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Items: 14

1.

Germline de novo mutation clusters arise during oocyte aging in genomic regions with high double-strand-break incidence.

Goldmann JM, Seplyarskiy VB, Wong WSW, Vilboux T, Neerincx PB, Bodian DL, Solomon BD, Veltman JA, Deeken JF, Gilissen C, Niederhuber JE.

Nat Genet. 2018 Apr;50(4):487-492. doi: 10.1038/s41588-018-0071-6. Epub 2018 Mar 5.

PMID:
29507425
2.

Running-wheel activity delays mitochondrial respiratory flux decline in aging mouse muscle via a post-transcriptional mechanism.

Stolle S, Ciapaite J, Reijne AC, Talarovicova A, Wolters JC, Aguirre-Gamboa R, van der Vlies P, de Lange K, Neerincx PB, van der Vries G, Deelen P, Swertz MA, Li Y, Bischoff R, Permentier HP, Horvatovitch PL, Groen AK, van Dijk G, Reijngoud DJ, Bakker BM.

Aging Cell. 2018 Feb;17(1). doi: 10.1111/acel.12700. Epub 2017 Nov 9.

3.

Rapid Targeted Genomics in Critically Ill Newborns.

van Diemen CC, Kerstjens-Frederikse WS, Bergman KA, de Koning TJ, Sikkema-Raddatz B, van der Velde JK, Abbott KM, Herkert JC, Löhner K, Rump P, Meems-Veldhuis MT, Neerincx PBT, Jongbloed JDH, van Ravenswaaij-Arts CM, Swertz MA, Sinke RJ, van Langen IM, Wijmenga C.

Pediatrics. 2017 Oct;140(4). pii: e20162854. doi: 10.1542/peds.2016-2854.

4.

The Genome of the Netherlands: design, and project goals.

Boomsma DI, Wijmenga C, Slagboom EP, Swertz MA, Karssen LC, Abdellaoui A, Ye K, Guryev V, Vermaat M, van Dijk F, Francioli LC, Hottenga JJ, Laros JF, Li Q, Li Y, Cao H, Chen R, Du Y, Li N, Cao S, van Setten J, Menelaou A, Pulit SL, Hehir-Kwa JY, Beekman M, Elbers CC, Byelas H, de Craen AJ, Deelen P, Dijkstra M, den Dunnen JT, de Knijff P, Houwing-Duistermaat J, Koval V, Estrada K, Hofman A, Kanterakis A, Enckevort Dv, Mai H, Kattenberg M, van Leeuwen EM, Neerincx PB, Oostra B, Rivadeneira F, Suchiman EH, Uitterlinden AG, Willemsen G, Wolffenbuttel BH, Wang J, de Bakker PI, van Ommen GJ, van Duijn CM.

Eur J Hum Genet. 2014 Feb;22(2):221-7. doi: 10.1038/ejhg.2013.118. Epub 2013 May 29.

5.

Deep proteome profiling of Trichoplax adhaerens reveals remarkable features at the origin of metazoan multicellularity.

Ringrose JH, van den Toorn HW, Eitel M, Post H, Neerincx P, Schierwater B, Altelaar AF, Heck AJ.

Nat Commun. 2013;4:1408. doi: 10.1038/ncomms2424.

PMID:
23360999
6.

Cleavage specificities of the brother and sister proteases Lys-C and Lys-N.

Raijmakers R, Neerincx P, Mohammed S, Heck AJ.

Chem Commun (Camb). 2010 Dec 14;46(46):8827-9. doi: 10.1039/c0cc02523b. Epub 2010 Oct 18.

PMID:
20953479
7.

Gene expression in chicken reveals correlation with structural genomic features and conserved patterns of transcription in the terrestrial vertebrates.

Nie H, Crooijmans RP, Lammers A, van Schothorst EM, Keijer J, Neerincx PB, Leunissen JA, Megens HJ, Groenen MA.

PLoS One. 2010 Aug 5;5(8):e11990. doi: 10.1371/journal.pone.0011990.

8.

Microarray data mining using Bioconductor packages.

Nie H, Neerincx PB, van der Poel J, Ferrari F, Bicciato S, Leunissen JA, Groenen MA.

BMC Proc. 2009 Jul 16;3 Suppl 4:S9. doi: 10.1186/1753-6561-3-S4-S9.

9.

Methods for interpreting lists of affected genes obtained in a DNA microarray experiment.

Hedegaard J, Arce C, Bicciato S, Bonnet A, Buitenhuis B, Collado-Romero M, Conley LN, SanCristobal M, Ferrari F, Garrido JJ, Groenen MA, Hornshøj H, Hulsegge I, Jiang L, Jiménez-Marín Á, Kommadath A, Lagarrigue S, Leunissen JA, Liaubet L, Neerincx PB, Nie H, Poel JV, Prickett D, Ramirez-Boo M, Rebel JM, Robert-Granié C, Skarman A, Smits MA, Sørensen P, Tosser-Klopp G, Watson M.

BMC Proc. 2009 Jul 16;3 Suppl 4:S5.

10.

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

Neerincx PB, Rauwerda H, Nie H, Groenen MA, Breit TM, Leunissen JA.

BMC Proc. 2009 Jul 16;3 Suppl 4:S4. doi: 10.1186/1753-6561-3-S4-S4.

11.

Comparison of three microarray probe annotation pipelines: differences in strategies and their effect on downstream analysis.

Neerincx PB, Casel P, Prickett D, Nie H, Watson M, Leunissen JA, Groenen MA, Klopp C.

BMC Proc. 2009 Jul 16;3 Suppl 4:S1. doi: 10.1186/1753-6561-3-S4-S1.

12.

Using R in Taverna: RShell v1.2.

Wassink I, Rauwerda H, Neerincx PB, van der Vet PE, Breit TM, Leunissen JA, Nijholt A.

BMC Res Notes. 2009 Jul 16;2:138. doi: 10.1186/1756-0500-2-138.

13.

Interoperability with Moby 1.0--it's better than sharing your toothbrush!

BioMoby Consortium, Wilkinson MD, Senger M, Kawas E, Bruskiewich R, Gouzy J, Noirot C, Bardou P, Ng A, Haase D, Saiz Ede A, Wang D, Gibbons F, Gordon PM, Sensen CW, Carrasco JM, Fernández JM, Shen L, Links M, Ng M, Opushneva N, Neerincx PB, Leunissen JA, Ernst R, Twigger S, Usadel B, Good B, Wong Y, Stein L, Crosby W, Karlsson J, Royo R, Párraga I, Ramírez S, Gelpi JL, Trelles O, Pisano DG, Jimenez N, Kerhornou A, Rosset R, Zamacola L, Tarraga J, Huerta-Cepas J, Carazo JM, Dopazo J, Guigo R, Navarro A, Orozco M, Valencia A, Claros MG, Pérez AJ, Aldana J, Rojano M, Fernandez-Santa Cruz R, Navas I, Schiltz G, Farmer A, Gessler D, Schoof H, Groscurth A.

Brief Bioinform. 2008 May;9(3):220-31. doi: 10.1093/bib/bbn003. Epub 2008 Jan 31. Review.

PMID:
18238804
14.

Evolution of web services in bioinformatics.

Neerincx PB, Leunissen JA.

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

PMID:
15975226

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