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Publications
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--- Key Publications ---
Han R, Wong AJY, Tang Z, Truco MJ, Lavelle DO, Kozik A, Jin Y, Michelmore RW. (2021) Drone phenotyping and machine learning enable discovery of loci regulating daily floral opening in lettuce. Journal of Experimental Botany, 2021. 72(8): 2979-2994. 
Gurdon C, Kozik A, Tao R, Poulev A, Armas I, Michelmore RW, Raskin I. (2021) Isolating an active and inactive CACTA transposon from lettuce color mutants and characterizing their family. Plant Physiology. 2021.
Kozik, A., Rowan, B.A., Lavelle, D., Berke, L., Schranz, M.E., Michelmore, R.W., Christensen, A.C. (2019) The alternative reality of plant mitochondrial DNA: One ring does not rule them all.PL PLoS Genet. 2019. Aug 30;15(8):e1008373. doi: 10.1371/journal.pgen.1008373.
Reyes-Chin-Wo, S., Wang, Z., Yang, X., Kozik, A., Arikit, S., Song, C., Xia, L., Froenicke, L., Lavelle, D.O., Truco, M-J., Xia, R., Zhu, S., Xu, C., Xu, H., Xu, X., Cox, K., Korf, I., Meyers, B.C., Michelmore, R.W. (2017) Genome assembly with in vitro proximity ligation data and whole genome triplication in lettuce. Nature Comm. 2017. 8:14953. 
Christopoulou M, McHale L, Kozik A, Reyes-Chin Wo S, Wroblewski T, Michelmore RW. (2015) Dissection 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. (2015) Genome-Wide Architecture of Disease Resistance Genes in Lettuce G3 (Bethesda) 2015. Oct 8;5(12):2655-69.
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. (2014) Genomics 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. (2014) A target enrichment method for gathering phylogenetic information from hundreds of loci: An example from the Compositae. Appl Plant Sci. 2014. Feb 6;2(2).
Wroblewski T, Matvienko M, Piskurewicz U, Xu H, Martineau B, Wong J, Govindarajulu M, Kozik A, Michelmore RW. (2014) Distinctive 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.
Matvienko M, Kozik A, Froenicke L, Lavelle D, Martineau B, Perroud B, Michelmore R. (2013) Consequences of normalizing transcriptomic and genomic libraries of plant genomes using a duplex-specific nuclease and tetramethylammonium chloride. PLoS One. 2013. 8(2), e55913.
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. (2013) An 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. (2013) Characterization 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]
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. (2012) Genomics 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. (2012) Development 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.
Ashrafi, H., Hill, T., Stoffel, K., Kozik, A., Yao, J., Chin-Wo, S. R., & Van Deynze, A. (2012) De 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.
Cantu, D., Govindarajulu, M., Kozik, A., Wang, M., Chen, X., Michelmore, R.W., Dubcovsky, J. (2011) Next 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.
Cantu, D., Govindarajulu, M., Kozik, A., Wang, M., Chen, X., Michelmore, R.W., Dubcovsky, J. (2011) Next-generation sequencing provides rapid access to the genes of wheat stripe rust. Plos One 2011. 6:e24230.
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. 
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.
Chapman MA, Hvala J, Strever J, Matvienko M, Kozik A, Michelmore RW, Tang S, Knapp SJ, Burke JM. (2009) Development, polymorphism, and cross-taxon utility of EST-SSR markers from safflower (Carthamus tinctorius L.). Theor Appl Genet. 2009. 120(1):85-91.
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
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 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 (2008) SSRs and INDELs mined from the sunflower EST database: abundance, polymorphisms, and crosstaxa utility. Theor Appl Genet. 2008. 117(7):1021-9.
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
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. 0.330555556
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.
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.
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
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.
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 ---
Kozik A, Froenicke L, Lavelle D, Truco MJ, Xu H, Reyes-Chin-Wo S, Michelmore RW. (2014) Chromosome-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. (2014) Lettuce 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 (2009) Candidate Gene Analysis In Lactuca spp. Plant & Animal Genomes XVII Conference 2009 January 10-14, 2009 Town & Country Convention Center San Diego,
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
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., 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
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. (2004) Identification 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. (2002) Candidate Gene Approaches to Agriculturally Important Traits in Lettuce. X Plant and Animal Genome Conference, San Diego. 2002
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