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Items: 1 to 50 of 82

1.

Targeted therapy in acute myeloid leukemia: current status and new insights from a proteomic perspective.

van Dijk AD, de Bont ESJM, Kornblau SM.

Expert Rev Proteomics. 2020 Jan 23:1-10. doi: 10.1080/14789450.2020.1717951. [Epub ahead of print]

PMID:
31945303
2.

Meiotic recombination profiling of interspecific hybrid F1 tomato pollen by linked read sequencing.

Rommel Fuentes R, Hesselink T, Nieuwenhuis R, Bakker L, Schijlen E, van Dooijeweert W, Diaz Trivino S, de Haan JR, Sanchez Perez G, Zhang X, Fransz P, de Jong H, van Dijk ADJ, de Ridder D, Peters SA.

Plant J. 2019 Dec 9. doi: 10.1111/tpj.14640. [Epub ahead of print]

PMID:
31820490
3.

Designing Eukaryotic Gene Expression Regulation Using Machine Learning.

de Jongh RPH, van Dijk ADJ, Julsing MK, Schaap PJ, de Ridder D.

Trends Biotechnol. 2020 Feb;38(2):191-201. doi: 10.1016/j.tibtech.2019.07.007. Epub 2019 Aug 17. Review.

PMID:
31431299
4.

Comprehensive phenotyping reveals interactions and functions of Arabidopsis thaliana TCP genes in yield determination.

van Es SW, van der Auweraert EB, Silveira SR, Angenent GC, van Dijk ADJ, Immink RGH.

Plant J. 2019 Jul;99(2):316-328. doi: 10.1111/tpj.14326. Epub 2019 Apr 29.

5.

An analysis of characterized plant sesquiterpene synthases.

Durairaj J, Di Girolamo A, Bouwmeester HJ, de Ridder D, Beekwilder J, van Dijk AD.

Phytochemistry. 2019 Feb;158:157-165. doi: 10.1016/j.phytochem.2018.10.020. Epub 2018 Nov 13.

PMID:
30446165
6.

Improved inference of intermolecular contacts through protein-protein interaction prediction using coevolutionary analysis.

Correa Marrero M, Immink RGH, de Ridder D, van Dijk ADJ.

Bioinformatics. 2019 Jun 1;35(12):2036-2042. doi: 10.1093/bioinformatics/bty924.

PMID:
30398547
7.

Comparative analysis of binding patterns of MADS-domain proteins in Arabidopsis thaliana.

Aerts N, de Bruijn S, van Mourik H, Angenent GC, van Dijk ADJ.

BMC Plant Biol. 2018 Jun 25;18(1):131. doi: 10.1186/s12870-018-1348-8.

8.

DNA sequence and shape are predictive for meiotic crossovers throughout the plant kingdom.

Demirci S, Peters SA, de Ridder D, van Dijk ADJ.

Plant J. 2018 May 29. doi: 10.1111/tpj.13979. [Epub ahead of print]

9.

Histone Modification Patterns Using RPPA-Based Profiling Predict Outcome in Acute Myeloid Leukemia Patients.

van Dijk AD, Hu CW, de Bont ESJM, Qiu Y, Hoff FW, Yoo SY, Coombes KR, Qutub AA, Kornblau SM.

Proteomics. 2018 Apr;18(8):e1700379. doi: 10.1002/pmic.201700379. Epub 2018 Apr 2.

PMID:
29505696
10.

Corrigendum: Towards recommendations for metadata and data handling in plant phenotyping.

Krajewski P, Chen D, Cwiek H, van Dijk ADJ, Fiorani F, Kersey P, Klukas C, Lange M, Markiewicz A, Nap JP, van Oeveren J, Pommier C, Scholz U, van Schriek M, Usadel B, Weise S.

J Exp Bot. 2018 Mar 24;69(7):1819. doi: 10.1093/jxb/ery006. No abstract available.

PMID:
29471492
11.

Divergent regulation of Arabidopsis SAUR genes: a focus on the SAUR10-clade.

van Mourik H, van Dijk ADJ, Stortenbeker N, Angenent GC, Bemer M.

BMC Plant Biol. 2017 Dec 19;17(1):245. doi: 10.1186/s12870-017-1210-4.

12.

Transcription Factor-Mediated Control of Anthocyanin Biosynthesis in Vegetative Tissues.

Outchkourov NS, Karlova R, Hölscher M, Schrama X, Blilou I, Jongedijk E, Simon CD, van Dijk ADJ, Bosch D, Hall RD, Beekwilder J.

Plant Physiol. 2018 Feb;176(2):1862-1878. doi: 10.1104/pp.17.01662. Epub 2017 Nov 30.

13.

Tulipa gesneriana and Lilium longiflorum PEBP Genes and Their Putative Roles in Flowering Time Control.

Leeggangers HACF, Rosilio-Brami T, Bigas-Nadal J, Rubin N, van Dijk ADJ, Nunez de Caceres Gonzalez FF, Saadon-Shitrit S, Nijveen H, Hilhorst HWM, Immink RGH, Zaccai M.

Plant Cell Physiol. 2018 Jan 1;59(1):90-106. doi: 10.1093/pcp/pcx164.

PMID:
29088399
14.

Similarities between plant traits based on their connection to underlying gene functions.

Nap JP, Sanchez-Perez GF, van Dijk ADJ.

PLoS One. 2017 Aug 10;12(8):e0182097. doi: 10.1371/journal.pone.0182097. eCollection 2017.

15.

Sequence-based analysis of protein degradation rates.

Correa Marrero M, van Dijk ADJ, de Ridder D.

Proteins. 2017 Sep;85(9):1593-1601. doi: 10.1002/prot.25323. Epub 2017 Jun 10.

PMID:
28547871
16.

Floral pathway integrator gene expression mediates gradual transmission of environmental and endogenous cues to flowering time.

van Dijk ADJ, Molenaar J.

PeerJ. 2017 Apr 19;5:e3197. doi: 10.7717/peerj.3197. eCollection 2017.

17.

An interactomics overview of the human and bovine milk proteome over lactation.

Zhang L, van Dijk ADJ, Hettinga K.

Proteome Sci. 2017 Jan 5;15:1. doi: 10.1186/s12953-016-0110-0. eCollection 2016.

18.

Selected proceedings of Machine Learning in Systems Biology: MLSB 2016.

van Dijk AD, Lähdesmäki H, de Ridder D, Rousu J.

BMC Bioinformatics. 2016 Dec 13;17(Suppl 16):437. doi: 10.1186/s12859-016-1305-1. No abstract available.

19.

Species-Specific Genome Sequence Databases: A Practical Review.

van Dijk AD.

Methods Mol Biol. 2017;1533:173-181. Review.

PMID:
27987170
20.

Cross-Family Transcription Factor Interactions: An Additional Layer of Gene Regulation.

Bemer M, van Dijk ADJ, Immink RGH, Angenent GC.

Trends Plant Sci. 2017 Jan;22(1):66-80. doi: 10.1016/j.tplants.2016.10.007. Epub 2016 Nov 1. Review.

PMID:
27814969
21.

Distribution, position and genomic characteristics of crossovers in tomato recombinant inbred lines derived from an interspecific cross between Solanum lycopersicum and Solanum pimpinellifolium.

Demirci S, van Dijk AD, Sanchez Perez G, Aflitos SA, de Ridder D, Peters SA.

Plant J. 2017 Feb;89(3):554-564. doi: 10.1111/tpj.13406. Epub 2017 Feb 3.

22.

An expanded evaluation of protein function prediction methods shows an improvement in accuracy.

Jiang Y, Oron TR, Clark WT, Bankapur AR, D'Andrea D, Lepore R, Funk CS, Kahanda I, Verspoor KM, Ben-Hur A, Koo da CE, Penfold-Brown D, Shasha D, Youngs N, Bonneau R, Lin A, Sahraeian SM, Martelli PL, Profiti G, Casadio R, Cao R, Zhong Z, Cheng J, Altenhoff A, Skunca N, Dessimoz C, Dogan T, Hakala K, Kaewphan S, Mehryary F, Salakoski T, Ginter F, Fang H, Smithers B, Oates M, Gough J, Törönen P, Koskinen P, Holm L, Chen CT, Hsu WL, Bryson K, Cozzetto D, Minneci F, Jones DT, Chapman S, Bkc D, Khan IK, Kihara D, Ofer D, Rappoport N, Stern A, Cibrian-Uhalte E, Denny P, Foulger RE, Hieta R, Legge D, Lovering RC, Magrane M, Melidoni AN, Mutowo-Meullenet P, Pichler K, Shypitsyna A, Li B, Zakeri P, ElShal S, Tranchevent LC, Das S, Dawson NL, Lee D, Lees JG, Sillitoe I, Bhat P, Nepusz T, Romero AE, Sasidharan R, Yang H, Paccanaro A, Gillis J, Sedeño-Cortés AE, Pavlidis P, Feng S, Cejuela JM, Goldberg T, Hamp T, Richter L, Salamov A, Gabaldon T, Marcet-Houben M, Supek F, Gong Q, Ning W, Zhou Y, Tian W, Falda M, Fontana P, Lavezzo E, Toppo S, Ferrari C, Giollo M, Piovesan D, Tosatto SC, Del Pozo A, Fernández JM, Maietta P, Valencia A, Tress ML, Benso A, Di Carlo S, Politano G, Savino A, Rehman HU, Re M, Mesiti M, Valentini G, Bargsten JW, van Dijk AD, Gemovic B, Glisic S, Perovic V, Veljkovic V, Veljkovic N, Almeida-E-Silva DC, Vencio RZ, Sharan M, Vogel J, Kansakar L, Zhang S, Vucetic S, Wang Z, Sternberg MJ, Wass MN, Huntley RP, Martin MJ, O'Donovan C, Robinson PN, Moreau Y, Tramontano A, Babbitt PC, Brenner SE, Linial M, Orengo CA, Rost B, Greene CS, Mooney SD, Friedberg I, Radivojac P.

Genome Biol. 2016 Sep 7;17(1):184. doi: 10.1186/s13059-016-1037-6.

23.

Towards recommendations for metadata and data handling in plant phenotyping.

Krajewski P, Chen D, Ćwiek H, van Dijk AD, Fiorani F, Kersey P, Klukas C, Lange M, Markiewicz A, Nap JP, van Oeveren J, Pommier C, Scholz U, van Schriek M, Usadel B, Weise S.

J Exp Bot. 2015 Sep;66(18):5417-27. doi: 10.1093/jxb/erv271. Epub 2015 Jun 4. Erratum in: J Exp Bot. 2018 Mar 24;69(7):1819.

PMID:
26044092
24.

A quantitative and dynamic model of the Arabidopsis flowering time gene regulatory network.

Leal Valentim F, Mourik Sv, Posé D, Kim MC, Schmid M, van Ham RC, Busscher M, Sanchez-Perez GF, Molenaar J, Angenent GC, Immink RG, van Dijk AD.

PLoS One. 2015 Feb 26;10(2):e0116973. doi: 10.1371/journal.pone.0116973. eCollection 2015.

25.

Prioritization of candidate genes in QTL regions based on associations between traits and biological processes.

Bargsten JW, Nap JP, Sanchez-Perez GF, van Dijk AD.

BMC Plant Biol. 2014 Dec 10;14:330. doi: 10.1186/s12870-014-0330-3.

26.

Rice cytochrome P450 MAX1 homologs catalyze distinct steps in strigolactone biosynthesis.

Zhang Y, van Dijk AD, Scaffidi A, Flematti GR, Hofmann M, Charnikhova T, Verstappen F, Hepworth J, van der Krol S, Leyser O, Smith SM, Zwanenburg B, Al-Babili S, Ruyter-Spira C, Bouwmeester HJ.

Nat Chem Biol. 2014 Dec;10(12):1028-33. doi: 10.1038/nchembio.1660. Epub 2014 Oct 26.

PMID:
25344813
27.

The (r)evolution of gene regulatory networks controlling Arabidopsis plant reproduction: a two-decade history.

Pajoro A, Biewers S, Dougali E, Leal Valentim F, Mendes MA, Porri A, Coupland G, Van de Peer Y, van Dijk AD, Colombo L, Davies B, Angenent GC.

J Exp Bot. 2014 Sep;65(17):4731-45. doi: 10.1093/jxb/eru233. Epub 2014 Jun 9. Review.

PMID:
24913630
28.

Inferring the gene network underlying the branching of tomato inflorescence.

Astola L, Stigter H, van Dijk AD, van Daelen R, Molenaar J.

PLoS One. 2014 Apr 3;9(4):e89689. doi: 10.1371/journal.pone.0089689. eCollection 2014.

29.

Structural determinants of DNA recognition by plant MADS-domain transcription factors.

Muiño JM, Smaczniak C, Angenent GC, Kaufmann K, van Dijk AD.

Nucleic Acids Res. 2014 Feb;42(4):2138-46. doi: 10.1093/nar/gkt1172. Epub 2013 Nov 25.

30.

Analysis of functional redundancies within the Arabidopsis TCP transcription factor family.

Danisman S, van Dijk AD, Bimbo A, van der Wal F, Hennig L, de Folter S, Angenent GC, Immink RG.

J Exp Bot. 2013 Dec;64(18):5673-85. doi: 10.1093/jxb/ert337. Epub 2013 Oct 15.

31.

Valencene synthase from the heartwood of Nootka cypress (Callitropsis nootkatensis) for biotechnological production of valencene.

Beekwilder J, van Houwelingen A, Cankar K, van Dijk AD, de Jong RM, Stoopen G, Bouwmeester H, Achkar J, Sonke T, Bosch D.

Plant Biotechnol J. 2014 Feb;12(2):174-82. doi: 10.1111/pbi.12124. Epub 2013 Sep 25.

32.

N-glycan occupancy of Arabidopsis N-glycoproteins.

Song W, Mentink RA, Henquet MG, Cordewener JH, van Dijk AD, Bosch D, America AH, van der Krol AR.

J Proteomics. 2013 Nov 20;93:343-55. doi: 10.1016/j.jprot.2013.07.032. Epub 2013 Aug 27.

PMID:
23994444
33.

Mining minimal motif pair sets maximally covering interactions in a protein-protein interaction network.

Boyen P, Neven F, van Dyck D, Valentim FL, van Dijk AD.

IEEE/ACM Trans Comput Biol Bioinform. 2013 Jan-Feb;10(1):73-86. doi: 10.1109/TCBB.2012.165.

PMID:
23702545
34.

Gene Ontology consistent protein function prediction: the FALCON algorithm applied to six eukaryotic genomes.

Kourmpetis YA, van Dijk ADj, Ter Braak CJ.

Algorithms Mol Biol. 2013 Mar 27;8(1):10. doi: 10.1186/1748-7188-8-10.

35.

Multidimensional health locus of control and depressive symptoms in the multi-ethnic population of the Netherlands.

van Dijk TK, Dijkshoorn H, van Dijk A, Cremer S, Agyemang C.

Soc Psychiatry Psychiatr Epidemiol. 2013 Dec;48(12):1931-9. doi: 10.1007/s00127-013-0678-y. Epub 2013 Mar 19.

PMID:
23508370
36.

A large-scale evaluation of computational protein function prediction.

Radivojac P, Clark WT, Oron TR, Schnoes AM, Wittkop T, Sokolov A, Graim K, Funk C, Verspoor K, Ben-Hur A, Pandey G, Yunes JM, Talwalkar AS, Repo S, Souza ML, Piovesan D, Casadio R, Wang Z, Cheng J, Fang H, Gough J, Koskinen P, Törönen P, Nokso-Koivisto J, Holm L, Cozzetto D, Buchan DW, Bryson K, Jones DT, Limaye B, Inamdar H, Datta A, Manjari SK, Joshi R, Chitale M, Kihara D, Lisewski AM, Erdin S, Venner E, Lichtarge O, Rentzsch R, Yang H, Romero AE, Bhat P, Paccanaro A, Hamp T, Kaßner R, Seemayer S, Vicedo E, Schaefer C, Achten D, Auer F, Boehm A, Braun T, Hecht M, Heron M, Hönigschmid P, Hopf TA, Kaufmann S, Kiening M, Krompass D, Landerer C, Mahlich Y, Roos M, Björne J, Salakoski T, Wong A, Shatkay H, Gatzmann F, Sommer I, Wass MN, Sternberg MJ, Škunca N, Supek F, Bošnjak M, Panov P, Džeroski S, Šmuc T, Kourmpetis YA, van Dijk AD, ter Braak CJ, Zhou Y, Gong Q, Dong X, Tian W, Falda M, Fontana P, Lavezzo E, Di Camillo B, Toppo S, Lan L, Djuric N, Guo Y, Vucetic S, Bairoch A, Linial M, Babbitt PC, Brenner SE, Orengo C, Rost B, Mooney SD, Friedberg I.

Nat Methods. 2013 Mar;10(3):221-7. doi: 10.1038/nmeth.2340. Epub 2013 Jan 27.

37.

Solvated protein-protein docking using Kyte-Doolittle-based water preferences.

Kastritis PL, Visscher KM, van Dijk AD, Bonvin AM.

Proteins. 2013 Mar;81(3):510-8. doi: 10.1002/prot.24210. Epub 2012 Dec 24.

PMID:
23161727
38.

Interactome-wide prediction of protein-protein binding sites reveals effects of protein sequence variation in Arabidopsis thaliana.

Leal Valentim F, Neven F, Boyen P, van Dijk AD.

PLoS One. 2012;7(10):e47022. doi: 10.1371/journal.pone.0047022. Epub 2012 Oct 15.

39.

Characterization of SOC1's central role in flowering by the identification of its upstream and downstream regulators.

Immink RG, Posé D, Ferrario S, Ott F, Kaufmann K, Valentim FL, de Folter S, van der Wal F, van Dijk AD, Schmid M, Angenent GC.

Plant Physiol. 2012 Sep;160(1):433-49. doi: 10.1104/pp.112.202614. Epub 2012 Jul 12. Erratum in: Plant Physiol. 2013 Aug;162(4):2151.

40.

Arabidopsis class I and class II TCP transcription factors regulate jasmonic acid metabolism and leaf development antagonistically.

Danisman S, van der Wal F, Dhondt S, Waites R, de Folter S, Bimbo A, van Dijk AD, Muino JM, Cutri L, Dornelas MC, Angenent GC, Immink RG.

Plant Physiol. 2012 Aug;159(4):1511-23. doi: 10.1104/pp.112.200303. Epub 2012 Jun 20.

41.

Integrating two patterning processes in the flower.

van Mourik S, van Dijk AD, Angenent GC, Merk RM, Molenaar J.

Plant Signal Behav. 2012 Jun;7(6):682-4. doi: 10.4161/psb.20017. Epub 2012 May 14.

42.

Mutational robustness of gene regulatory networks.

van Dijk AD, van Mourik S, van Ham RC.

PLoS One. 2012;7(1):e30591. doi: 10.1371/journal.pone.0030591. Epub 2012 Jan 25.

43.

Predicting the impact of alternative splicing on plant MADS domain protein function.

Severing EI, van Dijk AD, Morabito G, Busscher-Lange J, Immink RG, van Ham RC.

PLoS One. 2012;7(1):e30524. doi: 10.1371/journal.pone.0030524. Epub 2012 Jan 25.

44.

Simulation of organ patterning on the floral meristem using a polar auxin transport model.

van Mourik S, Kaufmann K, van Dijk AD, Angenent GC, Merks RM, Molenaar J.

PLoS One. 2012;7(1):e28762. doi: 10.1371/journal.pone.0028762. Epub 2012 Jan 23.

45.

Explicit treatment of water molecules in data-driven protein-protein docking: the solvated HADDOCKing approach.

Kastritis PL, van Dijk AD, Bonvin AM.

Methods Mol Biol. 2012;819:355-74. doi: 10.1007/978-1-61779-465-0_22.

PMID:
22183547
46.

Correlated mutations via regularized multinomial regression.

Sreekumar J, ter Braak CJ, van Ham RC, van Dijk AD.

BMC Bioinformatics. 2011 Nov 14;12:444. doi: 10.1186/1471-2105-12-444.

47.

PRI-CAT: a web-tool for the analysis, storage and visualization of plant ChIP-seq experiments.

Muiño JM, Hoogstraat M, van Ham RC, van Dijk AD.

Nucleic Acids Res. 2011 Jul;39(Web Server issue):W524-7. doi: 10.1093/nar/gkr373. Epub 2011 May 24.

48.

Assessing the contribution of alternative splicing to proteome diversity in Arabidopsis thaliana using proteomics data.

Severing EI, van Dijk AD, van Ham RC.

BMC Plant Biol. 2011 May 16;11(1):82. doi: 10.1186/1471-2229-11-82.

49.

SLIDER: a generic metaheuristic for the discovery of correlated motifs in protein-protein interaction networks.

Boyen P, Van Dyck D, Neven F, van Ham RC, van Dijk AD.

IEEE/ACM Trans Comput Biol Bioinform. 2011 Sep-Oct;8(5):1344-57. doi: 10.1109/TCBB.2011.17.

PMID:
21282865
50.

Sequence motifs in MADS transcription factors responsible for specificity and diversification of protein-protein interaction.

van Dijk AD, Morabito G, Fiers M, van Ham RC, Angenent GC, Immink RG.

PLoS Comput Biol. 2010 Nov 24;6(11):e1001017. doi: 10.1371/journal.pcbi.1001017.

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