Professor and Chair Nicholas Provart

Nicholas J. Provart

Professor & Chair


St. George (downtown)

CSB Appointment


Research Areas

Bioinformatics / Computational Biology, Genetics / Genomics, Molecular Biology, Plant Biology, Structural Biology, Systems Biology


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

Primary Undergraduate Department

Cell & Systems Biology

Graduate Programs

Cell & Systems Biology

Academic or Administrative Appointments

Chair, Department of Cell & Systems Biology
Member, Multinational Arabidopsis Steering Committee and the International Arabidopsis Informatics Consortium
Interim Director, Bioinformatics and Computational Biology Program

Research Description

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,; 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.

Contact Information

Office Phone: 416-978-3500/416-978-7141
Office: RW 434A/ESC3072
Lab: ESC3078
Lab Phone: 416-946-8149

Mailing Address

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

Visit lab’s website

Recent News

Excellence and excitement at CSB Research Day 2024

The wide variety of cutting-edge science in the Department of Cell & Systems Biology was on full display in the distinguished halls of Hart House…

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Global Biodata Coalition designates UofT’s Bio-Analytic Resource as a Global Core Biodata Resource

The Bio-Analytic Resource for Plant Biology is thrilled to have been designated as a Global Core Biodata Resource by the Global Biodata Coalition.…

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Janssen Award for Equity and Inclusion to improve opportunities for CSB graduate students

CSB is grateful for a new endowment to U of T from Jannsen Canada that will help address health inequity and provide ongoing support to future…

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Multi‐omics atlas of combinatorial abiotic stress responses in wheat

Da Ros L, Bollina V, Soolanayakanahally R, Pahari S, Elferjani R, Kulkarni M, Vaid N, Risseuw E, Cram D, Pasha A, Esteban E, Konkin D, Provart N, Nambara E, Kagale S
2023, The Plant Journal, 10.1111/tpj.16332

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The red flower wintersweet genome provides insights into the evolution of magnoliids and the molecular mechanism for tepal color development

Shen Z, Li W, Li Y, Liu M, Cao H, Provart N, Ding X, Sun M, Tang Z, Yue C, Cao Y, Yuan D, Zhang L
2021, The Plant Journal, 10.1111/tpj.15533

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An abscisic acid-responsive protein interaction network for sucrose non-fermenting related kinase1 in abiotic stress response

Carianopol CS, Chan AL, Dong S, Provart NJ, Lumba S, Gazzarrini S
2020, Communications Biology, 10.1038/s42003-020-0866-8

Light-responsive expression atlas reveals the effects of light quality and intensity in Kalanchoë fedtschenkoi, a plant with crassulacean acid metabolism

Yang X, Tuskan GA, Muchero W, Chen J, Provart NJ, Pasha A, Borland AM, Cushman JC, Schmutz J, Ng V, Liu D, Yerramsetty P, Wang M, Lipzen A, Garcia TM, Sreedasyam A, Hu R, Zhang J
2020, GigaScience, 10.1093/gigascience/giaa018

Transcriptomics at Maize Embryo/Endosperm Interfaces Identifies a Transcriptionally Distinct Endosperm Subdomain Adjacent to the Embryo Scutellum

Doll NM, Just J, Brunaud V, Caïus J, Grimault A, Depège-Fargeix N, Esteban E, Pasha A, Provart NJ, Ingram GC, Rogowsky PM, Widiez T
2020, The Plant Cell, 10.1105/tpc.19.00756

Expression Atlas of Selaginella moellendorffii Provides Insights into the Evolution of Vasculature, Secondary Metabolism, and Roots

Ferrari C, Shivhare D, Hansen BO, Pasha A, Esteban E, Provart NJ, Kragler F, Fernie A, Tohge T, Mutwil M
2020, The Plant Cell, 10.1105/tpc.19.00780

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Editorial: Resistance to Salinity and Water Scarcity in Higher Plants. Insights From Extremophiles and Stress-Adapted Plants: Tools, Discoveries and Future Prospects.

Grene R, Provart NJ, Pardo JM
2019, Frontiers in plant science, 10, 373, 31001299

High Temporal-Resolution Transcriptome Landscape of Early Maize Seed Development.

Yi F, Gu W, Chen J, Song N, Gao X, Zhang X, Zhou Y, Ma X, Song W, Zhao H, Esteban E, Pasha A, Provart NJ, Lai J
2019, The Plant cell, 31, 974-992, 30914497

Map of physical interactions between extracellular domains of Arabidopsis leucine-rich repeat receptor kinases.

Mott GA, Smakowska-Luzan E, Pasha A, Parys K, Howton TC, Neuhold J, Lehner A, Grünwald K, Stolt-Bergner P, Provart NJ, Mukhtar MS, Desveaux D, Guttman DS, Belkhadir Y
2019, Scientific data, 6, 190025, 30806640

Proteome-wide, Structure-Based Prediction of Protein-Protein Interactions/New Molecular Interactions Viewer.

Dong S, Lau V, Song R, Ierullo M, Esteban E, Wu Y, Sivieng T, Nahal H, Gaudinier A, Pasha A, Oughtred R, Dolinski K, Tyers M, Brady SM, Grene R, Usadel B, Provart NJ
2019, Plant physiology, 179, 1893-1907, 30679268

An updated gene atlas for maize reveals organ-specific and stress-induced genes.

Hoopes GM, Hamilton JP, Wood JC, Esteban E, Pasha A, Vaillancourt B, Provart NJ, Buell CR
2019, The Plant journal : for cell and molecular biology, 97, 1154-1167, 30537259

A gene expression map of shoot domains reveals regulatory mechanisms.

Tian C, Wang Y, Yu H, He J, Wang J, Shi B, Du Q, Provart NJ, Meyerowitz EM, Jiao Y
2019, Nature communications, 10, 141, 30635575

Tung Tree (Vernicia fordii) Genome Provides A Resource for Understanding Genome Evolution and Improved Oil Production

Zhang L, Liu M, Long H, Dong W, Pasha A, Esteban E, Li W, Yang X, Li Z, Song A, Ran D, Zhao G, Zeng Y, Chen H, Zou M, Li J, Liang F, Xie M, Hu J, Wang D, Cao H, Provart NJ, Zhang L, Tan X
2019, Genomics, Proteomics & Bioinformatics, 10.1016/j.gpb.2019.03.006

The Transcriptional Landscape of Polyploid Wheats and Their Diploid Ancestors during Embryogenesis and Grain Development

Xiang D, Quilichini TD, Liu Z, Gao P, Pan Y, Li Q, Nilsen KT, Venglat P, Esteban E, Pasha A, Wang Y, Wen R, Zhang Z, Hao Z, Wang E, Wei Y, Cuthbert R, Kochian LV, Sharpe A, Provart N, Weijers D, Gillmor CS, Pozniak C, Datla R
2019, The Plant Cell, 10.1105/tpc.19.00397

An eFP‐Seq Browser for visualizing and exploring RNA sequencing data

Sullivan A, Purohit PK, Freese NH, Pasha A, Esteban E, Waese J, Wu A, Chen M, Chin CY, Song R, Watharkar SR, Chan AP, Krishnakumar V, Vaughn MW, Town C, Loraine AE, Provart NJ
2019, The Plant Journal, 10.1111/tpj.14468

Arabidopsis bioinformatics resources: The current state, challenges, and priorities for the future

2019, Plant Direct, 10.1002/pld3.109

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Regulation of Root Angle and Gravitropism.

Toal TW, Ron M, Gibson D, Kajala K, Splitt B, Johnson LS, Miller ND, Slovak R, Gaudinier A, Patel R, de Lucas M, Provart NJ, Spalding EP, Busch W, Kliebenstein DJ, Brady SM
2018, G3 (Bethesda, Md.), 8, 3841-3855, 30322904

The transcriptional landscape of polyploid wheat.

Ramírez-González RH, Borrill P, Lang D, Harrington SA, Brinton J, Venturini L, Davey M, Jacobs J, van Ex F, Pasha A, Khedikar Y, Robinson SJ, Cory AT, Florio T, Concia L, Juery C, Schoonbeek H, Steuernagel B, Xiang D, Ridout CJ, Chalhoub B, Mayer KFX, Benhamed M, Latrasse D, Bendahmane A, , Wulff BBH, Appels R, Tiwari V, Datla R, Choulet F, Pozniak CJ, Provart NJ, Sharpe AG, Paux E, Spannagl M, Bräutigam A, Uauy C
2018, Science (New York, N.Y.), 361, 30115782

Analyses of Protein Interaction Networks Using Computational Tools.

Dong S, Provart NJ
2018, Methods in molecular biology (Clifton, N.J.), 1794, 97-117, 29855953

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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
2015, The New phytologist, 26465351

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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
2014, Nature biotechnology, 25306245

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
2014, Developmental cell, 29, 360-72, 24823379

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
2014, PloS one, 9, e94808, 24733489

Bioinformatic tools in Arabidopsis research

de Lucas M, Provart NJ, Brady SM
2014, Methods in molecular biology (Clifton, N.J.), 1062, 97-136, 24057362

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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
2013, BMC genomics, 14, 578, 23984645

Developmental transcriptional profiling reveals key insights into Triticeae reproductive development

Tran F, Penniket C, Patel RV, Provart NJ, Laroche A, Rowland O, Robert LS
2013, The Plant journal : for cell and molecular biology, 74, 971-88, 23581995

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
2013, The Plant journal : for cell and molecular biology, 73, 798-813, 23181633

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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
2012, The Plant journal : for cell and molecular biology, 71, 1038-50, 22607031

A predicted protein interactome for rice

Ho CL, Wu Y, Shen HB, Provart NJ, Geisler M
2012, Rice (New York, N.Y.), 5, 15, 24279740

Taking the next step: building an Arabidopsis information portal

2012, The Plant cell, 24, 2248-56, 22751211

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
2012, BMC biology, 10, 8, 22348746

The role of the Arabidopsis FUSCA3 transcription factor during inhibition of seed germination at high temperature

Chiu RS, Nahal H, Provart NJ, Gazzarrini S
2012, BMC plant biology, 12, 15, 22279962

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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
2011, PloS one, 6, e29123, 22195004

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
2012, Nucleic acids research, 40, D1250-4, 22139927

Changes in stomatal function and water use efficiency in potato plants with altered sucrolytic activity

Antunes WC, Provart NJ, Williams TC, Loureiro ME
2012, Plant, cell & environment, 35, 747-59, 21999376

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
2011, The Plant journal : for cell and molecular biology, 67, 715-25, 21518053

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
2011, Molecular plant, 4, 1074-91, 21653281

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
2011, Proceedings of the National Academy of Sciences of the United States of America, 108, 9709-14, 21593420

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
2011, Bioinformatics (Oxford, England), 27, 877-8, 21252074

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
2011, PloS one, 6, e15237, 21249219

Seed bioinformatics

Bassel GW, Holdsworth MJ, Provart NJ
2011, Methods in molecular biology (Clifton, N.J.), 773, 403-19, 21898268

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An international bioinformatics infrastructure to underpin the Arabidopsis community

2010, The Plant cell, 22, 2530-6, 20807877

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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
2010, Plant physiology, 152, 566-78, 20023150

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
2009, Molecular plant pathology, 10, 621-34, 19694953

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
2009, Plant, cell & environment, 32, 1633-51, 19712066

Genotype and time of day shape the Populus drought response

Wilkins O, Waldron L, Nahal H, Provart NJ, Campbell MM
2009, The Plant journal : for cell and molecular biology, 60, 703-15, 19682285

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
2009, Science (New York, N.Y.), 324, 1068-71, 19407142

Web-queryable large-scale data sets for hypothesis generation in plant biology

Brady SM, Provart NJ
2009, The Plant cell, 21, 1034-51, 19401381

Gene expression analyses for elucidating mechanisms of hormonal action in plants

Bassel GW, Provart NJ
2009, Methods in molecular biology (Clifton, N.J.), 495, 21-37, 19085149

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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
2009, Plant physiology, 149, 981-93, 19091872

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
2008, BMC plant biology, 8, 47, 18433503

Elucidating the germination transcriptional program using small molecules

Bassel GW, Fung P, Chow TF, Foong JA, Provart NJ, Cutler SR
2008, Plant physiology, 147, 143-55, 18359847

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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
2007, BMC bioinformatics, 8, 358, 17888165

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
2007, PloS one, 2, e718, 17684564

A predicted interactome for Arabidopsis

Geisler-Lee J, O'Toole N, Ammar R, Provart NJ, Millar AH, Geisler M
2007, Plant physiology, 145, 317-29, 17675552

C-terminal motif prediction in eukaryotic proteomes using comparative genomics and statistical over-representation across protein families

Austin RS, Provart NJ, Cutler SR
2007, BMC genomics, 8, 191, 17594486

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CapsID: a web-based tool for developing parsimonious sets of CAPS molecular markers for genotyping

Taylor J, Provart NJ
2006, BMC genetics, 7, 27, 16686952

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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
2005, The Plant journal : for cell and molecular biology, 43, 153-63, 15960624

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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
2004, Plant & cell physiology, 45, 1875-81, 15653807

Systems approaches to understanding cell signaling and gene regulation

Provart NJ, McCourt P
2004, Current opinion in plant biology, 7, 605-9, 15337105

A comparative genomic analysis of ESTs from Ustilago maydis

Austin R, Provart NJ, Sacadura NT, Nugent KG, Babu M, Saville BJ
2004, Functional & integrative genomics, 4, 207-18, 15349794

BlastDigester–a web-based program for efficient CAPS marker design

Ilic K, Berleth T, Provart NJ
2004, Trends in genetics : TIG, 20, 280-3, 15219390

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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
2003, Plant physiology, 132, 893-906, 12805619

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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
2002, The Plant cell, 14, 559-74, 11910004

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