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olympos' library [160 articles]

Senaste artiklarna i olympos' bibliotek ordnat efter prioritet.
  • Co-evolution of transcriptional and post-translational cell-cycle regulation
    Nature (27 September 2006)
    by Lars J Jensen, Thomas S Jensen, Ulrik de Lichtenberg, Søren Brunak, Peer Bork
    posted to no-tag by olympos on 2007-04-02 22:16:05 as **** along with 7 people and 1 group JAShapiro adepace koller ccr cjeans kluck larsjuhljensen EisenLab
  • Identification of long-range regulatory elements in the protocadherin-alpha gene cluster
    PNAS, Vol. 103, No. 52. (26 December 2006), pp. 19719-19724.
    by Scott Ribich, Bosiljka Tasic, Tom Maniatis
    posted to longrange by olympos on 2007-01-30 14:06:57 as ****
  • Genome-wide analysis of Arabidopsis thaliana DNA methylation uncovers an interdependence between methylation and transcription
    Nature Genetics, Vol. 39, No. 1. (26 November 2006), pp. 61-69.
    by Daniel Zilberman, Mary Gehring, Robert K Tran, Tracy Ballinger, Steven Henikoff
    posted to methylation by olympos on 2007-01-02 23:34:42 as **** along with 2 people saru vmsr
  • A chromatin-mediated mechanism for specification of conditional transcription factor targets
    Nature Genetics, Vol. 38, No. 12. (12 November 2006), pp. 1446-1451.
    by Michael J Buck, Jason D Lieb
    posted to chromatin by olympos on 2007-04-17 19:09:02 as *** along with 2 people and 2 groups nickluscombe kengg EBI-regulation Plantandetc
  • Computational identification of promoters and first exons in the human genome.
    Nat Genet, Vol. 29, No. 4. (December 2001), pp. 412-417.
    by RV Davuluri, I Grosse, MQ Zhang
    posted to no-tag by olympos on 2007-01-29 21:24:00 as *** along with 1 person saxonov
  • Heterotachy in mammalian promoter evolution.
    PLoS Genet, Vol. 2, No. 4. (April 2006)
    by MS Taylor, C Kai, J Kawai, P Carninci, Y Hayashizaki, CA Semple
    posted to transposable_element regulatoryelement evolution by olympos on 2007-01-24 14:00:47 as *** along with 4 people and 1 group kentsis aprasad cisevol gjuggler cis-regulatory-evolution
  • Evolution of a polymorphic regulatory element in interferon-gamma through transposition and mutation.
    Mol Biol Evol, Vol. 19, No. 6. (June 2002), pp. 884-890.
    by H Ackerman, I Udalova, J Hull, D Kwiatkowski
    posted to regulatoryelement evolution by olympos on 2007-01-24 13:57:30 as *** along with 1 person and 1 group cisevol cis-regulatory-evolution
  • Locally Weighted Naive Bayes
    by Eibe Frank, Mark Hall, Bernhard Pfahringer
    posted to machinelearning bayesian by olympos on 2007-01-09 14:35:29 as *** along with 2 people sdvillal flavian_vasile
  • CpG Island Methylation in Human Lymphocytes Is Highly Correlated with DNA Sequence, Repeats, and Predicted DNA Structure
    PLoS Genetics, Vol. 2, No. 3. (1 March 2006), e26.
    by Christoph Bock, Martina Paulsen, Sascha Tierling, Thomas Mikeska, Thomas Lengauer, Jörn Walter
    posted to cpg by olympos on 2006-12-20 21:34:35 as *** along with 3 people rdiaz cberry inesdesantiago
  • 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 motif by olympos on 2006-12-14 15:47:54 as *** along with 25 people and 6 groups bryankr icases ana barry aalibes aprasad jfr tuck chad_davis lyongu tabu dquest neveaire ranb johncumbers noano xiaobeizhao GustavoLacerda nklee mdimon dandaman vietanh0 ep161302 nuin Stew structural_bioinformatics Biostatistics Computational-Genomics Bioinformatics Neuroscience TNT
  • Regulation of gene expression and cocaine reward by CREB and [Delta]FosB
    Nat Neurosci, Vol. 6, No. 11. (November 2003), pp. 1208-1215.
    by Colleen A Mcclung, Eric J Nestler
    posted to cocaine mouse by olympos on 2006-12-14 15:46:08 as *** along with 1 person makikasahara
  • A functional gene array for detection of bacterial virulence elements.
    PLoS ONE, Vol. 3, No. 5. (2008)
    by C Jaing, S Gardner, K McLoughlin, N Mulakken, M Alegria-Hartman, P Banda, P Williams, P Gu, M Wagner, C Manohar, T Slezak
    posted to antibiotic nimblegen u01 by olympos on 2008-07-31 18:13:57 as **
  • Broad-spectrum respiratory tract pathogen identification using resequencing DNA microarrays
    Genome Res., Vol. 16, No. 4. (1 April 2006), pp. 527-535.
    by Baochuan Lin, Zheng Wang, Gary J Vora, Jennifer A Thornton, Joel M Schnur, Dzung C Thach, Kate M Blaney, Adam G Ligler, Anthony P Malanoski, Jose Santiago, Elizabeth A Walter, Brian K Agan, David Metzgar, Donald Seto, Luke T Daum, Russell Kruzelock, Robb K Rowley, Eric H Hanson, Clark Tibbetts, David A Stenger
    posted to resequencing u01 by olympos on 2008-07-29 22:21:29 as **
  • Microarray-Based Detection of 90 Antibiotic Resistance Genes of Gram-Positive Bacteria
    J. Clin. Microbiol., Vol. 43, No. 5. (1 May 2005), pp. 2291-2302.
    by Vincent Perreten, Lorianne Vorlet-Fawer, Peter Slickers, Ralf Ehricht, Peter Kuhnert, Joachim Frey
    posted to antibiotic u01 by olympos on 2008-07-28 19:03:33 as **
  • Environmental Shotgun Sequencing: Its Potential and Challenges for Studying the Hidden World of Microbes
    PLoS Biology, Vol. 5, No. 3. (1 March 2007), e82.
    by Jonathan A Eisen
    posted to metagenomics microbe review sequencing by olympos on 2008-07-26 00:39:00 as ** along with 7 people and 3 groups jmeppley jdelcampo azazello beatrizfernandez xingxu jlgreen djkt Microbial-Ecology Green Lab iSEEM
  • Rapid quantification and taxonomic classification of environmental DNA from both prokaryotic and eukaryotic origins using a microarray.
    FEMS microbiology letters, Vol. 245, No. 2. (15 April 2005), pp. 271-278.
    by TZ Desantis, CE Stone, SR Murray, JP Moberg, GL Andersen
    posted to phylochip by olympos on 2008-07-16 01:44:41 as ** along with 1 person mcox
  • Novel Microarray Design Strategy To Study Complex Bacterial Communities
    Appl. Environ. Microbiol., Vol. 74, No. 6. (15 March 2008), pp. 1876-1885.
    by Antoine Huyghe, Patrice Francois, Yvan Charbonnier, Manuela Tangomo-Bento, Eve-Julie Bonetti, Bruce J Paster, Ignacio Bolivar, Denise Baratti-Mayer, Didier Pittet, Jacques Schrenzel, And
    posted to phylochip by olympos on 2008-07-16 01:28:35 as ** along with 1 person vrich
  • Integrated analysis of experimental data sets reveals many novel promoters in 1% of the human genome
    Genome Res., Vol. 17, No. 6. (1 June 2007), pp. 720-731.
    by Nathan D Trinklein, Ulas Karaoz, Jiaqian Wu, Anason Halees, Force, Patrick J Collins, Deyou Zheng, Zhengdong D Zhang, Mark B Gerstein, Michael Snyder, Richard M Myers, Zhiping Weng
    posted to tez by olympos on 2007-11-26 22:28:32 as ** along with 5 people jyuh djkt cjeans Garamonfok jasonflannick
  • Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project.
    Nature, Vol. 447, No. 7146. (14 June 2007), pp. 799-816.
    by E Encode
    posted to tez by olympos on 2007-11-26 04:50:28 as ** along with 10 people and 2 groups jyuh jfr chad_davis kengg blobbybirdman shikin fpattyn yevishere elfar eskay Bioinformatics UH - Computational Biology
  • Comprehensive analysis of transcriptional promoter structure and function in 1% of the human genome.
    Genome Res, Vol. 16, No. 1. (January 2006), pp. 1-10.
    by SJ Cooper, ND Trinklein, ED Anton, L Nguyen, RM Myers
    posted to tez by olympos on 2007-11-24 04:17:34 as ** along with 2 people troels_marstrand xiaobeizhao
  • BLAT--the BLAST-like alignment tool.
    Genome Res, Vol. 12, No. 4. (April 2002), pp. 656-664.
    by WJ Kent
    posted to tez by olympos on 2007-11-24 04:16:40 as ** along with 18 people and 1 group operon miguel pcahan1 Ayest indigoviolet mtagaya treangen michC djkt timflutre cjeans wenhan natstreet antonkratz yoanjacquemin talponer bozdagd gpappas EisenLab
  • Cap analysis gene expression for high-throughput analysis of transcriptional starting point and identification of promoter usage.
    Proc Natl Acad Sci U S A, Vol. 100, No. 26. (23 December 2003), pp. 15776-15781.
    by T Shiraki, S Kondo, S Katayama, K Waki, T Kasukawa, H Kawaji, R Kodzius, A Watahiki, M Nakamura, T Arakawa, S Fukuda, D Sasaki, A Podhajska, M Harbers, J Kawai, P Carninci, Y Hayashizaki
    posted to tez by olympos on 2007-11-24 04:14:59 as ** along with 6 people setar troels_marstrand xiaobeizhao gjuggler antonkratz jyuh
  • Evidence for variation in abundance of antisense transcripts between multicellular animals but no relationship between antisense transcription and organismic complexity.
    Genome Res (12 June 2006)
    by Miao Sun, Laurence D D Hurst, Gordon G G Carmichael, Jianjun Chen
    posted to antisense tez by olympos on 2007-11-18 22:13:01 as ** along with 2 people and 1 group xwbcn stajich Berkeley Mycology
  • 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
    posted to faire tez by olympos on 2007-11-18 21:19:02 as ** along with 2 people and 1 group dpollard uz_labu_laimi EisenLab
  • Evidence for nucleosome depletion at active regulatory regions genome-wide.
    Nat Genet, Vol. 36, No. 8. (August 2004), pp. 900-905.
    by CK Lee, Y Shibata, B Rao, BD Strahl, JD Lieb
    posted to faire tez by olympos on 2007-11-18 21:18:36 as ** along with 1 person nucleosome
  • Pseudogenes in the ENCODE regions: Consensus annotation, analysis of transcription, and evolution.
    Genome Res, Vol. 17, No. 6. (June 2007), pp. 839-851.
    by D Zheng, A Frankish, R Baertsch, P Kapranov, A Reymond, SW Choo, Y Lu, F Denoeud, SE Antonarakis, M Snyder, Y Ruan, CL Wei, TR Gingeras, R Guigó, J Harrow, MB Gerstein
    posted to pseudogene tez by olympos on 2007-11-18 21:17:37 as ** along with 2 people and 3 groups dchughes ghattem Bioinformatics G4ID Genetics-of-Gambling
  • GENCODE: producing a reference annotation for ENCODE
    Genome Biology, Vol. 7, No. Suppl 1. (2006)
    by Jennifer Harrow, France Denoeud, Adam Frankish, Alexandre Reymond, Chao K Chen, Jacqueline Chrast, Julien Lagarde, James Gilbert, Roy Storey, David Swarbreck, Colette Rossier, Catherine Ucla, Tim Hubbard, Stylianos Antonarakis, Roderic Guigo
    posted to tez by olympos on 2007-11-18 20:47:51 as ** along with 1 person wenhan
  • Origin of a substantial fraction of human regulatory sequences from transposable elements
    Trends in Genetics, Vol. 19, No. 2. (February 2003), pp. 68-72.
    by King I Jordan, Igor B Rogozin, Galina V Glazko, Eugene V Koonin
    posted to tez transposable_element by olympos on 2007-11-18 20:47:30 as **
  • Genome-scale mapping of DNase I sensitivity in vivo using tiling DNA microarrays
    Nature Methods, Vol. 3, No. 7. (21 June 2006), pp. 511-518.
    by Peter J Sabo, Michael S Kuehn, Robert Thurman, Brett E Johnson, Ericka M Johnson, Hua Cao, Man Yu, Elizabeth Rosenzweig, Jeff Goldy, Andrew Haydock, Molly Weaver, Anthony Shafer, Kristin Lee, Fidencio Neri, Richard Humbert, Michael A Singer, Todd A Richmond, Michael O Dorschner, Michael Mcarthur, Michael Hawrylycz, Roland D Green, Patrick A Navas, William S Noble, John A Stamatoyannopoulos
    posted to dhs tez by olympos on 2007-11-18 20:46:29 as ** along with 1 person tuck
  • Pseudogenes: are they "junk" or functional DNA?
    Annu Rev Genet, Vol. 37 (2003), pp. 123-151.
    by ES Balakirev, FJ Ayala
    posted to pseudogene tez by olympos on 2007-11-18 20:45:02 as **
  • Integrated Pseudogene Annotation for Human Chromosome 22: Evidence for Transcription
    Journal of Molecular Biology, Vol. 349, No. 1. (27 May 2005), pp. 27-45.
    by Deyou Zheng, Zhaolei Zhang, Paul M Harrison, John Karro, Nick Carriero, Mark Gerstein
    posted to pseudogene tez by olympos on 2007-11-18 20:44:04 as **
  • The UCSC Table Browser data retrieval tool.
    Nucleic Acids Res, Vol. 32, No. Database issue. (1 January 2004)
    by D Karolchik, AS Hinrichs, TS Furey, KM Roskin, CW Sugnet, D Haussler, WJ Kent
    posted to tez by olympos on 2007-11-18 20:42:56 as ** along with 2 people miguel heliopais
  • Histone methylation in transcriptional control
    Current Opinion in Genetics & Development, Vol. 12, No. 2. (1 April 2002), pp. 198-209.
    by Tony Kouzarides
    posted to methylation tez by olympos on 2007-11-12 21:48:35 as **
  • A high-resolution map of active promoters in the human genome
    Nature (29 June 2005)
    by Tae H Kim, Leah O Barrera, Ming Zheng, Chunxu Qu, Michael A Singer, Todd A Richmond, Yingnian Wu, Roland D Green, Bing Ren
    posted to tez by olympos on 2007-11-12 21:47:51 as ** along with 6 people and 1 group imouthesmp okarsligil jfr tuck balicea sebastien_vigneau Bioinformatics
  • Antisense transcription in the mammalian transcriptome.
    Science, Vol. 309, No. 5740. (2 September 2005), pp. 1564-1566.
    by S Katayama, Y Tomaru, T Kasukawa, K Waki, M Nakanishi, M Nakamura, H Nishida, CC Yap, M Suzuki, J Kawai, H Suzuki, P Carninci, Y Hayashizaki, C Wells, M Frith, T Ravasi, KC Pang, J Hallinan, J Mattick, DA Hume, L Lipovich, S Batalov, PG Engström, Y Mizuno, MA Faghihi, A Sandelin, AM Chalk, S Mottagui-Tabar, Z Liang, B Lenhard, C Wahlestedt, , ,
    posted to antisense tez transcriptome by olympos on 2007-11-12 21:46:06 as ** along with 1 person xwbcn
  • Translating the Histone Code
    Science, Vol. 293, No. 5532. (10 August 2001), pp. 1074-1080.
    by Thomas Jenuwein, David C Allis
    posted to tez by olympos on 2007-11-12 21:45:11 as ** along with 1 person johncumbers
  • The landscape of histone modifications across 1% of the human genome in five human cell lines
    Genome Res., Vol. 17, No. 6. (1 June 2007), pp. 691-707.
    by Christoph M Koch, Robert M Andrews, Paul Flicek, Shane C Dillon, Ulas Karaoz, Gayle K Clelland, Sarah Wilcox, David M Beare, Joanna C Fowler, Phillippe Couttet, Keith D James, Gregory C Lefebvre, Alexander W Bruce, Oliver M Dovey, Peter D Ellis, Pawandeep Dhami, Cordelia F Langford, Zhiping Weng, Ewan Birney, Nigel P Carter, David Vetrie, Ian Dunham
    posted to tez by olympos on 2007-11-12 21:35:44 as ** along with 7 people and 1 group jyuh djkt ghattem epigenetics maximilianh xingxu jasonflannick Bioinformatics
  • R: A Language for Data Analysis and Graphics
    Journal of Computational and Graphical Statistics, Vol. 5, No. 3. (1996), pp. 299-314.
    by Ross Ihaka, Robert Gentleman
    posted to tez by olympos on 2007-11-12 16:30:29 as ** along with 3 people dgruiz incovoma xingxu
  • Genomic Maps and Comparative Analysis of Histone Modifications in Human and Mouse
    Cell, Vol. 120, No. 2. (28 January 2005), pp. 169-181.
    by Bradley E Bernstein, Michael Kamal, Kerstin Lindblad-Toh, Stefan Bekiranov, Dione K Bailey, Dana J Huebert, Scott Mcmahon, Elinor K Karlsson, Edward J Kulbokas, Thomas R Gingeras, Stuart L Schreiber, Eric S Lander
    posted to tez by olympos on 2007-11-11 21:04:46 as ** along with 4 people caseybrown jasonflannick inesdesantiago dquest
  • Genome-wide map of nucleosome acetylation and methylation in yeast.
    Cell, Vol. 122, No. 4. (26 August 2005), pp. 517-527.
    by DK Pokholok, CT Harbison, S Levine, M Cole, NM Hannett, TI Lee, GW Bell, K Walker, PA Rolfe, E Herbolsheimer, J Zeitlinger, F Lewitter, DK Gifford, RA Young
    posted to tez by olympos on 2007-11-11 20:53:01 as ** along with 4 people and 1 group nucleosome kengg koller redfish99213 Plantandetc
  • Significance analysis of microarrays applied to the ionizing radiation response.
    Proc Natl Acad Sci U S A, Vol. 98, No. 9. (24 April 2001), pp. 5116-5121.
    by VG Tusher, R Tibshirani, G Chu
    posted to tez by olympos on 2007-11-11 18:37:18 as ** along with 10 people paszkows miguel jen_drake gpalidwor ccr incovoma ugengma shikin askrajiv renatomilani
  • Histone H3 lysine 4 methylation patterns in higher eukaryotic genes
    Nat Cell Biol, Vol. 6, No. 1. (January 2004), pp. 73-77.
    by Robert Schneider, Andrew J Bannister, Fiona A Myers, Alan W Thorne, Colyn Crane-Robinson, Tony Kouzarides
    posted to tez by olympos on 2007-11-11 18:36:31 as **
  • Targeted Recruitment of Set1 Histone Methylase by Elongating Pol II Provides a Localized Mark and Memory of Recent Transcriptional Activity
    Molecular Cell, Vol. 11, No. 3. (March 2003), pp. 709-719.
    by Huck H Ng, Francois Robert, Richard A Young, Kevin Struhl
    posted to tez by olympos on 2007-11-11 18:35:57 as **
  • Active genes are tri-methylated at K4 of histone H3
    Nature, Vol. 419, No. 6905. (2002), pp. 407-411.
    by Helena Santos-Rosa, Robert Schneider, Andrew J Bannister, Julia Sherriff, Bradley E Bernstein, Tolga NC Emre, Stuart L Schreiber, Jane Mellor, Tony Kouzarides
    posted to tez by olympos on 2007-11-11 18:35:14 as **
  • Methylation of histone H3 Lys 4 in coding regions of active genes
    Proceedings of the National Academy of Sciences, Vol. 99, No. 13. (25 June 2002), pp. 8695-8700.
    by Bradley E Bernstein, Emily L Humphrey, Rachel L Erlich, Robert Schneider, Peter Bouman, Jun S Liu, Tony Kouzarides, Stuart L Schreiber
    posted to tez by olympos on 2007-11-11 18:34:39 as **
  • Regulation of chromatin structure by site-specific histone H3 methyltransferases
    Nature, Vol. 406, No. 6796. (2000), pp. 593-599.
    by Stephen Rea, Frank Eisenhaber, Donal O'Carroll, Brian D Strahl, Zu-Wen Sun, Manfred Schmid, Susanne Opravil, Karl Mechtler, Chris P Ponting, David C Allis, Thomas Jenuwein
    posted to tez by olympos on 2007-11-11 18:18:55 as **
  • Regulation of Transcription by a Protein Methyltransferase
    Science, Vol. 284, No. 5423. (25 June 1999), pp. 2174-2177.
    by Dagang Chen, Han Ma, Heng Hong, Stephen S Koh, Shih-Ming Huang, Brandon T Schurter, Dana W Aswad, Michael R Stallcup
    posted to tez by olympos on 2007-11-11 18:16:00 as **
  • Role of Histone H3 Lysine 27 Methylation in Polycomb-Group Silencing
    Science, Vol. 298, No. 5595. (1 November 2002), pp. 1039-1043.
    by Ru Cao, Liangjun Wang, Hengbin Wang, Li Xia, Hediye Erdjument-Bromage, Paul Tempst, Richard S Jones, Yi Zhang
    posted to histone tez by olympos on 2007-11-11 00:25:15 as **
  • Analysis of genome-wide histone acetylation state and enzyme binding using DNA microarrays.
    Methods Enzymol, Vol. 376 (2004), pp. 289-304.
    by D Robyr, SK Kurdistani, M Grunstein
    posted to acetylation histone tez by olympos on 2007-11-10 22:39:04 as **
  • The occurrence of Epsilon-N-Methyl. lysine in histones.
    Biochemistry, Vol. 3 (January 1964), pp. 10-15.
    by K Murray
    posted to tez by olympos on 2007-11-10 21:50:43 as **
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