Research Output

2008

Benchmarking protein classification algorithms via supervised cross-validation

Kertész-Farkas, A., Dhir, S., Sonego, P., Pacurar, M., Netoteia, S., Nijveen, H., Kuzniar, A., Leunissen, J. A. M., Kocsor, A. & Pongor, S., 2008, In : Journal of Biochemical and Biophysical Methods. 70, 6, p. 1215-1223

Research output: Contribution to journalArticleAcademicpeer-review

13 Citations (Scopus)

Comparative BAC end sequence analysis of tomato and potato reveals overrepresentation of specific gene families in potato

Datema, E., Mueller, L. A., Buels, R., Giovannoni, J. J., Visser, R. G. F., Stiekema, W. & van Ham, R. C. H. J., 2008, In : BMC Plant Biology. 8, 34.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
23 Citations (Scopus)

Cross-species BAC-FISH painting of the tomato and potato chromosome 6 reveals undescribed chromosomal rearrangements

Tang, X., Szinay, D., Ramanna, M. S., van der Vossen, E. A. G., Datema, E., Klein Lankhorst, R. M., de Boer, J. M., Peters, S. A., Bachem, C. W. B., Stiekema, W. J., Visser, R. G. F., de Jong, J. H. & Bai, Y., 2008, In : Genetics. 180, p. 1319-1328

Research output: Contribution to journalArticleAcademicpeer-review

62 Citations (Scopus)

FISH mapping and molecular organization of the major repetitive sequences of tomato

Chang, S. B., Yang, T. J., Datema, E., van Vugt, J., Vosman, B., Kuipers, A., Meznikova, M., Szinay, D., Klein Lankhorst, R. M., Jacobsen, E. & de Jong, J. H. S. G. M., 2008, In : Chromosome Research. 16, 7, p. 919-933

Research output: Contribution to journalArticleAcademicpeer-review

50 Citations (Scopus)

Genetic and functional characterization of the gene cluster directing the biosynthesis of putisolvin I and II in Pseudomonas putida strain PCL1445

Dubern, J. F., Coppoolse, E. R., Stiekema, W. J. & Bloemberg, G. V., 2008, In : Microbiology. 154, p. 2070-2083

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
40 Citations (Scopus)

HaploSNPer: a web-based allele and SNP detection tool

Tang, J., Leunissen, J. A. M., Voorrips, R. E., van der Linden, C. G. & Vosman, B., 2008, In : BMC Genetics. 9, 7 p., 23.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
21 Citations (Scopus)

High-resolution chromosome mapping of BACs using multi-colour FISH and pooled-BAC FISH as a backbone for sequencing tomato chromosome 6

Szinay, D., Chang, S. B., Khrustaleva, L. I., Peters, S. A., Schijlen, E. G. W. M., Bai, Y., Stiekema, W., van Ham, R. C. H. J., de Jong, H. & Klein Lankhorst, R. M., 2008, In : The Plant Journal. 56, 4, p. 627-637

Research output: Contribution to journalArticleAcademicpeer-review

63 Citations (Scopus)

High-throughput bioinformatics with the Cyrille2 pipeline system.

Fiers, M. W. E. J., van der Burgt, A., Datema, E., de Groot, J. C. W. & van Ham, R. C. H. J., 2008, In : BMC Bioinformatics. 9, 10 p., 96.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
11 Citations (Scopus)

Interoperability with Moby 1.0 - It-s better than sharing your toothbrush!

Wilkinson, M. D., Senger, M., Kawas, E., Neerincx, P. B. T. & Leunissen, J. A. M., 2008, In : Briefings in Bioinformatics. 9, 3, p. 220-231

Research output: Contribution to journalArticleAcademicpeer-review

73 Citations (Scopus)

Large-scale identification of polymorphic microsatellites using an in silico approach

Tang, J., Baldwin, S. J., Jacobs, J. M. E., van der Linden, C. G., Voorrips, R. E., Leunissen, J. A. M., van Eck, H. J. & Vosman, B., 2008, In : BMC Bioinformatics. 9, 13 p., 374.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
51 Citations (Scopus)

Predicting sub-Golgi localization of type II membrane proteins

van Dijk, A. D. J., Bosch, H. J., ter Braak, C. J. F., van der Krol, A. R. & van Ham, R. C. H. J., 2008, In : Bioinformatics. 24, 16, p. 1779-1786

Research output: Contribution to journalArticleAcademicpeer-review

28 Citations (Scopus)

SEQATOMS: a web tool for identifying missing regions in PDB in sequence context

Brandt, B. W., Heringa, J. & Leunissen, J. A. M., 2008, In : Nucleic acids research. 36, 2, p. W255-W259

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
10 Citations (Scopus)

The quest for orthologs: finding the corresponding gene across genomes

Kuzniar, A., van Ham, R. C. H. J., Pongor, S. & Leunissen, J. A. M., 2008, In : Trends in Genetics. 24, 11, p. 539-551

Research output: Contribution to journalArticleAcademicpeer-review

174 Citations (Scopus)
2007

A Protein Classification Benchmark collection for machine learning

Sonego, P., Pacurar, M., Dhir, S., Kertész-Farkas, A., Kocsor, A., Gáspári, Z., Leunissen, J. A. M. & Pongor, S., 2007, In : Nucleic acids research. 35, p. D232-D236

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
37 Citations (Scopus)

Local coexpression domains in the genome of rice show no microsynteny with Arabidopsis domains

Ren, X. Y., Stiekema, W. J. & Nap, J. P. H., 2007, In : Plant Molecular Biology. 65, 1-2, p. 205-217

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
23 Citations (Scopus)
Open Access

Primer3Plus, an enhanced web interface to Primer3

Untergasser, A., Nijveen, H., Rao, X., Bisseling, T., Geurts, R. & Leunissen, J. A. M., 2007, In : Nucleic acids research. 35, suppl2, p. W71-W74

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
1433 Citations (Scopus)

Role of the synthase domain of Ags1p in cell wall alfa-glucan biosynthesis in fission yeast

Vos, A., Dekker, N., Distel, B., Leunissen, J. A. M. & Hochstenbach, F., 2007, In : Journal of Biological Chemistry. 282, 26, p. 18969-18979

Research output: Contribution to journalArticleAcademicpeer-review

16 Citations (Scopus)

The use of multiple hierarchically independent gene ontology terms in gene function prediction and genome annotation

Kourmpetis, Y. I. A., van der Burgt, A., Bink, M. C. A. M., ter Braak, C. J. F. & van Ham, R. C. H. J., 2007, In : In Silico Biology. 7, 0050

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
4 Citations (Scopus)
2006

A text-mining analysis of the human phenome

van Driel, M. A., Bruggeman, J., Vriend, G., Brunner, H. G. & Leunissen, J. A. M., 2006, In : European Journal of Human Genetics. 14, 5, p. 535-542

Research output: Contribution to journalArticleAcademicpeer-review

419 Citations (Scopus)

Bioinformatics for plant genome annotation

Fiers, M. W. E. J., 2006, [S.l.]. 141 p.

Research output: Thesisinternal PhD, WU

Open Access

Comparative genomics of the relationship between gene structure and expression

Ren, X., 2006, [S.l.]. 160 p.

Research output: Thesisinternal PhD, WU

Open Access

In plants, highly expressed genes are least compact

Ren, X. Y., Vorst, O. F. J., Fiers, M. W. E. J., Stiekema, W. J. & Nap, J. P. H., 2006, In : Trends in Genetics. 22, 10, p. 528-532

Research output: Contribution to journalArticleAcademicpeer-review

95 Citations (Scopus)

In silico identification of putative promoter motifs of White Spot syndrome virus

Marks, H., Ren, X. Y., Sandbrink, H., van Hulten, M. C. W. & Vlak, J. M., 2006, In : BMC Bioinformatics. 7, 309, 13 p.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
18 Citations (Scopus)

PROREPEAT: a comprehensive directory of exact tandem repeats in proteins

Leunissen, J. A. M., van den Bosch, M., Kappé, G., Hong Luo, H. & de Jong, W. W., 2006, In Silico Analysis of Proteins; Celebrating the 20th anniversary of Swiss-Prot, July 30-August 4, 2006, Fortaleza - Brazil. [S.l.], p. 34

Research output: Chapter in Book/Report/Conference proceedingAbstractAcademic

QualitySNP: a pipeline for detecting single nucleotide polymorphisms and insertions/deletions in EST data from diploid and polyploid species

Tang, J., Vosman, B., Voorrips, R. E., van der Linden, C. G. & Leunissen, J. A. M., 2006, In : BMC Bioinformatics. 7, 15 p., 438.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
102 Citations (Scopus)

Testing statistical significance scores of sequence comparison methods with structure similarity

Hulsen, T., de Vlieg, J., Leunissen, J. A. M. & Groenen, P., 2006, In : BMC Bioinformatics. 7, 13 p., 444.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
8 Citations (Scopus)

The PROREPEAT database: a directory of exact tandem repeats in proteins

Leunissen, J. A. M., van den Bosch, M., Luo, H., Kappé, G. & de Jong, W. W., 2006, 9th Croatian Biological Conference with international participation, Rovinj, September 23-29, 2006. Besendorfer, V. & Klobucar, G. I. V. (eds.). Zagreb: Croation Biological Society, p. 53

Research output: Chapter in Book/Report/Conference proceedingAbstract

TreeDomViewer: a tool for the visualization of phylogeny and protein domain structure

Alako, B. T. F., Rainey, D., Nijveen, H. & Leunissen, J. A. M., 2006, In : Nucleic acids research. 34, p. W104-W109

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
8 Citations (Scopus)
2005

Application of bioinformatics in plant breeding

Vassilev, D., Leunissen, J., Atanassov, A., Nenov, A. & Dimov, G., 2005, In : Biotechnology and Biotechnological Equipment. 19, spec. iss., p. 139-152

Research output: Contribution to journalArticleAcademicpeer-review

7 Citations (Scopus)

Biochemical and molecular aspects of haploid embryogenesis

Boutilier, K. A., Fiers, M. A., Liu, C. M. & van der Geest, A. H. M., 2005, Haploids in crop improvement II. Palmer, C. E., Keller, W. A. & Kasha, K. J. (eds.). Heidelberg, p. 73-96 300 p. (Biotechnology in agriculture and forestry; no. 56).

Research output: Chapter in Book/Report/Conference proceedingChapter

11 Citations (Scopus)

CoPub Mapper: mining MEDLINE based on search term co-publication

Alako, B. T. F., Veldhoven, A., van Baal, S., Jelier, R., Verhoeven, S., Rullman, T., Polman, J. & Jenster, G., 2005, In : BMC Bioinformatics. 6, 15 p., 51.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
52 Citations (Scopus)

Evolution of web services in bioinformatics

Neerincx, P. B. T. & Leunissen, J. A. M., 2005, In : Briefings in Bioinformatics. 6, 2, p. 178-188

Research output: Contribution to journalArticleAcademicpeer-review

54 Citations (Scopus)

GeneSeeker: extraction and integration of human disease-related information from web-based genetic databases

van Driel, M. A., Cuelenaere, K., Kemmeren, P. P. C. W., Leunissen, J. A. M., Brunner, H. G. & Vriend, G., 2005, In : Nucleic acids research. 33, SUPP/2, p. w758-w761

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
75 Citations (Scopus)

Local coexpression domains of two to four genes in the genome of Arabidopsis

Ren, X. Y., Fiers, M. W. E. J., Stiekema, W. J. & Nap, J. P. H., 2005, In : Plant Physiology. 138, 2, p. 923-934

Research output: Contribution to journalArticleAcademicpeer-review

43 Citations (Scopus)

Molecular genetics of White Spot Syndrome Virus

Marks, H., Ren, X., Witteveldt, J., Sandbrink, H., Vlak, J. M. & van Hulten, M. C. W., 2005, Diseases in Asian Aquaculture. Walker, P. J., Lester, R. G. & Bondad-Reantaso, M. G. (eds.). Manila: Asian Fisheries Society, p. 363-378 16 p.

Research output: Chapter in Book/Report/Conference proceedingChapterAcademicpeer-review

Protein secondary structure prediction : Comparison of ten common prediction algorithms using a neural network

de Haan, J. R. & Leunissen, J. A. M., 2005, Essays in Bioinformatics. Moss, D. S., Jelaska, S. & Pongor, S. (eds.). Amsterdam, p. 149-161 (NATO Science Series: Life and Behavioural Sciences; no. 368).

Research output: Chapter in Book/Report/Conference proceedingChapter

Size does matter: Cre-mediated somatic deletion efficiency depends on the distance between the target lox-sites

Coppoolse, E. R., de Vroomen, M. J., van Gennip, F., Hersmus, B. J. M. & van Haaren, M. J., 2005, In : Plant Molecular Biology. 58, 5, p. 687-698

Research output: Contribution to journalArticleAcademicpeer-review

16 Citations (Scopus)

The 14-Amino acid CLV3, CLE19 and CLE40 peptides trigger consumption of the root meristem in Arabidopsis through a CLAVATA2-dependent pathway

Fiers, M. A., Golemiec, E., Xu, J., van der Geest, L., Heidstra, R., Stiekema, W. & Liu, C. M., 2005, In : The Plant Cell. 17, p. 2542-2553

Research output: Contribution to journalArticleAcademicpeer-review

208 Citations (Scopus)

The Tomato Sequencing Project, the first cornerstone of the International Solanaceae Project (SOL)

Mueller, L. A., Tanksley, S. D., Giovannoni, J. J., van Eck, J., Stack, S., Choi, D., Dong Kim, B., Chen, M., Cheng, Z., Li, C., Ling, H., Xue, Y., Seymour, G. B., Bishop, G., Bryan, G. J., Sharma, R., Khurana, J., Tyagi, A., Chattopadhyay, D., Singh, N. K. & 13 others, Stiekema, W., Lindhout, P., Jesse, T., Klein Lankhorst, R. M., Bouzayen, M., Shibata, D., Tabata, S., Granell, A., Botella, M. A., Giuliano, G., Frusciante, L., Causse, M. & Zamir, D., 2005, In : Comparative and Functional Genomics. 6, 3, p. 153-158

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
101 Citations (Scopus)
2004

A high-resolution map of the H1 locus harbouring resistance to the potato cyst nematode Globodera rostochiensis

Bakker, E. H., Achenbach, U., Bakker, J. D., van Vliet, J. M., Peleman, J., Segers, B., van der Heijden, S., van der Linde, P., Graveland, R., Hutten, R. C. B., van Eck, H. J., Coppoolse, E. R., van der Vossen, E. A. G. & Goverse, A., 2004, In : Theoretical and Applied Genetics. 109, 1, p. 146-152

Research output: Contribution to journalArticleAcademicpeer-review

50 Citations (Scopus)

Allermatch, a webtool for the prediction of potential allergenicity according to current FAO/WHO Codex alimentarius guidelines

Fiers, M. W. E. J., Kleter, G. A., Nijland, H., Peijnenburg, A. A. C. M., Nap, J. P. H. & van Ham, R. C. H. J., 2004, In : BMC Bioinformatics. 5, 6 p., 133.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
88 Citations (Scopus)

Bioinformatics for biosafety: predicting the potential allergenicity of GM food

Stiekema, W. J. & Nap, J. P. H., 2004, Genomics for Biosafety in Plant Biotechnology. Nap, J. P., Atanassov, A. & Stiekema, W. J. (eds.). Amsterdam, p. 98-114 (NATO Science Series; no. 359).

Research output: Chapter in Book/Report/Conference proceedingChapter

Chromosomal co-expression domains in the Arabidopsis thaliana genome

Ren, X. Y., Fiers, M. W. E. J., Nap, J. P. H. & Stiekema, W. J., 2004, Book of Abstracts Congress Centre Hotel De Wageningse Berg, Wageningen, The Netherlands, 31 March 2004 - 2 April 2004. p. 26

Research output: Chapter in Book/Report/Conference proceedingAbstractAcademic

Chromosomal co-expression domains in the Arabidopsis thaliana genome

Ren, X. Y., Fiers, M. W. E. J., Nap, J. P. H. & Stiekema, W. J., 2004.

Research output: Contribution to conferenceAbstractAcademic

Identification and expression of the first nonmammalian amyloid-ß precursor-like protein APLP2 in the amphibian Xenopus laevis

Collin, R. W. J., van Strien, D., Leunissen, J. A. M. & Martens, G. J. M., 2004, In : European Journal of Biochemistry. 271, 10, p. 1906-1912

Research output: Contribution to journalArticleAcademicpeer-review

9 Citations (Scopus)

Satellite repeats in the functional centromere and pericentromeric heterochromatin of Medicago truncatula

Kulikova, O., Geurts, R., Lamine, M., Kim, D. J., Cook, D. R., Leunissen, J., de Jong, J. H. S. G. M., Roe, B. A. & Bisseling, T., 2004, In : Chromosoma. 113, 6, p. 276-283

Research output: Contribution to journalArticleAcademicpeer-review

49 Citations (Scopus)

Towards a better understanding of the role of reactive oxygen species in legume root nodules

Ramos Escribano, J., 2004, [S.l.]. 125 p.

Research output: Thesisinternal PhD, WU

Open Access
2003

An ancient R gene from Solanum bulbocastanum confers broad-spectrum resistance to late Phytophthora infestans in cultivated potato and tomato

van der Vossen, E. A. G., Sikkema, A., te Lintel Hekkert, B., Gross, J., Stevens, P., Muskens, M., Wouters, T. C. A. E., Pereira, A. B., Stiekema, W. J. & Allefs, S., 2003, In : The Plant Journal. 36, 6, p. 867-882

Research output: Contribution to journalArticleAcademicpeer-review

288 Citations (Scopus)

A new web-based data mining tool for the identification of candidate genes for human genetic disorders

van Driel, M. A., Cuelenaere, K., Kemmeren, P. P. C. W., Leunissen, J. A. M. & Brunner, H. G., 2003, In : European Journal of Human Genetics. 11, p. 57-63

Research output: Contribution to journalArticleAcademicpeer-review

72 Citations (Scopus)