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Ключевое слово motifpaper [151 articles]

Recent papers classified by the tag motifpaper.
  • notes POCO: discovery of regulatory patterns from promoters of oppositely expressed gene sets.
    Nucleic Acids Res, Vol. 33, No. Web Server issue. (1 July 2005)
    by M Kankainen, L Holm
    posted to motifpaper by dquest on 2006-10-02 17:33:01 as ** along with 1 person Terkko
  • notes BioProspector: discovering conserved DNA motifs in upstream regulatory regions of co-expressed genes.
    Pac Symp Biocomput (2001), pp. 127-138.
    by X Liu, DL Brutlag, JS Liu
    posted to motifpaper by dquest on 2006-09-29 21:37:15 as **
  • notes rVista for comparative sequence-based discovery of functional transcription factor binding sites.
    Genome Res, Vol. 12, No. 5. (May 2002), pp. 832-839.
    by GG Loots, I Ovcharenko, L Pachter, I Dubchak, EM Rubin
    posted to motifpaper by dquest on 2006-09-28 21:33:11 as *
  • notes Algorithms for extracting structured motifs using a suffix tree with an application to promoter and regulatory site consensus identification.
    J Comput Biol, Vol. 7, No. 3-4. (2000), pp. 345-362.
    by L Marsan, MF Sagot
    posted to motifpaper by dquest on 2006-09-29 21:35:59 as **
  • notes Detecting seeded motifs in DNA sequences.
    Nucleic Acids Res, Vol. 33, No. 15. (2005)
    by C Pizzi, S Bortoluzzi, A Bisognin, A Coppe, GA Danieli
    posted to motifpaper by dquest on 2006-10-02 17:30:25 as ** along with 2 people Cortel imouthesmp
  • notes Informative priors based on transcription factor structural class improve de novo motif discovery
    Bioinformatics, Vol. 22, No. 14. (15 July 2006), pp. e384-392.
    by Leelavati Narlikar, Raluca Gordan, Uwe Ohler, Alexander J Hartemink
    posted to motifpaper by dquest on 2007-08-17 07:25:41 as ** along with 3 people nklee idonaldson yevishere
  • notes Extracting regulatory sites from the upstream region of yeast genes by computational analysis of oligonucleotide frequencies.
    J Mol Biol, Vol. 281, No. 5. (4 September 1998), pp. 827-842.
    by J van Helden, B André, J Collado-Vides
    posted to motifpaper by dquest on 2006-09-28 21:32:14 as * along with 3 people johncumbers smiddha ale
  • notes From the Cover: Building a dictionary for genomes: Identification of presumptive regulatory sites by statistical analysis
    PNAS, Vol. 97, No. 18. (29 August 2000), pp. 10096-10100.
    by Harmen J Bussemaker, Hao Li, Eric D Siggia
    posted to motifpaper by dquest on 2006-09-29 21:33:35 as ** along with 3 people and 2 groups ep161302 ana johncumbers structural_bioinformatics Bioinformatics
  • notes Regulatory element detection using a probabilistic segmentation model.
    Proc Int Conf Intell Syst Mol Biol, Vol. 8 (2000), pp. 67-74.
    by HJ Bussemaker, H Li, ED Siggia
    posted to motifpaper by dquest on 2006-09-29 21:33:05 as **
  • notes RSIR: regularized sliced inverse regression for motif discovery.
    Bioinformatics, Vol. 21, No. 22. (15 November 2005), pp. 4169-4175.
    by W Zhong, P Zeng, P Ma, JS Liu, Y Zhu
    posted to motifpaper by dquest on 2006-10-02 17:29:07 as **
  • Finding DNA regulatory motifs within unaligned noncoding sequences clustered by whole-genome mRNA quantitation.
    Nat Biotechnol, Vol. 16, No. 10. (October 1998), pp. 939-945.
    by FP Roth, JD Hughes, PW Estep, GM Church
    posted to motifpaper by dquest on 2006-09-28 21:22:40 as ** along with 2 people and 1 group isimpson kengg Plantandetc
  • notes Finding exact optimal motifs in matrix representation by partitioning.
    Bioinformatics, Vol. 21 Suppl 2 (1 September 2005)
    by HC Leung, FY Chin
    posted to motifpaper by dquest on 2006-10-02 17:26:54 as **
  • Identification of consensus patterns in unaligned DNA sequences known to be functionally related.
    Comput Appl Biosci, Vol. 6, No. 2. (April 1990), pp. 81-92.
    by GZ Hertz, GW Hartzell, GD Stormo
    posted to motifpaper by dquest on 2006-09-28 21:18:41 as read
  • notes NestedMICA: sensitive inference of over-represented motifs in nucleic acid sequence
    Nucleic Acids Research, Vol. 33, No. 5. (2005), pp. 1445-1453.
    by Thomas A Down, Tim J Hubbard
    posted to motifpaper by dquest on 2006-10-02 17:25:24 as ** along with 3 people and 1 group waszak lyongu dpollard EisenLab
  • notes PhyME: a probabilistic algorithm for finding motifs in sets of orthologous sequences.
    BMC Bioinformatics, Vol. 5 (28 October 2004)
    by S Sinha, M Blanchette, M Tompa
    posted to motifpaper by dquest on 2006-09-28 21:17:45 as read along with 4 people eckart_bindewald adsmitty lusk xili03
  • notes Discovery of novel transcription factor binding sites by statistical overrepresentation.
    Nucleic Acids Res, Vol. 30, No. 24. (15 December 2002), pp. 5549-5560.
    by S Sinha, M Tompa
    posted to motifpaper by dquest on 2006-09-29 21:19:03 as ** along with 8 people wenhan ep161302 kaarsinogen xiaobeizhao smiddha GeeSharpMinor xi03 xili03
  • notes A multistep bioinformatic approach detects putative regulatory elements in gene promoters.
    BMC Bioinformatics, Vol. 6 (2005)
    by S Bortoluzzi, A Coppe, A Bisognin, C Pizzi, GA Danieli
    posted to motifpaper by dquest on 2006-10-02 17:24:15 as **
  • notes A statistical method for finding transcription factor binding sites.
    Proc Int Conf Intell Syst Mol Biol, Vol. 8 (2000), pp. 344-354.
    by S Sinha, M Tompa
    posted to motifpaper by dquest on 2006-09-29 21:17:52 as **
  • notes Quantitative analysis of the relationship between nucleotide sequence and functional activity.
    Nucleic Acids Res, Vol. 14, No. 16. (26 August 1986), pp. 6661-6679.
    by GD Stormo, TD Schneider, L Gold
    posted to motifpaper by dquest on 2006-10-03 20:41:24 as **
  • Discovery of Regulatory Elements by a Computational Method for Phylogenetic Footprinting
    Genome Res., Vol. 12, No. 5. (1 May 2002), pp. 739-748.
    by Mathieu Blanchette, Martin Tompa
    posted to motifpaper by dquest on 2006-09-28 21:13:38 as read along with 5 people and 2 groups chad_davis balajis lyongu dpollard csdhwang EisenLab cis-regulatory-evolution
  • Promoter region-based classification of genes.
    Pac Symp Biocomput (2001), pp. 151-163.
    by P Pavlidis, TS Furey, M Liberto, D Haussler, WN Grundy
    posted to motifpaper by dquest on 2007-05-12 23:08:50 as **
  • Detecting putative orthologs.
    Bioinformatics, Vol. 19, No. 13. (1 September 2003), pp. 1710-1711.
    by DP Wall, HB Fraser, AE Hirsh
    posted to motifpaper orthalog by dquest on 2007-11-23 21:06:21 as ** along with 3 people and 3 groups ana indigoviolet ninch structural_bioinformatics Bioinformatics EisenLab
  • Orthologous Transcription Factors in Bacteria Have Different Functions and Regulate Different Genes
    PLoS Computational Biology, Vol. 3, No. 9. (1 September 2007), e175.
    by Morgan N Price, Paramvir S Dehal, Adam P Arkin
    posted to motifpaper by dquest on 2007-11-23 21:02:52 as ** along with 6 people and 3 groups dpollard djkt zwang cabbagezs heliopais blobbybirdman EisenLab cis-regulatory-evolution Myxo group
  • notes Computational identification of cis-acting elements affecting post-transcriptional control of gene expression in Saccharomyces cerevisiae.
    Nucleic Acids Res, Vol. 28, No. 7. (1 April 2000), pp. 1604-1617.
    by JS Jacobs Anderson, R Parker
    posted to motifpaper by dquest on 2006-09-29 21:08:55 as **
  • Factors influencing the identification of transcription factor binding sites by cross-species comparison.
    Genome Res, Vol. 12, No. 10. (October 2002), pp. 1523-1532.
    by LA McCue, W Thompson, CS Carmack, CE Lawrence
    posted to motifpaper by dquest on 2006-09-28 21:05:10 as ***** along with 2 people kaarsinogen nklee
  • notes Efficient detection of unusual words.
    J Comput Biol, Vol. 7, No. 1-2. (r 2000), pp. 71-94.
    by A Apostolico, ME Bock, S Lonardi, X Xu
    posted to motifpaper by dquest on 2006-09-29 21:07:09 as ** along with 1 person suizan
  • notes Combinatorial approaches to finding subtle signals in DNA sequences.
    Proc Int Conf Intell Syst Mol Biol, Vol. 8 (2000), pp. 269-278.
    by PA Pevzner, SH Sze
    posted to motifpaper by dquest on 2006-09-29 21:04:23 as ** along with 3 people ep161302 lesliehong xili03
  • LAGAN and Multi-LAGAN: efficient tools for large-scale multiple alignment of genomic DNA.
    Genome Res, Vol. 13, No. 4. (April 2003), pp. 721-731.
    by M Brudno, CB Do, GM Cooper, MF Kim, E Davydov, ED Green, A Sidow, S Batzoglou,
    posted to motifpaper by dquest on 2007-11-23 20:55:06 as ** along with 12 people and 1 group Neeperando operon balajis dpollard xwbcn adepace hdopazo lusk Garamonfok adijr natstreet nklee EisenLab
  • notes Phylogenetic footprinting of transcription factor binding sites in proteobacterial genomes.
    Nucleic Acids Res, Vol. 29, No. 3. (1 February 2001), pp. 774-782.
    by L McCue, W Thompson, C Carmack, MP Ryan, JS Liu, V Derbyshire, CE Lawrence
    posted to motifpaper by dquest on 2006-09-28 21:03:12 as read along with 2 people and 1 group adepace nklee EisenLab
  • KEGG: kyoto encyclopedia of genes and genomes.
    Nucleic Acids Res, Vol. 28, No. 1. (1 January 2000), pp. 27-30.
    by M Kanehisa, S Goto
    posted to motifpaper by dquest on 2007-11-23 20:49:45 as ** along with 11 people jerome_ucsf_slb natstreet grottenolm Evangelia j3xucite fisherp koerner ruvido noby naegele katerinakal
  • notes Discovering regulatory elements in non-coding sequences by analysis of spaced dyads.
    Nucleic Acids Res, Vol. 28, No. 8. (15 April 2000), pp. 1808-1818.
    by J van Helden, AF Rios, J Collado-Vides
    posted to motifpaper by dquest on 2006-09-29 21:03:08 as **
  • notes Automatic extraction of motifs represented in the hidden Markov model from a number of DNA sequences.
    Bioinformatics, Vol. 14, No. 4. (1998), pp. 317-325.
    by T Yada, Y Totoki, M Ishikawa, K Asai, K Nakai
    posted to motifpaper by dquest on 2006-09-29 21:02:06 as **
  • notes Use of the 'Perceptron' algorithm to distinguish translational initiation sites in E. coli.
    Nucleic Acids Res, Vol. 10, No. 9. (11 May 1982), pp. 2997-3011.
    by GD Stormo, TD Schneider, L Gold, A Ehrenfeucht
    posted to motifpaper by dquest on 2006-10-03 20:05:51 as read
  • WeederH: an algorithm for finding conserved regulatory motifs and regions in homologous sequences
    BMC Bioinformatics, Vol. 8 (07 February 2007), 46.
    by Giulio Pavesi, Federico Zambelli, Graziano Pesole
    posted to motifpaper by dquest on 2007-05-12 23:02:17 as ** along with 2 people nuin GustavoLacerda
  • notes Combinatorial pattern discovery in biological sequences: The TEIRESIAS algorithm.
    Bioinformatics, Vol. 14, No. 1. (1998), pp. 55-67.
    by I Rigoutsos, A Floratos
    posted to motifpaper by dquest on 2006-09-29 21:00:46 as ** along with 3 people and 1 group thaliana okarsligil heliopais Bioinformatics
  • 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 motifpaper motifsampling by dquest on 2007-11-23 13:58:08 as ** along with 3 people and 1 group chad_davis dpollard yevishere EisenLab
  • Algorithms for phylogenetic footprinting.
    J Comput Biol, Vol. 9, No. 2. (2002), pp. 211-223.
    by M Blanchette, B Schwikowski, M Tompa
    posted to motifpaper by dquest on 2006-09-28 20:54:55 as read along with 1 person chad_davis
  • notes Over- and underrepresentation of short DNA words in herpesvirus genomes.
    J Comput Biol, Vol. 3, No. 3. (1996), pp. 345-360.
    by MY Leung, GM Marsh, TP Speed
    posted to motifpaper by dquest on 2006-09-29 20:39:15 as **
  • notes Identification of functional elements in unaligned nucleic acid sequences by a novel tuple search algorithm.
    Comput Appl Biosci, Vol. 12, No. 1. (February 1996), pp. 71-80.
    by F Wolfertstetter, K Frech, G Herrmann, T Werner
    posted to motifpaper by dquest on 2006-09-29 20:37:58 as **
  • Approaches to the automatic discovery of patterns in biosequences.
    J Comput Biol, Vol. 5, No. 2. (1998), pp. 279-305.
    by A Brazma, I Jonassen, I Eidhammer, D Gilbert
    posted to motifpaper motifsampling by dquest on 2007-11-23 13:48:37 as ** along with 1 person treangen
  • notes Fitting a mixture model by expectation maximization to discover motifs in biopolymers.
    Proc Int Conf Intell Syst Mol Biol, Vol. 2 (1994), pp. 28-36.
    by TL Bailey, C Elkan
    posted to motifpaper by dquest on 2006-09-29 20:26:31 as ** along with 1 person lusk
  • notes Linguistics of nucleotide sequences. I: The significance of deviations from mean statistical characteristics and prediction of the frequencies of occurrence of words.
    J Biomol Struct Dyn, Vol. 6, No. 5. (April 1989), pp. 1013-1026.
    by PA Pevzner, Borodovsky MYu, AA Mironov
    posted to motifpaper by dquest on 2006-09-29 20:24:25 as **
  • notes DBTBS: a database of Bacillus subtilis promoters and transcription factors
    Nucl. Acids Res., Vol. 29, No. 1. (1 January 2001), pp. 278-280.
    by Takahiro Ishii, Ken-Ichi Yoshida, Goro Terai, Yasutaro Fujita, Kenta Nakai
    posted to motifpaper by dquest on 2006-11-03 19:04:22 as read
  • notes Methods for discovering novel motifs in nucleic acid sequences.
    Comput Appl Biosci, Vol. 5, No. 4. (October 1989), pp. 293-298.
    by R Staden
    posted to motifpaper by dquest on 2006-09-29 20:17:23 as **
  • notes Identifying DNA and protein patterns with statistically significant alignments of multiple sequences
    Bioinformatics, Vol. 15, No. 7. (1 July 1999), pp. 563-577.
    by Gz Hertz, Gd Stormo
    posted to motifpaper by dquest on 2006-09-29 20:16:29 as ** along with 4 people and 1 group chad_davis tuck indigoviolet lusk EisenLab
  • notes Recognition of characteristic patterns in sets of functionally equivalent DNA sequences.
    Comput Appl Biosci, Vol. 3, No. 3. (September 1987), pp. 223-227.
    by G Mengeritsky, TF Smith
    posted to motifpaper by dquest on 2006-09-29 20:15:22 as **
  • notes Bipartite pattern discovery by entropy minimization-based multiple local alignment.
    Nucleic Acids Res, Vol. 32, No. 17. (2004), pp. 4979-4991.
    by C Bi, PK Rogan
    posted to motifpaper by dquest on 2006-10-02 16:13:59 as **
  • notes An algorithm for finding protein-DNA binding sites with applications to chromatin-immunoprecipitation microarray experiments.
    Nat Biotechnol, Vol. 20, No. 8. (August 2002), pp. 835-839.
    by XS Liu, DL Brutlag, JS Liu
    posted to motifpaper by dquest on 2006-09-28 20:43:59 as read along with 4 people troels_marstrand opheliav yevishere xili03
  • Rigorous pattern-recognition methods for DNA sequences. Analysis of promoter sequences from Escherichia coli.
    J Mol Biol, Vol. 186, No. 1. (5 November 1985), pp. 117-128.
    by DJ Galas, M Eggert, MS Waterman
    posted to motifpaper by dquest on 2006-09-29 20:14:45 as **
  • Microarray-Based Analysis of the Staphylococcus aureus sigmaB Regulon
    J. Bacteriol., Vol. 186, No. 13. (1 July 2004), pp. 4085-4099.
    by Markus Bischoff, Paul Dunman, Jan Kormanec, Daphne Macapagal, Ellen Murphy, William Mounts, Brigitte Berger-Bachi, Steven Projan
    posted to motifpaper by dquest on 2007-05-12 21:54:56 as ** along with 1 person daniel_quest
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