Current knowledge about biological pathways is scarce and not all genes that participate in and affect function of these pathways are known. Prime examples of information gaps are biosynthetic pathways leading to secondary metabolites in plants. Filling the gaps in our current knowledge about biological pathways and gene discovery is a fundamental challenge and also happen to be my biggest scientific desire. Novel powerful computational approaches such as machine learning and statistically robust methods along with the rapidly increasing availability of ‘omics’ data sets (e.g., genomics, proteomics, metabolomics, and fluxomics), carries the potential for detecting ‘electronic signatures’ of the biological network of secondary metabolism in plants.
My research motivated me to develop algorithms to associate candidate genes with a given target pathway, as well as developing user-friendly interfaces for construction and analysis of co-expression-based-regulatory networks of genes from specific pathways. Looking to the future, I plan to play a role in the training of the next generation of biologists capable of maximizing computer and mathematical techniques, and keep devising solutions based on comparative genomics approaches (homology information and conserved gene expression of orthologous genes), for enhancing the identification of key players genes in secondary metabolism in crop plants.
Papers(17) Lashbrooke, J., Cohen, H., Levy-Samocha, D., Tzfadia, O., Panizel, I., Zeisler, V., Massalha, H., Stern, A., Trainotti, L., Schreiber, F., Costa, F., Aharoni, A. (2016) MYB107 and MYB9 Homologs Regulate Suberin Deposition in Angiosperms. The Plant Cell (In press).
(16) Fernandez-Moreno, JP., Tzfadia, O., Forment, J., Presa, S., Rogachev, I., Meir, S., Orzaez, D., Aharoni, A., Granell, A. (2016) Characterization of a New Pink-Fruited Tomato Mutant Results in the Identification of a Null Allele of the SlMYB12 Transcription Factor. Plant Physiology 171(3):1821-1836.
(15) Xie, G.-C., Tzfadia, O., Levy, AA., Weithorn, E., Peled-Zehavi, H., Van Parys, T., Van de Peer, Y., Galili, G. (2016) hfAIM: a reliable bioinformatics approach for in silico genome-wide identification of autophagy-associated atg8-interacting motifs in various organisms. Autophagy 12(5):876-87.
(14) Tzfadia, O., Diels, T., De Meyer, S., Vandepoele, K., Aharoni, A., Van de Peer, Y. (2016) CoExpNetViz: the Construction and Vizualisation of Co-expression Networks. Frontiers in Plant Science 6:1194.
(13) Amar, M., Frades, I., Chazanov, D., Nethanel, N., Hedley, PE., Erik Alexandersson, A., Tzfadia, O., Ron, Shamir. (2014) The MORPH-R web and software tool for predicting missing genes in biological pathways. Physiologia Plantarum 155(1):12-20.
(12) Toubiana, D., Batushansky, A., Tzfadia, O., Scossa, F., Khan, A., Barak, S., Zamir, D., Fernie, A., Nikoloski, Z., Fait, A. (2014) Combined correlation-based network and mQTL analyses efficiently identified loci for branched chain amino acid, serine to threonine, and proline metabolism in tomato seeds. The Plant Journal 81(1):121-33.
(11) Amar, M., Frades, I., Danek, A., Goldberg, J., Sharma, A., Hedley, PE., Proux-Wera, E., Andreasson E Shamir, R., Tzfadia, O., Alexandersson, E. (2014) Evaluation and integration of functional annotation pipelines for newly sequenced organisms: the potato genome as a test case. BMC Plant Biology 14:329.
(10) Rosenwasser, S., Mausz, M., Schatz, M., Sheyn, U., Malitsky, S., Aharoni, A., Weinstock, E., Tzfadia, O., Ben-Dor, S., Feldmesser, E., Pohnert, G., Vardi, A. (2014) Rewiring host lipid metabolism by large viruses determines the fate of Emiliania huxleyia bloom-forming alga in the ocean. The Plant Cell 26(6):2689-2707.
(9) Rosenwasser, S., Graff, van Creveld, S., Schatz, M., Malitsky, S., Tzfadia, O., Aharoni, A., Levin, J., Gabashvili, A., Feldmesser, E., Vardi, A. (2014) Mapping the diatom redox-sensitive proteome provides insights into response to nitrogen stress in the marine environment. Proceedings of the National Academy of Sciences 111(7):2740-5.
(8) Itkin, M., Heinig, U., Tzfadia, O., Bhide, PA., Shinde, B., Cardenas, P., Bocobza, SE., Unger, T., Malitsky, S., Finkers, R., Tikunov, Y., Bovy, A., Chikate, Y., Singh, N., Rogachev, I., Beekwilder, J., Giri, AP., Aharoni, A. (2013) Biosynthesis of anti-nutritional glycoalkaloids in Solanaceous crops is mediated by clustered pathway genes. Science 341,175-179.
(7) Tzfadia, O., Galili, G. (2013) The Arabidopsis exocyst subcomplex subunits involved in a golgi-independent transport into the vacuole possess consensus autophagy-associated ATG8 interacting motifs. Plant Signaling and Behavior 9.
(6) Levy, AA., Ben-Abu, Y., Tishler, Y., Elbaum, R., Tzfadia, O., Rogachev, I., Meir, S., Aharoni, A. (2013) Lessons from 12,000 years of wheat evolution under domestication. International Plant and Animal Genome Conference XXI 2013
(5) Bradbury, LMT., Shumskaya, M., Tzfadia, O., Kennellyt, EJ., Wurtzel, ET. (2012) CruP protects against ROS in oxygenic photosynthetic organisms. Proceedings of the National Academy of Sciences. 109,E1888-97.
(4) Tzfadia, O., Amar, M., Bradbury, LMT., Wurtzel, ET., Shamir, R. (2012) The MORPH algorithm: ranking candidate genes for membership in Arabidopsis thaliana pathways. The Plant Cell 24,4389-406.
(3) Meier, S., Tzfadia, O., Vallabhaneni, R., Gehring, C., Wurtzel, ET. (2011) A transcriptional analysis of carotenoid, chlorophyll and plastidial isoprenoid biosynthesis genes during development and osmotic stress responses in Arabidopsis thaliana. BMC Systems Biology 5,77.
(2) Li, F., Tzfadia, O., Wurtzel, ET. (2009) The Phytoene Synthase gene family in the Grasses: Subfunctionalization provides tissue-specific control of carotenogenesis. Plant Signaling and Behavior 4,208-211.
(1) Tzfadia, O., Azrielli, A., Falach, L., Zada, A., Roelofs, WL., Rafaeli, A. (2008) Pheromone biosynthetic pathways: PBAN-regulated rate-limiting steps and differential expression of desaturase genes in moth species. Insect Biochemistry and Molecular Biology 38,552-67.
VIB / UGent
Bioinformatics & Evolutionary Genomics
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