Scribbles & Snippets
... of low and no utility ...

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Recovery of corrupt XFS partition.
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Retrieve large batches of rows from mysql
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General

I guess everybody gets this feeling once in a while... You are facing a particular problem you already solved in the past, but you just can't rember how you did it. So you start all over again, scan the internet for tips & tricks, and after hours of wasted time you probably have the exact same solution as you had a few months ago. Then a year later, facing the exact same problem, you're thinking: hmm... I do think I already had a solution for this...

And that's why I decided to put those solutions online, mainly for my own reference, but perhaps someone will find these snippets of use. If you have better or more elegant solutions, feel free to leave comments! I've sorted them into some categories and add the mighty tags for easy navigation and better search results :-)

Biography

Personal

  • Name: Geert Vandeweyer
  • Birthday: January 20, 1983
  • Living: Ekeren, Belgium; together with my fiancee Valérie
  • Past Activities Years of scoutism; Passive interest in various styles of music

Education

  • High School: Sint-Michiels College, Brasschaat
  • University: University of Leuven : Bio-Engineer in Cell And Gene Biotechnology
  • University: University of Leuven : Advanced Master in Bio-Informatics
  • PhD: University of Antwerp: Detection and Interpretation of Genomic Structural Variation in Patients with Cognitive Disorders.

Professional

  • 2013-current:University of Antwerp: FWO Post-doctoral Fellowship: Deciphering hidden inheritance patterns using advanced data mining techniques on high throughput genomic data
  • 2011-2013: University of Antwerp: Post Doctoral Researcher in Bio-Informatics: Implementation of Next-Generation Sequencing Data analysis in the context of medical genetics.

Specialties

  • Programming Languages: Perl, MatLab, R, PHP, BASH, Visual Basic
  • Database Management:SQL, MySQL, MS Access
  • Linux Administration:Ubuntu/Fedora/Gentoo/SLES/...; HPC Clustering using Torque/PBS and DRMAA-perl interfaces
  • Bio-data-analysis Illumina Genotyping/CNV and Expression applications; Ensembl/UCSC data structures ; Next-Gen Resequencing, Galaxy, CLC-Bio

Digital Whereabouts

Projects

  • CNV-WebStore : Online CNV Analysis and Interpretation Platform
  • BITS : BioInformatic Tools collection for daily routine Automation
  • Cash Register Program : Cash register program written in Access for orthopedic company
  • VariantDB : A flexible annotation and filtering portal for NGS data

Scientific Bibliography

 

  1. van der Werf I., Kooy R.F., Vandeweyer G..A Robust Protocol to Increase NimbleGen SeqCap EZ Multiplexing Capacity to 96 Samples PLoS ONE 2015 Apr 14.
  2. Vandeweyer G., Helsmoortel C., Van Dijck A., Vulto-van Silfhout A.T., Coe B.P., Bernier R., Gerdts J., Rooms L., van den Ende J., Bakshi M., Wilson M., Nordgren A., Hendon L.G., Abdulrahman O.A., Romano C., de Vries B.B., Kleefstra T., Eichler E.E., Van der Aa N., Kooy R.F. The transcriptional regulator ADNP links the BAF (SWI/SNF) complexes with autism. American Journal of Medical Genetics Part C, Seminars in Medical Genetics 2014 Sept;166(3):315-26
  3. Helsmoortel C., Vandeweyer G., Ordoukhanian P., Van Nieuwerburgh F., Van der Aa N., Kooy R.F. Challenges and opportunities in the investigation of unexplained intellectual disability using family based whole exome sequencing. Clinical Genetics 2014 Aug 1 (epub ahead of print)
  4. Metsu S., Rooms L., Rainger J., Taylor M.S., Bengani H., Wilson D.I., Chilamakuri C.S., Morrison H., Vandeweyer G., Reyniers E., Douglas E., Thompson G., Haan E., Gecz J., Fitzpatrick D.R., Kooy R.F. FRA2A is a CGG repeat expansion associated with silencing of AFF3. PLoS Genetics 2014 Apr 24;10(4):e1004242
  5. Helsmoortel C., Vulto-van Silfhout A.T., Coe B.P., Vandeweyer G., Rooms L., van den Ende J., Schuurs-Hoeijmakers J.H., Marcelis C.L., Willemsen M.H., Vissers L.E., Yntema H.G., Bakshi M., Wilson M., Witherspoon K.T., Malmgren H., Nordgren A., Annerén G., Fichera M., Bosco P., Romano C., de Vries B.B., Kleefstra T., Kooy R.F., Eichler E.E., Van der Aa N. A SWI/SNF-related autism syndrome caused by de novo mutations in ADNP. Nature Genetics 2014 Apr;46(4):380-4
  6. Van Den Bossche, M., Strazisar, M., Cammaerts, S., Liekens, A., Vandeweyer, G., Depreeuw, V., Mattheijssens, M., Lenaerts, A., De Zutter, S., De Rijk, P., Sabbe, B., Del-Favero, J. Identification of rare copy number variants in high burden schizophrenia families. American Journal of Medical Genetics part B Neuropsychiatric Genetics 2013 Apr;162B(3):273-82
  7. Ajit Bolar N., Vanlander A.V., Wilbrecht C., Van der Aa N., Smet J., De Paepe B., Vandeweyer G., Kooy F., Eyskens F., De Latter E., Delanghe G., Govaert P., Leroy J.G., Loeys B., Lill R., Van Laer L., Van Coster R. Mutation of the iron-sulfur cluster assembly gene IBA57 causes severe myopathy and encephalopathy. Human Molecular Genetics 2013 Jul 1;22(13):2590-602
  8. Iqbal Z., Vandeweyer G.,van der Voet M., Waryah A.M., Zahoor M.Y., Besseling J., Roca1 L.T.,Vulto-van Silfhout A.T., Nijhof B., Kramer J., Van der Aa N., Ansar M., Peeters H., Helsmoortel C., Gilissen C., Vissers L., Veltman J.A., de Brouwer A.P.M, Kooy, R.F., Riazuddin S., Schenck A., van Bokhoven H.,Rooms L. Homozygous and heterozygous disruptions of ANK3: at the crossroads of neurodevelopmental and psychiatric disorders. Human Molecular Genetics. (in press)
  9. Vandeweyer G., Kooy R.F. Detection and interpretation of genomic structural variation in health and disease. Expert Review of Molecular Diagnostics. 2013 Jan;13(1):61-82
  10. Helsmoortel C., Vandeweyer G., Kooy RF. On the spot: very local chromosomal rearrangements. F1000 Biology Reports. 2012;4:22
  11. Van der Aa N., Vandeweyer G., Reyniers E., Kenis S., Dom L., Mortier G., Rooms L., Kooy R.F. Haploinsufficiency of CMIP in a girl with autism spectrum disorder and developmental delay due to a de novo deletion on chromosome 16q23.2. Autism Research. 2012 Aug;5(4):277-81
  12. Vandeweyer G., Van der Aa N., Reyniers E. Kooy R.F. The Contribution of CLIP2 Haploinsuffiency to the Clinical Manifestations of the Williams-Beuren Syndrome. Americal Journal of Human Genetics. American Journal of Human Genetics. 2012 Jun 8;90(6):1071-8.
  13. Vandeweyer G., Van der Aa N., Ceulemans B., van Bon B.W., Rooms L., Kooy R.F. A de novo balanced t(2;6)(p15;p22.3) in a patient with West Syndrome disrupts a lnc-RNA. Epilepsy Research. 2012; 99:346-349.
  14. Vandeweyer G., Reyniers E., Wuyts W., Rooms L., Kooy R.F. CNV-WebStore: online CNV analysis, storage and interpretation. BMC Bioinformatics. 2011 Jan 5;12:4.
  15. Rooms L., Vandeweyer G., Reyniers E., van Mol K., de Canck I., Van der Aa N., Rossau R., Kooy R.F. Array-Based MLPA to detect recurrent copy number variations in patients with idiopathic mental retardation. American Journal of Medical Genetics A. 2011;155(2):343-348.
  16. Van der Aa N., Vandeweyer G., Kooy R.F. A boy with mental retardation, obesity and hypertrichosis caused by a microdeletion of 19p13.12. European Journal of Medical Genetics. 2010;53(5):291-293.
  17. Bruno D.L., Anderlid B.M., Lindstrand A., van Ravenswaaij-Arts C., Ganesamoorthy D., Lundin J., Martin C.L., Douglas J., Nowak C., Adam M.P., Kooy R.F., Van der Aa N., Reyniers E., Vandeweyer G., Stolte-Dijkstra I., Dijkhuizen T., Yeung A., Delatycki M., Borgstrom B., Thelin L., Cardoso C., van Bon B., Pfundt R., de Vries B.B., Wallin A., Amor D.J., James P.A., Slater H.R., Schoumans J. Further Molecular and clinical delineation of co-locating 17p13.3 microdeletions and microduplications that show distinctive phenotypes. Journal of Medical Genetics. 2010;47(5):299-311.
  18. van Bon, B. W. M., Mefford, H. C., Menten, B., Koolen, D. A., Sharp, A. J., Nillesen, W. M., Innis, J. W., de Ravel, T. J. L., Mercer, C. L., Fichera, M., Stewart, H., Connell, L. E., Õunap, K., Lachlan, K., Castle, B., Van der Aa, N., van Ravenswaaij, C., Nobrega, M. A., Serra-Juhé, C., Simonic, I., de Leeuw, N., R. Pfundt, R., Bongers, E. M., Baker, C., Finnemore, P., Huang, S., Maloney, V. K., Crolla, J. A., van Kalmthout, M., Elia, M., Vandeweyer, G., Fryns, J. P., Janssens, S., Foulds, N., Reitano, S., Smith, K., Parkel, S., Loeys, B., Woods, C. G., Oostra, A., Speleman, F., Pereira, A. C., Kurg, A., Willatt, L., Knight, S. L. J., Vermeesch, J. R., Romano, C., Barber, J. C., Mortier, G., Pérez-Jurado, L. A., Kooy, F., Brunner, H. G., Eichler, E. E., Kleefstra, T., de Vries, B. B. A. Further delineation of the 15q13 microdeletion and duplication syndromes: A clinical spectrum varying from non-pathogenic to a severe outcome. Journal of Medical Genetics 2009:46,511-523.
  19. Kooy R.F., Van der Aa N., Vandeweyer G., Reyniers E., Rooms L. Genetic overlaps in mental retardation, autism and schizophrenia. Monographs in Human Genetics, Volume 18: Genetics of Mental Retardation
  20. Van der Aa, N., Rooms, L., Vandeweyer, G., van den Ende, J., Reyniers, E., Fichera, M., Romano, C., Delle Chiaie, B., Mortier, G., Menten, B., Destree, A., Maystadt, I., Mannik, K., Kurg, A., Reimand, T., McMullan, D., Oley, C., Brueton, L., Bongers, E. M. H. F., van Bon, B. W. M., Pfund, R., Jacquemont, S., Ferrarini, A., Martinet, D., Schrander-Stumpel, C., Stegmann, A. P. A., Frints, S. G. M., de Vries, B. B. A., Ceulemans, B., Kooy, R. F. Fourteen new cases contribute to the characterization of the 7q11.23 microduplication syndrome. European Journal of Medical Genetics 2009:52,94-100.
  21. Vandeweyer, G., Kooy, RF. Balanced translocations in mental retardation. Hum Genet 2009:126,133-147.