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Tag popgenie-ms [45 articles]

Recent papers classified by the tag popgenie-ms.
  • SynView: a GBrowse-compatible approach to visualizing comparative genome data
    Bioinformatics, Vol. 22, No. 18. (15 September 2006), pp. 2308-2309.
    by Wang, Haiming, Su, Yanqi, Mackey, J Aaron, Kraemer, T Eileen, Kissinger, C Jessica
    posted to popgenie-ms by natstreet on 2008-02-12 08:42:56 as **
  • BLAT--the BLAST-like alignment tool.
    Genome Res, Vol. 12, No. 4. (April 2002), pp. 656-664.
    by WJ Kent
    posted to popgenie-ms by natstreet on 2008-02-12 12:27:04 as ** along with 23 people and 1 group daforerog pwais umit mmartin paszkows operon miguel pcahan1 Ayest indigoviolet mtagaya treangen michC djkt timflutre olympos cjeans wenhan antonkratz yoanjacquemin talponer bozdagd gpappas EisenLab
  • A Molecular Timetable for Apical Bud Formation and Dormancy Induction in Poplar.
    Plant Cell, Vol. 19, No. 8. (10 August 2007), pp. 2370-2390.
    by Tom Ruttink, Matthias Arend, Kris Morreel, Véronique Storme, Stephane Rombauts, Jörg Fromm, Rishikesh PP Bhalerao, Wout Boerjan, Antje Rohde
    posted to popgenie-ms omics-chapter by natstreet on 2007-08-19 15:25:03 as ** along with 1 person bjbecerra
  • An "electronic fluorescent pictograph" browser for exploring and analyzing large-scale biological data sets.
    PLoS ONE, Vol. 2 (2007), e718.
    by D Winter, B Vinegar, H Nahal, R Ammar, GV Wilson, NJ Provart
    posted to popgenie-ms omics-chapter by natstreet on 2008-07-02 11:41:00 as ** along with 1 person guhjy
  • The Arabidopsis Information Resource (TAIR): gene structure and function annotation
    Nucleic Acids Research, Vol. 36 (5 November 2008), pp. 1009-1014.
    by David Swarbreck, Christopher Wilks, Philippe Lamesch, Tanya Z Berardini, Margarita Garcia-Hernandez, Hartmut Foerster, Donghui Li, Tom Meyer, Robert Muller, Larry Ploetz, Amie Radenbaugh, Shanker Singh, Vanessa Swing, Christophe Tissier, Peifen Zhang, Eva Huala
    posted to popgenie-ms by natstreet on 2008-02-12 08:40:29 as ** along with 1 person moborg
  • Global expression profiling in leaves of free-growing aspen
    BMC Plant Biology, Vol. 8, No. 1. (2008), 61.
    by Andreas Sjodin, Kirsten Wissel, Max Bylesjo, Johan Trygg, Stefan Jansson
    posted to popgenie-ms omics-chapter by natstreet on 2008-05-23 13:27:50 as ** along with 1 person druvus
  • High efficiency poplar transformation.
    Plant Cell Reports, Vol. 26, No. 9. (11 May 2007), pp. 1529-1538.
    by Leland J Cseke, Sarah B Cseke, Gopi K Podila
    posted to popgenie-ms by natstreet on 2007-08-03 10:25:03 as **
  • Genetic Transformation of Populus trichocarpa Genotype Nisqually-1: A Functional Genomic Tool for Woody Plants
    Plant and Cell Physiology, Vol. 47, No. 11. (November 2006), pp. 1582-1589.
    by Song, Jingyuan, Lu, Shanfa, Chen, Zenn-Zong, Lourenco, Rodrigo, Chiang, L Vincent
    posted to popgenie-ms by natstreet on 2008-07-01 15:49:03 as **
  • Comparative analysis of orthologous cellulose synthase promoters from Arabidopsis, Populus and Eucalyptus: evidence of conserved regulatory elements in angiosperms.
    The New phytologist (10 June 2008), 10.1111/j.1469-8137.2008.02517.x.
    by Nicole, Martin Ranik, David, Alexander
    posted to popgenie-ms by natstreet on 2008-06-14 10:13:27 as **
  • Protease gene families in Populus and Arabidopsis
    BMC Plant Biology, Vol. 6 (20 December 2006), 30.
    by Maribel Garcia-Lorenzo, Andreas Sjodin, Stefan Jansson, Christiane Funk
    posted to popgenie-ms by natstreet on 2008-03-25 09:23:36 as ** along with 1 person druvus
  • KEGG for linking genomes to life and the environment
    Nucleic Acids Research, Vol. 36 (12 December 2008), pp. 480-484.
    by Minoru Kanehisa, Michihiro Araki, Susumu Goto, Masahiro Hattori, Mika Hirakawa, Masumi Itoh, Toshiaki Katayama, Shuichi Kawashima, Shujiro Okuda, Toshiaki Tokimatsu, Yoshihiro Yamanishi
    posted to popgenie-ms by natstreet on 2008-07-02 09:15:21 as ** along with 12 people daforerog reyez namunet irenas guhjy raiyar barriot renatomilani shung hpaces massivemayhem TheresaNiederberger
  • Analysis of 70,000 EST sequences to study divergence between two closely related Populus species
    Tree Genetics & Genomes, Vol. 1, No. 3. (6 November 2005), pp. 109-115.
    by Per Unneberg, Michael Strömberg, Joakim Lundeberg, Stefan Jansson, Fredrik Sterky
    posted to popgenie-ms by natstreet on 2008-03-03 13:07:49 as **
  • Web-based analysis of the mouse transcriptome using Genevestigator
    BMC Bioinformatics, Vol. 7 (21 June 2006), 311.
    by Oliver Laule, Matthias Hirsch-Hoffmann, Tomas Hruz, Wilhelm Gruissem, Philip Zimmermann
    posted to popgenie-ms by natstreet on 2008-07-02 11:26:08 as **
  • QTL for yield in bioenergy Populus : identifying G×E interactions from growth at three contrasting sites
    Tree Genetics & Genomes, Vol. 4, No. 1. (2008), pp. 1614-2950.
    by Anne Rae, Matthieu Pinel, Catherine Bastien, Maurizio Sabatti, Nathaniel Street, James Tucker, Caroline Dixon, Nicolas Marron, Sophie Dillen, Gail Taylor
    posted to family-331 o3-paper popgenie-ms src-paper by natstreet on 2008-03-17 15:22:33 as ** along with 1 person kathrynmrobinson
  • KEGG: kyoto encyclopedia of genes and genomes.
    Nucleic Acids Res, Vol. 28, No. 1. (1 January 2000), pp. 27-30.
    by M Kanehisa, S Goto
    posted to popgenie-ms by natstreet on 2008-07-02 09:14:57 as ** along with 14 people sgoetz namunet csanford dquest j3xucite fisherp koerner ruvido noby naegele katerinakal grottenolm Evangelia jerome_ucsf_slb
  • PlnTFDB: An integrative plant transcription factor database
    BMC Bioinformatics, Vol. 8 (07 February 2007), 42.
    by Diego M Riano-Pachon, Slobodan Ruzicic, Ingo Dreyer, Bernd Mueller-Roeber
    posted to regulon-paper popgenie-ms omics-chapter by natstreet on 2007-10-29 18:16:22 as **
  • Suppression subtractive hybridization-mediated transcriptome analysis from multiple tissues of aspen ( Populus tremuloides) altered in phenylpropanoid metabolism
    Planta, Vol. 219, No. 4. (2004), pp. 694-704.
    by Priya Ranjan, Yu-Ying Kao, Hongying Jiang, Chandrashekhar P Joshi, Scott A Harding, Chung-Jui Tsai
    posted to popgenie-ms omics-chapter by natstreet on 2008-06-18 15:32:40 as **
  • VISTA : visualizing global DNA sequence alignments of arbitrary length.
    Bioinformatics (Oxford, England), Vol. 16, No. 11. (November 2000), pp. 1046-1047.
    by C Mayor, M Brudno, JR Schwartz, A Poliakov, EM Rubin, KA Frazer, LS Pachter, I Dubchak
    posted to popgenie-ms by natstreet on 2008-07-02 11:31:37 as ** along with 2 people treangen AaronDarling
  • Pfam: clans, web tools and services.
    Nucleic Acids Res, Vol. 34, No. Database issue. (1 January 2006), pp. 247-251.
    by RD Finn, J Mistry, B Schuster-Böckler, S Griffiths-Jones, V Hollich, T Lassmann, S Moxon, M Marshall, A Khanna, R Durbin, SR Eddy, EL Sonnhammer, A Bateman
    posted to popgenie-ms by natstreet on 2008-07-02 09:19:27 as ** along with 11 people cerca gbart dullhunk massivemayhem cjeans siebertm lpfernandes pablomendes antonkratz Lombardo_7 phoenixzxl
  • A transcriptional roadmap to wood formation
    Proceedings of the National Academy of Sciences, Vol. 98, No. 25. (27 November 2001), pp. 14732-14737.
    by Magnus Hertzberg, Henrik Aspeborg, Jarmo Schrader, Anders Andersson, Rikard Erlandsson, Kristina Blomqvist, Rupali Bhalerao, Mathias Uhlen, Tuula T Teeri, Joakim Lundeberg, Bjorn Sundberg, Peter Nilsson, Goran Sandberg
    posted to src-paper regulon-paper popgenie-ms omics-chapter by natstreet on 2007-08-03 15:09:43 as **
  • A dense linkage map of hybrid cottonwood (Populus fremontii x P. angustifolia) contributes to long-term ecological research and comparison mapping in a model forest tree.
    Heredity, Vol. 100 (26 September 2008), pp. 59-70.
    by SAA Woolbright, SPP Difazio, T Yin, GDD Martinsen, X Zhang, GJJ Allan, TGG Whitham, P Keim
    posted to popgenie-ms by natstreet on 2007-09-28 07:54:16 as ** along with 2 people druvus kathrynmrobinson
  • A High-Resolution Transcript Profile across the Wood-Forming Meristem of Poplar Identifies Potential Regulators of Cambial Stem Cell Identity
    Plant Cell, Vol. 16, No. 9. (1 September 2004), pp. 2278-2292.
    by Jarmo Schrader, Jeanette Nilsson, Ewa Mellerowicz, Anders Berglund, Peter Nilsson, Magnus Hertzberg, Goran Sandberg
    posted to popgenie-ms omics-chapter by natstreet on 2008-02-01 14:15:14 as **
  • Abundantly and Rarely Expressed Lhc Protein Genes Exhibit Distinct Regulation Patterns in Plants
    Plant Physiol., Vol. 140, No. 3. (1 March 2006), pp. 793-804.
    by Frank Klimmek, Andreas Sjodin, Christos Noutsos, Dario Leister, Stefan Jansson
    posted to popgenie-ms by natstreet on 2008-03-25 09:24:02 as ** along with 2 people dandaman druvus
  • Intragenomic Matching Reveals a Huge Potential for miRNA-Mediated Regulation in Plants
    PLoS Computational Biology, Vol. 3, No. 11. (1 November 2007), e238.
    by Morten Lindow, Anders Jacobsen, Sanne Nygaard, Yuan Mang, Anders Krogh
    posted to popgenie-ms by natstreet on 2007-12-10 08:27:45 as ** along with 1 person megraw
  • ViroBLAST: A standalone BLAST web server for flexible queries of multiple databases and user's datasets.
    Bioinformatics, Vol. 23 (5 July 2007), pp. 2334-2336.
    by Wenjie Deng, David CC Nickle, Gerald HH Learn, Brandon Maust, James II Mullins
    posted to popgenie-ms by natstreet on 2008-06-23 12:37:30 as ** along with 1 person guhjy
  • Cambial meristem dormancy in trees involves extensive remodelling of the transcriptome
    The Plant Journal, Vol. 40, No. 2. (2004), pp. 173-187.
    by Jarmo Schrader, Richard Moyle, Rupali Bhalerao, Magnus Hertzberg, Joakim Lundeberg, Peter Nilsson, Rishikesh P Bhalerao
    posted to popgenie-ms omics-chapter by natstreet on 2008-02-28 09:56:11 as **
  • DBD: a transcription factor prediction database.
    Nucleic Acids Res, Vol. 34, No. Database issue. (1 January 2006), pp. 74-81.
    by SK Kummerfeld, SA Teichmann
    posted to popgenie-ms by natstreet on 2008-07-02 11:38:09 as ** along with 5 people and 1 group troels_marstrand gpalidwor nickluscombe nklee mariakmejia EBI-regulation
  • The Genome of Black Cottonwood, Populus trichocarpa (Torr. & Gray)
    Science, Vol. 313, No. 5793. (15 September 2006), pp. 1596-1604.
    by GA Tuskan, S Difazio, S Jansson, J Bohlmann, I Grigoriev, U Hellsten, N Putnam, S Ralph, S Rombauts, A Salamov, J Schein, L Sterck, A Aerts, RR Bhalerao, RP Bhalerao, D Blaudez, W Boerjan, A Brun, A Brunner, V Busov, M Campbell, J Carlson, M Chalot, J Chapman, GL Chen, D Cooper, PM Coutinho, J Couturier, S Covert, Q Cronk, R Cunningham, J Davis, S Degroeve, A Dejardin, C Depamphilis, J Detter, B Dirks, I Dubchak, S Duplessis, J Ehlting, B Ellis, K Gendler, D Goodstein, M Gribskov, J Grimwood, A Groover, L Gunter, B Hamberger, B Heinze, Y Helariutta, B Henrissat, D Holligan, R Holt, W Huang, N Islam-Faridi, S Jones, M Jones-Rhoades, R Jorgensen, C Joshi, J Kangasjarvi, J Karlsson, C Kelleher, R Kirkpatrick, M Kirst, A Kohler, U Kalluri, F Larimer, J Leebens-Mack, JC Leple, P Locascio, Y Lou, S Lucas, F Martin, B Montanini, C Napoli, DR Nelson, C Nelson, K Nieminen, O Nilsson, V Pereda, G Peter, R Philippe, G Pilate, A Poliakov, J Razumovskaya, P Richardson, C Rinaldi, K Ritland, P Rouze, D Ryaboy, J Schmutz, J Schrader, B Segerman, H Shin, A Siddiqui, F Sterky, A Terry, CJ Tsai, E Uberbacher, P Unneberg, J Vahala, K Wall, S Wessler, G Yang, T Yin, C Douglas, M Marra, G Sandberg, Y Van de Peer, D Rokhsar
    posted to popgenie-ms omics-chapter by natstreet on 2008-06-06 17:39:57 as ** along with 2 people mlog kathrynmrobinson
  • Environmental and hormonal regulation of the activitydormancy cycle in the cambial meristem involves stage-specific modulation of transcriptional and metabolic networks
    The Plant Journal, Vol. 50, No. 4. (May 2007), pp. 557-573.
    by Druart, Nathalie, Johansson, Annika, Baba, Kyoko, Schrader, Jarmo, Sjodin, Andreas, Bhalerao, R Rupali, Resman, Lars, Trygg, Johan, Moritz, Thomas, Bhalerao, P Rishikesh
    posted to popgenie-ms omics-chapter by natstreet on 2008-02-29 09:54:38 as ** along with 1 person druvus
  • Extending Genomics to Natural Communities and Ecosystems
    Science, Vol. 320, No. 5875. (25 April 2008), pp. 492-495.
    by Thomas G Whitham, Stephen P Difazio, Jennifer A Schweitzer, Stephen M Shuster, Gery J Allan, Joseph K Bailey, Scott A Woolbright
    posted to popgenie-ms omics-chapter by natstreet on 2008-05-21 14:57:26 as ** along with 6 people and 3 groups ArtemPankin neteler farhat brant jago jlgreen Khavkin's lab Green Lab iSEEM
  • Populus: Arabidopsis for Forestry. Do We Need a Model Tree?
    Ann Bot, Vol. 90, No. 6. (1 December 2002), pp. 681-689.
    by GAIL Taylor
    posted to popgenie-ms by natstreet on 2008-07-02 11:08:54 as **
  • OPLS discriminant analysis: combining the strengths of PLS-DA and SIMCA classification
    Journal of Chemometrics, Vol. 20, No. 8-10. (2006), pp. 341-351.
    by Max Bylesjö, Mattias Rantalainen, Olivier Cloarec, Jeremy K Nicholson, Elaine Holmes, Johan Trygg
    posted to popgenie-ms regulon-paper by natstreet on 2007-10-29 16:22:50 as **
  • DBD--taxonomically broad transcription factor predictions: new content and functionality.
    Nucleic acids research, Vol. 36, No. Database issue. (January 2008), pp. 88-92.
    by D Wilson, V Charoensawan, SK Kummerfeld, SA Teichmann
    posted to popgenie-ms omics-chapter by natstreet on 2008-07-02 11:36:28 as **
  • Characterization of genes with tissue-specific differential expression patterns in Populus
    Tree Genetics & Genomes, Vol. 3, No. 4. (26 October 2007), pp. 351-362.
    by Bo Segerman, Stefan Jansson, Jan Karlsson
    posted to regulon-paper popgenie-ms omics-chapter by natstreet on 2007-10-29 18:14:10 as **
  • GENEVESTIGATOR. Arabidopsis microarray database and analysis toolbox.
    Plant Physiol, Vol. 136, No. 1. (September 2004), pp. 2621-2632.
    by P Zimmermann, M Hirsch-Hoffmann, L Hennig, W Gruissem
    posted to popgenie-ms by natstreet on 2008-07-02 11:25:19 as ** along with 1 person and 1 group kengg Plantandetc
  • The generic genome browser: a building block for a model organism system database.
    Genome Res, Vol. 12, No. 10. (October 2002), pp. 1599-1610.
    by LD Stein, C Mungall, S Shu, M Caudy, M Mangone, A Day, E Nickerson, JE Stajich, TW Harris, A Arva, S Lewis
    posted to popgenie-ms by natstreet on 2008-03-30 11:18:31 as ** along with 7 people and 1 group Cortel indigoviolet dquest stajich dullhunk tharris farhat EisenLab
  • SynBrowse: a synteny browser for comparative sequence analysis
    Bioinformatics, Vol. 21, No. 17. (1 September 2005), pp. 3461-3468.
    by Xiaokang Pan, Lincoln Stein, Volker Brendel
    posted to popgenie-ms by natstreet on 2008-04-01 11:06:11 as **
  • Visualization-based discovery and analysis of genomic aberrations in microarray data.
    BMC Bioinformatics, Vol. 6 (2005), 146.
    by CL Myers, X Chen, OG Troyanskaya
    posted to popgenie-ms by natstreet on 2008-07-10 10:22:18 as ** along with 2 people srp33 bioguru2000
  • UPSC-BASE Populus transcriptomics online
    The Plant Journal, Vol. 48, No. 5. (December 2006), pp. 806-817.
    by Sjodin, Andreas, Bylesjo, Max, Skogstrom, Oskar, Eriksson, Daniel, Nilsson, Peter, Ryden, Patrik, Jansson, Stefan, Karlsson, Jan
    posted to regulon-paper popgenie-ms omics-chapter by natstreet on 2007-10-29 16:12:07 as ** along with 1 person druvus
  • PlantTFDB: a comprehensive plant transcription factor database.
    Nucleic acids research, Vol. 36, No. Database issue. (January 2008), pp. 966-969.
    by AY Guo, X Chen, G Gao, H Zhang, QH Zhu, XC Liu, YF Zhong, X Gu, K He, J Luo
    posted to popgenie-ms by natstreet on 2008-07-02 09:20:03 as **
  • The COG database: an updated version includes eukaryotes.
    BMC Bioinformatics, Vol. 4 (11 September 2003), 41.
    by RL Tatusov, ND Fedorova, JD Jackson, AR Jacobs, B Kiryutin, EV Koonin, DM Krylov, R Mazumder, SL Mekhedov, AN Nikolskaya, BS Rao, S Smirnov, AV Sverdlov, S Vasudevan, YI Wolf, JJ Yin, DA Natale
    posted to popgenie-ms by natstreet on 2008-07-02 09:16:42 as ** along with 8 people and 2 groups tharris dmp arve indigoviolet j3xucite treangen bluto westoll C. elegans / WormBase EisenLab
  • From genomics to chemical genomics: new developments in KEGG.
    Nucleic Acids Res, Vol. 34, No. Database issue. (1 January 2006), pp. 354-357.
    by M Kanehisa, S Goto, M Hattori, KF Aoki-Kinoshita, M Itoh, S Kawashima, T Katayama, M Araki, M Hirakawa
    posted to popgenie-ms by natstreet on 2008-07-02 09:15:11 as ** along with 14 people namunet guhjy aalibes kuhn balajis alexg eweaver tny dullhunk michC frohike incovoma sgoetz yggdrasil
  • VISTA: computational tools for comparative genomics.
    Nucleic acids research, Vol. 32, No. Web Server issue. (1 July 2004), pp. 273-279.
    by KA Frazer, L Pachter, A Poliakov, EM Rubin, I Dubchak
    posted to popgenie-ms by natstreet on 2008-07-02 11:29:19 as ** along with 1 person and 1 group Auger Dead 60's
  • FlyBase: integration and improvements to query tools.
    Nucleic Acids Res, Vol. 36, No. Database issue. (January 2008), pp. 588-593.
    by RJ Wilson, JL Goodman, VB Strelets
    posted to popgenie-ms by natstreet on 2008-07-02 09:21:13 as ** along with 1 person guhjy
  • Accurate detection of aneuploidies in array CGH and gene expression microarray data
    Bioinformatics, Vol. 20, No. 18. (2004), pp. 3533-3543.
    by Chad L Myers, Maitreya J Dunham, SY Kung, Olga G Troyanskaya
    posted to popgenie-ms by natstreet on 2008-07-10 10:23:19 as **
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