui, Feng Qian, Ruth R Montgomery, Sima Lev, Peter W Mason, Raymond A Koski, Stephen J Elledge, Ramnik J Xavier, Herve Agaisse, Erol Fikrig
    posted to host-pathogen host-pathogen-dataset by tmmurali on 2008-08-14 21:46:01 as ***** along with 1 person shuzhens
  • An empirical Bayes approach to inferring large-scale gene association networks.
    Bioinformatics, Vol. 21, No. 6. (March 2005), pp. 754-764.
    by J Schäfer, K Strimmer
    posted to reverse_engineering by tmmurali on 2008-08-07 20:24:55 as ***** along with 5 people and 1 group eldan gangli wnpx Ao_Li2007 StatAnika tulip
  • The discovery of structural form.
    Proceedings of the National Academy of Sciences of the United States of America (31 July 2008)
    by Charles Kemp, Joshua B B Tenenbaum
    posted to actex graph-grammars by tmmurali on 2008-08-06 23:09:02 as ***** along with 18 people and 3 groups nojhan stringertheory thefillm amatos markstoehr uhhhhhhhhhhm A_Olympia jmchauvet shigepong rsantana tbloomf OriginalLurch markusd jborn deubel jyuh Zephyrus jago Optimization logics of knowledge Roswell Cancer Crosstalk
  • Discerning static and causal interactions in genome-wide reverse engineering problems.
    Bioinformatics (Oxford, England) (8 May 2008)
    by M Zampieri, N Soranzo, C Altafini
    posted to actex reverse_engineering by tmmurali on 2008-08-06 18:24:05 as ***** along with 4 people roys jyuh verdicchio balicea
  • Unraveling Protein Networks with Power Graph Analysis
    PLoS Comput Biol, Vol. 4, No. 7. (11 July 2008), e1000108.
    by Loïc Royer, Matthias Reimann, Bill Andreopoulos, Michael Schroeder
    posted to network-models network_modules network_structure by tmmurali on 2008-07-17 19:26:39 as ***** along with 18 people and 2 groups aramesh2 AbnerCYH jmuhlich MatthiasReimann royerloic Ema lptolik kengg roys reyez nuin Borelli askrajiv renatomilani chad_davis stajich sebk rsantana Berkeley Mycology OPIG
  • Association analysis-based transformations for protein interaction networks: a function prediction case study
    (2007), pp. 540-549.
    by Gaurav Pandey, Michael Steinbach, Rohit Gupta, Tushar Garg, Vipin Kumar
    posted to gene-function-prediction ppi_network_quality ppi-prediction by tmmurali on 2008-07-15 20:14:01 as *****
  • Uncovering the overlapping community structure of complex networks in nature and society
    Nature, Vol. 435, No. 7043., pp. 814-818.
    by Gergely Palla, Imre Derényi, Illés Farkas, Tamás Vicsek
    posted to network_modules by tmmurali on 2008-06-18 15:32:07 as ***** along with 12 people and 2 groups kuhn jfr lfriedl wilmegape gcalda ltabourier michaelmampaey Scis0000002 maralena lmichan ellakat betaparticle kdl ADMiRes
  • Integrating large-scale functional genomic data to dissect the complexity of yeast regulatory networks.
    Nature genetics (15 June 2008)
    by Jun Zhu, Bin Zhang, Erin N N Smith, Becky Drees, Rachel B B Brem, Leonid Kruglyak, Roger E E Bumgarner, Eric E E Schadt
    posted to actex data_integration reverse_engineering transcriptional_regulatory_networks by tmmurali on 2008-06-18 14:56:33 as ***** along with 10 people realzhang kengg maralena ptrobajo jyuh roys marck caseybrown djkt srp33
  • Use and misuse of the gene ontology annotations.
    Nature reviews. Genetics (13 May 2008)
    by Seung Yon Rhee, Valerie Wood, Kara Dolinski, Sorin Draghici
    posted to functional_enrichment by tmmurali on 2008-06-18 14:52:25 as ***** along with 20 people and 2 groups djkt jyuh aheilbut mariakmejia cmzmasek A_Olympia realzhang carlk roys gjuggler fpattyn RamuAnandakrishnan ptrobajo giovenko cabbagesofdoom renatomilani capitall marck rvosa bpcusack logics of knowledge FAB-lab
  • Predicting synthetic rescues in metabolic networks
    Mol Syst Biol, Vol. 4 (12 February 2008)
    by Adilson E Motter, Natali Gulbahce, Eivind Almaas, Albert-Laszlo Barabasi
    posted to actex by tmmurali on 2008-05-28 04:52:30 as ***** along with 9 people kentsis zwang bootsy biomcgary cabbagezs westoll shikin shung debasis
  • Estimating the size of the human interactome
    Proceedings of the National Academy of Sciences (12 May 2008), 0708078105.
    by Michael P Stumpf, Thomas Thorne, Eric de Silva, Ronald Stewart, Hyeong J An, Michael Lappe, Carsten Wiuf
    posted to ppi_network by tmmurali on 2008-05-13 18:25:50 as ***** along with 20 people zwang chrissp100 sanchezbuelna jyuh phoenixzxl neils paolomarcatili mjoach xingxu Ema cabbagesofdoom balicea marck friendpine brianb roys Evangelia dragonrez chad_davis bpcusack
  • A modular approach for integrative analysis of large-scale gene-expression and drug-response data
    Nature Biotechnology, Vol. 26, No. 5. (08 May 2008), pp. 531-539.
    by Zoltán Kutalik, Jacques S Beckmann, Sven Bergmann
    posted to biclustering gene_expression_compendium gene_expression_mining by tmmurali on 2008-05-13 16:06:30 as ***** along with 4 people jfr stringertheory oelemento ptrobajo
  • A Simple Model of the Modular Structure of Transcriptional Regulation in Yeast
    Journal of Computational Biology, Vol. 15, No. 4. (2008), pp. 393-405.
    by Vladimir Filkov, Nameeta Shah
    posted to actex reverse_engineering transcriptional_regulatory_networks by tmmurali on 2008-05-09 05:30:23 as ***** along with 1 person eskay
  • Hierarchical structure and the prediction of missing links in networks
    Nature, Vol. 453, No. 7191., pp. 98-101.
    by Aaron Clauset, Cristopher Moore, MEJ Newman
    posted to actex network_structure by tmmurali on 2008-05-02 15:36:33 as ***** along with 36 people pbull gtgt15 Ema jago cmor balicea kengg jjray soramame_0518 deanmalmgren briordan hryk tny AbnerCYH cactus akshat bryanhughes gagliol margaritis jyuh craigwilson06 cmmorel eyliu markusd elsantosneto pinney i-stevenson fbaroni nedwards apwesolowski Borelli ptrobajo dpf rds lfriedl sen_cheng
  • Direct targets of the TRP63 transcription factor revealed by a combination of gene expression profiling and reverse engineering
    Genome Res. (25 April 2008), gr.073601.107.
    by Giusy Della Gatta, Mukesh Bansal, Alberto Ambesi-Impiombato, Dario Antonini, Caterina Missero, Diego di Bernardo
    posted to actex reverse_engineering transcriptional_regulatory_networks by tmmurali on 2008-04-29 22:17:55 as ***** along with 1 person roys
  • Nested effects models for high-dimensional phenotyping screens
    Bioinformatics, Vol. 23, No. 13. (1 July 2007), pp. i305-312.
    by Florian Markowetz, Dennis Kostka, Olga G Troyanskaya, Rainer Spang
    posted to phenotype_maps by tmmurali on 2008-04-13 03:51:07 as ***** along with 3 people jyuh jiny czeller
  • Non-transcriptional pathway features reconstructed from secondary effects of RNA interference.
    Bioinformatics (Oxford, England), Vol. 21, No. 21. (1 November 2005), pp. 4026-4032.
    by F Markowetz, J Bloch, R Spang
    posted to actex reverse_engineering by tmmurali on 2008-04-12 17:39:38 as *****
  • A systems biology approach to prediction of oncogenes and molecular perturbation targets in B-cell lymphomas
    Mol Syst Biol, Vol. 4 (12 February 2008)
    by Kartik M Mani, Celine Lefebvre, Kai Wang, Wei K Lim, Katia Basso, Riccardo Dalla-Favera, Andrea Califano
    posted to actex active-networks reverse_engineering by tmmurali on 2008-04-12 17:24:07 as ***** along with 5 people jfr ealloza shikin dap5087 dragonrez
  • MMG: a probabilistic tool to identify submodules of metabolic pathways
    Bioinformatics, Vol. 24, No. 8. (15 April 2008), pp. 1078-1084.
    by Guido Sanguinetti, Josselin Noirel, Phillip C Wright
    posted to pathway_perturbation_network_based by tmmurali on 2008-04-11 15:31:57 as ***** along with 1 person mdstobbe
  • Host pathogen protein interactions predicted by comparative modeling.
    Protein Sci, Vol. 16, No. 12. (December 2007), pp. 2585-2596.
    by FP Davis, DT Barkan, N Eswar, JH McKerrow, A Sali
    posted to host-pathogen by tmmurali on 2008-04-08 21:27:44 as ***** along with 1 person bicko
  • Genome-wide inference of protein interaction sites: lessons from the yeast high-quality negative protein-protein interaction dataset.
    Nucleic Acids Res (14 February 2008)
    by Jie Guo, Xiaomei Wu, Da-Yong Y Zhang, Kui Lin
    posted to ppi-prediction by tmmurali on 2008-04-03 13:29:38 as ***** along with 4 people neils kluck stef_lise paolomarcatili
  • Protein networks in disease
    Genome Res., Vol. 18, No. 4. (1 April 2008), pp. 644-652.
    by Trey Ideker, Roded Sharan
    posted to ppi_network by tmmurali on 2008-04-01 19:32:16 as ***** along with 19 people jyuh balicea Borelli jwdietrich frohike bootsy nedwards roys mclarenv phoenixzxl brianb schuylrp jfr paolomarcatili gracio thomaskelder ptrobajo raiyar zwang
  • Quantitative evidence for conserved longevity pathways between divergent eukaryotic species
    Genome Res., Vol. 18, No. 4. (1 April 2008), pp. 564-570.
    by Erica D Smith, Mitsuhiro Tsuchiya, Lindsay A Fox, Nick Dang, Di Hu, Emily O Kerr, Elijah D Johnston, Bie N Tchao, Diana N Pak, Linnea K Welton, Daniel E Promislow, James H Thomas, Matt Kaeberlein, Brian K Kennedy
    posted to aging by tmmurali on 2008-04-01 19:27:23 as ***** along with 2 people wilbur ptrobajo
  • Systematic identification of mammalian regulatory motifs' target genes and functions
    Nature Methods, Vol. 5, No. 4. (02 March 2008), pp. 347-353.
    by Jason B Warner, Anthony A Philippakis, Savina A Jaeger, Fangxue S He, Jolinta Lin, Martha L Bulyk
    posted to actex transcriptional_regulatory_networks transcription-modules by tmmurali on 2008-03-31 17:02:05 as ***** along with 4 people and 1 group zwang ptrobajo jyuh isimpson Jarman Lab
  • Validation and refinement of gene-regulatory pathways on a network of physical interactions.
    Genome Biol, Vol. 6, No. 7. (2005)
    by CH Yeang, HC Mak, S McCuine, C Workman, T Jaakkola, T Ideker
    posted to actex by tmmurali on 2008-03-28 23:57:34 as ***** along with 11 people and 1 group snuppepuppan abhik textoris wnpx noano koller ccr cdppublications AlexanderPico carlk jago CDP
  • Computing Knock-Out Strategies in Metabolic Networks
    Journal of Computational Biology, Vol. 15, No. 3. (2008), pp. 259-268.
    by Utz-Uwe Haus, Steffen Klamt, Tamon Stephen
    posted to actex by tmmurali on 2008-03-28 19:17:09 as ***** along with 5 people and 1 group ptrobajo balicea jiny Borelli longoka Frontiers in Diabetes and Obesity
  • Probabilistic protein function prediction from heterogeneous genome-wide data.
    PLoS ONE, Vol. 2, No. 3. (2007)
    by N Nariai, ED Kolaczyk, S Kasif
    posted to gene-function-prediction by tmmurali on 2008-03-18 21:29:07 as *****
  • A simple and exact Laplacian clustering of complex networking phenomena: Application to gene expression profiles
    Proceedings of the National Academy of Sciences, Vol. 105, No. 11. (18 March 2008), pp. 4083-4087.
    by Choongrak Kim, Mookyung Cheon, Minho Kang, Iksoo Chang
    posted to cancer_classification gene_expression_mining by tmmurali on 2008-03-18 18:43:06 as ***** along with 3 people roys ptrobajo jyuh
  • Biological network design strategies: discovery through dynamic optimization.
    Mol Biosyst, Vol. 2, No. 12. (December 2006), pp. 650-659.
    by BS Adiwijaya, PI Barton, B Tidor
    posted to actex by tmmurali on 2008-03-17 21:13:57 as ***** along with 2 people and 1 group jrbanga cdppublications CDP
  • Stimulus Design for Model Selection and Validation in Cell Signaling.
    PLoS Comput Biol, Vol. 4, No. 2. (15 February 2008)
    by Joshua F F Apgar, Jared E E Toettcher, Drew Endy, Forest M M White, Bruce Tidor
    posted to actex by tmmurali on 2008-03-17 21:12:41 as ***** along with 1 person aheilbut
  • A systems biology approach for pathway level analysis
    Genome Res. (4 September 2007), gr.6202607.
    by Sorin Draghici, Purvesh Khatri, Adi L Tarca, Kashyap Amin, Arina Done, Calin Voichita, Constantin Georgescu, Roberto Romero
    posted to pathway_perturbation_network_based by tmmurali on 2008-03-13 17:35:32 as ***** along with 15 people and 3 groups dragonrez jfr gurkanbebek grahamc shigepong zwang cabbagezs cerami xingxu shikin idonaldson Pao-Yang thomaskelder heliopais AlexanderPico Bioinformatics ParkinsonLab_at_MaRS OPIG
  • Protein Function Assignment through Mining Cross-Species Protein-Protein Interactions.
    PLoS ONE, Vol. 3, No. 2. (2008)
    by XW Chen, M Liu, R Ward
    posted to gene-function-prediction by tmmurali on 2008-02-22 19:06:05 as ***** along with 1 person jyuh
  • A Gene Recommender Algorithm to Identify Coexpressed Genes in C. elegans
    Genome Res., Vol. 13, No. 8. (1 August 2003), pp. 1828-1837.
    by Art B Owen, Josh Stuart, Kathy Mach, Anne M Villeneuve, Stuart Kim
    posted to pathway_perturbation_gene_set_based by tmmurali on 2008-02-22 18:41:08 as ***** along with 2 people balajis tvdbulck
  • A search engine to identify pathway genes from expression data on multiple organisms
    BMC Systems Biology, Vol. 1, No. 1. (2007)
    by Chunnuan Chen, Matthew Weirauch, Corey Powell, Alexander Zambon, Joshua Stuart
    posted to gene-function-prediction pathway_perturbation_gene_set_based by tmmurali on 2008-02-22 18:40:15 as ***** along with 5 people jyuh jfr rsandie waszak AlexanderPico
  • Deductive biocomputing
    PLoS ONE, Vol. 2 (2007)
    by J Shrager, R Waldinger, M Stickel, JP Massar
    posted to actex by tmmurali on 2008-02-22 17:57:54 as ***** along with 3 people jyuh dullhunk aheilbut
  • On the Sparse Reconstruction of Gene Networks
    Journal of Computational Biology, Vol. 15, No. 1. (2008), pp. 21-30.
    by M Andrecut, SA Kauffman
    posted to reverse_engineering by tmmurali on 2008-02-14 15:15:10 as *****
  • A single gene network accurately predicts phenotypic effects of gene perturbation in Caenorhabditis elegans
    Nature Genetics, Vol. 40, No. 2. (27 January 2008), pp. 181-188.
    by Insuk Lee, Ben Lehner, Catriona Crombie, Wendy Wong, Andrew G Fraser, Edward M Marcotte
    posted to no-tag by tmmurali on 2008-02-01 17:42:45 as ***** along with 7 people balicea capitall roys jiny kintoki meiklej jfr
  • Successful anti-cancer drug targets able to pass FDA review demonstrate the identifiable signature distinct from the signatures of random genes and initially proposed targets
    Bioinformatics, Vol. 24, No. 3. (1 February 2008), pp. 389-395.
    by Anatoly L Mayburd, Inna Golovchikova, James L Mulshine
    posted to drug-prioritisation by tmmurali on 2008-01-31 16:53:02 as *****
  • MetaReg: A platform for modeling, analysis and visualization of biological systems using large-scale experimental data
    Genome Biology, Vol. 9 (02 January 2008), R1.
    by Igor Ulitsky, Irit Gat-Viks, Ron Shamir
    posted to actex reverse_engineering by tmmurali on 2008-01-30 15:41:00 as ***** along with 4 people jyuh waszak ptrobajo jfr
  • High-confidence prediction of global interactomes based on genome-wide coevolutionary networks
    Proceedings of the National Academy of Sciences (16 January 2008), 0709671105.
    by David Juan, Florencio Pazos, Alfonso Valencia
    posted to ppi-prediction by tmmurali on 2008-01-22 19:15:56 as ***** along with 12 people and 1 group brant balicea sebastien_vigneau bluto cjeans aconesa Katje roys friendpine huali mdstobbe paolomarcatili microbiology_nijmegen
  • Protein-protein interaction networks and biology—what's the connection?
    Nature Biotechnology, Vol. 26, No. 1., pp. 69-72.
    by Luke Hakes, John W Pinney, David L Robertson, Simon C Lovell
    posted to ppi_network ppi_network_quality by tmmurali on 2008-01-09 18:34:19 as ***** along with 15 people and 1 group Yanno jyuh jfr balicea dullhunk neils mikaelhuss cjeans nedwards biehl shikin mclarenv Yumyai paolomarcatili zdai GeneGo
  • Distinct physiological states of Plasmodium falciparum in malaria-infected patients
    Nature (28 November 2007)
    by JP Daily, D Scanfeld, N Pochet, K Le Roch, D Plouffe, M Kamal, O Sarr, S Mboup, O Ndir, D Wypij, K Levasseur, E Thomas, P Tamayo, C Dong, Y Zhou, ES Lander, D Ndiaye, D Wirth, EA Winzeler, JP Mesirov, A Regev
    posted to host-pathogen host-pathogen-dataset by tmmurali on 2008-01-08 23:22:25 as ***** along with 2 people aswin shuzhens
  • Population Fitness and the Regulation of Escherichia coli Genes by Bacterial Viruses
    PLoS Biology, Vol. 3, No. 7. (1 July 2005), e229.
    by Ying Chen, Ido Golding, Satoshi Sawai, Ling Guo, Edward C Cox
    posted to actex_phage by tmmurali on 2008-01-07 16:34:18 as *****
  • Inferring cellular networks - a review
    BMC Bioinformatics, Vol. 8, No. Suppl 6. (2007)
    by Florian Markowetz, Rainer Spang
    posted to actex reverse_engineering by tmmurali on 2008-01-07 01:58:50 as ***** along with 6 people jyuh shigepong dejori heliopais bertelsen czeller
  • A probabilistic methodology for integrating knowledge and experiments on biological networks.
    J Comput Biol, Vol. 13, No. 2. (March 2006), pp. 165-181.
    by I Gat-Viks, A Tanay, D Raijman, R Shamir
    posted to actex by tmmurali on 2008-01-07 00:12:41 as ***** along with 1 person carlk
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