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Items: 38

1.

CiliaCarta: An integrated and validated compendium of ciliary genes.

van Dam TJP, Kennedy J, van der Lee R, de Vrieze E, Wunderlich KA, Rix S, Dougherty GW, Lambacher NJ, Li C, Jensen VL, Leroux MR, Hjeij R, Horn N, Texier Y, Wissinger Y, van Reeuwijk J, Wheway G, Knapp B, Scheel JF, Franco B, Mans DA, van Wijk E, Képès F, Slaats GG, Toedt G, Kremer H, Omran H, Szymanska K, Koutroumpas K, Ueffing M, Nguyen TT, Letteboer SJF, Oud MM, van Beersum SEC, Schmidts M, Beales PL, Lu Q, Giles RH, Szklarczyk R, Russell RB, Gibson TJ, Johnson CA, Blacque OE, Wolfrum U, Boldt K, Roepman R, Hernandez-Hernandez V, Huynen MA.

PLoS One. 2019 May 16;14(5):e0216705. doi: 10.1371/journal.pone.0216705. eCollection 2019.

2.

Whole Exome Sequencing Is the Preferred Strategy to Identify the Genetic Defect in Patients With a Probable or Possible Mitochondrial Cause.

Theunissen TEJ, Nguyen M, Kamps R, Hendrickx AT, Sallevelt SCEH, Gottschalk RWH, Calis CM, Stassen APM, de Koning B, Mulder-Den Hartog ENM, Schoonderwoerd K, Fuchs SA, Hilhorst-Hofstee Y, de Visser M, Vanoevelen J, Szklarczyk R, Gerards M, de Coo IFM, Hellebrekers DMEI, Smeets HJM.

Front Genet. 2018 Oct 12;9:400. doi: 10.3389/fgene.2018.00400. eCollection 2018.

3.

Genetic defects in mtDNA-encoded protein translation cause pediatric, mitochondrial cardiomyopathy with early-onset brain disease.

Kamps R, Szklarczyk R, Theunissen TE, Hellebrekers DMEI, Sallevelt SCEH, Boesten IB, de Koning B, van den Bosch BJ, Salomons GS, Simas-Mendes M, Verdijk R, Schoonderwoerd K, de Coo IFM, Vanoevelen JM, Smeets HJM.

Eur J Hum Genet. 2018 Apr;26(4):537-551. doi: 10.1038/s41431-017-0058-2. Epub 2018 Feb 13.

4.

Selection and Characterization of Palmitic Acid Responsive Patients with an OXPHOS Complex I Defect.

Theunissen TEJ, Gerards M, Hellebrekers DMEI, van Tienen FH, Kamps R, Sallevelt SCEH, Hartog ENMM, Scholte HR, Verdijk RM, Schoonderwoerd K, de Coo IFM, Szklarczyk R, Smeets HJM.

Front Mol Neurosci. 2017 Oct 18;10:336. doi: 10.3389/fnmol.2017.00336. eCollection 2017.

5.

A comprehensive strategy for exome-based preconception carrier screening.

Sallevelt SCEH, de Koning B, Szklarczyk R, Paulussen ADC, de Die-Smulders CEM, Smeets HJM.

Genet Med. 2017 May;19(5):583-592. doi: 10.1038/gim.2016.153. Epub 2016 Oct 27.

PMID:
28492530
6.

Network topology of NaV1.7 mutations in sodium channel-related painful disorders.

Kapetis D, Sassone J, Yang Y, Galbardi B, Xenakis MN, Westra RL, Szklarczyk R, Lindsey P, Faber CG, Gerrits M, Merkies IS, Dib-Hajj SD, Mantegazza M, Waxman SG, Lauria G; PROPANE Study Group.

BMC Syst Biol. 2017 Feb 24;11(1):28. doi: 10.1186/s12918-016-0382-0.

7.

Rapid Resolution of Blended or Composite Multigenic Disease in Infants by Whole-Exome Sequencing.

Theunissen TEJ, Sallevelt SCEH, Hellebrekers DMEI, de Koning B, Hendrickx ATM, van den Bosch BJC, Kamps R, Schoonderwoerd K, Szklarczyk R, Mulder-Den Hartog ENM, de Coo IFM, Smeets HJM.

J Pediatr. 2017 Mar;182:371-374.e2. doi: 10.1016/j.jpeds.2016.12.032. Epub 2017 Jan 9.

PMID:
28081892
8.

A homozygous FITM2 mutation causes a deafness-dystonia syndrome with motor regression and signs of ichthyosis and sensory neuropathy.

Zazo Seco C, Castells-Nobau A, Joo SH, Schraders M, Foo JN, van der Voet M, Velan SS, Nijhof B, Oostrik J, de Vrieze E, Katana R, Mansoor A, Huynen M, Szklarczyk R, Oti M, Tranebjærg L, van Wijk E, Scheffer-de Gooyert JM, Siddique S, Baets J, de Jonghe P, Kazmi SA, Sadananthan SA, van de Warrenburg BP, Khor CC, Göpfert MC, Qamar R, Schenck A, Kremer H, Siddiqi S.

Dis Model Mech. 2017 Feb 1;10(2):105-118. doi: 10.1242/dmm.026476. Epub 2016 Dec 15.

9.

Specific MRI Abnormalities Reveal Severe Perrault Syndrome due to CLPP Defects.

Theunissen TE, Szklarczyk R, Gerards M, Hellebrekers DM, Mulder-Den Hartog EN, Vanoevelen J, Kamps R, de Koning B, Rutledge SL, Schmitt-Mechelke T, van Berkel CG, van der Knaap MS, de Coo IF, Smeets HJ.

Front Neurol. 2016 Nov 16;7:203. eCollection 2016.

10.

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

Szklarczyk R, Megchelenbrink W, Cizek P, Ledent M, Velemans G, Szklarczyk D, Huynen MA.

Nucleic Acids Res. 2016 Jan 4;44(D1):D567-73. doi: 10.1093/nar/gkv1228. Epub 2015 Nov 17.

11.

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

van der Lee R, Feng Q, Langereis MA, Ter Horst R, Szklarczyk R, Netea MG, Andeweg AC, van Kuppeveld FJ, Huynen MA.

PLoS Comput Biol. 2015 Oct 20;11(10):e1004553. doi: 10.1371/journal.pcbi.1004553. eCollection 2015 Oct.

12.

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

van der Lee R, Szklarczyk R, Smeitink J, Smeets HJ, Huynen MA, Vogel R.

BMC Genomics. 2015 Sep 15;16:691. doi: 10.1186/s12864-015-1883-8.

13.

Olfactory receptor genes cooperate with protocadherin genes in human extreme obesity.

Mariman EC, Szklarczyk R, Bouwman FG, Aller EE, van Baak MA, Wang P.

Genes Nutr. 2015 Jul;10(4):465. doi: 10.1007/s12263-015-0465-3. Epub 2015 May 6.

14.

CLPB mutations cause 3-methylglutaconic aciduria, progressive brain atrophy, intellectual disability, congenital neutropenia, cataracts, movement disorder.

Wortmann SB, Ziętkiewicz S, Kousi M, Szklarczyk R, Haack TB, Gersting SW, Muntau AC, Rakovic A, Renkema GH, Rodenburg RJ, Strom TM, Meitinger T, Rubio-Gozalbo ME, Chrusciel E, Distelmaier F, Golzio C, Jansen JH, van Karnebeek C, Lillquist Y, Lücke T, Õunap K, Zordania R, Yaplito-Lee J, van Bokhoven H, Spelbrink JN, Vaz FM, Pras-Raves M, Ploski R, Pronicka E, Klein C, Willemsen MA, de Brouwer AP, Prokisch H, Katsanis N, Wevers RA.

Am J Hum Genet. 2015 Feb 5;96(2):245-57. doi: 10.1016/j.ajhg.2014.12.013. Epub 2015 Jan 15.

15.

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

Wanschers BF, Szklarczyk R, van den Brand MA, Jonckheere A, Suijskens J, Smeets R, Rodenburg RJ, Stephan K, Helland IB, Elkamil A, Rootwelt T, Ott M, van den Heuvel L, Nijtmans LG, Huynen MA.

Hum Mol Genet. 2014 Dec 1;23(23):6356-65. doi: 10.1093/hmg/ddu357. Epub 2014 Jul 9.

PMID:
25008109
16.

How to deal with oxygen radicals stemming from mitochondrial fatty acid oxidation.

Speijer D, Manjeri GR, Szklarczyk R.

Philos Trans R Soc Lond B Biol Sci. 2014 Jul 5;369(1646):20130446. doi: 10.1098/rstb.2013.0446. Review.

17.

Control of mitochondrial integrity in ageing and disease.

Szklarczyk R, Nooteboom M, Osiewacz HD.

Philos Trans R Soc Lond B Biol Sci. 2014 Jul 5;369(1646):20130439. doi: 10.1098/rstb.2013.0439. Review.

18.

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

Tucker EJ, Wanschers BF, Szklarczyk R, Mountford HS, Wijeyeratne XW, van den Brand MA, Leenders AM, Rodenburg RJ, Reljić B, Compton AG, Frazier AE, Bruno DL, Christodoulou J, Endo H, Ryan MT, Nijtmans LG, Huynen MA, Thorburn DR.

PLoS Genet. 2013;9(12):e1004034. doi: 10.1371/journal.pgen.1004034. Epub 2013 Dec 26.

19.

A mutation in the FAM36A gene, the human ortholog of COX20, impairs cytochrome c oxidase assembly and is associated with ataxia and muscle hypotonia.

Szklarczyk R, Wanschers BF, Nijtmans LG, Rodenburg RJ, Zschocke J, Dikow N, van den Brand MA, Hendriks-Franssen MG, Gilissen C, Veltman JA, Nooteboom M, Koopman WJ, Willems PH, Smeitink JA, Huynen MA, van den Heuvel LP.

Hum Mol Genet. 2013 Feb 15;22(4):656-67. doi: 10.1093/hmg/dds473. Epub 2012 Nov 2.

PMID:
23125284
20.

NDUFA4 is a subunit of complex IV of the mammalian electron transport chain.

Balsa E, Marco R, Perales-Clemente E, Szklarczyk R, Calvo E, Landázuri MO, Enríquez JA.

Cell Metab. 2012 Sep 5;16(3):378-86. doi: 10.1016/j.cmet.2012.07.015. Epub 2012 Aug 16.

21.

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

Huynen MA, Duarte I, Szklarczyk R.

Biochim Biophys Acta. 2013 Feb;1827(2):224-31. doi: 10.1016/j.bbabio.2012.08.001. Epub 2012 Aug 10. Review.

22.

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

Willems P, Wanschers BF, Esseling J, Szklarczyk R, Kudla U, Duarte I, Forkink M, Nooteboom M, Swarts H, Gloerich J, Nijtmans L, Koopman W, Huynen MA.

Antioxid Redox Signal. 2013 Jan 10;18(2):129-38. doi: 10.1089/ars.2011.4253. Epub 2012 Sep 11.

23.

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.

Szklarczyk R, Wanschers BF, Cuypers TD, Esseling JJ, Riemersma M, van den Brand MA, Gloerich J, Lasonder E, van den Heuvel LP, Nijtmans LG, Huynen MA.

Genome Biol. 2012 Feb 22;13(2):R12. doi: 10.1186/gb-2012-13-2-r12.

24.

C7orf30 specifically associates with the large subunit of the mitochondrial ribosome and is involved in translation.

Wanschers BF, Szklarczyk R, Pajak A, van den Brand MA, Gloerich J, Rodenburg RJ, Lightowlers RN, Nijtmans LG, Huynen MA.

Nucleic Acids Res. 2012 May;40(9):4040-51. doi: 10.1093/nar/gkr1271. Epub 2012 Jan 11.

25.

Unraveling the human dendritic cell phagosome proteome by organellar enrichment ranking.

Buschow SI, Lasonder E, Szklarczyk R, Oud MM, de Vries IJ, Figdor CG.

J Proteomics. 2012 Feb 16;75(5):1547-62. doi: 10.1016/j.jprot.2011.11.024. Epub 2011 Dec 3.

26.

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

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.

Mitochondrion. 2011 Nov;11(6):954-63. doi: 10.1016/j.mito.2011.08.012. Epub 2011 Sep 14.

PMID:
21945727
27.

FACIL: Fast and Accurate Genetic Code Inference and Logo.

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.

Bioinformatics. 2011 Jul 15;27(14):1929-33. doi: 10.1093/bioinformatics/btr316. Epub 2011 Jun 8.

28.

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

Huigsloot M, Nijtmans LG, Szklarczyk R, Baars MJ, van den Brand MA, Hendriksfranssen MG, van den Heuvel LP, Smeitink JA, Huynen MA, Rodenburg RJ.

Am J Hum Genet. 2011 Apr 8;88(4):488-93. doi: 10.1016/j.ajhg.2011.03.002. Epub 2011 Mar 31.

29.

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

Szklarczyk R, Wanschers BF, Nabuurs SB, Nouws J, Nijtmans LG, Huynen MA.

FEBS Lett. 2011 Mar 9;585(5):737-43. doi: 10.1016/j.febslet.2011.01.046. Epub 2011 Feb 22.

30.

Mosaic origin of the mitochondrial proteome.

Szklarczyk R, Huynen MA.

Proteomics. 2010 Nov;10(22):4012-24. doi: 10.1002/pmic.201000329. Epub 2010 Nov 3. Review.

PMID:
21080492
31.

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

Szklarczyk R, Huynen MA.

Genome Biol. 2009;10(11):R135. doi: 10.1186/gb-2009-10-11-r135. Epub 2009 Nov 24.

32.

Mitochondrial proteome evolution and genetic disease.

Huynen MA, de Hollander M, Szklarczyk R.

Biochim Biophys Acta. 2009 Dec;1792(12):1122-9. doi: 10.1016/j.bbadis.2009.03.005. Epub 2009 Mar 26. Review.

33.

Complex fate of paralogs.

Szklarczyk R, Huynen MA, Snel B.

BMC Evol Biol. 2008 Dec 18;8:337. doi: 10.1186/1471-2148-8-337.

34.

Rapid asymmetric evolution of a dual-coding tumor suppressor INK4a/ARF locus contradicts its function.

Szklarczyk R, Heringa J, Pond SK, Nekrutenko A.

Proc Natl Acad Sci U S A. 2007 Jul 31;104(31):12807-12. Epub 2007 Jul 24.

35.

A first look at ARFome: dual-coding genes in mammalian genomes.

Chung WY, Wadhawan S, Szklarczyk R, Pond SK, Nekrutenko A.

PLoS Comput Biol. 2007 May;3(5):e91.

36.

AuberGene--a sensitive genome alignment tool.

Szklarczyk R, Heringa J.

Bioinformatics. 2006 Jun 15;22(12):1431-6. Epub 2006 Apr 10.

PMID:
16606686
37.

Tracking repeats using significance and transitivity.

Szklarczyk R, Heringa J.

Bioinformatics. 2004 Aug 4;20 Suppl 1:i311-7.

PMID:
15262814
38.

Contextual alignment of biological sequences (Extended abstract).

Gambin A, Lasota S, Szklarczyk R, Tiuryn J, Tyszkiewicz J.

Bioinformatics. 2002;18 Suppl 2:S116-27.

PMID:
12385993

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