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Group: EisenLab - with tag prediction [56 articles]

Recent papers posted by members of the EisenLab group with tag prediction
  • Levers and fulcrums: progress in cis-regulatory motif models
    Nature Methods, Vol. 5, No. 4., pp. 297-298.
    by Ewan Birney
    posted to cis-regulatory comparative_genomics methods motif prediction by stajich to the group EisenLab on 2008-04-07 16:11:40 as ** along with 3 people and 1 group isimpson pradiptaray emptyhb Berkeley Mycology
  • 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 to the group EisenLab on 2008-02-01 06:21:42 as ** along with 1 person bootsy
  • 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 to the group EisenLab on 2007-12-05 22:46:33 as read along with 2 people ep161302 indigoviolet
  • 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 to the group EisenLab on 2007-11-21 02:56:16 as read along with 2 people stajich caseybrown
  • 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 to the group EisenLab on 2007-11-17 00:01:35 as *** along with 7 people and 1 group lp2 nklee maximilianh roys caseybrown emptyhb barwil cis-regulatory-evolution
  • 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 to the group EisenLab on 2007-11-01 00:41:11 as read along with 5 people and 1 group chad_davis balajis lyongu dquest csdhwang 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 to the group EisenLab on 2007-11-01 00:10:36 as read along with 4 people and 1 group isimpson tvdbulck nickluscombe heliopais 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 to the group EisenLab on 2007-10-25 02:20:56 as ** along with 1 person and 1 group maximilianh 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 motif_detection prediction by dpollard to the group EisenLab on 2007-10-25 01:20:27 as *** along with 5 people cjeans nklee niallhaslam maximilianh idonaldson
  • 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 to the group EisenLab on 2007-10-25 01:18:08 as ** along with 9 people and 1 group pradiptaray gpappas timflutre GustavoLacerda cabbagezs maximilianh cisevol urgi yoanjacquemin BergmanLab
  • Applied bioinformatics for the identification of regulatory elements.
    Nat Rev Genet, Vol. 5, No. 4. (April 2004), pp. 276-287.
    by WW Wasserman, A Sandelin
    posted to review prediction cis-regulatory by Stew to the group EisenLab on 2007-09-18 18:26:40 as read along with 15 people and 7 groups mariakmejia icases ana chad_davis moborg gpalidwor dchughes nickluscombe johncumbers giovanni xiaobeizhao bertelsen nklee jdiezperezj ArtemPankin structural_bioinformatics Bioinformatics G4ID EBI-regulation GeschwindLab TNT Genetics-of-Gambling
  • Cracking the genome's second code: enhancer detection by combined phylogenetic footprinting and transgenic fish and frog embryos.
    Methods, Vol. 39, No. 3. (July 2006), pp. 212-219.
    by ML Allende, M Manzanares, JJ Tena, CG Feijóo, JL Gómez-Skarmeta
    posted to prediction phlyogenetic frog footprinting fish cis-regulatory by Stew to the group EisenLab on 2007-09-18 01:19:46 as read
  • Computational prediction of transcription-factor binding site locations.
    Genome Biol, Vol. 5, No. 1. (2003)
    by ML Bulyk
    posted to review prediction clustering cis-regulatory by Stew to the group EisenLab on 2007-09-17 20:40:18 as ** along with 5 people kaarsinogen lusk nklee yevishere xili03
  • Exploiting transcription factor binding site clustering to identify cis-regulatory modules involved in pattern formation in the Drosophila genome.
    Proc Natl Acad Sci U S A, Vol. 99, No. 2. (22 January 2002), pp. 757-762.
    by BP Berman, Y Nibu, BD Pfeiffer, P Tomancak, SE Celniker, M Levine, GM Rubin, MB Eisen
    posted to prediction modules drosophila clustering cis-regulatory by Stew to the group EisenLab on 2007-09-17 20:14:51 as read along with 3 people indigoviolet emptyhb csdhwang
  • Different words, same meaning: understanding the languages of the genome.
    Trends Genet (27 September 2006)
    by Greg Elgar
    posted to review prediction elgar cis-regulatory by Stew to the group EisenLab on 2007-07-27 22:32:32 as read along with 2 people and 4 groups nickluscombe WJST EBI-regulation asthma humangenetics SNP
  • 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 regulatory prediction cis by Stew to the group EisenLab on 2007-07-27 22:17:11 as *** along with 2 people indigoviolet csdhwang
  • Prediction of Gene Expression in Embryonic Structures of Drosophila melanogaster
    PLoS Computational Biology, Vol. 3, No. 7. (1 July 2007), e144.
    by Anastasia A Samsonova, Mahesan Niranjan, Steven Russell, Alvis Brazma
    posted to tissue prediction expression drosophila by brant to the group EisenLab on 2007-07-24 19:58:38 as ** along with 2 people dpollard sebastien_vigneau
  • Using multiple alignments to improve gene prediction.
    J Comput Biol, Vol. 13, No. 2. (March 2006), pp. 379-393.
    by SS Gross, MR Brent
    posted to prediction gene 12flies by indigoviolet to the group EisenLab on 2007-07-15 13:54:12 as ** along with 1 person wenhan
  • Prediction of gene structure.
    J Mol Biol, Vol. 226, No. 1. (5 July 1992), pp. 141-157.
    by R Guigó, S Knudsen, N Drake, T Smith
    posted to prediction gene 12flies by indigoviolet to the group EisenLab on 2007-07-15 13:52:20 as ** along with 1 person wenhan
  • Gene finding in novel genomes.
    BMC Bioinformatics, Vol. 5 (14 May 2004)
    by I Korf
    posted to prediction gene 12flies by indigoviolet to the group EisenLab on 2007-07-15 13:51:00 as ** along with 5 people alexl LeightonP wenhan GustavoLacerda cmzmasek
  • 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 venky_presented snp sequence_properties round_robin regulatory_polymorphism prediction eisen_journal_club cis_regulatory_elements by dpollard to the group EisenLab on 2007-06-15 22:54:33 as *** along with 1 person and 2 groups cisevol Bioinformatics cis-regulatory-evolution
  • 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 prediction in_depth_suggestion experssion_pattern enhancer eisen_journal_club by dpollard to the group EisenLab on 2007-06-13 22:22:18 as **
  • 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 prediction drosophila crm cis_regulatory_elements binding_site by dpollard to the group EisenLab on 2007-06-13 22:20:42 as ***
  • 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 prediction method cis_regulatory_elements by dpollard to the group EisenLab on 2007-05-31 23:16:30 as ** along with 2 people adepace ajgentles
  • 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 prediction method clustering cis_regulatory_elements binding_site by dpollard to the group EisenLab on 2007-05-23 01:10:50 as **
  • 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 prediction motif method discovery clustering cis_regulatory_elements by dpollard to the group EisenLab on 2007-05-23 00:29:25 as ** along with 2 people sconlan cjeans
  • 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 prediction method enhancer drosophila comparative clustering by dpollard to the group EisenLab on 2007-04-09 17:43:36 as ** along with 4 people and 1 group isimpson Stew maximilianh cisevol 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 round_robin pwm prediction motif eisen_journal_club dan_presented chip_chip by dpollard to the group EisenLab on 2007-03-23 00:19:21 as *** along with 3 people chad_davis dquest yevishere
  • 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 pwm prediction chip_chip by dpollard to the group EisenLab on 2007-03-22 23:37:15 as ** along with 3 people and 1 group grahamc cjeans ghattem 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 gene_expression method prediction by dpollard to the group EisenLab on 2007-03-15 00:30:41 as *** along with 3 people and 1 group bertelsen barry koller Bioinformatics
  • 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 to the group EisenLab on 2007-03-15 00:27:26 as *** along with 1 person brant
  • 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 to the group EisenLab on 2007-03-15 00:24:34 as *** along with 6 people and 1 group brant troels_marstrand kaspermunch adepace lusk Stew Bioinformatics
  • Good enhancer hunting.
    Nat Methods, Vol. 4, No. 1. (January 2007), pp. 8-9.
    by J Potash
    posted to prediction enhancer by dpollard to the group EisenLab on 2007-02-09 01:57:00 as **
  • 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 to the group EisenLab on 2007-02-09 01:34:13 as read along with 1 person aalibes
  • 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 to the group EisenLab on 2007-02-01 19:56:05 as *** along with 8 people indigoviolet dquest sebastien_vigneau shigepong SeungjoonOh GustavoLacerda nklee xili03
  • 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 to the group EisenLab on 2007-02-01 19:41:57 as ** along with 3 people dquest lusk nklee
  • 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 to the group EisenLab on 2006-12-13 22:18:54 as ****
  • 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 to the group EisenLab on 2006-11-07 00:22:07 as read along with 6 people and 1 group emptyhb briann adepace lusk nklee cisevol 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 to the group EisenLab on 2006-10-18 20:12:50 as * along with 4 people xwbcn kengg nklee xili03
  • 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 to the group EisenLab on 2006-09-30 00:26:22 as ** along with 1 person uz_labu_laimi
  • 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 to the group EisenLab on 2006-09-30 00:22:15 as ** along with 2 people and 1 group indigoviolet dmc Durbin group
  • 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 enhancer_finding prediction tools by brant to the group EisenLab on 2006-09-13 14:20:55 as *** along with 3 people dpollard gpalidwor natstreet
  • Expression-Guided In Silico Evaluation of Candidate Cis Regulatory Codes for Drosophila Muscle Founder Cells
    PLoS Computational Biology, Vol. 2, No. 5. (1 May 2006), e53.
    by Anthony A Philippakis, Brian W Busser, Stephen S Gisselbrecht, Fangxue S He, Beatriz Estrada, Alan M Michelson, Martha L Bulyk
    posted to enhancer prediction by emilyhare to the group EisenLab on 2006-07-06 01:26:10 as ** along with 1 person maximilianh
  • Integrated Assessment and Prediction of Transcription Factor Binding
    PLoS Computational Biology, Vol. 2, No. 6. (1 June 2006), e70.
    by Andreas Beyer, Christopher Workman, Jens Hollunder, Dörte Radke, Ulrich Möller, Thomas Wilhelm, Trey Ideker
    posted to prediction target tf by emilyhare to the group EisenLab on 2006-06-24 00:47:46 as ** along with 6 people jfr balajis wnpx samal reidy Ao_Li2007
  • 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 to the group EisenLab on 2006-06-16 20:40:23 as ** along with 2 people samal nklee
  • 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 drosophila expression network prediction transcription by dpollard to the group EisenLab on 2006-06-09 23:01:14 as ** along with 1 person emilyhare
  • 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 to the group EisenLab on 2006-03-21 19:53:19 as ** along with 3 people malcook adsmitty nklee
  • Mapping Dmef2-binding regulatory modules by using a ChIP-enriched in silico targets approach
    PNAS, Vol. 102, No. 51. (20 December 2005), pp. 18479-18484.
    by Guillaume Junion, Teresa Jagla, Sebastien Duplant, Romain Tapin, Jean-Philippe Da Ponte, Krzysztof Jagla
    posted to chip-chip enhancer mef2 prediction by emilyhare to the group EisenLab on 2006-01-13 02:04:51 as read along with 1 person postrational
  • Genome-wide Prediction of Mammalian Enhancers Based on Analysis of Transcription-Factor Binding Affinity
    Cell, Vol. 124, No. 1. (13 January 2006), pp. 47-59.
    by Outi Hallikas, Kimmo Palin, Natalia Sinjushina, Reetta Rautiainen, Juha Partanen, Esko Ukkonen, Jussi Taipale
    posted to enhancer mammalian prediction by brant to the group EisenLab on 2006-01-13 01:55:31 as ** along with 12 people and 4 groups Terkko kaarsinogen tuck xwbcn dchughes nickluscombe olympos cabbagezs karfunkel maximilianh heliopais oelemento Bioinformatics G4ID EBI-regulation Genetics-of-Gambling
  • Using hexamers to predict cis-regulatory modules in Drosophila.
    BMC Bioinformatics, Vol. 6, No. 1. (27 October 2005)
    by Bob Y Chan, Dennis Kibler
    posted to cis-regulation drosophila prediction by indigoviolet to the group EisenLab on 2005-11-18 06:30:11 as *** along with 4 people brant troels_marstrand postrational wrowell
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