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dpollards prediction [43 articles]

Neue Publikationen in dpollards Bibliothek eingetragen unter dem Bezeichner: prediction. You can also see everyone's prediction.
  • Using DNA duplex stability information for transcription factor binding site discovery.
    Pac Symp Biocomput (2008), pp. 453-464.
    by R Gordân, AJ Hartemink
    posted to binding_site biophysical_model method motif_detection prediction transcription_factor by dpollard on 2008-02-01 06:21:41 as ** along with 1 person and 1 group bootsy 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 ab_initio cis_regulatory_elements clustering method prediction by dpollard on 2007-12-05 22:46:33 as read along with 2 people and 1 group ep161302 indigoviolet 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 cis_regulatory_elements clustering drosophila embryonic_patterning method prediction by dpollard on 2007-12-05 20:41:26 as read along with 1 person and 1 group indigoviolet EisenLab
  • Accurate gene-tree reconstruction by learning gene- and species-specific substitution rates across multiple complete genomes
    Genome Res. (7 November 2007), gr.7105007.
    by Matthew D Rasmussen, Manolis Kellis
    posted to drosophila method phylogeny prediction yeast by dpollard on 2007-11-21 02:56:16 as read along with 2 people and 1 group stajich caseybrown EisenLab
  • Reliable prediction of regulator targets using 12 Drosophila genomes.
    Genome Res (7 November 2007)
    by Alexander Stark, Pouya Kheradpour, Sushmita Roy, Manolis Kellis
    posted to cis_regulatory_elements drosophila eisen_journal_club matt_presented prediction round_robin by dpollard on 2007-11-17 00:01:32 as *** along with 7 people and 2 groups lp2 nklee maximilianh roys caseybrown emptyhb barwil EisenLab cis-regulatory-evolution
  • Transcriptional Control in the Segmentation Gene Network of Drosophila
    PLoS Biology, Vol. 2, No. 9. (1 September 2004), e271.
    by Mark D Schroeder, Michael Pearce, John Fak, Hongqing Fan, Ulrich Unnerstall, Eldon Emberly, Nikolaus Rajewsky, Eric D Siggia, Ulrike Gaul
    posted to cis_regulatory_elements embryonic_patterning expression_pattern method modeling prediction by dpollard on 2007-11-07 22:44:52 as read along with 5 people and 3 groups indigoviolet adepace wrowell emptyhb dlmace EisenLab Cline_lab UH - Computational Biology
  • 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 ab_initio binding_site conservation method prediction by dpollard on 2007-11-01 00:41:11 as read along with 5 people and 2 groups chad_davis balajis lyongu dquest csdhwang EisenLab cis-regulatory-evolution
  • Regulatory element detection using correlation with expression.
    Nat Genet, Vol. 27, No. 2. (February 2001), pp. 167-171.
    by HJ Bussemaker, H Li, ED Siggia
    posted to ab_initio binding_site gene_expression prediction by dpollard on 2007-11-01 00:10:36 as read along with 2 people and 2 groups nickluscombe heliopais EisenLab EBI-regulation
  • Incorporating evolution of transcription factor binding sites into annotated alignments.
    J Biosci, Vol. 32, No. 5. (August 2007), pp. 841-850.
    by AS Bais, S Grossmann, M Vingron
    posted to alignment binding_site conserved method prediction by dpollard on 2007-10-25 02:20:56 as ** along with 1 person and 2 groups maximilianh EisenLab cis-regulatory-evolution
  • Discriminative motif discovery in DNA and protein sequences using the DEME Algorithm
    BMC Bioinformatics, Vol. 8, No. 1. (2007)
    by Emma Redhead, Timothy Bailey
    posted to dan_presented eisen_journal_club motif_detection prediction round_robin by dpollard on 2007-10-25 01:20:26 as *** along with 5 people and 1 group cjeans nklee niallhaslam maximilianh idonaldson EisenLab
  • Discovering and detecting transposable elements in genome sequences.
    Brief Bioinform (10 October 2007)
    by Casey M M Bergman, Hadi Quesneville
    posted to prediction te transposable_elements by dpollard on 2007-10-25 01:18:08 as ** along with 8 people and 2 groups gpappas timflutre GustavoLacerda cabbagezs maximilianh cisevol urgi yoanjacquemin EisenLab BergmanLab
  • A Survey of Genomic Properties for the Detection of Regulatory Polymorphisms
    PLoS Computational Biology, Vol. 3, No. 6. (1 June 2007), e106.
    by Stephen B Montgomery, Obi L Griffith, Johanna M Schuetz, Angela Brooks-Wilson, Steven J Jones
    posted to cis_regulatory_elements eisen_journal_club prediction regulatory_polymorphism round_robin sequence_properties snp venky_presented by dpollard on 2007-06-15 22:54:33 as *** along with 1 person and 3 groups cisevol Bioinformatics EisenLab cis-regulatory-evolution
  • Systematic detection of statistically overrepresented DNA motif association rules.
    Genome Inform, Vol. 17, No. 1. (2006), pp. 124-133.
    by JM Lin, Z Weng
    posted to ab_initio binding_site eisen_journal_club method motif_detection prediction round_robin rules venky_presented by dpollard on 2007-06-15 00:04:13 as ** along with 1 person and 1 group indigoviolet EisenLab
  • Enhancer responses to similarly distributed antagonistic gradients in development.
    PLoS Comput Biol, Vol. 3, No. 5. (11 May 2007)
    by RP Zinzen, D Papatsenko
    posted to eisen_journal_club enhancer experssion_pattern in_depth_suggestion prediction by dpollard on 2007-06-13 22:22:18 as ** along with 1 group EisenLab
  • Computational annotation of transcription factor binding sites in D. Melanogaster developmental genes.
    Genome Inform, Vol. 17, No. 2. (2006), pp. 14-24.
    by V Narang, WK Sung, A Mittal
    posted to binding_site cis_regulatory_elements crm drosophila prediction by dpollard on 2007-06-13 22:20:42 as *** along with 1 group EisenLab
  • Localizing Recent Adaptive Evolution in the Human Genome
    PLoS Genetics, Vol. 3, No. 6. (1 June 2007), e90.
    by Scott H Williamson, Melissa J Hubisz, Andrew G Clark, Bret A Payseur, Carlos D Bustamante, Rasmus Nielsen
    posted to adaptive_evolution dan_presented eisen_journal_club human method prediction round_robin by dpollard on 2007-05-31 23:22:20 as *** along with 6 people and 2 groups brant madhadron candypmcg emarker iris42 dmc EisenLab Durbin group
  • 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 cis_regulatory_elements method prediction by dpollard on 2007-05-31 23:16:30 as ** along with 2 people and 1 group adepace ajgentles EisenLab
  • SPACER: identification of cis-regulatory elements with non-contiguous critical residues.
    Bioinformatics, Vol. 23, No. 8. (15 April 2007), pp. 1029-1031.
    by A Chakravarty, JM Carlson, RS Khetani, CE DeZiel, RH Gross
    posted to binding_site cis_regulatory_elements clustering method prediction by dpollard on 2007-05-23 01:10:50 as ** along with 1 group EisenLab
  • A phylogenetic Gibbs sampler that yields centroid solutions for cis regulatory site prediction.
    Bioinformatics (8 May 2007)
    by Lee A A Newberg, William A A Thompson, Sean Conlan, Thomas M M Smith, Lee Ann A McCue, Charles E E Lawrence
    posted to cis_regulatory_elements clustering discovery method motif prediction by dpollard on 2007-05-23 00:29:25 as ** along with 1 person and 1 group cjeans EisenLab
  • Discovering transcriptional regulatory regions in Drosophila by a nonalignment method for phylogenetic footprinting.
    Proc Natl Acad Sci U S A (29 March 2007)
    by Alona Sosinsky, Barry Honig, Richard S S Mann, Andrea Califano
    posted to clustering comparative drosophila enhancer method prediction by dpollard on 2007-04-09 17:43:36 as ** along with 3 people and 2 groups Stew maximilianh cisevol EisenLab cis-regulatory-evolution
  • 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 chip_chip dan_presented eisen_journal_club motif prediction pwm round_robin by dpollard on 2007-03-23 00:19:21 as *** along with 2 people and 1 group dquest yevishere EisenLab
  • GAPWM: A Genetic Algorithm Method for Optimizing a Position Weight Matrix.
    Bioinformatics (6 March 2007)
    by Leping Li, Yu Liang, Robert L L Bass
    posted to chip_chip prediction pwm by dpollard on 2007-03-22 23:37:15 as ** along with 3 people and 2 groups grahamc cjeans ghattem EisenLab ParkinsonLab_at_MaRS
  • Computational methods for transcriptional regulation.
    Curr Opin Genet Dev, Vol. 15, No. 2. (April 2005), pp. 214-221.
    by ED Siggia
    posted to cis_regulatory_elements expression_pattern gene_expression method modeling prediction by dpollard on 2007-03-15 00:30:41 as *** along with 3 people and 2 groups bertelsen barry koller Bioinformatics EisenLab
  • The identification and functional characterisation of conserved regulatory elements in developmental genes.
    Brief Funct Genomic Proteomic, Vol. 3, No. 4. (February 2005), pp. 332-350.
    by T Dickmeis, F Müller
    posted to cis_regulatory_elements conserved development prediction regulatory_sequence transcription_factor by dpollard on 2007-03-15 00:27:26 as *** along with 1 person and 1 group brant EisenLab
  • Prediction of cis-regulatory elements using binding site matrices--the successes, the failures and the reasons for both.
    Curr Opin Genet Dev, Vol. 15, No. 4. (August 2005), pp. 395-402.
    by T Vavouri, G Elgar
    posted to binding_site cis_regulatory_elements method motif pattern prediction pwm regulatory_sequence by dpollard on 2007-03-15 00:24:34 as *** along with 6 people and 2 groups brant troels_marstrand kaspermunch adepace lusk Stew Bioinformatics EisenLab
  • Evolution of cis-regulatory sequence and function in Diptera
    Heredity, Vol. aop, No. current.
    by PJ Wittkopp,
    posted to evolution prediction regulatory_sequence structure variation by dpollard on 2007-03-15 00:20:50 as read along with 5 people and 2 groups emptyhb indigoviolet adepace emmahe cisevol EisenLab cis-regulatory-evolution
  • Good enhancer hunting.
    Nat Methods, Vol. 4, No. 1. (January 2007), pp. 8-9.
    by J Potash
    posted to prediction enhancer by dpollard on 2007-02-09 01:57:00 as ** along with 1 group EisenLab
  • Structure-based prediction of C2H2 zinc-finger binding specificity: sensitivity to docking geometry.
    Nucleic Acids Res (30 January 2007)
    by Trevor W W Siggers, Barry Honig
    posted to affinity binding_site dan_presented eisen_journal_club prediction round_robin structure transcription_factor by dpollard on 2007-02-09 01:34:13 as read along with 1 person and 1 group aalibes EisenLab
  • Statistical significance of cis-regulatory modules
    BMC Bioinformatics, Vol. 8, No. 1. (2007)
    by Dustin Schones, Andrew Smith, Michael Zhang
    posted to prediction method crm by dpollard on 2007-02-01 19:56:05 as *** along with 8 people and 1 group indigoviolet dquest sebastien_vigneau shigepong SeungjoonOh GustavoLacerda nklee xili03 EisenLab
  • Simultaneous alignment and annotation of cis-regulatory regions.
    Bioinformatics, Vol. 23, No. 2. (15 January 2007)
    by AS Bais, S Grossmann, M Vingron
    posted to prediction binding_site alignment by dpollard on 2007-02-01 19:45:23 as ** along with 2 people and 1 group indigoviolet bluto EisenLab
  • PhyloScan: Identification of transcription factor binding sites using cross-species evidence
    Algorithms for Molecular Biology, Vol. 2 (23 January 2007), 1.
    by Steven C Carmack, Lee A Mccue, Lee A Newberg, Charles E Lawrence
    posted to prediction phylogeny comparative binding_site by dpollard on 2007-02-01 19:41:57 as ** along with 3 people and 1 group dquest lusk nklee EisenLab
  • Large Scale Discovery of Promoter Motifs in Drosophila melanogaster
    PLoS Computational Biology, Vol. preprint, No. 2006. (1 December 2006), e7.eor.
    by Thomas A Down, Casey M Bergman, Jing Su, Tim J Hubbard
    posted to drosophila eisen_journal_club emily_presented motif prediction promoter round_robin by dpollard on 2006-12-13 22:18:54 as **** along with 1 group EisenLab
  • Position specific variation in the rate of evolution in transcription factor binding sites.
    BMC Evol Biol, Vol. 3, No. 1. (28 August 2003)
    by AM Moses, DY Chiang, M Kellis, ES Lander, MB Eisen
    posted to binding conserved constraint evolution noncoding pattern phylogeny prediction pwm rate selection specific transcription by dpollard on 2006-11-07 00:22:07 as read along with 6 people and 2 groups emptyhb briann adepace lusk nklee cisevol EisenLab cis-regulatory-evolution
  • Large-scale Cis-element Detection by Analysis of Correlated Expression and Sequence Conservation between Arabidopsis and Brassica oleracea.
    Plant Physiol (6 October 2006)
    by Georg Haberer, Michael T T Mader, Peter Kosarev, Manuel Spannagl, Li Yang, Klaus Fx F Mayer
    posted to coexpression conserved crm prediction by dpollard on 2006-10-18 20:12:50 as * along with 4 people and 1 group xwbcn kengg nklee xili03 EisenLab
  • Identifying cis-regulatory modules by combining comparative and compositional analysis of DNA.
    Bioinformatics (10 October 2006)
    by Nora Pierstorff, Casey M M Bergman, Thomas Wiehe
    posted to annotation comparative composition discovery drosophila eisen_journal_club emily_presented method prediction round_robin by dpollard on 2006-10-18 19:54:18 as read along with 3 people and 1 group plofje SeungjoonOh csdhwang EisenLab
  • Identifying gene regulatory elements by genomic microarray mapping of DNaseI hypersensitive sites.
    Genome Res (8 September 2006)
    by George A A Follows, Pawan Dhami, Berthold Göttgens, Alexander W W Bruce, Peter J J Campbell, Shane C C Dillon, Aileen M M Smith, Christoph Koch, Ian J J Donaldson, Mike A A Scott, Ian Dunham, Mary E E Janes, David Vetrie, Anthony R R Green
    posted to array dnasei hypersensitive prediction by dpollard on 2006-09-30 00:26:22 as ** along with 1 person and 1 group uz_labu_laimi EisenLab
  • Vertebrate gene finding from multiple-species alignments using a two-level strategy.
    Genome Biol, Vol. 7 Suppl 1 (2006)
    by D Carter, R Durbin
    posted to alignment gene prediction by dpollard on 2006-09-30 00:22:15 as ** along with 2 people and 2 groups indigoviolet dmc EisenLab Durbin group
  • Quantitative and predictive model of transcriptional control of the Drosophila melanogaster even skipped gene.
    Nat Genet (17 September 2006)
    by Hilde Janssens, Shuling Hou, Johannes Jaeger, Ah-Ram R Kim, Ekaterina Myasnikova, David Sharp, John Reinitz
    posted to drosophila embryo expression gene model pattern prediction transcription by dpollard on 2006-09-30 00:16:37 as *** along with 6 people and 2 groups okarsligil brant adepace allPowerde Stew emptyhb Bioinformatics EisenLab
  • Predicting transcription factor binding sites using local overrepresentation and comparative genomics
    BMC Bioinformatics, Vol. 7 (31 August 2006), 396.
    by Matthieu Defrance, Helene Touzet
    posted to binding comparative prediction transcription by dpollard on 2006-09-08 19:25:42 as ** along with 3 people and 1 group brant gpalidwor natstreet EisenLab
  • Close sequence comparisons are sufficient to identify human cis-regulatory elements.
    Genome Res (12 June 2006)
    by Shyam Prabhakar, Francis Poulin, Malak Shoukry, Veena Afzal, Edward M M Rubin, Olivier Couronne, Len A A Pennacchio
    posted to alignment annotation conserved constraint evolution human mammal prediction rate selection transcription turnover by dpollard on 2006-06-16 20:47:54 as ** along with 6 people and 2 groups mariakmejia indigoviolet samal nickluscombe olympos emptyhb EisenLab EBI-regulation
  • Enhancing the prediction of transcription factor binding sites by incorporating structural properties and nucleotide covariations.
    J Comput Biol, Vol. 13, No. 4. (May 2006), pp. 929-945.
    by S Gunewardena, P Jeavons, Z Zhang
    posted to binding motif prediction structure transcription by dpollard on 2006-06-16 20:40:23 as ** along with 2 people and 1 group samal nklee EisenLab
  • Computational Models for Neurogenic Gene Expression in the Drosophila Embryo.
    Curr Biol (1 June 2006)
    by Robert P P Zinzen, Kate Senger, Mike Levine, Dmitri Papatsenko
    posted to cis_regulatory_elements drosophila expression expression_pattern modeling network prediction transcription by dpollard on 2006-06-09 23:01:14 as ** along with 1 person and 1 group emilyhare EisenLab
  • Integrating genomic data to predict transcription factor binding.
    Genome Inform Ser Workshop Genome Inform, Vol. 16, No. 1. (2005), pp. 83-94.
    by DT Holloway, M Kon, C DeLisi
    posted to binding data genomic integration prediction transcription by dpollard on 2006-03-21 19:53:19 as ** along with 3 people and 1 group malcook adsmitty nklee EisenLab
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