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Ключевое слово eisen_journal_club [127 articles]

Recent papers classified by the tag eisen_journal_club.
  • Translational and rotational settings of H2A.Z nucleosomes across the Saccharomycescerevisiae genome
    Nature, Vol. 446, No. 7135., pp. 572-576.
    by Istvan Albert, Travis N Mavrich, Lynn P Tomsho, Ji Qi, Sara J Zanton, Stephan C Schuster, Franklin B Pugh
  • Cooperative assembly of higher-order Notch complexes functions as a switch to induce transcription.
    Proc Natl Acad Sci U S A, Vol. 104, No. 7. (13 February 2007), pp. 2103-2108.
    by Y Nam, P Sliz, WS Pear, JC Aster, SC Blacklow
  • Global identification and characterization of transcriptionally active regions in the rice genome.
    PLoS ONE, Vol. 2 (2007)
    by L Li, X Wang, R Sasidharan, V Stolc, W Deng, H He, J Korbel, X Chen, W Tongprasit, P Ronald, R Chen, M Gerstein, X Wang Deng
    posted to devin_presented eisen_journal_club round_robin by lusk on 2007-04-06 19:51:32 as **
  • The evolutionary significance of cis-regulatory mutations
    Nature Reviews Genetics, Vol. 8, No. 3., pp. 206-216.
    by Gregory A Wray
  • Direct estimation of per nucleotide and genomic deleterious mutation rates in Drosophila
    Nature, Vol. 445, No. 7123. (4 January 2007), pp. 82-85.
    by Cathy Haag-Liautard, Mark Dorris, Xulio Maside, Steven Macaskill, Daniel L Halligan, Brian Charlesworth, Peter D Keightley
  • Programming gene expression with combinatorial promoters
    Mol Syst Biol, Vol. 3 (13 November 2007)
    by Robert S Cox, Michael G Surette, Michael B Elowitz
  • High-throughput sequence alignment using Graphics Processing Units
    BMC Bioinformatics, Vol. 8, No. 1. (2007)
    by Michael Schatz, Cole Trapnell, Arthur Delcher, Amitabh Varshney
  • Pleiotropic scaling of gene effects and the ‘cost of complexity’
    Nature, Vol. 452, No. 7186., pp. 470-472.
    by Günter P Wagner, Jane P Kenney-Hunt, Mihaela Pavlicev, Joel R Peck, David Waxman, James M Cheverud
  • Shape and function of the Bicoid morphogen gradient in dipteran species with different sized embryos.
    Dev Biol (13 February 2008)
    by Thomas Gregor, Alistair P P McGregor, Eric F F Wieschaus
    posted to brant_presented eisen_journal_club by lusk on 2008-03-28 22:31:15 as ** along with 1 person emptyhb
  • Dynamic Remodeling of Individual Nucleosomes Across a Eukaryotic Genome in Response to Transcriptional Perturbation
    PLoS Biology, Vol. 6, No. 3. (1 March 2008), e65.
    by Sushma Shivaswamy, Akshay Bhinge, Yongjun Zhao, Steven Jones, Martin Hirst, Vishwanath R Iyer
  • Evolution of chromosome organization driven by selection for reduced gene expression noise
    Nature Genetics, Vol. 39, No. 8. (27 July 2007), pp. 945-949.
    by Nizar N Batada, Laurence D Hurst
  • Adaptation or biased gene conversion? Extending the null hypothesis of molecular evolution.
    Trends Genet (4 April 2007)
    by Nicolas Galtier, Laurent Duret
  • An RNA gene expressed during cortical development evolved rapidly in humans
    Nature (16 August 2006)
    by Katherine S Pollard, Sofie R Salama, Nelle Lambert, Marie-Alexandra Lambot, Sandra Coppens, Jakob S Pedersen, Sol Katzman, Bryan King, Courtney Onodera, Adam Siepel, Andrew D Kern, Colette Dehay, Haller Igel, Manuel Ares, Pierre Vanderhaeghen, David Haussler
  • Flexible interaction of Drosophila Smad complexes with bipartite binding sites.
    Biochim Biophys Acta, Vol. 1769, No. 7-8. (g 2007), pp. 484-496.
    by S Gao, A Laughon
    posted to brant_presented eisen_journal_club by lusk on 2007-08-12 22:22:06 as **
  • Human gene organization driven by the coordination of replication and transcription
    Genome Res. (3 August 2007), gr.6533407.
    by Maxime Huvet, Samuel Nicolay, Marie Touchon, Benjamin Audit, Yves D'aubenton-Carafa, Alain Arneodo, Claude Thermes
  • A periodic pattern of SNPs in the human genome
    Genome Res. (2 August 2007), gr.6223207.
    by Bo E Madsen, Palle Villesen, Carsten Wiuf
  • 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
  • Divergence of Transcription Factor Binding Sites Across Related Yeast Species
    Science, Vol. 317, No. 5839. (10 August 2007), pp. 815-819.
    by Anthony R Borneman, Tara A Gianoulis, Zhengdong D Zhang, Haiyuan Yu, Joel Rozowsky, Michael R Seringhaus, Lu Y Wang, Mark Gerstein, Michael Snyder
  • Rapid evolution of smell and taste receptor genes during host specialization in Drosophila sechellia.
    Proc Natl Acad Sci U S A (9 March 2007)
    by Carolyn S S McBride
  • Species-specific positive selection of the male-specific lethal complex that participates in dosage compensation in Drosophila.
    Proc Natl Acad Sci U S A, Vol. 104, No. 39. (25 September 2007), pp. 15412-15417.
    by MA Rodriguez, D Vermaak, JJ Bayes, HS Malik
  • Paired-End Mapping Reveals Extensive Structural Variation in the Human Genome.
    Science (27 September 2007)
    by Jan O O Korbel, Alexander Eckehart E Urban, Jason P P Affourtit, Brian Godwin, Fabian Grubert, Jan Fredrik F Simons, Philip M M Kim, Dean Palejev, Nicholas J J Carriero, Lei Du, Bruce E E Taillon, Zhoutao Chen, Andrea Tanzer, A C Eugenia C Saunders, Jianxiang Chi, Fengtang Yang, Nigel P P Carter, Matthew E E Hurles, Sherman M M Weissman, Timothy T T Harkins, Mark B B Gerstein, Michael Egholm, Michael Snyder
  • Members of a large retroposon family are determinants of post-transcriptional gene expression in leishmania.
    PLoS Pathog, Vol. 3, No. 9. (7 September 2007)
    posted to eisen_journal_club lenny_presented round_robin by dpollard to the group EisenLab on 2007-10-19 21:44:19 as **
  • Quantitative prediction of NF-kappa B DNA-protein interactions.
    Proc Natl Acad Sci U S A, Vol. 99, No. 12. (11 June 2002), pp. 8167-8172.
    by IA Udalova, R Mott, D Field, D Kwiatkowski
  • Half a century of neural prepatterning: the story of a few bristles and many genes.
    Nat Rev Neurosci, Vol. 4, No. 7. (July 2003), pp. 587-598.
    posted to eisen_journal_club in_depth by dpollard to the group EisenLab on 2007-02-14 00:47:18 as read
  • Sequence Diversity, Reproductive Isolation and Species Concepts in Saccharomyces
    Genetics, Vol. 174, No. 2. (1 October 2006), pp. 839-850.
    by Gianni Liti, David B Barton, Edward J Louis
    posted to eisen_journal_club lenny_presented round_robin by dpollard to the group EisenLab on 2007-02-14 00:28:23 as **
  • Heritable Stochastic Switching Revealed by Single-Cell Genealogy
    PLoS Biology, Vol. 5, No. 9. (1 September 2007), e239.
    by Benjamin B Kaufmann, Qiong Yang, Jerome T Mettetal, Alexander van Oudenaarden
  • The highly cooperative folding of small naturally occurring proteins is likely the result of natural selection.
    Cell, Vol. 128, No. 3. (9 February 2007), pp. 613-624.
    by AL Watters, P Deka, C Corrent, D Callender, G Varani, T Sosnick, D Baker
  • Relative Impact of Nucleotide and Copy Number Variation on Gene Expression Phenotypes
    Science, Vol. 315, No. 5813. (9 February 2007), pp. 848-853.
    by Barbara E Stranger, Matthew S Forrest, Mark Dunning, Catherine E Ingle, Claude Beazley, Natalie Thorne, Richard Redon, Christine P Bird, Anna de Grassi, Charles Lee, Chris Tyler-Smith, Nigel Carter, Stephen W Scherer, Simon Tavare, Panagiotis Deloukas, Matthew E Hurles, Emmanouil T Dermitzakis
  • Structure-based prediction of C2H2 zinc-finger binding specificity: sensitivity to docking geometry.
    Nucleic Acids Res (30 January 2007)
    by Trevor W W Siggers, Barry Honig
  • Splicing and the Evolution of Proteins in Mammals
    PLoS Biology, Vol. 5, No. 2. (1 February 2007), e14.
    by Joanna L Parmley, Araxi O Urrutia, Lukasz Potrzebowski, Henrik Kaessmann, Laurence D Hurst
  • Pre-Steady-State Decoding of the Bicoid Morphogen Gradient
    PLoS Biology, Vol. 5, No. 2. (1 February 2007), e46.
    by Sven Bergmann, Oded Sandler, Hila Sberro, Sara Shnider, Eyal Schejter, Ben-Zion Shilo, Naama Barkai
  • Thymine Dimerization in DNA Is an Ultrafast Photoreaction
    Science, Vol. 315, No. 5812. (2 February 2007), pp. 625-629.
    by Wolfgang J Schreier, Tobias E Schrader, Florian O Koller, Peter Gilch, Carlos E Crespo-Hernandez, Vijay N Swaminathan, Thomas Carell, Wolfgang Zinth, Bern Kohler
    posted to eisen_journal_club rich_presented round_robin by dpollard to the group EisenLab on 2007-02-14 00:04:57 as ** along with 1 person lusk
  • FAIRE (Formaldehyde-Assisted Isolation of Regulatory Elements) isolates active regulatory elements from human chromatin.
    Genome Res (19 December 2006)
    by Paul G G Giresi, Jonghwan Kim, Ryan M M McDaniell, Vishwanath R R Iyer, Jason D D Lieb
  • A "Silent" Polymorphism in the MDR1 Gene Changes Substrate Specificity.
    Science (21 December 2006)
    by Chava Kimchi-Sarfaty, Jung Mi M Oh, In-Wha W Kim, Zuben E E Sauna, Anna Maria M Calcagno, Suresh V V Ambudkar, Michael M M Gottesman
  • A Systems Approach to Measuring the Binding Energy Landscapes of Transcription Factors
    Science, Vol. 315, No. 5809. (12 January 2007), pp. 233-237.
    by Sebastian J Maerkl, Stephen R Quake
  • 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 to the group EisenLab on 2006-12-13 22:18:54 as ****
  • Evolution of the ventral midline in insect embryos.
    Dev Cell, Vol. 11, No. 6. (December 2006), pp. 895-902.
  • Two Dobzhansky-Muller genes interact to cause hybrid lethality in Drosophila.
    Science, Vol. 314, No. 5803. (24 November 2006), pp. 1292-1295.
    by NJ Brideau, HA Flores, J Wang, S Maheshwari, X Wang, DA Barbash
  • Evidence that the adaptive allele of the brain size gene microcephalin introgressed into Homo sapiens from an archaic Homo lineage
    PNAS, Vol. 103, No. 48. (28 November 2006), pp. 18178-18183.
    by Patrick D Evans, Nitzan Mekel-Bobrov, Eric J Vallender, Richard R Hudson, Bruce T Lahn
  • 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
  • Global variation in copy number in the human genome
    Nature, Vol. 444, No. 7118. (23 November 2006), pp. 444-454.
    by Richard Redon, Shumpei Ishikawa, Karen R Fitch, Lars Feuk, George H Perry, Daniel T Andrews, Heike Fiegler, Michael H Shapero, Andrew R Carson, Wenwei Chen, Eun K Cho, Stephanie Dallaire, Jennifer L Freeman, Juan R Gonzalez, Monica Gratacos, Jing Huang, Dimitrios Kalaitzopoulos, Daisuke Komura, Jeffrey R Macdonald, Christian R Marshall, Rui Mei, Lyndal Montgomery, Kunihiro Nishimura, Kohji Okamura, Fan Shen, Martin J Somerville, Joelle Tchinda, Armand Valsesia, Cara Woodwark, Fengtang Yang, Junjun Zhang, Tatiana Zerjal, Jane Zhang, Lluis Armengol, Donald F Conrad, Xavier Estivill, Chris Tyler-Smith, Nigel P Carter, Hiroyuki Aburatani, Charles Lee, Keith W Jones, Stephen W Scherer, Matthew E Hurles
  • Two or Four Bristles: Functional Evolution of an Enhancer of scute in Drosophilidae
    PLoS Biology, Vol. 4, No. 12. (1 November 2006), e386.
    by Sylvain Marcellini, Pat Simpson
  • 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
  • Compact, universal DNA microarrays to comprehensively determine transcription-factor binding site specificities.
    Nat Biotechnol (24 September 2006)
    by Michael F F Berger, Anthony A A Philippakis, Aaron M M Qureshi, Fangxue S S He, Preston W W Estep, Martha L L Bulyk
  • Genetics of global gene expression
    Nature Reviews Genetics, Vol. 7, No. 11., pp. 862-872.
    by Matthew V Rockman, Leonid Kruglyak
  • Reliable prediction of regulator targets using 12 Drosophila genomes.
    Genome Res (7 November 2007)
    by Alexander Stark, Pouya Kheradpour, Sushmita Roy, Manolis Kellis
  • Dissecting Timing Variability in Yeast Meiosis
    Cell, Vol. 131, No. 3. (2 November 2007), pp. 544-556.
    by Iftach Nachman, Aviv Regev, Sharad Ramanathan
  • 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
  • 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
  • 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
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