Nicholas Provart

faculty_img Academic TitleProfessor

Campus: St. George

CSB Appointment: Full

Primary Undergraduate Department:
Cell & Systems Biology

Graduate Programs:
Cell & Systems Biology

Titles and Honors:
Academic or Administrative Appointments:
Member, North American Arabidopsis Steering Committee and the International Arabidopsis Informatics Consortium

Education:
Ph.D. Freie Universitaet Berlin 1996
M.Sc. University of Toronto 1993
B.Sc. University of Toronto 1990.

 

Mailing Address
Department of Cell & Systems Biology
University of Toronto
25 Willcocks St.
Toronto, ON M5S 3B2
Canada

 

Contact Information
Office phone: 416-978-7141
Office: ESC 3072
Lab: ESC 3078
Lab phone: 416-946-8149
Email: nicholas.provart@utoronto.ca
URL: http://labs.csb.utoronto.ca/provart

 

Research Areas
Bioinformatics & Computational Biology
Comparative Genomics
Functional Genomics
Molecular Biology
Plant Biology
Structural Biology
Systems Biology

 

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, http://bar.utoronto.ca; http://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.

 

Publications

2016

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New BAR tools for mining expression data and exploring Cis-elements in Arabidopsis thaliana..Austin, Ryan S, Shu Hiu, Jamie Waese, Matthew Ierullo, Asher Pasha, Ting Ting Wang, Jim Fan, et al. The Plant journal : for cell and molecular biology ( 5). 2016.
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A Human “eFP” Browser for Generating Gene Expression Anatograms.Patel, Rohan V, Erin T Hamanishi, and Nicholas J Provart. PloS one, no. 3 ( 8) 2016.
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Gene Slider: sequence logo interactive data-visualization for education and research..Waese, Jamie, Asher Pasha, Ting Ting Wang, Anna van Weringh, David S Guttman, and Nicholas J Provart. Bioinformatics (Oxford, England) ( 13). 2016.
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NIN-like protein 8 is a master regulator of nitrate-promoted seed germination in Arabidopsis.Yan, Dawei, Vanathy Easwaran, Vivian Chau, Masanori Okamoto, Matthew Ierullo, Mitsuhiro Kimura, Akira Endo, et al. Nature communications ( 12). 2016.
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2015

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Inference of Longevity-Related Genes from a Robust Coexpression Network of Seed Maturation Identifies Regulators Linking Seed Storability to Biotic Defense-Related Pathways.Righetti, Karima, Joseph Ly Vu, Sandra Pelletier, Benoit Ly Vu, Enrico Glaab, David Lalanne, Asher Pasha, et al. The Plant cell, no. 10 ( 26) 2015.
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50 years of Arabidopsis research: highlights and future directions.Provart NJ, Alonso J, Assmann SM, Bergmann D, Brady SM, Brkljacic J, Browse J, Chapple C, Colot V, Cutler S, Dangl J, Ehrhardt D, Friesner JD, Frommer WB, Grotewold E, Meyerowitz E, Nemhauser J, Nordborg M, Pikaard C, Shanklin J, Somerville C, Stitt M, Torii KU, Waese J, Wagner D, McCourt P.New Phytol. 2015 Oct;
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2014

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Comparative analyses of C4 and C3 photosynthesis in developing leaves of maize and rice.Wang L, Czedik-Eysenberg A, Mertz RA, Si Y, Tohge T, Nunes-Nesi A, Arrivault S, Dedow LK, Bryant DW, Zhou W, Xu J, Weissmann S, Studer A, Li P, Zhang C, LaRue T, Shao Y, Ding Z, Sun Q, Patel RV, Turgeon R, Zhu X, Provart NJ, Mockler TC, Fernie AR, Stitt M, Liu P, Brutnell TP.Nat. Biotechnol. 2014 Oct;
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A mesoscale abscisic acid hormone interactome reveals a dynamic signaling landscape in Arabidopsis.Lumba S, Toh S, Handfield LF, Swan M, Liu R, Youn JY, Cutler SR, Subramaniam R, Provart N, Moses A, Desveaux D, McCourt P.Dev. Cell 2014 May;29(3):360-72
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New insights into Dehalococcoides mccartyi metabolism from a reconstructed metabolic network-based systems-level analysis of D. mccartyi transcriptomes.Islam MA, Waller AS, Hug LA, Provart NJ, Edwards EA, Mahadevan R.PLoS ONE 2014;9(4):e94808
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Bioinformatic tools in Arabidopsis research.de Lucas M, Provart NJ, Brady SM.Methods Mol. Biol. 2014;1062:97-136
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2013

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RNA-Seq effectively monitors gene expression in Eutrema salsugineum plants growing in an extreme natural habitat and in controlled growth cabinet conditions.Champigny MJ, Sung WW, Catana V, Salwan R, Summers PS, Dudley SA, Provart NJ, Cameron RK, Golding GB, Weretilnyk EA.BMC Genomics 2013;14:578
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Developmental transcriptional profiling reveals key insights into Triticeae reproductive development.Tran F, Penniket C, Patel RV, Provart NJ, Laroche A, Rowland O, Robert LS.Plant J. 2013 Jun;74(6):971-88
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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.Chatfield SP, Capron R, Severino A, Penttila PA, Alfred S, Nahal H, Provart NJ.Plant J. 2013 Mar;73(5):798-813
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2012

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A predicted protein interactome for rice.Ho CL, Wu Y, Shen HB, Provart NJ, Geisler M.Rice (N Y) 2012;5(1):15
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Taking the next step: building an Arabidopsis information portal. .Plant Cell 2012 Jun;24(6):2248-56
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BAR expressolog identification: expression profile similarity ranking of homologous genes in plant species.Patel RV, Nahal HK, Breit R, Provart NJ.Plant J. 2012 Sep;71(6):1038-50
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The embryonic leaf identity gene FUSCA3 regulates vegetative phase transitions by negatively modulating ethylene-regulated gene expression in Arabidopsis.Lumba S, Tsuchiya Y, Delmas F, Hezky J, Provart NJ, Shi Lu Q, McCourt P, Gazzarrini S.BMC Biol. 2012;10:8
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The role of the Arabidopsis FUSCA3 transcription factor during inhibition of seed germination at high temperature.Chiu RS, Nahal H, Provart NJ, Gazzarrini S.BMC Plant Biol. 2012;12:15
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MetaBase–the wiki-database of biological databases.Bolser DM, Chibon PY, Palopoli N, Gong S, Jacob D, Del Angel VD, Swan D, Bassi S, González V, Suravajhala P, Hwang S, Romano P, Edwards R, Bishop B, Eargle J, Shtatland T, Provart NJ, Clements D, Renfro DP, Bhak D, Bhak J.Nucleic Acids Res. 2012 Jan;40(Database issue):D1250-4
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Changes in stomatal function and water use efficiency in potato plants with altered sucrolytic activity.Antunes WC, Provart NJ, Williams TC, Loureiro ME.Plant Cell Environ. 2012 Apr;35(4):747-59
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2011

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The re-establishment of desiccation tolerance in germinated Arabidopsis thaliana seeds and its associated transcriptome.Maia J, Dekkers BJ, Provart NJ, Ligterink W, Hilhorst HW.PLoS ONE 2011;6(12):e29123
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Seed bioinformatics.Bassel GW, Holdsworth MJ, Provart NJ.Methods Mol. Biol. 2011;773:403-19
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Analysis of gene expression patterns during seed coat development in Arabidopsis.Dean G, Cao Y, Xiang D, Provart NJ, Ramsay L, Ahad A, White R, Selvaraj G, Datla R, Haughn G.Mol Plant 2011 Nov;4(6):1074-91
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Genome-wide network model capturing seed germination reveals coordinated regulation of plant cellular phase transitions.Bassel GW, Lan H, Glaab E, Gibbs DJ, Gerjets T, Krasnogor N, Bonner AJ, Holdsworth MJ, Provart NJ.Proc. Natl. Acad. Sci. U.S.A. 2011 Jun;108(23):9709-14
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Next-generation mapping of Arabidopsis genes.Austin RS, Vidaurre D, Stamatiou G, Breit R, Provart NJ, Bonetta D, Zhang J, Fung P, Gong Y, Wang PW, McCourt P, Guttman DS.Plant J. 2011 Aug;67(4):715-25
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PhyloPro: a web-based tool for the generation and visualization of phylogenetic profiles across Eukarya.Xiong X, Song H, On T, Lochovsky L, Provart NJ, Parkinson J.Bioinformatics 2011 Mar;27(6):877-8
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ePlant and the 3D data display initiative: integrative systems biology on the world wide web.Fucile G, Di Biase D, Nahal H, La G, Khodabandeh S, Chen Y, Easley K, Christendat D, Kelley L, Provart NJ.PLoS ONE 2011;6(1):e15237
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2010

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An international bioinformatics infrastructure to underpin the Arabidopsis community. .Plant Cell 2010 Aug;22(8):2530-6
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AtMetExpress development: a phytochemical atlas of Arabidopsis development.Matsuda F, Hirai MY, Sasaki E, Akiyama K, Yonekura-Sakakibara K, Provart NJ, Sakurai T, Shimada Y, Saito K.Plant Physiol. 2010 Feb;152(2):566-78
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2009

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Co-expression tools for plant biology: opportunities for hypothesis generation and caveats.Usadel B, Obayashi T, Mutwil M, Giorgi FM, Bassel GW, Tanimoto M, Chow A, Steinhauser D, Persson S, Provart NJ.Plant Cell Environ. 2009 Dec;32(12):1633-51
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Forward and reverse genetics to identify genes involved in the age-related resistance response in Arabidopsis thaliana.Carviel JL, Al-Daoud F, Neumann M, Mohammad A, Provart NJ, Moeder W, Yoshioka K, Cameron RK.Mol. Plant Pathol. 2009 Sep;10(5):621-34
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Genotype and time of day shape the Populus drought response.Wilkins O, Waldron L, Nahal H, Provart NJ, Campbell MM.Plant J. 2009 Nov;60(4):703-15
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Abscisic acid inhibits type 2C protein phosphatases via the PYR/PYL family of START proteins.Park SY, Fung P, Nishimura N, Jensen DR, Fujii H, Zhao Y, Lumba S, Santiago J, Rodrigues A, Chow TF, Alfred SE, Bonetta D, Finkelstein R, Provart NJ, Desveaux D, Rodriguez PL, McCourt P, Zhu JK, Schroeder JI, Volkman BF, Cutler SR.Science 2009 May;324(5930):1068-71
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Web-queryable large-scale data sets for hypothesis generation in plant biology.Brady SM, Provart NJ.Plant Cell 2009 Apr;21(4):1034-51
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Expansion and diversification of the Populus R2R3-MYB family of transcription factors.Wilkins O, Nahal H, Foong J, Provart NJ, Campbell MM.Plant Physiol. 2009 Feb;149(2):981-93
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Gene expression analyses for elucidating mechanisms of hormonal action in plants.Bassel GW, Provart NJ.Methods Mol. Biol. 2009;495:21-37
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2008

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An extensive (co-)expression analysis tool for the cytochrome P450 superfamily in Arabidopsis thaliana.Ehlting J, Sauveplane V, Olry A, Ginglinger JF, Provart NJ, Werck-Reichhart D.BMC Plant Biol. 2008;8:47
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Elucidating the germination transcriptional program using small molecules.Bassel GW, Fung P, Chow TF, Foong JA, Provart NJ, Cutler SR.Plant Physiol. 2008 May;147(1):143-55
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2007

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Combining classifiers to predict gene function in Arabidopsis thaliana using large-scale gene expression measurements.Lan H, Carson R, Provart NJ, Bonner AJ.BMC Bioinformatics 2007;8:358
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An “Electronic Fluorescent Pictograph” browser for exploring and analyzing large-scale biological data sets.Winter D, Vinegar B, Nahal H, Ammar R, Wilson GV, Provart NJ.PLoS ONE 2007;2(8):e718
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A predicted interactome for Arabidopsis.Geisler-Lee J, O’Toole N, Ammar R, Provart NJ, Millar AH, Geisler M.Plant Physiol. 2007 Oct;145(2):317-29
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C-terminal motif prediction in eukaryotic proteomes using comparative genomics and statistical over-representation across protein families.Austin RS, Provart NJ, Cutler SR.BMC Genomics 2007;8:191
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2006

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CapsID: a web-based tool for developing parsimonious sets of CAPS molecular markers for genotyping.Taylor J, Provart NJ.BMC Genet. 2006;7:27
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2005

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The Botany Array Resource: e-Northerns, Expression Angling, and promoter analyses.Toufighi K, Brady SM, Austin R, Ly E, Provart NJ.Plant J. 2005 Jul;43(1):153-63
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2004

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A comprehensive expression analysis of the Arabidopsis proline-rich extensin-like receptor kinase gene family using bioinformatic and experimental approaches.Nakhamchik A, Zhao Z, Provart NJ, Shiu SH, Keatley SK, Cameron RK, Goring DR.Plant Cell Physiol. 2004 Dec;45(12):1875-81
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A comparative genomic analysis of ESTs from Ustilago maydis.Austin R, Provart NJ, Sacadura NT, Nugent KG, Babu M, Saville BJ.Funct. Integr. Genomics 2004 Oct;4(4):207-18
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Systems approaches to understanding cell signaling and gene regulation.Provart NJ, McCourt P.Curr. Opin. Plant Biol. 2004 Oct;7(5):605-9
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BlastDigester–a web-based program for efficient CAPS marker design.Ilic K, Berleth T, Provart NJ.Trends Genet. 2004 Jul;20(7):280-3
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2003

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Gene expression phenotypes of Arabidopsis associated with sensitivity to low temperatures.Provart NJ, Gil P, Chen W, Han B, Chang HS, Wang X, Zhu T.Plant Physiol. 2003 Jun;132(2):893-906
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2002

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Expression profile matrix of Arabidopsis transcription factor genes suggests their putative functions in response to environmental stresses.Chen W, Provart NJ, Glazebrook J, Katagiri F, Chang HS, Eulgem T, Mauch F, Luan S, Zou G, Whitham SA, Budworth PR, Tao Y, Xie Z, Chen X, Lam S, Kreps JA, Harper JF, Si-Ammour A, Mauch-Mani B, Heinlein M, Kobayashi K, Hohn T, Dangl JL, Wang X, Zhu T.Plant Cell 2002 Mar;14(3):559-74
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