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Items: 1 to 50 of 59

1.

Analyses of Protein Interaction Networks Using Computational Tools.

Dong S, Provart NJ.

Methods Mol Biol. 2018;1794:97-117. doi: 10.1007/978-1-4939-7871-7_7.

PMID:
29855953
2.

An extracellular network of Arabidopsis leucine-rich repeat receptor kinases.

Smakowska-Luzan E, Mott GA, Parys K, Stegmann M, Howton TC, Layeghifard M, Neuhold J, Lehner A, Kong J, Grünwald K, Weinberger N, Satbhai SB, Mayer D, Busch W, Madalinski M, Stolt-Bergner P, Provart NJ, Mukhtar MS, Zipfel C, Desveaux D, Guttman DS, Belkhadir Y.

Nature. 2018 Jan 18;553(7688):342-346. doi: 10.1038/nature25184. Epub 2018 Jan 10.

PMID:
29320478
3.

The Next Generation of Training for Arabidopsis Researchers: Bioinformatics and Quantitative Biology.

Friesner J, Assmann SM, Bastow R, Bailey-Serres J, Beynon J, Brendel V, Buell CR, Bucksch A, Busch W, Demura T, Dinneny JR, Doherty CJ, Eveland AL, Falter-Braun P, Gehan MA, Gonzales M, Grotewold E, Gutierrez R, Kramer U, Krouk G, Ma S, Markelz RJC, Megraw M, Meyers BC, Murray JAH, Provart NJ, Rhee S, Smith R, Spalding EP, Taylor C, Teal TK, Torii KU, Town C, Vaughn M, Vierstra R, Ware D, Wilkins O, Williams C, Brady SM.

Plant Physiol. 2017 Dec;175(4):1499-1509. doi: 10.1104/pp.17.01490. No abstract available.

PMID:
29208732
4.

ePlant: Visualizing and Exploring Multiple Levels of Data for Hypothesis Generation in Plant Biology.

Waese J, Fan J, Pasha A, Yu H, Fucile G, Shi R, Cumming M, Kelley LA, Sternberg MJ, Krishnakumar V, Ferlanti E, Miller J, Town C, Stuerzlinger W, Provart NJ.

Plant Cell. 2017 Aug;29(8):1806-1821. doi: 10.1105/tpc.17.00073. Epub 2017 Aug 14.

5.

Topo-phylogeny: Visualizing evolutionary relationships on a topographic landscape.

Waese J, Provart NJ, Guttman DS.

PLoS One. 2017 May 1;12(5):e0175895. doi: 10.1371/journal.pone.0175895. eCollection 2017.

6.

ccNET: Database of co-expression networks with functional modules for diploid and polyploid Gossypium.

You Q, Xu W, Zhang K, Zhang L, Yi X, Yao D, Wang C, Zhang X, Zhao X, Provart NJ, Li F, Su Z.

Nucleic Acids Res. 2017 Jan 4;45(D1):D1090-D1099. doi: 10.1093/nar/gkw910. Epub 2016 Oct 7.

7.

The Bio-Analytic Resource for Plant Biology.

Waese J, Provart NJ.

Methods Mol Biol. 2017;1533:119-148.

PMID:
27987167
8.

Gene Slider: sequence logo interactive data-visualization for education and research.

Waese J, Pasha A, Wang TT, van Weringh A, Guttman DS, Provart NJ.

Bioinformatics. 2016 Dec 1;32(23):3670-3672. Epub 2016 Aug 13.

PMID:
27522081
9.

The developmental transcriptome atlas of the biofuel crop Camelina sativa.

Kagale S, Nixon J, Khedikar Y, Pasha A, Provart NJ, Clarke WE, Bollina V, Robinson SJ, Coutu C, Hegedus DD, Sharpe AG, Parkin IA.

Plant J. 2016 Dec;88(5):879-894. doi: 10.1111/tpj.13302.

10.

New BAR tools for mining expression data and exploring Cis-elements in Arabidopsis thaliana.

Austin RS, Hiu S, Waese J, Ierullo M, Pasha A, Wang TT, Fan J, Foong C, Breit R, Desveaux D, Moses A, Provart NJ.

Plant J. 2016 Nov;88(3):490-504. doi: 10.1111/tpj.13261. Epub 2016 Oct 5.

11.

A Human "eFP" Browser for Generating Gene Expression Anatograms.

Patel RV, Hamanishi ET, Provart NJ.

PLoS One. 2016 Mar 8;11(3):e0150982. doi: 10.1371/journal.pone.0150982. eCollection 2016.

12.

ccNET: Database of co-expression networks with functional modules for diploid and polyploid Gossypium.

You Q, Xu W, Zhang K, Zhang L, Yi X, Yao D, Wang C, Zhang X, Zhao X, Provart NJ, Li F, Su Z.

Nucleic Acids Res. 2017 May 19;45(9):5625-5626. doi: 10.1093/nar/gkw1342. No abstract available.

13.

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. 2016 Feb;209(3):921-44. doi: 10.1111/nph.13687. Epub 2015 Oct 14. Review.

14.

Inference of Longevity-Related Genes from a Robust Coexpression Network of Seed Maturation Identifies Regulators Linking Seed Storability to Biotic Defense-Related Pathways.

Righetti K, Vu JL, Pelletier S, Vu BL, Glaab E, Lalanne D, Pasha A, Patel RV, Provart NJ, Verdier J, Leprince O, Buitink J.

Plant Cell. 2015 Oct;27(10):2692-708. doi: 10.1105/tpc.15.00632. Epub 2015 Sep 26.

15.

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 Nov;32(11):1158-65. doi: 10.1038/nbt.3019. Epub 2014 Oct 12.

PMID:
25306245
16.

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 Apr 14;9(4):e94808. doi: 10.1371/journal.pone.0094808. eCollection 2014.

17.

Bioinformatic tools in Arabidopsis research.

de Lucas M, Provart NJ, Brady SM.

Methods Mol Biol. 2014;1062:97-136. doi: 10.1007/978-1-62703-580-4_5.

PMID:
24057362
18.

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 Aug 28;14:578. doi: 10.1186/1471-2164-14-578.

19.

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. doi: 10.1111/tpj.12206. Epub 2013 May 11.

20.

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. doi: 10.1111/tpj.12085.

21.

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. doi: 10.1111/j.1365-313X.2012.05055.x. Epub 2012 Jul 12.

22.

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 Feb 20;10:8. doi: 10.1186/1741-7007-10-8.

23.

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 Jan 27;12:15. doi: 10.1186/1471-2229-12-15.

24.

A predicted protein interactome for rice.

Ho CL, Wu Y, Shen HB, Provart NJ, Geisler M.

Rice (N Y). 2012 Jul 2;5(1):15. doi: 10.1186/1939-8433-5-15.

25.

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. doi: 10.1371/journal.pone.0029123. Epub 2011 Dec 14.

26.

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. doi: 10.1093/nar/gkr1099. Epub 2011 Dec 1.

27.

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. doi: 10.1111/j.1365-3040.2011.02448.x. Epub 2011 Nov 23.

28.

Seed bioinformatics.

Bassel GW, Holdsworth MJ, Provart NJ.

Methods Mol Biol. 2011;773:403-19. doi: 10.1007/978-1-61779-231-1_23.

PMID:
21898268
29.

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. doi: 10.1093/mp/ssr040. Epub 2011 Jun 7.

30.

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 7;108(23):9709-14. doi: 10.1073/pnas.1100958108. Epub 2011 May 18.

31.

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. doi: 10.1111/j.1365-313X.2011.04619.x. Epub 2011 Jul 18.

32.

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 15;27(6):877-8. doi: 10.1093/bioinformatics/btr023. Epub 2011 Jan 19.

PMID:
21252074
33.

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 Jan 10;6(1):e15237. doi: 10.1371/journal.pone.0015237.

34.

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. doi: 10.1104/pp.109.148031. Epub 2009 Dec 18.

35.

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. doi: 10.1111/j.1365-3040.2009.02040.x. Epub 2009 Aug 27. Review.

36.

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. doi: 10.1111/j.1364-3703.2009.00557.x.

PMID:
19694953
37.

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. doi: 10.1111/j.1365-313X.2009.03993.x. Epub 2009 Aug 8.

38.

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 22;324(5930):1068-71. doi: 10.1126/science.1173041. Epub 2009 Apr 30.

39.

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

Brady SM, Provart NJ.

Plant Cell. 2009 Apr;21(4):1034-51. doi: 10.1105/tpc.109.066050. Epub 2009 Apr 28. Review.

40.

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. doi: 10.1104/pp.108.132795. Epub 2008 Dec 17.

41.

Gene expression analyses for elucidating mechanisms of hormonal action in plants.

Bassel GW, Provart NJ.

Methods Mol Biol. 2009;495:21-37. doi: 10.1007/978-1-59745-477-3_3.

PMID:
19085149
42.

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 Apr 23;8:47. doi: 10.1186/1471-2229-8-47.

43.

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. doi: 10.1104/pp.107.110841. Epub 2008 Mar 21.

44.
45.

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 Aug 8;2(8):e718.

46.

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. Epub 2007 Aug 3.

48.

Functional annotation of the Arabidopsis P450 superfamily based on large-scale co-expression analysis.

Ehlting J, Provart NJ, Werck-Reichhart D.

Biochem Soc Trans. 2006 Dec;34(Pt 6):1192-8.

PMID:
17073783
49.
50.

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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