College of Arts & Sciences Biology

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Abdelali Barakat

Abdelali Barakat
Assistant Professor
Biology, College of Arts & Sciences
UCL Churchill-Haines Labs 170A
Phone: 605-677-6180
Teaching Interests:
Genomics - Bioinformatics Molecular genetics Molecular biology
Research Interests:
Epigenetic regulation of stress responses in plants, plant phenotypic responses to environmental inputs (phenotypic plasticity), small RNA-mediated gene regulation in plant development, plant comparative genomics and evolution
Education:
  • Ph D, Plant Molecular and Cellular Biology, University of Paris XI, 1996
  • MS, Plant Molecular and Cellular Biology, University of Paris XI, 1993
  • BS, Plant Sciences, University Cadi Ayyad, 1989
Grants:
  • College of Arts & Sciences Travel Grant, University of South Dakota, (2013 - 2014)
  • Genomic Resources for the Fine Hardwood Black Cherry, Prunus serotina, USDA-NIFA, (2008 - 2011)
Publications:
  • Bagniewska-Zadworna, A., Barakat, A., Lakomy, P., Smolinski, D., Zadworny, M., (2014), Lignin and lignans in plant defence: Insight from expression profiling of cinnamyl alcohol dehydrogenase genes during development and following fungal infection in Populus, Plant Journal, vol. 229, p. 111–121.
  • Akond, M., Richard, B., Ragin, B., Herrera, H., Kaodi, U., Akbay, C., Kantartzi, S. K., Njiti, V., Barakat, A., Meksem, K., Lightfoot, D. A., Kassem, M., (2013), Additional Quantitative Trait Loci and Candidate Genes for Seed Isoflavone Content in Soybean, Journal of Agricultural Science, vol. 5, iss. 11, pp. 20-33.
  • Fang, G., Blackmon, B. P., Staton, M. E., Nelson, C. D., Kubisiak, T. L., Olukolu, B., Henry, D., Zhebentyayeva, T., Saski, C. A., Cheng, C., Monsanto, M., Ficklin, S., Atkins, M., Georgi, L., Barakat, A., Wheeler, N., Carlson, J. E., Sederoff, R., Abbott, A. G., (2013), Physical mapping of the Chinese chestnut genome: A genome resource for Fagaceae species, Tree Genetics and Genome, vol. 9, pp. 525-537.
  • The International Peach Genome Initiative, Verde, I., Abbott, A. G., Scalabrin, S., Jung, S., Shu, S., Marroni, F., Zhebentyayeva, T., Dettori, M., Grimwood, J., Cattonaro, F., Zuccolo, A., Rossini, L., Jenkins, J., Vendramin, E., Meisel, L. A., Decroocq, V., Sosinski, B., Prochnik, S., Mitros, T., Policriti, A., Cipriani, G., Dondini, L., Ficklin, S., Goodstein, D. M., Xuan, P., Del Fabbro, C., Aramini, V., Copetti, D., Gonzalez, S., Horner, D., Falchi, R., Lucas, S., Mica, E., Maldonado, J., Lazzari, B., Bielenberg, D., Pirona, R., Miculan, M., Barakat, A., Testolin, R., Stella, A., Tartarini, S., Tonutti, P., Arús, P., Orellana, A., Wells, C., Main, D., Vizzotto, G., Silva, H., Salamini, F., Schmutz, J., Morgante, M., Rokhsar, D. S., (2013), The high-quality draft genome of peach (Prunus persica) identifies unique patterns of genetic diversity, domestication and genome evolution, Nature Genetics, vol. 45, p. 487–494.
  • Bliss, B. J., Wanke, S., Barakat, A., Ayyampalayam, S., Wickett, N., Wall, P. K., Jiao, Y., Landherr, L., Ralph, P. E., Hu, Y., Neinhuis, C., Leebens-Mack, J., Arumuganathan, K., Clifton, S. W., Maximova, S. N., Ma, H., dePamphili, C. W., , (2013), Characterization of the basal angiosperm Aristolochia fimbriata: a potential experimental system for genetic studies., BMC Plant Biology, vol. 13, p. 13.
  • Hsu, C., Adams, J. P., No, K., Liang, H., Meilan, R., Pechanova, O., Barakat, A., Carlson, J. E., Page, G. P., Luthe, D. S., Yuceer, C., , (2012), Overexpression of constans homologs co1 and co2 fails to alter normal reproductive onset and fall bud set in woody perennial poplar., PLoS ONE, vol. 7, p. e45448.
  • Barakat, A., Sriram, A., Park, J., Zhebentyayeva, T., Main, D., Abbott, A., (2012), Genome-wide identification of chilling responsive microRNAs in Prunus persica, BMC Genomics, vol. 13, p. 481.
  • Barakat, A., Staton, M., Cheng, C., Park, J., Yassin, N., Ficklin, S., Yeh, C., Hebard, F., Baier, K., Powell, W., Schuster, S., Wheeler, N., Abbott, A., Carlson, J., Sederoff, R., , (2012), Chestnut resistance to the blight disease: insights from transcriptome analysis., BMC Plant Biology, vol. 12, p. 38.
  • Williams, B., Kantartzi, S. K., Meksem, K., Grier, R. L., Barakat, A., Lightfoot, D. A., Kassem, M. A., (2012), Genetic analysis of root and shoot traits in the ‘Essex’ by ‘Forrest’ recombinant inbred line (RIL) population of soybean [Glycine max (L.) Merr.], Journal of Plant Sciences, vol. 1, pp. 1-9.
  • Barakat, A., Norzawani, B., Park, J., Choi, A., Herr, J., Carlson, J., , (2011), Comparative and phylogenomic analyses of cinnamoyl-CoA reductase and cinnamoyl-CoA-reductase-like gene family in land plants, Plant Sciience, vol. 181, pp. 249-57.
  • Bagniewska, A., Zenkteler, M., Zenkteler, E., Wojciechowicz, K., Barakat, A., , J., (2011), A successful application of embryo rescue technique as a model for studying crosses between Salix viminalis and Populus species, Australian Journal of Botany, vol. 59, pp. 382-392.
  • Hsu, C., Adams, J. P., Kim, H., No, K., Main, C., Strauss, S. H., Drnevich, J., Vandervelde, L., Ellis, J. D., Rice, B. M., Wickett, N., Gunter, L. E., Tuskan, G. A., Brunner, A. M., Page, G. P., Barakat, A., Carlson, J. E., dePamphilis, C., Luthe, D. S., Yuceer, C., , (2011), FT duplication coordinates reproductive and vegetative growth, Proc. Natl. Acad. Sci. USA., vol. 108, pp. 10756-10761.
  • Barakat, A., Choi, A., Norzawani, B., Park, J., Carlson, J., , (2011), Comparative genomics and evolutionary analyses of the O-methyltransferase gene family in Populus, Gene, vol. 479, pp. 37-46.
  • Liang, H., Ayyampalayam, S., Wickett, N., Barakat, A., Xu, Y., Landherr, L., Ralph, P., Xu, T., Schlarbaum, S. E., Ma, H., Leebens-Mack, J., dePamphilis, C. W., , (2011), Generation of a large-scale genomic resources for functional and comparative genomics in Liriodendron tulipifera L, Tree Genetics and Genome, vol. 7, pp. 941-954.
  • Schlarbaum, S. E., Barakat, A., Liang, H., Carlson, J., (2010), Organization of the chromosome region harboring a FLORICAULA/LEAFY gene in Liriodendron., Tree Genetics and Genome, vol. 7, pp. 373-384.
  • Liang, H., Barakat, A., Schlarbaum, S. E., Plock, S., Mandoli, D. F., Carlson, J. E., (2010), Comparison of genome organization of Gigantea homologs in yellow-poplar in monocots and eudicots, Genome, vol. 53, pp. 533-544.
  • Barakat, A., Bagniewska-Zadworna, A., Frost, C., Carlson, J., (2010), Phylogeny and expression profiling of CAD and CAD-like genes in hybrid Populus (P. deltoides x P. nigra): evidence from herbivore damage for subfunctionalization and functional divergence, BMC Plant Biology, vol. 10, p. 100.
  • Wall, P. K., LeebensMack, J., Chanderbali, A., Barakat, A., Wolcott, E., Liang, H., Landherr, L., Tomsho, L. P., Hu, Y., Carlson, J., Ma, H., Schuster, S., Soltis, D., Soltis, P., Altman, N., depamphilis, C. W., (2009), Comparison of next generation sequencing technologies for transcriptome characterization, BMC Genomics, vol. 10, p. 347.
  • Barakat, A., Diloreto, S., Zhang, Y., Smith, C., Baier, K., Powell, B., Wheeler, W., Sederoff, R., Carlson, J. E., (2009), Comparison of the transcriptomes of American chestnut (Castanea dentata) and Chinese chestnut (Castanea mollissima) in response to the chestnut blight infection, BMC Plant Biology, vol. 9, p. 51.
  • Barakat, A., Bagniewska-Zadworna, A., Plakkat, U., Choi, A., Diloreto, S., Carlson, J. E., (2009), The cinnamyl alcohol dehydrogenase gene family in Populus: Genome organization, phylogeny, and expression, BMC Plant Biology, vol. 9, p. 26.
  • Barakat, A., Wall, P. K., Diloreto, S., dePamphilis, C. W., , (2007), Conservation and divergence, dynamic of microRNAs in Populus balsamifera, ssp. trichocarpa. , BMC Genomics, vol. 8, p. 481.
  • Barakat, A., Muller, K., Sáenz de MierA, L. E., , (2007), Molecular evolutionary analyses of Arabidopsis L7 ribosomal protein gene family, Gene, vol. 403, pp. 143-150.
  • Barakat, A., Wall, P. K., LeebensMack, J., Wang, J., Carlson, J. E., depamPhilis, C. W., (2007), Large-scale identification of microRNAs from a basal eudicot (Eschscholzia californica) and conservation in flowering plants, Plant Journal, vol. 51, pp. 991-1003.
  • Cui, L., Wall, P. K., Leebens-Mack, J., Lindsay, B. G., Barakat, A., Soltis, D., Doyle, J. J., Soltis, P., Carlson, J., Albert, V., Arumuganathan, A., Ma, H., depamPhilis, C. W., (2006), Widespread genome duplications throughout the history of flowering plants, Genome Research, vol. 16, pp. 738-749.
  • Badula, A., Kaczmarek, D., Barakat, A., Delseny, M., Quiros , C. F., (2003), Comparative mapping of Brassica olereacea and Arabidopsis thaliana chromosomes based on ESTs from A. thaliana, Mol Genet Genomics., vol. 268, pp. 656-65.
  • Dominguez, I., Graziano, E., Gebhardt, C., Barakat, A., Berry, S., Arùs, P., Delseny, M., Barnes, S., (2003), Plant genome archeology: evidence for conserved ancestral chromosome segments in dicotyledonous plant species, Plant Biotechnology Journal, vol. 1, pp. 91-99.
  • Gebhardt, G., Walkemeier, B., Henselewski, H., Barakat, A., Delseny, M., Stüber, K., (2003), Comparative mapping between potato (Solanum tuberosum) and Arabidopsis thaliana reveals structurally conserved domains and ancient duplications in the potato genome, Plant Journal, vol. 34, pp. 529-41.
  • Lin, B., Wang, J., Chen, R., Liu, H., Meyer, Y., Barakat, A., Delseny, M., , (2001), Genomic analysis of the Hsp70 superfamily in Arabidopsis thaliana, Cell Stress & Chaperones, vol. 6, pp. 301-208.
  • Barakat, A., Szick-Miranda, K., Chang, I., Guyot, R., Blanc, G., Cooke, R., Delseny, M., Bailey-Serres, J., (2001), The organization of cytoplasmic ribosomal protein genes in the Arabidopsis Genome, Plant Physiology, vol. 127, pp. 1-18.
  • Blanc, G., Barakat, A., Guyot, R., Cooke, R., Delseny, M., , (2001), Extensive duplication and reshuffling in the Arabidopsis thaliana genome, Plant Cell, vol. 12, pp. 1093-1102.
  • Barakat, A., Szick-Miranda, K., Chang, I., Guyot, R., Blanc, G., Cooke, R., , M., Bailey-Serres, J., (2001), The organization of cytoplasmic ribosomal protein genes in the Arabidopsis Genome, Plant Physiology, vol. 127, pp. 1-18.
  • Barakat, A., Gallois, G., Raynal, M., Mestre-Ortega, D., Sallaud, C., Guiderdoni, E., Delseny, M., Bernardi, G., (2000), The distribution of T-DNA in the genomes of transgenic Arabidopsis and rice, FEBS Letters, vol. 471, pp. 161-164.
  • Delseny, M., Barakat, A., Sadowski, J., Grellet, F., Cooke, R., (2000), The Arabidopsis genome : A model of analysis of crop plant genomes and their diversity, Harwood Academic Publishers.
  • Barakat, A., (1999), The gene distribution in the genomes of pea, tomato and date palm, FEBS Letters, vol. 463, pp. 139-142.
  • Barakat, A., Matassi, G., Bernardi, G., (1998), Distribution of genes in the Arabidopsis thaliana genome and its implication in the genome organisation of plant, Proc. Natl. Acad. Sci. USA. , vol. 95, pp. 10044-10049.
  • Barakat, A., Carels, N., Berrnardi, G., (1997), The distribution of genes in the genomes of Gramineae, Proceedings of the National Academy of Sciences of the United States of America, vol. 94, pp. 6857-6861.
  • Carels, N., Barakat, A., Bernardi, G., (1995), The gene distribution in the maize genome, Proc. Natl. Acad. Sci. USA. , vol. 92 , pp. 11057-11060.
  • Barakat, A., (1994), Genetic heterogeneity of Pseudomonas aeruginosa. clinical isolates revealed by esterase electrophoretic polymorphism and restriction fragment length polymorphism of the ribosomal RNA gene region, Journal Of Clinical Microbiology, vol. 40, pp. 313-322.
Presentations:
  • Barakat, A., Bagniewska-Zadworna, A., Lakomy, P., Smolinski, D. J., Zadworny, M. (2014, July). Lignin and lignans in plant defence: Insight from expression profiling of cinnamyl alcohol dehydrogenase following Populus plant infection by fungal pathogens. Presented at the Plant Biology 2014, Portland OR.
  • Akond, M., Bazzelle, R., Ragin, B., Herrera, H., Kaodi, U., Akbay, C., Kantartzi, S. K., Njiti, V., Barakat, A., Meksem, K., Lightfoot, D. A., Kassem, M. A. (2014, January). Additional Quantitative Trait Loci and Candidate Genes for Seed Isoflavone Content in Soybean. Presented at the Plant & Animal Genome XXII Conference, San Diego, CA.
  • Barakat, A., Shumaker, K., Hsu, C., Wei, H., Yuceer, C., Carlson, J. (2014, January). Microrna Expression Profiles Associated with Vegetative Bud Initiation and Development in Populus. Presented at the Plant & Animal Genome XXII, San Diego.
  • Barakat, A. (2013, November). Blight Disease Resistance in Chestnut: Insights from Transcriptome and Comparative Genomics Analyses. Presented at the Plant Biology Department seminar - Invited speaker, Brookings.