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Ключевое слово actex [56 articles]

Recent papers classified by the tag actex.
  • 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
  • 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
  • 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
  • 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
  • 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 bottom-up approach to gene regulation
    Nature, Vol. 439, No. 7078. (16 February 2006), pp. 856-860.
    by Nicholas J Guido, Xiao Wang, David Adalsteinsson, David Mcmillen, Jeff Hasty, Charles R Cantor, Timothy C Elston, JJ Collins
    posted to actex by tmmurali on 2008-05-14 20:12:44 as ** along with 14 people and 2 groups rklancer snuppepuppan jyuh okarsligil bayesian balicea samal madhadron balabu johncumbers mmt proulx dbikard nklee Bioinformatics SynBioSys
  • 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
  • Evaluation of different biological data and computational classification methods for use in protein interaction prediction
    Proteins: Structure, Function, and Bioinformatics, Vol. 63, No. 3. (2006), pp. 490-500.
    by Yanjun Qi, Ziv Bar-Joseph, Judith Klein-Seetharaman
    posted to actex ppi-prediction by tmmurali on 2008-01-07 04:19:20 as read along with 2 people and 1 group lfriedl balajis kdl
  • 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
  • Designing biological systems.
    Genes Dev, Vol. 21, No. 3. (1 February 2007), pp. 242-254.
    by DA Drubin, JC Way, PA Silver
    posted to actex synthetic-biology by tmmurali on 2007-12-18 17:49:25 as ** along with 6 people and 1 group choonpeng hslee snowcrash jonsta247 dbikard grahamc SynBioSys
  • Analyzing Pathways Using SAT-Based Approaches
    Algebraic Biology (2007), pp. 155-169.
    by Ashish Tiwari, Carolyn Talcott, Merrill Knapp, Patrick Lincoln, Keith Laderoute
    posted to actex network-dynamics by tmmurali on 2008-01-06 22:06:24 as **
  • 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 5 people saman_vp Borelli ryang wnpx jhatrimatri
  • 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
  • Genetic interactions in yeast: is robustness going bust?
    Mol Syst Biol, Vol. 3 (27 March 2007)
    by Martin Kupiec, Roded Sharan, Eytan Ruppin
    posted to actex genetic_interactions by tmmurali on 2007-12-09 08:10:53 as *****
  • Multiple knockout analysis of genetic robustness in the yeast metabolic network
    Nature Genetics, Vol. 38, No. 9. (29 August 2006), pp. 993-998.
    by David Deutscher, Isaac Meilijson, Martin Kupiec, Eytan Ruppin
    posted to actex genetic_interactions by tmmurali on 2007-12-09 08:21:48 as ** along with 7 people and 1 group koller raiyar cjeans patrycja_missiuro edwardmorrissey hryk jiny steinmetzlab
  • Estimating Maximum Likelihood Parameters for Stochastic Context-Free Graph Grammars
    Inductive Logic Programming (2003), pp. 281-298.
    by Tim Oates, Shailesh Doshi, Fang Huang
    posted to actex graph-grammars by tmmurali on 2008-01-06 18:54:50 as **
  • Systematic pathway analysis using high-resolution fitness profiling of combinatorial gene deletions
    Nature Genetics, Vol. 39, No. 2. (07 January 2007), pp. 199-206.
    by Robert P St Onge, Ramamurthy Mani, Julia Oh, Michael Proctor, Eula Fung, Ronald W Davis, Corey Nislow, Frederick P Roth, Guri Giaever
    posted to actex genetic_interactions by tmmurali on 2008-01-05 07:27:52 as * along with 5 people aalibes wnpx Ao_Li2007 gwcarter raiyar
  • 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
  • Minimal cut sets in biochemical reaction networks.
    Bioinformatics, Vol. 20, No. 2. (22 January 2004), pp. 226-234.
    by S Klamt, ED Gilles
    posted to actex by tmmurali on 2007-12-09 08:54:31 as ** along with 3 people alexg AbnerCYH jiny
  • 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
  • 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
  • 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 *****
  • 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
  • 2020 ComputingExceeding human limits
    Nature, Vol. 440, No. 7083. (22 March 2006), pp. 409-410.
    by Stephen H Muggleton
    posted to actex by tmmurali on 2007-12-17 21:37:22 as ***** along with 4 people ddahlem dullhunk bigbossman nicklynch
  • Modular epistasis in yeast metabolism
    Nature Genetics, Vol. 37, No. 1. (12 December 2004), 77.
    by Daniel Segrè, Alexander Deluna, George M Church, Roy Kishony
    posted to actex genetic_interactions by tmmurali on 2007-12-09 08:11:44 as ** along with 6 people RMGraze balajis i41m nirfriedman koller edwardmorrissey
  • Learning Factor Graphs in Polynomial Time and Sample Complexity
    J. Mach. Learn. Res., Vol. 7 (2006), pp. 1743-1788.
    by Pieter Abbeel, Daphne Koller, Andrew Y Ng
    posted to actex reverse_engineering by tmmurali on 2008-01-06 22:01:06 as **
  • 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 7 people jyuh raiyar oelemento emptyhb megraw roys Borelli
  • 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
  • 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 phoenixzxl VirtualPlants Plantandetc compneur
  • Prediction of phenotype and gene expression for combinations of mutations
    Mol Syst Biol, Vol. 3 (27 March 2007)
    by Gregory W Carter, Susanne Prinz, Christine Neou, Patrick J Shelby, Bruz Marzolf, Vesteinn Thorsson, Timothy Galitski
    posted to actex genetic_interactions by tmmurali on 2008-05-14 19:58:34 as ** along with 5 people balabu nicoleq zwang gwcarter jo_davies
  • 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 **
  • 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
  • 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 actex transcriptional_regulatory_networks by tmmurali on 2008-04-23 06:29:29 as ** along with 5 people biozhang2001 jfr nirfriedman cconboy koller
  • 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
  • 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 **
  • Increasing the Power to Detect Causal Associations by Combining Genotypic and Expression Data in Segregating Populations
    PLoS Computational Biology, Vol. 3, No. 4. (1 April 2007), e69.
    by Jun Zhu, Matthew C Wiener, Chunsheng Zhang, Arthur Fridman, Eric Minch, Pek Y Lum, Jeffrey R Sachs, Eric E Schadt
    posted to actex data_integration reverse_engineering by tmmurali on 2008-07-07 21:18:33 as ** along with 5 people jfr hms jo_davies semrich beete
  • Comparing association network algorithms for reverse engineering of large-scale gene regulatory networks: synthetic versus real data
    Bioinformatics, Vol. 23, No. 13. (1 July 2007), pp. 1640-1647.
    by Nicola Soranzo, Ginestra Bianconi, Claudio Altafini
    posted to actex reverse_engineering by tmmurali on 2008-08-07 19:55:52 as ** along with 2 people heliopais roys
  • 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
  • Programming biomolecular self-assembly pathways
    Nature, Vol. 451, No. 7176. (17 January 2008), pp. 318-322.
    by Peng Yin, Harry M Choi, Colby R Calvert, Niles A Pierce
    posted to actex by tmmurali on 2008-01-17 18:58:42 as ** along with 3 people cjeans cactus austin
  • Metabolic network analysis of the causes and evolution of enzyme dispensability in yeast.
    Nature, Vol. 429, No. 6992. (10 June 2004), pp. 661-664.
    by B Papp, C Pál, LD Hurst
    posted to actex genetic_interactions by tmmurali on 2007-12-09 08:26:54 as ***** along with 5 people bjorns edwardmorrissey stefanoallesina hryk Takayuki
  • 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 *****
  • 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
  • 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
  • The environmental contribution to gene expression profiles
    Nature Reviews Genetics, Vol. 9, No. 8., pp. 575-581.
    by Greg Gibson
    posted to actex gene_expression_mining by tmmurali on 2008-07-18 15:28:03 as *** along with 3 people jmjimenez lp2 jyuh
  • Programming gene expression with combinatorial promoters
    Mol Syst Biol, Vol. 3 (13 November 2007)
    by Robert S Cox, Michael G Surette, Michael B Elowitz
    posted to actex transcription-modules by tmmurali on 2007-12-18 16:48:07 as ** along with 14 people and 2 groups Retchless austin dpollard balicea kengg dbikard margaritis lusk cjeans zwang discreteonyxorb cabbagezs Ema tresch EisenLab SynBioSys
  • 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
  • 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
  • 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
  • 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
  • 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
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