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emptyhb library [208 articles]

Статьи, недавно добавленные в библиотеку emptyhb library ordered by importance.
  • notes Comparative genomics at the vertebrate extremes.
    Nat Rev Genet, Vol. 5, No. 6. (June 2004), pp. 456-465.
    by D Boffelli, MA Nobrega, EM Rubin
    posted to cis_regulatory_elements cis_regulatory_evolution review by emptyhb on 2008-04-14 05:25:41 as ***** along with 2 people olympos blobbybirdman
  • Evolution and Selection in Yeast Promoters: Analyzing the Combined Effect of Diverse Transcription Factor Binding Sites
    PLoS Computational Biology, Vol. 4, No. 1. (1 January 2008), e7.
    by Daniela Raijman, Ron Shamir, Amos Tanay
    posted to no-tag by emptyhb on 2008-03-21 02:15:40 as ***** along with 8 people and 1 group xili03 aalibes chad_davis sebastien_vigneau lusk Garamonfok nklee maximilianh BioinfoCIPF
  • notes Evolution of Transcription Factor Binding Sites in Mammalian Gene Regulatory Regions: Conservation and Turnover
    Mol Biol Evol, Vol. 19, No. 7. (1 July 2002), pp. 1114-1121.
    by Emmanouil T Dermitzakis, Andrew G Clark
    posted to binding_sites_turnover cis_regulatory_elements by emptyhb on 2007-12-09 16:53:51 as ***** along with 3 people and 2 groups adepace cisevol xili03 EisenLab cis-regulatory-evolution
  • Rewiring of the Yeast Transcriptional Network Through the Evolution of Motif Usage
    Science, Vol. 309, No. 5736. (05 August 2005), pp. 938-940.
    by Jan Ihmels, Sven Bergmann, Maryam Gerami-Nejad, Itai Yanai, Mark Mcclellan, Judith Berman, Naama Barkai
    posted to cis_regulatory_evolution species_divergence transcriptional_regulation by emptyhb on 2008-04-05 19:55:05 as **** along with 9 people and 3 groups roys Ema aalibes monod arve marcius adepace entropy janek04 EisenLab BioinfoCIPF SGU-CIPF
  • Gene Regulation by Transcription Factors and MicroRNAs
    Science, Vol. 319, No. 5871. (28 March 2008), pp. 1785-1786.
    by Oliver Hobert
    posted to mirna review transcriptional_regulation by emptyhb on 2008-04-01 07:19:00 as **** along with 8 people and 1 group jfr ealloza zwang biomcgary heliopais maralena bootsy siebert microRNA
  • 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 drosophila motif_searching pattern_formation transcriptional_regulation by emptyhb on 2008-01-19 22:49:02 as **** along with 7 people and 3 groups indigoviolet dpollard adepace wrowell dlmace pradiptaray balicea EisenLab Cline_lab UH - Computational Biology
  • notes Evaluating the role of natural selection in the evolution of gene regulation
    Heredity, Vol. aop, No. current.
    by JC Fay, PJ Wittkopp
    posted to cis_regulatory_elements detecting_selection review transcriptional_regulation by emptyhb on 2007-12-31 18:07:55 as **** along with 4 people and 2 groups dpollard djkt cisevol gjuggler EisenLab cis-regulatory-evolution
  • Rapid analysis of the DNA-binding specificities of transcription factors with DNA microarrays
    Nature Genetics, Vol. 36, No. 12. (14 November 2004), 1331.
    by Sonali Mukherjee, Michael F Berger, Ghil Jona, Xun S Wang, Dale Muzzey, Michael Snyder, Richard A Young, Martha L Bulyk
    posted to biophysics dna-protein_interaction in-vivo_binding_sites by emptyhb on 2008-04-05 23:00:57 as *** along with 5 people johncumbers olympos nklee yevishere kristallreiner
  • Close sequence comparisons are sufficient to identify human cis-regulatory elements.
    Genome Res (12 June 2006)
    by Shyam Prabhakar, Francis Poulin, Malak Shoukry, Veena Afzal, Edward M M Rubin, Olivier Couronne, Len A A Pennacchio
    posted to cis_regulatory_elements cis_regulatory_evolution motif_searching by emptyhb on 2008-02-27 06:32:09 as *** along with 8 people and 2 groups indigoviolet dpollard samal nickluscombe olympos bpcusack mariakmejia kcrawlik EisenLab EBI-regulation
  • notes Conservation of regulatory elements between two species of Drosophila.
    BMC Bioinformatics, Vol. 4 (20 November 2003)
    by E Emberly, N Rajewsky, ED Siggia
    posted to cis_regulatory_elements cis_regulatory_evolution drosophila motif_searching by emptyhb on 2008-02-24 21:43:41 as *** along with 1 person and 1 group dquest Bioinformatics
  • Comprehensive identification of Drosophila dorsal-ventral patterning genes using a whole-genome tiling array
    Proceedings of the National Academy of Sciences, Vol. 103, No. 34. (22 August 2006), pp. 12763-12768.
    by Frederic Biemar, David A Nix, Jessica Piel, Brant Peterson, Matthew Ronshaugen, Victor Sementchenko, Ian Bell, Robert J Manak, Michael S Levine
    posted to cis_regulatory_elements drosophila mirna pattern_formation by emptyhb on 2008-01-11 16:48:18 as *** along with 1 person and 1 group Stew EisenLab
  • Evolution of functionally conserved enhancers can be accelerated in large populations: a population-genetic model.
    Proc Biol Sci, Vol. 269, No. 1494. (7 May 2002), pp. 953-960.
    by AJ Carter, GP Wagner
    posted to binding_sites_turnover cis_regulatory_elements population_genetics_modeling by emptyhb on 2007-12-11 20:55:48 as *** along with 1 person and 1 group cisevol cis-regulatory-evolution
  • Intragenic Recombination and Diversifying Selection Contribute to the Evolution of Downy Mildew Resistance at the RPP8 Locus of Arabidopsis
    Plant Cell, Vol. 10, No. 11. (1 November 1998), pp. 1861-1874.
    by John M Mcdowell, Murali Dhandaydham, Terri A Long, Mark G Aarts, Stephen Goff, Eric B Holub, Jeffery L Dangl
    posted to immune plant by emptyhb on 2007-11-28 14:15:42 as ***
  • Genomic islands of speciation in Anopheles gambiae.
    PLoS Biol, Vol. 3, No. 9. (September 2005)
    by TL Turner, MW Hahn, SV Nuzhdin
    posted to microarray by emptyhb on 2008-10-09 01:27:49 as ** along with 2 people RMGraze natstreet
  • Getting started in tiling microarray analysis.
    PLoS Comput Biol, Vol. 3, No. 10. (26 October 2007), pp. 1842-1844.
    by XS Liu
    posted to microarray by emptyhb on 2008-10-08 04:14:50 as ** along with 7 people cassj jfr cabbagezs waszak yevishere Ayest GeeSharpMinor
  • Microarray Analysis
    PLoS Biology, Vol. 1, No. 1. (1 October 2003), e15.
    by Greg Gibson
    posted to microarray by emptyhb on 2008-10-07 19:40:00 as ** along with 1 person and 2 groups ana structural_bioinformatics Bioinformatics
  • DNA binding sites: representation and discovery.
    Bioinformatics, Vol. 16, No. 1. (January 2000), pp. 16-23.
    by GD Stormo
    posted to dna-protein_interaction cis_regulatory_elements by emptyhb on 2008-10-06 23:47:08 as ** along with 7 people isimpson kaarsinogen mbj dquest lusk ezralanglois xili03
  • Selection of DNA binding sites by regulatory proteins. Statistical-mechanical theory and application to operators and promoters.
    J Mol Biol, Vol. 193, No. 4. (20 February 1987), pp. 723-750.
    by OG Berg, PH von Hippel
    posted to dna-protein_interaction cis_regulatory_elements by emptyhb on 2008-10-06 23:39:58 as ** along with 8 people and 2 groups jjray indigoviolet lusk discreteonyxorb cisevol Ema brant zambujo EisenLab cis-regulatory-evolution
  • Conservation and Rewiring of Functional Modules Revealed by an Epistasis Map in Fission Yeast
    Science (25 September 2008), 1162609.
    by Assen Roguev, Sourav Bandyopadhyay, Martin Zofall, Ke Zhang, Tamas Fischer, Sean R Collins, Hongjing Qu, Michael Shales, Han-Oh Park, Jacqueline Hayles, Kwang-Lae Hoe, Dong-Uk Kim, Trey Ideker, Shiv I Grewal, Jonathan S Weissman, Nevan J Krogan
    posted to systems_biology epigenetics by emptyhb on 2008-10-06 21:24:26 as ** along with 3 people caseybrown bpcusack brembs
  • Indel-Based Evolutionary Distance and Mouse-Human Divergence
    Genome Res., Vol. 14, No. 8. (1 August 2004), pp. 1610-1616.
    by Aleksey Y Ogurtsov, Shamil Sunyaev, Alexey S Kondrashov
    posted to population_genetics by emptyhb on 2008-10-06 17:07:32 as ** along with 1 person aprasad
  • Apobec3 Encodes Rfv3, a Gene Influencing Neutralizing Antibody Control of Retrovirus Infection
    Science, Vol. 321, No. 5894. (5 September 2008), pp. 1343-1346.
    by Mario L Santiago, Mauricio Montano, Robert Benitez, Ronald J Messer, Wes Yonemoto, Bruce Chesebro, Kim J Hasenkrug, Warner C Greene
    posted to no-tag by emptyhb on 2008-10-06 06:43:03 as ** along with 1 person rjreinhard
  • Speciation through sensory drive in cichlid fish
    Nature, Vol. 455, No. 7213. (2 October 2008), pp. 620-626.
    by Ole Seehausen, Yohey Terai, Isabel S Magalhaes, Karen L Carleton, Hillary D Mrosso, Ryutaro Miyagi, Inke van der Sluijs, Maria V Schneider, Martine E Maan, Hidenori Tachida, Hiroo Imai, Norihiro Okada
    posted to species_divergence natural_selection by emptyhb on 2008-10-06 06:17:57 as ** along with 2 people jbsaltz stevanspringer
  • Genome-wide transcription and the implications for genomic organization.
    Nat Rev Genet (8 May 2007)
    by Philipp Kapranov, Aarron T T Willingham, Thomas R R Gingeras
    posted to transcriptional_regulation systems_biology by emptyhb on 2008-10-05 05:34:38 as ** along with 17 people and 5 groups pengchy jyuh balicea xico dchughes kengg sebastien_vigneau zwang ajgentles Ema asddd hanansh antonkratz vietanh0 maximilianh GeeSharpMinor inesdesantiago Bioinformatics WetBiology G4ID Plantandetc Genetics-of-Gambling
  • Biological function of unannotated transcription during the early development of Drosophila melanogaster
    Nature Genetics, Vol. 38, No. 10. (03 September 2006), pp. 1151-1158.
    by Robert J Manak, Sujit Dike, Victor Sementchenko, Philipp Kapranov, Frederic Biemar, Jeff Long, Jill Cheng, Ian Bell, Srinka Ghosh, Antonio Piccolboni, Thomas R Gingeras
    posted to no-tag by emptyhb on 2008-10-05 03:51:46 as ** along with 7 people and 6 groups GeeSharpMinor dpollard neveaire djkt wrowell Stew xingxu Biostatistics Computational-Genomics Bioinformatics EisenLab Neuroscience Cline_lab
  • Probabilistic Phylogenetic Inference with Insertions and Deletions
    PLoS Comput Biol, Vol. 4, No. 9. (2008), e1000172.
    by Elena Rivas, Sean R Eddy
    posted to no-tag by emptyhb on 2008-09-22 06:14:34 as ** along with 6 people nuin timflutre druvus djkt aprasad gjuggler
  • An Approximate Bayesian Estimator Suggests Strong, Recurrent Selective Sweeps in Drosophila
    PLoS Genet, Vol. 4, No. 9. (2008), e1000198.
    by Jeffrey D Jensen, Kevin R Thornton, Peter Andolfatto
    posted to population_genetics drosophila by emptyhb on 2008-09-22 06:13:25 as ** along with 2 people maren jbsaltz
  • Assessing computational tools for the discovery of transcription factor binding sites
    Nature Biotechnology, Vol. 23, No. 1. (06 January 2005), pp. 137-144.
    by Martin Tompa, Nan Li, Timothy L Bailey, George M Church, Bart D De Moor, Eleazar Eskin, Alexander V Favorov, Martin C Frith, Yutao Fu, James J Kent, Vsevolod J Makeev, Andrei A Mironov, William S Noble, Giulio Pavesi, Graziano Pesole, Mireille Régnier, Nicolas Simonis, Saurabh Sinha, Gert Thijs, Jacques v van Helden, Mathias Vandenbogaert, Zhiping Weng, Christopher Workman, Chun Ye, Zhou Zhu
    posted to review motif_searching by emptyhb on 2008-09-16 22:44:24 as ** along with 26 people and 6 groups bryankr icases ana barry aalibes aprasad jfr tuck chad_davis lyongu tabu dquest neveaire ranb johncumbers noano xiaobeizhao olympos GustavoLacerda nklee mdimon dandaman vietanh0 ep161302 nuin Stew structural_bioinformatics Biostatistics Computational-Genomics Bioinformatics Neuroscience TNT
  • Metabolic gene regulation in a dynamically changing environment
    Nature (30 July 2008)
    by Matthew R Bennett, Wyming L Pang, Natalie A Ostroff, Bridget L Baumgartner, Sujata Nayak, Lev S Tsimring, Jeff Hasty
    posted to transcriptional_regulation systems_biology by emptyhb on 2008-09-15 19:55:09 as ** along with 5 people erel10 caseybrown bayesian klo margaritis
  • The origins of genome complexity.
    Science, Vol. 302, No. 5649. (21 November 2003), pp. 1401-1404.
    by M Lynch, JS Conery
    posted to review population_genetics natural_selection by emptyhb on 2008-09-15 04:44:23 as ** along with 7 people and 1 group operon madhadron bluto timflutre jwestbrook cmzmasek HugoMarcelo King_Lab
  • Species-Specific Transcription in Mice Carrying Human Chromosome 21
    Science (11 September 2008), 1160930.
    by Michael D Wilson, Nuno L Barbosa-Morais, Dominic Schmidt, Caitlin M Conboy, Lesley Vanes, Victor L Tybulewicz, Elizabeth M Fisher, Simon Tavare, Duncan T Odom
    posted to transcriptional_regulation experimental_method cis_regulatory_evolution by emptyhb on 2008-09-13 02:26:57 as ** along with 4 people and 1 group Zephyrus sebastien_vigneau Stew bpcusack Roswell Cancer Crosstalk
  • Human-Specific Gain of Function in a Developmental Enhancer
    Science, Vol. 321, No. 5894. (5 September 2008), pp. 1346-1350.
    by Shyam Prabhakar, Axel Visel, Jennifer A Akiyama, Malak Shoukry, Keith D Lewis, Amy Holt, Ingrid Plajzer-Frick, Harris Morrison, David R Fitzpatrick, Veena Afzal, Len A Pennacchio, Edward M Rubin, James P Noonan
    posted to experimental_method cis_regulatory_evolution by emptyhb on 2008-09-12 13:53:08 as ** along with 11 people and 1 group Stew shoshin bpcusack Zephyrus sebastien_vigneau djkt natstreet isimpson maximilianh caseybrown eskay Roswell Cancer Crosstalk
  • Levels of naturally occurring DNA polymorphism correlate with recombination rates in D. melanogaster.
    Nature, Vol. 356, No. 6369. (9 April 1992), pp. 519-520.
    by DJ Begun, CF Aquadro
    posted to population_genetics natural_selection by emptyhb on 2008-09-11 23:09:35 as **
  • A Catalog of Neutral and Deleterious Polymorphism in Yeast
    PLoS Genet, Vol. 4, No. 8. (2008), e1000183.
    by Scott W Doniger, Hyun S Kim, Devjanee Swain, Daniella Corcuera, Morgan Williams, Shiaw-Pyng Yang, Justin C Fay
    posted to population_genetics natural_selection by emptyhb on 2008-09-11 23:00:06 as ** along with 2 people bpcusack caseybrown
  • Quantitative specificity of the Mnt repressor
    Journal of Molecular Biology, Vol. 271, No. 2. (15 August 1997), pp. 178-194.
    by Dana S Fields, Yi-Yuan He, Ahmed Y Al-Uzri, Gary D Stormo
    posted to dna-protein_interaction by emptyhb on 2008-09-11 16:33:12 as **
  • Insights into Protein–DNA Interactions through Structure Network Analysis
    PLoS Comput Biol, Vol. 4, No. 9. (2008), e1000170.
    by R Sathyapriya, MS Vijayabaskar, Saraswathi Vishveshwara
    posted to dna-protein_interaction by emptyhb on 2008-09-11 15:41:33 as ** along with 7 people and 1 group Zephyrus Ema aalibes AbnerCYH Totobox zwang hmk Roswell Cancer Crosstalk
  • A survey of DNA motif finding algorithms
    BMC Bioinformatics, Vol. 8, No. Suppl 7. (2007)
    by Modan Das, Ho K Dai
    posted to review motif_searching by emptyhb on 2008-09-10 22:38:01 as ** along with 8 people dquest nklee maximilianh yevishere csdhwang brant xili03 pradiptaray
  • NestedMICA: sensitive inference of over-represented motifs in nucleic acid sequence
    Nucleic Acids Research, Vol. 33, No. 5. (2005), pp. 1445-1453.
    by Thomas A Down, Tim J Hubbard
    posted to motif_searching by emptyhb on 2008-09-10 22:30:21 as ** along with 4 people and 1 group lyongu dpollard dquest waszak EisenLab
  • DNA binding sites: representation and discovery
    Bioinformatics, Vol. 16, No. 1. (1 January 2000), pp. 16-23.
    by Gary D Stormo
    posted to motif_searching by emptyhb on 2008-09-02 05:07:44 as ** along with 1 person kaarsinogen
  • BioSAVE: Display of scored annotation within a sequence context
    BMC Bioinformatics, Vol. 9 (20 March 2008), 157.
    by Richard F Pollock, Boris Adryan
    posted to software motif_searching cis_regulatory_elements by emptyhb on 2008-09-01 17:56:15 as ** along with 2 people jyuh dquest
  • Noise Reduction by Diffusional Dissipation in a Minimal Quorum Sensing Motif
    PLoS Comput Biol, Vol. 4, No. 8. (2008), e1000167.
    by Yu Tanouchi, Dennis Tu, Jungsang Kim, Lingchong You
    posted to noiserobustness by emptyhb on 2008-08-31 20:21:10 as ** along with 4 people raik erel10 margaritis jjray
  • PhyloGibbs-MP: Module Prediction and Discriminative Motif-Finding by Gibbs Sampling
    PLoS Comput Biol, Vol. 4, No. 8. (2008), e1000156.
    by Rahul Siddharthan
    posted to motif_searching by emptyhb on 2008-08-31 20:03:28 as ** along with 2 people and 1 group nuin sabahkadri BenosLab
  • A Feature-Based Approach to Modeling Protein–DNA Interactions
    PLoS Comput Biol, Vol. 4, No. 8. (2008), e1000154.
    by Eilon Sharon, Shai Lubliner, Eran Segal
    posted to dna-protein_interaction transcriptional_regulation by emptyhb on 2008-08-25 15:29:39 as ** along with 4 people dakelley Stew zwang aalibes
  • Evolution of yellow Gene Regulation and Pigmentation in Drosophila
    Current Biology, Vol. 12, No. 18. (17 September 2002), pp. 1547-1556.
    by Patricia J Wittkopp, Kathy Vaccaro, Sean B Carroll
    posted to cis_regulatory_evolution drosophila by emptyhb on 2008-08-22 16:38:10 as **
  • Comparative genome sequencing of Drosophila pseudoobscura: chromosomal, gene, and cis-element evolution.
    Genome Res, Vol. 15, No. 1. (January 2005), pp. 1-18.
    by S Richards, Y Liu, BR Bettencourt, P Hradecky, S Letovsky, R Nielsen, K Thornton, MJ Hubisz, R Chen, RP Meisel, O Couronne, S Hua, MA Smith, P Zhang, J Liu, HJ Bussemaker, MF van Batenburg, SL Howells, SE Scherer, E Sodergren, BB Matthews, MA Crosby, AJ Schroeder, D Ortiz-Barrientos, CM Rives, ML Metzker, DM Muzny, G Scott, D Steffen, DA Wheeler, KC Worley, P Havlak, KJ Durbin, A Egan, R Gill, J Hume, MB Morgan, G Miner, C Hamilton, Y Huang, L Waldron, D Verduzco, KP Clerc-Blankenburg, I Dubchak, MA Noor, W Anderson, KP White, AG Clark, SW Schaeffer, W Gelbart, GM Weinstock, RA Gibbs
    posted to cis_regulatory_evolution drosophila by emptyhb on 2008-08-22 15:40:54 as ** along with 9 people and 3 groups briann tsackton jshapiro operon indigoviolet penka adepace cisevol skumagai EisenLab Nie cis-regulatory-evolution
  • 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 population_genetics by emptyhb on 2008-08-14 02:25:07 as ** along with 4 people and 1 group dpollard djkt usagi-kirin mimulus_99 EisenLab
  • Patterns of Evolutionary Constraints in Intronic and Intergenic DNA of Drosophila
    Genome Res., Vol. 14, No. 2. (1 February 2004), pp. 273-279.
    by Daniel L Halligan, Adam Eyre-Walker, Peter Andolfatto, Peter D Keightley
    posted to drosophila natural_selection by emptyhb on 2008-08-14 02:24:58 as ** along with 1 person and 1 group penka Nie
  • Positive and negative selection on noncoding DNA in Drosophila simulans.
    Molecular biology and evolution (29 May 2008)
    by Penelope R R Haddrill, Doris Bachtrog, Peter Andolfatto
    posted to drosophila natural_selection population_genetics by emptyhb on 2008-08-13 21:32:07 as ** along with 2 people Stew caseybrown
  • Contrasting patterns of X-linked and autosomal nucleotide variation in Drosophila melanogaster and Drosophila simulans.
    Molecular biology and evolution, Vol. 18, No. 3. (March 2001), pp. 279-290.
    by P Andolfatto
    posted to drosophila natural_selection population_genetics by emptyhb on 2008-08-13 20:11:40 as **
  • Rationalization of gene regulation by a eukaryotic transcription factor: calculation of regulatory region occupancy from predicted binding affinities.
    Journal of molecular biology, Vol. 323, No. 1. (11 October 2002), pp. 1-8.
    by X Liu, ND Clarke
    posted to cis_regulatory_evolution dna-protein_interaction by emptyhb on 2008-08-11 21:13:28 as **
  • Canalization of segmentation and its evolution in Drosophila.
    Proc Natl Acad Sci U S A (14 June 2007)
    by Susan E E Lott, Martin Kreitman, Arnar Palsson, Elena Alekseeva, Michael Z Z Ludwig
    posted to genetic_buffering by emptyhb on 2008-08-10 18:33:52 as ** along with 1 person and 1 group dpollard EisenLab
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