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Items: 1 to 20 of 111

1.

TF2Network: predicting transcription factor regulators and gene regulatory networks in Arabidopsis using publicly available binding site information.

Kulkarni SR, Vaneechoutte D, Van de Velde J, Vandepoele K.

Nucleic Acids Res. 2017 Dec 20. doi: 10.1093/nar/gkx1279. [Epub ahead of print]

PMID:
29272447
2.

The P. 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 S, 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 A 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 J, Maumus F, Salse J, Schmutz J, Rensing SA.

Plant J. 2017 Dec 13. doi: 10.1111/tpj.13801. [Epub ahead of print]

PMID:
29237241
3.

Ensemble gene function prediction database reveals genes important for complex I formation in Arabidopsis thaliana.

Hansen BO, Meyer EH, Ferrari C, Vaid N, Movahedi S, Vandepoele K, Nikoloski Z, Mutwil M.

New Phytol. 2017 Dec 4. doi: 10.1111/nph.14921. [Epub ahead of print]

PMID:
29205376
4.

The Plastid Genome in Cladophorales Green Algae Is Encoded by Hairpin Chromosomes.

Del Cortona A, Leliaert F, Bogaert KA, Turmel M, Boedeker C, Janouškovec J, Lopez-Bautista JM, Verbruggen H, Vandepoele K, De Clerck O.

Curr Biol. 2017 Dec 18;27(24):3771-3782.e6. doi: 10.1016/j.cub.2017.11.004. Epub 2017 Nov 30.

PMID:
29199074
5.

JASPAR 2018: update of the open-access database of transcription factor binding profiles and its web framework.

Khan A, Fornes O, Stigliani A, Gheorghe M, Castro-Mondragon JA, van der Lee R, Bessy A, Chèneby J, Kulkarni SR, Tan G, Baranasic D, Arenillas DJ, Sandelin A, Vandepoele K, Lenhard B, Ballester B, Wasserman WW, Parcy F, Mathelier A.

Nucleic Acids Res. 2018 Jan 4;46(D1):D1284. doi: 10.1093/nar/gkx1188. No abstract available.

6.

JASPAR 2018: update of the open-access database of transcription factor binding profiles and its web framework.

Khan A, Fornes O, Stigliani A, Gheorghe M, Castro-Mondragon JA, van der Lee R, Bessy A, Chèneby J, Kulkarni SR, Tan G, Baranasic D, Arenillas DJ, Sandelin A, Vandepoele K, Lenhard B, Ballester B, Wasserman WW, Parcy F, Mathelier A.

Nucleic Acids Res. 2018 Jan 4;46(D1):D260-D266. doi: 10.1093/nar/gkx1126.

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.

Genome-wide characterization of differential transcript usage in Arabidopsis thaliana.

Vaneechoutte D, Estrada AR, Lin YC, Loraine AE, Vandepoele K.

Plant J. 2017 Dec;92(6):1218-1231. doi: 10.1111/tpj.13746. Epub 2017 Nov 20.

PMID:
29031026
9.

Cancer-related mRNA expression analysis using a novel flow cytometry-based assay.

Depreter B, Philippé J, Meul M, Denys B, Vandepoele K, De Moerloose B, Lammens T.

Cytometry B Clin Cytom. 2017 Oct 5. doi: 10.1002/cyto.b.21593. [Epub ahead of print] Review.

PMID:
28980766
10.

Gearing up to handle the mosaic nature of life in the quest for orthologs.

Forslund K, Pereira C, Capella-Gutierrez S, Sousa da Silva A, Altenhoff A, Huerta-Cepas J, Muffato M, Patricio M, Vandepoele K, Ebersberger I, Blake J, Fernández Breis JT; Quest for Orthologs Consortium, Boeckmann B, Gabaldón T, Sonnhammer E, Dessimoz C, Lewis S.

Bioinformatics. 2017 Aug 30. doi: 10.1093/bioinformatics/btx542. [Epub ahead of print]

PMID:
28968857
11.

Whole blood Fe isotopic signature in a sub-Saharan African population.

Cikomola JC, Flórez MR, Costas-Rodríguez M, Anoshkina Y, Vandepoele K, Katchunga PB, Kishabongo AS, Speeckaert MM, Vanhaecke F, Delanghe JR.

Metallomics. 2017 Aug 16;9(8):1142-1149. doi: 10.1039/c7mt00170c.

PMID:
28737806
12.

Evolutionary relationships and expression analysis of EUL domain proteins in rice (Oryza sativa).

De Schutter K, Tsaneva M, Kulkarni SR, Rougé P, Vandepoele K, Van Damme EJM.

Rice (N Y). 2017 Dec;10(1):26. doi: 10.1186/s12284-017-0164-3. Epub 2017 May 30.

13.

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
14.

The transcriptional repressor complex FRS7-FRS12 regulates flowering time and growth in Arabidopsis.

Ritter A, Iñigo S, Fernández-Calvo P, Heyndrickx KS, Dhondt S, Shi H, De Milde L, Vanden Bossche R, De Clercq R, Eeckhout D, Ron M, Somers DE, Inzé D, Gevaert K, De Jaeger G, Vandepoele K, Pauwels L, Goossens A.

Nat Commun. 2017 May 11;8:15235. doi: 10.1038/ncomms15235.

15.

The Transcription Factor MYB29 Is a Regulator of ALTERNATIVE OXIDASE1a.

Zhang X, Ivanova A, Vandepoele K, Radomiljac J, Van de Velde J, Berkowitz O, Willems P, Xu Y, Ng S, Van Aken O, Duncan O, Zhang B, Storme V, Chan KX, Vaneechoutte D, Pogson BJ, Van Breusegem F, Whelan J, De Clercq I.

Plant Physiol. 2017 Mar;173(3):1824-1843. doi: 10.1104/pp.16.01494. Epub 2017 Feb 6.

PMID:
28167700
16.

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.

PMID:
28161902
17.

A Guide to the PLAZA 3.0 Plant Comparative Genomic Database.

Vandepoele K.

Methods Mol Biol. 2017;1533:183-200.

PMID:
27987171
18.

The mutation nrpb1-A325V in the largest subunit of RNA polymerase II suppresses compromised growth of Arabidopsis plants deficient in a function of the general transcription factor IIF.

Babiychuk E, Hoang KT, Vandepoele K, Van De Slijke E, Geelen D, De Jaeger G, Obokata J, Kushnir S.

Plant J. 2017 Feb;89(4):730-745. doi: 10.1111/tpj.13417. Epub 2017 Feb 10.

PMID:
27862530
19.

Protocadherin-1 Localization and Cell-Adhesion Function in Airway Epithelial Cells in Asthma.

Faura Tellez G, Willemse BW, Brouwer U, Nijboer-Brinksma S, Vandepoele K, Noordhoek JA, Heijink I, de Vries M, Smithers NP, Postma DS, Timens W, Wiffen L, van Roy F, Holloway JW, Lackie PM, Nawijn MC, Koppelman GH.

PLoS One. 2016 Oct 4;11(10):e0163967. doi: 10.1371/journal.pone.0163967. eCollection 2016.

20.

Functional characterization of the Arabidopsis transcription factor bZIP29 reveals its role in leaf and root development.

Van Leene J, Blomme J, Kulkarni SR, Cannoot B, De Winne N, Eeckhout D, Persiau G, Van De Slijke E, Vercruysse L, Vanden Bossche R, Heyndrickx KS, Vanneste S, Goossens A, Gevaert K, Vandepoele K, Gonzalez N, Inzé D, De Jaeger G.

J Exp Bot. 2016 Oct;67(19):5825-5840. Epub 2016 Sep 22.

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