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lusks library [186 articles]

Senaste artiklarna i lusks bibliotek.
  • Modeling Promoter Grammars with Evolving Hidden Markov Models.
    Bioinformatics (Oxford, England) (5 June 2008)
    by Kyoung-Jae J Won, Albin Sandelin, Troels Torben T Marstrand, Anders Krogh
    posted to module_inference spacing by lusk on 2008-06-19 19:25:37 as ** along with 2 people maximilianh niallhaslam
  • RNA-seq: An assessment of technical reproducibility and comparison with gene expression arrays
    Genome Res. (11 June 2008), gr.079558.108.
    by John Marioni, Cristopher Mason, Shrikant Mane, Matthew Stephens, Yoav Gilad
    posted to illumina microarray sequencing by lusk on 2008-06-19 19:17:06 as ** along with 16 people and 1 group dakelley caseybrown Ema balicea vega semrich vmarshal fpattyn stajich giovanni ela503 Stew jyuh kengg shurjo GustavoLacerda Berkeley Mycology
  • Inferring Natural Selection on Fine-Scale Chromatin Organization in Yeast.
    Molecular biology and evolution (29 May 2008)
    by G A A Babbitt, Y Kim
    posted to evolution nucleosome by lusk on 2008-06-12 21:21:20 as **
  • Regulation of a segmentation stripe by overlapping activators and repressors in the Drosophila embryo.
    Science (New York, N.Y.), Vol. 254, No. 5036. (29 November 1991), pp. 1385-1387.
    by D Stanojevic, S Small, M Levine
    posted to eve overlap by lusk on 2008-05-14 22:31:45 as **
  • The origin of subfunctions and modular gene regulation.
    Genetics, Vol. 170, No. 1. (May 2005), pp. 433-446.
    by A Force, WA Cresko, FB Pickett, SR Proulx, C Amemiya, M Lynch
    posted to flies null by lusk on 2008-04-30 04:51:10 as ** along with 3 people brant bluto Stew
  • The evolution of genetic networks by non-adaptive processes
    Nature Reviews Genetics, Vol. 8, No. 10., pp. 803-813.
    by Michael Lynch
    posted to flies null by lusk on 2008-04-30 04:50:16 as ** along with 10 people and 2 groups brant balicea dchughes aswin stajich margaritis zwang nosada17 Stew lilith G4ID Genetics-of-Gambling
  • A systems view of Drosophila segmentation
    Genome Biology, Vol. 9 (11 February 2008), 207.
    by Mike Levine
    posted to inside segmentation by lusk on 2008-04-30 04:49:19 as ** along with 1 person grahamc
  • Sequence Context affects the rate of short insertions and deletions in flies and primates
    Genome Biology, Vol. 9 (21 February 2008), R37.
    by Amos Tanay, Eric D Siggia
    posted to deletion insertion inside by lusk on 2008-04-15 02:02:12 as ** along with 5 people djkt biomcgary gjuggler brant aprasad
  • 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 eve flies inside by lusk on 2008-04-13 01:46:37 as ** along with 1 person and 1 group dpollard EisenLab
  • 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 eisen_journal_club ryan_presented by lusk on 2008-03-28 22:33:23 as ** along with 14 people and 2 groups Retchless tmmurali austin dpollard balicea kengg dbikard margaritis cjeans zwang discreteonyxorb cabbagezs Ema tresch EisenLab SynBioSys
  • High-throughput sequence alignment using Graphics Processing Units
    BMC Bioinformatics, Vol. 8, No. 1. (2007)
    by Michael Schatz, Cole Trapnell, Arthur Delcher, Amitabh Varshney
    posted to eisen_journal_club stuart_presented by lusk on 2008-03-28 22:32:51 as ** along with 10 people and 1 group Yanno jyuh sephy laughcry nedwards mdimon cndewey heliopais urgi tpreeprem gatech-compgenomics
  • 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
    posted to colin_presented eisen_journal_club by lusk on 2008-03-28 22:32:14 as ** along with 2 people biomcgary natstreet
  • 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
    posted to eisen_journal_club nucleosome rich_presented by lusk on 2008-03-28 22:30:43 as ** along with 2 people djkt vega
  • The Downstream Promoter Element DPE Appears To Be as Widely Used as the TATA Box in Drosophila Core Promoters
    Mol. Cell. Biol., Vol. 20, No. 13. (1 July 2000), pp. 4754-4764.
    by Alan K Kutach, James T Kadonaga
    posted to genny by lusk on 2008-01-25 19:08:40 as ** along with 2 people zhlei bpcusack
  • 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 evolution tfbs by lusk on 2008-01-21 22:07:56 as ***** along with 7 people and 1 group aalibes chad_davis sebastien_vigneau Garamonfok nklee maximilianh emptyhb BioinfoCIPF
  • Extensive low-affinity transcriptional interactions in the yeast genome.
    Genome Res (29 June 2006)
    by Amos Tanay
    posted to inside by lusk on 2007-09-25 03:01:44 as ** along with 6 people and 1 group devin indigoviolet dpollard balicea koller emptyhb EisenLab
  • From promoter sequence to expression: a probabilistic framework
    by Eran Segal, Yoseph Barash, Itamar Simon, Nir Friedman, Daphne Koller
    edited by Sorin Istrail, Michael S Waterman, Andrew G Clark
    posted to inside by lusk on 2007-09-25 02:59:55 as **
  • A feature-based approach to modeling protein-DNA interactions
    by E Sharon, E Segal
    edited by T Speed, H Huang
    posted to inside by lusk on 2007-09-25 02:54:17 as **
  • 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
    posted to eisen_journal_club stuart_presented by lusk on 2007-08-12 22:28:16 as ** along with 5 people and 2 groups jjray dpollard ealloza djkt zwang EisenLab BioinfoCIPF
  • 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
    posted to danr_presented eisen_journal_club by lusk on 2007-08-12 22:21:32 as ** along with 4 people operon djkt cabbagezs bpcusack
  • A periodic pattern of SNPs in the human genome
    Genome Res. (2 August 2007), gr.6223207.
    by Bo E Madsen, Palle Villesen, Carsten Wiuf
    posted to danr_presented eisen_journal_club by lusk on 2007-08-12 22:20:47 as ** along with 2 people and 3 groups dchughes ljs Bioinformatics G4ID Genetics-of-Gambling
  • 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 eisen_journal_club emily_presented by lusk on 2007-08-12 22:19:33 as ** along with 4 people and 1 group dpollard cjeans maximilianh isimpson EisenLab
  • 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
    posted to devin_presented eisen_journal_club rich_presented by lusk on 2007-08-12 22:19:04 as ** along with 17 people and 2 groups bryankr aalibes chad_davis dpollard djkt mikaelhuss cjeans sujaikumar zwang GustavoLacerda Jporci maximilianh cisevol njcitulike emptyhb nklee anka EisenLab cis-regulatory-evolution
  • A large-scale full-length cDNA analysis to explore the budding yeast transcriptome.
    Proc Natl Acad Sci U S A, Vol. 103, No. 47. (21 November 2006), pp. 17846-17851.
    by F Miura, N Kawaguchi, J Sese, A Toyoda, M Hattori, S Morishita, T Ito
    posted to tss by lusk on 2007-07-20 22:49:04 as **
  • Backup without redundancy: genetic interactions reveal the cost of duplicate gene loss.
    Mol Syst Biol, Vol. 3 (2007)
    by J Ihmels, SR Collins, M Schuldiner, NJ Krogan, JS Weissman
    posted to next_project by lusk on 2007-07-16 22:04:58 as **** along with 2 people aprasad bpcusack
  • Distance preferences in the arrangement of binding motifs and hierarchical levels in organization of transcription regulatory information.
    Nucleic Acids Res, Vol. 31, No. 20. (15 October 2003), pp. 6016-6026.
    by VJ Makeev, AP Lifanov, AG Nazina, DA Papatsenko
    posted to affin_cut by lusk on 2007-07-15 02:50:33 as ** along with 2 people and 2 groups dpollard oannes EisenLab Regulomics_UCHSC
  • Periodical distribution of transcription factor sites in promoter regions and connection with chromatin structure.
    Proc Natl Acad Sci U S A, Vol. 96, No. 6. (16 March 1999), pp. 2891-2895.
    by I Ioshikhes, EN Trifonov, MQ Zhang
    posted to affin_cut by lusk on 2007-07-15 02:50:10 as **
  • Cooperative DNA-protein interactions. Effects of changing the spacing between adjacent binding sites.
    J Mol Biol, Vol. 235, No. 2. (14 January 1994), pp. 532-544.
    by C Mao, NG Carlson, JW Little
    posted to affin_cut by lusk on 2007-07-15 02:49:41 as **
  • Molecular determinants of the cell-cycle regulated Mcm1p-Fkh2p transcription factor complex.
    Nucleic Acids Res, Vol. 31, No. 9. (1 May 2003), pp. 2279-2288.
    by J Boros, FL Lim, Z Darieva, A Pic-Taylor, R Harman, BA Morgan, AD Sharrocks
    posted to affin_cut by lusk on 2007-07-15 02:49:15 as **
  • Genome-wide regulatory complexity in yeast promoters: Separation of functionally conserved and neutral sequence.
    Genome Res, Vol. 15, No. 2. (February 2005), pp. 205-213.
    by CS Chin, JH Chuang, H Li
    posted to affin_cut by lusk on 2007-07-15 02:47:49 as ** along with 3 people and 1 group briann nklee cisevol cis-regulatory-evolution
  • An improved map of conserved regulatory sites for Saccharomyces cerevisiae.
    BMC Bioinformatics, Vol. 7, No. 1. (7 March 2006)
    by Kenzie D Macisaac, Ting Wang, Benjamin D Gordon, David K Gifford, Gary D Stormo, Ernest Fraenkel
    posted to affin_cut by lusk on 2007-07-15 02:46:52 as ** along with 7 people tuck eckart_bindewald cconboy raiyar nklee barwil kristallreiner
  • SGD: Saccharomyces Genome Database.
    Nucleic Acids Res, Vol. 26, No. 1. (1 January 1998), pp. 73-79.
    by JM Cherry, C Adler, C Ball, SA Chervitz, SS Dwight, ET Hester, Y Jia, G Juvik, T Roe, M Schroeder, S Weng, D Botstein
    posted to affin_cut by lusk on 2007-07-15 02:45:48 as ** along with 4 people and 1 group irenas RMGraze nklee CitoJam dbk-lab
  • Rapid and sensitive protein similarity searches.
    Science, Vol. 227, No. 4693. (22 March 1985), pp. 1435-1441.
    by DJ Lipman, WR Pearson
    posted to affin_cut by lusk on 2007-07-15 02:45:21 as ** along with 2 people dgront CitoJam
  • Neural networks for determining protein specificity and multiple alignment of binding sites.
    Proc Int Conf Intell Syst Mol Biol, Vol. 2 (1994), pp. 188-194.
    by JM Heumann, AS Lapedes, GD Stormo
    posted to affin_cut by lusk on 2007-07-15 02:44:58 as **
  • Locating mammalian transcription factor binding sites: A survey of computational and experimental techniques.
    Genome Res (19 October 2006)
    by Laura Elnitski, Victor X X Jin, Peggy J J Farnham, Steven J M J Jones
    posted to affin_cut by lusk on 2007-07-15 02:43:21 as ** along with 6 people and 1 group bryankr giovanni SeungjoonOh cabbagezs maximilianh gdb GeschwindLab
  • Transcriptional regulatory networks in Saccharomyces cerevisiae.
    Science, Vol. 298, No. 5594. (25 October 2002), pp. 799-804.
    by TI Lee, NJ Rinaldi, F Robert, DT Odom, Z Bar-Joseph, GK Gerber, NM Hannett, CT Harbison, CM Thompson, I Simon, J Zeitlinger, EG Jennings, HL Murray, DB Gordon, B Ren, JJ Wyrick, JB Tagne, TL Volkert, E Fraenkel, DK Gifford, RA Young
    posted to affin_cut review by lusk on 2007-07-15 02:42:54 as ** along with 26 people and 2 groups camster snuppepuppan icases forluvoft ggrot alokm opheliav samal sameetmehta cconboy koller jguinney franklin timflutre jpoyatos nklee karfunkel mimulus_99 roys njcitulike brant kristallreiner Borelli Takayuki dquest siebert dbk-lab TNT
  • Transcription of eukaryotic protein-coding genes.
    Annu Rev Genet, Vol. 34 (2000), pp. 77-137.
    by TI Lee, RA Young
    posted to affin_cut review by lusk on 2007-07-15 02:42:25 as ** along with 1 person hplatero
  • The spacing between binding sites controls the mode of cooperative DNA-protein interactions: implications for evolution of regulatory circuitry
    Journal of Molecular Biology, Vol. 278, No. 2. (1 May 1998), pp. 331-338.
    by Zane Liu, John W Little
    posted to cooperativity spacing by lusk on 2007-07-10 19:52:00 as **
  • Mechanisms controlling differential promoter-occupancy by the yeast forkhead proteins Fkh1p and Fkh2p: implications for regulating the cell cycle and differentiation
    Genes Dev., Vol. 15, No. 18. (15 September 2001), pp. 2445-2456.
    by Peter C Hollenhorst, Gregory Pietz, Catherine A Fox
    posted to cutoff_model fkh1 by lusk on 2007-05-17 02:16:04 as **
  • The different (sur)faces of Rap1p
    Molecular Genetics and Genomics, Vol. 268, No. 6. (1 March 2003), pp. 791-798.
    by B Piña, J Fernández-Larrea, N García-Reyero, FZ Idrissi
    posted to cutoff_model rap1 by lusk on 2007-05-17 00:17:38 as ** along with 1 person hplatero
  • Yap1 and Skn7 control two specialized oxidative stress response regulons in yeast.
    J Biol Chem, Vol. 274, No. 23. (4 June 1999), pp. 16040-16046.
    by J Lee, C Godon, G Lagniel, D Spector, J Garin, J Labarre, MB Toledano
    posted to cutoff_model yap1 by lusk on 2007-05-16 23:55:40 as **
  • Association of the Cell Cycle Transcription Factor Mbp1 with the Skn7 Response Regulator in Budding Yeast
    Mol. Biol. Cell, Vol. 10, No. 10. (1 October 1999), pp. 3389-3400.
    by Nicolas Bouquin, Anthony L Johnson, Brian A Morgan, Leland H Johnston
    posted to cutoff_model skn7 by lusk on 2007-05-16 23:47:44 as **
  • The Skn7 Response Regulator of Saccharomyces cerevisiae Interacts with Hsf1 In Vivo and Is Required for the Induction of Heat Shock Genes by Oxidative Stress
    Mol. Biol. Cell, Vol. 11, No. 7. (1 July 2000), pp. 2335-2347.
    by Desmond C Raitt, Anthony L Johnson, Alexander M Erkine, Kozo Makino, Brian Morgan, David S Gross, Leland H Johnston
    posted to cutoff_model skn7 by lusk on 2007-05-16 23:41:32 as **
  • Mcm1 Binds Replication Origins
    J. Biol. Chem., Vol. 278, No. 8. (14 February 2003), pp. 6093-6100.
    by Victoria K Chang, Michael J Fitch, Justin J Donato, Tim W Christensen, Margaret A Merchant, Bik K Tye
    posted to cutoff_model mcm1 by lusk on 2007-05-16 22:23:14 as **
  • MCM proteins and DNA replication
    Current Opinion in Cell Biology, Vol. 18, No. 2. (April 2006), pp. 130-136.
    by Domenico Maiorano, Malik Lutzmann, Marcel Mechali
    posted to cutoff_model mcm1 by lusk on 2007-05-16 22:17:17 as **
  • NDD1, a High-Dosage Suppressor of cdc28-1N, Is Essential for Expression of a Subset of Late-S-Phase-Specific Genes in Saccharomyces cerevisiae
    Mol. Cell. Biol., Vol. 19, No. 5. (1 May 1999), pp. 3312-3327.
    by Chong J Loy, David Lydall, Uttam Surana
    posted to cutoff_model ndd1 by lusk on 2007-05-16 21:22:18 as **
  • Genome-wide prediction and characterization of interactions between transcription factors in Saccharomyces cerevisiae.
    Nucleic Acids Res, Vol. 34, No. 3. (2006), pp. 917-927.
    by X Yu, J Lin, T Masuda, N Esumi, DJ Zack, J Qian
    posted to cooperativity cutoff_model by lusk on 2007-05-16 19:40:31 as **** along with 3 people and 1 group balajis malcook oannes Regulomics_UCHSC
  • Identifying cooperative transcriptional regulations using protein-protein interactions.
    Nucleic Acids Res, Vol. 33, No. 15. (2005), pp. 4828-4837.
    by N Nagamine, Y Kawada, Y Sakakibara
    posted to cooperativity cutoff_model by lusk on 2007-05-16 19:29:52 as **
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