Jack A Leunissen

Jack A M Leunissen

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Jack A Leunissen

Jack A M Leunissen

Publications by authors named "Jack A M Leunissen"

39Publications

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1PubMed Central Citations

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

PLoS One 2015 25;10(3):e0119016. Epub 2015 Mar 25.

Centre for Integrative Bioinformatics, VU University, Amsterdam, The Netherlands; Netherlands Consortium for Systems Biology (NCSB), Amsterdam, The Netherlands; Section Functional Genomics, Dept. Clinical Genetics, VU University Medical Center,Amsterdam, The Netherlands.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0119016PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4373785PMC
February 2016

A comparison of database systems for XML-type data.

In Silico Biol 2010 ;10(3):193-205

Laboratory for Bioinformatics, Wageningen University and Research Centre, Wageningen, The Netherlands.

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http://dx.doi.org/10.3233/ISB-2010-0433DOI Listing
September 2013

The human leukocyte antigen-presented ligandome of B lymphocytes.

Mol Cell Proteomics 2013 Jul 12;12(7):1829-43. Epub 2013 Mar 12.

Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, The Netherlands.

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http://dx.doi.org/10.1074/mcp.M112.024810DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3708169PMC
July 2013

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

Nucleic Acids Res 2012 Jan 18;40(Database issue):D394-9. Epub 2011 Nov 18.

Laboratory of Bioinformatics, Wageningen University and Research Centre, PO Box 569, 6700 AN Wageningen, Netherlands.

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http://dx.doi.org/10.1093/nar/gkr1019DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3245022PMC
January 2012

MADMAX - Management and analysis database for multiple ~omics experiments.

J Integr Bioinform 2011 Jul 21;8(2):160. Epub 2011 Jul 21.

Laboratory of Bioinformatics, P.O. Box 569, 6700 AN Wageningen, the Netherlands.

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http://dx.doi.org/10.2390/biecoll-jib-2011-160DOI Listing
July 2011

Evidence for RNA recombination between distinct isolates of Pepino mosaic virus.

Acta Biochim Pol 2010 19;57(3):385-8. Epub 2010 Aug 19.

Institute of Plant Protection, National Research Institute, Department of Virology and Bacteriology, Poznań, Poland.

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January 2011

Multi-netclust: an efficient tool for finding connected clusters in multi-parametric networks.

Bioinformatics 2010 Oct 2;26(19):2482-3. Epub 2010 Aug 2.

Laboratory of Bioinformatics, Wageningen University and Research Centre, PO Box 569, 6700 AN Wageningen, The Netherlands.

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http://dx.doi.org/10.1093/bioinformatics/btq435DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2944197PMC
October 2010

An evaluation of the performance of three semantic background knowledge sources in comparative anatomy.

J Integr Bioinform 2010 Mar 25;7(3). Epub 2010 Mar 25.

Laboratory of Bioinformatics, Wageningen University, Droevendaalsesteeg 1, 6708PB, Wageningen, The Netherlands.

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http://dx.doi.org/10.2390/biecoll-jib-2010-124DOI Listing
March 2010

A comprehensive overview of the vertebrate p24 family: identification of a novel tissue-specifically expressed member.

Mol Biol Evol 2009 Aug 8;26(8):1707-14. Epub 2009 May 8.

Department of Molecular Animal Physiology, Donders Centre for Neuroscience and Nijmegen Centre for Molecular Life Sciences (NCMLS), Faculty of Science, Radboud University, Nijmegen, The Netherlands.

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http://dx.doi.org/10.1093/molbev/msp099DOI Listing
August 2009

ProGMap: an integrated annotation resource for protein orthology.

Nucleic Acids Res 2009 Jul 3;37(Web Server issue):W428-34. Epub 2009 Jun 3.

Laboratory of Bioinformatics, Wageningen University and Research Centre (WUR), Dreijenlaan 3, 6703 HA Wageningen, The Netherlands.

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http://dx.doi.org/10.1093/nar/gkp462DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2703891PMC
July 2009

Using R in Taverna: RShell v1.2.

BMC Res Notes 2009 Jul 16;2:138. Epub 2009 Jul 16.

Human Media Interaction Group, University of Twente, Enschede, The Netherlands.

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http://dx.doi.org/10.1186/1756-0500-2-138DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2717104PMC
July 2009

OligoRAP - an Oligo Re-Annotation Pipeline to improve annotation and estimate target specificity.

BMC Proc 2009 Jul 16;3 Suppl 4:S4. Epub 2009 Jul 16.

Laboratory of Bioinformatics, Wageningen University and Research centre (WUR), P,O, Box 569, 6700 AN Wageningen, The Netherlands.

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http://dx.doi.org/10.1186/1753-6561-3-S4-S4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2712747PMC
July 2009

Microarray data mining using Bioconductor packages.

BMC Proc 2009 Jul 16;3 Suppl 4:S9. Epub 2009 Jul 16.

Animal Breeding and Genomics Centre, Wageningen University, Marijkeweg 40, P,O, Box 338, 6700 AH, Wageningen, The Netherlands.

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http://dx.doi.org/10.1186/1753-6561-3-S4-S9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2712752PMC
July 2009

The quest for orthologs: finding the corresponding gene across genomes.

Trends Genet 2008 Nov 24;24(11):539-51. Epub 2008 Sep 24.

Laboratory of Bioinformatics, Wageningen University, Dreijenlaan 3, 6703 HA Wageningen, The Netherlands.

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http://dx.doi.org/10.1016/j.tig.2008.08.009DOI Listing
November 2008

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

Nucleic Acids Res 2008 Jul 7;36(Web Server issue):W255-9. Epub 2008 May 7.

Centre for Integrative Bioinformatics (IBIVU), VU University Amsterdam, De Boelelaan 1081a, 1081 HV Amsterdam, The Netherlands.

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https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/
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http://dx.doi.org/10.1093/nar/gkn237DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2447787PMC
July 2008

Benchmarking protein classification algorithms via supervised cross-validation.

J Biochem Biophys Methods 2008 Apr 31;70(6):1215-23. Epub 2007 May 31.

Research Group on Artificial Intelligence of the Hungarian Academy of Sciences and University of Szeged, Aradi vértanúk tere 1., H-6720 Szeged, Hungary.

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http://dx.doi.org/10.1016/j.jbbm.2007.05.011DOI Listing
April 2008

HaploSNPer: a web-based allele and SNP detection tool.

BMC Genet 2008 Feb 28;9:23. Epub 2008 Feb 28.

Laboratory of Bioinformatics, Wageningen University, PO Box 8128, 6700 ET Wageningen, The Netherlands.

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http://dx.doi.org/10.1186/1471-2156-9-23DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2288614PMC
February 2008

Primer3Plus, an enhanced web interface to Primer3.

Nucleic Acids Res 2007 Jul 7;35(Web Server issue):W71-4. Epub 2007 May 7.

Laboratory of Molecular Biology, Department of Plant Science, Wageningen University, Dreijenlaan 3, 6703HA, Wageningen, The Netherlands.

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http://dx.doi.org/10.1093/nar/gkm306DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1933133PMC
July 2007

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

J Biol Chem 2007 Jun 30;282(26):18969-79. Epub 2007 Apr 30.

Department of Medical Biochemistry, Academic Medical Center, University of Amsterdam, Meibergdreef 15, 1105 AZ Amsterdam, The Netherlands.

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http://dx.doi.org/10.1074/jbc.M605147200DOI Listing
June 2007

A Protein Classification Benchmark collection for machine learning.

Nucleic Acids Res 2007 Jan 16;35(Database issue):D232-6. Epub 2006 Nov 16.

Protein Structure and Bioinformatics Group, International Centre for Genetic Engineering and Biotechnology, Padriciano 99, 34012 Trieste, Italy.

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http://dx.doi.org/10.1093/nar/gkl812DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1669728PMC
January 2007

Testing statistical significance scores of sequence comparison methods with structure similarity.

BMC Bioinformatics 2006 Oct 12;7:444. Epub 2006 Oct 12.

Centre for Molecular and Biomolecular Informatics, Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands.

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http://dx.doi.org/10.1186/1471-2105-7-444DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1618413PMC
October 2006

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

Nucleic Acids Res 2006 Jul;34(Web Server issue):W104-9

Laboratory of Bioinformatics, Wageningen University and Research Centre, PO Box 8128, 6700 ET Wageningen, The Netherlands.

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https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/
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http://dx.doi.org/10.1093/nar/gkl171DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1538806PMC
July 2006

A text-mining analysis of the human phenome.

Eur J Hum Genet 2006 May;14(5):535-42

Centre for Molecular and Biomolecular Informatics, Radboud University Nijmegen, Toernooiveld 1, 6525ED Nijmegen, the Netherlands.

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http://dx.doi.org/10.1038/sj.ejhg.5201585DOI Listing
May 2006

Evolution of web services in bioinformatics.

Brief Bioinform 2005 Jun;6(2):178-88

Laboratory of Bioinformatics, Department of Plant Sciences, Wageningen University and Research Centre (WUR), Wageningen, the Netherlands.

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http://dx.doi.org/10.1093/bib/6.2.178DOI Listing
June 2005

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

Eur J Biochem 2004 May;271(10):1906-12

Department of Molecular Animal Physiology, Nijmegen Center for Molecular Life Sciences (NCMLS), University of Nijmegen, The Netherlands.

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http://dx.doi.org/10.1111/j.1432-1033.2004.04100.xDOI Listing
May 2004

The human genome encodes 10 alpha-crystallin-related small heat shock proteins: HspB1-10.

Cell Stress Chaperones 2003 ;8(1):53-61

Department of Biochemistry, 161 NCMLS, University of Nijmegen, PO Box 9101, 6500 HB Nijmegen, The Netherlands.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC514853PMC
http://dx.doi.org/10.1379/1466-1268(2003)8<53:thgecs>2.0.co;2DOI Listing
January 2004

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

Eur J Hum Genet 2003 Jan;11(1):57-63

Centre for Molecular and Biomolecular Informatics, University of Nijmegen, The Netherlands.

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http://dx.doi.org/10.1038/sj.ejhg.5200918DOI Listing
January 2003

Chimera: construction of chimeric sequences for phylogenetic analysis.

Bioinformatics 2003 Jan;19(2):303-4

Dalicon BV, Toernooiveld 218, 6525 EC Nijmegen (NL).

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http://dx.doi.org/10.1093/bioinformatics/19.2.303DOI Listing
January 2003

Evolution and diversity of prokaryotic small heat shock proteins.

Prog Mol Subcell Biol 2002 ;28:1-17

Department of Biochemistry, University of Nijmegen, P.O. Box 9101, 6500 HB Nijmegen, The Netherlands.

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http://dx.doi.org/10.1007/978-3-642-56348-5_1DOI Listing
September 2002

EXProt--a database for EXPerimentally verified Protein functions.

In Silico Biol 2002 ;2(1):1-4

Centre for Molecular and Biomolecular Informatics, University of Nijmegen, The Netherlands.

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June 2002

EXProt: a database for proteins with an experimentally verified function.

Nucleic Acids Res 2002 Jan;30(1):50-1

Centre for Molecular and Biomolecular Informatics (CMBI), University of Nijmegen, PO Box 9010, 6500 GL Nijmegen, The Netherlands.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC99155PMC
http://dx.doi.org/10.1093/nar/30.1.50DOI Listing
January 2002