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eckart_bindewald's prediction [106 articles]

Recent papers added to eckart_bindewald's library classified by the tag prediction. You can also see everyone's prediction.
  • GORouter: an RDF model for providing semantic query and inference services for Gene Ontology and its associations
    BMC Bioinformatics, Vol. 9, No. Suppl 1. (2008)
    by Qingwei Xu, Yixiang Shi, Qiang Lu, Guoqing Zhang, Qingming Luo, Yixue Li
    posted to gene go ontology prediction rdf semantic by eckart_bindewald on 2008-03-25 19:23:35 as **** along with 1 person jyuh
  • Enhanced automated function prediction using distantly related sequences and contextual association by PFP
    Protein Sci, Vol. 15, No. 6. (1 June 2006), pp. 1550-1556.
    by Troy Hawkins, Stanislav Luban, Daisuke Kihara
    posted to automated function prediction protein by eckart_bindewald on 2008-03-18 17:31:40 as ** along with 1 person sgoetz
  • Function prediction of uncharacterized proteins.
    J Bioinform Comput Biol, Vol. 5, No. 1. (February 2007), pp. 1-30.
    by T Hawkins, D Kihara
    posted to function prediction protein by eckart_bindewald on 2008-03-18 17:29:55 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 3d function phylogenetic prediction protein by eckart_bindewald on 2008-03-18 17:26:00 as ***** along with 4 people skhadar zwang asddd hpaces
  • GOtcha: a new method for prediction of protein function assessed by the annotation of seven genomes.
    BMC Bioinformatics, Vol. 5 (18 November 2004)
    by DM Martin, M Berriman, GJ Barton
    posted to function go prediction protein by eckart_bindewald on 2008-03-18 17:21:27 as **** along with 3 people Sharpshoot sgoetz bootsy
  • Global self-organization of all known protein sequences reveals inherent biological signatures
    Journal of Molecular Biology, Vol. 268, No. 2. (2 May 1997), pp. 539-556.
    by Michal Linial, Nathan Linial, Naftali Tishby, Golan Yona
    posted to fingerprint function gene prediction protein signature by eckart_bindewald on 2008-03-14 16:41:33 as ****
  • Predicting expression patterns from regulatory sequence in Drosophila segmentation
    Nature (02 January 2008)
    by Eran Segal, Tali Raveh-Sadka, Mark Schroeder, Ulrich Unnerstall, Ulrike Gaul
    posted to expression gene microrna prediction profile promoter by eckart_bindewald on 2008-03-13 15:34:23 as ***** along with 11 people tresch tmmurali djkt bootsy biomcgary idonaldson roys emptyhb pkharchenko meiklej jrest
  • Computational analysis of biological functions and pathways collectively targeted by co-expressed microRNAs in cancer
    BMC Bioinformatics, Vol. 8, No. Suppl 7. (2007)
    by Yuriy Gusev, Thomas Schmittgen, Megan Lerner, Russell Postier, Daniel Brackett
    posted to analysis cancer function microrna pathway prediction protein by eckart_bindewald on 2008-03-03 16:07:17 as *** along with 5 people jfr ealloza vinithepooh yugusev maralena
  • Term-tissue specific models for prediction of gene ontology biological processes using transcriptional profiles of aging in drosophila melanogaster
    BMC Bioinformatics, Vol. 9 (28 February 2008), 129.
    by Wensheng Zhang, Sige Zou, Jiuzhou Song
    posted to function microarray prediction protein by eckart_bindewald on 2008-03-03 15:19:20 as ****
  • How RNA folds.
    J Mol Biol, Vol. 293, No. 2. (22 October 1999), pp. 271-281.
    by I Tinoco, C Bustamante
    posted to folding prediction rna by eckart_bindewald on 2007-12-06 14:40:49 as *** along with 8 people and 3 groups dayjm marcius perrywoo arcticrasta condon Hosna apop physics beta BioinfoCIPF SGU-CIPF
  • Automated de novo prediction of native-like RNA tertiary structures
    PNAS (28 August 2007), 0703836104.
    by Rhiju Das, David Baker
    posted to fragment prediction rna structure by eckart_bindewald on 2007-12-06 14:36:50 as read along with 6 people and 2 groups reyez jwm marcius zwang physics Ema BioinfoCIPF SGU-CIPF
  • High-resolution structure prediction and the crystallographic phase problem
    Nature (14 October 2007)
    by Bin Qian, Srivatsan Raman, Rhiju Das, Philip Bradley, Airlie J Mccoy, Randy J Read, David Baker
    posted to ab_initio crystallography nmr prediction protein star3 structure x-ray by eckart_bindewald on 2007-11-19 12:47:07 as ***** along with 15 people and 2 groups ardalby apaydin aheilbut jwm chad_davis ffranca dgront massivemayhem cjeans zwang cactus sobolevnrm boris_aguilar Ema chenway OPIG baker-group
  • Detecting genetic variation in microarray expression data
    Genome Res. (3 July 2007), gr.6307307.
    by Jennifer A Greenhall, Matthew A Zapala, Mario Caceres, Ondrej Libiger, Carrolee Barlow, Nicholas J Schork, David J Lockhart
    posted to detection expression microarray pattern prediction by eckart_bindewald on 2007-11-06 18:09:08 as **** along with 6 people and 2 groups jyuh jfr rdiaz giovanni qmwwallace msomel Bioinformatics GeschwindLab
  • Fast-Find: a novel computational approach to analyzing combinatorial motifs.
    BMC Bioinformatics, Vol. 7 (2006)
    by M Hamady, E Peden, R Knight, R Singh
    posted to database motif prediction rna search by eckart_bindewald on 2007-10-26 13:30:28 as ***
  • Evolutionary rates vary among rRNA structural elements
    Nucl. Acids Res., Vol. 35, No. 10. (11 May 2007), pp. 3339-3354.
    by S Smit, J Widmann, R Knight
    posted to evolution mutation prediction ribosome rna structure by eckart_bindewald on 2007-10-26 13:26:48 as *** along with 5 people and 3 groups marcius balicea penka i000 cjeans BioinfoCIPF SGU-CIPF YY1
  • Identification of homologs in insignificant BLAST hits by exploiting extrinsic gene properties
    BMC Bioinformatics, Vol. 8 (21 September 2007), 356.
    by Jos Boekhorst, Berend Snel
    posted to accuracy blast gene homology prediction sequence by eckart_bindewald on 2007-10-24 14:12:45 as *** along with 2 people julesyoo dandaman
  • Discovering Motifs in Ranked Lists of DNA Sequences
    PLoS Computational Biology, Vol. 3, No. 3. (1 March 2007), e39.
    by Eran Eden, Doron Lipson, Sivan Yogev, Zohar Yakhini
    posted to dna microarray motif pattern prediction rna by eckart_bindewald on 2007-10-18 12:53:32 as ***** along with 6 people isimpson zwang GeeSharpMinor ppark idonaldson hpaces
  • Stem kernels for RNA sequence analyses.
    J Bioinform Comput Biol, Vol. 5, No. 5. (October 2007), pp. 1103-1122.
    by Y Sakakibara, K Popendorf, N Ogawa, K Asai, K Sato
    posted to alignment noncoding prediction rna sequence by eckart_bindewald on 2007-10-17 18:33:48 as **
  • Detailed estimation of bioinformatics prediction reliability through the Fragmented Prediction Performance Plots
    BMC Bioinformatics, Vol. 8, No. 1. (2007)
    by Oliviero Carugo
    posted to accuracy measure prediction by eckart_bindewald on 2007-10-17 18:31:50 as read
  • How to infer gene networks from expression profiles
    Mol Syst Biol, Vol. 3 (13 February 2007)
    by Mukesh Bansal, Vincenzo Belcastro, Alberto Ambesi-Impiombato, Diego di Bernardo
    posted to gene network prediction by eckart_bindewald on 2007-10-09 13:56:06 as read along with 12 people and 2 groups mariakmejia jfr wnpx nickluscombe kengg mikaelhuss jrbanga BIBLIOma RockHI lp2 natstreet heliopais EBI-regulation Plantandetc
  • A Bayesian framework for combining heterogeneous data sources for gene function prediction (in Saccharomyces cerevisiae).
    Proc Natl Acad Sci U S A, Vol. 100, No. 14. (8 July 2003), pp. 8348-8353.
    by OG Troyanskaya, K Dolinski, AB Owen, RB Altman, D Botstein
    posted to bayesian function gene microarray prediction statistics by eckart_bindewald on 2007-10-09 13:25:34 as **** along with 17 people and 2 groups frohike kallberg srp33 carlk isimpson BioGeek serak dragonrez okarsligil lfriedl balajis eweaver luispedro opheliav wnpx nedwards Evangelia kdl Bioinformatics
  • Prediction of small, noncoding RNAs in bacteria using heterogeneous data.
    J Math Biol (13 March 2007)
    by Brian Tjaden
    posted to ecoli hmm markov noncoding prediction rna secondary_structure by eckart_bindewald on 2007-03-15 19:26:37 as ****
  • Small libraries of protein fragments model native protein structures accurately.
    J Mol Biol, Vol. 323, No. 2. (18 October 2002), pp. 297-307.
    by R Kolodny, P Koehl, L Guibas, M Levitt
    posted to assembly fragment prediction protein structure by eckart_bindewald on 2007-03-09 17:30:58 as ** along with 3 people and 2 groups ana barry j3xucite structural_bioinformatics Bioinformatics
  • On the nature of the protein folding code.
    Proc Natl Acad Sci U S A, Vol. 90, No. 2. (15 January 1993), pp. 644-648.
    by S Rackovsky
    posted to assembly fragment prediction protein structure by eckart_bindewald on 2007-03-09 17:23:49 as **
  • Predicting novel protein folds by using FRAGFOLD.
    Proteins, Vol. Suppl 5 (2001), pp. 127-132.
    by DT Jones
    posted to assembly fragment prediction protein structure by eckart_bindewald on 2007-03-09 17:15:43 as **
  • Combining local-structure, fold-recognition, and new fold methods for protein structure prediction.
    Proteins, Vol. 53 Suppl 6 (2003), pp. 491-496.
    by K Karplus, R Karchin, J Draper, J Casper, Y Mandel-Gutfreund, M Diekhans, R Hughey
    posted to fragment library prediction protein structure by eckart_bindewald on 2007-03-09 17:14:18 as ** along with 1 person j3xucite
  • Some fundamental aspects of building protein structures from fragment libraries.
    Protein Sci, Vol. 13, No. 6. (June 2004), pp. 1636-1650.
    by JB Holmes, J Tsai
    posted to fragment library prediction protein structure by eckart_bindewald on 2007-03-09 17:11:21 as ** along with 2 people and 2 groups barry wouterboomsma structural_bioinformatics Bioinformatics
  • Shaping up the protein folding funnel by local interaction: Lesson from a structure prediction study
    PNAS, Vol. 103, No. 9. (28 February 2006), pp. 3141-3146.
    by George Chikenji, Yoshimi Fujitsuka, Shoji Takada
    posted to assembly fragment prediction protein structure by eckart_bindewald on 2007-03-09 17:08:04 as ** along with 4 people wouterboomsma sotaro rsantana saunders
  • ArchPRED: a template based loop structure prediction server.
    Nucleic Acids Res, Vol. 34, No. Web Server issue. (1 July 2006)
    by N Fernandez-Fuentes, J Zhai, A Fiser
    posted to loop prediction protein secondary_structure by eckart_bindewald on 2007-03-09 17:06:27 as ** along with 2 people vavi cdeane
  • Hon-yaku: a biology-driven Bayesian methodology for identifying translation initiation sites in prokaryotes
    BMC Bioinformatics, Vol. 8 (08 February 2007), 47.
    by Yuko Makita, Michiel JL de Hoon, Antoine Danchin
    posted to translation prokaryote prediction initiation by eckart_bindewald on 2007-02-09 11:54:17 as *** along with 1 person dquest
  • Considerations in the identification of functional RNA structural elements in genomic alignments
    BMC Bioinformatics, Vol. 8 (30 January 2007), 33.
    by Tomas Babak, Benjamin J Blencowe, Timothy R Hughes
    posted to z-score rna prediction noncoding energy by eckart_bindewald on 2007-02-02 14:52:46 as ***** along with 1 person and 1 group andersbj microRNA
  • Secondary structure computer prediction of the poliovirus 5' non-coding region is improved by a genetic algorithm.
    Comput Appl Biosci, Vol. 13, No. 1. (February 1997), pp. 1-12.
    by KM Currey, BA Shapiro
    posted to structure secondary robustness rna prediction persistence mutation genetic algorithm by eckart_bindewald on 2007-01-23 16:22:01 as read
  • Secondary structure alone is generally not statistically significant for the detection of noncoding RNAs.
    Bioinformatics, Vol. 16, No. 7. (July 2000), pp. 583-605.
    by E Rivas, SR Eddy
    posted to energy noncoding prediction rna z-score by eckart_bindewald on 2007-01-08 10:40:29 as read along with 9 people and 3 groups evaf marcius eweaver andersbj arcticrasta mtagaya dquest Eonwe ilh microRNA BioinfoCIPF SGU-CIPF
  • Noncoding RNA gene detection using comparative sequence analysis.
    BMC Bioinformatics, Vol. 2, No. 1. (2001)
    by E Rivas, SR Eddy
    posted to alignment noncoding prediction rna secondary_structure by eckart_bindewald on 2007-01-05 20:01:59 as **** along with 4 people and 2 groups evaf marcius arcticrasta jarasch BioinfoCIPF SGU-CIPF
  • MSARI: Multiple sequence alignments for statistical detection of RNA secondary structure
    PNAS, Vol. 101, No. 33. (17 August 2004), pp. 12102-12107.
    by Alex Coventry, Daniel J Kleitman, Bonnie Berger
    posted to noncoding prediction rna secondary_structure by eckart_bindewald on 2007-01-05 19:54:57 as read
  • Predicting non-coding RNA genes in <it>Escherichia coli</it> with boosted genetic programming
    Nucleic Acids Research, Vol. 33, No. 10. (2005), pp. 3263-3270.
    by Pal Saetrom, Ragnhild Sneve, Knut I Kristiansen, Ola Snove, Thomas Grunfeld, Torbjorn Rognes, Erling Seeberg
    posted to genetic_programming noncoding prediction rna by eckart_bindewald on 2006-12-28 16:07:01 as read
  • RNAs everywhere: genome-wide annotation of structured RNAs.
    J Exp Zoolog B Mol Dev Evol (14 December 2006)
    by Rolf Backofen, Stephan H H Bernhart, Christoph Flamm, Claudia Fried, Guido Fritzsch, Jörg Hackermüller, Jana Hertel, Ivo L L Hofacker, Kristin Missal, Axel Mosig, Sonja J J Prohaska, Dominic Rose, Peter F F Stadler, Andrea Tanzer, Stefan Washietl, Sebastian Will
    posted to alignment conserved noncoding prediction rna by eckart_bindewald on 2006-12-21 14:32:50 as read along with 11 people and 5 groups jfr bala marcius tardigrade andersbj penka cdawson ilh raylim jayster4 maralena microRNA BioinfoCIPF SGU-CIPF DictyosteliumGroup GIG
  • Thousands of corresponding human and mouse genomic regions unalignable in primary sequence contain common RNA structure.
    Genome Res (2 June 2006)
    by Elfar Torarinsson, Milena Sawera, Jakob H H Havgaard, Merete Fredholm, Jan Gorodkin
    posted to alignment conserved noncoding prediction rna by eckart_bindewald on 2006-12-21 14:29:08 as **** along with 2 people and 1 group dpollard mtagaya EisenLab
  • ddbRNA: detection of conserved secondary structures in multiple alignments.
    Bioinformatics, Vol. 19, No. 13. (1 September 2003), pp. 1606-1611.
    by D di Bernardo, T Down, T Hubbard
    posted to alignment conserved noncoding prediction rna by eckart_bindewald on 2006-12-21 14:09:32 as **** along with 2 people and 2 groups arcticrasta bsmagic Bioinformatics bioinplant
  • Computational identification of microRNAs and their targets.
    Comput Biol Chem (21 November 2006)
    by Baohong Zhang, Xiaoping Pan, Qinglian Wang, George P P Cobb, Todd A A Anderson
    posted to microrna prediction target by eckart_bindewald on 2006-11-27 17:07:05 as *** along with 5 people and 2 groups jfr tardigrade cdawson GustavoLacerda heliopais microRNA GIG
  • Comparative analysis of secondary structure of insect mitochondrial small subunit ribosomal RNA using maximum weighted matching.
    Nucleic Acids Res, Vol. 28, No. 20. (15 October 2000), pp. 3839-3845.
    by RD Page
    posted to circles graph matching prediction rna secondary_structure by eckart_bindewald on 2006-10-26 15:05:01 as ***
  • Secondary Structure Prediction of Interacting RNA Molecules
    Journal of Molecular Biology, Vol. 345, No. 5., pp. 987-1001.
    by Mirela Andronescu, Zhi C Zhang, Anne Condon
    posted to prediction rna secondary_structure by eckart_bindewald on 2006-10-20 17:53:45 as ** along with 4 people and 2 groups marcius Hosna cthachuk physics BioinfoCIPF SGU-CIPF
  • Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure.
    Proc Natl Acad Sci U S A, Vol. 101, No. 19. (11 May 2004), pp. 7287-7292.
    by DH Mathews, MD Disney, JL Childs, SJ Schroeder, M Zuker, DH Turner
    posted to constraint experimental prediction rna secondary_structure by eckart_bindewald on 2006-10-20 17:27:53 as read along with 4 people and 1 group austin arcticrasta condon Hosna beta
  • Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes.
    Genome Res, Vol. 15, No. 8. (August 2005), pp. 1034-1050.
    by A Siepel, G Bejerano, JS Pedersen, AS Hinrichs, M Hou, K Rosenbloom, H Clawson, J Spieth, LW Hillier, S Richards, GM Weinstock, RK Wilson, RA Gibbs, WJ Kent, W Miller, D Haussler
    posted to conserved noncoding prediction rna secondary structure by eckart_bindewald on 2006-09-22 19:20:36 as **** along with 14 people and 2 groups pradiptaray bpb aprasad balajis indigoviolet brant adepace djkt olympos sujaikumar Stew cisevol dmc elfar EisenLab cis-regulatory-evolution
  • Computational prediction of methylation status in human genomic sequences.
    Proc Natl Acad Sci U S A, Vol. 103, No. 28. (11 July 2006), pp. 10713-10716.
    by R Das, N Dimitrova, Z Xuan, RA Rollins, F Haghighi, JR Edwards, J Ju, TH Bestor, MQ Zhang
    posted to dna genome human methylation prediction by eckart_bindewald on 2006-09-18 14:54:22 as ** along with 2 people olympos epigenetics
  • CpG island methylation in human lymphocytes is highly correlated with DNA sequence, repeats, and predicted DNA structure.
    PLoS Genet, Vol. 2, No. 3. (March 2006)
    by C Bock, M Paulsen, S Tierling, T Mikeska, T Lengauer, J Walter
    posted to dna methylation prediction by eckart_bindewald on 2006-09-18 14:53:49 as ** along with 3 people kaarsinogen olympos epigenetics
  • Computational methods for RNA structure determination.
    Curr Opin Struct Biol, Vol. 11, No. 3. (June 2001), pp. 282-286.
    by F Major, R Griffey
    posted to prediction review rna star2 structure by eckart_bindewald on 2006-09-13 13:52:23 as read along with 3 people and 2 groups lillekatt P2324548 marcius BioinfoCIPF SGU-CIPF
  • Efficient pairwise RNA structure prediction and alignment using sequence alignment constraints.
    BMC Bioinformatics, Vol. 7 (04 September 2006), 400.
    by Robin D Dowell, Sean R Eddy
    posted to constraint prediction rna secondary_structure by eckart_bindewald on 2006-09-07 20:44:24 as ** along with 4 people and 2 groups reyez marcius dquest ilh BioinfoCIPF SGU-CIPF
  • An Interactive Framework for RNA Secondary Structure Prediction with a Dynamical Treatment of Constraints
    Journal of Molecular Biology, Vol. 254, No. 2. (24 November 1995), pp. 163-174.
    by Christine Gaspin, Eric Westhof
    posted to contraint interactive prediction rna secondary_structure by eckart_bindewald on 2006-08-29 16:08:19 as read along with 1 person Hosna
  • Computer modeling 16 S ribosomal RNA
    Journal of Molecular Biology, Vol. 221, No. 3. (5 October 1991), pp. 889-907.
    by John M Hubbard, John E Hearst
    posted to 16s 3d distance_geometry prediction structure by eckart_bindewald on 2006-08-29 14:30:29 as read along with 1 person and 2 groups marcius BioinfoCIPF SGU-CIPF
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