Radek Szklarczyk
Comparative Genomics Group (link) Tel: +31-24-36-19-774
Radboud University Nijmegen Medical Centre    Fax: +31-24-36-19-395
Nijmegen Email:
the Netherlands (full address)

Publications

Bas F. J. Wanschers*, Radek Szklarczyk*, Aleksandra Pajak, Mariël A. M. van den Brand, Jolein Gloerich, Richard J. T. Rodenburg, Robert N. Lightowlers, Leo G. Nijtmans, Martijn A. Huynen, C7orf30 specifically associates with the large subunit of the mitochondrial ribosome and is involved in translation, Nucl. Acids Res. published online January 11, 2012 paper
*) Contributed equally

Sonja I. Buschow, Edwin Lasonder, Radek Szklarczyk, Machteld M. Oud, I. Jolanda M. de Vries , Carl G. Figdor, Unraveling the human dendritic cell phagosome proteome by organellar enrichment ranking, Journal of Proteomics 2011, in press pubmed

Jonckheere AI, Huigsloot M, Lammens M, Jansen J, van den Heuvel LP, Spiekerkoetter U, von Kleist-Retzow JC, Forkink M, Koopman WJ, Szklarczyk R, Huynen MA, Fransen JA, Smeitink JA, Rodenburg RJ, Restoration of complex V deficiency caused by a novel deletion in the human TMEM70 gene normalizes mitochondrial morphology, Mitochondrion 2011 Sep 14. [Epub ahead of print] pubmed

Dutilh BE, Jurgelenaite R, Szklarczyk R, van Hijum SA, Harhangi HR, Schmid M, de Wild B, Françoijs KJ, Stunnenberg HG, Strous M, Jetten MS, Op den Camp HJ, Huynen MA. FACIL: fast and accurate genetic code inference and logo, Bioinformatics 2011 Jun 8. [Epub ahead of print] pubmed

M. Huigsloot, L.G. Nijtmans, R. Szklarczyk, M.J.H. Baars, M.A.M. van den Brand, M.G.M. Hendriks-Franssen, L.P. van den Heuvel, J.A.M. Smeitink, M.A. Huynen, R.J.T. Rodenburg, A mutation in C2orf64 causes impaired cytochrome c oxidase assembly and mitochondrial cardiomyopathy, American Journal of Human Genetics 2011 Mar 30. [Epub ahead of print] pubmed

R. Szklarczyk*, B. Wanschers*, S.B. Nabuurs, J. Nouws, L.G. Nijtmans, M.A. Huynen, NDUFB7 and NDUFA8 are located at the intermembrane surface of complex I, FEBS Letters 2011, Feb 21 (Epub ahead of print). pubmed
*) Contributed equally

R. Szklarczyk, M.A. Huynen, Mosaic origin of the mitochondrial proteome, Proteomics 2010, 10, 4012–4024, pubmed

R. Szklarczyk, M.A. Huynen, Expansion of the human mitochondrial proteome by intra- and inter-compartmental protein duplication, Genome Biology 2009, 10:R135, paper

M.A. Huynen, M. de Hollander, R. Szklarczyk, Mitochondrial proteome evolution and genetic disease, Biochimica et Biophysica Acta - Molecular Basis of Disease 2009 December 1792(12):1122-9, pubmed

R. Szklarczyk, M.A. Huynen, B. Snel, Complex fate of paralogs, BMC Evol Biol. 2008 Dec 18;8(1):337, paper

R. Szklarczyk, J. Heringa, S. Kosakovsky Pond, A. Nekrutenko, Rapid asymmetric evolution of a dual-coding tumor suppressor INK4a/ARF locus contradicts its function, Proceedings of the National Academy of Sciences 2007 Jul 31;104(31):12807-12, pdf, List of dual-coding regions

W.-Y. Chung, S. Wadhawan, R. Szklarczyk, S. Kosakovsky Pond, A. Nekrutenko, A First Look at ARFome: Dual-Coding Genes in Mammalian Genomes, PLoS Computational Biology, 2007 May 18;3(5):e91, pdf.

R. Szklarczyk, J. Heringa, AuberGene - a sensitive genome alignment tool, Bioinformatics, 15 June 2006; 22: 1431 - 1436. pdf web

R. Szklarczyk, J. Heringa, Tracking Repeats Using Significance and Transitivity Bioinformatics. 2004 Aug 4;20 Suppl 1:i311-i317 ISMB/ECCB 2004 conference pdf

A. Gambin, S. Lasota, R. Szklarczyk, J. Tiuryn, J. Tyszkiewicz, Contextual Alignment of Biological Sequences Bioinformatics. 2002 Oct; 18 Suppl 2: S116-27, pdf

Research interests
Computational genomics. Comparative genomics. Genome evolution.

No-less-important interests
Skiing. Photography.

Lectures and talks
Title Part of...
 Download/Viewing of Slides
Algorithms for Genomes Course
 A course for Exact Sciences students, 3rd/4th year
 Course website
Comparative Genomics: Phylogenetic footprinting
 Genomics course, 3rd year Biology
 Download in PDF
Alignments (local+global) and BLAST
 Sequence Analysis course, Master Bioinformatics
 Download in PDF
Yeast genome duplication
 Literature discussion
 Download in PDF
TRUST method
 ISMB/ECCB 2004 conference, see Publications above
 Download in PDF
BLAST algorithm
 Data Mining Techiniques lecture
Introduction to Molecular Biology
 Data Mining Techiniques lecture
 Download in PDF
Global Alignment
 Data Mining Techiniques lecture
Local Alignments
 Data Mining Techiniques lecture
Sesil: Repeat detection tool
Repeat statistics
 IBIVU biweekly meetings
 Download in MS Powerpoint
Genomics: Sequencing genomes 
 Bioinformatics course, 2nd year MNW
 Download in PDF
Genomics: Introduction
 Bioinformatics course, 2nd year MNW
 Download in PDF
Contextual alignment
 Own research
 Download in PDF