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Items: 32

1.

Appropriate thiamin pyrophosphate levels are required for acclimation to changes in photoperiod.

Rosado-Souza L, Proost S, Moulin M, Bergmann S, Bocobza S, Aharoni A, Fitzpatrick TB, Mutwil M, Fernie AR, Obata T.

Plant Physiol. 2019 Mar 5. pii: pp.01346.2018. doi: 10.1104/pp.18.01346. [Epub ahead of print]

2.

Correction to: Transcriptomics of manually isolated Amborella trichopoda egg apparatus cells.

Flores-Tornero M, Proost S, Mutwil M, Scutt CP, Dresselhaus T, Sprunck S.

Plant Reprod. 2019 Feb 25. doi: 10.1007/s00497-019-00367-8. [Epub ahead of print]

PMID:
30805714
3.

Kingdom-wide comparison reveals the evolution of diurnal gene expression in Archaeplastida.

Ferrari C, Proost S, Janowski M, Becker J, Nikoloski Z, Bhattacharya D, Price D, Tohge T, Bar-Even A, Fernie A, Stitt M, Mutwil M.

Nat Commun. 2019 Feb 13;10(1):737. doi: 10.1038/s41467-019-08703-2.

4.

Transcriptomics of manually isolated Amborella trichopoda egg apparatus cells.

Flores-Tornero M, Proost S, Mutwil M, Scutt CP, Dresselhaus T, Sprunck S.

Plant Reprod. 2019 Mar;32(1):15-27. doi: 10.1007/s00497-019-00361-0. Epub 2019 Feb 1. Erratum in: Plant Reprod. 2019 Feb 25;:.

PMID:
30707279
5.

Multi-tissue integration of transcriptomic and specialized metabolite profiling provides tools for assessing the common bean (Phaseolus vulgaris) metabolome.

Perez de Souza L, Scossa F, Proost S, Bitocchi E, Papa R, Tohge T, Fernie AR.

Plant J. 2018 Nov 27. doi: 10.1111/tpj.14178. [Epub ahead of print]

PMID:
30480348
6.

AtRsgA from Arabidopsis thaliana is important for maturation of the small subunit of the chloroplast ribosome.

Janowski M, Zoschke R, Scharff LB, Martinez Jaime S, Ferrari C, Proost S, Ng Wei Xiong J, Omranian N, Musialak-Lange M, Nikoloski Z, Graf A, Schöttler MA, Sampathkumar A, Vaid N, Mutwil M.

Plant J. 2018 Oct;96(2):404-420. doi: 10.1111/tpj.14040. Epub 2018 Sep 8.

PMID:
30044525
7.

CoNekT: an open-source framework for comparative genomic and transcriptomic network analyses.

Proost S, Mutwil M.

Nucleic Acids Res. 2018 Jul 2;46(W1):W133-W140. doi: 10.1093/nar/gky336.

8.

PhytoNet: comparative co-expression network analyses across phytoplankton and land plants.

Ferrari C, Proost S, Ruprecht C, Mutwil M.

Nucleic Acids Res. 2018 Jul 2;46(W1):W76-W83. doi: 10.1093/nar/gky298.

9.

LSTrAP: efficiently combining RNA sequencing data into co-expression networks.

Proost S, Krawczyk A, Mutwil M.

BMC Bioinformatics. 2017 Oct 10;18(1):444. doi: 10.1186/s12859-017-1861-z.

10.

Expression atlas and comparative coexpression network analyses reveal important genes involved in the formation of lignified cell wall in Brachypodium distachyon.

Sibout R, Proost S, Hansen BO, Vaid N, Giorgi FM, Ho-Yue-Kuang S, Legée F, Cézart L, Bouchabké-Coussa O, Soulhat C, Provart N, Pasha A, Le Bris P, Roujol D, Hofte H, Jamet E, Lapierre C, Persson S, Mutwil M.

New Phytol. 2017 Aug;215(3):1009-1025. doi: 10.1111/nph.14635. Epub 2017 Jun 15.

11.

Phylogenomic analysis of gene co-expression networks reveals the evolution of functional modules.

Ruprecht C, Proost S, Hernandez-Coronado M, Ortiz-Ramirez C, Lang D, Rensing SA, Becker JD, Vandepoele K, Mutwil M.

Plant J. 2017 May;90(3):447-465. doi: 10.1111/tpj.13502. Epub 2017 Mar 23.

12.

Beyond Genomics: Studying Evolution with Gene Coexpression Networks.

Ruprecht C, Vaid N, Proost S, Persson S, Mutwil M.

Trends Plant Sci. 2017 Apr;22(4):298-307. doi: 10.1016/j.tplants.2016.12.011. Epub 2017 Jan 23. Review.

PMID:
28126286
13.

PlaNet: Comparative Co-Expression Network Analyses for Plants.

Proost S, Mutwil M.

Methods Mol Biol. 2017;1533:213-227.

PMID:
27987173
14.

Novel allelic variants in ACD6 cause hybrid necrosis in local collection of Arabidopsis thaliana.

Świadek M, Proost S, Sieh D, Yu J, Todesco M, Jorzig C, Rodriguez Cubillos AE, Plötner B, Nikoloski Z, Chae E, Giavalisco P, Fischer A, Schröder F, Kim ST, Weigel D, Laitinen RA.

New Phytol. 2017 Jan;213(2):900-915. doi: 10.1111/nph.14155. Epub 2016 Sep 2.

15.

Tools of the trade: studying molecular networks in plants.

Proost S, Mutwil M.

Curr Opin Plant Biol. 2016 Apr;30:143-50. doi: 10.1016/j.pbi.2016.02.010. Epub 2016 Mar 15. Review.

PMID:
26990519
16.

Corrigendum: The genome sequence of the orchid Phalaenopsis equestris.

Cai J, Liu X, Vanneste K, Proost S, Tsai WC, Liu KW, Chen LJ, He Y, Xu Q, Bian C, Zheng Z, Sun F, Liu W, Hsiao YY, Pan ZJ, Hsu CC, Yang YP, Hsu YC, Chuang YC, Dievart A, Dufayard JF, Xu X, Wang JY, Wang J, Xiao XJ, Zhao XM, Du R, Zhang GQ, Wang M, Su YY, Xie GC, Liu GH, Li LQ, Huang LQ, Luo YB, Chen HH, Van de Peer Y, Liu ZJ.

Nat Genet. 2015 Mar;47(3):304. doi: 10.1038/ng0315-304a. No abstract available.

PMID:
25711871
17.

Growth-Regulating Factors (GRFs): A Small Transcription Factor Family with Important Functions in Plant Biology.

Omidbakhshfard MA, Proost S, Fujikura U, Mueller-Roeber B.

Mol Plant. 2015 Jul;8(7):998-1010. doi: 10.1016/j.molp.2015.01.013. Epub 2015 Jan 22. Review.

18.

The genome sequence of the orchid Phalaenopsis equestris.

Cai J, Liu X, Vanneste K, Proost S, Tsai WC, Liu KW, Chen LJ, He Y, Xu Q, Bian C, Zheng Z, Sun F, Liu W, Hsiao YY, Pan ZJ, Hsu CC, Yang YP, Hsu YC, Chuang YC, Dievart A, Dufayard JF, Xu X, Wang JY, Wang J, Xiao XJ, Zhao XM, Du R, Zhang GQ, Wang M, Su YY, Xie GC, Liu GH, Li LQ, Huang LQ, Luo YB, Chen HH, Van de Peer Y, Liu ZJ.

Nat Genet. 2015 Jan;47(1):65-72. doi: 10.1038/ng.3149. Epub 2014 Nov 24. Erratum in: Nat Genet. 2015 Mar;47(3):304.

PMID:
25420146
19.

PLAZA 3.0: an access point for plant comparative genomics.

Proost S, Van Bel M, Vaneechoutte D, Van de Peer Y, Inzé D, Mueller-Roeber B, Vandepoele K.

Nucleic Acids Res. 2015 Jan;43(Database issue):D974-81. doi: 10.1093/nar/gku986. Epub 2014 Oct 16.

20.

Reversal of senescence by N resupply to N-starved Arabidopsis thaliana: transcriptomic and metabolomic consequences.

Balazadeh S, Schildhauer J, Araújo WL, Munné-Bosch S, Fernie AR, Proost S, Humbeck K, Mueller-Roeber B.

J Exp Bot. 2014 Jul;65(14):3975-92. doi: 10.1093/jxb/eru119. Epub 2014 Apr 1.

21.

TRAPID: an efficient online tool for the functional and comparative analysis of de novo RNA-Seq transcriptomes.

Van Bel M, Proost S, Van Neste C, Deforce D, Van de Peer Y, Vandepoele K.

Genome Biol. 2013 Dec 13;14(12):R134. doi: 10.1186/gb-2013-14-12-r134.

22.

FLOWERING LOCUS C in monocots and the tandem origin of angiosperm-specific MADS-box genes.

Ruelens P, de Maagd RA, Proost S, Theißen G, Geuten K, Kaufmann K.

Nat Commun. 2013;4:2280. doi: 10.1038/ncomms3280.

PMID:
23955420
23.

Gamma paleohexaploidy in the stem lineage of core eudicots: significance for MADS-box gene and species diversification.

Vekemans D, Proost S, Vanneste K, Coenen H, Viaene T, Ruelens P, Maere S, Van de Peer Y, Geuten K.

Mol Biol Evol. 2012 Dec;29(12):3793-806. doi: 10.1093/molbev/mss183. Epub 2012 Jul 20.

PMID:
22821009
24.

Dissecting plant genomes with the PLAZA comparative genomics platform.

Van Bel M, Proost S, Wischnitzki E, Movahedi S, Scheerlinck C, Van de Peer Y, Vandepoele K.

Plant Physiol. 2012 Feb;158(2):590-600. doi: 10.1104/pp.111.189514. Epub 2011 Dec 23.

25.

i-ADHoRe 3.0--fast and sensitive detection of genomic homology in extremely large data sets.

Proost S, Fostier J, De Witte D, Dhoedt B, Demeester P, Van de Peer Y, Vandepoele K.

Nucleic Acids Res. 2012 Jan;40(2):e11. doi: 10.1093/nar/gkr955. Epub 2011 Nov 18.

26.

The Medicago genome provides insight into the evolution of rhizobial symbioses.

Young ND, Debellé F, Oldroyd GE, Geurts R, Cannon SB, Udvardi MK, Benedito VA, Mayer KF, Gouzy J, Schoof H, Van de Peer Y, Proost S, Cook DR, Meyers BC, Spannagl M, Cheung F, De Mita S, Krishnakumar V, Gundlach H, Zhou S, Mudge J, Bharti AK, Murray JD, Naoumkina MA, Rosen B, Silverstein KA, Tang H, Rombauts S, Zhao PX, Zhou P, Barbe V, Bardou P, Bechner M, Bellec A, Berger A, Bergès H, Bidwell S, Bisseling T, Choisne N, Couloux A, Denny R, Deshpande S, Dai X, Doyle JJ, Dudez AM, Farmer AD, Fouteau S, Franken C, Gibelin C, Gish J, Goldstein S, González AJ, Green PJ, Hallab A, Hartog M, Hua A, Humphray SJ, Jeong DH, Jing Y, Jöcker A, Kenton SM, Kim DJ, Klee K, Lai H, Lang C, Lin S, Macmil SL, Magdelenat G, Matthews L, McCorrison J, Monaghan EL, Mun JH, Najar FZ, Nicholson C, Noirot C, O'Bleness M, Paule CR, Poulain J, Prion F, Qin B, Qu C, Retzel EF, Riddle C, Sallet E, Samain S, Samson N, Sanders I, Saurat O, Scarpelli C, Schiex T, Segurens B, Severin AJ, Sherrier DJ, Shi R, Sims S, Singer SR, Sinharoy S, Sterck L, Viollet A, Wang BB, Wang K, Wang M, Wang X, Warfsmann J, Weissenbach J, White DD, White JD, Wiley GB, Wincker P, Xing Y, Yang L, Yao Z, Ying F, Zhai J, Zhou L, Zuber A, Dénarié J, Dixon RA, May GD, Schwartz DC, Rogers J, Quétier F, Town CD, Roe BA.

Nature. 2011 Nov 16;480(7378):520-4. doi: 10.1038/nature10625.

27.

Journey through the past: 150 million years of plant genome evolution.

Proost S, Pattyn P, Gerats T, Van de Peer Y.

Plant J. 2011 Apr;66(1):58-65. doi: 10.1111/j.1365-313X.2011.04521.x.

28.

A greedy, graph-based algorithm for the alignment of multiple homologous gene lists.

Fostier J, Proost S, Dhoedt B, Saeys Y, Demeester P, Van de Peer Y, Vandepoele K.

Bioinformatics. 2011 Mar 15;27(6):749-56. doi: 10.1093/bioinformatics/btr008. Epub 2011 Jan 6.

PMID:
21216775
29.

The genome of the domesticated apple (Malus × domestica Borkh.).

Velasco R, Zharkikh A, Affourtit J, Dhingra A, Cestaro A, Kalyanaraman A, Fontana P, Bhatnagar SK, Troggio M, Pruss D, Salvi S, Pindo M, Baldi P, Castelletti S, Cavaiuolo M, Coppola G, Costa F, Cova V, Dal Ri A, Goremykin V, Komjanc M, Longhi S, Magnago P, Malacarne G, Malnoy M, Micheletti D, Moretto M, Perazzolli M, Si-Ammour A, Vezzulli S, Zini E, Eldredge G, Fitzgerald LM, Gutin N, Lanchbury J, Macalma T, Mitchell JT, Reid J, Wardell B, Kodira C, Chen Z, Desany B, Niazi F, Palmer M, Koepke T, Jiwan D, Schaeffer S, Krishnan V, Wu C, Chu VT, King ST, Vick J, Tao Q, Mraz A, Stormo A, Stormo K, Bogden R, Ederle D, Stella A, Vecchietti A, Kater MM, Masiero S, Lasserre P, Lespinasse Y, Allan AC, Bus V, Chagné D, Crowhurst RN, Gleave AP, Lavezzo E, Fawcett JA, Proost S, Rouzé P, Sterck L, Toppo S, Lazzari B, Hellens RP, Durel CE, Gutin A, Bumgarner RE, Gardiner SE, Skolnick M, Egholm M, Van de Peer Y, Salamini F, Viola R.

Nat Genet. 2010 Oct;42(10):833-9. doi: 10.1038/ng.654. Epub 2010 Aug 29.

PMID:
20802477
30.

PLAZA: a comparative genomics resource to study gene and genome evolution in plants.

Proost S, Van Bel M, Sterck L, Billiau K, Van Parys T, Van de Peer Y, Vandepoele K.

Plant Cell. 2009 Dec;21(12):3718-31. doi: 10.1105/tpc.109.071506. Epub 2009 Dec 29.

31.

The flowering world: a tale of duplications.

Van de Peer Y, Fawcett JA, Proost S, Sterck L, Vandepoele K.

Trends Plant Sci. 2009 Dec;14(12):680-8. doi: 10.1016/j.tplants.2009.09.001. Epub 2009 Oct 7. Review.

PMID:
19818673
32.

Predicting protein-protein interactions in Arabidopsis thaliana through integration of orthology, gene ontology and co-expression.

De Bodt S, Proost S, Vandepoele K, Rouzé P, Van de Peer Y.

BMC Genomics. 2009 Jun 29;10:288. doi: 10.1186/1471-2164-10-288.

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