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At-TAX: a whole genome tiling array resource for developmental expression analysis and transcript identification in Arabidopsis thaliana
Sascha Laubinger, Georg Zeller, Stefan R Henz, Timo Sachsenberg, Christian K Widmer, Naïra Naouar, Marnik Vuylsteke, Bernhard Schölkopf, Gunnar Rätsch, Detlef Weigel
Genome Biol. 2008; 9(7): R112. Published online 2008 July 9. doi: 10.1186/gb-2008-9-7-r112
PMCID:
PMC2530869
Abstract Full Text PDF–2.5M Supplementary Material
 Is Cited by the Following 23 Articles in this Archive:
The Functions of RNA-Dependent RNA Polymerases in Arabidopsis
Matthew R. Willmann, Matthew W. Endres, Rebecca T. Cook, Brian D. Gregory
Arabidopsis Book. 2011; 9: e0146. Published online 2011 July 31. doi: 10.1199/tab.0146
PMCID:
PMC3268507
Abstract Full Text PDF–4.7M
Complex Evolutionary Events at a Tandem Cluster of Arabidopsis thaliana Genes Resulting in a Single-Locus Genetic Incompatibility
Lisa M. Smith, Kirsten Bomblies, Detlef Weigel
PLoS Genet. 2011 July; 7(7): e1002164. Published online 2011 July 14. doi: 10.1371/journal.pgen.1002164
PMCID:
PMC3136440
Abstract Full Text PDF–2.7M Supplementary Material
The ROOT DETERMINED NODULATION1 Gene Regulates Nodule Number in Roots of Medicago truncatula and Defines a Highly Conserved, Uncharacterized Plant Gene Family
Elise L. Schnabel, Tessema K. Kassaw, Lucinda S. Smith, John F. Marsh, Giles E. Oldroyd, Sharon R. Long, Julia A. Frugoli
Plant Physiol. 2011 September; 157(1): 328–340. Published online 2011 July 8. doi: 10.1104/pp.111.178756
PMCID:
PMC3165882
Abstract Full Text PDF–1.0M
Reference-guided assembly of four diverse Arabidopsis thaliana genomes
Korbinian Schneeberger, Stephan Ossowski, Felix Ott, Juliane D. Klein, Xi Wang, Christa Lanz, Lisa M. Smith, Jun Cao, Joffrey Fitz, Norman Warthmann, Stefan R. Henz, Daniel H. Huson, Detlef Weigel
Proc Natl Acad Sci U S A. 2011 June 21; 108(25): 10249–10254. Published online 2011 June 6. doi: 10.1073/pnas.1107739108
PMCID:
PMC3121819
Abstract Full Text PDF–203K Supplementary Material
RNA 3′ processing functions of Arabidopsis FCA and FPA limit intergenic transcription
Cagla Sonmez, Isabel Bäurle, Andreas Magusin, Rene Dreos, Sascha Laubinger, Detlef Weigel, Caroline Dean
Proc Natl Acad Sci U S A. 2011 May 17; 108(20): 8508–8513. Published online 2011 May 2. doi: 10.1073/pnas.1105334108
PMCID:
PMC3100917
Abstract Full Text PDF–548K Supplementary Material
AnyExpress: Integrated toolkit for analysis of cross-platform gene expression data using a fast interval matching algorithm
Jihoon Kim, Kiltesh Patel, Hyunchul Jung, Winston P Kuo, Lucila Ohno-Machado
BMC Bioinformatics. 2011; 12: 75. Published online 2011 March 17. doi: 10.1186/1471-2105-12-75
PMCID:
PMC3076267
Abstract Full Text PDF–873K Supplementary Material
Ratio-Based Analysis of Differential mRNA Processing and Expression of a Polyadenylation Factor Mutant pcfs4 Using Arabidopsis Tiling Microarray
Jianti Zheng, Denghui Xing, Xiaohui Wu, Yingjia Shen, Diana M. Kroll, Guoli Ji, Qingshun Quinn Li
PLoS One. 2011; 6(2): e14719. Published online 2011 February 25. doi: 10.1371/journal.pone.0014719
PMCID:
PMC3045369
Abstract Full Text PDF–628K Supplementary Material
A Modular Cloning System for Standardized Assembly of Multigene Constructs
Ernst Weber, Carola Engler, Ramona Gruetzner, Stefan Werner, Sylvestre Marillonnet
PLoS One. 2011; 6(2): e16765. Published online 2011 February 18. doi: 10.1371/journal.pone.0016765
PMCID:
PMC3041749
Abstract Full Text PDF–1.9M Supplementary Material
Support vector machines-based identification of alternative splicing in Arabidopsis thaliana from whole-genome tiling arrays
Johannes Eichner, Georg Zeller, Sascha Laubinger, Gunnar Rätsch
BMC Bioinformatics. 2011; 12: 55. Published online 2011 February 16. doi: 10.1186/1471-2105-12-55
PMCID:
PMC3051901
Abstract Full Text PDF–792K Supplementary Material
A spatial and temporal map of C. elegans gene expression
W. Clay Spencer, Georg Zeller, Joseph D. Watson, Stefan R. Henz, Kathie L. Watkins, Rebecca D. McWhirter, Sarah Petersen, Vipin T. Sreedharan, Christian Widmer, Jeanyoung Jo, Valerie Reinke, Lisa Petrella, Susan Strome, Stephen E. Von Stetina, Menachem Katz, Shai Shaham, Gunnar Rätsch, David M. Miller, III
Genome Res. 2011 February; 21(2): 325–341. doi: 10.1101/gr.114595.110
PMCID:
PMC3032935
Abstract Full Text PDF–2.0M
Transposable elements and small RNAs contribute to gene expression divergence between Arabidopsis thaliana and Arabidopsis lyrata
Jesse D. Hollister, Lisa M. Smith, Ya-Long Guo, Felix Ott, Detlef Weigel, Brandon S. Gaut
Proc Natl Acad Sci U S A. 2011 February 8; 108(6): 2322–2327. Published online 2011 January 20. doi: 10.1073/pnas.1018222108
PMCID:
PMC3038775
Abstract Full Text PDF–631K Supplementary Material
High throughput generation of promoter reporter (GFP) transgenic lines of low expressing genes in Arabidopsis and analysis of their expression patterns
Yong-Li Xiao, Julia C Redman, Erin L Monaghan, Jun Zhuang, Beverly A Underwood, William A Moskal, Wei Wang, Hank C Wu, Christopher D Town
Plant Methods. 2010; 6: 18. Published online 2010 August 6. doi: 10.1186/1746-4811-6-18
PMCID:
PMC2927586
Abstract Full Text PDF–3.6M Supplementary Material
Genomics and Bioinformatics Resources for Crop Improvement
Keiichi Mochida, Kazuo Shinozaki
Plant Cell Physiol. 2010 April; 51(4): 497–523. Published online 2010 April 8. doi: 10.1093/pcp/pcq027
PMCID:
PMC2852516
Abstract Full Text PDF–1.1M
The Arabidopsis Floral Homeotic Proteins APETALA3 and PISTILLATA Negatively Regulate the BANQUO Genes Implicated in Light Signaling
Chloe D. Mara, Tengbo Huang, Vivian F. Irish
Plant Cell. 2010 March; 22(3): 690–702. Published online 2010 March 19. doi: 10.1105/tpc.109.065946
PMCID:
PMC2861465
Abstract Full Text PDF–1.4M Supplementary Material
Analysis of DNA strand-specific differential expression with high density tiling microarrays
Luis Quintales, Mar Sánchez, Francisco Antequera
BMC Bioinformatics. 2010; 11: 136. Published online 2010 March 17. doi: 10.1186/1471-2105-11-136
PMCID:
PMC2858035
Abstract Full Text PDF–938K Supplementary Material
PhiC31 recombination system demonstrates heritable germinal transmission of site-specific excision from the Arabidopsis genome
James G Thomson, Ronald Chan, Roger Thilmony, Yuan-Yeu Yau, David W Ow
BMC Biotechnol. 2010; 10: 17. Published online 2010 February 23. doi: 10.1186/1472-6750-10-17
PMCID:
PMC2837860
Abstract Full Text PDF–1.9M
Stimulation of Nonselective Amino Acid Export by Glutamine Dumper Proteins
Réjane Pratelli, Lars M. Voll, Robin J. Horst, Wolf B. Frommer, Guillaume Pilot
Plant Physiol. 2010 February; 152(2): 762–773. doi: 10.1104/pp.109.151746
PMCID:
PMC2815850
Abstract Full Text PDF–1.0M Supplementary Material
AGRONOMICS1: A New Resource for Arabidopsis Transcriptome Profiling
Hubert Rehrauer, Catharine Aquino, Wilhelm Gruissem, Stefan R. Henz, Pierre Hilson, Sascha Laubinger, Naira Naouar, Andrea Patrignani, Stephane Rombauts, Huan Shu, Yves Van de Peer, Marnik Vuylsteke, Detlef Weigel, Georg Zeller, Lars Hennig
Plant Physiol. 2010 February; 152(2): 487–499. doi: 10.1104/pp.109.150185
PMCID:
PMC2815891
Abstract Full Text PDF–1.2M Supplementary Material
Advances in Genetical Genomics of Plants
R.V.L. Joosen, W. Ligterink, H.W.M. Hilhorst, J.J.B. Keurentjes
Curr Genomics. 2009 December; 10(8): 540–549. doi: 10.2174/138920209789503914
PMCID:
PMC2817885
Abstract Full Text PDF–251K
Web-Queryable Large-Scale Data Sets for Hypothesis Generation in Plant Biology
Siobhan M. Brady, Nicholas J. Provart
Plant Cell. 2009 April; 21(4): 1034–1051. doi: 10.1105/tpc.109.066050
PMCID:
PMC2685637
Abstract Full Text PDF–887K
SEPALLATA3: the 'glue' for MADS box transcription factor complex formation
Richard GH Immink, Isabella AN Tonaco, Stefan de Folter, Anna Shchennikova, Aalt DJ van Dijk, Jacqueline Busscher-Lange, Jan W Borst, Gerco C Angenent
Genome Biol. 2009; 10(2): R24. Published online 2009 February 25. doi: 10.1186/gb-2009-10-2-r24
PMCID:
PMC2688274
Abstract Full Text PDF–2.3M Supplementary Material
Next is now: new technologies for sequencing of genomes, transcriptomes and beyond
Ryan Lister, Brian D. Gregory, Joseph R. Ecker
Curr Opin Plant Biol. Author manuscript; available in PMC 2010 April 1.
Published in final edited form as: Curr Opin Plant Biol. 2009 April; 12(2): 107–118. Published online 2009 January 20. doi: 10.1016/j.pbi.2008.11.004
PMCID:
PMC2723731
Abstract Full Text PDF–693K
Whole genome transcriptome polymorphisms in Arabidopsis thaliana
Xu Zhang, Jake K Byrnes, Thomas S Gal, Wen-Hsiung Li, Justin O Borevitz
Genome Biol. 2008; 9(11): R165. Published online 2008 November 24. doi: 10.1186/gb-2008-9-11-r165
PMCID:
PMC2614497
Abstract Full Text PDF–1.1M Supplementary Material
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