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Tag prediction [955 articles]

Recent papers classified by the tag prediction.
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  • An integrative approach for predicting interactions of protein regions
    Bioinformatics, Vol. 24, No. 16. (15 August 2008), pp. i35-41.
    by Sven-Eric Schelhorn, Thomas Lengauer, Mario Albrecht
    posted to domain interaction prediction protein by zwang on 2008-08-11 04:13:26 as **** along with 2 people neils kluck
  • Computational prediction of small-molecule catalysts
    Nature, Vol. 455, No. 7211. (17 September 2008), pp. 309-313.
    by KN Houk, Paul H Cheong
    posted to structure prediction by zwang on 2008-10-16 14:04:21 as **
  • Predicting Protein Function with Hierarchical Phylogenetic Profiles: The Gene3D Phylo-Tuner Method Applied to Eukaryotic Genomes
    PLoS Computational Biology, Vol. 3, No. 11. (1 November 2007), e237.
    by Juan A Ranea, Corin Yeats, Alastair Grant, Christine A Orengo
    posted to eukaryota genome hierarchical phylogeny prediction protein by zwang on 2007-12-10 04:43:48 as *** along with 5 people and 1 group marti eckart_bindewald skhadar asddd hpaces Orengo Group functional genomics watchlist
  • De Novo Computational Design of Retro-Aldol Enzymes
    Science, Vol. 319, No. 5868. (7 March 2008), pp. 1387-1391.
    by Lin Jiang, Eric A Althoff, Fernando R Clemente, Lindsey Doyle, Daniela Rothlisberger, Alexandre Zanghellini, Jasmine L Gallaher, Jamie L Betker, Fujie Tanaka, Carlos F Barbas, Donald Hilvert, Kendall N Houk, Barry L Stoddard, David Baker
    posted to design prediction protein by zwang on 2008-03-07 03:02:39 as ** along with 13 people and 3 groups alexknight barry aalibes jwm aprasad dgront sobolevnrm davidlott msuarezdiez scienbox ucbcjbm joseph_x_zhou cambray structural_bioinformatics baker-group McCammon
  • Predicting novel RNA-RNA interactions.
    Current opinion in structural biology (14 May 2008)
    by Irmtraud M M Meyer
    posted to interaction prediction rna structure by zwang on 2008-06-16 03:49:12 as ***** along with 2 people and 1 group Hosna marck beta
  • Prediction of Functional Sites Based on the Fuzzy Oil Drop Model
    PLoS Computational Biology, Vol. 3, No. 5. (1 May 2007), e94.
    by Michał Bryliński, Katarzyna Prymula, Wiktor Jurkowski, Marek Kochańczyk, Ewa Stawowczyk, Leszek Konieczny, Irena Roterman
    posted to prediction site by zwang on 2007-05-26 05:09:12 as * along with 1 person and 1 group Einat structural_bioinformatics
  • 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 protein structure by zwang on 2008-06-27 03:37:25 as ** along with 5 people kgutwin chad_davis barry phoenixzxl marck
  • Systematic evaluation of objective functions for predicting intracellular fluxes in Escherichia coli
    Mol Syst Biol, Vol. 3 (10 July 2007)
    by Robert Schuetz, Lars Kuepfer, Uwe Sauer
    posted to bacterial prediction systematic by zwang on 2007-07-11 19:28:02 as ** along with 4 people and 1 group alexg fishtank Ema michaelbarton Bioinformatics
  • Characterization of Protein Hubs by Inferring Interacting Motifs from Protein Interactions
    PLoS Computational Biology, Vol. 3, No. 9. (1 September 2007), e178.
    by Ramon Aragues, Andrej Sali, Jaume Bonet, Marc A Marti-Renom, Baldo Oliva
    posted to interaction interface motif prediction protein by zwang on 2007-10-22 05:23:09 as **** along with 3 people marti winterschlaefer Ema
  • Network-based global inference of human disease genes
    Mol Syst Biol, Vol. 4 (6 May 2008)
    by Xuebing Wu, Rui Jiang, Michael Q Zhang, Shao Li
    posted to gene human network prediction by zwang on 2008-05-09 02:59:01 as **** along with 10 people saket tmmurali diamantis jfr maralena bootsy biomcgary guhjy ptrobajo Borelli
  • A statistical approach using network structure in the prediction of protein characteristics
    Bioinformatics (28 June 2007), btm342.
    by Pao-Yang Chen, Charlotte M Deane, Gesine Reinert
    posted to network prediction protein statistical structure by zwang on 2007-08-15 03:41:38 as * along with 5 people and 1 group grahamc iris_2001 cabbagezs cdeane Pao-Yang ParkinsonLab_at_MaRS
  • Genome-wide prediction of matrix attachment regions that increase gene expression in mammalian cells
    Nat Meth, Vol. 4, No. 9. (2007), pp. 747-753.
    by Pierre-Alain Girod, Duc-Quang Nguyen, David Calabrese, Stefania Puttini, Melanie Grandjean, Danielle Martinet, Alexandre Regamey, Damien Saugy, Jacques S Beckmann, Philipp Bucher, Nicolas Mermod
    posted to expression gene genome-wide mammal prediction by zwang on 2007-08-31 16:22:46 as * along with 2 people sebastien_vigneau uz_labu_laimi
  • Integration of Genome and Chromatin Structure with Gene Expression Profiles To Predict c-MYC Recognition Site Binding and Function.
    PLoS Comput Biol, Vol. 3, No. 4. (6 April 2007)
    by Yili Chen, Thomas W W Blackwell, Ji Chen, Jing Gao, Angel W W Lee, David J J States
    posted to chromatin gene genome integration prediction structure by zwang on 2007-04-28 12:36:42 as ** along with 1 person and 2 groups kengg Bioinformatics Plantandetc
  • InPrePPI: an integrated evaluation method based on genomic context for predicting protein-protein interactions in prokaryotic genomes
    BMC Bioinformatics, Vol. 8 (26 October 2007), 414.
    by Jingchun Sun, Yan Sun, Guohui Ding, Qi Liu, Chuan Wang, Youyu He, Tieliu Shi, Yixue Li, Zhongming Zhao
    posted to bacterial genome interaction prediction protein by zwang on 2007-10-29 13:11:19 as ** along with 2 people and 1 group tmmurali iris_2001 csb_journal_club_public
  • Probabilistic prediction and ranking of human protein-protein interactions
    BMC Bioinformatics, Vol. 8 (05 July 2007), 239.
    by Michelle S Scott, Geoffrey J Barton
    posted to interaction prediction protein by zwang on 2007-07-13 17:19:17 as **** along with 4 people and 1 group cerca wnpx grahamc mingzhi ParkinsonLab_at_MaRS
  • Detecting Coevolution in and among Protein Domains
    PLoS Computational Biology, Vol. 3, No. 11. (1 November 2007), e211.
    by Chen-Hsiang Yeang, David Haussler
    posted to co-evolution domain prediction protein by zwang on 2007-12-10 04:24:46 as ***** along with 11 people and 1 group balicea skhadar sobolevnrm niallhaslam hpaces mingzhi Ema phoenixzxl penpen926 friendpine pradiptaray baker-group
  • Structure Prediction of Domain Insertion Proteins from Structures of Individual Domains
    Structure, Vol. 16, No. 4. (8 April 2008), pp. 513-527.
    by Monica Berrondo, Marc Ostermeier, Jeffrey J Gray
    posted to structure prediction peptide domain by zwang on 2008-11-12 01:40:59 as **** along with 2 people raik choonpeng
  • Structure-Templated Predictions of Novel Protein Interactions from Sequence Information
    PLoS Computational Biology, Vol. 3, No. 9. (1 September 2007), e182.
    by Doron Betel, Kevin E Breitkreuz, Ruth Isserlin, Danielle Dewar-Darch, Mike Tyers, Christopher W Hogue
    posted to interaction prediction protein sequence structure by zwang on 2007-10-22 05:11:20 as **** along with 3 people agustinarce cjeans winterschlaefer
  • Binding Site Graphs: A New Graph Theoretical Framework for Prediction of Transcription Factor Binding Sites
    PLoS Computational Biology, Vol. 3, No. 5. (1 May 2007), e90.
    by Timothy E Reddy, Charles Delisi, Boris E Shakhnovich
    posted to binding prediction transcription by zwang on 2007-05-12 10:40:13 as *****
  • Predicting protein function from domain content
    Bioinformatics (30 June 2008), btn312.
    by Kristoffer Forslund, Erik L Sonnhammer
    posted to domain prediction protein by zwang on 2008-07-01 02:44:42 as *** along with 4 people saket druvus phoenixzxl reyez
  • Phylogenetic tree information aids supervised learning for predicting protein-protein interaction based on distance matrices
    BMC Bioinformatics, Vol. 8 (09 January 2007), 6.
    by Roger A Craig, Li Liao
    posted to interaction phylogeny prediction protein by zwang on 2007-04-16 13:57:11 as *** along with 2 people marti iris_2001
  • Accurate prediction of protein-protein interactions from sequence alignments using a Bayesian method
    Mol Syst Biol, Vol. 4 (12 February 2008)
    by Lukas Burger, Erik van Nimwegen
    posted to alignment bayesian interaction prediction protein sequence by zwang on 2008-02-17 10:10:43 as **** along with 12 people raik sjcockell kengg grahamc laughcry biomcgary cabbagezs roys cdeane gjuggler phoenixzxl pansapiens
  • Network-based prediction of human tissue-specific metabolism.
    Nature biotechnology (17 August 2008)
    by Tomer Shlomi, Moran N N Cabili, Markus J J Herrgård, Bernhard Ø O Palsson, Eytan Ruppin
    posted to prediction network metabolism by zwang on 2008-09-10 07:26:54 as ** along with 8 people jfr roys mdstobbe klo peterli ptrobajo renatomilani guhjy
  • Trawler: de novo regulatory motif discovery pipeline for chromatin immunoprecipitation
    Nature Methods, Vol. 4, No. 7. (24 June 2007), pp. 563-565.
    by Laurence Ettwiller, Benedict Paten, Mirana Ramialison, Ewan Birney, Joachim Wittbrodt
    posted to chromatin motif prediction regulatory by zwang on 2007-08-28 03:56:29 as * along with 3 people and 1 group brant maximilianh fpattyn EisenLab
  • Protein-Protein Interaction Hotspots Carved into Sequences.
    PLoS Comput Biol, Vol. 3, No. 7. (13 July 2007)
    by Yanay Ofran, Burkhard Rost
    posted to insilico interaction prediction protein sequence by zwang on 2007-08-29 02:25:39 as *** along with 7 people and 3 groups bicko dchughes grahamc cjeans Jporci Pao-Yang higueruelo G4ID ParkinsonLab_at_MaRS Genetics-of-Gambling
  • Toward high-resolution prediction and design of transmembrane helical protein structures
    Proceedings of the National Academy of Sciences, Vol. 104, No. 40. (2 October 2007), pp. 15682-15687.
    by P Barth, J Schonbrun, D Baker
    posted to expression prediction protein structure by zwang on 2007-10-08 19:01:24 as * along with 3 people hmk biehl Ema
  • Systematic Identification of cis-Regulatory Sequences Active in Mouse and Human Embryonic Stem Cells
    PLoS Genetics, Vol. 3, No. 8. (1 August 2007), e145.
    by Marica Grskovic, Christina Chaivorapol, Alexandre Gaspar-Maia, Hao Li, Miguel Ramalho-Santos
    posted to human motif prediction regulatory sequence systematic by zwang on 2007-09-03 04:40:58 as **
  • MicroRNA Targeting Specificity in Mammals: Determinants beyond Seed Pairing.
    Mol Cell, Vol. 27, No. 1. (6 July 2007), pp. 91-105.
    by Andrew Grimson, Kyle Kai-How K Farh, Wendy K K Johnston, Philip Garrett-Engele, Lee P P Lim, David P P Bartel
    posted to mammal microrna prediction target by zwang on 2007-08-15 04:15:51 as ** along with 7 people and 1 group giovenko jfr andersbj bootsy heliopais fpattyn maralena microRNA
  • 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 metabolism network prediction by zwang on 2008-02-17 10:43:10 as ** along with 9 people kentsis bootsy biomcgary cabbagezs westoll shikin shung debasis tmmurali
  • How does eukaryotic gene prediction work?
    Nature Biotechnology, Vol. 25, No. 8., pp. 883-885.
    by Michael R Brent
    posted to eukaryota gene prediction by zwang on 2007-08-14 08:01:16 as **** along with 7 people and 3 groups guhjy indigoviolet dchughes wenhan cabbagezs nklee ale EisenLab G4ID Genetics-of-Gambling
  • Prediction of structures of multidomain proteins from structures of the individual domains.
    Protein Sci (22 December 2006)
    by Andrew M M Wollacott, Alexandre Zanghellini, Paul Murphy, David Baker
    posted to domain prediction protein structure by zwang on 2007-04-16 13:37:00 as ** along with 5 people dgront wouterboomsma choonpeng IrinaMoreira rph
  • ProCope - Protein Complex Prediction and Evaluation
    Bioinformatics (17 July 2008), btn376.
    by Jan Krumsiek, Caroline C Friedel, Ralf Zimmer
    posted to complex prediction protein by zwang on 2008-07-26 10:52:18 as ** along with 3 people saket guhjy chad_davis
  • A Universal Framework for Regulatory Element Discovery across All Genomes and Data Types.
    Mol Cell, Vol. 28, No. 2. (26 October 2007), pp. 337-350.
    by O Elemento, N Slonim, S Tavazoie
    posted to clustering genome motif prediction yeast by zwang on 2007-11-01 02:15:02 as *** along with 12 people and 2 groups ana brant cwbrown aswin cjeans cabbagezs nklee maximilianh idonaldson sb_journal_club kristen barwil EisenLab Motif Discovery
  • I-TASSER server for protein 3D structure prediction
    BMC Bioinformatics, Vol. 9 (23 January 2008), 40.
    by Yang Zhang
    posted to prediction protein structure by zwang on 2008-02-24 13:43:46 as ** along with 4 people chad_davis mkurc rabio mclarenv
  • High-throughput identification of Interacting Protein-Protein Binding Sites
    BMC Bioinformatics, Vol. 8 (27 June 2007), 223.
    by Jo-Lan Chung, Wei Wang, Philip E Bourne
    posted to binding interaction prediction protein site svm by zwang on 2007-08-27 08:57:42 as ***** along with 3 people and 1 group bicko grahamc Evangelia ParkinsonLab_at_MaRS
  • Detecting Coevolution in and among Protein Domains
    PLoS Computational Biology, Vol. 3, No. 11. (1 November 2007), e211.
    by Chen-Hsiang Yeang, David Haussler
    posted to co-evolution domain prediction protein by zwang on 2007-11-03 03:07:56 as **** along with 1 person cjeans
  • Structure-Templated Predictions of Novel Protein Interactions from Sequence Information
    PLoS Computational Biology, Vol. 3, No. 9. (1 September 2007), e182.
    by Doron Betel, Kevin E Breitkreuz, Ruth Isserlin, Danielle Dewar-Darch, Mike Tyers, Christopher W Hogue
    posted to interaction prediction protein sequence structure by zwang on 2007-11-02 08:05:43 as *** along with 2 people bicko dquest
  • NucPred--Predicting nuclear localization of proteins
    Bioinformatics, Vol. 23, No. 9. (1 May 2007), pp. 1159-1160.
    by Markus Brameier, Andrea Krings, Robert M Maccallum
    posted to localization nuclear prediction protein by zwang on 2007-05-10 08:12:27 as ** along with 2 people neils zdai
  • 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 interaction prediction protein svm by zwang on 2008-06-16 03:51:12 as **** along with 4 people guhjy marck phoenixzxl tmmurali
  • Efficient pairwise RNA structure prediction using probabilistic alignment constraints in Dynalign
    BMC Bioinformatics, Vol. 8 (19 April 2007), 130.
    by Arif O Harmanci, Gaurav Sharma, David H Mathews
    posted to prediction rna structure by zwang on 2007-05-29 12:26:56 as ** along with 1 person puranjoy_b
  • A Bayesian Estimator of Protein-Protein Association Probabilities
    Bioinformatics (22 May 2008), btn238.
    by JM Gilmore, DL Auberry, JL Sharp, AM White, KK Anderson, DS Daly
    posted to bayesian interaction prediction protein by zwang on 2008-06-03 04:01:29 as ** along with 2 people guhjy renatomilani
  • Predicting transcription factor specificity with all-atom models.
    Nucleic acids research (1 October 2008)
    by Sahand Jamal J Rahi, Peter Virnau, Leonid A A Mirny, Mehran Kardar
    posted to structure protein prediction interaction dna by zwang on 2008-11-04 09:08:12 as ***** along with 4 people reyez maximilianh lptolik aalibes
  • The MC-Fold and MC-Sym pipeline infers RNA structure from sequence data
    Nature, Vol. 452, No. 7183., pp. 51-55.
    by Marc Parisien, François Major
    posted to prediction rna sequence structure by zwang on 2008-03-07 02:48:26 as *** along with 4 people puranjoy_b austin elfar reyez
  • CpG Island Mapping by Epigenome Prediction.
    PLoS Comput Biol, Vol. 3, No. 6. (8 June 2007)
    by Christoph Bock, Jörn Walter, Martina Paulsen, Thomas Lengauer
    posted to cpg-island genome prediction by zwang on 2007-08-18 15:22:12 as *** along with 7 people bpcusack kaarsinogen sebastien_vigneau oelemento fpattyn rschulz inesdesantiago
  • Predicting functionally important residues from sequence conservation
    Bioinformatics (22 May 2007), btm270.
    by John A Capra, Mona Singh
    posted to prediction residue by zwang on 2007-06-10 16:23:10 as ** along with 7 people and 2 groups grahamc azazello cabbagezs Jporci niallhaslam santiago dgront ParkinsonLab_at_MaRS MBLAB
  • Structure-Guided Comparative Analysis of Proteins: Principles, Tools, and Applications for Predicting Function
    PLoS Comput Biol, Vol. 4, No. 9. (2008), e1000151.
    by Raja Mazumder, Sona Vasudevan
    posted to structure protein prediction function by zwang on 2008-10-07 11:19:53 as ** along with 9 people and 2 groups i000 pengchy raik chad_davis druvus reyez mdstobbe barry jameswasmuth structural_bioinformatics Bioinformatics
  • Predicting protein function from sequence and structure
    Nat Rev Mol Cell Biol, Vol. 8, No. 12. (December 2007), pp. 995-1005.
    by David Lee, Oliver Redfern, Christine Orengo
    posted to function prediction protein review sequence structure by zwang on 2007-12-08 08:55:16 as *** along with 9 people and 1 group skhadar neils cjeans Evangelia hpaces Ema renatomilani kluck janasont MuraLab
  • Accurate prediction of stability changes in protein mutants by combining machine learning with structure based computational mutagenesis
    Bioinformatics, Vol. 24, No. 18. (15 September 2008), pp. 2002-2009.
    by Majid Masso, Iosif I Vaisman
    posted to svm structure stability protein prediction by zwang on 2008-10-09 08:57:06 as ** along with 2 people kluck afon
  • Control of Membrane Fusion Mechanism by Lipid Composition: Predictions from Ensemble Molecular Dynamics
    PLoS Computational Biology, Vol. 3, No. 11. (1 November 2007), e220.
    by Peter M Kasson, Vijay S Pande
    posted to dynamics prediction by zwang on 2007-12-10 04:34:31 as * along with 3 people and 1 group sobolevnrm paulschlesinger Ema baker-group
  • An Approach to Predict Transcription Factor DNA Binding Site Specificity Based upon Gene and Transcription Factor Functional Categorization
    Bioinformatics (10 July 2007), btm348.
    by Ziliang Qian, Lingyi Lu, Xiaojun Liu, Yu-Dong Cai, Yixue Li
    posted to binding dna gene prediction site transcription by zwang on 2007-08-15 03:43:07 as *** along with 2 people druvus xili03
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