Radek Szklarczyk

With January 2014 I moved to the Clinical Genetics department of Maastricht University Medical Centre.
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Publications

Radek Szklarczyk, Bas F.J. Wanschers, Leo G. Nijtmans, Richard J. Rodenburg, Johannes Zschocke, Nicola Dikow, Mariël A.M. van den Brand, Marthe G.M. Hendriks-Franssen, Christian Gilissen, Joris A. Veltman, Marco Nooteboom, Werner J.H. Koopman, Peter H.G.M. Willems, Jan A.M. Smeitink, Martijn A. Huynen, and Lambertus P. van den Heuvel, A mutation in the FAM36A gene, the human ortholog of COX20, impairs cytochrome c oxidase assembly and is associated with ataxia and muscle hypotonia, Hum. Mol. Genet. 2013 pubmed

Peter Willems, Bas Wanschers, John Esseling, Radek Szklarczyk, Urszula Kudla, Isabel Duarte, Marleen Forkink, Marco Nooteboom, Herman Swarts, Jolein Gloerich, Leo Nijtmans, Werner Koopman, and Martijn A. Huynen BOLA1 is an aerobic protein that prevents mitochondrial morphology changes induced by glutathione depletion, Antioxidant and Redox Signalling 2013 pubmed

Martijn A. Huynen, Isabel Duarte, Radek Szklarczyk, Loss, replacement and gain of proteins at the origin of the mitochondria, Biochim. Biophys. Acta 2013 pubmed

Eduardo Balsa, Ricardo Marco, Ester Perales-Clemente, Radek Szklarczyk, Enrique Calvo, Manuel O. Landázuri, José A. Enríquez, Redefinition of the Electron Transport Chain Complexes I and IV: the Mismatched Subunit NDUFA4, Cell Metabolism 2012 pubmed

Radek Szklarczyk*, Bas F.J. Wanschers*, Thomas D. Cuypers, John J. Esseling, Moniek Riemersma, Mariël A.M. van den Brand, Jolein Gloerich, Edwin Lasonder, Lambert P. van den Heuvel, Leo G. Nijtmans, Martijn A. Huynen, Iterative orthology prediction uncovers new mitochondrial proteins and identifies C12orf62 as the human ortholog of COX14, a protein involved in the assembly of cytochrome c oxidase, Genome Biology 2012 paper
*) Contributed equally

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 2012 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 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 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 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 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

Lectures and talks
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Algorithms for Genomes Course
A course for Exact Sciences students, 3rd/4th year
Course website
Comparative Genomics: Phylogenetic footprinting
Genomics course, 3rd year Biology
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Alignments (local+global) and BLAST
Sequence Analysis course, Master Bioinformatics
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Yeast genome duplication
Literature discussion
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TRUST method
ISMB/ECCB 2004 conference, see Publications above
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BLAST algorithm
Data Mining Techiniques lecture
Introduction to Molecular Biology
Data Mining Techiniques lecture
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Global Alignment
Data Mining Techiniques lecture
Local Alignments
Data Mining Techiniques lecture
Sesil: Repeat detection tool
Repeat statistics

IBIVU biweekly meetings
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Genomics: Sequencing genomes 
Bioinformatics course, 2nd year MNW
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Genomics: Introduction
Bioinformatics course, 2nd year MNW
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Contextual alignment
Own research
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