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indigoviolets library [368 articles]

Neue Artikel in indigoviolets Bibliothek.
  • The Making of a Fly: The Genetics of Animal Design
    (15 April 1992)
    by Peter A Lawrence
    posted to no-tag by indigoviolet on 2007-12-15 03:00:50 as ** along with 1 group EisenLab
  • WebLogo: A Sequence Logo Generator
    Genome Res., Vol. 14, No. 6. (1 June 2004), pp. 1188-1190.
    by Gavin E Crooks, Gary Hon, John-Marc Chandonia, Steven E Brenner
    posted to no-tag by indigoviolet on 2007-12-12 15:10:45 as ** along with 4 people and 2 groups analogAI xiaobeizhao sobolevnrm yevishere EisenLab baker-group
  • Sequence logos: a new way to display consensus sequences.
    Nucleic Acids Res, Vol. 18, No. 20. (25 October 1990), pp. 6097-6100.
    by TD Schneider, RM Stephens
    posted to no-tag by indigoviolet on 2007-12-12 15:07:59 as ** along with 2 people and 1 group analogAI yevishere EisenLab
  • Selection of DNA binding sites by regulatory proteins. Statistical-mechanical theory and application to operators and promoters.
    J Mol Biol, Vol. 193, No. 4. (20 February 1987), pp. 723-750.
    by OG Berg, PH von Hippel
    posted to no-tag by indigoviolet on 2007-12-12 15:05:58 as ** along with 7 people and 2 groups zambujo brant jjray lusk discreteonyxorb cisevol Ema EisenLab cis-regulatory-evolution
  • An overview of the structures of protein-DNA complexes.
    Genome Biol, Vol. 1, No. 1. (2000)
    by NM Luscombe, SE Austin, HM Berman, JM Thornton
    posted to no-tag by indigoviolet on 2007-12-12 14:49:58 as ** along with 4 people and 1 group kaarsinogen medic0747 emptyhb jonsta247 EisenLab
  • Drosophila DNase I footprint database: a systematic genome annotation of transcription factor binding sites in the fruitfly, Drosophila melanogaster.
    Bioinformatics, Vol. 21, No. 8. (15 April 2005), pp. 1747-1749.
    by CM Bergman, JW Carlson, SE Celniker
    posted to no-tag by indigoviolet on 2007-12-12 14:40:40 as ** along with 1 person and 2 groups yas EisenLab T_lab
  • GOstat: find statistically overrepresented Gene Ontologies within a group of genes.
    Bioinformatics, Vol. 20, No. 9. (12 June 2004), pp. 1464-1465.
    by T Beissbarth, TP Speed
    posted to no-tag by indigoviolet on 2007-12-12 14:40:11 as ** along with 5 people and 1 group Yanno miguel RMGraze jdiggans yevishere EisenLab
  • Gene ontology: tool for the unification of biology. The Gene Ontology Consortium.
    Nat Genet, Vol. 25, No. 1. (May 2000), pp. 25-29.
    by M Ashburner, CA Ball, JA Blake, D Botstein, H Butler, JM Cherry, AP Davis, K Dolinski, SS Dwight, JT Eppig, MA Harris, DP Hill, L Issel-Tarver, A Kasarskis, S Lewis, JC Matese, JE Richardson, M Ringwald, GM Rubin, G Sherlock
    posted to no-tag by indigoviolet on 2007-12-12 14:35:50 as ** along with 27 people and 5 groups CitoJam aalibes miguel dragonrez lfriedl chad_davis yas balajis benny dullhunk nirfriedman fisherp caporaso helliontroy zlu gurkanbebek djkt massivemayhem incovoma leechuck aconesa sgoetz javamint bootsy PunkRock natstreet naegele kdl Bioinformatics EisenLab T_lab biomedical-nlp
  • Temporal patterns of fruit fly (Drosophila) evolution revealed by mutation clocks.
    Mol Biol Evol, Vol. 21, No. 1. (January 2004), pp. 36-44.
    by K Tamura, S Subramanian, S Kumar
    posted to no-tag by indigoviolet on 2007-12-12 14:32:29 as ** along with 1 group EisenLab
  • Gene Recognition Via Spliced Sequence Alignment
    Proceedings of the National Academy of Sciences of the United States of America, Vol. 93, No. 17. (1996), pp. 9061-9066.
    by Mikhail S Gelfand, Andrey A Mironov, Pavel A Pevzner
    posted to no-tag by indigoviolet on 2007-12-12 14:20:24 as ** along with 1 group EisenLab
  • TRANSFAC: a database on transcription factors and their DNA binding sites.
    Nucleic Acids Res, Vol. 24, No. 1. (1 January 1996), pp. 238-241.
    by E Wingender, P Dietze, H Karas, R Knüppel
    posted to database by indigoviolet on 2007-12-12 14:09:36 as ** along with 2 people and 1 group ea dquest EisenLab
  • Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase.
    Science, Vol. 249, No. 4968. (3 August 1990), pp. 505-510.
    by C Tuerk, L Gold
    posted to no-tag by indigoviolet on 2007-12-12 14:09:06 as ** along with 1 person and 1 group leelarcombe EisenLab
  • 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 algorithm motif by indigoviolet on 2007-12-12 14:01:38 as ** along with 3 people and 1 group tuck dquest lusk EisenLab
  • A computational genomics approach to the identification of gene networks
    Nucl. Acids Res., Vol. 25, No. 18. (15 September 1997), pp. 3594-3604.
    by A Wagner
    posted to motif by indigoviolet on 2007-12-12 11:05:07 as ** along with 1 group EisenLab
  • 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 motif by indigoviolet on 2007-12-12 11:00:03 as ** along with 3 people and 1 group xili03 nklee yevishere EisenLab
  • Combining evidence using p-values: application to sequence homology searches.
    Bioinformatics, Vol. 14, No. 1. (1998), pp. 48-54.
    by TL Bailey, M Gribskov
    posted to algorithm by indigoviolet on 2007-12-12 10:57:32 as ** along with 1 group EisenLab
  • Methods and statistics for combining motif match scores.
    J Comput Biol, Vol. 5, No. 2. (1998), pp. 211-221.
    by TL Bailey, M Gribskov
    posted to motif by indigoviolet on 2007-12-12 10:56:53 as ** along with 1 group EisenLab
  • Statistical extraction of Drosophila cis-regulatory modules using exhaustive assessment of local word frequency.
    BMC Bioinformatics, Vol. 4 (22 December 2003)
    by AG Nazina, DA Papatsenko
    posted to algorithm enhancer-prediction by indigoviolet on 2007-12-12 09:21:45 as ** along with 1 group EisenLab
  • Detection of cis -element clusters in higher eukaryotic DNA
    Bioinformatics, Vol. 17, No. 10. (1 October 2001), pp. 878-889.
    by Martin C Frith, Ulla Hansen, Zhiping Weng
    posted to algorithm enhancer-prediction by indigoviolet on 2007-12-12 09:15:36 as ** along with 1 group 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 algorithm enhancer-prediction by indigoviolet on 2007-12-12 09:15:32 as ** along with 1 person and 1 group xili03 EisenLab
  • JASPAR: an open-access database for eukaryotic transcription factor binding profiles.
    Nucleic Acids Res, Vol. 32, No. Database issue. (1 January 2004)
    by A Sandelin, W Alkema, P Engström, WW Wasserman, B Lenhard
    posted to database motif by indigoviolet on 2007-12-12 09:14:43 as ** along with 4 people and 2 groups aalibes jguinney nklee heliopais EisenLab Motif Discovery
  • ClusterDraw web server: a tool to identify and visualize clusters of binding motifs for transcription factors
    Bioinformatics, Vol. 23, No. 8. (15 April 2007), pp. 1032-1034.
    by Papatsenko, Dmitri
    posted to algorithm enhancer-prediction by indigoviolet on 2007-12-12 09:12:26 as ** along with 1 person and 1 group jyuh EisenLab
  • Cluster-Buster: finding dense clusters of motifs in DNA sequences
    Nucl. Acids Res., Vol. 31, No. 13. (1 July 2003), pp. 3666-3668.
    by Martin C Frith, Michael C Li, Zhiping Weng
    posted to algorithm enhancer-prediction by indigoviolet on 2007-12-12 09:10:09 as ** along with 1 group EisenLab
  • Decoding human regulatory circuits.
    Genome Res, Vol. 14, No. 10A. (October 2004), pp. 1967-1974.
    by W Thompson, MJ Palumbo, WW Wasserman, JS Liu, CE Lawrence
    posted to algorithm enhancer-prediction by indigoviolet on 2007-12-12 09:09:40 as ** along with 1 person and 1 group chad_davis EisenLab
  • CisModule: de novo discovery of cis-regulatory modules by hierarchical mixture modeling.
    Proc Natl Acad Sci U S A, Vol. 101, No. 33. (17 August 2004), pp. 12114-12119.
    by Q Zhou, WH Wong
    posted to algorithm enhancer-prediction by indigoviolet on 2007-12-12 08:38:23 as ** along with 2 people and 1 group ep161302 dpollard EisenLab
  • De novo cis-regulatory module elicitation for eukaryotic genomes
    PNAS, Vol. 102, No. 20. (17 May 2005), pp. 7079-7084.
    by Mayetri Gupta, Jun S Liu
    posted to algorithm enhancer-prediction by indigoviolet on 2007-12-12 08:37:52 as ** along with 2 people and 1 group tuck lusk EisenLab
  • Modulefinder: a tool for computational discovery of cis regulatory modules.
    Pac Symp Biocomput (2005), pp. 519-530.
    by AA Philippakis, FS He, ML Bulyk
    posted to algorithm enhancer-prediction by indigoviolet on 2007-12-12 07:50:58 as ** along with 1 person and 1 group ccr EisenLab
  • 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 algorithm enhancer-prediction by indigoviolet on 2007-12-12 07:47:27 as ** along with 1 person and 1 group xili03 EisenLab
  • MAPPER: a search engine for the computational identification of putative transcription factor binding sites in multiple genomes.
    BMC Bioinformatics, Vol. 6 (2005)
    by VD Marinescu, IS Kohane, A Riva
    posted to algorithm motif by indigoviolet on 2007-12-12 05:44:21 as ** along with 1 group EisenLab
  • CREME: a framework for identifying cis-regulatory modules in human-mouse conserved segments.
    Bioinformatics, Vol. 19 Suppl 1 (2003)
    by R Sharan, I Ovcharenko, A Ben-Hur, RM Karp
    posted to algorithm enhancer-prediction by indigoviolet on 2007-12-12 05:41:45 as ** along with 1 person and 1 group dquest EisenLab
  • Identification of regulatory regions which confer muscle-specific gene expression
    Journal of Molecular Biology, Vol. 278, No. 1. (24 April 1998), pp. 167-181.
    by Wyeth W Wasserman, James W Fickett
    posted to algorithm enhancer-prediction by indigoviolet on 2007-12-12 05:40:08 as ** along with 1 person and 1 group gpalidwor EisenLab
  • Prediction of similarly acting cis-regulatory modules by subsequence profiling and comparative genomics in Drosophila melanogaster and D.pseudoobscura.
    Bioinformatics, Vol. 20, No. 16. (1 November 2004), pp. 2738-2750.
    by YH Grad, FP Roth, MS Halfon, GM Church
    posted to algorithm enhancer-prediction by indigoviolet on 2007-12-11 10:22:44 as ** along with 1 person and 1 group maximilianh EisenLab
  • Finding cis-regulatory modules in Drosophila using phylogenetic hidden Markov models
    Bioinformatics, Vol. 23, No. 16. (15 August 2007), pp. 2031-2037.
    by Wendy S Wong, Rasmus Nielsen
    posted to algorithm enhancer-prediction by indigoviolet on 2007-12-11 05:05:47 as ** along with 2 people and 1 group cabbagezs csdhwang EisenLab
  • Searching for statistically significant regulatory modules.
    Bioinformatics, Vol. 19 Suppl 2 (October 2003)
    by TL Bailey, WS Noble
    posted to algorithm enhancer-prediction by indigoviolet on 2007-12-05 13:00:37 as ** along with 2 people and 2 groups xili03 stajich EisenLab Berkeley Mycology
  • Homotypic regulatory clusters in Drosophila.
    Genome Res, Vol. 13, No. 4. (April 2003), pp. 579-588.
    by AP Lifanov, VJ Makeev, AG Nazina, DA Papatsenko
    posted to algorithm enhancer-prediction by indigoviolet on 2007-12-05 12:56:45 as ** along with 1 group EisenLab
  • Genome-wide analysis of clustered Dorsal binding sites identifies putative target genes in the Drosophila embryo.
    Proc Natl Acad Sci U S A, Vol. 99, No. 2. (22 January 2002), pp. 763-768.
    by M Markstein, P Markstein, V Markstein, MS Levine
    posted to algorithm enhancer-prediction by indigoviolet on 2007-12-05 12:38:23 as ** along with 1 person and 1 group dpollard EisenLab
  • SCORE: A computational approach to the identification of cis-regulatory modules and target genes in whole-genome sequence data
    Proceedings of the National Academy of Sciences, Vol. 99, No. 15. (23 July 2002), pp. 9888-9893.
    by Mark Rebeiz, Nick L Reeves, James W Posakony
    posted to algorithm enhancer-prediction by indigoviolet on 2007-12-05 12:37:56 as ** along with 1 group EisenLab
  • Identifying cis-regulatory modules by combining comparative and compositional analysis of DNA
    Bioinformatics, Vol. 22, No. 23. (1 December 2006), pp. 2858-2864.
    by Pierstorff, Nora, Bergman, M Casey, Wiehe, Thomas
    posted to algorithm enhancer-prediction by indigoviolet on 2007-12-05 12:15:18 as ** along with 2 people and 1 group brant emilyhare EisenLab
  • Stubb: a program for discovery and analysis of cis-regulatory modules.
    Nucleic Acids Res, Vol. 34, No. Web Server issue. (1 July 2006)
    by S Sinha, Y Liang, E Siggia
    posted to algorithm enhancer-prediction by indigoviolet on 2007-12-05 12:14:38 as ** along with 2 people and 1 group Stew csdhwang EisenLab
  • Cross-species comparison significantly improves genome-wide prediction of cis-regulatory modules in Drosophila.
    BMC Bioinformatics, Vol. 5 (9 September 2004)
    by S Sinha, MD Schroeder, U Unnerstall, U Gaul, ED Siggia
    posted to algorithm enhancer-prediction by indigoviolet on 2007-12-05 12:14:10 as ** along with 1 group EisenLab
  • Computational detection of genomic cis-regulatory modules applied to body patterning in the early Drosophila embryo.
    BMC Bioinformatics, Vol. 3 (24 October 2002)
    by N Rajewsky, M Vergassola, U Gaul, ED Siggia
    posted to algorithm enhancer-prediction by indigoviolet on 2007-12-05 12:13:43 as ** along with 5 people and 1 group ansobol adepace koller Stew csdhwang EisenLab
  • BLAT--the BLAST-like alignment tool.
    Genome Res, Vol. 12, No. 4. (April 2002), pp. 656-664.
    by WJ Kent
    posted to algorithm alignment by indigoviolet on 2007-12-03 20:27:15 as ** along with 17 people and 1 group talponer operon miguel pcahan1 Ayest mtagaya treangen michC djkt timflutre olympos cjeans wenhan natstreet antonkratz inesdesantiago yoanjacquemin EisenLab
  • NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins.
    Nucleic Acids Res, Vol. 35, No. Database issue. (January 2007)
    by KD Pruitt, T Tatusova, DR Maglott
    posted to database by indigoviolet on 2007-12-03 18:17:47 as ** along with 4 people and 1 group ninch kuhn jjray incovoma EisenLab
  • DroSpeGe: rapid access database for new Drosophila species genomes.
    Nucleic Acids Res, Vol. 35, No. Database issue. (January 2007)
    by DG Gilbert
    posted to database by indigoviolet on 2007-12-03 18:15:01 as ** along with 1 group EisenLab
  • Drosophila melanogaster: a case study of a model genomic sequence and its consequences.
    Genome Res, Vol. 15, No. 12. (December 2005), pp. 1661-1667.
    by M Ashburner, CM Bergman
    posted to annotation review by indigoviolet on 2007-12-03 18:11:52 as ** along with 2 people and 2 groups emilyhare penka EisenLab Nie
  • The FlyBase database of the Drosophila Genome Projects and community literature. The FlyBase Consortium.
    Nucleic Acids Res, Vol. 27, No. 1. (1 January 1999), pp. 85-88.
    by Flybase Consortium
    posted to database by indigoviolet on 2007-12-03 18:10:04 as ** along with 1 person and 1 group CitoJam EisenLab
  • PAML: a program package for phylogenetic analysis by maximum likelihood.
    Comput Appl Biosci, Vol. 13, No. 5. (October 1997), pp. 555-556.
    by Z Yang
    posted to algorithm molecular-evolution by indigoviolet on 2007-12-03 18:07:12 as ** along with 9 people and 3 groups bjorns chrn chad_davis penka BioNica stajich pv usagi-kirin jmjimenez EisenLab Nie Berkeley Mycology
  • T-Coffee: A novel method for fast and accurate multiple sequence alignment.
    J Mol Biol, Vol. 302, No. 1. (8 September 2000), pp. 205-217.
    by C Notredame, DG Higgins, J Heringa
    posted to algorithm alignment by indigoviolet on 2007-12-03 18:04:40 as ** along with 8 people and 1 group miguel dayjm ffranca treangen Haggan siebertm adijr marti EisenLab
  • Whole-genome sequence assembly for mammalian genomes: Arachne 2.
    Genome Res, Vol. 13, No. 1. (January 2003), pp. 91-96.
    by DB Jaffe, J Butler, S Gnerre, E Mauceli, K Lindblad-Toh, JP Mesirov, MC Zody, ES Lander
    posted to algorithm assembly by indigoviolet on 2007-12-03 12:32:59 as ** along with 4 people and 1 group bpb AaronDarling wenhan farhat EisenLab
  • Base-calling of automated sequencer traces using phred. II. Error probabilities.
    Genome Res, Vol. 8, No. 3. (March 1998), pp. 186-194.
    by B Ewing, P Green
    posted to algorithm by indigoviolet on 2007-12-03 12:32:33 as ** along with 2 people and 2 groups balajis giovanni Bioinformatics EisenLab
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