Nicholas Provart

provart2011.jpg
Associate Professor
Education: 
Ph.D., Freie Universitaet Berlin, 1996
Department: 
Cell & Systems Biology
Research Areas: 
Systems Biology & Bioinformatics, Plant Biology, Molecular Biology & Biotechnology, Functional Genomics & Genetics
Graduate Programs: 
Cell & Systems Biology, Genome Biology & Bioinformatics
Office phone: 
416-978-7141
Lab phone: 
416-946-8149
Fax: 
416-978-5878
Office: 
ESC 3051
Lab: 
ESC 3078

nicholas [dot] provart (at)utoronto [dot] ca

Address: 

Department of Cell & Systems Biology
University of Toronto
25 Willcocks Street
Toronto, Ontario
Canada M5S 3B2

Research: 

My interests lie in the use of bioinformatics tools (some of which my lab has developed and which are available at the Bio-Analytic Resource, bar.utoronto.ca; facebook.com/BioAnalyticResource) to identify novel aspects of plant biology, especially in the area of plant stress biology. For instance, cluster analysis of gene expression data from plants subjected to different abiotic and biotic stresses has provided putative functional roles for several plant transcription factors, cytochrome P450s, and other members within multigene families. Furthermore, gene expression analyses can also provide inferential mechanistic insights into the development of various organs or tissues, e.g. rice seed, at the metabolic or signal transduction level. Being a founding member of the Centre for the Analysis of Genome Evolution and Function, CAGEF - with its numerous high-throughput technology platforms, my lab is well positioned to utilize and generate large amounts of sequence and gene expression data, following a systems biology approach.

 Bio-Analytic Resource by Toufighi et al. (2005)

2014
de Lucas, M., Provart, N.J., Brady, S. (2014).  Bioinformatic Tools in Arabidopsis Research. Arabidopsis Protocols. 1062, 97-136. Abstract
Lumba, S., Toh, S., Handfield, L., Swan, M., Liu, R., Youn, J., Cutler, S.R., Subramaniam, R., Provart, N.J., Moses, A., Desveaux, D., McCourt, P. (2014).  A Mesoscale Abscisic Acid Hormone Interactome Reveals a Dynamic Signaling Landscape in Arabidopsis. Developmental Cell. 29(3), 360-372. Abstract
2013
Tran, F., Penniket, C., Patel, R.V., Provart, N.J., Laroche, A., Rowland, O., Robert, L.S. (2013).  Developmental transcriptional profiling reveals key insights into Triticeae reproductive development. The Plant Journal. Abstract
Champigny, M.J., Sung, W.W., Catana, V., Salwan, R., Summers, P.S., Dudley, S.A., Provart, N.J., Cameron, R.K., Golding, G.B., Weretilnyk1*, E.A. (2013).  RNA-Seq effectively monitors gene expression in Eutrema salsugineum plants growing in an extreme natural habitat and in controlled growth cabinet conditions. BMC Genomics. 14, 23. Abstract
2012
Lumba, S., Tsuchiya, Y., Delmas, F., Hezky, J., Provart, N.J., Lu, Q.S., McCourt, P., Gazzarrini, S. (2012).  The embryonic leaf identity gene FUSCA3 regulates vegetative phase transitions by negatively modulating ethylene-regulated gene expression in Arabidopsis. BMC Biology. 10, 8. Abstract
Chiu, R.S., Nahal, H., Provart, N.J., Gazzarrini, S. (2012).  The role of the Arabidopsis FUSCA3 transcription factor during inhibition of seed germination at high temperature. BMC Plant Biology. 12, 15. Abstract
Patel, R.V., Nahal, H.K., Breit, R., Provart, N.J. (2012).  BAR expressolog identification: expression profile similarity ranking of homologous genes in plant species. The Plant Journal. 71(6), 1038–1050. Abstract
International-Arabidopsis-Informatics-Consortium, (2012).  Taking the Next Step: Building an Arabidopsis Information Portal. The Plant Cell. 24(6), 2248-2256. Abstract
Provart, N.J. (2012).  Correlation Networks Visualization. Frontiers in Plant Systems Biology. 3, 240. Abstract
Chatfield, S.P., Capron, R., Severino, A., Penttila, P., Alfred, S., Nahal, H., Provart, N.J. (2012).  Incipient stem cell niche conversion in tissue culture: Using a systems approach to probe early events in WUSCHEL-dependent conversion of lateral root primordia into shoot meristems. The Plant Journal. 2012, 1. Abstract
Ho, C., Wu, Y., Shen, H., Provart, N.J., Geisler, M. (2012).  A predicted protein interactome for rice. Rice. 5, 15. Abstract
The-EPIC-Planning-Committee, (2012).  Reading the Second Code:Mapping Epigenomes to Understand Plant Growth, Development, and Adaptation to the Environment. The Plant Cell. 24, 2257–2261.
2011
Maia, J., Dekkers, B.J.W., Provart, N.J., Ligterink, W., Hilhorst, H.W.M. (2011).  The Re-Establishment of Desiccation Tolerance in Germinated Arabidopsis thaliana Seeds and Its Associated Transcriptome. PLoS ONE. 6(12), e29123. Abstract
Fucile, G., DiBiase, D., Nahal, H., La, G., Khodabandeh, S., Chen, Y., Easley, K., Christendat, D., Kelley, L., Provart, N.J. (2011).  ePlant and the 3D Data Display Initiative: Integrative Systems Biology on the World Wide Web. PLoS ONE. 6(1), e15237. Abstract
Xiong, X., Song, H., On, T., Lochovsky, L., Provart, N.J., Parkinson, J. (2011).  Phylopro: A web based tool for the generation and visualization of phylogenetic profiles across Eukarya. Bioinformatics. ePub, 2. Abstract
Bassel, G.W., Lan, H., Glaab, E., Gibbs, D.J., Gerjets, T., Krasnogor, N., Bonner, A.J., Holdsworth, M.J., Provart, N.J. (2011).  Genome-wide network model capturing seed germination reveals coordinated regulation of plant cellular phase transitions. Proc. Natl. Acad. Sci. USA. 108(23), 9709-9714. Abstract
Dean, G., Cao, Y., Xiang, D., Provart, N.J., Ramsay, L., Ahad, A., White, R., Selvaraj, G., Datla, R., Haughn, G. (2011).  Analysis of Gene Expression Patterns during Seed Coat Development in Arabidopsis. Molecular Plant. 4, 1074-1091. Abstract
Austin, R.S., Vidaurre, D., Stamatiou, G., Breit, R., Provart, N.J., Bonetta, D., Zhang, J., Fung, P., Gong, Y., Wang, P.W., McCourt, P., Guttman, D.S. (2011).  Next-Generation Mapping of Arabidopsis Genes. The Plant Journal. 67, 715–725. Abstract
ANTUNES, W.C., PROVART, N.J., WILLIAMS, T.C.R., LOUREIRO, M.E. (2011).  Changes in stomatal function and water use efficiency in potato plants with altered sucrolytic activity. Plant, Cell & Environment. 35, 747-759. Abstract
Bolser, D., Chibon, P., others, 4., Swan, D., Bassi, S., González, V., Suravajhala, P., Hwang, S., Romano, P., Edwards, R., Bishop, B., Eargle, J., Shtatland, T., Provart, N., Clements, D., Renfro, D., Bhak, D., Bahk, J.. (2011).  MetaBase--the wiki-database of biological databases. Nucleic Acids Research. 40(D1), D1250-D1254. Abstract
2010
Matsuda, F., Hirai, M., Sasaki, E., Akiyama, K., Yonekura-Sakakibara, K., Provart, N., Sakurai, T., Shimada, Y., Saito, K. (2010).  AtMetExpress Development: A Phytochemical Atlas of Arabidopsis Development. Plant Physiology. 152, 566–578. Abstract
Li, P., Ponnala, L., Gandotra, N., Wang, L., Si, Y., Tausta, L., Kebrom, T., Provart, N., Patel, R., Myers, C., Reidel, E., Turgeon, R., Liu, P., Sun, Q., Nelson, T., Brutnell, T. (2010).  The developmental dynamics of the maize leaf transcriptome. Nature Genetics. 42, 1060-1067. Abstract
International-Arabidopsis-Informatics-Consortium, (2010).  An International Bioinformatics Infrastructure to Underpin the Arabidopsis Community. The Plant Cell. 22, 2530-2536. Abstract
2009
Park, S.-Y., Fung, P., Nishimura, N., Jensen, D., Fujii, H., Zhao, Y., Lumba, S., Santiago, J., Rodrigues, A., Chow, T., Alfred, S., Bonetta, D., Finkelstein, R., Provart, N., Desveaux, D., Rodriguez, P., McCourt, P., Zhu, J.-K., Schroeder, J.I., Volkman, B., Cutler, S. (2009).  Abscisic Acid Inhibits Type 2C Protein Phosphatases via the PYR/PYL Family of START Proteins. Science. 324, 1068-1071. Abstract
CARVIEL, J.L., AL-DAOUD, F., NEUMANN, M., MOHAMMAD, A., PROVART, N.J., MOEDER, W., YOSHIOKA, K., CAMERON, R.K. (2009).  Forward and reverse genetics to identify genes involved in the age-related resistance response in Arabidopsis thaliana. MOLECULAR PLANT PATHOLOGY. 10(5), 621-634. Abstract
Morris, P.F., Schlosser, L.R., Onasch, K.D., Wittenschlaeger, T., Austin, R., Provart, N. (2009).  Multiple Horizontal Gene Transfer Events and Domain Fusions Have Created Novel Regulatory and Metabolic Networks in the Oomycete Genome. PLoS ONE. 4(7), e6133. Abstract
Ba, A.N.N., Pogoutse, A., Provart, N., Moses, A. (2009).  NLStradamus: a simple Hidden Markov Model for nuclear localization signal prediction. BMC Bioinformatics. 10, 202. Abstract
USADEL, B., OBAYASHI, T., MUTWIL, M., GIORGI, F.M., BASSEL, G.W., TANIMOTO, M., CHOW, A., STEINHAUSER, D., PERSSON, S., PROVART, N.J. (2009).  Co-expression tools for plant biology: opportunities for hypothesis generation and caveats. Plant, Cell & Environment. Abstract
Wilkins, O., Waldron, L., Nahal, H., Provart, N.J., Campbell, M.M. (2009).  Genotype and time of day shape the Populus drought response. The Plant Journal. 60, 703-715. Abstract
Wilkins, O., Nahal, H., Foong, J., Provart, N.J., Campbell, M.M. (2009).  Expansion and Diversification of the Populus R2R3-MYB Family of Transcription Factors. Plant Physiology. 149(2), 981-993. Abstract
Brady, S.M., Provart, N.J. (2009).  Web-Queryable Large-Scale Data Sets for Hypothesis Generation in Plant Biology. The Plant Cell. 21(4), 1034-1051. Abstract
2008
Ehlting, J., Sauveplane, V., Olry, A., Ginglinger, J., Provart, N., Werck-Reichhart, D. (2008).  An extensive (co-)expression analysis tool for the cytochrome P450 superfamily in Arabidopsis thaliana. BMC Plant Biology 2008. 8, 47.
Bassel, G., Fung, P., Chow, T., Foong, J., Provart, N., Cutler, S. (2008).  Elucidating the germination transcriptional program using small molecules. Plant Physiology. 147, 143-155.
2007
Geisler-Lee, J., O'Toole, N., Ammar, R., Provart, N.J., Millar, A.H., Geisler, M. (2007).  A Predicted Interactome for Arabidopsis thaliana. Plant Physiology . 145, 317-329. Abstract
Brady, S., Provart, N.J. (2007).  Extreme breeding: Leveraging genomics for crop improvement. Journal of the Science of Food and Agriculture. 87(6), 925-929. Abstract
Austin, R.S., Provart, N.J., Cutler, S.R. (2007).  C-terminal motif prediction in eukaryotic proteomes using comparative genomics and statistical over-representation across protein families. BMC Genomics. 8, 191. Abstract
Lan, H., Carson, R., Provart, N., Bonner, A. (2007).  Combining classifiers to predict gene function in Arabidopsis thaliana using large-scale gene expression measurements. BMC Bioinformatics 2007. 8, 358.
Winter, D., Vinegar, B., Nahal, H., Ammar, R., Wilson, G.V., Provart, N.J. (2007).  An 'Electronic Fluorescent Pictograph' Browser for Exploring and Analyzing Large-Scale Biological Data Sets. PLoS One. 2(8), e718. Abstract
2006
Ehlting, J., Provart, N.J., Werck-Reichhart, D. (2006).  Functional annotation of the Arabidopsis P450 superfamily based on large-scale co-expression analysis. Biochem. Soc. Trans. 34(6), 1192-1198. Abstract
Taylor, J., Provart, N. (2006).  CapsID: a web-based tool for developing parsimonious sets of CAPS molecular markers for genotyping. BMC Genetics. 7, 27. Abstract
2005
Toufighi, K., Brady, S., Austin, R., Ly, E., Provart, N. (2005).  The Bio-Array Resource: e-Northerns, Expression Angling,and promoter analyses. The Plant Journal. 43, 153-163. Abstract
2004
Ilic, K., Berleth, T., Provart, N. (2004).  BlastDigester - a web-based program for efficient CAPS marker design. TRENDS in Genetics. 20 (7), 280-283. Abstract
Provart, N. (2004).  Developments in Plant and Animal Genome Research. Journal of the Science of Food and Agriculture (JSFA). 84, 473-474. Abstract
Nakhamchik, A., Zhao, Z., Provart, N., Shiu, S., Keatley, S., Cameron, R., Goring, D. (2004).  A Comprehensive Expression Analysis of the Arabidopsis Proline-rich Extensin-like Receptor Kinase Gene Family using Bioinformatic and Experimental Approaches. Plant Cell Physiol. 45(12), 1875-1881. Abstract
Austin, R., Provart, N., Sacadura, N., Nugent, K., Babu, M., Saville, B. (2004).  A comparative genomic analysis of ESTs from Ustilago maydis. Funct Integr Genomics. 4(4), 207-218. Abstract
Provart, N., McCourt, P. (2004).  Systems approaches to understanding cell signaling and gene regulation. Curr Opin Plant Biol. 7(5), 605-9. Abstract
2003
Zhu, T., Budworth, P., Chen, W., Provart, N., Chang, H.-S., Guimil, S., Zou, G., Wang, X. (2003).  Transcriptional Control of Nutrient Partitioning During Rice Grain Filling. Plant Biotech. J. 1, 59-70. Abstract
Provart, N., Zhu, T. (2003).  A Browser-based Functional Classification SuperViewer for Arabidopsis Genomics. Currents in Computational Molecular Biology. 271-272. Abstract
Provart, N., Gil, P., Han, B., Chen, W., Chang, H.-S., Wang, X., Zhu, T. (2003).  Gene Expression Phenotypes of Arabidopsis Associated with Sensitivity to Low Temperatures. Plant Physiol. 132, 893-906. Abstract
Zhu, T., Provart, N. (2003).  Transcriptional responses to low temperature and their regulation in Arabidopsis. Can. J. Bot. 81, 1168-1174. Abstract
2002
Chen, W., Provart, N., Glazebrook, J., Katagiri, F., Chang, H.-S., Eulgem, T., Mauch, F. (2002).  Expression Profile Matrix of Arabidopsis Transcription Factor Genes Suggests Their Putative Functions in Response to Environmental Stresses. The Plant Cell. 14, 559-574. Abstract
1993
Provart, N., Majeau, N., Coleman, J.R. (1993).  Characterization of chloroplastic carbonic anhydrase. Expression in E. coli and site-directed mutagenesis. Plant Molec. Biol. 22, 937-943.