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Items: 28

1.

Neoproterozoic origin and multiple transitions to macroscopic growth in green seaweeds.

Del Cortona A, Jackson CJ, Bucchini F, Van Bel M, D'hondt S, Škaloud P, Delwiche CF, Knoll AH, Raven JA, Verbruggen H, Vandepoele K, De Clerck O, Leliaert F.

Proc Natl Acad Sci U S A. 2020 Jan 7. pii: 201910060. doi: 10.1073/pnas.1910060117. [Epub ahead of print]

PMID:
31911467
2.

Comparative transcriptomics enables the identification of functional orthologous genes involved in early leaf growth.

Vercruysse J, Van Bel M, Osuna-Cruz CM, Kulkarni SR, Storme V, Nelissen H, Gonzalez N, Inzé D, Vandepoele K.

Plant Biotechnol J. 2020 Feb;18(2):553-567. doi: 10.1111/pbi.13223. Epub 2019 Aug 12.

3.

Capturing the phosphorylation and protein interaction landscape of the plant TOR kinase.

Van Leene J, Han C, Gadeyne A, Eeckhout D, Matthijs C, Cannoot B, De Winne N, Persiau G, Van De Slijke E, Van de Cotte B, Stes E, Van Bel M, Storme V, Impens F, Gevaert K, Vandepoele K, De Smet I, De Jaeger G.

Nat Plants. 2019 Mar;5(3):316-327. doi: 10.1038/s41477-019-0378-z. Epub 2019 Mar 4.

PMID:
30833711
4.

Gene space completeness in complex plant genomes.

Van Bel M, Bucchini F, Vandepoele K.

Curr Opin Plant Biol. 2019 Apr;48:9-17. doi: 10.1016/j.pbi.2019.01.001. Epub 2019 Feb 21. Review.

PMID:
30797187
5.

Insights into the Evolution of Multicellularity from the Sea Lettuce Genome.

De Clerck O, Kao SM, Bogaert KA, Blomme J, Foflonker F, Kwantes M, Vancaester E, Vanderstraeten L, Aydogdu E, Boesger J, Califano G, Charrier B, Clewes R, Del Cortona A, D'Hondt S, Fernandez-Pozo N, Gachon CM, Hanikenne M, Lattermann L, Leliaert F, Liu X, Maggs CA, Popper ZA, Raven JA, Van Bel M, Wilhelmsson PKI, Bhattacharya D, Coates JC, Rensing SA, Van Der Straeten D, Vardi A, Sterck L, Vandepoele K, Van de Peer Y, Wichard T, Bothwell JH.

Curr Biol. 2018 Sep 24;28(18):2921-2933.e5. doi: 10.1016/j.cub.2018.08.015. Epub 2018 Sep 13.

6.

The Physcomitrella patens chromosome-scale assembly reveals moss genome structure and evolution.

Lang D, Ullrich KK, Murat F, Fuchs J, Jenkins J, Haas FB, Piednoel M, Gundlach H, Van Bel M, Meyberg R, Vives C, Morata J, Symeonidi A, Hiss M, Muchero W, Kamisugi Y, Saleh O, Blanc G, Decker EL, van Gessel N, Grimwood J, Hayes RD, Graham SW, Gunter LE, McDaniel SF, Hoernstein SNW, Larsson A, Li FW, Perroud PF, Phillips J, Ranjan P, Rokshar DS, Rothfels CJ, Schneider L, Shu S, Stevenson DW, Thümmler F, Tillich M, Villarreal Aguilar JC, Widiez T, Wong GK, Wymore A, Zhang Y, Zimmer AD, Quatrano RS, Mayer KFX, Goodstein D, Casacuberta JM, Vandepoele K, Reski R, Cuming AC, Tuskan GA, Maumus F, Salse J, Schmutz J, Rensing SA.

Plant J. 2018 Feb;93(3):515-533. doi: 10.1111/tpj.13801.

7.

PLAZA 4.0: an integrative resource for functional, evolutionary and comparative plant genomics.

Van Bel M, Diels T, Vancaester E, Kreft L, Botzki A, Van de Peer Y, Coppens F, Vandepoele K.

Nucleic Acids Res. 2018 Jan 4;46(D1):D1190-D1196. doi: 10.1093/nar/gkx1002.

8.

Reciprocally Retained Genes in the Angiosperm Lineage Show the Hallmarks of Dosage Balance Sensitivity.

Tasdighian S, Van Bel M, Li Z, Van de Peer Y, Carretero-Paulet L, Maere S.

Plant Cell. 2017 Nov;29(11):2766-2785. doi: 10.1105/tpc.17.00313. Epub 2017 Oct 23.

9.

Plant-RRBS, a bisulfite and next-generation sequencing-based methylome profiling method enriching for coverage of cytosine positions.

Schmidt M, Van Bel M, Woloszynska M, Slabbinck B, Martens C, De Block M, Coppens F, Van Lijsebettens M.

BMC Plant Biol. 2017 Jul 6;17(1):115. doi: 10.1186/s12870-017-1070-y.

10.

PhyD3: a phylogenetic tree viewer with extended phyloXML support for functional genomics data visualization.

Kreft L, Botzki A, Coppens F, Vandepoele K, Van Bel M.

Bioinformatics. 2017 Sep 15;33(18):2946-2947. doi: 10.1093/bioinformatics/btx324.

PMID:
28525531
11.

Proteome Profiling of Wheat Shoots from Different Cultivars.

Vu LD, Verstraeten I, Stes E, Van Bel M, Coppens F, Gevaert K, De Smet I.

Front Plant Sci. 2017 Mar 13;8:332. doi: 10.3389/fpls.2017.00332. eCollection 2017.

12.

Exploring Plant Co-Expression and Gene-Gene Interactions with CORNET 3.0.

Van Bel M, Coppens F.

Methods Mol Biol. 2017;1533:201-212.

PMID:
27987172
13.

Up-to-Date Workflow for Plant (Phospho)proteomics Identifies Differential Drought-Responsive Phosphorylation Events in Maize Leaves.

Vu LD, Stes E, Van Bel M, Nelissen H, Maddelein D, Inzé D, Coppens F, Martens L, Gevaert K, De Smet I.

J Proteome Res. 2016 Dec 2;15(12):4304-4317. Epub 2016 Oct 4.

PMID:
27643528
14.

A Collection of Conserved Noncoding Sequences to Study Gene Regulation in Flowering Plants.

Van de Velde J, Van Bel M, Vaneechoutte D, Vandepoele K.

Plant Physiol. 2016 Aug;171(4):2586-98. doi: 10.1104/pp.16.00821. Epub 2016 Jun 3.

15.

PP2A-3 interacts with ACR4 and regulates formative cell division in the Arabidopsis root.

Yue K, Sandal P, Williams EL, Murphy E, Stes E, Nikonorova N, Ramakrishna P, Czyzewicz N, Montero-Morales L, Kumpf R, Lin Z, van de Cotte B, Iqbal M, Van Bel M, Van De Slijke E, Meyer MR, Gadeyne A, Zipfel C, De Jaeger G, Van Montagu M, Van Damme D, Gevaert K, Rao AG, Beeckman T, De Smet I.

Proc Natl Acad Sci U S A. 2016 Feb 2;113(5):1447-52. doi: 10.1073/pnas.1525122113. Epub 2016 Jan 20.

16.

It's Time for Some "Site"-Seeing: Novel Tools to Monitor the Ubiquitin Landscape in Arabidopsis thaliana.

Walton A, Stes E, Cybulski N, Van Bel M, Iñigo S, Durand AN, Timmerman E, Heyman J, Pauwels L, De Veylder L, Goossens A, De Smet I, Coppens F, Goormachtig S, Gevaert K.

Plant Cell. 2016 Jan;28(1):6-16. doi: 10.1105/tpc.15.00878. Epub 2016 Jan 7. Review.

17.

A Conserved Core of Programmed Cell Death Indicator Genes Discriminates Developmentally and Environmentally Induced Programmed Cell Death in Plants.

Olvera-Carrillo Y, Van Bel M, Van Hautegem T, Fendrych M, Huysmans M, Simaskova M, van Durme M, Buscaill P, Rivas S, Coll NS, Coppens F, Maere S, Nowack MK.

Plant Physiol. 2015 Dec;169(4):2684-99. doi: 10.1104/pp.15.00769. Epub 2015 Oct 5.

18.

BLSSpeller: exhaustive comparative discovery of conserved cis-regulatory elements.

De Witte D, Van de Velde J, Decap D, Van Bel M, Audenaert P, Demeester P, Dhoedt B, Vandepoele K, Fostier J.

Bioinformatics. 2015 Dec 1;31(23):3758-66. doi: 10.1093/bioinformatics/btv466. Epub 2015 Aug 8.

19.

Dynamic Changes in ANGUSTIFOLIA3 Complex Composition Reveal a Growth Regulatory Mechanism in the Maize Leaf.

Nelissen H, Eeckhout D, Demuynck K, Persiau G, Walton A, van Bel M, Vervoort M, Candaele J, De Block J, Aesaert S, Van Lijsebettens M, Goormachtig S, Vandepoele K, Van Leene J, Muszynski M, Gevaert K, Inzé D, De Jaeger G.

Plant Cell. 2015 Jun;27(6):1605-19. doi: 10.1105/tpc.15.00269. Epub 2015 Jun 2.

20.

Drought tolerance conferred to sugarcane by association with Gluconacetobacter diazotrophicus: a transcriptomic view of hormone pathways.

Vargas L, Santa Brígida AB, Mota Filho JP, de Carvalho TG, Rojas CA, Vaneechoutte D, Van Bel M, Farrinelli L, Ferreira PC, Vandepoele K, Hemerly AS.

PLoS One. 2014 Dec 9;9(12):e114744. doi: 10.1371/journal.pone.0114744. eCollection 2014.

21.

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.

22.

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.

23.

pico-PLAZA, a genome database of microbial photosynthetic eukaryotes.

Vandepoele K, Van Bel M, Richard G, Van Landeghem S, Verhelst B, Moreau H, Van de Peer Y, Grimsley N, Piganeau G.

Environ Microbiol. 2013 Aug;15(8):2147-53. doi: 10.1111/1462-2920.12174. Epub 2013 Jul 4.

PMID:
23826978
24.

Gene functionalities and genome structure in Bathycoccus prasinos reflect cellular specializations at the base of the green lineage.

Moreau H, Verhelst B, Couloux A, Derelle E, Rombauts S, Grimsley N, Van Bel M, Poulain J, Katinka M, Hohmann-Marriott MF, Piganeau G, Rouzé P, Da Silva C, Wincker P, Van de Peer Y, Vandepoele K.

Genome Biol. 2012 Aug 24;13(8):R74. doi: 10.1186/gb-2012-13-8-r74.

25.

Comparative co-expression analysis in plant biology.

Movahedi S, Van Bel M, Heyndrickx KS, Vandepoele K.

Plant Cell Environ. 2012 Oct;35(10):1787-98. doi: 10.1111/j.1365-3040.2012.02517.x. Epub 2012 May 10. Review.

26.

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.

27.

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.

28.

FunSiP: a modular and extensible classifier for the prediction of functional sites in DNA.

Van Bel M, Saeys Y, Van de Peer Y.

Bioinformatics. 2008 Jul 1;24(13):1532-3. doi: 10.1093/bioinformatics/btn225. Epub 2008 May 12.

PMID:
18474505

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