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Tag modeling [979 articles]

Recent papers classified by the tag modeling.
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  • MORPH: Probabilistic Alignment Combined with Hidden Markov Models of cis-Regulatory Modules
    PLoS Computational Biology, Vol. 3, No. 11. (1 November 2007), e216.
    by Saurabh Sinha, Xin He
    posted to alignment hmm modeling module regulatory by zwang on 2007-12-10 04:29:31 as *** along with 7 people and 2 groups ana dpollard cjeans maximilianh hpaces Ema uwe EisenLab cis-regulatory-evolution
  • Simulating replica exchange simulations of protein folding with a kinetic network model
    Proceedings of the National Academy of Sciences, Vol. 104, No. 39. (25 September 2007), pp. 15340-15345.
    by Weihua Zheng, Michael Andrec, Emilio Gallicchio, Ronald M Levy
    posted to folding modeling network protein by zwang on 2007-11-01 02:13:25 as ** along with 1 person Diego_Prada
  • Ensemble modeling for analysis of cell signaling dynamics
    Nature Biotechnology, Vol. 25, No. 9. (10 September 2007), pp. 1001-1006.
    by Lars Kuepfer, Matthias Peter, Uwe Sauer, Jörg Stelling
    posted to dynamics modeling by zwang on 2007-09-14 04:59:00 as **
  • Network-Based Analysis of Affected Biological Processes in Type 2 Diabetes Models
    PLoS Genetics, Vol. 3, No. 6. (1 June 2007), e96.
    by Manway Liu, Arthur Liberzon, Sek W Kong, Weil R Lai, Peter J Park, Isaac S Kohane, Simon Kasif
    posted to modeling network by zwang on 2007-08-29 02:18:26 as * along with 6 people ptrobajo roys tmmurali ajgentles cabbagezs chrisamiller
  • An Evolutionary-Network Model Reveals Stratified Interactions in the V3 Loop of the HIV-1 Envelope
    PLoS Computational Biology, Vol. 3, No. 11. (1 November 2007), e231.
    by Art F Poon, Fraser I Lewis, Sergei L Pond, Simon D Frost
    posted to evolution interaction modeling network protein by zwang on 2007-12-10 04:40:29 as **** along with 1 person gokhan
  • Understanding the limits to generalizability of experimental evolutionary models
    Nature, Vol. 455, No. 7210. (2008), pp. 220-223.
    by Samantha E Forde, Robert E Beardmore, Ivana Gudelj, Sinan S Arkin, John N Thompson, Laurence D Hurst
    posted to modeling evolution by zwang on 2008-09-11 13:04:51 as ** along with 10 people and 1 group qwermish pradiptaray jasonn DanHodson druvus Zephyrus Ema Katje skoddet tmmurali Roswell Cancer Crosstalk
  • A First-Principles Model of Early Evolution: Emergence of Gene Families, Species, and Preferred Protein Folds
    PLoS Computational Biology, Vol. 3, No. 7. (1 July 2007), e139.
    by Konstantin B Zeldovich, Peiqiu Chen, Boris E Shakhnovich, Eugene I Shakhnovich
    posted to evolution folding gene modeling protein specy by zwang on 2007-08-28 07:39:34 as ** along with 6 people and 1 group BioNica grahamc cjeans Jporci farhat biinins ParkinsonLab_at_MaRS
  • The Functional Genomics Experiment model (FuGE): an extensible framework for standards in functional genomics
    Nat Biotech, Vol. 25, No. 10. (October 2007), pp. 1127-1133.
    by Andrew R Jones, Michael Miller, Ruedi Aebersold, Rolf Apweiler, Catherine A Ball, Alvis Brazma, James Degreef, Nigel Hardy, Henning Hermjakob, Simon J Hubbard, Peter Hussey, Mark Igra, Helen Jenkins, Randall K Julian, Kent Laursen, Stephen G Oliver, Norman W Paton, Susanna-Assunta Sansone, Ugis Sarkans, Christian J Stoeckert, Chris F Taylor, Patricia L Whetzel, Joseph A White, Paul Spellman, Angel Pizarro
    posted to function genome insilico modeling by zwang on 2007-10-11 17:03:39 as ** along with 4 people and 1 group guhjy jfr alanrw fgibson GelML
  • A modular network model of aging
    Mol Syst Biol, Vol. 3 (4 December 2007)
    by Huiling Xue, Bo Xian, Dong Dong, Kai Xia, Shanshan Zhu, Zhongnan Zhang, Lei Hou, Qingpeng Zhang, Yi Zhang, Jing-Dong J Han
    posted to modeling network by zwang on 2007-12-05 10:50:12 as ** along with 11 people and 1 group carlfulp cerca tharris tmmurali muraken grahamc cjeans biehl mingzhi renatomilani dap5087 C. elegans / WormBase
  • The Ascent of the Abundant: How Mutational Networks Constrain Evolution
    PLoS Comput Biol, Vol. 4, No. 7. (18 July 2008), e1000110.
    by Matthew C Cowperthwaite, Evan P Economo, William R Harcombe, Eric L Miller, Lauren A Meyers
    posted to evolution modeling mutation network rna by zwang on 2008-07-22 06:59:06 as ** along with 6 people Ema djkt friendpine biomcgary provero shoshin
  • Biology by numbers: mathematical modelling in developmental biology
    Nat Rev Genet, Vol. 8, No. 5. (May 2007), pp. 331-340.
    by Claire J Tomlin, Jeffrey D Axelrod
    posted to mathematic modeling by zwang on 2007-04-24 15:56:43 as ** along with 1 group Bioinformatics
  • A generative, probabilistic model of local protein structure
    Proceedings of the National Academy of Sciences, Vol. 105, No. 26. (1 July 2008), pp. 8932-8937.
    by Wouter Boomsma, Kanti V Mardia, Charles C Taylor, Jesper Ferkinghoff-Borg, Anders Krogh, Thomas Hamelryck
    posted to modeling protein structure by zwang on 2008-07-02 11:49:14 as * along with 5 people j3xucite bertelsen biehl apaydin mijam
  • Estimating dynamic models for gene regulation networks
    Bioinformatics (27 May 2008), btn246.
    by Jiguo Cao, Hongyu Zhao
    posted to dynamics gene modeling network regulation by zwang on 2008-06-03 04:00:45 as **
  • From Pathways Databases to Network Models of Switching Behavior
    PLoS Computational Biology, Vol. 3, No. 9. (1 September 2007), e152.
    by Baltazar D Aguda, Andrew B Goryachev
    posted to database modeling network pathway by zwang on 2007-11-02 08:00:02 as ** along with 4 people giovenko bayesian julius Ema
  • On State-Space Reduction in Multi-Strain Pathogen Models, with an Application to Antigenic Drift in Influenza A
    PLoS Computational Biology, Vol. 3, No. 8. (1 August 2007), e159.
    by Sergey Kryazhimskiy, Ulf Dieckmann, Simon A Levin, Jonathan Dushoff
    posted to influenza modeling by zwang on 2007-09-03 01:53:41 as * along with 2 people e3bo bpb
  • Mathematical modeling of pathogenicity of Cryptococcus neoformans
    Mol Syst Biol, Vol. 4 (15 April 2008)
    by Jacqueline Garcia, John Shea, Fernando Alvarez-Vasquez, Asfia Qureshi, Chiara Luberto, Eberhard O Voit, Maurizio Del Poeta
    posted to mathematic modeling by zwang on 2008-06-13 12:18:14 as **
  • New models of collaboration in genome-wide association studies: the Genetic Association Information Network
    Nat Genet, Vol. 39, No. 9. (2007), pp. 1045-1051.
    posted to genetic genome-wide modeling network by zwang on 2007-09-05 01:53:35 as * along with 4 people guhjy hpiwowar cabbagezs mfm11
  • Evolutionary models for formation of network motifs and modularity in the Saccharomyces transcription factor network.
    PLoS Comput Biol, Vol. 3, No. 10. (26 October 2007), pp. 1993-2002.
    by JJ Ward, JM Thornton
    posted to evolution modeling motif network transcription yeast by zwang on 2007-11-20 08:52:20 as ** along with 2 people cabbagezs grottenolm
  • Structured analysis approaches for large Markov chains
    Applied Numerical Mathematics: Transactions of IMACS, Vol. 31, No. 4. (1999), pp. 375-404.
    by Peter Buchholz
    posted to kronecker markov modeling by znmeb on 2007-04-23 23:23:20 as ** along with 1 person peg
  • Multiple structural alignment by secondary structures: algorithm and applications.
    Protein Sci, Vol. 12, No. 11. (November 2003), pp. 2492-2507.
    by O Dror, H Benyamini, R Nussinov, HJ Wolfson
    posted to bioinformatics modeling molecular by ziquje on 2005-02-23 16:18:08 as ** along with 2 people dimka analogAI
  • I want a new drug: G-protein-coupled receptors in drug development.
    Drug Discov Today, Vol. 11, No. 11-12. (June 2006), pp. 481-493.
    by S Schlyer, R Horuk
    posted to specificity silico modeling in homology gpcr by zimbo1 on 2008-10-21 11:14:15 as ** along with 1 person and 1 group xdeupi LabCompMed
  • An early history of the molecular modeling industry
    Drug Discovery Today, Vol. In Press, Corrected Proof
    by Allen B Richon
    posted to modeling molecular by zimbo1 on 2008-08-25 08:05:04 as ** along with 1 person middledomain
  • Current status and future direction of the molecular modeling industry
    Drug Discovery Today, Vol. 13, No. 15-16. (August 2008), pp. 665-669.
    by Allen B Richon
    posted to modeling molecular by zimbo1 on 2008-08-25 08:06:15 as **
  • A quantitative description of membrane current and its application to conduction and excitation in nerve.
    J Physiol, Vol. 117, No. 4. (August 1952), pp. 500-544.
    by AL HODGKIN, AF HUXLEY
    posted to action-potential differential-equations modeling neuron by zibdum on 2007-11-19 03:11:10 as **** along with 11 people and 1 group lumiste sylvain_chevallier brocktice mrkrause muraken elferdo suizan lenov mattions kb mdagtek TulaneCEP
  • Bayesian comparison of spatially regularised general linear models
    Human Brain Mapping, Vol. 28, No. 4. (2007), pp. 275-293.
    by Will Penny, Guillaume Flandin, Nelson Trujillo-Barreto
    posted to bayes jc-hbm modeling by zhi1984 on 2007-03-28 16:50:54 as * along with 1 person rwilliamson
  • Evaluating modeling techniques based on models of learning
    Communications of the ACM, Vol. 46, No. 10. (October 2003), pp. 79-84.
    by Andrew Gemino, Yair Wand
    posted to evaluation modeling by zemeigo on 2005-07-27 08:39:04 as **
  • A proposed framework for the analysis and evaluation of business models
    (2004), pp. 210-215.
    by Jean-Paul Van Belle
    posted to evaluation modeling quality by zemeigo on 2005-07-27 08:44:15 as **
  • An Ontological Model of an Information System
    IEEE Trans. Softw. Eng., Vol. 16, No. 11. (November 1990), pp. 1282-1292.
    by Yair Wand, Ron Weber
    posted to information model modeling system by zemeigo on 2005-10-28 11:47:23 as ** along with 3 people rrbarb intention23 balduzzi
  • Performance modeling of optical-burst switching with fiber delay lines
    Communications, IEEE Transactions on, Vol. 52, No. 12. (2004), pp. 2175-2183.
    by Xiaomin Lu, BL Mark
    posted to available balking channel fdl filling latest lauc lauc-vf markov modeling obs queue unscheduled void by ze on 2008-08-08 15:34:35 as read along with 1 person gvb
  • QoS performance of optical burst switching in IP-over-WDM networks
    Selected Areas in Communications, IEEE Journal on, Vol. 18, No. 10. (2000), pp. 2062-2071.
    by Myungsik Yoo, Chunming Qiao, Sudhir Dixit
    posted to switch modeling burst by ze on 2008-09-24 16:37:06 as read
  • Example-based model synthesis
    (2007), pp. 105-112.
    by Paul Merrell
    posted to modeling by yodha on 2007-05-28 07:10:51 as *****
  • notes Modeling and performance analysis of BitTorrent-like peer-to-peer networks
    SIGCOMM Comput. Commun. Rev., Vol. 34, No. 4. (October 2004), pp. 367-378.
    by Dongyu Qiu, R Srikant
    posted to bittorrent modeling by yishuai on 2005-12-29 12:41:57 as ** along with 6 people and 1 group georgiad aliku root p2p-sec jenine fq0520 SITCRC
  • On formal requirements modeling languages: RML revisited
    (1994), pp. 135-147.
    by Sol Greenspan, John Mylopoulos, Alex Borgida
    posted to modeling requirements rml by yijunyu on 2006-12-30 13:15:28 as read
  • Plucked-String Models: From the Karplus-Strong Algorithm to Digital Waveguides and beyond
    Computer Music Journal, Vol. 22, No. 3. (1998), pp. 17-32.
    by Matti Karjalainen, Vesa Välimäki, Tero Tolonen
    posted to modeling physical synthesis by yaxu on 2007-11-29 17:53:25 as read
  • Towards high-quality sound synthesis of the guitar and string instruments
    (1993)
    by M Karjalainen, V Valimaki, Z J'anosy
    posted to modeling physical synthesis by yaxu on 2007-11-29 17:50:54 as *****
  • Physical Modeling of Membranes for Percussion Instruments
    pp. 529-542.
    by Federico Fontana
    posted to modeling physical by yaxu on 2008-01-16 11:49:57 as **** along with 1 person spillage
  • 10 Criteria for Evaluating Physical Modeling Schemes for Music Creation
    (2003)
    by Nicolas Castagne, Claude Cadoz
    posted to modeling physical by yaxu on 2007-11-29 17:30:05 as *****
  • Shape modeling with point-sampled geometry
    ACM Trans. Graph., Vol. 22, No. 3. (July 2003), pp. 641-650.
    by Mark Pauly, Richard Keiser, Leif P Kobbelt, Markus Gross
    posted to geometry modeling point by yalding on 2005-07-25 14:46:06 as ** along with 4 people kutabar krissp cw veal
  • notes Data assimilation (4D-VAR) to forecast flood in shallow-waters with sediment erosion
    Journal of Hydrology, Vol. 300, No. 1-4. (10 January 2005), pp. 114-125.
    by Eric Belanger, Alain Vincent
    posted to assimilation flood modeling by xjlai on 2006-11-27 13:15:11 as **
  • Chaos Theory, Optimal Embedding and Evolutionary Algorithms
    by Viadan Babovic, Maarten Keijzer, Magnus Stefansson
    posted to evolution modeling by xingxu on 2007-08-17 17:32:19 as ** along with 1 person scis0000001
  • Integrative molecular concept modeling of prostate cancer progression
    Nature Genetics, Vol. 39, No. 1. (17 December 2006), pp. 41-51.
    by Scott A Tomlins, Rohit Mehra, Daniel R Rhodes, Xuhong Cao, Lei Wang, Saravana M Dhanasekaran, Shanker Kalyana-Sundaram, John T Wei, Mark A Rubin, Kenneth J Pienta, Rajal B Shah, Arul M Chinnaiyan
    posted to modeling prostate by xingxu on 2007-08-17 16:49:27 as ** along with 6 people ptrobajo kentsis jfr shigepong daed srp33
  • Climate Cycles and Forecasts of Cutaneous Leishmaniasis, a Nonstationary Vector-Borne Disease
    PLoS Medicine, Vol. 3, No. 8. (1 August 2006), e295.
    by Luis F Chaves, Mercedes Pascual
    posted to climate leishmania modeling by xingxu on 2008-01-26 18:18:33 as **
  • Using Likelihood-Free Inference to Compare Evolutionary Dynamics of the Protein Networks of H. pylori and P. falciparum
    PLoS Computational Biology, Vol. 3, No. 11. (1 November 2007), e230.
    by Oliver Ratmann, Ole Jørgensen, Trevor Hinkley, Michael Stumpf, Sylvia Richardson, Carsten Wiuf
    posted to bioinformatics evolution malaria modeling network pylori by xingxu on 2008-01-14 18:04:59 as ** along with 5 people TheresaNiederberger zwang hpaces Ema tresch
  • From classical genetics to quantitative genetics to systems biology: modeling epistasis.
    PLoS genetics, Vol. 4, No. 3. (March 2008)
    by DL Aylor, ZB Zeng
    posted to epistasis modeling quantitative_genetics systems by xingxu on 2008-04-17 12:57:40 as ** along with 2 people Ayest guhjy
  • Gene Network Inference via Structural Equation Modeling in Genetical Genomics Experiments.
    Genetics (3 February 2008)
    by Bing Liu, Alberto de la Fuente, Ina Hoeschele
    posted to epistasis genomics modeling by xingxu on 2008-02-24 03:01:20 as ** along with 6 people and 1 group orzenil dpollard raiyar caseybrown smgomez guhjy EisenLab
  • Pharmacokinetic-pharmacodynamic modeling of the antinociceptive effect of buprenorphine and fentanyl in rats: role of receptor equilibration kinetics.
    J Pharmacol Exp Ther, Vol. 313, No. 3. (June 2005), pp. 1136-1149.
    by A Yassen, E Olofsen, A Dahan, M Danhof
    posted to antinociceptive buprenorphine fentanyl modeling opioid pharmacodynamic pharmacoknetic pk-pd rat by xico on 2007-02-24 02:03:34 as ** along with 1 group WetBiology
  • Structural systems biology: modelling protein interactions
    Nature Reviews Molecular Cell Biology, Vol. 7, No. 3., pp. 188-197.
    by Patrick Aloy, Robert B Russell
    posted to interaction modeling protein structure system by xico on 2006-09-02 00:22:24 as ** along with 19 people and 3 groups ana aalibes bicko dgront drastic choonpeng henschel ruvido massivemayhem cat_worth fishtank iris_2001 gvuister lpfernandes Evangelia andreas_foersch higueruelo chad_davis jteyra structural_bioinformatics Bioinformatics WetBiology
  • notes Protein-Protein Docking with Backbone Flexibility
    Journal of Molecular Biology, Vol. 373, No. 2. (19 October 2007), pp. 503-519.
    by Chu Wang, Philip Bradley, David Baker
    posted to docking flexibility modeling theory by xdeupi on 2008-04-07 14:23:45 as ** along with 4 people and 2 groups csrocha barry jwm Ema structural_bioinformatics Bioinformatics
  • A structure-based simulation approach for electron paramagnetic resonance spectra using molecular and stochastic dynamics simulations.
    Biophys J, Vol. 91, No. 7. (1 October 2006), pp. 2647-2664.
    by C Beier, HJ Steinhoff
    posted to dynamics loops md modeling spin_labeling structure by xdeupi on 2006-10-30 18:37:07 as ** along with 1 group LabCompMed
  • Complex of an active mu-opioid receptor with a cyclic peptide agonist modeled from experimental constraints.
    Biochemistry, Vol. 43, No. 50. (21 December 2004), pp. 15796-15810.
    by CB Fowler, ID Pogozheva, AL Lomize, H LeVine, HI Mosberg
    posted to active-state gproteins modeling opioid structure by xdeupi on 2007-07-11 16:50:15 as ** along with 1 group LabCompMed
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