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Items: 1 to 50 of 134

1.

Inference of plant gene regulatory networks using data-driven methods: A practical overview.

Kulkarni SR, Vandepoele K.

Biochim Biophys Acta Gene Regul Mech. 2019 Oct 31:194447. doi: 10.1016/j.bbagrm.2019.194447. [Epub ahead of print] Review.

PMID:
31678628
2.

A new evolutionary model for the vertebrate actin family including two novel groups.

Witjes L, Van Troys M, Vandekerckhove J, Vandepoele K, Ampe C.

Mol Phylogenet Evol. 2019 Dec;141:106632. doi: 10.1016/j.ympev.2019.106632. Epub 2019 Sep 24.

PMID:
31560986
3.

Associated Bacteria Affect Sexual Reproduction by Altering Gene Expression and Metabolic Processes in a Biofilm Inhabiting Diatom.

Cirri E, De Decker S, Bilcke G, Werner M, Osuna-Cruz CM, De Veylder L, Vandepoele K, Werz O, Vyverman W, Pohnert G.

Front Microbiol. 2019 Aug 2;10:1790. doi: 10.3389/fmicb.2019.01790. eCollection 2019.

4.

TARP is an immunotherapeutic target in acute myeloid leukemia expressed in the leukemic stem cell compartment.

Depreter B, Weening KE, Vandepoele K, Essand M, De Moerloose B, Themeli M, Cloos J, Hanekamp D, Moors I, D' Hont I, Denys B, Uyttebroeck A, Van Damme A, Dedeken L, Snauwaert S, Goetgeluk G, De Munter S, Kerre T, Vandekerckhove B, Lammens T, Philippé J.

Haematologica. 2019 Aug 1. pii: haematol.2019.222612. doi: 10.3324/haematol.2019.222612. [Epub ahead of print]

5.

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. 2019 Jul 30. doi: 10.1111/pbi.13223. [Epub ahead of print]

6.

Enhanced Maps of Transcription Factor Binding Sites Improve Regulatory Networks Learned from Accessible Chromatin Data.

Kulkarni SR, Jones DM, Vandepoele K.

Plant Physiol. 2019 Oct;181(2):412-425. doi: 10.1104/pp.19.00605. Epub 2019 Jul 25.

7.

Neofunctionalization of Mitochondrial Proteins and Incorporation into Signaling Networks in Plants.

Lama S, Broda M, Abbas Z, Vaneechoutte D, Belt K, Säll T, Vandepoele K, Van Aken O.

Mol Biol Evol. 2019 May 1;36(5):974-989. doi: 10.1093/molbev/msz031.

8.

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
9.

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
10.

Clinical implications of measurable residual disease in AML: Review of current evidence.

Moors I, Vandepoele K, Philippé J, Deeren D, Selleslag D, Breems D, Straetmans N, Kerre T, Denys B.

Crit Rev Oncol Hematol. 2019 Jan;133:142-148. doi: 10.1016/j.critrevonc.2018.11.010. Epub 2018 Nov 24. Review.

PMID:
30661650
11.

Curse: building expression atlases and co-expression networks from public RNA-Seq data.

Vaneechoutte D, Vandepoele K.

Bioinformatics. 2019 Aug 15;35(16):2880-2881. doi: 10.1093/bioinformatics/bty1052.

PMID:
30590391
12.

A widespread alternative squalene epoxidase participates in eukaryote steroid biosynthesis.

Pollier J, Vancaester E, Kuzhiumparambil U, Vickers CE, Vandepoele K, Goossens A, Fabris M.

Nat Microbiol. 2019 Feb;4(2):226-233. doi: 10.1038/s41564-018-0305-5. Epub 2018 Nov 26.

PMID:
30478288
13.

Pinpointing a potential role for CLEC12B in cancer predisposition through familial exome sequencing.

Derpoorter C, Vandepoele K, Diez-Fraile A, Vandemeulebroecke K, De Wilde B, Speleman F, Van Roy N, Lammens T, Laureys G.

Pediatr Blood Cancer. 2019 Feb;66(2):e27513. doi: 10.1002/pbc.27513. Epub 2018 Oct 23.

PMID:
30350915
14.

Overcoming challenges in variant calling: exploring sequence diversity in candidate genes for plant development in perennial ryegrass (Lolium perenne).

Veeckman E, Van Glabeke S, Haegeman A, Muylle H, van Parijs FRD, Byrne SL, Asp T, Studer B, Rohde A, Roldán-Ruiz I, Vandepoele K, Ruttink T.

DNA Res. 2019 Feb 1;26(1):1-12. doi: 10.1093/dnares/dsy033.

15.

The NF1 hotspot in acute myeloid leukemia: what's in a name?

Vandepoele K, Van der Meulen J, Denys B.

Leukemia. 2018 Dec;32(12):2715. doi: 10.1038/s41375-018-0266-y. Epub 2018 Oct 1. No abstract available.

PMID:
30275525
16.

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.

17.

Genome Analyses of the Microalga Picochlorum Provide Insights into the Evolution of Thermotolerance in the Green Lineage.

Krasovec M, Vancaester E, Rombauts S, Bucchini F, Yau S, Hemon C, Lebredonchel H, Grimsley N, Moreau H, Sanchez-Brosseau S, Vandepoele K, Piganeau G.

Genome Biol Evol. 2018 Sep 1;10(9):2347-2365. doi: 10.1093/gbe/evy167.

18.

A case of chronic eosinophilic leukemia with secondary transformation to acute myeloid leukemia.

Hofmans M, Delie A, Vandepoele K, Van Roy N, Van der Meulen J, Philippé J, Moors I.

Leuk Res Rep. 2018 Apr 9;9:45-47. doi: 10.1016/j.lrr.2018.04.001. eCollection 2018.

19.

KIRA1 and ORESARA1 terminate flower receptivity by promoting cell death in the stigma of Arabidopsis.

Gao Z, Daneva A, Salanenka Y, Van Durme M, Huysmans M, Lin Z, De Winter F, Vanneste S, Karimi M, Van de Velde J, Vandepoele K, Van de Walle D, Dewettinck K, Lambrecht BN, Nowack MK.

Nat Plants. 2018 Jun;4(6):365-375. doi: 10.1038/s41477-018-0160-7. Epub 2018 May 28.

PMID:
29808023
20.

Understanding genetic control of root system architecture in soybean: Insights into the genetic basis of lateral root number.

Prince SJ, Valliyodan B, Ye H, Yang M, Tai S, Hu W, Murphy M, Durnell LA, Song L, Joshi T, Liu Y, Van de Velde J, Vandepoele K, Grover Shannon J, Nguyen HT.

Plant Cell Environ. 2019 Jan;42(1):212-229. doi: 10.1111/pce.13333. Epub 2018 Jun 15.

PMID:
29749073
21.

GSyellow, a Multifaceted Tag for Functional Protein Analysis in Monocot and Dicot Plants.

Besbrugge N, Van Leene J, Eeckhout D, Cannoot B, Kulkarni SR, De Winne N, Persiau G, Van De Slijke E, Bontinck M, Aesaert S, Impens F, Gevaert K, Van Damme D, Van Lijsebettens M, Inzé D, Vandepoele K, Nelissen H, De Jaeger G.

Plant Physiol. 2018 Jun;177(2):447-464. doi: 10.1104/pp.18.00175. Epub 2018 Apr 20.

22.

RNA-based FLT3-ITD allelic ratio is associated with outcome and ex vivo response to FLT3 inhibitors in pediatric AML.

Cucchi DGJ, Denys B, Kaspers GJL, Janssen JJWM, Ossenkoppele GJ, de Haas V, Zwaan CM, van den Heuvel-Eibrink MM, Philippé J, Csikós T, Kwidama Z, de Moerloose B, de Bont ESJM, Lissenberg-Witte BI, Zweegman S, Verwer F, Vandepoele K, Schuurhuis GJ, Sonneveld E, Cloos J.

Blood. 2018 May 31;131(22):2485-2489. doi: 10.1182/blood-2017-12-819508. Epub 2018 Apr 18.

PMID:
29669779
23.

Author Correction: 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, Bossche RV, De Clercq R, Eeckhout D, Ron M, Somers DE, Inzé D, Gevaert K, De Jaeger G, Vandepoele K, Pauwels L, Goossens A.

Nat Commun. 2018 Apr 10;9:16213. doi: 10.1038/ncomms16213.

24.

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. 2018 Apr 6;46(6):e31. doi: 10.1093/nar/gkx1279.

25.

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.

26.

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. 2018 Mar;217(4):1521-1534. doi: 10.1111/nph.14921. Epub 2017 Dec 4.

27.

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.

28.

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.

29.

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. Erratum in: Nucleic Acids Res. 2018 Jan 4;46(D1):D1284.

30.

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.

31.

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.

32.

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. 2018 Jul;94(4):565-575. doi: 10.1002/cyto.b.21593. Epub 2017 Nov 2. Review.

33.

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]

34.

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
35.

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.

36.

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
37.

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. Erratum in: Nat Commun. 2018 Apr 10;9:16213.

38.

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.

39.

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.

40.

A Guide to the PLAZA 3.0 Plant Comparative Genomic Database.

Vandepoele K.

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

PMID:
27987171
41.

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.

42.

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.

43.

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.

44.

Are We There Yet? Reliably Estimating the Completeness of Plant Genome Sequences.

Veeckman E, Ruttink T, Vandepoele K.

Plant Cell. 2016 Aug;28(8):1759-68. doi: 10.1105/tpc.16.00349. Epub 2016 Aug 10.

45.

The association between fructosamine-3 kinase 900C/G polymorphism, transferrin polymorphism and human herpesvirus-8 infection in diabetics living in South Kivu.

Cikomola JC, Vandepoele K, Katchunga PB, Kishabongo AS, Padalko EY, Speeckaert MM, Delanghe JR.

Acta Trop. 2016 Nov;163:14-9. doi: 10.1016/j.actatropica.2016.07.011. Epub 2016 Jul 25.

PMID:
27461879
46.

A novel approach for BCR-ABL1 standardization to improve International Scale estimation.

Maes B, Bakkus M, Boeckx N, Boone E, Cauwelier B, Denys B, De Schouwer P, Devos T, El Housni H, Hillen F, Jacobs K, Lambert F, Louagie H, Maes MB, Meeus P, Moreau E, Nollet F, Peeters K, Saussoy P, Van Lint P, Vaerman JL, Vaeyens F, Vandepoele K, Vannuffel P, Ver Elst K, Vermeulen K, Bruyndonckx R; Belgian working group on BCR-ABL1 IS standardization.

Int J Lab Hematol. 2016 Dec;38(6):674-684. doi: 10.1111/ijlh.12556. Epub 2016 Jul 27.

PMID:
27460189
47.

A simple colorimetric assay for measuring fructosamine 3 kinase activity.

Cikomola JC, Kishabongo AS, Vandepoele K, Mulder M, Katchunga PB, Laukens B, Schie LV, Grootaert H, Callewaert N, Speeckaert MM, Delanghe JR.

Clin Chem Lab Med. 2017 Jan 1;55(1):154-159. doi: 10.1515/cclm-2016-0441.

PMID:
27394048
48.

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.

49.

CoExpNetViz: Comparative Co-Expression Networks Construction and Visualization Tool.

Tzfadia O, Diels T, De Meyer S, Vandepoele K, Aharoni A, Van de Peer Y.

Front Plant Sci. 2016 Jan 5;6:1194. doi: 10.3389/fpls.2015.01194. eCollection 2015.

50.

The YPEL5-PPP1CB fusion transcript is detected in different hematological malignancies and in normal samples.

Vandepoele K, Philippé J, Denys B.

Leuk Res Rep. 2015 Aug 6;4(2):51-4. doi: 10.1016/j.lrr.2015.07.001. eCollection 2015.

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