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Alex Kozik

Alex Kozik

4302 UC Davis Genome Center-GBSF
451 Health Sciences Drive
University of California
Davis, California 95616

Phone: (530)754-9127
Fax: (530)752-9658
Email: akozik@atgc.org
Web page:
http://www.atgc.org

Position Assistant Researcher
Education 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.
Research Topic Bioinformatics, genome data visualization and comparison, high-throughput data analysis and management, database design and software development.Search for common sense in modern science.
Research Summary 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/)

Publications

--- Key Publications ---

  • Christopoulou M, McHale L, Kozik A, Reyes-Chin Wo S, Wroblewski T, Michelmore RW. (2015Dissection of Two Complex Clusters of Resistance Genes in Lettuce (Lactuca sativa) Mol Plant Microbe Interact. 2015. Feb 4.     
  • Christopoulou M, Wo SR, Kozik A, McHale LK, Truco MJ, Wroblewski T, Michelmore RW. (2015Genome-Wide Architecture of Disease Resistance Genes in Lettuce G3 (Bethesda) 2015. Oct 8;5(12):2655-69.     
  • Wroblewski T, Matvienko M, Piskurewicz U, Xu H, Martineau B, Wong J, Govindarajulu M, Kozik A, Michelmore RW. (2014Distinctive profiles of small RNA couple inverted repeat-induced post-transcriptional gene silencing with endogenous RNA silencing pathways in Arabidopsis. RNA. 2014. Dec;20(12):1987-99.     
  • Hodgins KA, Lai Z, Oliveira LO, Still DW, Scascitelli M, Barker MS, Kane NC, Dempewolf H, Kozik A, Kesseli RV, Burke JM, Michelmore RW, Rieseberg LH. (2014Genomics of Compositae crops: reference transcriptome assemblies and evidence of hybridization with wild relatives Mol Ecol Resour. 2014. Jan;14(1):166-77.     
  • Mandel JR, Dikow RB, Funk VA, Masalia RR, Staton SE, Kozik A, Michelmore RW, Rieseberg LH, Burke JM4. (2014A target enrichment method for gathering phylogenetic information from hundreds of loci: An example from the Compositae. Appl Plant Sci. 2014. Feb 6;2(2).     
  • Truco, M. J., Ashrafi, H., Kozik, A., van Leeuwen, H., Bowers, J., Wo, S. R. C., Stoffel, K., Xu, H., Hill, T., Deynze, A. V., & Michelmore, R. W.  (2013An Ultra High-Density, Transcript-Based, Genetic Map of Lettuce G3: Genes| Genomes| Genetics. 2013.   
  • Hill TA, Ashrafi H, Reyes-Chin-Wo S, Yao J, Stoffel K, Truco MJ, Kozik A, Michelmore RW, Van Deynze A. (2013Characterization of Capsicum annuum genetic diversity and population structure based on parallel polymorphism discovery with a 30K unigene pepper GeneChip PLoS One 2013. Feb 8. [Epub]     
  • Matvienko M, Kozik A, Froenicke L, Lavelle D, Martineau B, Perroud B, Michelmore R. (2013Consequences of normalizing transcriptomic and genomic libraries of plant genomes using a duplex-specific nuclease and tetramethylammonium chloride. PLoS One. 2013. 8(2), e55913.     
  • Ashrafi, H., Hill, T., Stoffel, K., Kozik, A., Yao, J., Chin-Wo, S. R., & Van Deynze, A.  (2012De novo assembly of the pepper transcriptome (Capsicum annuum): a benchmark for in silico discovery of SNPs, SSRs and candidate genes.  BMC genomics 2012.  13(1), 571.     
  • Lai, Z., Kane, N.C., Kozik, A., Hodgins, K.A., Dlugosch, K.M., Barker, M.S., Matvienko, M., Yu, Q., Pearl, S.A., Bell, G.D.M., Turner, K.G., Zou, Y., Guggisberg, A., Adams, K.L., Anderson, J.V., Horvath, D.P., Kesseli, R.V., Burke, J.M., Michelmore, R.W.  (2012Genomics of Compositae weeds: EST libraries, microarrays, and evidence of introgression. Am. J. Bot. 2012. 99: 209?218.     
  • Stoffel, K., van Leeuwen, H., Kozik, A., Caldwell, D., Ashrafi, H., Cui, X., Tan, X., Hill, Reyes Chin-Wo, M.J., Truco, Michelmore, R.W., Van Deynze, A.  (2012Development and application of a 6.6 Million Feature Affymetrix GeneChip? for massively parallel discovery of single position polymorphisms in lettuce (Lactuca spp.). BMC Genomics. 2012. 13:185. doi: 10.1186/1471-2164-13-185.     
  • Cantu, D., Govindarajulu, M., Kozik, A., Wang, M., Chen, X., Michelmore, R.W., Dubcovsky, J. (2011Next-generation sequencing provides rapid access to the genes of wheat stripe rust. Plos One 2011. 6:e24230.     
  • Cantu, D., Govindarajulu, M., Kozik, A., Wang, M., Chen, X., Michelmore, R.W., Dubcovsky, J.  (2011Next generation sequencing provides rapid access to the genome of Puccinia striiformis f. sp. tritici, the causal agent of wheat stripe rust. Plos One  2011. 6:e24230.     
  • Chapman MA, Hvala J, Strever J, Matvienko M, Kozik A, Michelmore RW, Tang S, Knapp SJ, Burke JM. (2009Development, polymorphism, and cross-taxon utility of EST-SSR markers from safflower (Carthamus tinctorius L.). Theor Appl Genet. 2009. 120(1):85-91.     
  • 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 (2009Comparative 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.  
  • McHale LK, Truco MJ, Kozik A, Wroblewski T, Ochoa OE, Lahre KA, Knapp SJ, Michelmore RW. (2009The genomic architecture of disease resistance in lettuce. Theor Appl Genet. 2009. 118(3):565-80.     
  • Radwan O, Gandhi S, Heesacker A, Whitaker B, Taylor C, Plocik A, Kesseli R, Kozik A, Michelmore RW, Knapp SJ. (2008Genetic diversity and genomic distribution of homologs encoding NBS-LRR disease resistance proteins in sunflower. Mol Genet Genomics. 2008. 280(2):111-125     
  • Barker MS, Kane NC, Matvienko M, Kozik A, Michelmore RW, Knapp SJ, Rieseberg LH. (2008Multiple paleopolyploidizations during the evolution of the Compositae reveal parallel patterns of duplicate gene retention after millions of years. 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 (2008SSRs and INDELs mined from the sunflower EST database: abundance, polymorphisms, and crosstaxa utility. Theor Appl Genet. 2008. 117(7):1021-9.     
  • Tan X, Meyers BC, Kozik A, West MA, Morgante M, St Clair DA, Bent AF, Michelmore RW. (2007Global Expression Analysis of NBS-LRR Encoding Genes in Arabidopsis BMC Plant Biology. 2007. 0.330555556     
  • Church SA, Livingstone K, Lai Z, Kozik A, Knapp SJ, Michelmore RW, Rieseberg LH. (2007Using 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.     
  • Truco MJ, Antonise R, Lavelle D, Ochoa O, Kozik A, Witsenboer H, Fort SB, Jeuken MJ, Kesseli RV, Lindhout P, Michelmore RW, Peleman J. (2007A high-density, integrated genetic linkage map of lettuce (Lactuca spp.). Theor Appl Genet. 2007. 115(6):735-46     
  • Konstantin??V.??Krutovsky, Christine??G.??Elsik, Marta??Matvienko, Alex??Kozik and David??B.??Neale. (2006Conserved ortholog sets in forest trees. Tree Genetics & Genomes 2006. 3:61-70  
  • Konstantin V. Krutovsky, Christine G. Elsik, Marta Matvienko, Alex Kozik, David B. Neale.  (2006Conserved ortholog sets in forest trees.  Tree Genetics & Genomics. 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. (2006Analyses of synteny between Arabidopsis thaliana and species in the Asteraceae reveal a complex network of small syntenic. Genetics. 2006. Aug;173(4):2227-2235.      
  • West MA, van Leeuwen H, Kozik A, Kliebenstein DJ, Doerge RW, St Clair DA, Michelmore RW. (2006High-density haplotyping with microarray-based expression and single feature polymorphism markers in Arabidopsis. Genome Res 2006. Jun;16(6):787-95.     
  • Bernal, A., Pan, Q., Pollack, J., Rose, L., Willets, N., Kozik, A., Michelmore, R.  (2005Functional 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.  (2003DiagHunter 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. (2003Genome-wide analysis of NBS-LRR-encoding genes in Arabidopsis. Plant Cell. 2003. 15(4):809-34.     
  • Kozik A, Kochetkova E, Michelmore R. (2002GenomePixelizer - a visualization program for comparative genomics within and between species. Bioinformatics. 2002. 18(2):335-6.     
  • Kozik, A, M. Matvienko, B. Scheres, T. Bisseling, A. Van Kammen, T.H.N. Ellis, T. LaRue, N. Weeden.  (1996Characterization 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  (1995Plant genes involved in root-nodule development on legumes.  Philosophical Transactions of the Royal Society of London B Biol 1995. 350(1331): 101-107.  
  • --- Presentations ---

  • Kozik A, Froenicke L, Lavelle D, Truco MJ, Xu H, Reyes-Chin-Wo S, Michelmore RW. (2014Chromosome-Scale Assembly of the Lettuce (Lactuca sativa) Genome Using Genotyping By Shotgun Sequencing (GBSS) Plant and Animal Genome XXII 2014 Jan. 11-15  
  • Truco MJ, Reyes-Chin-Wo S, Lavelle D, Kozik A, Froenicke L, Xu H, Michelmore RW. (2014Lettuce Genome Assembly, Structure and Annotation. Plant and Animal Genome XXII 2014 Jan. 11-15  
  • Dean O. Lavelle, Leah K. McHale, Marilena Christopoulou, María José Truco, Oswaldo E. Ochoa , Jim Cervantes , Jason M. Argyris , Marta Matvienko , Alex Kozik , Huaqin Xu, Kent J. Bradford , RW. Michelmore (2009Candidate Gene Analysis In Lactuca spp. Plant & Animal Genomes XVII Conference 2009 January 10-14, 2009 Town & Country Convention Center San Diego,   
  • 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. (2007Large-Scale Analysis of Interactions between Several Crop Species and Effector Repertoires from Multiple Bacterial Pathogens.  XIII International Congress on Molecular Plant-Microbe Interacti 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. (2007Comparative Large-Scale Analysis of Resistance Gene Evolution.  Plant and Animal Genomes XV Conference, January 13-17, 2007; P76 2007   
  • McHale, L., Truco, M.-J., Kozik, A., Wroblewski, T., Lavelle, D., Ochoa, O., Lahre, K., Mathrakott, S. and Michelmore, R. (2007Utilizing 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. (2007Genes 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., Piskurewicz, U., Luo, Y., Cavanaugh, K., Jelenska, J., McHale, L., Kozik, A., Ochoa, O., Greenberg, J. and Michelmore, R. (2006Large-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. (2005Large-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. (2004Identification and mapping of candidate genes involved in disease resistance in lettuce.  XII Plant and Animal Genome Conference, San Diego. 2004   
  • Truco M., Van Damme M., Lavelle D., Kozik A., Wroblewski T., Ochoa O., Van Wijk R., Kesseli R., Michelmore R. (2002Candidate Gene Approaches to Agriculturally Important Traits in Lettuce.  X Plant and Animal Genome Conference, San Diego. 2002   
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