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phoenixzxl's library [119 articles]

最近录入 phoenixzxl's 文献库.
  • GridCell: a stochastic particle-based biological system simulator
    BMC Systems Biology, Vol. 2, No. 1. (2008)
    by Laurier Boulianne, Sevin A Assaad, Michel Dumontier, Warren Gross
    posted to simulation by phoenixzxl on 2008-07-24 02:55:24 as **
  • Cooperativity and biological complexity
    Nat Chem Biol, Vol. 4, No. 8. (2008), pp. 435-439.
    by Adrian Whitty
    posted to cooperativity by phoenixzxl on 2008-07-23 07:58:57 as *** along with 1 person paulschlesinger
  • Cooperativity in macromolecular assembly
    Nat Chem Biol, Vol. 4, No. 8. (2008), pp. 458-465.
    by James R Williamson
    posted to cooperativity assembly by phoenixzxl on 2008-07-23 07:55:40 as **** along with 1 person paulschlesinger
  • Stochastic dynamics of macromolecular-assembly networks.
    Mol Syst Biol, Vol. 2 (2006)
    by L Saiz, JM Vilar
    posted to network_dynamic dynamics assembly by phoenixzxl on 2008-07-23 07:51:30 as **** along with 1 person wilsoros
  • Message-Passing Algorithms for the Prediction of Protein Domain Interactions from Protein-Protein Interaction Data
    Bioinformatics (17 July 2008), btn366.
    by Mudassar Iqbal, Alex A Freitas, Colin G Johnson, Massimo Vergassola
    posted to prediction_ddi by phoenixzxl on 2008-07-21 07:20:25 as *** along with 1 person iris_2001
  • A Dominant Conformational Role for Amino Acid Diversity in Minimalist Protein-Protein Interfaces
    Journal of Molecular Biology, Vol. 381, No. 2. (29 August 2008), pp. 407-418.
    by Ryan N Gilbreth, Kaori Esaki, Akiko Koide, Sachdev S Sidhu, Shohei Koide
    posted to prediction_interface by phoenixzxl on 2008-07-18 02:47:47 as ** along with 2 people mapplab zwang
  • Cross-species de novo identification of cis-regulatory modules with GibbsModule: application to gene regulation in embryonic stem cells
    Genome Res. (15 May 2008), gr.072769.107.
    by Dan Xie, Jun Cai, Na-Yu Chia, Huck Ng, Sheng Zhong
    posted to synthetic_biology by phoenixzxl on 2008-07-16 07:29:32 as ** along with 4 people isimpson GustavoLacerda ihpark idonaldson
  • Analyzing Protein Interaction Networks Using Structural Information
    Annual Review of Biochemistry, Vol. 77, No. 1. (2008)
    by Christina Kiel, Pedro Beltrao, Luis Serrano
    posted to structure_aided network_ppi by phoenixzxl on 2008-07-16 02:09:43 as **** along with 5 people zwang paolomarcatili grahamc neils Evangelia
  • Integrating Diverse Data for Structure Determination of Macromolecular Assemblies.
    Annu Rev Biochem (4 March 2008)
    by Frank Alber, Friedrich Förster, Dmitry Korkin, Maya Topf, Andrej Sali
    posted to review data_integration complex by phoenixzxl on 2008-07-16 02:08:04 as **** along with 1 person chad_davis
  • Seeded Bayesian Networks: constructing genetic networks from microarray data
    BMC Systems Biology, Vol. 2, No. 1. (2008)
    by Amira Djebbari, John Quackenbush
    posted to bayesian by phoenixzxl on 2008-07-08 07:06:08 as ** along with 3 people jyuh beete renatomilani
  • A stringent test for hydrophobicity scales: Two proteins with 88% sequence identity but different structure and function
    Proceedings of the National Academy of Sciences (30 June 2008), 0803264105.
    by Alexander E Kister, James C Phillips
    posted to prediction_structure insight by phoenixzxl on 2008-07-01 02:04:44 as *** along with 1 person bcondon
  • Predicting protein function from domain content
    Bioinformatics (30 June 2008), btn312.
    by Kristoffer Forslund, Erik L Sonnhammer
    posted to prediction_function by phoenixzxl on 2008-07-01 01:58:09 as ** along with 2 people reyez zwang
  • Optimization in computational systems biology
    BMC Systems Biology, Vol. 2, No. 1. (2008)
    by Julio Banga
    posted to system_biology insight by phoenixzxl on 2008-06-30 01:35:09 as *** along with 5 people balicea biehl reyez jrbanga tmmurali
  • Assessing the limits of genomic data integration for predicting protein networks.
    Genome Res, Vol. 15, No. 7. (July 2005), pp. 945-953.
    by LJ Lu, Y Xia, A Paccanaro, H Yu, M Gerstein
    posted to network_ppi insight data_integration by phoenixzxl on 2008-06-28 09:13:00 as **** along with 13 people and 2 groups carlk brianb iris_2001 okarsligil lfriedl balajis maryee opheliav wnpx mbeautru eukfn grahamc nedwards kdl Bioinformatics
  • A Genome-wide Ras-Effector Interaction Network.
    J Mol Biol (22 May 2007)
    by Christina Kiel, Mathilde Foglierini, Nico Kuemmerer, Pedro Beltrao, Luis Serrano
    posted to specificity prediction_ddi by phoenixzxl on 2008-06-28 08:58:28 as ** along with 1 person cjeans
  • Assembly reflects evolution of protein complexes
    Nature (18 June 2008)
    by Emmanuel D Levy, Elisabetta B Erba, Carol V Robinson, Sarah A Teichmann
    posted to evolution complex by phoenixzxl on 2008-06-27 12:06:08 as *** along with 7 people marck faion psique zwang jwm neils paulschlesinger
  • Protein Design by Directed Evolution
    Annual Review of Biophysics, Vol. 37, No. 1. (2008), pp. 153-173.
    by Christian Jackel, Peter Kast, Donald Hilvert
    posted to synthetic_biology review protein_design by phoenixzxl on 2008-06-25 08:26:36 as ** along with 1 person zwang
  • A theoretical framework for specificity in cell signaling
    Molecular Systems Biology, Vol. 1, No. 1. (18 October 2005), pp. msb4100031-E1-msb4100031-E5.
    by Natalia L Komarova, Xiufen Zou, Qing Nie, Lee Bardwell
    posted to specificity by phoenixzxl on 2008-06-24 07:24:12 as **** along with 1 person and 1 group arne dIEMoSIRIS
  • BADASP: predicting functional specificity in protein families using ancestral sequences.
    Bioinformatics, Vol. 21, No. 22. (15 November 2005), pp. 4190-4191.
    by RJ Edwards, DC Shields
    posted to specificity prediction_function by phoenixzxl on 2008-06-24 07:23:42 as ** along with 1 person dlr
  • Mathematical models of specificity in cell signaling.
    Biophys J, Vol. 92, No. 10. (15 May 2007), pp. 3425-3441.
    by L Bardwell, X Zou, Q Nie, NL Komarova
    posted to specificity by phoenixzxl on 2008-06-24 07:22:37 as ** along with 3 people and 1 group jtaylor ibschwartz arne dIEMoSIRIS
  • Automated design of specificity in molecular recognition.
    Nat Struct Biol, Vol. 10, No. 1. (January 2003), pp. 45-52.
    by JJ Havranek, PB Harbury
    posted to specificity protein_design coiled_coil by phoenixzxl on 2008-06-24 02:54:54 as *** along with 1 person bethbromley
  • Design of Multi-Specificity in Protein Interfaces
    PLoS Computational Biology, Vol. 3, No. 8. (1 August 2007), e164.
    by Elisabeth L Humphris, Tanja Kortemme
    posted to synthetic_biology specificity prediction_interface by phoenixzxl on 2008-06-23 11:03:15 as ** along with 6 people and 3 groups marck jwm bicko Einat dpollard Scis0000002 structural_bioinformatics Bioinformatics EisenLab
  • Specificity and Evolvability in Eukaryotic Protein Interaction Networks
    PLoS Computational Biology, Vol. 3, No. 2. (1 February 2007), e25.
    by Pedro Beltrao, Luis Serrano
    posted to specificity network_ppi network_evolution by phoenixzxl on 2008-06-23 10:57:55 as *** along with 1 person pedrobeltrao
  • Phylogeny-Aware Gap Placement Prevents Errors in Sequence Alignment and Evolutionary Analysis
    Science, Vol. 320, No. 5883. (20 June 2008), pp. 1632-1635.
    by Ari Loytynoja, Nick Goldman
    posted to sequence_alignment evolution by phoenixzxl on 2008-06-20 04:08:46 as **** along with 16 people and 1 group bpcusack bmaust gulsacan Schmidtc bpb zwang aprasad imtechnology marck ArtemPankin djkt gjuggler hpaces dinnes chad_davis jago Khavkin's lab
  • Progress and challenges in protein structure prediction
    Current Opinion in Structural Biology, Vol. 18, No. 3. (June 2008), pp. 342-348.
    by Yang Zhang
    posted to prediction_structure by phoenixzxl on 2008-06-17 13:08:55 as ** along with 2 people zwang marck
  • Structural specificity in coiled-coil interactions
    Current Opinion in Structural Biology, Vol. In Press, Corrected Proof
    by Gevorg Grigoryan, Amy E Keating
    posted to specificity coiled_coil by phoenixzxl on 2008-06-17 02:24:31 as ** along with 2 people zwang marck
  • Whole-cell simulation: a grand challenge of the 21st century.
    Trends Biotechnol, Vol. 19, No. 6. (June 2001), pp. 205-210.
    by M Tomita
    posted to simulation by phoenixzxl on 2008-06-16 08:42:07 as ***** along with 4 people wnpx Doug josepe fishtank
  • Modeling and simulation of genetic regulatory systems: a literature review.
    Journal of Computational Biology, Vol. 9, No. 1. (2002), pp. 67-103.
    by Hidde de Jong
    posted to simulation by phoenixzxl on 2008-06-16 08:40:38 as **** along with 14 people and 3 groups eldan tmmurali bayesian balicea Happybene wnpx kengg noano sstoma josepe dagmar jo_davies roys maburkitt VirtualPlants Plantandetc compneur
  • Implications from a Network-Based Topological Analysis of Ubiquitin Unfolding Simulations
    PLoS ONE, Vol. 3, No. 5. (14 May 2008), e2149.
    by Arun Krishnan, Alessandro Giuliani, Joseph P Zbilut, Masaru Tomita
    posted to simulation by phoenixzxl on 2008-06-16 08:05:33 as ** along with 1 person zwang
  • Simulation for Continuous-time Markov Chains
    (2002)
    by C Baier, J Katoen, H Hermanns, B Haverkort
    posted to simulation by phoenixzxl on 2008-06-16 08:03:38 as ** along with 1 person znmeb
  • A study of communication pathways in methionyl- tRNA synthetase by molecular dynamics simulations and structure network analysis
    Proceedings of the National Academy of Sciences, Vol. 104, No. 40. (2 October 2007), pp. 15711-15716.
    by Amit Ghosh, Saraswathi Vishveshwara
    posted to simulation by phoenixzxl on 2008-06-16 08:02:50 as ** along with 3 people and 1 group zwang cactus sobolevnrm baker-group
  • Dynamic Properties of Network Motifs Contribute to Biological Network Organization.
    PLoS Biol, Vol. 3, No. 11. (4 October 2005)
    by Robert J J Prill, Pablo A A Iglesias, Andre Levchenko
    posted to network_motif by phoenixzxl on 2008-06-10 15:29:16 as ** along with 10 people and 1 group marck tmmurali monod textoris bayesian luispedro xinian jdiggans watson stefanoallesina NeuralNetworks
  • A review on models and algorithms for motif discovery in protein-protein interaction networks
    Brief Funct Genomic Proteomic (28 April 2008), eln015.
    by Giovanni Ciriello, Concettina Guerra
    posted to network_ppi network_motif by phoenixzxl on 2008-06-10 13:34:50 as **
  • How to succeed in science: a concise guide for young biomedical scientists. Part II: making discoveries.
    Nature reviews. Molecular cell biology (10 April 2008)
    by Jonathan W W Yewdell
    posted to others by phoenixzxl on 2008-06-07 02:12:58 as **** along with 5 people sci91078 renatomilani iramjohn tayzerhouse05 jyuh
  • How to succeed in science: a concise guide for young biomedical scientists. Part I: taking the plunge
    Nat Rev Mol Cell Biol, Vol. 9, No. 5. (May 2008), pp. 413-416.
    by Jonathan W Yewdell
    posted to others by phoenixzxl on 2008-06-07 02:11:00 as **** along with 9 people and 1 group sci91078 kengg sobolevnrm iramjohn tayzerhouse05 jyuh bmaust GeeSharpMinor lp2 baker-group
  • Detection of topological patterns in complex networks: correlation profile of the internet
    Physica A: Statistical and Theoretical Physics, Vol. 333 (15 February 2004), pp. 529-540.
    by Sergei Maslov, Kim Sneppen, Alexei Zaliznyak
    posted to network_motif network_dynamic by phoenixzxl on 2008-06-06 08:06:21 as ** along with 2 people gcalda cjeans
  • Network motif analysis of a multi-mode genetic-interaction network
    Genome Biology, Vol. 8 (02 August 2007), R160.
    by James R Taylor, Andrew F Siegel, Timothy Galitski
    posted to network_motif by phoenixzxl on 2008-06-03 11:08:50 as ** along with 3 people marck tmmurali maralena
  • Coevolution at protein complex interfaces can be detected by the complementarity trace with important impact for predictive docking.
    Proceedings of the National Academy of Sciences of the United States of America (29 May 2008)
    by Hocine Madaoui, Raphaël Guerois
    posted to prediction_interface complex co-evolution by phoenixzxl on 2008-06-03 07:10:50 as ** along with 3 people chad_davis bicko cabbagesofdoom
  • Efficient functional clustering of protein sequences using the Dirichlet process
    Bioinformatics (29 May 2008), btn244.
    by Duncan P Brown
    posted to others by phoenixzxl on 2008-06-02 07:31:47 as **
  • Predicting protein-protein interactions based only on sequences information
    PNAS, Vol. 104, No. 11. (13 March 2007), pp. 4337-4341.
    by Juwen Shen, Jian Zhang, Xiaomin Luo, Weiliang Zhu, Kunqian Yu, Kaixian Chen, Yixue Li, Hualiang Jiang
    posted to svm prediction_ppi by phoenixzxl on 2008-05-30 08:01:01 as ** along with 5 people and 1 group samjlord Dualsystems ruvido cjeans huyun110 moernerlab
  • Using support vector machine combined with auto covariance to predict protein-protein interactions from protein sequences
    Nucl. Acids Res. (4 April 2008), gkn159.
    by Yanzhi Guo, Lezheng Yu, Zhining Wen, Menglong Li
    posted to svm prediction_ppi by phoenixzxl on 2008-05-23 02:57:16 as ** along with 4 people zwang marck tmmurali jyuh
  • Evolutionary conservation of domain-domain interactions
    Genome Biology, Vol. 7 (21 December 2006), R125.
    by Zohar Itzhaki, Eyal Akiva, Yael Altuvia, Hanah Margalit
    posted to prediction_ddi evolution by phoenixzxl on 2008-05-16 09:42:25 as *** along with 2 people and 1 group grahamc winterschlaefer ParkinsonLab_at_MaRS
  • 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 statistical prediction_ppi network_evolution evolution by phoenixzxl on 2008-05-13 08:35:44 as ** along with 18 people chad_davis Evangelia balicea marck paolomarcatili sanchezbuelna cabbagesofdoom xingxu mjoach jyuh chrissp100 zwang roys brianb friendpine Ema neils tmmurali
  • Comprehensive inventory of protein complexes in the Protein Data Bank from consistent classification of interfaces
    BMC Bioinformatics, Vol. 9, No. 1. (2008)
    by Andrew Bordner, Andrey Gorin
    posted to prediction_interface data_integration complex by phoenixzxl on 2008-05-13 07:28:04 as *** along with 1 person neils
  • An in Vivo Map of the Yeast Protein Interactome
    Science (8 May 2008), 1153878.
    by Kirill Tarassov, Vincent Messier, Christian R Landry, Stevo Radinovic, Mercedes M Molina, Igor Shames, Yelena Malitskaya, Jackie Vogel, Howard Bussey, Stephen W Michnick
    posted to data by phoenixzxl on 2008-05-12 01:31:12 as ** along with 7 people tmmurali aubinhon grahamc jyuh brianb neils cabbagesofdoom
  • The mismeasurement of science
    Current Biology, Vol. 17, No. 15. (7 August 2007), pp. R583-R585.
    by Peter A Lawrence
    posted to science by phoenixzxl on 2008-05-09 04:08:27 as ** along with 4 people and 1 group ukppdadsr dullhunk madhadron wrowell Cline_lab
  • The evolution of modularity in bacterial metabolic networks
    Proceedings of the National Academy of Sciences (6 May 2008), 0712149105.
    by Anat Kreimer, Elhanan Borenstein, Uri Gophna, Eytan Ruppin
    posted to network_evolution by phoenixzxl on 2008-05-07 01:59:36 as ** along with 11 people carlk mjoach saket qwermish deanmalmgren tmmurali skato_toyaku jjray hryk pinney roys
  • Synthetic gene brushes: a structure-function relationship
    Mol Syst Biol, Vol. 4 (15 April 2008)
    by Amnon Buxboim, Shirley S Daube, Roy Bar-Ziv
    posted to synthetic_biology by phoenixzxl on 2008-04-21 03:14:46 as **
  • Scaffolds, levers, rods and springs: diverse cellular functions of long coiled-coil proteins.
    Cellular and molecular life sciences : CMLS, Vol. 61, No. 16. (August 2004), pp. 1996-2009.
    by A Rose, I Meier
    posted to coiled_coil by phoenixzxl on 2008-04-16 03:19:04 as **
  • 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 data_integration gene_expression prediction_ppi by phoenixzxl on 2008-04-16 02:12:11 as **** along with 7 people and 1 group ptrobajo zwang grahamc ardalby giovanni tmmurali biomcgary OPIG
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