SCIENTIFIC PAPERS
Selected Publications of Ceres Scientists
Apuya, N.R., Park, J.-H., Zhang, L., Ahyow, M., Davidow, P., Fleet, J.V., Rarang, J.C., Hippley, M., Johnson, T.W., Yoo, H.-D., Trieu, A., Krueger, S., Wu, C.-y., Lu, Y.-p., Flavell, R.B. and Bobzin, S.C. (2008) Enhancement of alkaloid production in Opium and California poppy by transactivation using heterologous regulatory factors. Plant Biotechnol J, 6, 160-175.
Doukhanina, E.V., Apuya, N.R., Yoo, H.-D., Wu, C.-y., Davidow, P., Krueger, S., Flavell, R.B., Hamilton, R. and Bobzin, S.C. (2007) Expression of human nuclear receptors in plants for the discovery of plant-derived ligands. J Biomol Screen, 12, 385-395.
Ragab AS, Van Fleet J, Jankowski B, Park J-H, Bobzin SC. 2006 “Detection and Quantitation of Resveratrol in Tomato Fruit (Lycopersicon esculentum Mill.)” J. Ag. Food Chem. 54, 7175.
Tatarinova T, Schumitzky A. Multiple Collapse Clustering. Proceedings of the Fifth International Conference on Bioinformatics and Genome Regulation and Structure (BGRS'2006), Vol. 1: 184-7.
Tatarinova T, Brover V, Troukhan M, Alexandrov N. Skew in CG content near the transcription start site in Arabidopsis thaliana. Bioinformatics. 2003:19 Suppl. 1:i313-4.
Joshi T, Chen Y, Alexandrov N, Xu D. Genome-scale gene function prediction using multiple sources of high-throughput data in yeast Saccharomyces cerevisiae. OMICS. 2004 Winter;8(4):322-33.
Alexandrov N, Troukhan M, Brover S, Tatarinova T, Flavell R, Feldmann K. Features of Arabidopsis genes and genome discovered using full-length cDNAs. Plant Mol. Biol. (2006) 60: 69-85.
Joshi T, Chen Y, Alexandrov N, Xu D. Cellular function prediction and biological pathway discovery in Arabidopsis thaliana using microarray data. Int. J. Bioinformatics Research and Applications. Vol 1, No. 3, 2006.
Goodwin SM, Rashotte AM, Rahman M, Feldmann K., Jenks MA. 2005. Wax constituents on the inflorescence stems of double eceriferum mutants in Arabidopsis reveal complex gene interactions. Phytochemistry 66:771-80.
Kim H-B, Schaller H, Goh C-H, Kwon M, Choi, HS, Choe S, An CS, Durst F, Feldmann KA, Feyereisen R. 2005. Obtusifoliol 14-demethylase (AtCYP51A2) mutants reveal that sterols regulate plant growth and development via brassinosteroid-dependent and -independent pathways. Plant Physiology (in press).
Schneeberger RG, Zhang K, Tatarinova T, Troukhan M, Kwok SF, Drais J, Klinger K, Orejudos F, Macy K, Bhakta A, Burns J, Subramanian G, Donson J, Flavell R, Feldmann KA. 2005. Agrobacterium T-DNA integration in Arabidopsis is correlated with DNA sequence compositions that occur frequently in gene promoter regions. Functional and Integrative Genomics. Functional Integrative Genomics (Epub Mar 3).
Joshi T, Chen Y, Becker JM, Alexandrov N, Xu D. 2004. Genome-scale gene function prediction using multiple sources of high-throughput data in yeast Saccharomyces cerevisiae. OMICS. 8:322-33.
Mascia PN, Flavell RB. 2004. Safe and acceptable strategies for producing foreign molecules in plants. Current Opinions in Plant Biology. 7:189-95.
Rashotte AM, Jenks MA, Ross AS, Feldmann KA. 2004. Novel eceriferum Mutants in Arabidopsis thaliana. Planta, Novel eceriferum mutants in Arabidopsis thaliana. Planta 219:5-13.
Veretnik S, Bourne PE, Alexandrov NN, Shindyalov IN. 2004. Toward consistent assignment of structural domains in proteins. Journal Molecular Biology. 339:647-78.
Alexandrov N, Shindyalov I. 2003. PDP: protein domain parser. Bioinformatics. 19:429-30
Haas BJ, Volfovsky N, Town CD, Troukhan M, Alexandrov N, Feldmann KA, Flavell RB, White O, Salzberg SL. 2003. Full-length messenger RNA sequences greatly improve genome annotation. Genome Biology. 3:RESEARCH0029.
Li WW, Quinn GB, Alexandrov NN, Bourne PE, Shindyalov IN. 2003. A comparative proteomics resource: proteins of Arabidopsis thaliana. Genome Biology. 4:R51. http://arabidopsis.sdsc.edu.
Park JH, Halitschke R, Kim HB, Baldwin IT, Feldmann KA, Feyereisen R. 2003. A knock-out mutation in allene oxide synthase results in male sterility and defective wound signal transduction in Arabidopsis due to a block in jasmonic acid biosynthesis. The Plant Journal. 31:1-12.
Volkmuth W, Alexandrov N. 2003. Evidence for sequence-independent evolutionary traces in genomics data. Pacific Symposium Biocomputing. 247-58.
Volkmuth W, Turk S, Shapiro A, Fang Y, Kiegle E, van Haaren M, Donson J. 2003. Technical advances: genome-wide cDNA-AFLP analysis of the Arabidopsis transcriptome. OMICS. 7:143-59.
Xiao W, Gehring M, Choi Y, Margossian L, Pu H, Harada JJ, Goldberg RB, Pennell RI, Fischer RL. 2003. Imprinting of the MEA polycomb gene is controlled by antagonism between MET1 methyltransferase and DME glycosylase. Developmental Cell. 5:891-901.
Choe S, Schmitz RJ, Fujioka S, Takatsuto S, Lee MO, Yoshida S, Feldmann KA, Tax FE. 2002. Arabidopsis brassinosteroid-insensitive dwarf12 mutants are semidominant and defective in a GSK-3 β-like kinase. Plant Physiol. 130:1506-15.
Donson J, Fang Y, Espiritu-Santo G, Xing W, Salazar A, Miyamoto S, Armendarez V, Volkmuth W. 2002. Comprehensive gene expression analysis by transcript profiling.
Plant Molecular Biology. 48:75-97.
Feldmann KA, Choe S, Kim H, Park J-H. 2002. Functional genomics of cytochromes P450 in plants. In: Phytochemistry in the genomics and post-genomics eras. Romero, J.T. and R.A. Dixon (eds). Pergamon, Boston. Pp. 125-143.
Pennell R. 2002. Seeds don't need dads. The Daily Telegraph (London). July 10.
Bak S, Tax FE, Feldmann KA, Galbraith DW, Feyereisen R. 2001. CYP83B1, a cytochrome P450 at the metabolic branch point in auxin and indole glucosinolate biosynthesis in Arabidopsis. Plant Cell. 13:101-11.
Choe S, Fujioka S, Noguchi T, Takatsuto S, Yoshida S, Feldmann KA. 2001. Overexpression of DWARF4 in the brassinosteroid biosynthetic pathway results in increased vegetative growth and seed yield in Arabidopsis. The Plant Journal. 26:573-82.
Feldmann KA. Cytochrome P450s as genes for crop improvement. 2001. Current Opinions in Plant Biology. 4:162-7.
Rashotte AM, Jenks MA, Feldmann KA. 2001. Cuticular waxes on eceriferum mutants of Arabidopsis thaliana. Phytochemistry 57:115-123.
Choe S., A. Tanaka, T. Noguchi, S. Fujioka, S. Takatsuto, A.S. Ross, F.E. Tax, S. Yoshida, and K.A. Feldmann. 2000. Lesions in the sterol Δ7 reductase gene of Arabidopsis cause dwarfism due to a block in brassinosteroid biosynthesis. Plant J. 21:431-443.
Flavell, RB. 2000. A Floral Boost. Current Biology. 10 R1-R2.
Flavell, RB. 2000 Agriculture: a path of experiment and change. Nature Biotechnology. Vol 17 Supplement 1999 BV7.
Flavell, RB. 2000. Plant Biotechnology Moral Dilemmas: editorial overview. Current Opinion in Plant Biology. 3(2) 143-146.
Noguchi T, Fujioka S, Choe S, Takatsuto S, Tax FE, Yoshida S, Feldmann KA. 2000. Biosynthetic pathways of brassinolide in Arabidopsis. Plant Physiol. 124:201-299.
Clouse SD, Feldmann KA. 1999. Molecular genetics of brassinosteroid action. In: Brassinosteoids: Steroidal plant hormones. Eds. Sakari, et al., Springer, pp. 163-190.
Feldmann KA. 1999. The greening of chimeric oligonucleotides. Nature Biotechnology 17:857-858.
Flavell. RB. 1999. Biotechnology and Food and Nutrition Needs in Developing Countries. 2020 Briefs on Biotechnology, IFPRI.
Flavell, RB. 1999. Science Technology and Social Responsibility: the case of genetically modified plants for food. Proceedings of The Royal Society. Science Technology and Social Responsibility. 45-49.
Noguchi I, Fujioka S, Choe S, Takatsuto S, Yoshida S, Yuan H, Feldmann KA, Tax FE. 1999. Brassinosteroid-insensitive dwarf mutants of Arabidopsis accumulate brassinosteroids. Plant Physiol. 121:743-752.
Choe S, Feldmann KA. 1998. T-DNA mediated gene tagging. In: Transgenic plant research. K. Lindsey (ed.). Harwood Academic Publishers, Switzerland, pgs 57-73.
Coury DA, Feldmann KA. 1998. T-DNA insertional mutagenesis in plants. In: Somaclonal variation and induced mutation in crop improvement. S. Mohan Jain, B.S. Ahloowalia and D.S. Brar (eds.). Kluwer Academic Pub., The Netherlands.
Dilkes BP, Feldmann KA 1998. Gene isolation from T-DNA tagged transformants. In: Methods in molecular biology, Arabidopsis protocols. Martinez-Zapater, J.M and Salinas J. (eds.). 82:339-351.
Pennell R. 1998. Cell walls: structures and signals. Current Opinions in Plant Biology. 1:504-10.
Winkler R, Feldmann KA. 1998. Identifying T-DNA insertion mutants in Arabidopsis using PCR. In: Methods in molecular biology, Arabidopsis protocols. Martinez-Zapater, J.M and Salinas J. (eds.). 82:129-136.
Winkler R, Frank M, Galbraith DW, Feyereisen R, Feldmann KA. 1998. Systematic reverse genetics of the P450 superfamily in Arabidopsis. Plant Physiol. 118:743-749