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Alex Kozik4302 UC Davis Genome Center-GBSF
451 Health Sciences Drive
University of California
Davis, California 95620
Phone: (530)754-9127
Fax: (530)752-9658
Email: akozik@atgc.org
Web page: http://www.atgc.org
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Position
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Assistant Researcher |
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Education
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PhD in Genetics. 1995. Wageningen Agricultural University (http://www.wau.nl/),Dr. Ton Bisseling lab, Wageningen, The Netherlands.
M.S. in Chemistry. 1987. St Petersburg State University (http://www.spbu.ru/),Russia. |
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Research Topic
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Bioinformatics, genome data visualization and comparison, high-throughput data analysis and management, database design and software development.Search for common sense in modern science. |
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Research Summary
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Despite the fact that bioinformatics has been one of the fastest growing sectors in biology, there is still a lot of work to be done. Because of the absence of uniform data standards and a high level of corruption in current genome sequence data, particular problems in computational biology include_once individual and creative approaches to solve them.
Our bioinformatics group designed and developed new generation tools (computer programs) to study segmental duplications and syntenic regions of assembled genomes, as well as a new approach to SNP/InDel (Single Nucleotide Polymorphism/Insertion-Deletion) discovery and visualization of EST clustering.
You can access software developed by me and our bioinformatics group at:
GenomePixelizer (http://www.atgc.org/GenomePixelizer/)
GenoPix2D plotter (http://www.atgc.org/GenoPix_2D_Plotter/)
PhyloGrapher (http://www.atgc.org/PhyloGrapher/)
SNP/InDel discovery pipeline (http://cgpdb.ucdavis.edu/SNP_Discovery/) |
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Publications
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--- Key Publications ---
Barker MS, Kane NC, Matvienko M, Kozik A, Michelmore RW, Knapp SJ, Rieseberg LH. (2008) Multiple paleopolyploidizations during the evolution of the Compositae reveal parallel patterns of duplicate gene retention afte Mol Biol Evol. 2008. 25(11):2445-55. 
Heesacker A, Kishore VK, Gao W, Tang S, Kolkman JM, Gingle A, Matvienko M, Kozik A, Michelmore RM, Lai Z, Rieseberg LH, Knapp SJ (2008) SSRs and INDELs mined from the sunflower EST database: abundance, polymorphisms, and crosstaxa utility. Theor Appl Genet. 2008. 117(7):1021-9.
Radwan O, Gandhi S, Heesacker A, Whitaker B, Taylor C, Plocik A, Kesseli R, Kozik A, Michelmore RW, Knapp SJ. (2008) Genetic diversity and genomic distribution of homologs encoding NBS-LRR disease resistance proteins in sunflower. Mol Genet Genomics. 2008. 280(2):111-125
Truco MJ, Antonise R, Lavelle D, Ochoa O, Kozik A, Witsenboer H, Fort SB, Jeuken MJ, Kesseli RV, Lindhout P, Michelmore RW, Peleman J. (2007) A high-density, integrated genetic linkage map of lettuce (Lactuca spp.). Theor Appl Genet. 2007. 115(6):735-46
Church SA, Livingstone K, Lai Z, Kozik A, Knapp SJ, Michelmore RW, Rieseberg LH. (2007) Using Variable Rate Models to Identify Genes Under Selection in Sequence Pairs: Their Validity and Limitations for EST Sequences Journal of Molecular Evolution 2007. 64(2):171-80.
Tan X, Meyers BC, Kozik A, West MA, Morgante M, St Clair DA, Bent AF, Michelmore RW. (2007) Global Expression Analysis of NBS-LRR Encoding Genes in Arabidopsis BMC Plant Biology. 2007. 7:56
West MA, van Leeuwen H, Kozik A, Kliebenstein DJ, Doerge RW, St Clair DA, Michelmore RW. (2006) High-density haplotyping with microarray-based expression and single feature polymorphism markers in Arabidopsis. Genome Res 2006. Jun;16(6):787-95.
Konstantin V. Krutovsky, Christine G. Elsik, Marta Matvienko, Alex Kozik and David B. Neale. (2006) Conserved ortholog sets in forest trees. Tree Genetics & Genomes 2006. 3:61–70 
Timms L, Jimenez R, Chase M, Lavelle D, McHale L, Kozik A, Lai Z, Heesacker A, Knapp S, Rieseberg L, Michelmore R, Kesseli R. (2006) Analyses of synteny between Arabidopsis thaliana and species in the Asteraceae reveal a complex network of small syntenic. Genetics. 2006. Aug;173(4):2227-2235.
Konstantin V. Krutovsky, Christine G. Elsik, Marta Matvienko, Alex Kozik, David B. Neale. (2006) Conserved ortholog sets in forest trees. Tree Genetics & Genomics. 2006. 3: 61-70.
Bernal, A., Pan, Q., Pollack, J., Rose, L., Willets, N., Kozik, A., Michelmore, R. (2005) Functional dissection of the Pto resistance gene using DNA shuffling. J. Biol. Chem. 2005. 280:23073-83
Cannon S.B., Kozik A., Chan B., Michelmore R., Young N.D. (2003) DiagHunter and GenoPix2D: programs for genomic comparisons, large-scale homology-discovery, and visualization Genome Biology. 2003. 4:R68
Meyers BC, Kozik A, Griego A, Kuang H, Michelmore RW. (2003) Genome-wide analysis of NBS-LRR-encoding genes in Arabidopsis Plant Cell. 2003. 15(4):809-34. 
Kozik A, Kochetkova E, Michelmore R. (2002) GenomePixelizer - a visualization program for comparative genomics within and between species Bioinformatics. 2002. 18(2):335-6.
McHale LK, Truco MJ, Kozik A, Wroblewski T, Ochoa OE, Lahre KA, Knapp SJ, Michelmore RW. (2009) The genomic architecture of disease resistance in lettuce. Theor Appl Genet. 2009. 118(3):565-80.
Wroblewski T, Caldwell KS, Piskurewicz U, Cavanaugh KA, Xu H, Kozik A, Ochoa O, McHale LK, Lahre K, Jelenska J, Castillo JA, Blumenthal D, Vinatzer BA, Greenberg JT and Michelmore RW (2009) Comparative large-scale analysis of interactions between several crop species and the effector repertoires from multiple pathovars of Pseudomonas and Ralstonia. Plant Physiology. 2009. 10.1104/pp.109. 
Kozik, A, M. Matvienko, B. Scheres, T. Bisseling, A. Van Kammen, T.H.N. Ellis, T. LaRue, N. Weeden. (1996) Characterization of novel early nodulin ENOD7 of pea. Plant Molecular Biology. 1996. vol 31, p.149-156
Franssen H; Mylona P; Pawlowski K; Van De Sande K; Heidstra R; Geurts R; Kozik A; Matvienko M; Yang W.-C; Hadri AE; Martinez-Abarca F; Bisseling T (1995) Plant genes involved in root-nodule development on legumes. Philosophical Transactions of the Royal Society of London B Biol 1995. 350(1331): 101-107.
--- Presentations ---
Wroblewski, T., Caldwell, K., Vinatzer, B., Piskurewicz, U., Cavanaugh, K., Jelenska, J., McHale, L., Xu, H., Kozik, A., Ochoa, O., Williams, L., Greenberg, J. and Michelmore, R. (2007) Large-Scale Analysis of Interactions between Several Crop Species and Effector Repertoires from Multiple Bacterial Pathogens. XIII International Congress on Molecular Plant-Microbe Interacti 2007
McHale, L., Truco, M.-J., Kozik, A., Wroblewski, T., Lavelle, D., Ochoa, O., Lahre, K., Mathrakott, S. and Michelmore, R. (2007) Utilizing of Compositae Genome Project to Dissect the Genomic Architecture of Disease Resistance in Lettuce. XIII International Congress on Molecular Plant-Microbe Interact 2007
Caldwell, K., Wroblewski, T., Vinatzer, B., Williams, L., Piskurewicz, U., Cavanaugh, K., Jelenska, J., McHale, L., Kozik, A., Castillo, J., Ochoa, O., Greenberg, J., and Michelmore, R. (2007) Genes Encoding Defense Signaling Proteins in Plants are More Conserved than Those Encoding Recognition Proteins. The 8-th International Conference on Arabidopsis Research. June 2007
Wroblewski, T., Vinatzer, B., Caldwell, K.S., Piskurewicz, U., Cavanaugh, K.A., Jelenska, J., Teitzel, G., McHale, L.K., Xu, H., Kozik, A., Ochoa, O., Williams, L.A., Greenberg, J.T. and Michelmore, R.W. (2007) Comparative Large-Scale Analysis of Resistance Gene Evolution. Plant and Animal Genomes XV Conference, January 13-17, 2007; P76 2007
Wroblewski, T. , Vinatzer, B., Caldwell, K., Piskurewicz, U., Luo, Y., Cavanaugh, K., Jelenska, J., McHale, L., Kozik, A., Ochoa, O., Greenberg, J. and Michelmore, R. (2006) Large-scale analysis of interactions between multiple Pseudomonas spp. and several crop species. XIII Plant and Animal Genome Conference, San Diego, CA. January 2006
Wroblewski, T., Vinatzer, B., Caldwell, K., Piskurewicz, U., Cavanaugh, C., Jelenska, J., McHale, L., Kozik, A., Lee, M-W., Hotton, S., Fairfax, K., Teitzel, G., Castillo, J., Ochoa, O., Blumenthal, D., Greenberg, J. and Michelmore, R. (2005) Large-scale analysis of recognition of effector proteins from multiple Pseudomonas spp. by several crop species. MPMI Conference, December 2005, Merida, Mexico. 2005
McHale L., Lavelle D.O., Pande B., Wroblewski T., Jose-Truco M., Suresh S., Kozik A., Ochoa O. and Michelmore R. (2003) Identification and mapping of candidate genes involved in disease resistance in lettuce. XI Plant and Animal Genome Conference, San Diego. 2003
Truco M., Van Damme M., Lavelle D., Kozik A., Wroblewski T., Ochoa O., Van Wijk R., Kesseli R., Michelmore R. (2002) Candidate Gene Approaches to Agriculturally Important Traits in Lettuce. X Plant and Animal Genome Conference, San Diego. 2002
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