Research Output

2015

Single-molecule protein sequencing through fingerprinting: computational assessment

Yao, Y., Docter, M., van Ginkel, J., de Ridder, D. & Joo, C., 2015, In : Physical Biology. 12, 5, 6 p., 055003.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
19 Citations (Scopus)

The cell size distribution of tomato fruit can be changed by overexpression of CDKA1

Czerednik, A., Busscher, M., Angenent, G. C. & de Maagd, R. A., 2015, In : Plant Biotechnology Journal. 13, 2, p. 259-268

Research output: Contribution to journalArticleAcademicpeer-review

14 Citations (Scopus)
Open Access
39 Citations (Scopus)

Time-series analysis of the transcriptome of the re-establishment of desiccation tolerance by ABA in germinated Arabidopsis thaliana seeds

Dias Costa, M. C., Nijveen, H., Ligterink, W., Buitink, J. & Hilhorst, H. W. M., 2015, In : Genomics Data. 5, p. 154-156

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
2 Citations (Scopus)

Unbiased quantitative models of protein translation derived from ribosome profiling data

Gritsenko, A. A., Hulsman, M., Reinders, M. J. T. & de Ridder, D., 2015, In : PLoS Computational Biology. 11, 8, 26 p., e1004336.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
13 Citations (Scopus)

Using bioconductor package BiGGR for metabolic flux estimation based on gene expression changes in brain

Gavai, A. K., Supandi, F., Hettling, H., Murrell, P., Leunissen, J. A. M. & van Beek, J. H. G. M., 2015, In : PLoS ONE. 10, 3, 21 p., e0119016.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
10 Citations (Scopus)
2014

A novel Cry9Aa with increased toxicity for Spodoptera exigua (Hübner)

Naimov, S., Nedyalkova, R., Staykov, N., Weemen-Hendriks, M., Minkov, I. & de Maagd, R. A., 2014, In : Journal of Invertebrate Pathology. 115, p. 99-101

Research output: Contribution to journalArticleAcademicpeer-review

8 Citations (Scopus)

Beyond genomic variation - comparison and functional annotation in three Brassica rapa genotypes: a turnip, a rapid cycling and a Chinese cabbage

Lin, K., Zhang, N., Severing, E. I., Nijveen, H., Cheng, F., Visser, R. G. F., Wang, X., de Ridder, D. & Bonnema, A. B., 2014, In : BMC Genomics. 15, 34 p., 250.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
40 Citations (Scopus)

Birth, death, and diversification of mobile promoters in prokaryotes

van Passel, M. W. J., Nijveen, H. & Wahl, L. M., 2014, In : Genetics. 197, 1, p. 291-299

Research output: Contribution to journalArticleAcademicpeer-review

4 Citations (Scopus)

Can interactions between Bt proteins be predicted and how should effects on non-target organisms of GM crops with multiple Bt Proteins be assessed?

De Schrijver, A., de Clercq, P., Booij, K., de Maagd, R. A. & van Frankenhuyzen, K., 2014, Bilthoven: Cogem. 95 p. (CGM; no. 2014-05)

Research output: Book/ReportReportProfessional

Open Access
170 Citations (Scopus)

Fluorescence in situ hybridization and optical mapping to correct scaffold arrangement in the tomato genome

Shearer, L. A., Anderson, L. K., de Jong, H., Smit, S., Goicoechea, J. L., Roe, B. A., Hua, A., Giovannoni, J. J. & Stack, S. M., 2014, In : G3 : Genes Genomes Genetics. 4, 8, p. 1395-1405

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
50 Citations (Scopus)

Genetic dissection of leaf development in Brassica rapa using a ‘geneticalgenomics’ approach

Xiao, D., Wang, H., Basnet, R. K., Jianjun Zhao, J., Lin, K., Hou, X. & Bonnema, A. B., 2014, In : Plant Physiology. 164, 3, p. 1309-1325

Research output: Contribution to journalArticleAcademicpeer-review

25 Citations (Scopus)
Open Access
65 Citations (Scopus)

Interaction between parental environment and genotype affects plant and seed performance in Arabidopsis

He, H., De Souza Vidigal, D., Snoek, L. B., Schnabel, S. K., Nijveen, H., Hilhorst, H. & Bentsink, L., 2014, In : Journal of Experimental Botany. 65, 22, p. 6603-6615

Research output: Contribution to journalArticleAcademicpeer-review

81 Citations (Scopus)

Next-gen genetical genomics; RNA-sequencing of a new multi-parent recombinant inbred line population of Caenorhabditis elegans

Snoek, L. B., Volkers, R. J. M., Nijveen, H., Sterken, M. G., Riksen, J. A. G., Braeckman, B., Schulenburg, H. J. G. & Kammenga, J. E., 2014, Proceedings of Evolutionary Biology of Caenorhabditis and other Nematodes. p. 77-77

Research output: Chapter in Book/Report/Conference proceedingAbstract

Plant metabolomics is not ripe for environmental risk assessment

Hall, R. D. & de Maagd, R. A., 2014, In : Trends in Biotechnology. 32, 8, p. 391-392

Research output: Contribution to journalLetterAcademicpeer-review

12 Citations (Scopus)

Protein redesign by learning from data

van den Berg, B. A., Reinders, M. J. T., van der Laan, J. M., Roubos, J. A. & de Ridder, D., 2014, In : Protein Engineering, Design & Selection. 27, 9, p. 281-288

Research output: Contribution to journalArticleAcademicpeer-review

4 Citations (Scopus)

Text mining for metabolic reaction extraction from scientific literature

Risse, J. E., 2014, Wageningen: Wageningen University. 138 p.

Research output: Thesisinternal PhD, WU

Open Access

The genome of the stress-tolerant wild tomato species Solanum pennellii

Bolger, A., Scossa, F., Bolger, M. E., Aflitos, S. A., Schijlen, E. G. W. M., van Ham, R. C. H. J. & Klein Lankhorst, R. M., 2014, In : Nature Genetics. 46, 9, p. 1034-1038

Research output: Contribution to journalArticleAcademicpeer-review

177 Citations (Scopus)

Transcriptional control of fleshy fruit development and ripening

Karlova, R. B., Chapman, N., David, K., Angenent, G. C., Seymour, G. B. & de Maagd, R. A., 2014, In : Journal of Experimental Botany. 65, 16, p. 4527-4541

Research output: Contribution to journalArticleAcademicpeer-review

133 Citations (Scopus)

Understanding and identifying amino acid repeats

Luo, H. & Nijveen, H., 2014, In : Briefings in Bioinformatics. 15, 4, p. 582-591

Research output: Contribution to journalArticleAcademicpeer-review

30 Citations (Scopus)
2013

Applications in computer-assisted biology

Nijveen, H., 2013, Wageningen: Wageningen UR. 106 p.

Research output: Thesisinternal PhD, WU

Open Access

Discovery of T cell epitopes implementing HLA-peptidomics into a reverse immunology approach

Hombrink, P., Hassan, C., Kester, M. G. D., Ru, A. H., Bergen, C. A. M., Nijveen, H., Drijfhout, J. W., Falkenburg, J. H. F., Heemskerk, M. H. M. & van Veelen, P. A., 2013, In : The Journal of Immunology. 190, 8, p. 3869-3877

Research output: Contribution to journalArticleAcademicpeer-review

21 Citations (Scopus)
Open Access
19 Citations (Scopus)

Improving hierarchical clustering of genotypic data via principal component analysis

Odong, T. L., van Heerwaarden, J., van Hintum, T. J. L., van Eeuwijk, F. A. & Jansen, J., 2013, In : Crop Science. 53, p. 1546-1554

Research output: Contribution to journalArticleAcademicpeer-review

9 Citations (Scopus)

Obituary: In memory of Jack Leunissen

Luo, J., Nijveen, H., Attwood, T., Judge, D., Pongor, S., Landsman, D. & Bishop, M., 2013, In : Briefings in Bioinformatics. 14, 3, p. 261-262

Research output: Contribution to journalArticleAcademic

QualitySNPng: a user-friendly SNP detection and visualization tool

Nijveen, H., van Kaauwen, M. P. W., Esselink, G., Hoegen, B. & Vosman, B., 2013, In : Nucleic acids research. 41, p. W587-W590

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
18 Citations (Scopus)

The Brassica rapa FLC homologue FLC2 is a key regulator of flowering time, identified through transcriptional co-expression networks

Xiao, D., Jianjun Zhao, J., Hou, X. L., Basnet, R. K., Carpio, D. P., Zhang, N., Bucher, J., Lin, K., Cheng, F., Wang, X. W. & Bonnema, A. B., 2013, In : Journal of Experimental Botany. 64, 14, p. 4503-4516

Research output: Contribution to journalArticleAcademicpeer-review

61 Citations (Scopus)

The human leukocyte antigen-presented ligandome of B lymphocytes

Hassan, C., Kester, M. G. D., Ru, A. H., Hombrink, P., Drijfhout, J. W., Nijveen, H., Leunissen, J. A. M., Heemskerk, M. H. M., Falkenburg, J. H. F. & van Veelen, P. A., 2013, In : Molecular and Cellular Proteomics. 12, p. 1829-1843

Research output: Contribution to journalArticleAcademicpeer-review

73 Citations (Scopus)

The mechanism of introner-like element multiplication in fungi

van der Burgt, I. A., Severing, E. I., Ochoa Tufiño, V., de Wit, P. J. G. M. & Collemare, J. A. R., 2013, Book of Abstracts 27th Fungal Genetics Conference, Asilomar, Pacific Grove, California, USA, 12-17 March 2013. p. 205

Research output: Chapter in Book/Report/Conference proceedingAbstract

Using fluorescence in situ hybridization (FISH) to improve the assembly of the tomato genome

Shearer, L. A., Anderson, L. K., de Jong, J. H. S. G. M., Smit, S., Goicoechea, J. L., Roe, B. A., Hua, A., Giovannoni, J. J. & Stack, S. M., 2013, In : Tomato Genetics Cooperative Report. 63, p. 5-14

Research output: Contribution to journalArticleAcademicpeer-review

2012

Beyond structural variation- whole genome comparison and functional annotation in three Brassica rapa genotypes: a Turnip, a Rapid cycling and a Chinese cabbage

Lin, K., Zhang, N., Servering, E., Nijveen, H., Cheng, F., Visser, R. G. F., Wang, X. & Bonnema, A. B., 2012.

Research output: Contribution to conferencePosterProfessional

Biased Gene Fractionation and Dominant Gene Expression among the Subgenomes of Brassica rapa

Cheng, F., Wu, J., Fang, L., Sun, S., Liu, B., Lin, K., Bonnema, A. B. & Wang, X., 2012, In : PLoS ONE. 7, 5, e36442.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
155 Citations (Scopus)

Bin mapping of tomato diversity array (DArT) markers to genomic regions of Solanum lycopersicum × Solanum pennellii introgression lines

Schalkwyk, A., Wenzl, P., Smit, S., Lopez-Cobollo, R., Kilian, A., Bishop, G., Hefer, C. & Berger, D. K., 2012, In : Theoretical and Applied Genetics. 124, 5, p. 947-956

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
15 Citations (Scopus)

Birth of new spliceosomal introns in fungi by multiplication of introner-like elements

van der Burgt, A., Severing, E. I., Collemare, J. & de Wit, P. J. G. M., 2012, In : Current Biology. 22, 13, p. 1260-1265

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
33 Citations (Scopus)

De novo sequencing, assembly and analysis of the genome of the laboratory strain Saccharomyces cerevisiae CEN.PK113-7D, a model for modern industrial biotechnology

Nijkamp, J. F., van den Broek, M., Datema, E., de Kok, S., Bosman, L., Luttik, M. A., Daran-Lapujade, P., Vongsangnak, W., Nielsen, J., Heijne, W. H. M., Klaassen, P., Paddon, C. J., Platt, D., Kotter, P., van Ham, R. C. H. J., Reinders, M. J. T., Pronk, J. T., de Ridder, D. & Daran, J. M., 2012, In : Microbial Cell Factories. 11, 36.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
159 Citations (Scopus)

Predicting the Impact of Alternative Splicing on Plant MADS Domain Protein Function

Severing, E. I., van Dijk, A. D. J., Morabito, G., Busscher-Lange, J., Immink, G. H. & van Ham, R. C. H. J., 2012, In : PLoS ONE. 7, 1, 13 p., e30524.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
43 Citations (Scopus)

Promoter propagation in prokaryotes

Matus-Garcia, M., Nijveen, H. & van Passel, M. W. J., 2012, In : Nucleic acids research. 40, 20, p. 10032-10040

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
11 Citations (Scopus)

Promoter reuse in prokaryotes

Nijveen, H., Matus-Garcia, M. & van Passel, M. W. J., 2012, In : Mobile Genetic Elements. 2, 6, p. 1-3

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

ProRepeat: an integrated repository for studying amino acid tandem repeats in proteins

Luo, H., Lin, K., David, A., Nijveen, H. & Leunissen, J. A. M., 2012, In : Nucleic acids research. 40, D1, p. D394-D399 6 p.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
8 Citations (Scopus)

RNASTAR: An RNA STructural Alignment Repository that provides insight into the evolution of natural and artificial RNAs

Widmann, J., Stombaugh, J., Mcdonald, D., Chocholousova, J., Gardner, P., Iyer, M. K., Liu, Z. Z., Lozupone, C. A., Quinn, J., Smit, S., Wikman, S., Zaneveld, J. R. R. & Knight, R., 2012, In : RNA-A Publication of the RNA Society. 18, 7, p. 1319-1327

Research output: Contribution to journalArticleAcademicpeer-review

18 Citations (Scopus)

The Genomes of the Fungal Plant Pathogens Cladosporium fulvum and Dothistroma septosporum Reveal Adaptation to Different Hosts and Lifestyles But Also Signatures of Common Ancestry

de Wit, P. J. G. M., van der Burgt, I. A., Ökman, B., Stergiopoulos, I., Abd-Elsalam, K. A., Aerts, A. L., Bahkali, A. H., Beenen, H. G., Chettri, P., Cox, M. P., Datema, E., de Vries, R. P., Dhillon, B., Ganley, A. R., Griffiths, S. A., Guo, Y., Hamelin, R. C., Henrissat, B., Karimi Jashni, M., Kema, G. H. J. & 14 others, Klaubauf, S., Lapidus, A., Levasseur, A., Lindquist, E., Mehrabi, R., Ohm, R. A., Owen, T. J., Salamov, A., Schwelm, A., van den Burg, H. A., van Ham, R. C. H. J., Zhang, S., Goodwin, S. B. & Collemare, J., 2012, In : Plos Genetics. 8, 11, e1003088.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
155 Citations (Scopus)

The tomato genome sequence provides insights into fleshy fruit evolution

Sato, S., Tabata, S., Hirakawa, H., Klein Lankhorst, R. M., de Jong, H., van Ham, R. C. H. J., Datema, E., Smit, S., Schijlen, E. G. W. M., van Haarst, J. C., Peters, S. A., Henkens, M. H. C., van Staveren, M. J., Mooijman, P. J. W., Hesselink, T., van de Belt, J., Szinay, D., Bai, Y. & Visser, R. G. F., 2012, In : Nature. 485, p. 635-641

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
1706 Citations (Scopus)

The turbulent life of Sirevirus retrotransposons and the evolution of the maize genome: more than ten thousand elements tell the story

Bousios, A., Kourmpetis, Y. I. A., Pavlidis, P., Minga, E., Tsaftaris, A. & Darzentas, N., 2012, In : The Plant Journal. 69, 3, p. 475-488

Research output: Contribution to journalArticleAcademicpeer-review

18 Citations (Scopus)
2011

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

Severing, E. I., van Dijk, A. D. J. & van Ham, R. C. H. J., 2011, In : BMC Plant Biology. 11, 10 p., 82.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
27 Citations (Scopus)

Assessing the impact of alternative splicing on the diversity and evolution of the proteome in plants

Severing, E. I., 2011, [S.l.]. 119 p.

Research output: Thesisinternal PhD, WU

Open Access

Bayesian Markov random field analysis for integrated network-based protein function prediction

Kourmpetis, Y. I. A., 2011, [S.l.]. 113 p.

Research output: Thesisinternal PhD, WU

Open Access

ChIP-seq Analysis in R (CSAR): An R package for the statistical detection of protein-bound genomic regions

Muino, J. M., Kaufmann, K., van Ham, R. C. H. J., Angenent, G. C. & Krajewski, P., 2011, In : Plant Methods. 7, 11.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
44 Citations (Scopus)

Comparative genomics of the secretome of the Dothideomycete fungus Cladosporium fulvum

van der Burgt, A., van den Burg, H., Stergiopoulos, I., Ökmen, B., Mehrabi, R., Karimi, M., Collemare, J., Beenen, H., Kema, G. H. J., Bradshaw, R., Bahkali, A. & de Wit, P. J. G. M., 2011, Proceeding of the 26th Fungal Genetics Conference, Asilomar, Pacific Grove, California, USA, 15-20 March 2011. p. 133

Research output: Chapter in Book/Report/Conference proceedingAbstractAcademic