Recent publications of the Bioinformatics staff

  • Luo H, Lin K, David A, Nijveen H, Leunissen JAM (2011) ProRepeat: an integrated repository for studying amino acid tandem repeats in proteins. Nucleic Acids Res.2011; doi: 10.1093/nar/gkr1019.

  • Via A, De Las Rivas J, Attwood TK, Landsman D, Brazas MD, Leunissen JAM, Tramontano A, Schneider MV (2011) 10 simple rules for developing a short bioinformatics training course. PLoS Computational Biology, in press.

  • Risse JE, Leunissen JAM (2011) A comparison of database systems for XML-type data. In Silico Biology, in press.

  • Lin K, Kools H, de Groot PJ, Gavai AK, Basnet RK, Cheng F, Wu J, Wang X, Lommen A, Hooiveld GJEJ, Bonnema G, Visser RGF, Muller MR, Leunissen JAM (2011) MADMAX - Management and analysis database for multiple ~omics experiments. J. Integrative Bioinformatics, 8(2):160, 2011. Online Journal: http://journal.imbio.de/index.php?paper_id=160.

  • Muiño JM, Hoogstraat M, van Ham RCHJ, van Dijk ADJ (2011) PRI-CAT: A web-tool for the analysis, storage and visualization of plant ChIP-seq experiments. Nucleic Acids Res., accepted for publication.

  • Nijveen H, Kester, M, Viars A, de Ru AH, de Jager M, Falkenburg JHF, Leunissen JAM, van Veelen P (2010) HSPVdb - the Human Short Peptide Variation database for improved mass spectrometry-based detection of polymorphic HLA-ligands. Immunogenetics 63(3), 143-153.

  • Kourmpetis YAI, van Dijk ADJ, Bink MCAM, van Ham RCHJ, ter Braak CJF (2010) Bayesian Markov Random Field Analysis for Protein Function Prediction. PLoS ONE 5(2): e9293. doi:10.1371/journal.pone.0009293.

  • Wassink I, Ooms M, Neerincx P, van der Veer G, Rauwerda H, Leunissen JAM, Breit TM, Nijholt A, van der Vet P (2010) e-BioFlow: Improving Practical Use of Workflow Systems in Bioinformatics. In: Information Technology in Bio- and Medical Informatics, ITBAM 2010, Lecture Notes in Computer Science. Khuri S, Lhotská L, Pisanti N (eds), Springer-Verlag Berlin Heidelberg, Germany. Volume 6266, 1-15, DOI: 10.1007/978-3-642-15020-3_1.

  • Hasiów-Jaroszewska B, Kuzniar A, Peters SA, Leunissen JAM, Pospieszny H (2010) Evidence for RNA recombination between distinct isolates of Pepino mosaic virus. Acta Biochim Pol. 57, 385-388.

  • Kuzniar A, Dhir S, Nijveen H, Pongor S, Leunissen JAM (2010) Multi-netclust: A tool for finding connected clusters in multi-parametric data networks. Bioinformatics, 26, 2482-2483.

  • Nie HS, Crooijmans RPMA, Lammers A, van Schothorst EM, Keijer J, Neerincx PBT, Leunissen JAM, Megens HJ, Groenen MAM (2010) Gene Expression in Chicken Reveals Correlation with Structural Genomic Features and Conserved Patterns of Transcription in the Terrestrial Vertebrates. PLOS ONE 5(8), e11990.

  • van Ophuizen EAA, Leunissen JAM (2010) An evaluation of the performance of three semantic background knowledge sources in comparative anatomy. J. Integrative Bioinformatics 7, 124, doi:10.2390/biecoll-jib-2010-124.

  • Anithakumari AM, Tang J, van Eck HJ, Visser RGF, Leunissen JAM, Vosman B, van der Linden GC (2010) Reliable application of SNPs from EST databases to high throughput genotyping in potato. Mol. Breeding 26, 65-75, doi:10.1007/s11032-009-9377-5.

  • Kuzniar A (2009) Graph-based methods for large-scale protein classification and orthology inference. Ph.D. thesis, Wageningen University.

  • Neerincx PBT (2009) Web services for transcriptomics. Ph.D. thesis, Wageningen University.

  • Neerincx PBT, Casel P, Prickett D, Nie H, Watson M, Leunissen JAM, Groenen MAM, Klopp C (2009) Comparison of three Microarray Probe Annotation Pipelines: Differences in Strategies and their Effect on Downstream Analysis. BMC Proceedings 3 (Suppl 4), S1.

  • Neerincx PBT, Rauwerda H, Nie H, Groenen MAM, Breit TM, Leunissen JAM (2009) OligoRAP - An Oligo Re-Annotation Pipeline to improve annotation and estimate target specificity. BMC Proceedings 3 (Suppl 4), S4.

  • Hedegaard J, Bicciato S, Bonnet A, Ramirez Boo M, Buitenhuis B, Collado-Romero M, Nagstrup Conley L, San Cristobal M, Ferrari F, Groenen MAM, Hornshøj H, Hulsegge I, Jiang L, Arce Jiménez C, Jiménez-Marín A, Kommadath A, Lagarrigue S, Leunissen JAM, Liaubet L, Neerincx PBT, Nie H, Garrido Pavón JJ, Prickett D, Rebel JMJ, Robert-Granié C, Skarman A, Smits MA, Sørensen P, Tosser-Klopp G, van der Poel J, Watson M (2009) Methods for interpreting lists of affected genes obtained in a DNA microarray experiment. BMC Proceeding 3 (Suppl 4), S5.
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  • Nie H, Neerincx PBT, Poel JVD, Ferrari F, Bicciato S, Leunissen JAM, Groenen MAM (2009) Microarray data mining using Bioconductor packages. BMC Proceedings 3 (Suppl 4), S9.

  • Wassink I, Rauwerda H, Neerincx PBT, van der Vet PE, Breit TM, Leunissen JAM, Nijholt A (2009) Using R in Taverna: RShell v1.2. BMC Research Notes 2, 138.

  • Gavai AK (2009) Bayesian Networks for -omics data analysis. Ph.D. thesis, Wageningen University.

  • Kuzniar A, Lin K, He Y, Nijveen H, Pongor S, Leunissen JAM (2009) ProGMap: an integrated annotation resource for protein orthology. Nucleic Acids Res. 37, W428-W434; doi:10.1093/nar/gkp462.

  • Gavai AK, Tikunov Y, Ursem R, Bovy A, van Eeuwijk F, Nijveen H, Lucas PJF, Leunissen JAM (2009) Constraint-based probabilistic learning of metabolic pathways from tomato volatiles. Metabolomics, doi:10.1007/s11306-009-0166-2.

  • Strating JRPM, van Bakel NN, Leunissen JAM, Martens GJM (2009) A comprehensive overview of the vertebrate p24 family: identification of a novel tissue-specifically expressed member. Mol. Biol. Evol. 26 (8), 1707-1714; doi:10.1093/molbev/msp099.

  • Kuzniar A, van Ham RCHJ, Pongor S, Leunissen JAM (2008) The quest for orthologs: finding the corresponding gene across genomes. Trends in Genetics 24 (11), 539-551; doi:10.1016/j.tig.2008.08.009.

  • Tang J, Baldwin SJ, Jacobs JME, van der Linden CG, Voorrips RE, Leunissen JAM, van Eck H, Vosman B (2008) Large-scale Identification of polymorphic microsatellites using an in silico approach. BMC Bioinformatics 9, 374; doi:10.1186/1471-2105-9-374.

  • Brandt BW, Heringa J, Leunissen JAM (2008) SEQATOMS: a web tool for identifying missing regions in PDB in sequence context. Nucleic Acids Res. 36, W255-W259; doi:10.1093/nar/gkn237.

  • The BioMoby Consortium: Wilkinson MD, Senger M, Kawas E, Bruskiewich R, Gouzy J, Noirot C, Bardou P, Ng A, Haase D, Saiz Ede A, Wang D, Gibbons F, Gordon PM, Sensen CW, Carrasco JM, Fernández JM, Shen L, Links M, Ng M, Opushneva N, Neerincx PB, Leunissen JAM, Ernst R, Twigger S, Usadel B, Good B, Wong Y, Stein L, Crosby W, Karlsson J, Royo R, Párraga I, Ramírez S, Gelpi JL, Trelles O, Pisano DG, Jimenez N, Kerhornou A, Rosset R, Zamacola L, Tarraga J, Huerta-Cepas J, Carazo JM, Dopazo J, Guigo R, Navarro A, Orozco M, Valencia A, Claros MG, Pérez AJ, Aldana J, Rojano MM, Fernandez-Santa Cruz R, Navas I, Schiltz G, Farmer A, Gessler D, Schoof H, Groscurth A (2008) Interoperability with Moby 1.0 - It's better than sharing your toothbrush! Briefings in Bioinformatics 9, 220-231.

  • Tang J, Leunissen JAM, Voorrips RE, van der Linden CG, Vosman B (2008) HaploSNPer: a web-based allele and SNP detection tool. BMC Genetics 9, 23; doi:10.1186/1471-2156-9-23.

  • Alako BTF (2008) Integrative algorithmic approach towards knowledge discovery by bioinformatics. Ph.D. thesis, Wageningen University.

  • Tang J (2008) A bioinformatics approach to marker development. Ph.D. thesis, Wageningen University.

  • Kertész-Farkas A, Dhir S, Sonego P, Pacurar M, Netoteia S, Nijveen H, Kuzniar A, Leunissen JAM, Kocsor A, Pongor S (2008) Benchmarking protein classification algorithms via supervised cross-validation. J. Biochem. Biophys. Methods 70, 1215-1223, doi:10.1016/j.jbbm.2007.05.011

  • Vos A, Dekker N, Distel B, Leunissen JAM, Hochstenbach F (2007) Role of the SYN domain of Ags1p in cell wall α-glucan biosynthesis in fission yeast. J. Biol. Chem. 282, 18969-18979.

  • Untergasser A, Nijveen H, Rao X, Bisseling T, Geurts R, Leunissen JAM (2007) Primer3Plus, an enhanced web interface to Primer3. Nucleic Acids Res. 35, W71-W74; doi:10.1093/nar/gkm306

  • Sonego P, Pacurar M, Dhir S, Kertész-Farkas A, Kocsor A, Gáspári Z, Leunissen J, Pongor S (2007) A Protein Classification Benchmark collection for machine learning. Nucleic Acids Res. 35, D232-D236.

  • Hulsen T, de Vlieg J, Leunissen JAM, Groenen P (2006) Testing statistical significance scores of sequence comparison methods with structure similarity. BMC Bioinformatics 2006, 7:444.

  • Tang J, Vosman B, Voorrips RE, van der Linden CG, Leunissen JAM (2006) QualitySNP: a pipeline for detecting single nucleotide polymorphisms and insertions/deletions in EST data from diploid and polyploid species. BMC Bioinformatics 2006, 7:438.

  • Alako B, Rainey D, Nijveen H, Leunissen JAM (2006) TreeDomViewer: a tool for the visualization of phylogeny and protein domain structure. Nucleic Acids Res. 34, W104-W109.

  • van Driel MA, Bruggeman J, Vriend G, Brunner HG, Leunissen JAM (2006) A text-mining analysis of the human phenome. Eur. J. Human Genet. 14, 535-542.

  • Coppoolse ER, de Vroomen MJ, van Gennip F, Hersmus BJM, van Haaren MJJ (2005) Size does matter: Cre-mediated somatic deletion efficiency depends on the distance between the target lox-sites. Plant Mol. Biol. 58, 687-698.

  • de Haan JR, Leunissen JAM (2005) Protein secondary structure prediction. Comparison of ten common prediction algorithms using a neural network. In: Essays in Bioinformatics. Moss DS, Jelaska S, and Pongor S., editors. IOS Press, Amsterdam. pp. 149-161.

  • Vassilev D, Leunissen J, Atanassov A, Nenov A, Dimov G (2005) Application of bioinformatics in plant breeding. Biotech. Biotech. Equip. 19, 139-152.

  • van Driel MA, Cuelenaere K, Kemmeren PPCW, Leunissen JAM, Brunner HG, Vriend G (2005) GeneSeeker: extraction and integration of human disease-related information from web-based genetic databases. Nucleic Acids Res. 33, W758-761.

  • Neerincx P, Leunissen JAM (2005) Evolution of web services in bioinformatics. Briefings in Bioinformatics 6, 178-188.

  • Alako BT, Veldhoven A, van Baal S, Jelier R, Verhoeven S, Rullmann T, Polman J, Jenster G. (2005) CoPub Mapper: mining MEDLINE based on search term co-publication. BMC Bioinformatics. 2005 6, 51.

  • Bakker EH, Achenbach U, Bakker J, van Vliet J, Peleman J, Segers B, van der Heijden S, van der Linde P, Graveland P, Hutten RCB, van Eck HJ, Coppoolse ER, Vossen EAG, Goverse A (2004) A high-resolution map of the H1 locus harbouring resistance to the potato cyst nematode Globodera rostochiensis. Theor. Appl. Genetics 109, 146-152.

  • Kulikova O, Geurts R, Lamine M, Kim DJ, Cook DR, Leunissen J, de Jong JHSGM, Roe BA, Bisseling T (2004) Satellite repeats in the functional centromere and pericentromeric heterochromatin of Medicago truncatula. Chromosoma 113, 276-283.

  • Collin RWJ, van Strien D, Leunissen JAM, Martens GJM (2004) Identification and expression of the first nonmammalian amyloid-β precursor-like protein APLP2 in the amphibian Xenopus laevis. Eur. J. Biochem 271, 1906-1912.

  • Kappé G, Franck E, Verschuure P, Boelens WC, Leunissen JAM, de Jong WW (2003) The human genome encodes ten alpha-crystallin-related small heat shock proteins: HspB1-10. Cell Stress & Chaperones 8, 53-61.

  • Leunissen JAM (2003) Chimera: construction of chimeric sequences for phylogenetic analysis. Bioinformatics 19, 303-304.

  • van Driel MA, Cuelenaere K, Kemmeren PPCW, Leunissen JAM, Brunner HG (2003) A new web-based data mining tool for the identification of candidate genes for human genetic disorders. Eur. J. Human Genet. 11, 57-63.

Last modified November 19, 2011, by JL

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