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Agricultural Publications Publications Agricultural publications Bioinformatics McCarthy F. M., et al. AgBase: supporting functional modeling in agricultural organisms. Nucleic Acids Research 39(suppl 1):D497-506 (2011). Ogata Y., Suzuki H., Sakurai N., Shibata D. CoP: a database for characterizing co-expressed gene modules with biological information in plants. Bioinformatics 26(9):1267-8 (2010). Baginsky S., Hennig L., Zimmermann P., Gruissem W. Gene expression analysis, proteomics, and network discovery. Plant Physiology 152:402-10 (2010). Mochida K., Shinozaki K. Genomics and bioinformatics resources for crop improvement. Plant and Cell Physiology 51(4):497–523 (2010). Zeisel A., Amir A., Köstler W. J., Domany E. Intensity dependent estimation of noise in microarrays improves detection of differentially expressed genes. BMC Bioinformatics 11:400 (2010). Sakurai N., et al. KaPPA-View4: a metabolic pathway database for representation and analysis of correlation networks of gene co-expression and metabolite co-accumulation and omics data. Nucleic Acids Research 39(suppl 1):D677-84 (2011). Watson-Haigh N. S., Kadarmideen H. N., Reverter A. PCIT: an R package for weighted gene co-expression networks based on partial correlation and information theory approaches. Bioinformatics 26(3):411-3 (2010). Lohse M., et al. Robin: an intuitive wizard application for R-based expression microarray quality assessment and analysis. Plant Physiology 153(2):642-51 (2010). Dai X., et al. TrichOME: a comparative omics database for plant trichomes. Plant Physiology 152(1):44–54 (2010). Multiple organisms Oikawa A., et al. An integrative approach to the identification of Arabidopsis and rice genes involved in xylan and secondary wall development. PLoS One 5(11):e15481 (2010). Narsai R., Castleden I., Whelan J. Common and distinct organ and stress responsive transcriptomic patterns in Oryza sativa and Arabidopsis thaliana. BMC Plant Biology 10:262 (2010). Dinkins, R. D., Barnes A., Waters W. Microarray analysis of endophyte-infected and endophyte-free tall fescue. Journal of Plant Physiology 167(14):1197-1203 (2010). Anopheles/Plasmodium White B. J. Ecological genomics of the malaria mosquito Anopheles gambiae. PhD dissertation, University of Notre Dame (2010). White B. J., Cheng C., Simard F., Costantini C., Besansky N. Genetic association of physically unlinked islands of genomic divergence in incipient species of Anopheles gambiae. Molecular Ecology 19(5):925–39 (2010). Mu J., et al. Plasmodium falciparum genome-wide scans for positive selection, recombination hot spots and resistance to antimalarial drugs. Nature Genetics 42(3):268-71 (2010). Arabidoposis Das, Ma., et al. A composite transcriptional signature differentiates responses towards closely related herbicides in Arabidopsis thaliana and Brassica napus. Plant Molecular Biology 72(4-5):545-56 (2010). Seymour G. B., et al. A SEPALLATA gene is involved in the development and ripening of strawberry (Fragaria×ananassa Duch.) fruit, a non-climacteric tissue. Journal of Experimental Botany. Published online November 29, 2010. doi:10.1093/jxb/erq360. Kato N., He H., Steger A. P. A systems model of vesicle trafficking in Arabidopsis pollen tubes. Plant Physiology 152(2):590–601 (2010). Rehrauer H. et al. AGRONOMICS1: A new resource for Arabidopsis transcriptome profiling. Plant Physiology 152(2):487-99 (2010). Gilding E. K., Marks M. D. Analysis of purified glabra3-shapeshifter trichomes reveals a role for NOECK in regulating early trichome morphogenic events. Plant Journal 64(2):304-17 (2010). Truman W. M., Bennett M. H., Turnbull C. G. N., Grant M. R. Arabidopsis auxin mutants are compromised in systemic acquired resistance and exhibit aberrant accumulation of various indolic compounds. Plant Physiology 152:1562-73 (2010). Li L., Ye H., Guo H., Yin Y. Arabidopsis IWS1 interacts with transcription factor BES1 and is involved in plant steroid hormone brassinosteroid regulated gene expression. Proceedings of the National Academy of Sciences of the United States of America 107(8):3918–23 (2010). Zakrzewska-Placzek M., Souret F. F., Sobczyk G. J., Green P. J., Kufel J. Arabidopsis thaliana XRN2 is required for primary cleavage in the pre-ribosomal RNA. Nucleic Acids Research 38(13):4487-502 (2010). Matsui A, et al. Arabidopsis tiling array analysis to identify the stress-responsive genes. Methods in Molecular Biology 639:141-55 (2010). Borghi L., et al. Arabidopsis RETINOBLASTOMA-RELATED is required for stem cell maintenance, cell differentiation, and lateral organ production. Plant Cell 22:1792-811 (2010). Liu J.-X., Howell S. H. bZIP28 and NF-Y transcription factors are activated by ER stress and assemble into a transcriptional complex to regulate stress response genes in Arabidopsis. Plant Cell 22:782-96 (2010). Ruhlmann J. M., Kram B. W., Carter C. J. CELL WALL INVERTASE 4 is required for nectar production in Arabidopsis. Journal of Experimental Botany 61(2):395-404 (2010). Chen K., Zhang Y., Tang T., Shi S. Cis-regulatory change and expression divergence between duplicate genes formed by genome duplication of Arabidopsis thaliana. Chinese Science Bulletin 55(22):2359-65 (2010). Hannah M. A., et al. Combined transcript and metabolite profiling of Arabidopsis grown under widely variant growth conditions facilitates the identification of novel metabolite-mediated regulation of gene expression. Plant Physiology 152:2120-9 (2010). Tsuchiya T., Eulgem T. Co-option of EDM2 to distinct regulatory modules in Arabidopsis thaliana development. BMC Plant Biology (10):203 (2010). Liu D., et al. cpSecA, a thylakoid protein translocase subunit, is essential for photosynthetic development in Arabidopsis. Journal of Experimental Botany 61(6):1655-69 (2010). Rowe H. C., et al. Deficiencies in jasmonate-mediated plant defense reveal quantitative variation in Botrytis cinerea pathogenesis. PLoS Pathogens 6(4):e1000861 (2010). Pantelides I. S., Tjamos S. E., Paplomatas E. J. Ethylene perception via ETR1 is required in Arabidopsis infection by Verticillium dahlia. Molecular Plant Pathology 11(2):191–202 (2010). Kleindt C. K., Stracke R., Mehrtens F., Weisshaar B. Expression analysis of flavonoid biosynthesis genes during Arabidopsis thaliana silique and seed development with a primary focus on the proanthocyanidin biosynthetic pathway. BMC Research Notes 3:255 (2010). Juenger T. E., et al. Exploring genetic and expression differences between physiologically extreme ecotypes: comparative genomic hybridization and gene expression studies of Kas-1 and Tsu-1 accessions of Arabidopsis thaliana. Plant, Cell & Environment 33(8):1268-84 (2010). Okamoto M. Genome-wide analysis of endogenous abscisic acid-mediated transcription in dry and imbibed seeds of Arabidopsis using tiling arrays. Plant Journal 62(1):39-51 (2010). Le B. H., et al. Global analysis of gene activity during Arabidopsis seed development and identification of seed- specific transcription factors. Proceedings of the National Academy of Sciences of the United States of America 107(18):8063-70 (2010). Laubinger S., et al. Global effects of the small RNA biogenesis machinery on the Arabidopsis thaliana transcriptome. Proceedings of the National Academy of Sciences of the United States of America. 107(41):17466–73 (2010). Streitner C., Hennig L., Korneli C., Staiger D. Global transcript profiling of transgenic plants constitutively overexpressing the RNA-binding protein AtGRP7. BMC Plant Biology 10:221 (2010). Xiao Y. L., et al. High throughput generation of promoter reporter (GFP) transgenic lines of low expressing genes in Arabidopsis and analysis of their expression patterns. Plant Methods 6:18 (2010). Licausi F., et al. HRE1 and HRE2, two hypoxia-inducible ethylene response factors, affect anaerobic responses in Arabidopsis thaliana. The Plant Journal 62(2):302–15 (2010). Drews G. N., Wang D., Steffen J. G., Schumaker K. S., Yadegari R. Identification of genes expressed in the angiosperm female gametophyte. Journal of Experimental Botany. Published online November 39, 2010. doi:10.1093/jxb/erq385. Kinoshita N., et al. Identification of growth insensitive to ABA3 (gia3), a recessive mutation affecting ABA signaling for the control of early post-germination growth in Arabidopsis thaliana. Plant and Cell Physiology 51(2):239-51 (2010). Xiao Y., Yu X., Chen J., Di P., Chen W., Zhang L. IiSDD1, a gene responsive to autopolyploidy and environmental factors in Isatis indigotica. Molecular Biology Reports 37(2):987-94 (2010). Larue C. T., Wen J., Walker J. C. Interactions between a NAC-domain transcription factor and the putative small protein encoding DVL/ROT gene family. Plant Molecular Biology Reporter 28(1):162-8 (2010). Sun Y., et al. Integration of brassinosteroid signal transduction with the transcription network for plant growth regulation in Arabidopsis. Developmental Cell 19(5):765-77 (2010). Nelson D. C., et al. Karrikins enhance light responses during germination and seedling development in Arabidopsis thaliana. Proceedings of the National Academy of Sciences of the United States of America 107(15):7095-100 (2010). Chandran D., Inada N., Hather G., Kleindt, C. K. Wildermuth M. C. Laser microdissection of Arabidopsis cells at the powdery mildew infection site reveals site-specific processes and regulators. Proceedings of the National Academy of Sciences of the United States of America 107(1):460-5 (2010). Jülke, S., Ludwig-Müller, J. Modulation of lipid transfer proteins alters clubroot development in Arabidopsis thaliana. Acta Horticulturae 867:165-72 (2010). Wang Y.-H.,
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