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xingxu さんのウォッチリスト [399 articles]

最近追加された論文の中で xingxu さんの設定条件に合うもののリストです
  • 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
  • Multi-scale correlations in continuous genomic data.
    Pac Symp Biocomput (2008), pp. 201-215.
    by RE Thurman, WS Noble, JA Stamatoyannopoulos
    posted to correlation histone hypersensitive nucleosome by dpollard on 2008-02-01 07:05:30 as ** along with 2 people and 1 group jyuh operon 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
  • Use of an evolutionary model to provide evidence for a wide heterogeneity of required affinities between transcription factors and their binding sites in yeast.
    Pac Symp Biocomput (2008), pp. 489-500.
    by RW Lusk, MB Eisen
    posted to affinity binding_site transcription_factor variation yeast by dpollard on 2008-02-01 06:19:08 as read along with 1 person and 2 groups maximilianh EisenLab cis-regulatory-evolution
  • 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 19 people and 2 groups adacier jyuh bpb aprasad dayjm tny djkt cjeans zwang lisa1 cactus biomcgary lilou kinestetika dandaman gjuggler renatomilani mclarenv youdon EisenLab microbiology_nijmegen
  • 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
  • Multiple RTK pathways downregulate Groucho-mediated repression in Drosophila embryogenesis.
    Development (23 January 2008)
    by Einat Cinnamon, Aharon Helman, Rachel Ben-Haroush Schyr, Amir Orian, Gerardo Jiménez, Ze'ev Paroush
    posted to post_transcriptional_modification repression by dpollard on 2008-02-01 06:09:59 as ** along with 1 group EisenLab
  • Delimiting the conserved features of hunchback function for the trunk organization of insects.
    Development (23 January 2008)
    by Henrique Marques-Souza, Manuel Aranda, Diethard Tautz
    posted to drosophila expression_pattern gene_function_evolution insects pattern targets transcription_factor tribolium by dpollard on 2008-02-01 06:06:53 as ** along with 1 group EisenLab
  • 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
  • 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
  • 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
  • Evolutionary changes in cis and trans gene regulation
    Nature, Vol. 430, No. 6995. (1 July 2004), pp. 85-88.
    by Patricia J Wittkopp, Belinda K Haerum, Andrew G Clark
    posted to cis_vs_trans drosophila expression_divergence expression_polymorphism hybrid regulatory_evolution regulatory_polymorphism by dpollard on 2007-12-05 22:58:32 as read along with 8 people and 2 groups lyongu balicea tabu adepace emmahe emarker mimulus_99 cisevol EisenLab cis-regulatory-evolution
  • Ancient and Recent Positive Selection Transformed Opioid cis-Regulation in Humans.
    PLoS Biol, Vol. 3, No. 12. (15 November 2005)
    by Matthew V V Rockman, Matthew W W Hahn, Nicole Soranzo, Fritz Zimprich, David B B Goldstein, Gregory A A Wray
    posted to binding_site cis_regulatory_elements human regulatory_evolution regulatory_polymorphism regulatory_sequence_evolution turnover by dpollard on 2007-12-05 22:55:41 as read along with 7 people and 3 groups imouthesmp indigoviolet Archaeogenetics happy_manatee djkt mgaldzic cisevol EisenLab CHIP 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
  • Chance caught on the wing: cis-regulatory evolution and the origin of pigment patterns in Drosophila.
    Nature, Vol. 433, No. 7025. (3 February 2005), pp. 481-487.
    by N Gompel, B Prud'homme, PJ Wittkopp, VA Kassner, SB Carroll
    posted to binding_site cis_regulatory_elements drosophila pigmentation regulatory_evolution regulatory_sequence_evolution turnover by dpollard on 2007-12-05 22:48:37 as read along with 4 people and 2 groups emilyhare adepace cisevol emptyhb EisenLab cis-regulatory-evolution
  • 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
  • Regulation of Body Pigmentation by the Abdominal-B Hox Protein and Its Gain and Loss in Drosophila Evolution
    Cell, Vol. 125, No. 7. (30 June 2006), pp. 1387-1399.
    by Sangyun Jeong, Antonis Rokas, Sean B Carroll
    posted to binding_site cis_regulatory_elements pigmentation regulatory_evolution regulatory_sequence_evolution turnover by dpollard on 2007-12-05 22:44:47 as read along with 1 person and 2 groups emilyhare EisenLab cis-regulatory-evolution
  • Quantitative models of developmental pattern formation.
    Dev Cell, Vol. 11, No. 3. (September 2006), pp. 289-300.
    by GT Reeves, CB Muratov, T Schüpbach, SY Shvartsman
    posted to expression_pattern modeling pattern review by dpollard on 2007-12-05 21:05:56 as read along with 1 person and 1 group brant 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
  • Transcriptional regulation of a pair-rule stripe in Drosophila.
    Genes Dev, Vol. 5, No. 5. (May 1991), pp. 827-839.
    by S Small, R Kraut, T Hoey, R Warrior, M Levine
    posted to drosophila embryonic_patterning grammar repression seminal_paper by dpollard on 2007-12-05 19:31:27 as ** along with 1 person and 1 group lusk EisenLab
  • Transcriptional regulatory code of a eukaryotic genome
    Nature, Vol. 431, No. 7004. (2004), pp. 99-104.
    by Christopher T Harbison, Benjamin D Gordon, Tong I Lee, Nicola J Rinaldi, Kenzie D Macisaac, Timothy W Danford, Nancy M Hannett, Jean-Bosco Tagne, David B Reynolds, Jane Yoo, Ezra G Jennings, Julia Zeitlinger, Dmitry K Pokholok, Manolis Kellis, Alex P Rolfe, Ken T Takusagawa, Eric S Lander, David K Gifford, Ernest Fraenkel, Richard A Young
    posted to chip_chip cis_regulatory_elements yeast by dpollard on 2007-12-04 00:29:15 as read along with 21 people and 8 groups mariakmejia brant alokm tuck chad_davis lyongu kaspermunch balicea kt dchughes nirfriedman cmm nickluscombe kengg gespim koller lusk nklee cisevol njcitulike xili03 Bioinformatics EisenLab FAB-lab G4ID EBI-regulation Plantandetc Genetics-of-Gambling BergmanLab
  • 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
  • Nucleotide sequence of an RNA polymerase binding site at an early T7 promoter.
    Proc Natl Acad Sci U S A, Vol. 72, No. 3. (March 1975), pp. 784-788.
    by D Pribnow
    posted to binding_site cis_regulatory_elements conservation seminal_paper by dpollard on 2007-11-26 00:28:07 as read 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
  • 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
  • Dynamics and function of intron sequences of the wingless gene during the evolution of the Drosophila genus.
    Evol Dev, Vol. 6, No. 5. (t 2004), pp. 325-335.
    by J Costas, PS Pereira, CP Vieira, S Pinho, J Vieira, F Casares
    posted to cis_regulatory_elements drosophila expression_divergence expression_pattern turnover by dpollard on 2007-11-21 01:23:45 as read along with 2 groups EisenLab cis-regulatory-evolution
  • Turnover of binding sites for transcription factors involved in early Drosophila development.
    Gene, Vol. 310 (22 May 2003), pp. 215-220.
    by J Costas, F Casares, J Vieira
    posted to binding_site cis_regulatory_elements drosophila turnover by dpollard on 2007-11-21 01:22:24 as read along with 1 person and 2 groups cisevol EisenLab cis-regulatory-evolution
  • 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 14 people and 5 groups 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
  • Polymorphism and divergence for island-model species.
    Genetics, Vol. 163, No. 1. (January 2003), pp. 411-420.
    by J Wakeley
    posted to population_genetics population_structure test_for_selection by dpollard on 2007-11-19 02:46:23 as ** along with 1 group EisenLab
  • Evolution of novel abdominal appendages in a sepsid fly from histoblasts, not imaginal discs
    Evolution & Development, Vol. 9, No. 4. (August 2007), pp. 347-354.
    by Bowsher, H Julia, Nijhout, H Frederik
    posted to eisen_journal_club emily_presented evo_devo round_robin by dpollard on 2007-11-17 00:12:25 as ** along with 1 person and 1 group brant EisenLab
  • In vivo dynamics of RNA polymerase II transcription.
    Nat Struct Mol Biol (5 August 2007)
    by Xavier Darzacq, Yaron Shav-Tal, Valeria de Turris, Yehuda Brody, Shailesh M M Shenoy, Robert D D Phair, Robert H H Singer
    posted to colin_presented eisen_journal_club modeling round_robin transcription by dpollard on 2007-11-17 00:11:00 as ** along with 5 people and 3 groups jjray dchughes madhadron cwbrown margaritis EisenLab G4ID Genetics-of-Gambling
  • Unmasking Activation of the Zygotic Genome Using Chromosomal Deletions in the Drosophila Embryo
    PLoS Biology, Vol. 5, No. 5. (1 May 2007), e117.
    by Stefano De Renzis, Olivier Elemento, Saeed Tavazoie, Eric F Wieschaus
    posted to drosophila eisen_journal_club embryo gene_expression matt_presented round_robin by dpollard on 2007-11-17 00:09:40 as ** along with 1 person and 2 groups wrowell EisenLab Cline_lab
  • Global analysis of patterns of gene expression during Drosophila embryogenesis
    Genome Biology, Vol. 8 (23 July 2007), R145.
    by Pavel Tomancak, Benjamin P Berman, Amy Beaton, Richard Weiszmann, Elaine Kwan, Volker Hartenstein, Susan E Celniker, Gerald M Rubin
    posted to drosophila eisen_journal_club embryonic_patterning expression_pattern gene_expression matt_presented round_robin by dpollard on 2007-11-17 00:04:12 as read along with 1 person and 1 group 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
  • Programming gene expression with combinatorial promoters
    Mol Syst Biol, Vol. 3 (13 November 2007)
    by Robert S Cox, Michael G Surette, Michael B Elowitz
    posted to cis_regulatory_elements eisen_journal_club grammar rich_presented round_robin by dpollard on 2007-11-16 23:56:56 as ** along with 13 people and 2 groups Retchless tmmurali austin balicea kengg dbikard margaritis lusk cjeans zwang discreteonyxorb cabbagezs Ema EisenLab SynBioSys
  • Dissecting Timing Variability in Yeast Meiosis
    Cell, Vol. 131, No. 3. (2 November 2007), pp. 544-556.
    by Iftach Nachman, Aviv Regev, Sharad Ramanathan
    posted to eisen_journal_club lenny_presented round_robin by dpollard on 2007-11-16 23:55:04 as ** along with 2 people and 1 group balabu margaritis 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
  • Constraint and turnover in sex-biased gene expression in the genus Drosophila
    Nature, Vol. 450, No. 7167., pp. 233-237.
    by Yu Zhang, David Sturgill, Michael Parisi, Sudhir Kumar, Brian Oliver
    posted to dan_presented drosophila eisen_journal_club expression_divergence gene_expression round_robin by dpollard on 2007-11-16 23:49:54 as read along with 1 person and 2 groups indigoviolet EisenLab cis-regulatory-evolution
  • Contamination of the genome by very slightly deleterious mutations: why have we not died 100 times over?
    J Theor Biol, Vol. 175, No. 4. (21 August 1995), pp. 583-594.
    by AS Kondrashov
    posted to mutational_load selection slightly_deleterious_mutations by dpollard on 2007-11-16 03:45:21 as read along with 1 group EisenLab
  • The regulatory content of intergenic DNA shapes genome architecture.
    Genome Biol, Vol. 5, No. 4. (2004)
    by CE Nelson, BM Hersh, SB Carroll
    posted to drosophila gene_expression genome_architecture nematode noncoding by dpollard on 2007-11-14 21:21:28 as read along with 4 people and 3 groups madhadron elzodw blobbybirdman cisevol EisenLab cis-regulatory-evolution BergmanLab
  • Large-Scale Discovery of Promoter Motifs in Drosophila melanogaster
    PLoS Computational Biology, Vol. 3, No. 1. (1 January 2007), e7.
    by Thomas A Down, Casey M Bergman, Jing Su, Tim J Hubbard
    posted to binding_site cis_regulatory_elements drosophila motif_detection by dpollard on 2007-11-14 21:19:05 as read along with 5 people and 1 group indigoviolet dquest SeungjoonOh nklee emptyhb EisenLab
  • Principles of Genome Evolution in the Drosophila melanogaster Species Group
    PLoS Biology, Vol. 5, No. 6. (1 June 2007), e152.
    by José M Ranz, Damien Maurin, Yuk S Chan, Marcin von Grotthuss, Ladeana W Hillier, John Roote, Michael Ashburner, Casey M Bergman
    posted to drosophila evolution genome_architecture inversion by dpollard on 2007-11-14 21:16:50 as ** along with 4 people and 1 group operon zwang nosada17 maximilianh EisenLab
  • Purifying Selection Maintains Highly Conserved Noncoding Sequences in Drosophila.
    Mol Biol Evol (23 July 2007)
    by Sònia Casillas, Antonio Barbadilla, Casey M M Bergman
    posted to conserved drosophila noncoding polymorphism population_genetics purifying selection by dpollard on 2007-11-14 21:15:01 as read along with 7 people and 2 groups brant operon emilyhare Garamonfok Stew cisevol emptyhb EisenLab cis-regulatory-evolution
  • Rapid sequence turnover at an intergenic locus in Drosophila.
    Mol Biol Evol, Vol. 21, No. 4. (April 2004), pp. 670-680.
    by ND Singh, DA Petrov
    posted to drosophila genome_architecture genome_size indels noncoding by dpollard on 2007-11-14 21:13:48 as read along with 1 group EisenLab
  • Pseudogene evolution in Drosophila suggests a high rate of DNA loss.
    Mol Biol Evol, Vol. 15, No. 11. (November 1998), pp. 1562-1567.
    by DA Petrov, YC Chao, EC Stephenson, DL Hartl
    posted to drosophila genome_architecture genome_size indels pseudogene by dpollard on 2007-11-14 21:12:54 as ** along with 1 group EisenLab
  • How intron splicing affects the deletion and insertion profile in Drosophila melanogaster.
    Genetics, Vol. 162, No. 3. (November 2002), pp. 1233-1244.
    by SE Ptak, DA Petrov
    posted to drosophila genome_architecture genome_size indels splicing by dpollard on 2007-11-14 21:12:02 as ** along with 1 group EisenLab
  • DNA loss and evolution of genome size in Drosophila.
    Genetica, Vol. 115, No. 1. (May 2002), pp. 81-91.
    by DA Petrov
    posted to drosophila genome_architecture genome_size indels by dpollard on 2007-11-14 21:11:15 as ** along with 1 person and 1 group timflutre EisenLab
  • Mutational equilibrium model of genome size evolution.
    Theor Popul Biol, Vol. 61, No. 4. (June 2002), pp. 531-544.
    by DA Petrov
    posted to genome_architecture genome_size indels model by dpollard on 2007-11-14 21:10:36 as ** along with 3 people and 1 group operon aprasad timflutre EisenLab
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