Nicholas J. Provart
Professor & Chair
Campus
St. George (downtown)
CSB Appointment
Full
Research Areas
Bioinformatics / Computational Biology, Genetics / Genomics, Molecular Biology, Plant Biology, Structural Biology, Systems Biology
Education
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, 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.
Contact Information
Office Phone: 416-978-3500/416-978-7141
Office: RW 434A/ESC3072
Lab: ESC3078
Lab Phone: 416-946-8149
Email
Mailing Address
Department of Cell & Systems Biology
University of Toronto
25 Willcocks St.
Toronto, ON M5S 3B2
Canada
Recent News
Publications
2024
20 years of the Bio-Analytic Resource for Plant Biology
Sullivan A, Lombardo M, Pasha A, Lau V, Zhuang J, Christendat A, Pereira B, Zhao T, Li Y, Wong R, Qureshi F, Provart N
2024, Nucleic Acids Research, 10.1093/nar/gkae920
2023
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
2021
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
2020
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
2019
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
2018
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
2015
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
2014
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
2013
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
2012
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
2011
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
2010
An international bioinformatics infrastructure to underpin the Arabidopsis community
2010, The Plant cell, 22, 2530-6, 20807877
2009
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
2008
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
2007
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
2006
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
2005
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
2004
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
2003
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
2002
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