Martijn A Huynen

Martijn A Huynen

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Martijn A Huynen

Publications by authors named "Martijn A Huynen"

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Diabetes is associated with genotypically drug-resistant tuberculosis.

Eur Respir J 2019 Dec 12. Epub 2019 Dec 12.

Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, the Netherlands.

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http://dx.doi.org/10.1183/13993003.01891-2019DOI Listing
December 2019

Mapping actionable pathways and mutations in brain tumours using targeted RNA next generation sequencing.

Acta Neuropathol Commun 2019 Nov 20;7(1):185. Epub 2019 Nov 20.

Department of Biochemistry, Radboud Institute for Molecular Life Sciences, Geert Grooteplein 26, 6525, GA, Nijmegen, The Netherlands.

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http://dx.doi.org/10.1186/s40478-019-0826-zDOI Listing
November 2019

A Combined Mass Spectrometry and Data Integration Approach to Predict the Mitochondrial Poly(A) RNA Interacting Proteome.

Front Cell Dev Biol 2019 15;7:283. Epub 2019 Nov 15.

Department of Pediatrics, Radboud Center for Mitochondrial Medicine, Radboud University Medical Centre, Nijmegen, Netherlands.

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http://dx.doi.org/10.3389/fcell.2019.00283DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6873792PMC
November 2019

COmplexome Profiling ALignment (COPAL) reveals remodeling of mitochondrial protein complexes in Barth syndrome.

Bioinformatics 2019 Sep;35(17):3083-3091

CMBI, Radboud Centre for Mitochondrial Medicine, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands.

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http://dx.doi.org/10.1093/bioinformatics/btz025DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6735710PMC
September 2019

Use of whole-genome sequencing to predict Mycobacterium tuberculosis drug resistance in Indonesia.

J Glob Antimicrob Resist 2019 03 29;16:170-177. Epub 2018 Aug 29.

Infectious Disease Research Center, Faculty of Medicine, Universitas Padjadjaran, Eijkman 38, Bandung 40161, Indonesia; Faculty of Medicine, Universitas Padjadjaran/Hasan Sadikin Hospital, Pasir Kaliki 38, Bandung 40161, Indonesia.

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http://dx.doi.org/10.1016/j.jgar.2018.08.018DOI Listing
March 2019

The Tudor protein Veneno assembles the ping-pong amplification complex that produces viral piRNAs in Aedes mosquitoes.

Nucleic Acids Res 2019 03;47(5):2546-2559

Department of Medical Microbiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, P.O. Box 9101, 6500 HB Nijmegen, The Netherlands.

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https://academic.oup.com/nar/advance-article/doi/10.1093/nar
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http://dx.doi.org/10.1093/nar/gky1266DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6411831PMC
March 2019

The assembly pathway of complex I in Arabidopsis thaliana.

Plant J 2019 02 27;97(3):447-459. Epub 2018 Nov 27.

Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany.

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http://dx.doi.org/10.1111/tpj.14133DOI Listing
February 2019

Allele-specific RNA-seq expression profiling of imprinted genes in mouse isogenic pluripotent states.

Epigenetics Chromatin 2019 02 15;12(1):14. Epub 2019 Feb 15.

Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences (RIMLS), Radboud University, 6500 HB, Nijmegen, The Netherlands.

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http://dx.doi.org/10.1186/s13072-019-0259-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6376749PMC
February 2019

Towards predicting the environmental metabolome from metagenomics with a mechanistic model.

Nat Microbiol 2018 04 12;3(4):456-460. Epub 2018 Mar 12.

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

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http://dx.doi.org/10.1038/s41564-018-0124-8DOI Listing
April 2018

Haemophilus is overrepresented in the nasopharynx of infants hospitalized with RSV infection and associated with increased viral load and enhanced mucosal CXCL8 responses.

Microbiome 2018 01 11;6(1):10. Epub 2018 Jan 11.

Laboratory of Pediatric Infectious Diseases, Radboud Center for Infectious Diseases, Radboud University Medical Center, Geert Grooteplein-Zuid 10 (Route 412), 6525, GA, Nijmegen, The Netherlands.

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http://dx.doi.org/10.1186/s40168-017-0395-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5765694PMC
January 2018

The Gene Ontology of eukaryotic cilia and flagella.

Cilia 2017 16;6:10. Epub 2017 Nov 16.

European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD UK.

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http://dx.doi.org/10.1186/s13630-017-0054-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5688719PMC
November 2017

Interspecies differences in PTH-mediated PKA phosphorylation of the epithelial calcium channel TRPV5.

Pflugers Arch 2017 10 22;469(10):1301-1311. Epub 2017 May 22.

Department of Physiology, Radboud University Medical Center, PO Box 9101, 6500 HB, Nijmegen, The Netherlands.

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http://dx.doi.org/10.1007/s00424-017-1996-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5590029PMC
October 2017

Whole-Genome Sequencing of Bacterial Pathogens: the Future of Nosocomial Outbreak Analysis.

Clin Microbiol Rev 2017 10;30(4):1015-1063

Department of Medical Microbiology, Radboud University Medical Centre, Nijmegen, The Netherlands.

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http://dx.doi.org/10.1128/CMR.00016-17DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5608882PMC
October 2017

Genome-scale detection of positive selection in nine primates predicts human-virus evolutionary conflicts.

Nucleic Acids Res 2017 Oct;45(18):10634-10648

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

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http://dx.doi.org/10.1093/nar/gkx704DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5737536PMC
October 2017

Regulatory remodeling in the allo-tetraploid frog Xenopus laevis.

Genome Biol 2017 10 24;18(1):198. Epub 2017 Oct 24.

Radboud University, Faculty of Science, Department of Molecular Developmental Biology, Radboud Institute for Molecular Life Sciences, 6500 HB, Nijmegen, The Netherlands.

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http://dx.doi.org/10.1186/s13059-017-1335-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5655803PMC
October 2017

Heterochromatic histone modifications at transposons in Xenopus tropicalis embryos.

Dev Biol 2017 06 14;426(2):460-471. Epub 2016 Sep 14.

Radboud University, Department of Molecular Developmental Biology, Radboud Institute for Molecular Life Sciences, Faculty of Science, PO Box 9101, 6500 HB Nijmegen, The Netherlands.

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http://dx.doi.org/10.1016/j.ydbio.2016.08.031DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5350053PMC
June 2017

Identification and evolutionary analysis of tissue-specific isoforms of mitochondrial complex I subunit NDUFV3.

Biochim Biophys Acta Bioenerg 2017 Mar 15;1858(3):208-217. Epub 2016 Dec 15.

Radboud Center for Mitochondrial Medicine, Radboud University Medical Center, Nijmegen, The Netherlands. Electronic address:

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http://dx.doi.org/10.1016/j.bbabio.2016.12.004DOI Listing
March 2017

Immunologic defects in severe mucocutaneous HSV-2 infections: Response to IFN-γ therapy.

J Allergy Clin Immunol 2016 09 7;138(3):895-898. Epub 2016 Apr 7.

Department of Internal Medicine, and RadboudUMC Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands. Electronic address:

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http://dx.doi.org/10.1016/j.jaci.2016.02.025DOI Listing
September 2016

Proteomics of Human Dendritic Cell Subsets Reveals Subset-Specific Surface Markers and Differential Inflammasome Function.

Cell Rep 2016 09;16(11):2953-2966

Department of Tumor Immunology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, P.O. Box 9101, 6500 HB Nijmegen, the Netherlands; Department of Gastroenterology and Hepatology, Erasmus MC-University Medical Center, 3015 CN Rotterdam, the Netherlands. Electronic address:

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5039226PMC
http://dx.doi.org/10.1016/j.celrep.2016.08.023DOI Listing
September 2016

The origin of the supernumerary subunits and assembly factors of complex I: A treasure trove of pathway evolution.

Biochim Biophys Acta 2016 Jul 15;1857(7):971-9. Epub 2016 Apr 15.

Centre for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands; Nijmegen Centre for Mitochondrial Disorders, Radboud University Medical Center, Nijmegen, The Netherlands. Electronic address:

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http://dx.doi.org/10.1016/j.bbabio.2016.03.027DOI Listing
July 2016

Estimating Metabolic Fluxes Using a Maximum Network Flexibility Paradigm.

PLoS One 2015 12;10(10):e0139665. Epub 2015 Oct 12.

Institute for Computing and Information Sciences (ICIS), Radboud University, Nijmegen, the Netherlands; Centre for Systems Biology and Bioenergetics (CSBB), Radboud University Medical Centre, Nijmegen, the Netherlands.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0139665PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4601694PMC
June 2016

CTCF-mediated chromatin loops enclose inducible gene regulatory domains.

BMC Genomics 2016 Mar 22;17:252. Epub 2016 Mar 22.

Department of Molecular Developmental Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University, Nijmegen, The Netherlands.

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http://dx.doi.org/10.1186/s12864-016-2516-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4804521PMC
March 2016

OFIP/KIAA0753 forms a complex with OFD1 and FOR20 at pericentriolar satellites and centrosomes and is mutated in one individual with oral-facial-digital syndrome.

Hum Mol Genet 2016 Feb 7;25(3):497-513. Epub 2015 Dec 7.

Equipe d'Accueil 4271, Génétique des Anomalies du Développement, Université Fédérale Bourgogne - Franche Comté, F-21079 Dijon, France, Fédération Hospitalo-Universitaire Médecine Translationnelle et Anomalies du Développement (TRANSLAD), Centre de Génétique et Centre de Référence Anomalies du Développement et Syndromes Malformatifs de l'Interrégion Est,

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http://dx.doi.org/10.1093/hmg/ddv488DOI Listing
February 2016

Predicting human genetic interactions from cancer genome evolution.

PLoS One 2015 1;10(5):e0125795. Epub 2015 May 1.

Department of Bioinformatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre, Nijmegen, The Netherlands; Centre for Systems Biology and Bioenergetics, Radboud University Medical Centre, Nijmegen, The Netherlands.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0125795PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4416779PMC
January 2016

Evolution and structural organization of the mitochondrial contact site (MICOS) complex and the mitochondrial intermembrane space bridging (MIB) complex.

Biochim Biophys Acta 2016 Jan 23;1863(1):91-101. Epub 2015 Oct 23.

Nijmegen Centre for Mitochondrial Disorders, Radboud University Medical Center, Nijmegen, The Netherlands; Cluster of Excellence Frankfurt "Macromolecular Complexes", Goethe-University, Germany.

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http://dx.doi.org/10.1016/j.bbamcr.2015.10.009DOI Listing
January 2016

WeGET: predicting new genes for molecular systems by weighted co-expression.

Nucleic Acids Res 2016 Jan 17;44(D1):D567-73. Epub 2015 Nov 17.

Centre for Molecular and Biomolecular Informatics (CMBI), Radboud University Medical Centre, Geert Grooteplein Zuid 26-28, 6525 GA Nijmegen, Nijmegen, The Netherlands Centre for Systems Biology and Bioenergetics (CSBB), Radboud University Medical Centre, Geert Grooteplein Zuid 10, 6500 HB Nijmegen, Nijmegen, The Netherlands

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http://dx.doi.org/10.1093/nar/gkv1228DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4702868PMC
January 2016

Systematic Phenomics Analysis Deconvolutes Genes Mutated in Intellectual Disability into Biologically Coherent Modules.

Am J Hum Genet 2016 Jan;98(1):149-64

Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud university medical center, 6525 GA Nijmegen, the Netherlands. Electronic address:

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http://dx.doi.org/10.1016/j.ajhg.2015.11.024DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4716705PMC
January 2016

Sequence specificity between interacting and non-interacting homologs identifies interface residues--a homodimer and monomer use case.

BMC Bioinformatics 2015 Oct 8;16:325. Epub 2015 Oct 8.

Center for Integrative Bioinformatics VU (IBIVU), Vrije University Amsterdam, De Boelelaan 1081A, 1081 HV, Amsterdam, The Netherlands.

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http://dx.doi.org/10.1186/s12859-015-0758-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4599308PMC
October 2015

Integrative Genomics-Based Discovery of Novel Regulators of the Innate Antiviral Response.

PLoS Comput Biol 2015 Oct 20;11(10):e1004553. Epub 2015 Oct 20.

Centre for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud university medical center, Nijmegen, The Netherlands.

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http://dx.doi.org/10.1371/journal.pcbi.1004553DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4618338PMC
October 2015

The pros and cons of vertebrate animal models for functional and therapeutic research on inherited retinal dystrophies.

Prog Retin Eye Res 2015 Sep 1;48:137-59. Epub 2015 May 1.

Department of Human Genetics, Radboud University Medical Center, Geert Grooteplein 10, 6525 GA, Nijmegen, The Netherlands; Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein 10, 6525 GA, Nijmegen, The Netherlands. Electronic address:

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http://dx.doi.org/10.1016/j.preteyeres.2015.04.004DOI Listing
September 2015

Transcriptome analysis of complex I-deficient patients reveals distinct expression programs for subunits and assembly factors of the oxidative phosphorylation system.

BMC Genomics 2015 Sep 15;16:691. Epub 2015 Sep 15.

Nijmegen Center for Mitochondrial Disorders, Department of Pediatrics, Radboud Institute for Molecular Life Sciences, Radboud university medical center, PO BOX 9101, 6500 HB, Nijmegen, The Netherlands.

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http://dx.doi.org/10.1186/s12864-015-1883-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4570683PMC
September 2015

An siRNA-based functional genomics screen for the identification of regulators of ciliogenesis and ciliopathy genes.

Nat Cell Biol 2015 Aug 13;17(8):1074-1087. Epub 2015 Jul 13.

Section of Ophthalmology and Neuroscience, Leeds Institutes of Molecular Medicine, University of Leeds, Leeds, LS9 7TF, UK.

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http://www.nature.com/articles/ncb3201
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http://dx.doi.org/10.1038/ncb3201DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4536769PMC
August 2015

A mutation in the human CBP4 ortholog UQCC3 impairs complex III assembly, activity and cytochrome b stability.

Hum Mol Genet 2014 Dec 9;23(23):6356-65. Epub 2014 Jul 9.

Centre for Molecular and Biomolecular Informatics, Nijmegen Centre for Molecular Life Sciences, Radboud University Medical Centre, PO Box 9101, 6500HB Nijmegen, The Netherlands,

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http://dx.doi.org/10.1093/hmg/ddu357DOI Listing
December 2014

Mutations in the UQCC1-interacting protein, UQCC2, cause human complex III deficiency associated with perturbed cytochrome b protein expression.

PLoS Genet 2013 26;9(12):e1004034. Epub 2013 Dec 26.

Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, Victoria, Australia ; Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia ; Victorian Clinical Genetics Services, Royal Children's Hospital, Melbourne, Victoria, Australia.

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http://dx.doi.org/10.1371/journal.pgen.1004034DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3873243PMC
August 2014

The symbiotic intestinal ciliates and the evolution of their hosts.

Eur J Protistol 2014 Apr 31;50(2):166-73. Epub 2014 Jan 31.

Department of Evolutionary Microbiology, Radboud University Nijmegen, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands. Electronic address:

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http://dx.doi.org/10.1016/j.ejop.2014.01.004DOI Listing
April 2014

Genome evolution predicts genetic interactions in protein complexes and reveals cancer drug targets.

Nat Commun 2013 ;4:2124

Department of Bioinformatics, Centre for Molecular Life Sciences, Radboud University Medical Centre, 6525GA Nijmegen, The Netherlands.

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http://dx.doi.org/10.1038/ncomms3124DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3717498PMC
January 2014

ODoSE: a webserver for genome-wide calculation of adaptive divergence in prokaryotes.

PLoS One 2013 6;8(5):e62447. Epub 2013 May 6.

European Centre for Environment and Human Health, The University of Exeter Medical School, University of Exeter, Truro, United Kingdom.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0062447PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3646019PMC
December 2013

Inferring metabolic states in uncharacterized environments using gene-expression measurements.

PLoS Comput Biol 2013 21;9(3):e1002988. Epub 2013 Mar 21.

Department of Bioinformatics (CMBI), Centre for Molecular Life Sciences, Radboud University Nijmegen, The Netherlands.

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http://dx.doi.org/10.1371/journal.pcbi.1002988DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3605102PMC
November 2013

Human intellectual disability genes form conserved functional modules in Drosophila.

PLoS Genet 2013 Oct 31;9(10):e1003911. Epub 2013 Oct 31.

Department of Human Genetics, Nijmegen Centre for Molecular Life Sciences, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Centre, Nijmegen, The Netherlands.

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http://dx.doi.org/10.1371/journal.pgen.1003911DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3814316PMC
October 2013

A complex V ATP5A1 defect causes fatal neonatal mitochondrial encephalopathy.

Brain 2013 May 18;136(Pt 5):1544-54. Epub 2013 Apr 18.

Department of Paediatrics, Nijmegen Centre for Mitochondrial Disorders, Laboratory for Genetic, Endocrine, and Metabolic Disorders, Radboud University Medical Centre, Nijmegen, The Netherlands.

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http://dx.doi.org/10.1093/brain/awt086DOI Listing
May 2013

The SYSCILIA gold standard (SCGSv1) of known ciliary components and its applications within a systems biology consortium.

Cilia 2013 May 31;2(1). Epub 2013 May 31.

Centre for Molecular and Biomolecular Informatics, Radboud University Medical Centre, Nijmegen 6500 HB, The Netherlands.

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http://dx.doi.org/10.1186/2046-2530-2-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3674929PMC
May 2013

Loss, replacement and gain of proteins at the origin of the mitochondria.

Biochim Biophys Acta 2013 Feb 10;1827(2):224-31. Epub 2012 Aug 10.

Centre for Molecular and Biomolecular Informatics, Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen Medical Centre, P.O. Box 9101, 6400 HB Nijmegen, The Netherlands.

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http://dx.doi.org/10.1016/j.bbabio.2012.08.001DOI Listing
February 2013

BOLA1 is an aerobic protein that prevents mitochondrial morphology changes induced by glutathione depletion.

Antioxid Redox Signal 2013 Jan 11;18(2):129-38. Epub 2012 Sep 11.

Department of Biochemistry, Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands.

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http://dx.doi.org/10.1089/ars.2011.4253DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3513987PMC
January 2013

A three-dimensional topology of complex I inferred from evolutionary correlations.

BMC Struct Biol 2012 Aug 3;12:19. Epub 2012 Aug 3.

Center for Molecular and Biomolecular Informatics/Nijmegen Center for Molecular Life Sciences, Radboud University Medical Center, PO Box 9101, Nijmegen, HB, 6500, The Netherlands.

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http://dx.doi.org/10.1186/1472-6807-12-19DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3436739PMC
August 2012

Structure based hypothesis of a mitochondrial ribosome rescue mechanism.

Biol Direct 2012 May 8;7:14. Epub 2012 May 8.

Centre for Molecular and Biomolecular Informatics, Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen Medical Centre, P,O, Box 9101, 6400, HB Nijmegen, The Netherlands.

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http://dx.doi.org/10.1186/1745-6150-7-14DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3418547PMC
May 2012

Analysis of genes regulated by the transcription factor LUMAN identifies ApoA4 as a target gene in dendritic cells.

Mol Immunol 2012 Feb 30;50(1-2):66-73. Epub 2011 Dec 30.

Department of Tumor Immunology, Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands.

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http://linkinghub.elsevier.com/retrieve/pii/S016158901100826
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http://dx.doi.org/10.1016/j.molimm.2011.12.003DOI Listing
February 2012

Restoration of complex V deficiency caused by a novel deletion in the human TMEM70 gene normalizes mitochondrial morphology.

Mitochondrion 2011 Nov 14;11(6):954-63. Epub 2011 Sep 14.

Department of Pediatrics, Nijmegen Center for Mitochondrial Disorders, Laboratory for Genetic, Endocrine, and Metabolic Disorders, Radboud University Nijmegen Medical Center, 6500 HB Nijmegen, The Netherlands.

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https://linkinghub.elsevier.com/retrieve/pii/S15677249110027
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http://dx.doi.org/10.1016/j.mito.2011.08.012DOI Listing
November 2011

Evidence for short-time divergence and long-time conservation of tissue-specific expression after gene duplication.

Brief Bioinform 2011 Sep 22;12(5):442-8. Epub 2011 Apr 22.

Centre for Genomic Regulation, Barcelona, Spain.

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http://dx.doi.org/10.1093/bib/bbr022DOI Listing
September 2011

The organellar genome and metabolic potential of the hydrogen-producing mitochondrion of Nyctotherus ovalis.

Mol Biol Evol 2011 Aug 4;28(8):2379-91. Epub 2011 Mar 4.

Department of Evolutionary Microbiology, Institute for Water and Wetland Research, Radboud University Nijmegen, Nijmegen, The Netherlands.

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http://dx.doi.org/10.1093/molbev/msr059DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3144386PMC
August 2011

FACIL: Fast and Accurate Genetic Code Inference and Logo.

Bioinformatics 2011 Jul 8;27(14):1929-33. Epub 2011 Jun 8.

Centre for Molecular and Biomolecular Informatics, Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen Medical Centre, Geert Grooteplein 28, 6525 GA, Nijmegen, Germany.

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http://dx.doi.org/10.1093/bioinformatics/btr316DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3129529PMC
July 2011

TEFM (c17orf42) is necessary for transcription of human mtDNA.

Nucleic Acids Res 2011 May 28;39(10):4284-99. Epub 2011 Jan 28.

MRC Mitochondrial Biology Unit, Wellcome Trust/MRC Building, Hills Road, Cambridge CB2 0XY, UK.

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http://dx.doi.org/10.1093/nar/gkq1224DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3105396PMC
May 2011

A mutation in C2orf64 causes impaired cytochrome c oxidase assembly and mitochondrial cardiomyopathy.

Am J Hum Genet 2011 Apr 31;88(4):488-93. Epub 2011 Mar 31.

Nijmegen Center for Mitochondrial Disorders, Department of Pediatrics, Radboud University Nijmegen Medical Centre, PO Box 9101, NL-6500HB, Nijmegen, The Netherlands.

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http://dx.doi.org/10.1016/j.ajhg.2011.03.002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3071910PMC
April 2011

NDUFB7 and NDUFA8 are located at the intermembrane surface of complex I.

FEBS Lett 2011 Mar 22;585(5):737-43. Epub 2011 Feb 22.

Centre for Molecular and Biomolecular Informatics, Radboud University Nijmegen Medical Centre, 6500 HB, Nijmegen, The Netherlands.

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http://dx.doi.org/10.1016/j.febslet.2011.01.046DOI Listing
March 2011

Measuring the physical cohesiveness of proteins using physical interaction enrichment.

Bioinformatics 2010 Nov 26;26(21):2737-43. Epub 2010 Aug 26.

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/10.1093/bioinformatics/btq474DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2958743PMC
November 2010

Mosaic origin of the mitochondrial proteome.

Proteomics 2010 Nov 3;10(22):4012-24. Epub 2010 Nov 3.

Radboud University Nijmegen Medical Centre, CMBI/NCMLS, Nijmegen, The Netherlands.

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http://dx.doi.org/10.1002/pmic.201000329DOI Listing
November 2010

Expansion of the human mitochondrial proteome by intra- and inter-compartmental protein duplication.

Genome Biol 2009 24;10(11):R135. Epub 2009 Nov 24.

Centre for Molecular and Biomolecular Informatics, NCMLS, Radboud University Medical Centre, 6500 HB Nijmegen, The Netherlands.

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http://dx.doi.org/10.1186/gb-2009-10-11-r135DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3091328PMC
July 2010

Dominant processes during human dendritic cell maturation revealed by integration of proteome and transcriptome at the pathway level.

J Proteome Res 2010 Apr;9(4):1727-37

Department of Tumor Immunology and CMBI at the Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands.

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http://dx.doi.org/10.1021/pr9008546DOI Listing
April 2010

The alpha-kinase family: an exceptional branch on the protein kinase tree.

Cell Mol Life Sci 2010 Mar 12;67(6):875-90. Epub 2009 Dec 12.

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

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http://dx.doi.org/10.1007/s00018-009-0215-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2827801PMC
March 2010

A functional peptidyl-tRNA hydrolase, ICT1, has been recruited into the human mitochondrial ribosome.

EMBO J 2010 Mar 25;29(6):1116-25. Epub 2010 Feb 25.

Mitochondrial Research Group, Institute for Ageing and Health, Medical School, Newcastle University, Newcastle upon Tyne, UK.

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http://dx.doi.org/10.1038/emboj.2010.14DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2845271PMC
March 2010

Mitochondrial proteome evolution and genetic disease.

Biochim Biophys Acta 2009 Dec 26;1792(12):1122-9. Epub 2009 Mar 26.

CMBI 260, Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen Medical Centre, Box 9101, 6500 HB Nijmegen, Netherlands.

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http://dx.doi.org/10.1016/j.bbadis.2009.03.005DOI Listing
December 2009

The hydrogenosomes of Psalteriomonas lanterna.

BMC Evol Biol 2009 Dec 9;9:287. Epub 2009 Dec 9.

Department of Evolutionary Microbiology, IWWR, Radboud University Nijmegen, The Netherlands.

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http://dx.doi.org/10.1186/1471-2148-9-287DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2796672PMC
December 2009

The biological coherence of human phenome databases.

Am J Hum Genet 2009 Dec;85(6):801-8

Centre for Molecular and Biomolecular Informatics, Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen Medical Centre, Geert Grooteplein 26-28, 6525 GA Nijmegen, The Netherlands.

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http://dx.doi.org/10.1016/j.ajhg.2009.10.026DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2790572PMC
December 2009

Increasing the coverage of a metapopulation consensus genome by iterative read mapping and assembly.

Bioinformatics 2009 Nov 19;25(21):2878-81. Epub 2009 Jun 19.

Center for Molecular and Biomolecular Informatics, Nijmegen Center for Molecular Life Sciences, Radboud University Nijmegen Medical Center, Geert Grooteplein 28, 6525 GA, Nijmegen, The Netherlands, Germany.

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http://dx.doi.org/10.1093/bioinformatics/btp377DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2781756PMC
November 2009

Clustering of codons with rare cognate tRNAs in human genes suggests an extra level of expression regulation.

PLoS Genet 2009 Jul 3;5(7):e1000548. Epub 2009 Jul 3.

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

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https://dx.plos.org/10.1371/journal.pgen.1000548
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http://dx.doi.org/10.1371/journal.pgen.1000548DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2697378PMC
July 2009

Asymmetric relationships between proteins shape genome evolution.

Genome Biol 2009 Feb 12;10(2):R19. Epub 2009 Feb 12.

Center for Molecular and Biomolecular Informatics, Nijmegen Center for Molecular Life Sciences, Radboud University Nijmegen Medical Center, Geert Grooteplein 26-28, 6525 GA, Nijmegen, The Netherlands.

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http://dx.doi.org/10.1186/gb-2009-10-2-r19DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2688278PMC
February 2009

Macronuclear genome structure of the ciliate Nyctotherus ovalis: single-gene chromosomes and tiny introns.

BMC Genomics 2008 Dec 5;9:587. Epub 2008 Dec 5.

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

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http://dx.doi.org/10.1186/1471-2164-9-587DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2633312PMC
December 2008

Complex fate of paralogs.

BMC Evol Biol 2008 Dec 18;8:337. Epub 2008 Dec 18.

Centre for Molecular and Biomolecular Informatics, NCMLS, Radboud University Medical Centre, PO Box 9101, 6500 HB Nijmegen, the Netherlands.

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http://dx.doi.org/10.1186/1471-2148-8-337DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2628386PMC
December 2008

Evolution of closely linked gene pairs in vertebrate genomes.

Mol Biol Evol 2008 Sep 19;25(9):1909-21. Epub 2008 Jun 19.

Biomolecular Chemistry, 271 Nijmegen Center of Molecular Life Science, Radboud University Nijmegen, Nijmegen, The Netherlands.

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http://dx.doi.org/10.1093/molbev/msn136DOI Listing
September 2008

Signature genes as a phylogenomic tool.

Mol Biol Evol 2008 Aug 19;25(8):1659-67. Epub 2008 May 19.

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

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http://dx.doi.org/10.1093/molbev/msn115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2464742PMC
August 2008

Signature, a web server for taxonomic characterization of sequence samples using signature genes.

Nucleic Acids Res 2008 Jul 17;36(Web Server issue):W470-4. Epub 2008 May 17.

Center for Molecular and Biomolecular Informatics/Nijmegen Center for Molecular Life Sciences, Radboud University Nijmegen Medical Centre, Geert Grooteplein 28, 6525 GA, Nijmegen, The Netherlands.

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http://dx.doi.org/10.1093/nar/gkn277DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2447722PMC
July 2008

Conserved co-expression for candidate disease gene prioritization.

BMC Bioinformatics 2008 Apr 23;9:208. Epub 2008 Apr 23.

Centre for Molecular and Biomolecular Informatics, Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen Medical Centre, Geert Grooteplein 26-28, 6525 GA, Nijmegen, The Netherlands.

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http://dx.doi.org/10.1186/1471-2105-9-208DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2383918PMC
April 2008