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Group: EisenLab - with tag method [39 articles]

Недавние статьи, отправленные по почте членами EisenLab группы with tag method
  • Gene Network Inference via Structural Equation Modeling in Genetical Genomics Experiments.
    Genetics (3 February 2008)
    by Bing Liu, Alberto de la Fuente, Ina Hoeschele
    posted to eqtl method network system by dpollard to the group EisenLab on 2008-02-12 23:12:26 as *** along with 5 people caseybrown jyuh raiyar xingxu smgomez
  • 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
  • The effect of the guide tree on multiple sequence alignments and subsequent phylogenetic analyses.
    Pac Symp Biocomput (2008), pp. 25-36.
    by S Nelesen, K Liu, D Zhao, CR Linder, T Warnow
    posted to accuracy alignment alignment_accuracy method multiple_alignment phylogeny reconstruction by dpollard to the group EisenLab on 2008-02-01 06:14:52 as **
  • 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
  • The cost of inbreeding in Arabidopsis.
    Nature, Vol. 416, No. 6880. (4 April 2002), pp. 531-534.
    by CD Bustamante, R Nielsen, SA Sawyer, KM Olsen, MD Purugganan, DL Hartl
    posted to method population_genetics test_for_selection by dpollard to the group EisenLab on 2007-11-19 07:32:25 as *** along with 1 person djkt
  • MORPH: Probabilistic Alignment Combined with Hidden Markov Models of cis-Regulatory Modules
    PLoS Computational Biology, Vol. 3, No. 11. (1 November 2007), e216.
    by Saurabh Sinha, Xin He
    posted to alignment alignment_accuracy binding_site_alignment brant_presented cis_regulatory_elements eisen_journal_club method round_robin by dpollard to the group EisenLab on 2007-11-16 23:53:34 as **** along with 7 people and 1 group ana cjeans zwang maximilianh hpaces Ema uwe cis-regulatory-evolution
  • Bayesian estimation of concordance among gene trees.
    Mol Biol Evol, Vol. 24, No. 2. (February 2007), pp. 412-426.
    by C Ané, B Larget, DA Baum, SD Smith, A Rokas
    posted to concordance gene_tree gene_vs_species_tree method phylogeny speciation by dpollard to the group EisenLab on 2007-11-06 22:35:21 as *** along with 1 person AaronDarling
  • 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
  • Enhancing the quality of phylogenetic analysis using fuzzy hidden Markov model alignments.
    Medinfo, Vol. 12, No. Pt 2. (2007), pp. 1245-1249.
    by C Collyda, S Diplaris, P Mitkas, N Maglaveras, C Pappas
    posted to alignment alignment_accuracy method phylogeny by dpollard to the group EisenLab on 2007-10-25 02:23:23 as **
  • 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
  • Computational and experimental approaches for modeling gene regulatory networks.
    Curr Pharm Des, Vol. 13, No. 14. (2007), pp. 1415-1436.
    by J Goutsias, NH Lee
    posted to review regulatory_network modeling method experimental computational by dpollard to the group EisenLab on 2007-06-14 23:48:35 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 yeast venky_presented round_robin motif method eisen_journal_club binding_site ab_initio by dpollard to the group EisenLab on 2007-06-14 23:38:43 as ** along with 5 people aalibes medic0747 GustavoLacerda mircea marti
  • Determination of local statistical significance of patterns in Markov sequences with application to promoter element identification.
    J Comput Biol, Vol. 11, No. 1. (2004), pp. 1-14.
    by H Huang, MC Kao, X Zhou, JS Liu, WH Wong
    posted to stuart_presented round_robin motif method markov eisen_journal_club binding_site ab_initio by dpollard to the group EisenLab on 2007-06-04 22:47:45 as * along with 1 person jguinney
  • 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
  • Imputation-based analysis of association studies: candidate regions and quantitative traits
    PLoS Genetics, Vol. preprint, No. 2007. (1 May 2007), e114.eor.
    by Bertrand Servin, Matthew Stephens
    posted to method association_mapping by dpollard to the group EisenLab on 2007-05-31 22:45:19 as **
  • 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 **
  • STAMP: a web tool for exploring DNA-binding motif similarities.
    Nucleic Acids Res (3 May 2007)
    by Shaun Mahony, Panayiotis V V Benos
    posted to website pwm motif method alignment by dpollard to the group EisenLab on 2007-05-23 00:40:45 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 3 people siebert sconlan cjeans
  • RE-MuSiC: a tool for multiple sequence alignment with regular expression constraints.
    Nucleic Acids Res (8 May 2007)
    by Yun-Sheng S Chung, Wei-Hsun H Lee, Chuan Yi Y Tang, Chin Lung L Lu
    posted to regular_expressions multiple_alignment method by dpollard to the group EisenLab on 2007-05-23 00:25:21 as **
  • 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
  • ChIP-on-chip protocol for genome-wide analysis of transcription factor binding in Drosophila melanogaster embryos.
    Nat Protoc, Vol. 1, No. 6. (2006), pp. 2839-2855.
    by T Sandmann, JS Jakobsen, EE Furlong
    posted to transcription_factor method drosophila chip_chip binding by dpollard to the group EisenLab on 2007-04-09 17:24:28 as ** along with 1 person johncumbers
  • Quantifying DNA-protein binding specificities by using oligonucleotide mass tags and mass spectroscopy
    PNAS, Vol. 104, No. 9. (27 February 2007), pp. 3061-3066.
    by Lingang Zhang, Simon Kasif, And C Cantor
    posted to transcription_factor method mass_spec dna_binding by cwbrown to the group EisenLab on 2007-03-29 22:07:00 as ** along with 2 people jyuh zwang
  • Quantifying similarity between motifs
    Genome Biology, Vol. 8 (26 February 2007), R24.
    by Shobhit Gupta, John A Stamatoyannopoulos, Timothy L Bailey, William S Noble
    posted to motif_finding motif_comparison method by cwbrown to the group EisenLab on 2007-03-29 21:08:57 as ** along with 3 people and 1 group grahamc nklee gracio ParkinsonLab_at_MaRS
  • DNA Familial Binding Profiles Made Easy: Comparison of Various Motif Alignment and Clustering Strategies
    PLoS Computational Biology, Vol. preprint, No. 2007. (1 February 2007), e61.eor.
    by Shaun Mahony, Philip Auron, Panayiotis Benos
    posted to transcription_factor motifs method dna_binding by cwbrown to the group EisenLab on 2007-03-29 20:45:40 as **
  • In vitro analysis of DNA-protein interactions by proximity ligation.
    Proc Natl Acad Sci U S A, Vol. 104, No. 9. (27 February 2007), pp. 3067-3072.
    by SM Gustafsdottir, J Schlingemann, A Rada-Iglesias, E Schallmeiner, M Kamali-Moghaddam, C Wadelius, U Landegren
    posted to transcription_factor round_robin method eisen_journal_club colin_presented binding by dpollard to the group EisenLab on 2007-03-23 19:28:14 as ** along with 2 people jyuh zwang
  • Global Discriminative Learning for Higher-Accuracy Computational Gene Prediction
    PLoS Computational Biology, Vol. 3, No. 3. (1 March 2007), e54.
    by Axel Bernal, Koby Crammer, Artemis Hatzigeorgiou, Fernando Pereira
    posted to method gene_prediction ab_initio by dpollard to the group EisenLab on 2007-03-23 00:33:15 as ** along with 1 person GustavoLacerda
  • Multiple Hypothesis Testing to Detect Lineages Under Positive Selection that Affects Only a Few Sites.
    Mol Biol Evol (5 March 2007)
    by Maria Anisimova, Ziheng Yang
    posted to multiple_testing method evolution adaptive by dpollard to the group EisenLab on 2007-03-22 23:51:26 as ** along with 2 people and 1 group stevanspringer operon FAB-lab
  • Incorporating Indel Information into Phylogeny Estimation for Rapidly Emerging Pathogens
    BMC Evolutionary Biology, Vol. 7 (14 March 2007), 40.
    by Benjamin D Redelings, Marc A Suchard
    posted to phylogeny method indels gene alignment by dpollard to the group EisenLab on 2007-03-22 22:56:37 as ** along with 2 people aprasad stajich
  • Global Discriminative Learning for Higher-Accuracy Computational Gene Prediction
    PLoS Computational Biology, Vol. 3, No. 3. (1 March 2007), e54.
    by Axel Bernal, Koby Crammer, Artemis Hatzigeorgiou, Fernando Pereira
    posted to ab_initio gene_prediction method by dpollard to the group EisenLab on 2007-03-16 21:10:40 as ** along with 4 people and 1 group alexl wenhan zwang acarbo Bioinformatics
  • 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 5 people and 1 group nklee Borelli bertelsen barry koller Bioinformatics
  • 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
  • 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 9 people sconlan indigoviolet dquest sebastien_vigneau shigepong SeungjoonOh GustavoLacerda nklee xili03
  • Multiple alignment by sequence annealing.
    Bioinformatics, Vol. 23, No. 2. (15 January 2007)
    by AS Schwartz, L Pachter
    posted to protein method alignment by dpollard to the group EisenLab on 2007-02-01 19:47:22 as **
  • Single-Molecule Detection of Transcription Factor Binding to DNA in Real Time: Specificity, Equilibrium, and Kinetic Parameters.
    Biochemistry, Vol. 45, No. 46. (21 November 2006), pp. 13794-13806.
    by Eric A Nalefski, Eugene Nebelitsky, Janice A Lloyd, Steven R Gullans
    posted to binding kenetics method motif by dpollard to the group EisenLab on 2006-11-17 13:00:37 as **
  • Exogean: a framework for annotating protein-coding genes in eukaryotic genomic DNA.
    Genome Biol, Vol. 7 Suppl 1 (2006)
    by S Djebali, F Delaplace, HR Crollius
    posted to annotation eukaryote gene method by dpollard to the group EisenLab on 2006-09-30 00:21:18 as ** along with 1 person indigoviolet
  • Quantification of the variation in percentage identity for protein sequence alignments
    BMC Bioinformatics, Vol. 7 (19 September 2006), 415.
    by Ps G Raghava, Geoffrey J Barton
    posted to accuracy alignment gene method protein by dpollard to the group EisenLab on 2006-09-30 00:20:09 as *** along with 5 people pansapiens bicko rabio medic0747 sujaikumar
  • Estimating Selection Pressures from Limited Comparative Data.
    Mol Biol Evol (5 June 2006)
    by Joshua B B Plotkin, Jonathan Dushoff, Michael M M Desai, Hunter B B Fraser
    posted to evolution gene method selection variation by dpollard to the group EisenLab on 2006-07-13 19:10:38 as *** along with 4 people friendpine bnchakraborty djkt BioNica
  • Comparing gene expression networks in a multi-dimensional space to extract similarities and differences between organisms.
    Bioinformatics (9 March 2006)
    by Gaëlle Lelandais, Pierre Vincens, Anne Badel-Chagnon, Stéphane Vialette, Claude Jacq, Serge Hazout
    posted to evolution expression gene method network by dpollard to the group EisenLab on 2006-03-21 18:55:30 as ** along with 1 person wnpx
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