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phoenixzxl library [162 articles]

最近 phoenixzxl ordered by to_read.
  • Higher criticism thresholding: Optimal feature selection when useful features are rare and weak
    Proceedings of the National Academy of Sciences, Vol. 105, No. 39. (2008), pp. 14790-14795.
    by David Donoho, Jiashun Jin
    posted to tutorial machine_learning by phoenixzxl on 2008-10-06 08:37:21 as ** along with 5 people jyuh sschurer rdiaz briordan sg45653
  • Physical protein-protein interactions predicted from microarrays
    Bioinformatics (1 October 2008), btn498.
    by Ta-Tsen Soong, Kazimierz O Wrzeszczynski, Burkhard Rost
    posted to prediction_ppi by phoenixzxl on 2008-10-06 03:16:17 as ** along with 5 people pengchy natstreet grahamc neils renatomilani
  • Bayesian statistical analysis of protein side-chain rotamer preferences.
    Protein Sci, Vol. 6, No. 8. (August 1997), pp. 1661-1681.
    by RL Dunbrack, FE Cohen
    posted to bayesian statistical structure_aided by phoenixzxl on 2008-08-29 03:44:46 as ** along with 12 people and 1 group karbak nknii j3xucite dgront blackbart kazemi rsantana hmk LamBras mijam jwm zwang TCR_Signaling
  • A Brief History of the Hypothesis
    Cell, Vol. 134, No. 3. (8 August 2008), pp. 378-381.
    by David J Glass, Ned Hall
    posted to science by phoenixzxl on 2008-08-29 03:43:30 as ** along with 14 people and 3 groups leonor HugoMarcelo druvus A_Olympia reyez barry paulschlesinger jjray robertlischke chad_davis Enro Zephyrus bpcusack Tominator logics of knowledge Centre de Recherches Interdisciplinaires Roswell Cancer Crosstalk
  • Formation of current coils in geodynamo simulations
    Nature, Vol. 454, No. 7208., pp. 1106-1109.
    by Akira Kageyama, Takehiro Miyagoshi, Tetsuya Sato
    posted to science simulation by phoenixzxl on 2008-08-28 13:05:03 as **
  • Puzzles, promises and a cure for ageing
    Nature, Vol. 454, No. 7208., pp. 1065-1071.
    by Jan Vijg, Judith Campisi
    posted to science by phoenixzxl on 2008-08-28 13:00:42 as ** along with 1 person and 1 group psique parkinson's disease references
  • Design of protein function leaps by directed domain interface evolution
    Proceedings of the National Academy of Sciences (29 April 2008), 0801097105.
    by Jin Huang, Akiko Koide, Koki Makabe, Shohei Koide
    posted to directed_evolution protein_design by phoenixzxl on 2008-08-27 08:23:52 as ** along with 4 people cmzmasek choonpeng zwang marck
  • Improving Subcellular Localization Prediction using Text Classification and the Gene Ontology
    Bioinformatics (26 August 2008), btn463.
    by Alona Fyshe, Yifeng Liu, Duane Szafron, Russ Greiner, Paul Lu
    posted to go localization by phoenixzxl on 2008-08-27 02:08:10 as **
  • Optimal Design of Thermally Stable Proteins
    Bioinformatics (22 August 2008), btn450.
    by Vanitha Suresh, Ryan M Bannen, George N Phillips, Stephen J Wright, Julie C Mitchell
    posted to protein_design structure_aided by phoenixzxl on 2008-08-27 02:04:46 as ** along with 2 people friendpine zwang
  • What is the expectation maximization algorithm?
    Nat Biotech, Vol. 26, No. 8. (2008), pp. 897-899.
    by Chuong B Do, Serafim Batzoglou
    posted to mle by phoenixzxl on 2008-08-15 10:56:14 as ** along with 4 people Tominator GeeSharpMinor jyuh zwang
  • Bringing models to life
    Nature Cell Biology, Vol. 10, No. 8., pp. 876-876.
    by Pierre-François Lenne
    posted to book by phoenixzxl on 2008-08-05 07:39:18 as **
  • A robust approach
    Nature, Vol. 439, No. 7072. (04 January 2006), pp. 19-20.
    by Eörs Szathmáry
    posted to book by phoenixzxl on 2008-08-05 07:38:18 as **
  • A surprising simplicity to protein folding.
    Nature, Vol. 405, No. 6782. (4 May 2000), pp. 39-42.
    by D Baker
    posted to protein by phoenixzxl on 2008-08-05 07:37:58 as ** along with 4 people and 1 group imouthesmp Einat gbart mirzazadeh structural_bioinformatics
  • Life, logic and information
    Nature, Vol. 454, No. 7203. (24 July 2008), pp. 424-426.
    by Paul Nurse
    posted to essay by phoenixzxl on 2008-08-05 04:12:34 as ** along with 5 people dullhunk bayesian reyez fgibson margaritis
  • How complete are current yeast and human protein-interaction networks?
    Genome Biology, Vol. 7 (01 December 2006), 120.
    by Traver G Hart, Arun K Ramani, Edward M Marcotte
    posted to network_ppi by phoenixzxl on 2008-07-31 09:43:17 as ** along with 4 people and 1 group eukfn shikin Pao-Yang carlk GeneGo
  • Correlated sequence-signatures as markers of protein-protein interaction.
    J Mol Biol, Vol. 311, No. 4. (24 August 2001), pp. 681-692.
    by E Sprinzak, H Margalit
    posted to prediction_ddi by phoenixzxl on 2008-07-31 03:23:28 as ** along with 9 people bicko chad_davis maryee dyermd grahamc cjeans lilith wilbur Rhys
  • Pfam: clans, web tools and services.
    Nucleic Acids Res, Vol. 34, No. Database issue. (1 January 2006)
    by RD Finn, J Mistry, B Schuster-Böckler, S Griffiths-Jones, V Hollich, T Lassmann, S Moxon, M Marshall, A Khanna, R Durbin, SR Eddy, EL Sonnhammer, A Bateman
    posted to domain by phoenixzxl on 2008-07-31 03:04:19 as ** along with 10 people gbart dullhunk massivemayhem cjeans siebertm lpfernandes pablomendes antonkratz natstreet Lombardo_7
  • SCOP database in 2004: refinements integrate structure and sequence family data.
    Nucleic Acids Res, Vol. 32, No. Database issue. (1 January 2004)
    by A Andreeva, D Howorth, SE Brenner, TJ Hubbard, C Chothia, AG Murzin
    posted to domain by phoenixzxl on 2008-07-31 03:00:43 as ** along with 3 people tjimenez chad_davis nuke2005
  • Comparative analysis of Saccharomyces cerevisiae WW domains and their interacting proteins.
    Genome biology, Vol. 7, No. 4. (2006)
    by JR Hesselberth, JP Miller, A Golob, JE Stajich, GA Michaud, S Fields
    posted to domain by phoenixzxl on 2008-07-31 02:35:49 as **
  • PDZ Domain Binding Selectivity Is Optimized Across the Mouse Proteome
    Science, Vol. 317, No. 5836. (20 July 2007), pp. 364-369.
    by Michael A Stiffler, Jiunn R Chen, Viara P Grantcharova, Ying Lei, Daniel Fuchs, John E Allen, Lioudmila A Zaslavskaia, Gavin Macbeath
    posted to domain by phoenixzxl on 2008-07-31 02:34:20 as ** along with 2 people zwang carlk
  • Integrating protein-protein interactions and text mining for protein function prediction
    BMC Bioinformatics, Vol. 9, No. Suppl 8. (2008)
    by Samira Jaeger, Sylvain Gaudan, Ulf Leser, Dietrich R Schuhmann
    posted to data_integration prediction_function by phoenixzxl on 2008-07-28 07:29:25 as ** along with 6 people raiyar farzanehs jiny bootsy reyez jyuh
  • Cytoprophet: A Cytoscape plug-in for protein and domain interaction networks inference
    Bioinformatics (24 July 2008), btn380.
    by Faruck Morcos, Charles Lamanna, Marcin Sikora, Jesus Izaguirre
    posted to soft by phoenixzxl on 2008-07-28 07:24:36 as ** along with 3 people grahamc marck natstreet
  • Predicting and Validating Protein Interactions Using Network Structure
    PLoS Comput Biol, Vol. 4, No. 7. (25 July 2008), e1000118.
    by Pao-Yang Chen, Charlotte M Deane, Gesine Reinert
    posted to network_ppi by phoenixzxl on 2008-07-28 04:05:49 as ** along with 4 people icq242500260 roys zwang mingzhi
  • 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 ** along with 1 person arjunan
  • 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 5 people maximilianh idonaldson isimpson GustavoLacerda yoonk
  • 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 5 people jfr frohike renatomilani beete jyuh
  • 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 3 people druvus zwang reyez
  • 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 prediction_ddi specificity by phoenixzxl on 2008-06-28 08:58:28 as ** along with 1 person cjeans
  • 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 protein_design review synthetic_biology by phoenixzxl on 2008-06-25 08:26:36 as ** along with 1 person zwang
  • 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 prediction_function specificity 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
  • 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 prediction_interface specificity synthetic_biology by phoenixzxl on 2008-06-23 11:03:15 as ** along with 7 people and 3 groups msuarezdiez jwm bicko Einat dpollard Scis0000002 marck structural_bioinformatics Bioinformatics EisenLab
  • 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 4 people chad_davis barry marck zwang
  • Structural specificity in coiled-coil interactions
    Current Opinion in Structural Biology, Vol. In Press, Corrected Proof
    by Gevorg Grigoryan, Amy E Keating
    posted to coiled_coil specificity by phoenixzxl on 2008-06-17 02:24:31 as ** along with 3 people marck zwang viktor21614
  • 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 tmmurali monod textoris bayesian luispedro xinian jdiggans watson stefanoallesina marck 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_motif network_ppi by phoenixzxl on 2008-06-10 13:34:50 as **
  • 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_dynamic network_motif 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 tmmurali maralena marck
  • 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 co-evolution complex prediction_interface by phoenixzxl on 2008-06-03 07:10:50 as ** along with 4 people cabbagesofdoom bicko chad_davis zwang
  • 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 prediction_ppi svm by phoenixzxl on 2008-05-30 08:01:01 as ** along with 6 people and 1 group winterschlaefer 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 prediction_ppi svm by phoenixzxl on 2008-05-23 02:57:16 as ** along with 4 people jyuh zwang marck tmmurali
  • 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 evolution network_evolution prediction_ppi statistical by phoenixzxl on 2008-05-13 08:35:44 as ** along with 21 people and 1 group tharris zwang chrissp100 sanchezbuelna jyuh tmmurali neils paolomarcatili mjoach xingxu Ema cabbagesofdoom balicea marck friendpine brianb roys Evangelia dragonrez chad_davis bpcusack C. elegans / WormBase
  • 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 cabbagesofdoom jyuh neils aubinhon brianb tmmurali grahamc
  • 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 madhadron wrowell dullhunk ukppdadsr 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 hryk qwermish deanmalmgren carlk jjray skato_toyaku mjoach tmmurali roys pinney saket
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