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xiaobeizhaos library [41 articles]

Neue Artikel in xiaobeizhaos library ordered by importance.
  • Tissue-specific functions based on information content of gene ontology using cap analysis gene expression.
    Medical & biological engineering & computing, Vol. 45, No. 11. (November 2007), pp. 1029-1036.
    by S Maekawa, A Matsumoto, Y Takenaka, H Matsuda
    posted to no-tag by xiaobeizhao on 2008-07-12 12:02:15 as ***** along with 1 person jyuh
  • Serial analysis of gene expression.
    Science, Vol. 270, No. 5235. (20 October 1995), pp. 484-487.
    by VE Velculescu, L Zhang, B Vogelstein, KW Kinzler
    posted to no-tag by xiaobeizhao on 2008-05-13 11:15:30 as ***** along with 5 people and 1 group bertelsen gurkanbebek jeremymiller epigenetics elzodw GeschwindLab
  • WebLogo: A Sequence Logo Generator
    Genome Res., Vol. 14, No. 6. (1 June 2004), pp. 1188-1190.
    by Gavin E Crooks, Gary Hon, John-Marc Chandonia, Steven E Brenner
    posted to weblogo by xiaobeizhao on 2006-12-13 20:05:53 as ***** along with 4 people and 2 groups analogAI indigoviolet sobolevnrm yevishere EisenLab baker-group
  • notes Where did the BLOSUM62 alignment score matrix come from?
    Nat Biotechnol, Vol. 22, No. 8. (August 2004), pp. 1035-1036.
    by SR Eddy
    posted to amino-acid primer sequence-alignment substitution-matrix by xiaobeizhao on 2006-10-08 22:31:06 as ***** along with 5 people reyez ziquje bicko gurkanbebek rabio
  • 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 algorithm analysis review tfbs by xiaobeizhao on 2006-10-09 06:03:55 as **** along with 23 people and 6 groups nuin ep161302 icases ana barry aalibes aprasad jfr tuck chad_davis lyongu tabu dquest neveaire ranb johncumbers noano olympos GustavoLacerda nklee mdimon dandaman vietanh0 structural_bioinformatics Biostatistics Computational-Genomics Bioinformatics Neuroscience TNT
  • Gibbs Recursive Sampler: finding transcription factor binding sites
    Nucl. Acids Res., Vol. 31, No. 13. (1 July 2003), pp. 3580-3585.
    by William Thompson, Eric C Rouchka, Charles E Lawrence
    posted to algorithm gibbs-sampler tfbs by xiaobeizhao on 2006-10-09 05:49:57 as **** along with 4 people lyongu dquest daniel_quest johncumbers
  • CAGE Basic/Analysis Databases: the CAGE resource for comprehensive promoter analysis.
    Nucleic Acids Res, Vol. 34, No. Database issue. (1 January 2006)
    by H Kawaji, T Kasukawa, S Fukuda, S Katayama, C Kai, J Kawai, P Carninci, Y Hayashizaki
    posted to no-tag by xiaobeizhao on 2008-05-13 11:05:12 as ** along with 4 people troels_marstrand olympos kkishore12 gjuggler
  • Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targets
    Genome Res. (7 February 2008), gr.7080508.
    by David S Johnson, Wei Li, Benjamin D Gordon, Arindam Bhattacharjee, Bo Curry, Jayati Ghosh, Leonardo Brizuela, Jason S Carroll, Myles Brown, Paul Flicek, Christopher M Koch, Ian Dunham, Mark Bieda, Xiaoqin Xu, Peggy J Farnham, Philipp Kapranov, David A Nix, Thomas R Gingeras, Xinmin Zhang, Heather Holster, Nan Jiang, Roland Green, Jun S Song, Scott A Mccuine, Elizabeth Anton, Loan Nguyen, Nathan D Trinklein, Zhen Ye, Keith Ching, David Hawkins, Bing Ren, Peter C Scacheri, Joel Rozowsky, Alexander Karpikov, Ghia Euskirchen, Sherman Weissman, Mark Gerstein, Michael Snyder, Annie Yang, Zarmik Moqtaderi, Heather Hirsch, Hennady P Shulha, Yutao Fu, Zhiping Weng, Kevin Struhl, Richard M Myers, Jason D Lieb, Shirley X Liu
    posted to chip-chip by xiaobeizhao on 2008-03-17 12:32:23 as ** along with 10 people and 2 groups gracio stajich lp2 magusina jfr kengg djkt cabbagezs idonaldson caseybrown Berkeley Mycology BergmanLab
  • Functional Demarcation of Active and Silent Chromatin Domains in Human HOX Loci by Noncoding RNAs.
    Cell, Vol. 129, No. 7. (29 June 2007), pp. 1311-1323.
    by JL Rinn, M Kertesz, JK Wang, SL Squazzo, X Xu, SA Brugmann, LH Goodnough, JA Helms, PJ Farnham, E Segal, HY Chang
    posted to no-tag by xiaobeizhao on 2008-03-08 22:38:57 as ** along with 4 people and 1 group jasonflannick kentsis andersbj mtagaya microRNA
  • Epigenetics: a landscape takes shape.
    Cell, Vol. 128, No. 4. (23 February 2007), pp. 635-638.
    by AD Goldberg, CD Allis, E Bernstein
    posted to epigenetics by xiaobeizhao on 2008-03-08 22:29:26 as ** along with 2 people and 1 group stefanjanusz grahamc ParkinsonLab_at_MaRS
  • Histone methylation: dynamic or static?
    Cell, Vol. 109, No. 7. (28 June 2002), pp. 801-806.
    by AJ Bannister, R Schneider, T Kouzarides
    posted to epigenetics by xiaobeizhao on 2008-03-08 22:28:03 as **
  • Analysis of epigenetic modifications of chromatin at specific gene loci by native chromatin immunoprecipitation of nucleosomes isolated using hydroxyapatite chromatography
    Nat. Protocols, Vol. 3, No. 3. (March 2008), pp. 398-409.
    by Marjorie Brand, Shravanti Rampalli, Chandra-Prakash Chaturvedi, Jeffrey F Dilworth
    posted to no-tag by xiaobeizhao on 2008-03-08 21:58:17 as **
  • 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 no-tag by xiaobeizhao on 2007-11-17 22:32:50 as ** along with 2 people troels_marstrand olympos
  • 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 no-tag by xiaobeizhao on 2007-11-17 01:39:02 as ** along with 5 people antonkratz setar troels_marstrand olympos gjuggler
  • Applied bioinformatics for the identification of regulatory elements.
    Nat Rev Genet, Vol. 5, No. 4. (April 2004), pp. 276-287.
    by WW Wasserman, A Sandelin
    posted to no-tag by xiaobeizhao on 2007-11-17 01:03:33 as ** along with 15 people and 8 groups mariakmejia icases ana chad_davis moborg gpalidwor dchughes nickluscombe johncumbers giovanni bertelsen Stew nklee jdiezperezj ArtemPankin structural_bioinformatics Bioinformatics EisenLab G4ID EBI-regulation GeschwindLab TNT Genetics-of-Gambling
  • Promoter classifier: software package for promoter database analysis.
    Appl Bioinformatics, Vol. 4, No. 3. (2005), pp. 205-209.
    by NI Gershenzon, IP Ioshikhes
    posted to no-tag by xiaobeizhao on 2007-11-16 22:01:00 as **
  • CAGE: cap analysis of gene expression
    Nature Methods, Vol. 3, No. 3., pp. 211-222.
    by Rimantas Kodzius, Miki Kojima, Hiromi Nishiyori, Mari Nakamura, Shiro Fukuda, Michihira Tagami, Daisuke Sasaki, Kengo Imamura, Chikatoshi Kai, Matthias Harbers, Yoshihide Hayashizaki, Piero Carninci
    posted to no-tag by xiaobeizhao on 2007-11-16 16:37:20 as ** along with 1 person jyuh
  • Demystified ...: Transcription
    Mol Pathol, Vol. 53, No. 1. (1 February 2000), pp. 1-7.
    by WM Macfarlane
    posted to no-tag by xiaobeizhao on 2007-11-16 15:49:58 as **
  • Weight matrix descriptions of four eukaryotic RNA polymerase II promoter elements derived from 502 unrelated promoter sequences.
    J Mol Biol, Vol. 212, No. 4. (20 April 1990), pp. 563-578.
    by P Bucher
    posted to no-tag by xiaobeizhao on 2007-11-16 14:54:49 as ** along with 1 person troels_marstrand
  • Analysis of E. coli promoter sequences.
    Nucleic Acids Res, Vol. 15, No. 5. (11 March 1987), pp. 2343-2361.
    by CB Harley, RP Reynolds
    posted to no-tag by xiaobeizhao on 2007-11-16 14:54:26 as ** along with 1 person mrzjh2
  • Mammalian RNA polymerase II core promoters: insights from genome-wide studies
    Nature Reviews Genetics, Vol. 8, No. 6. (08 May 2007), pp. 424-436.
    by Albin Sandelin, Piero Carninci, Boris Lenhard, Jasmina Ponjavic, Yoshihide Hayashizaki, David A Hume
    posted to no-tag by xiaobeizhao on 2007-11-15 22:25:24 as ** along with 5 people and 3 groups GeeSharpMinor dchughes zwang cabbagezs cisevol G4ID Genetics-of-Gambling cis-regulatory-evolution
  • Genome-wide analysis of mammalian promoter architecture and evolution
    Nature Genetics, Vol. 38, No. 6. (28 April 2006), pp. 626-635.
    by Piero Carninci, Albin Sandelin, Boris Lenhard, Shintaro Katayama, Kazuro Shimokawa, Jasmina Ponjavic, Colin AM Semple, Martin S Taylor, Pär G Engström, Martin C Frith, Alistair RR Forrest, Wynand B Alkema, Sin L Tan, Charles Plessy, Rimantas Kodzius, Timothy Ravasi, Takeya Kasukawa, Shiro Fukuda, Mutsumi Kanamori-Katayama, Yayoi Kitazume, Hideya Kawaji, Chikatoshi Kai, Mari Nakamura, Hideaki Konno, Kenji Nakano, Salim Mottagui-Tabar, Peter Arner, Alessandra Chesi, Stefano Gustincich, Francesca Persichetti, Harukazu Suzuki, Sean M Grimmond, Christine A Wells, Valerio Orlando, Claes Wahlestedt, Edison T Liu, Matthias Harbers, Jun Kawai, Vladimir B Bajic, David A Hume, Yoshihide Hayashizaki
    posted to no-tag by xiaobeizhao on 2007-11-15 21:29:20 as ** along with 10 people and 4 groups jasonflannick jfr xwbcn dchughes tabu samal nickluscombe cisevol eviledv gjuggler G4ID EBI-regulation Genetics-of-Gambling cis-regulatory-evolution
  • Secondary structure prediction for aligned RNA sequences.
    J Mol Biol, Vol. 319, No. 5. (21 June 2002), pp. 1059-1066.
    by IL Hofacker, M Fekete, PF Stadler
    posted to secondary-structure rna by xiaobeizhao on 2007-01-20 20:44:17 as ** along with 7 people evaf balajis eckart_bindewald ppgardne arcticrasta ilh raylim
  • Trans-splicing and polycistronic transcription in Caenorhabditis elegans.
    Trends Genet, Vol. 11, No. 4. (April 1995), pp. 132-136.
    by T Blumenthal
    posted to no-tag by xiaobeizhao on 2006-12-14 05:04:33 as **
  • A conserved sequence motif in 3' untranslated regions of ribosomal protein mRNAs in nematodes
    RNA, Vol. 12, No. 10. (1 October 2006), pp. 1786-1789.
    by Ashwin Hajarnavis, Richard Durbin
    posted to no-tag by xiaobeizhao on 2006-12-14 04:39:58 as **
  • U2AF binding selects for the high conservation of the C. elegans 3' splice site
    RNA, Vol. 11, No. 3. (1 March 2005), pp. 248-253.
    by Courtney Hollins, Diego A Zorio, Margaret Macmorris, Thomas Blumenthal
    posted to splicing by xiaobeizhao on 2006-12-14 04:17:48 as **
  • Functional analysis of a C. elegans trans-splice acceptor.
    Nucleic Acids Res, Vol. 21, No. 4. (25 February 1993), pp. 913-919.
    by R Conrad, RF Liou, T Blumenthal
    posted to splicing by xiaobeizhao on 2006-12-14 04:04:11 as **
  • Analysis of the role of Caenorhabditis elegans GC-AG introns in regulated splicing.
    Nucleic Acids Res, Vol. 30, No. 15. (1 August 2002), pp. 3360-3367.
    by T Farrer, AB Roller, WJ Kent, AM Zahler
    posted to splicing by xiaobeizhao on 2006-12-14 03:35:30 as **
  • A note on composite likelihood inference and model selection
    Biometrika, Vol. 92, No. 3. (1 September 2005), pp. 519-528.
    by Cristiano Varin, Paolo Vidoni
    posted to likelihood by xiaobeizhao on 2006-11-30 18:19:36 as **
  • Structure validation by Calpha geometry: phi,psi and Cbeta deviation.
    Proteins, Vol. 50, No. 3. (15 February 2003), pp. 437-450.
    by SC Lovell, IW Davis, WB Arendall, PI de Bakker, JM Word, MG Prisant, JS Richardson, DC Richardson
    posted to plot by xiaobeizhao on 2006-10-21 01:54:56 as ** along with 6 people and 2 groups aqeel jwm robert dgront martainn mijam Radiation_Damage Stressosome
  • Phi/psi-chology: Ramachandran revisited.
    Structure, Vol. 4, No. 12. (15 December 1996), pp. 1395-1400.
    by GJ Kleywegt, TA Jones
    posted to plot by xiaobeizhao on 2006-10-20 13:45:07 as ** along with 1 person aqeel
  • An algorithm with constant execution time for dynamic storage allocation
    Real-Time Computing Systems and Applications, 1995. Proceedings., Second International Workshop on (1995), pp. 21-25.
    by T Ogasawara
    posted to algorithm constant-execution-time by xiaobeizhao on 2006-10-10 18:22:42 as **
  • Gibbs motif sampling: detection of bacterial outer membrane protein repeats.
    Protein Sci, Vol. 4, No. 8. (August 1995), pp. 1618-1632.
    by AF Neuwald, JS Liu, CE Lawrence
    posted to algorithm gibbs-sampler motif protein by xiaobeizhao on 2006-10-09 16:36:24 as **
  • Discovery of novel transcription factor binding sites by statistical overrepresentation.
    Nucleic Acids Res, Vol. 30, No. 24. (15 December 2002), pp. 5549-5560.
    by S Sinha, M Tompa
    posted to algorithm tfbs by xiaobeizhao on 2006-10-09 15:33:50 as ** along with 8 people wenhan ep161302 kaarsinogen dquest smiddha GeeSharpMinor xi03 xili03
  • SCPD: a promoter database of the yeast Saccharomyces cerevisiae.
    Bioinformatics, Vol. 15, No. 7-8. (g 1999), pp. 607-611.
    by J Zhu, MQ Zhang
    posted to promoter by xiaobeizhao on 2006-10-09 15:33:09 as ** along with 4 people chad_davis lusk nklee njcitulike
  • Background rareness-based iterative multiple sequence alignment algorithm for regulatory element detection.
    Bioinformatics, Vol. 19, No. 15. (12 October 2003), pp. 1952-1963.
    by C Narasimhan, P LoCascio, E Uberbacher
    posted to algorithm sequence-alignment by xiaobeizhao on 2006-10-09 15:31:53 as ** along with 2 people nklee xili03
  • An algorithm for finding signals of unknown length in DNA sequences.
    Bioinformatics, Vol. 17 Suppl 1 (2001)
    by G Pavesi, G Mauri, G Pesole
    posted to algorithm pattern-discovery by xiaobeizhao on 2006-10-09 05:41:54 as ** along with 5 people ep161302 dquest smiddha nklee xili03
  • New Algorithms for Regular Expression Matching
    (28 Jun 2006)
    by Philip Bille
    posted to algorithm by xiaobeizhao on 2006-10-09 04:08:05 as ** along with 6 people ansobol jrw michael_hliao estrabd vidal31 oflazer
  • Sequence comparison and protein structure prediction.
    Curr Opin Struct Biol, Vol. 16, No. 3. (June 2006), pp. 374-384.
    by RL Dunbrack
    posted to protein-structure review by xiaobeizhao on 2006-10-09 04:00:40 as ** along with 4 people jwm wouterboomsma rabio schuylrp
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