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de xili03 library [100 articles]

Articles dernièrement stockés dans la bibliothèque de xili03 .
  • Evaluation of phylogenetic footprint discovery for predicting bacterial cis-regulatory elements and revealing their evolution
    BMC Bioinformatics, Vol. 9 (23 January 2008), 37.
    by Rekin's Janky, Jacques van Helden
    posted to footprinting by xili03 on 2008-08-11 08:58:36 as ** along with 1 person and 1 group cisevol cis-regulatory-evolution
  • Characterization and Identification of MicroRNA Core Promoters in Four Model Species.
    PLoS Comput Biol, Vol. 3, No. 3. (9 March 2007)
    by Xuefeng Zhou, Jianhua Ruan, Guandong Wang, Weixiong Zhang
    posted to microrna by xili03 on 2008-08-07 07:40:37 as ** along with 7 people and 2 groups bootsy jfr tardigrade andersbj cdawson ale maralena microRNA GIG
  • Comparative Sequence Analysis Reveals an Intricate Network Among REST, CREB and miRNA in Mediating Neuronal Gene Expression
    Genome Biology, Vol. 7 (26 September 2006), R85.
    by Jie Wu, Xiaohui Xie
    posted to microrna by xili03 on 2008-08-07 07:38:34 as ** along with 4 people and 1 group bootsy maralena diancu heliopais microRNA
  • Significant sequence similarities in promoters and precursors of Arabidopsis thaliana non-conserved microRNAs
    Bioinformatics, Vol. 22, No. 21. (1 November 2006), pp. 2585-2589.
    by Wang, Yu, Hindemitt, Tobias, Mayer, FX Klaus
    posted to microrna by xili03 on 2008-08-07 07:29:39 as **
  • MicroRNA promoter element discovery in Arabidopsis.
    RNA (3 August 2006)
    by Molly Megraw, Vesselin Baev, Ventsislav Rusinov, Shane T T Jensen, Kriton Kalantidis, Artemis G G Hatzigeorgiou
    posted to microrna by xili03 on 2008-08-07 07:12:33 as ** along with 6 people and 1 group maralena bootsy tardigrade cdawson byy ale GIG
  • MATLIGN: a motif clustering, comparison and matching tool
    BMC Bioinformatics, Vol. 8 (08 June 2007), 189.
    by Matti Kankainen, Ari Loytynoja
    posted to postprocessing by xili03 on 2008-07-29 04:53:51 as ** along with 3 people and 1 group isimpson smbe2008 idonaldson BergmanLab
  • Statistical mechanical modeling of genome-wide transcription factor occupancy data by MatrixREDUCE.
    Bioinformatics, Vol. 22, No. 14. (15 July 2006)
    by BC Foat, AV Morozov, HJ Bussemaker
    posted to affinity by xili03 on 2008-07-10 06:33:06 as ** along with 3 people dquest lusk yevishere
  • Predicting transcription factor affinities to DNA from a biophysical model.
    Bioinformatics (10 November 2006)
    by Helge Roider, Aditi Kanhere, Thomas Manke, Martin Vingron
    posted to affinity by xili03 on 2008-07-10 05:16:38 as ** along with 2 people and 1 group indigoviolet dpollard EisenLab
  • Whole-Genome Discovery of Transcription Factor Binding Sites by Network-Level Conservation
    Genome Res., Vol. 14, No. 1. (1 January 2004), pp. 99-108.
    by Moshe Pritsker, Yir-Chung Liu, Michael A Beer, Saeed Tavazoie
    posted to affinity by xili03 on 2008-07-10 05:13:22 as ** along with 2 people kaarsinogen koller
  • Rank order metrics for quantifying the association of sequence features with gene regulation.
    Bioinformatics, Vol. 19, No. 2. (22 January 2003), pp. 212-218.
    by ND Clarke, JA Granek
    posted to no-tag by xili03 on 2008-07-10 05:08:25 as ** along with 2 people and 1 group kaspermunch nklee Bioinformatics
  • A biophysical approach to transcription factor binding site discovery.
    Genome Res, Vol. 13, No. 11. (November 2003), pp. 2381-2390.
    by M Djordjevic, AM Sengupta, BI Shraiman
    posted to affinity by xili03 on 2008-07-10 02:59:48 as ** along with 2 people dquest discreteonyxorb
  • Predicting functional transcription factor binding through alignment-free and affinity-based analysis of orthologous promoter sequences
    Bioinformatics, Vol. 24, No. 13. (1 July 2008), pp. i165-171.
    by Lucas D Ward, Harmen J Bussemaker
    posted to affinity by xili03 on 2008-07-10 02:51:00 as ** along with 1 person maximilianh
  • On counting position weight matrix matches in a sequence, with application to discriminative motif finding.
    Bioinformatics, Vol. 22, No. 14. (15 July 2006)
    by S Sinha
    posted to algorithm by xili03 on 2008-07-09 06:03:48 as ** along with 2 people eckart_bindewald samal
  • Finding sequence motifs with Bayesian models incorporating positional information: an application to transcription factor binding sites
    BMC Bioinformatics, Vol. 9 (04 June 2008), 262.
    by Nak-Kyeong Kim, Kannan Tharakaraman, Leonardo Marino-Ramirez, John L Spouge
    posted to position information by xili03 on 2008-06-17 06:53:06 as ** along with 1 person maximilianh
  • Computational identification of transcriptional regulatory elements in DNA sequence
    Nucl. Acids Res., Vol. 34, No. 12. (19 July 2006), pp. 3585-3598.
    by Debraj Guhathakurta
    posted to survey by xili03 on 2008-05-07 03:08:27 as ** along with 8 people and 1 group tmmurali jfr johncumbers reidy giovanni cabbagezs ankur_iitg vietanh0 GeschwindLab
  • Studying the functional conservation of cis-regulatory modules and their transcriptional output
    BMC Bioinformatics, Vol. 9 (29 April 2008), 220.
    by Denis C Bauer, Timothy L Bailey
    posted to cis-element by xili03 on 2008-05-05 07:29:43 as ** along with 2 people and 1 group maximilianh cisevol cis-regulatory-evolution
  • A survey of DNA motif finding algorithms
    BMC Bioinformatics, Vol. 8, No. Suppl 7. (2007)
    by Modan Das, Ho K Dai
    posted to survey by xili03 on 2008-05-05 03:25:38 as ** along with 7 people pradiptaray brant dquest nklee maximilianh yevishere csdhwang
  • Multi-objective optimization using genetic algorithms: A tutorial
    Reliability Engineering & System Safety, Vol. 91, No. 9. (September 2006), pp. 992-1007.
    by Abdullah Konak, David W Coit, Alice E Smith
    posted to evolutionary by xili03 on 2008-04-30 14:54:17 as ** along with 1 person kutabar
  • A co-evolutionary framework for regulatory motif discovery
    Evolutionary Computation, 2007. CEC 2007. IEEE Congress on (2007), pp. 3894-3901.
    by Michael A Lones, Andy M Tyrrell
    posted to evolutionary by xili03 on 2008-04-30 14:26:07 as **
  • Comparative analysis of methods for representing and searching for transcription factor binding sites
    Bioinformatics, Vol. 20, No. 18., 3516.
    by Robert Osada, Elena Zaslavsky
    posted to information by xili03 on 2008-04-30 09:15:35 as **
  • Effective transcription factor binding site prediction using a combination of optimization, a genetic algorithm and discriminant analysis to capture distant interactions
    BMC Bioinformatics, Vol. 8, No. 1. (2007)
    by Victor Levitsky, Elena Ignatieva, Elena Ananko, Igor Turnaev, Tatyana Merkulova, Nikolay Kolchanov, T Hodgman
    posted to genetic algorithm by xili03 on 2008-04-30 09:04:09 as ** along with 4 people nklee maximilianh yevishere csdhwang
  • Composite Module Analyst: identification of transcription factor binding site combinations using genetic algorithm.
    Nucleic acids research, Vol. 34, No. Web Server issue. (1 July 2006)
    by T Waleev, D Shtokalo, T Konovalova, N Voss, E Cheremushkin, P Stegmaier, O Kel-Margoulis, E Wingender, A Kel
    posted to genetic algorithm by xili03 on 2008-04-29 08:10:02 as **
  • Composite Module Analyst: a fitness-based tool for identification of transcription factor binding site combinations
    Bioinformatics, Vol. 22, No. 10. (15 May 2006), pp. 1190-1197.
    by A Kel, T Konovalova, T Waleev, E Cheremushkin, O Kel-Margoulis, E Wingender
    posted to genetic algorithm by xili03 on 2008-04-29 08:01:34 as **
  • CREME: a framework for identifying cis-regulatory modules in human-mouse conserved segments
    Bioinformatics, Vol. 19, No. 1. (2003)
    by Roded
    posted to statistical by xili03 on 2008-04-29 07:38:34 as **
  • Identification of functional clusters of transcription factor binding motifs in genome sequences: the MSCAN algorithm.
    Bioinformatics, Vol. 19 Suppl 1 (2003)
    by O Johansson, W Alkema, WW Wasserman, J Lagergren
    posted to statistical by xili03 on 2008-04-29 07:34:26 as ** along with 2 people and 1 group isimpson indigoviolet EisenLab
  • Statistical significance of clusters of motifs represented by position specific scoring matrices in nucleotide sequences
    Nucl. Acids Res., Vol. 30, No. 14. (15 July 2002), pp. 3214-3224.
    by Martin C Frith, John L Spouge, Ulla Hansen, Zhiping Weng
    posted to statistical by xili03 on 2008-04-29 07:30:02 as ** along with 1 person and 1 group indigoviolet EisenLab
  • Searching for statistically significant regulatory modules.
    Bioinformatics, Vol. 19 Suppl 2 (October 2003)
    by TL Bailey, WS Noble
    posted to statistical by xili03 on 2008-04-29 07:27:27 as ** along with 2 people and 2 groups indigoviolet stajich EisenLab Berkeley Mycology
  • A GA Approach to the Definition of Regulatory Signals in Genomic Sequences
    Genetic and Evolutionary Computation – GECCO 2004 (2004), pp. 380-391.
    by Giancarlo Mauri, Roberto Mosca, Giulio Pavesi
    posted to genetic algorithm by xili03 on 2008-04-29 04:29:24 as **
  • Modeling within-motif dependence for transcription factor binding site predictions.
    Bioinformatics, Vol. 20, No. 6. (12 April 2004), pp. 909-916.
    by Q Zhou, JS Liu
    posted to dependency by xili03 on 2008-04-29 01:59:20 as ** along with 1 person dquest
  • A graph-based motif detection algorithm models complex nucleotide dependencies in transcription factor binding sites.
    Nucleic Acids Res, Vol. 34, No. 20. (2006), pp. 5730-5739.
    by BT Naughton, E Fratkin, S Batzoglou, DL Brutlag
    posted to dependency by xili03 on 2008-04-29 01:57:17 as ** along with 4 people and 1 group GustavoLacerda indigoviolet nklee yevishere EisenLab
  • A Clustering Method for Improving the Global Search Capability of Genetic Algorithms
    (2000)
    by Leizer Schnitman, Takashi Yoneyama
    posted to algorithm genetic by xili03 on 2008-04-22 02:00:15 as **
  • Fitness sharing and niching methods revisited
    Evolutionary Computation, IEEE Transactions on, Vol. 2, No. 3. (1998), pp. 97-106.
    by B Sareni, L Krahenbuhl
    posted to algorithm genetic by xili03 on 2008-04-22 00:41:00 as **
  • A self-adaptive mate selection model for genetic programming
    Evolutionary Computation, 2005. The 2005 IEEE Congress on, Vol. 3 (2005), pp. 2707-2714 Vol. 3.
    by R Fry, Smith, AM Tyrrell
    posted to algorithm genetic by xili03 on 2008-04-22 00:40:31 as **
  • Regulatory motif discovery using a population clustering evolutionary algorithm.
    IEEE/ACM Trans Comput Biol Bioinform, Vol. 4, No. 3. (p 2007), pp. 403-414.
    by MA Lones, AM Tyrrell
    posted to evolutionary by xili03 on 2008-04-22 00:11:54 as read along with 4 people isimpson nklee idonaldson csdhwang
  • Integrated analysis of yeast regulatory sequences for biologically linked clusters of genes.
    Funct Integr Genomics, Vol. 3, No. 3. (July 2003), pp. 125-134.
    by A Sandelin, A Höglund, B Lenhard, WW Wasserman
    posted to algorithm by xili03 on 2008-04-21 03:55:29 as ** along with 2 people aalibes nklee
  • Evolutionary computation method for pattern recognition of cis-acting sites
    Biosystems, Vol. 72, No. 1-2. (November 2003), pp. 19-27.
    by Daniel Howard, Karl Benson
    posted to evolutionary by xili03 on 2008-04-21 03:44:44 as **
  • Discovery of sequence motifs related to coexpression of genes using evolutionary computation.
    Nucleic Acids Res, Vol. 32, No. 13. (2004), pp. 3826-3835.
    by GB Fogel, DG Weekes, G Varga, ER Dow, HB Harlow, JE Onyia, C Su
    posted to evolutionary by xili03 on 2008-04-21 03:37:46 as ** along with 2 people gpalidwor dquest
  • Evolutionary computation in bioinformatics: a review
    Systems, Man, and Cybernetics, Part C: Applications and Reviews, IEEE Transactions on, Vol. 36, No. 5. (2006), pp. 601-615.
    by SK Pal, S Bandyopadhyay, SS Ray
    posted to survey by xili03 on 2008-04-21 03:30:22 as **
  • The state of the art of mammalian promoter recognition
    Brief Bioinform, Vol. 4, No. 1. (1 January 2003), pp. 22-30.
    by Thomas Werner
    posted to survey by xili03 on 2008-04-21 03:24:03 as **
  • DNA binding sites: representation and discovery.
    Bioinformatics, Vol. 16, No. 1. (January 2000), pp. 16-23.
    by GD Stormo
    posted to survey by xili03 on 2008-04-21 03:21:13 as read along with 5 people kaarsinogen mbj dquest lusk ezralanglois
  • Computational prediction of transcription-factor binding site locations.
    Genome Biol, Vol. 5, No. 1. (2003)
    by ML Bulyk
    posted to survey by xili03 on 2008-04-21 03:08:58 as read along with 6 people and 1 group aalibes kaarsinogen lusk Stew nklee yevishere EisenLab
  • Evolution of Transcription Factor Binding Sites in Mammalian Gene Regulatory Regions: Conservation and Turnover
    Mol Biol Evol, Vol. 19, No. 7. (1 July 2002), pp. 1114-1121.
    by Emmanouil T Dermitzakis, Andrew G Clark
    posted to regulatory site by xili03 on 2008-04-21 02:47:03 as read along with 3 people and 2 groups adepace cisevol emptyhb EisenLab cis-regulatory-evolution
  • Statistical analysis of over-represented words in human promoter sequences.
    Nucleic Acids Res, Vol. 32, No. 3. (2004), pp. 949-958.
    by L Mariño-Ramírez, JL Spouge, GC Kanga, D Landsman
    posted to statistical by xili03 on 2008-04-15 05:33:38 as ** along with 2 people and 1 group kaspermunch smiddha Bioinformatics
  • Detecting subtle sequence signals: a Gibbs sampling strategy for multiple alignment.
    Science, Vol. 262, No. 5131. (8 October 1993), pp. 208-214.
    by CE Lawrence, SF Altschul, MS Boguski, JS Liu, AF Neuwald, JC Wootton
    posted to gibbssampling by xili03 on 2008-04-13 05:52:39 as ** along with 6 people wenhan dquest AaronDarling johncumbers jguinney seitentaisei
  • Statistical significance in biological sequence analysis.
    Brief Bioinform, Vol. 7, No. 1. (March 2006), pp. 2-24.
    by AY Mitrophanov, M Borodovsky
    posted to p-value by xili03 on 2008-04-10 06:37:12 as read along with 2 people wenhan Ayest
  • Finding motifs using random projections.
    J Comput Biol, Vol. 9, No. 2. (2002), pp. 225-242.
    by J Buhler, M Tompa
    posted to algorithm by xili03 on 2008-04-08 12:22:20 as ** along with 1 person dquest
  • Detection of potential positive regulatory motifs of transcription in yeast introns by comparative analysis of oligonucleotide frequencies
    Computational Biology and Chemistry, Vol. 27, No. 4-5. (October 2003), pp. 497-506.
    by Jing Zhang, Jun Hu, Xiu-Fan Shi, Huai Cao, Wei-Bo Liu
    posted to intron by xili03 on 2008-04-08 02:09:54 as **
  • Finding motifs for insufficient number of sequences with strong binding to transcription facto
    (2004), pp. 125-132.
    by Francis YL Chin, Henry CM Leung, SM Yiu, TW Lam, Roni Rosenfeld, WW Tsang, David K Smith, Y Jiang
    posted to algorithm by xili03 on 2008-04-08 01:36:15 as read
  • DNA motif representation with nucleotide dependency.
    IEEE/ACM Trans Comput Biol Bioinform, Vol. 5, No. 1. (r 2008), pp. 110-119.
    by F Chin, HC Leung
    posted to dependency motif by xili03 on 2008-04-06 03:38:03 as read along with 3 people Stew AbnerCYH maximilianh
  • notes An algorithm for finding signals of unknown length in DNA sequences.
    Bioinformatics, Vol. 17 Suppl 1 (2001)
    by G Pavesi, G Mauri, G Pesole
    posted to algorithm by xili03 on 2008-04-06 03:11:28 as ** along with 5 people ep161302 dquest xiaobeizhao smiddha nklee
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