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tmmurali's library [350 articles]

最近录入 tmmurali's 文献库:按阅读优先等级排序.
  • 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_structure network_modules network-models by tmmurali on 2008-07-17 19:26:39 as ***** along with 14 people and 1 group lptolik MatthiasReimann jmuhlich AbnerCYH royerloic stajich chad_davis renatomilani askrajiv Borelli nuin reyez kengg Ema Berkeley Mycology
  • 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 ppi-prediction ppi_network_quality gene-function-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 betaparticle ellakat kuhn jfr lfriedl wilmegape gcalda ltabourier michaelmampaey Scis0000002 maralena lmichan 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 transcriptional_regulatory_networks network-inference data_integration actex by tmmurali on 2008-06-18 14:56:33 as ***** along with 9 people caseybrown djkt marck roys jyuh realzhang kengg ptrobajo maralena
  • 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 18 people and 1 group marck capitall realzhang gjuggler A_Olympia fpattyn cmzmasek djkt renatomilani giovenko cabbagesofdoom ptrobajo RamuAnandakrishnan roys carlk mariakmejia aheilbut jyuh logics of knowledge
  • 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 debasis kentsis zwang bootsy biomcgary cabbagezs westoll shikin shung
  • 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 18 people chad_davis Evangelia balicea marck paolomarcatili sanchezbuelna cabbagesofdoom xingxu mjoach jyuh chrissp100 zwang roys brianb friendpine Ema neils phoenixzxl
  • 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 gene_expression_mining gene_expression_compendium biclustering by tmmurali on 2008-05-13 16:06:30 as ***** along with 3 people ptrobajo oelemento stringertheory
  • 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 transcriptional_regulatory_networks reverse_engineering actex 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 network_structure actex by tmmurali on 2008-05-02 15:36:33 as ***** along with 35 people sen_cheng jjray rds Borelli ptrobajo apwesolowski dpf cmmorel fbaroni balicea cmor kengg pbull jago Ema gtgt15 hryk nedwards i-stevenson pinney elsantosneto markusd eyliu craigwilson06 jyuh margaritis gagliol bryanhughes akshat cactus AbnerCYH tny briordan deanmalmgren soramame_0518
  • 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 transcriptional_regulatory_networks reverse_engineering actex 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 czeller jyuh jiny
  • 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 network-inference 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 4 people dragonrez ealloza shikin dap5087
  • 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 paolomarcatili neils kluck stef_lise
  • 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 zwang balicea raiyar ptrobajo jfr brianb paolomarcatili thomaskelder gracio schuylrp jyuh Borelli jwdietrich frohike bootsy nedwards roys mclarenv phoenixzxl
  • 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 ptrobajo wilbur
  • 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 isimpson jyuh zwang ptrobajo
  • 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 jago carlk AlexanderPico snuppepuppan abhik textoris wnpx noano koller ccr cdppublications 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 1 person ptrobajo
  • 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 2 people roys ptrobajo
  • 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 AlexanderPico heliopais dragonrez jfr gurkanbebek grahamc shigepong zwang cabbagezs cerami xingxu shikin idonaldson Pao-Yang thomaskelder 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 tvdbulck balajis
  • 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 AlexanderPico jyuh jfr rsandie waszak
  • 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 aheilbut jyuh dullhunk
  • 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 jfr balicea capitall roys jiny kintoki meiklej
  • 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 network-inference by tmmurali on 2008-01-30 15:41:00 as ***** along with 4 people jfr jyuh waszak ptrobajo
  • 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 paolomarcatili brant balicea sebastien_vigneau bluto cjeans aconesa Katje roys friendpine huali mdstobbe 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 14 people and 1 group paolomarcatili Yanno jyuh jfr balicea dullhunk neils mikaelhuss cjeans nedwards biehl shikin mclarenv Yumyai 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 shuzhens aswin
  • 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 network-inference by tmmurali on 2008-01-07 01:58:50 as ***** along with 6 people czeller bertelsen jyuh shigepong dejori heliopais
  • 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
  • Perturbations to uncover gene networks.
    Trends Genet (10 November 2006)
    by Jesper Tegnér, Johan Björkegren
    posted to actex by tmmurali on 2008-01-05 07:40:30 as ***** along with 4 people aswin braingrind tvdbulck heliopais
  • A Predictive Model for Transcriptional Control of Physiology in a Free Living Cell
    Cell, Vol. 131, No. 7. (28 December 2007), pp. 1354-1365.
    by Richard Bonneau, Marc T Facciotti, David J Reiss, Amy K Schmid, Min Pan, Amardeep Kaur, Vesteinn Thorsson, Paul Shannon, Michael H Johnson, Christopher J Bare, William Longabaugh, Madhavi Vuthoori, Kenia Whitehead, Aviv Madar, Lena Suzuki, Tetsuya Mori, Dong-Eun Chang, Jocelyne Diruggiero, Carl H Johnson, Leroy Hood, Nitin S Baliga
    posted to actex network_modules by tmmurali on 2007-12-29 15:26:16 as ***** along with 4 people jyuh raiyar oelemento emptyhb
  • TABASCO: A single molecule, base-pair resolved gene expression simulator
    BMC Bioinformatics, Vol. 8 (19 December 2007), 480.
    by Sriram Kosuri, Jason R Kelly, Drew Endy
    posted to actex actex_phage by tmmurali on 2007-12-27 17:35:01 as *****
  • Combinatorics of feedback in cellular uptake and metabolism of small molecules
    Proceedings of the National Academy of Sciences (19 December 2007), 0706231105.
    by Sandeep Krishna, Szabolcs Semsey, Kim Sneppen
    posted to actex network_modules by tmmurali on 2007-12-26 19:32:52 as ***** along with 2 people coolger cjeans
  • Dialogue on Reverse-Engineering Assessment and Methods: The DREAM of High-Throughput Pathway Inference
    Annals of the New York Academy of Sciences, Vol. 1115, No. 1. (December 2007), pp. 1-22.
    by Gustavo Stolovitzky, Don Monroe, Andrea Califano
    posted to actex reverse_engineering by tmmurali on 2007-12-24 17:27:05 as ***** along with 2 people jyuh roys
  • The properties of high-dimensional data spaces: implications for exploring gene and protein expression data
    Nat Rev Cancer, Vol. 8, No. 1. (January 2008), pp. 37-49.
    by Robert Clarke, Habtom W Ressom, Antai Wang, Jianhua Xuan, Minetta C Liu, Edmund A Gehan, Yue Wang
    posted to data_integration gene_expression_mining by tmmurali on 2007-12-21 15:24:06 as ***** along with 8 people and 1 group brianb jyuh dwf frohike cjeans nedwards shikin blackm0k Bioinformatics
  • Transcription regulation by bacteriophage T4 AsiA
    Protein Expression and Purification, Vol. 41, No. 1. (May 2005), pp. 1-8.
    by Leonid Minakhin, Konstantin Severinov
    posted to actex_phage by tmmurali on 2007-12-20 23:29:42 as *****
  • Quantitative systems-level determinants of human genes targeted by successful drugs
    Genome Res. (14 December 2007), gr.6888208.
    by Lixia Yao, Andrey Rzhetsky
    posted to drug-prioritisation by tmmurali on 2007-12-20 20:06:36 as ***** along with 2 people jfr caseybrown
  • Global Changes in Cellular Gene Expression during Bacteriophage PRD1 Infection.
    J Virol, Vol. 80, No. 16. (August 2006), pp. 8081-8088.
    by MM Poranen, JJ Ravantti, AM Grahn, R Gupta, P Auvinen, DH Bamford
    posted to actex_phage by tmmurali on 2007-12-20 17:41:12 as ***** along with 1 person Terkko
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