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tmmurali's library [318 articles]

Recent papers added to tmmurali's library.
  • 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 1 person 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 *****
  • A relationship between gene expression and protein interactions on the proteome scale: analysis of the bacteriophage T7 and the yeast Saccharomyces cerevisiae.
    Nucleic Acids Res, Vol. 29, No. 17. (1 September 2001), pp. 3513-3519.
    by A Grigoriev
    posted to actex_phage by tmmurali on 2008-05-10 17:25:35 as ** along with 2 people gurkanbebek kintoki
  • Toward an AIDS Vaccine
    Science, Vol. 320, No. 5877. (9 May 2008), pp. 760-764.
    by Bruce D Walker, Dennis R Burton
    posted to host-pathogen by tmmurali on 2008-05-09 15:25:53 as ** along with 1 person becarmson
  • 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 *****
  • Stromal gene expression predicts clinical outcome in breast cancer
    Nat Med, Vol. 14, No. 5. (May 2008), pp. 518-527.
    by Greg Finak, Nicholas Bertos, Francois Pepin, Svetlana Sadekova, Margarita Souleimanova, Hong Zhao, Haiying Chen, Gulbeyaz Omeroglu, Sarkis Meterissian, Atilla Omeroglu, Michael Hallett, Morag Park
    posted to dataset-gene-expression-cancer cancer_classification by tmmurali on 2008-05-07 20:40:32 as **
  • Detecting cis-regulatory binding sites for cooperatively binding proteins
    Nucl. Acids Res., Vol. 36, No. 8. (1 May 2008), e46.
    by Liesbeth van Oeffelen, Pierre Cornelis, Wouter Van Delm, Fedor De Ridder, Bart De Moor, Yves Moreau
    posted to transcription-modules by tmmurali on 2008-05-06 14:27:20 as ** along with 2 people idonaldson maximilianh
  • 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 23 people jago Ema gtgt15 hryk nedwards i-stevenson pinney elsantosneto markusd eyliu craigwilson06 jyuh margaritis gagliol bryanhughes akshat cactus AbnerCYH tny briordan deanmalmgren soramame_0518 jjray
  • 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 *****
  • Stability puzzles in phage lambda.
    Physical review. E, Statistical, nonlinear, and soft matter physics, Vol. 65, No. 5 Pt 1. (May 2002)
    by E Aurell, S Brown, J Johanson, K Sneppen
    posted to actex_phage by tmmurali on 2008-04-28 03:19:54 as **
  • Real-time monitoring of single bacterium lysis and leakage events by chemiluminescence microscopy.
    Analytical chemistry, Vol. 79, No. 14. (15 July 2007), pp. 5373-5381.
    by Y Zhang, GJ Phillips, ES Yeung
    posted to actex_phage by tmmurali on 2008-04-28 03:18:34 as **
  • BicOverlapper: A tool for bicluster visualization
    Bioinformatics, Vol. 24, No. 9. (1 May 2008), pp. 1212-1213.
    by Rodrigo Santamaria, Roberto Theron, Luis Quintales
    posted to biclustering by tmmurali on 2008-04-25 13:51:52 as **
  • Using a logical model to predict the growth of yeast
    BMC Bioinformatics, Vol. 9 (12 February 2008), 97.
    by KE Whelan, RD King
    posted to actex by tmmurali on 2008-04-23 06:54:19 as ** along with 1 person heliopais
  • A Systems Approach to Mapping DNA Damage Response Pathways
    Science, Vol. 312, No. 5776. (19 May 2006), pp. 1054-1059.
    by Christopher T Workman, Craig H Mak, Scott Mccuine, Jean-Bosco Tagne, Maya Agarwal, Owen Ozier, Thomas J Begley, Leona D Samson, Trey Ideker
    posted to transcriptional_regulatory_networks actex by tmmurali on 2008-04-23 06:29:29 as ** along with 5 people biozhang2001 jfr nirfriedman cconboy koller
  • Discrimination of Direct and Indirect Interactions in a Network of Regulatory Effects
    Journal of Computational Biology, Vol. 14, No. 9. (2007), pp. 1217-1228.
    by Achim Tresch, T Beissbarth, H Sultmann, R Kuner, A Poustka, A Buness
    posted to actex reverse_engineering by tmmurali on 2008-04-20 21:23:04 as **
  • The Chemical Genomic Portrait of Yeast: Uncovering a Phenotype for All Genes
    Science, Vol. 320, No. 5874. (18 April 2008), pp. 362-365.
    by Maureen E Hillenmeyer, Eula Fung, Jan Wildenhain, Sarah E Pierce, Shawn Hoon, William Lee, Michael Proctor, St, Mike Tyers, Daphne Koller, Russ B Altman, Ronald W Davis, Corey Nislow, Guri Giaever
    posted to dataset_chemical_genomics by tmmurali on 2008-04-18 18:59:35 as ** along with 4 people and 1 group lp2 bala stajich nfreed Berkeley Mycology
  • Bayesian network analysis of signaling networks: a primer.
    Sci STKE, Vol. 2005, No. 281. (26 April 2005)
    by D Pe'er
    posted to actex reverse_engineering by tmmurali on 2008-04-17 17:08:41 as ** along with 4 people Borelli ryang wnpx jhatrimatri
  • Positional gene enrichment analysis of gene sets for high-resolution identification of overrepresented chromosomal regions.
    Nucleic Acids Res (16 March 2008)
    by Katleen De Preter, Roland Barriot, Frank Speleman, Jo Vandesompele, Yves Moreau
    posted to functional_enrichment by tmmurali on 2008-04-17 15:22:32 as **** along with 2 people and 1 group frohike bootsy Bioinformatics
  • Parameter Identifiability and Estimation of HIV/AIDS Dynamic Models.
    Bulletin of mathematical biology, Vol. 70, No. 3. (April 2008), pp. 785-799.
    by H Wu, H Zhu, H Miao, AS Perelson
    posted to actex host-pathogen by tmmurali on 2008-04-17 02:43:35 as **
  • Modeling and simulation of genetic regulatory systems: a literature review.
    J Comput Biol, Vol. 9, No. 1. (2002), pp. 67-103.
    by H de Jong
    posted to actex by tmmurali on 2008-04-17 02:42:05 as ** along with 14 people and 3 groups eldan bayesian balicea Happybene wnpx kengg noano sstoma josepe dagmar jo_davies roys maburkitt kentz VirtualPlants Plantandetc compneur
  • Combinatorial synthesis of genetic networks.
    Science, Vol. 296, No. 5572. (24 May 2002), pp. 1466-1470.
    by CC Guet, MB Elowitz, W Hsing, S Leibler
    posted to actex by tmmurali on 2008-04-17 02:37:17 as ** along with 5 people rklancer monod jjray johncumbers dbikard
  • A map of human protein interactions derived from co-expression of human mRNAs and their orthologs
    Mol Syst Biol, Vol. 4 (15 April 2008)
    by Arun K Ramani, Zhihua Li, Traver G Hart, Mark W Carlson, Daniel R Boutz, Edward M Marcotte
    posted to dataset_interactions ppi_network ppi-prediction by tmmurali on 2008-04-16 21:21:37 as ** along with 4 people and 1 group ardalby giovanni biomcgary phoenixzxl OPIG
  • Evolvability and hierarchy in rewired bacterial gene networks
    Nature, Vol. 452, No. 7189. (17 April 2008), pp. 840-845.
    by Mark Isalan, Caroline Lemerle, Konstantinos Michalodimitrakis, Carsten Horn, Pedro Beltrao, Emanuele Raineri, Mireia Garriga-Canut, Luis Serrano
    posted to actex transcriptional_regulatory_networks by tmmurali on 2008-04-16 21:20:44 as ** along with 12 people and 3 groups hryk margaritis cactus dbikard Garamonfok caseybrown biehl aalibes dullhunk neils cmzmasek josedavid SynBioSys Centre de Recherches Interdisciplinaires GEB
  • Artificial gene networks for objective comparison of analysis algorithms.
    Bioinformatics, Vol. 19 Suppl 2 (October 2003)
    by P Mendes, W Sha, K Ye
    posted to actex reverse_engineering by tmmurali on 2008-04-16 08:00:12 as ** along with 4 people and 2 groups camster dragonrez lfriedl pmendes dbk-lab kdl
  • Plasticity of the cis-Regulatory Input Function of a Gene.
    PLoS Biol, Vol. 4, No. 4. (April 2006)
    by AE Mayo, Y Setty, S Shavit, A Zaslaver, U Alon
    posted to actex transcriptional_regulatory_networks by tmmurali on 2008-04-16 04:47:43 as ** along with 4 people and 1 group rklancer stevanspringer bayesian discreteonyxorb FAB-lab
  • An ontology for a Robot Scientist.
    Bioinformatics, Vol. 22, No. 14. (15 July 2006)
    by LN Soldatova, A Clare, A Sparkes, RD King
    posted to actex by tmmurali on 2008-04-16 04:13:40 as **
  • Linking functionally related genes by sensitive and quantitative characterization of genetic interaction profiles
    Proceedings of the National Academy of Sciences, Vol. 105, No. 15. (15 April 2008), pp. 5821-5826.
    by Laurence Decourty, Cosmin Saveanu, Kenza Zemam, Florence Hantraye, Emmanuel Frachon, Jean-Claude Rousselle, Micheline Fromont-Racine, Alain Jacquier
    posted to dataset_interactions genetic_interactions by tmmurali on 2008-04-15 21:16:20 as **
  • From the Cover: Magnesium deficiency accelerates cellular senescence in cultured human fibroblasts
    Proceedings of the National Academy of Sciences, Vol. 105, No. 15. (15 April 2008), pp. 5768-5773.
    by David W Killilea, Bruce N Ames
    posted to aging by tmmurali on 2008-04-15 21:14:42 as **
  • Defining genetic interaction
    Proceedings of the National Academy of Sciences, Vol. 105, No. 9. (4 March 2008), pp. 3461-3466.
    by Ramamurthy Mani, St, John L Hartman, Guri Giaever, Frederick P Roth
    posted to genetic_interactions by tmmurali on 2008-04-13 04:27:46 as ** along with 1 person caseybrown
  • 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 2 people jyuh jiny
  • Context-sensitive data integration and prediction of biological networks
    Bioinformatics, Vol. 23, No. 17. (1 September 2007), pp. 2322-2330.
    by Chad L Myers, Olga G Troyanskaya
    posted to network-inference reverse_engineering by tmmurali on 2008-04-13 03:07:23 as ** along with 6 people jyuh rdiaz grahamc iris_2001 nedwards shung
  • Adaptively inferring human transcriptional subnetworks.
    Mol Syst Biol, Vol. 2 (2006)
    by D Das, Z Nahlé, MQ Zhang
    posted to transcriptional_regulatory_networks by tmmurali on 2008-04-12 21:49:50 as ** along with 4 people wnpx Ao_Li2007 kmdaily heliopais
  • 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 *****
  • Computational identification of cellular networks and pathways.
    Mol Biosyst, Vol. 3, No. 7. (July 2007), pp. 478-482.
    by F Markowetz, OG Troyanskaya
    posted to active-networks reverse_engineering by tmmurali on 2008-04-12 17:28:00 as ** along with 1 person jyuh
  • 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
  • Rapid comparative genomic analysis for clinical microbiology: The Francisella tularensis paradigm
    Genome Res. (11 April 2008), gr.071266.107.
    by Bernard La Scola, Khalid Elkarkouri, Wenjun Li, Tara Wahab, Ghislain Fournous, Jean-Marc Rolain, Silpak Biswas, Michel Drancourt, Catherine Robert, Stephane Audic, Sven Lofdahl, Didier Raoult
    posted to host-pathogen by tmmurali on 2008-04-11 21:58:02 as **
  • Fitting a Geometric Graph to a Protein-Protein Interaction Network.
    Bioinformatics (14 March 2008)
    by Desmond J J Higham, Marija Rasajski, Natasa Przulj
    posted to network-models by tmmurali on 2008-04-11 15:32:47 as **** along with 7 people jyuh AbnerCYH grahamc bootsy maralena scienbox lidaiqiang1981
  • 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
  • MicroRNAs accurately identify cancer tissue origin.
    Nat Biotechnol (23 March 2008)
    by Nitzan Rosenfeld, Ranit Aharonov, Eti Meiri, Shai Rosenwald, Yael Spector, Merav Zepeniuk, Hila Benjamin, Norberto Shabes, Sarit Tabak, Asaf Levy, Danit Lebanony, Yaron Goren, Erez Silberschein, Nurit Targan, Alex Ben-Ari, Shlomit Gilad, Netta Sion-Vardy, Ana Tobar, Meora Feinmesser, Oleg Kharenko, Ofer Nativ, Dvora Nass, Marina Perelman, Ady Yosepovich, Bruria Shalmon, Sylvie Polak-Charcon, Eddie Fridman, Amir Avniel, Isaac Bentwich, Zvi Bentwich, Dalia Cohen, Ayelet Chajut, Iris Barshack
    posted to microrna_cancer by tmmurali on 2008-04-08 21:33:39 as **** along with 5 people ealloza jyuh giovenko jdiezperezj maralena
  • Discovering microRNAs from deep sequencing data using miRDeep
    Nature Biotechnology, Vol. 26, No. 4., pp. 407-415.
    by Marc R Friedländer, Wei Chen, Catherine Adamidi, Jonas Maaskola, Ralf Einspanier, Signe Knespel, Nikolaus Rajewsky
    posted to microrna by tmmurali on 2008-04-08 21:32:40 as **** along with 2 people and 1 group stajich giovanni Berkeley Mycology
  • 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
  • Chemical Coevolution: Host-Parasite Arms Race Runs Hot and Cold
    Current Biology, Vol. 18, No. 7. (8 April 2008), pp. R306-R308.
    by Duncan E Jackson
    posted to host-pathogen by tmmurali on 2008-04-08 15:51:51 as *
  • Bacteria Subsisting on Antibiotics
    Science, Vol. 320, No. 5872. (4 April 2008), pp. 100-103.
    by Gautam Dantas, Morten O Sommer, Rantimi D Oluwasegun, George M Church
    posted to host-pathogen by tmmurali on 2008-04-04 15:03:30 as ** along with 6 people operon madhadron gvdh kjglennie melting osilander
  • ARACNE: an algorithm for the reconstruction of gene regulatory networks in a mammalian cellular context.
    BMC Bioinformatics, Vol. 7 Suppl 1 (2006)
    by AA Margolin, I Nemenman, K Basso, C Wiggins, G Stolovitzky, R Dalla Favera, A Califano
    posted to reverse_engineering by tmmurali on 2008-04-04 04:15:17 as *** along with 5 people kentsis jfr shigepong natstreet heliopais
  • 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 3 people 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 11 people gracio schuylrp jyuh Borelli jwdietrich frohike bootsy nedwards roys mclarenv phoenixzxl
  • Large-scale screening for novel low-affinity extracellular protein interactions
    Genome Res. (22 February 2008), gr.7187808.
    by Mark K Bushell, Christian Sollner, Benjamin Schuster-Boeckler, Alex Bateman, Gavin J Wright
    posted to ppi_network by tmmurali on 2008-04-01 19:30:00 as ** along with 7 people kluck niallhaslam jyuh neils Dualsystems grahamc 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 *****
  • 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 3 people jyuh zwang ptrobajo
  • Reverse-engineering transcription control networks
    Physics of Life Reviews, Vol. 2, No. 1. (March 2005), pp. 65-88.
    by Timothy S Gardner, Jeremiah J Faith
    posted to reverse_engineering by tmmurali on 2008-03-29 00:01:02 as ** along with 2 people rklancer heliopais
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