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dpollard's library [433 articles]

Recent papers added to dpollard's library ordered by importance.
  • 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 rockman_journal_club method expression array allele-specific by dpollard on 2008-06-27 21:03:45 as ***** along with 2 people and 1 group gjuggler nolodie 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 rockman_journal_club method massively_parallel_signature_sequencing expression allele-specific by dpollard on 2008-06-27 21:00:03 as ***** along with 1 group 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 rockman_journal_club method expression array allele-specific 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 rockman_journal_club method expression array allele-specific by dpollard on 2008-06-27 20:50:13 as ***** along with 1 person and 1 group 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 rockman_journal_club method expression allele-specific affy_array by dpollard on 2008-06-27 20:44:16 as ***** along with 4 people and 1 group RMGraze qfwills emarker mimulus_99 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 rockman_journal_club method illumina_beads expression allele-specific by dpollard on 2008-06-27 20:36:21 as ***** along with 1 person and 2 groups vplagnol RockmanLab cis-regulatory-evolution
  • PPW-1, a PAZ/PIWI protein required for efficient germline RNAi, is defective in a natural isolate of C. elegans.
    Curr Biol, Vol. 12, No. 17. (3 September 2002), pp. 1535-1540.
    by M Tijsterman, KL Okihara, K Thijssen, RH Plasterk
    posted to worms rockman_journal_club rnai natural_variation c_elegans by dpollard on 2008-05-29 00:22:53 as ***** along with 1 person and 1 group tardigrade RockmanLab
  • Mapping mendelian factors underlying quantitative traits using RFLP linkage maps.
    Genetics, Vol. 121, No. 1. (January 1989), pp. 185-199.
    by ES Lander, D Botstein
    posted to seminal_paper rockman_journal_club qtl interval_mapping by dpollard on 2008-05-22 21:34:29 as ***** along with 4 people and 1 group Ayest raiyar lp2 mcgannd RockmanLab
  • The evolutionary significance of cis-regulatory mutations
    Nature Reviews Genetics, Vol. 8, No. 3., pp. 206-216.
    by Gregory A Wray
    posted to cis_regulatory_elements polymorphism regulatory_evolution review variation by dpollard on 2007-11-08 00:12:33 as ***** along with 6 people and 4 groups emptyhb brant dchughes lusk mimulus_99 cisevol EisenLab G4ID Genetics-of-Gambling cis-regulatory-evolution
  • A stochastic model for the evolution of transcription factor binding site abundance.
    J Theor Biol (7 March 2007)
    by Günter P P Wagner, Wolfgang Otto, Vincent Lynch, Peter F F Stadler
    posted to binding_site model turnover by dpollard on 2007-05-23 01:02:56 as ***** along with 1 person and 2 groups cisevol EisenLab cis-regulatory-evolution
  • Flexible promoter architecture requirements for coactivator recruitment
    BMC Molecular Biology, Vol. 7, No. 1. (28 April 2006), 16.
    by Derek Y Chiang, David A Nix, Ryan K Shultzaberger, Audrey P Gasch, Michael B Eisen
    posted to binding expression grammar promoter spacing transcription yeast by dpollard on 2006-05-21 05:08:26 as ***** along with 1 person and 1 group postrational EisenLab
  • Strong region-specific heterogeneity in base composition evolution on the Drosophila X chromosome.
    Genetics (17 March 2006)
    by Wen-Ya Y Ko, Shengfu Piao, Hiroshi Akashi
    posted to base composition drosophila evolution gene nonstationary rate reconstruction tree variation by dpollard on 2006-03-31 23:50:30 as ***** along with 1 group EisenLab
  • Contrasting the Efficacy of Selection on the X and Autosomes in Drosophila.
    Mol Biol Evol (13 December 2007)
    by Nadia D D Singh, Amanda M M Larracuente, Andrew G G Clark
    posted to drosophila selection x_vs_autosomes by dpollard on 2008-01-11 18:03:53 as **** along with 1 group 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
  • THE LOCUS OF EVOLUTION: EVO DEVO AND THE GENETICS OF ADAPTATION
    Evolution, Vol. 61, No. 5. (2007), pp. 995-1016.
    by Hopi E Hoekstra, Jerry A Coyne
    posted to adaptation cis_vs_trans evo_devo regulatory_evolution review by dpollard on 2007-06-14 23:50:07 as **** along with 8 people and 2 groups mjoach stevanspringer mcphee balicea TaqSys epigenetics jayster4 mimulus_99 EisenLab FAB-lab
  • 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
  • Estimating the Neutral Rate of Nucleotide Substitution Using Introns.
    Mol Biol Evol (22 November 2006)
    by Michael M M Hoffman, Ewan Birney
    posted to evolution neutral rate by dpollard on 2006-12-01 23:24:04 as **** along with 1 group EisenLab
  • Evolutionary population genetics of promoters: Predicting binding sites and functional phylogenies.
    Proc Natl Acad Sci U S A, Vol. 102, No. 44. (1 November 2005), pp. 15936-15941.
    by V Mustonen, M Lässig
    posted to binding evolution polymorphism promoter selection transcription turnover by dpollard on 2006-06-10 00:48:36 as **** along with 4 people and 2 groups emptyhb kaarsinogen lusk cisevol EisenLab cis-regulatory-evolution
  • Ubiquitous selective constraints in the Drosophila genome revealed by a genome-wide interspecies comparison.
    Genome Res (2 June 2006)
    by Daniel L L Halligan, Peter D D Keightley
    posted to constraint drosophila evolution purifying selection by dpollard on 2006-06-09 22:48:45 as **** along with 5 people and 3 groups RMGraze penka jri cisevol emptyhb EisenLab Nie cis-regulatory-evolution
  • Recently evolved genes identified from Drosophila yakuba and D. erecta accessory gland ESTs.
    Genetics (16 December 2005)
    by David Begun, Heather Lindfors, Melissa Thompson, Alisha Holloway
    posted to adaptive drosophila evolution gene noncoding by dpollard on 2006-03-21 19:56:01 as **** along with 1 group EisenLab
  • Toward Automatic Reconstruction of a Highly Resolved Tree of Life
    Science, Vol. 311, No. 5765. (3 March 2006), pp. 1283-1287.
    by Francesca D Ciccarelli, Tobias Doerks, Christian von Mering, Christopher J Creevey, Berend Snel, Peer Bork
    posted to concatonation life phylogeny reconstruction tree by dpollard on 2006-03-21 19:02:31 as **** along with 12 people and 5 groups diamantis Retchless knaseanka tny dchughes nirfriedman cmm azazello wenhan maximilianh cmzmasek lonshy EisenLab FAB-lab G4ID Genetics-of-Gambling MBLAB
  • PLoS Computational Biology: Genome-Wide Identification of Human Functional DNA Using a Neutral Indel Model
    posted to drosophila evolution intergenic mutation by dpollard on 2006-01-13 01:59:45 as **** along with 1 group EisenLab
  • Hitchhiking effects of recurrent beneficial amino acid substitutions in the Drosophila melanogaster genome
    Genome Res. (7 November 2007), gr.6691007.
    by Peter Andolfatto
    posted to drosophila hitchhiking positive_selection by dpollard on 2008-02-13 06:38:24 as *** along with 3 people and 1 group djkt usagi-kirin mimulus_99 EisenLab
  • 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 5 people and 1 group caseybrown jyuh raiyar xingxu smgomez EisenLab
  • Alignment Uncertainty and Genomic Analysis
    Science, Vol. 319, No. 5862. (25 January 2008), pp. 473-476.
    by Karen M Wong, Marc A Suchard, John P Huelsenbeck
    posted to alignment alignment_accuracy by dpollard on 2008-02-01 06:16:50 as *** along with 23 people and 2 groups pradiptaray jdelcampo timflutre gracio adacier jyuh bpb aprasad dayjm tny djkt cjeans zwang lisa1 cactus biomcgary lilou kinestetika dandaman gjuggler renatomilani mclarenv youdon EisenLab microbiology_nijmegen
  • Inferring genome-scale rearrangement phylogeny and ancestral gene order: A Drosophila case study
    Genome Biology, Vol. 8 (08 November 2007), R236.
    by Arjun Bhutkar, William M Gelbart, Temple F Smith
    posted to drosophila phylogeny by dpollard on 2008-01-11 18:06:11 as *** along with 4 people and 1 group indigoviolet balicea maximilianh hpaces EisenLab
  • Characterization of the Duffy gene promoter: evidence for tissue-specific abolishment of expression in Fy(a-b-) of black individuals.
    Biochem Biophys Res Commun, Vol. 222, No. 3. (24 May 1996), pp. 852-859.
    by S Iwamoto, J Li, N Sugimoto, H Okuda, E Kajii
    posted to cis_regulatory_elements expression_divergence expression_pattern expression_polymorphism human modularity regulatory_evolution regulatory_sequence_evolution by dpollard on 2007-12-05 23:03:10 as *** along with 2 groups EisenLab cis-regulatory-evolution
  • Detection of the signature of natural selection in humans: evidence from the Duffy blood group locus.
    Am J Hum Genet, Vol. 66, No. 5. (May 2000), pp. 1669-1679.
    by MT Hamblin, A Di Rienzo
    posted to binding_site cis_regulatory_elements regulatory_evolution regulatory_polymorphism regulatory_sequence_evolution turnover by dpollard on 2007-12-05 22:53:19 as *** along with 2 groups EisenLab cis-regulatory-evolution
  • Disruption of a GATA motif in the Duffy gene promoter abolishes erythroid gene expression in Duffy-negative individuals.
    Nat Genet, Vol. 10, No. 2. (June 1995), pp. 224-228.
    by C Tournamille, Y Colin, JP Cartron, C Le Van Kim
    posted to binding_site cis_regulatory_elements regulatory_evolution regulatory_polymorphism regulatory_sequence_evolution turnover by dpollard on 2007-12-05 22:51:01 as *** along with 2 groups EisenLab cis-regulatory-evolution
  • Dominant gain-of-function mutations that lead to misregulation of the C. elegans heterochronic gene lin-14, and the evolutionary implications of dominant mutations in pattern-formation genes.
    Dev Suppl, Vol. 1 (1991), pp. 47-54.
    by G Ruvkun, B Wightman, T Bürglin, P Arasu
    posted to cis_regulatory_elements co_dominance dominance nematode semi_dominance seminal_paper by dpollard on 2007-11-26 00:38:21 as *** along with 1 group EisenLab
  • Accounting for Bias from Sequencing Error in Population Genetic Estimates.
    Mol Biol Evol (2 November 2007)
    by Philip L F L Johnson, Montgomery Slatkin
    posted to parameter_estimation polymorphism population_genetics sequencing_error by dpollard on 2007-11-25 05:46:42 as *** along with 2 people and 1 group bpb jmeppley EisenLab
  • Natural selection on protein-coding genes in the human genome
    Nature, Vol. 437, No. 7062., pp. 1153-1157.
    by Carlos D Bustamante, Adi Fledel-Alon, Scott Williamson, Rasmus Nielsen, Melissa T Hubisz, Stephen Glanowski, David M Tanenbaum, Thomas J White, John J Sninsky, Ryan D Hernandez, Daniel Civello, Mark D Adams, Michele Cargill, Andrew G Clark
    posted to gene human population_genetics test_for_selection by dpollard on 2007-11-19 07:34:51 as *** along with 15 people and 5 groups shoshin stevanspringer operon jwortman aprasad dayjm balajis marcius hdopazo djkt JBEgwa01 ramensky Garamonfok iris42 dmc EisenLab FAB-lab BioinfoCIPF SGU-CIPF Durbin group
  • 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
  • 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
  • Similar Levels of X-linked and Autosomal Nucleotide Variation in African and non-African populations of Drosophila melanogaster
    BMC Evolutionary Biology, Vol. 7 (25 October 2007), 202.
    by Nadia D Singh, Michael J Macpherson, Jeffrey D Jensen, Dmitri A Petrov
    posted to drosophila polymorphism population_genetics population_structure by dpollard on 2007-11-14 20:37:17 as *** along with 1 person and 1 group PetrovLab EisenLab
  • 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
  • The enhanceosome and transcriptional synergy.
    Cell, Vol. 92, No. 1. (9 January 1998), pp. 5-8.
    by M Carey
    posted to enhanceosome review transcription_factor by dpollard on 2007-10-31 20:42:02 as *** along with 1 group EisenLab
  • Enhanceosomes.
    Curr Opin Genet Dev, Vol. 11, No. 2. (April 2001), pp. 205-208.
    by M Merika, D Thanos
    posted to enhanceosome review transcription_factor by dpollard on 2007-10-31 20:41:32 as *** along with 1 group EisenLab
  • Context-dependent transcription: all politics is local.
    Gene, Vol. 313 (14 August 2003), pp. 43-57.
    by M Alvarez, SJ Rhodes, JP Bidwell
    posted to enhanceosome review transcription_factor by dpollard on 2007-10-31 20:40:55 as *** along with 1 group EisenLab
  • Phylogenetic Simulation of Promoter Evolution: Estimation and Modeling of Binding Site Turnover Events and Assessing Their Impact on Alignment Tools
    Genome Biology, Vol. 8 (24 October 2007), R225.
    by Weichun Huang, Joseph R Nevins, Uwe Ohler
    posted to alignment_accuracy cis_regulatory_elements simulation turnover by dpollard on 2007-10-30 18:55:43 as *** along with 4 people and 2 groups djkt stajich Garamonfok maximilianh EisenLab cis-regulatory-evolution
  • Functional Architecture and Evolution of Transcriptional Elements That Drive Gene Coexpression
    Science, Vol. 317, No. 5844. (14 September 2007), pp. 1557-1560.
    by Christopher D Brown, David S Johnson, Arend Sidow
    posted to cis_regulatory_elements colin_presented conservation eisen_journal_club grammar in_depth regulatory_evolution round_robin stew_presented by dpollard on 2007-10-29 18:57:23 as *** along with 9 people and 2 groups emptyhb djkt joepickrell zwang Garamonfok Stew mimulus_99 maximilianh cisevol EisenLab cis-regulatory-evolution
  • We gather together: insulators and genome organization.
    Curr Opin Genet Dev (1 October 2007)
    by Julie A A Wallace, Gary Felsenfeld
    posted to drosophila insulators by dpollard on 2007-10-25 02:00:08 as *** along with 3 people and 1 group dchughes sebastien_vigneau maximilianh EisenLab
  • Measuring the accuracy of genome-size multiple alignments
    Genome Biology, Vol. 8 (26 June 2007), R124.
    by Amol Prakash, Martin Tompa
    posted to alignment alignment_accuracy whole_genome by dpollard on 2007-10-25 01:39:42 as *** along with 3 people and 2 groups AaronDarling stajich lilou EisenLab Berkeley Mycology
  • 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
  • Global Analysis of mRNA Localization Reveals a Prominent Role in Organizing Cellular Architecture and Function
    Cell, Vol. 131, No. 1. (5 October 2007), pp. 174-187.
    by Eric Lecuyer, Hideki Yoshida, Neela Parthasarathy, Christina Alm, Tomas Babak, Tanja Cerovina, Timothy R Hughes, Pavel Tomancak, Henry M Krause
    posted to drosophila gene_expression in_situ by dpollard on 2007-10-19 23:10:47 as *** along with 2 people and 1 group wrowell oelemento EisenLab
  • Gene duplication and the adaptive evolution of a classic genetic switch
    Nature, Vol. 449, No. 7163. (11 October 2007), pp. 677-681.
    by Chris T Hittinger, Sean B Carroll
    posted to eisen_journal_club in-depth by dpollard on 2007-10-16 21:59:57 as *** along with 8 people and 2 groups clearbluespring skumagai mcphee dchughes djkt biomcgary blobbybirdman kjlipin EisenLab cis-regulatory-evolution
  • Widespread Lateral Gene Transfer from Intracellular Bacteria to Multicellular Eukaryotes
    Science (30 August 2007), 1142490.
    by Julie C Hotopp, Michael E Clark, Deodoro C Oliveira, Jeremy M Foster, Peter Fischer, Monica C Torres, Jonathan D Giebel, Nikhil Kumar, Nadeeza Ishmael, Shiliang Wang, Jessica Ingram, Rahul V Nene, Jessica Shepard, Jeffrey Tomkins, Stephen Richards, David J Spiro, Elodie Ghedin, Barton E Slatko, Herve Tettelin, John H Werren
    posted to eisen_journal_club round_robin stuart_presented by dpollard on 2007-10-09 18:13:31 as *** along with 7 people and 2 groups bluto zwang emmahe lp2 wrowell paulschlesinger Patola EisenLab Cline_lab
  • A high-resolution map of transcription in the yeast genome
    PNAS, Vol. 103, No. 14. (4 April 2006), pp. 5320-5325.
    by Lior David, Wolfgang Huber, Marina Granovskaia, Joern Toedling, Curtis J Palm, Lee Bofkin, Ted Jones, Ronald W Davis, Lars M Steinmetz
    posted to noncoding_transcription yeast by dpollard on 2007-07-02 22:54:06 as *** along with 6 people and 2 groups tuck alexg eckart_bindewald entropy raiyar xingxu EisenLab steinmetzlab
  • Large-scale analysis of transcriptional cis-regulatory modules reveals both common features and distinct subclasses
    Genome Biology, Vol. 8 (05 June 2007), R101.
    by Long Li, Qianqian Zhu, Xin He, Saurabh Sinha, Marc S Halfon
    posted to angela_presented cis_regulatory_elements crm drosophila eisen_journal_club enhancer regulatory_sequence_evolution round_robin by dpollard on 2007-07-02 21:12:58 as *** along with 4 people and 1 group isimpson lusk cjeans maximilianh EisenLab
  • The human phylome
    Genome Biology, Vol. 8 (13 June 2007), R109.
    by Jaime Huerta-Cepas, Hernán Dopazo, Joaquín Dopazo, Toni Gabaldón
    posted to dan_presented eisen_journal_club gene_tree genealogy genome_wide human phylogeny round_robin by dpollard on 2007-06-29 06:01:12 as *** along with 3 people and 2 groups aprasad grahamc cjeans EisenLab ParkinsonLab_at_MaRS
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