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dpollard's method [49 articles]

Recent papers added to dpollard's library classified by the tag method. You can also see everyone's method.
  • A genome-wide approach to identifying novel-imprinted genes.
    Hum Genet, Vol. 122, No. 6. (January 2008), pp. 625-634.
    by KS Pollard, D Serre, X Wang, H Tao, E Grundberg, TJ Hudson, AG Clark, K Frazer
    posted to allele-specific array expression method rockman_journal_club by dpollard on 2008-06-27 21:03:45 as ***** along with 2 people and 1 group nolodie gjuggler RockmanLab
  • Genome-wide allele-specific expression analysis using Massively Parallel Signature Sequencing (MPSS) reveals cis- and trans-effects on gene expression in maize hybrid meristem tissue.
    Plant molecular biology, Vol. 66, No. 5. (March 2008), pp. 551-563.
    by M Guo, S Yang, M Rupe, B Hu, DR Bickel, L Arthur, O Smith
    posted to allele-specific expression massively_parallel_signature_sequencing method rockman_journal_club by dpollard on 2008-06-27 21:00:03 as ***** along with 1 person and 1 group caseybrown RockmanLab
  • Analysis of allelic differential expression in human white blood cells
    Genome Res., Vol. 16, No. 3. (1 March 2006), pp. 331-339.
    by Krishna PV Pant, Heng Tao, Erica J Beilharz, Dennis G Ballinger, David R Cox, Kelly A Frazer
    posted to allele-specific array expression method rockman_journal_club by dpollard on 2008-06-27 20:54:12 as ***** along with 4 people and 1 group RMGraze qfwills emarker mimulus_99 RockmanLab
  • SNP-specific array-based allele-specific expression analysis.
    Genome Res (27 March 2008)
    by Hans T T Bjornsson, Thomas J J Albert, Christine M M Ladd-Acosta, Roland D D Green, Michael A A Rongione, Christina M M Middle, Rafael A A Irizarry, Karl W W Broman, Andrew P P Feinberg
    posted to allele-specific array expression method rockman_journal_club by dpollard on 2008-06-27 20:50:13 as ***** along with 2 people and 1 group jyuh rschulz RockmanLab
  • Allelic Variation in Gene Expression Is Common in the Human Genome
    Genome Res., Vol. 13, No. 8. (1 August 2003), pp. 1855-1862.
    by Shuen H Lo, Zhining Wang, Ying Hu, Howard H Yang, Sheryl Gere, Kenneth H Buetow, Maxwell P Lee
    posted to affy_array allele-specific expression method rockman_journal_club by dpollard on 2008-06-27 20:44:16 as ***** along with 4 people and 1 group RMGraze qfwills emarker mimulus_99 RockmanLab
  • Allele-Specific Chromatin Immunoprecipitation Studies Show Genetic Influence on Chromatin State in Human Genome
    PLoS Genetics, Vol. 3, No. 5. (1 May 2007), e81.
    by Mitsutaka Kadota, Howard H Yang, Nan Hu, Chaoyu Wang, Ying Hu, Philip R Taylor, Kenneth H Buetow, Maxwell P Lee
    posted to allele-specific chip_chip method by dpollard on 2008-06-27 20:41:19 as ** along with 1 group RockmanLab
  • Differential Allelic Expression in the Human Genome: A Robust Approach To Identify Genetic and Epigenetic Cis-Acting Mechanisms Regulating Gene Expression
    PLoS Genet, Vol. 4, No. 2. (29 February 2008), e1000006.
    by David Serre, Scott Gurd, Bing Ge, Robert Sladek, Donna Sinnett, Eef Harmsen, Marina Bibikova, Eugene Chudin, David L Barker, Todd Dickinson, Jian-Bing Fan, Thomas J Hudson
    posted to allele-specific expression illumina_beads method rockman_journal_club by dpollard on 2008-06-27 20:36:21 as ***** along with 3 people and 2 groups jyuh vplagnol caseybrown cis-regulatory-evolution RockmanLab
  • 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 on 2008-02-12 23:12:26 as *** along with 6 people and 1 group orzenil raiyar xingxu caseybrown smgomez jyuh EisenLab
  • 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
  • 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 on 2008-02-01 06:14:51 as ** along with 1 group 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 3 people and 1 group isimpson indigoviolet ep161302 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
  • 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 on 2007-11-19 07:32:25 as *** along with 1 person and 1 group djkt EisenLab
  • 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 on 2007-11-16 23:53:34 as **** along with 7 people and 2 groups ana cjeans zwang maximilianh hpaces Ema uwe 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 7 people and 3 groups indigoviolet adepace wrowell emptyhb dlmace pradiptaray balicea EisenLab Cline_lab UH - Computational Biology
  • 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 on 2007-11-06 22:35:21 as *** along with 1 person and 1 group AaronDarling EisenLab
  • 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
  • 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 on 2007-10-25 02:23:22 as ** along with 1 group EisenLab
  • 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
  • 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
  • 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 computational experimental method modeling regulatory_network review by dpollard on 2007-06-14 23:48:35 as ** along with 1 group EisenLab
  • 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 ab_initio binding_site eisen_journal_club method motif round_robin venky_presented yeast by dpollard on 2007-06-14 23:38:43 as ** along with 5 people and 1 group aalibes medic0747 GustavoLacerda mircea marti EisenLab
  • 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 ab_initio binding_site eisen_journal_club markov method motif round_robin stuart_presented by dpollard on 2007-06-04 22:47:45 as * along with 1 person and 1 group jguinney 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 7 people and 2 groups brant madhadron candypmcg shoshin 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
  • 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 association_mapping method by dpollard on 2007-05-31 22:45:19 as ** along with 1 group 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
  • 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 alignment method motif pwm website by dpollard on 2007-05-23 00:40:45 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 3 people and 1 group cjeans sconlan siebert EisenLab
  • 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 method multiple_alignment regular_expressions by dpollard on 2007-05-23 00:25:21 as ** along with 1 group 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 4 people and 2 groups Stew maximilianh cisevol isimpson EisenLab 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 binding chip_chip drosophila method transcription_factor by dpollard on 2007-04-09 17:24:28 as ** along with 1 person and 1 group johncumbers EisenLab
  • 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 binding colin_presented eisen_journal_club method round_robin transcription_factor by dpollard on 2007-03-23 19:28:14 as ** along with 2 people and 1 group jyuh zwang EisenLab
  • 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 on 2007-03-23 00:33:15 as ** along with 1 person and 1 group GustavoLacerda EisenLab
  • 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 adaptive evolution method multiple_testing by dpollard on 2007-03-22 23:51:26 as ** along with 3 people and 2 groups stevanspringer operon gjuggler EisenLab 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 alignment gene indels method phylogeny by dpollard on 2007-03-22 22:56:37 as ** along with 2 people and 1 group aprasad stajich EisenLab
  • 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 on 2007-03-16 21:10:40 as ** along with 4 people and 2 groups wenhan zwang acarbo alexl Bioinformatics EisenLab
  • 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 7 people and 2 groups barry koller bertelsen Borelli nklee balicea jjray Bioinformatics 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 troels_marstrand kaspermunch adepace lusk Stew brant Bioinformatics 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 9 people and 1 group indigoviolet dquest sebastien_vigneau shigepong SeungjoonOh GustavoLacerda nklee xili03 sconlan EisenLab
  • 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 on 2007-02-01 19:47:22 as ** along with 1 group EisenLab
  • 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 on 2006-11-17 13:00:37 as ** along with 1 group 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
  • 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 on 2006-09-30 00:21:18 as ** along with 1 person and 1 group indigoviolet EisenLab
  • 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 on 2006-09-30 00:20:09 as *** along with 5 people and 1 group pansapiens bicko rabio medic0747 sujaikumar EisenLab
  • 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 on 2006-07-13 19:10:38 as *** along with 4 people and 1 group bnchakraborty djkt BioNica friendpine EisenLab
  • Reference based annotation with GeneMapper.
    Genome Biol, Vol. 7, No. 4. (5 April 2006)
    by Sourav Chatterji, Lior Pachter
    posted to alignment annotation gene method by dpollard on 2006-04-08 23:24:07 as *** along with 4 people and 2 groups indigoviolet penka wenhan skumagai EisenLab Nie
  • 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 on 2006-03-21 18:55:30 as ** along with 1 person and 1 group wnpx EisenLab
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