Publications and references

In case you have designed primersets for your research using SNPbox, please refer to:

• SNPbox: a modular software package for large-scale primer design.
  Weckx S, De Rijk P, Van Broeckhoven C, Del-Favero J
  Bioinformatics. 2005 Feb 1;21(3):385-7. Epub 2004 Sep 3.
• SNPbox: web-based high-throughput primer design from gene to genome.
  Weckx S, De Rijk P, Van Broeckhoven C, Del-Favero J
  Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W170-2.
• SNPbox: web-based high-throughput primer design with an eye for repetitive sequences.
  Weckx,S., De Rijk,P., Glassee,W., Van Broeckhoven,C., Del-Favero,J.
  Methods in Molecular Biology: PCR primer design Edited by Anton Yuryev (Humana Press) (In Press)

  Articles applying the technology and/or software

  • Genome-wide linkage of febrile seizures and epilepsy to the FEB4 locus at 5q14.3-q23.1 and no MASS1 mutation.
    Deprez L, Claes LR, Claeys KG, Audenaert D, Van Dyck T, Goossens D, Van Paesschen W, Del-Favero J, Van Broeckhoven C, De Jonghe P
    Hum Genet. 2006 Jan;118(5):618-25. Epub 2005 Nov 5.
  • High-density SNP haplotyping suggests altered regulation of tau gene expression in progressive supranuclear palsy.
    Rademakers R, Melquist S, Cruts M, Theuns J, Del-Favero J, Poorkaj P, Baker M, Sleegers K, Crook R, De Pooter T, Bel Kacem S, Adamson J, Van den Bossche D, Van den Broeck M, Gass J, Corsmit E, De Rijk P, Thomas N, Engelborghs S, Heckman M, Litvan I, Crook J, De Deyn PP, Dickson D, Schellenberg GD, Van Broeckhoven C, Hutton ML
    Hum Mol Genet. 2005 Nov 1;14(21):3281-92. Epub 2005 Sep 29.
  • Patient-control association study of substance P-related genes in unipolar and bipolar affective disorders.
    Mendlewicz J, Oswald P, Claes S, Massat I, Souery D, Van Broeckhoven C, Del-Favero J
    Int J Neuropsychopharmacol. 2005 Dec;8(4):505-13. Epub 2005 Jun 1.
  • Linkage and association studies identify a novel locus for Alzheimer disease at 7q36 in a Dutch population-based sample.
    Rademakers R, Cruts M, Sleegers K, Dermaut B, Theuns J, Aulchenko Y, Weckx S, De Pooter T, Van den Broeck M, Corsmit E, De Rijk P, Del-Favero J, van Swieten J, van Duijn CM, Van Broeckhoven C
    Am J Hum Genet. 2005 Oct;77(4):643-52. Epub 2005 Aug 30.
  • Genomic architecture of human 17q21 linked to frontotemporal dementia uncovers a highly homologous family of low-copy repeats in the tau region.
    Cruts M, Rademakers R, Gijselinck I, van der Zee J, Dermaut B, de Pooter T, de Rijk P, Del-Favero J, van Broeckhoven C
    Hum Mol Genet. 2005 Jul 1;14(13):1753-62. Epub 2005 May 11.
  • De novo KCNQ2 mutations in patients with benign neonatal seizures.
    Claes LR, Ceulemans B, Audenaert D, Deprez L, Jansen A, Hasaerts D, Weckx S, Claeys KG, Del-Favero J, Van Broeckhoven C, De Jonghe P
    Neurology. 2004 Dec 14;63(11):2155-8.

  Articles refering to the technology and/or software

  • EasyExonPrimer: automated primer design for exon sequences.
    Wu X, Munroe DJ
    Appl Bioinformatics. 2006;5(2):119-20.
  • GENOMEMASKER package for designing unique genomic PCR primers.
    Andreson R, Reppo E, Kaplinski L, Remm M
    BMC Bioinformatics. 2006 Mar 27;7:172.
  • Computational tradeoffs in multiplex PCR assay design for SNP genotyping.
    Rachlin J, Ding C, Cantor C, Kasif S
    BMC Genomics. 2005 Jul 25;6:102.
  • SNPNB: analyzing neighboring-nucleotide biases on single nucleotide polymorphisms (SNPs).
    Zhang F, Zhao Z
    Bioinformatics. 2005 May 15;21(10):2517-9. Epub 2005 Mar 15.
  • SNPHunter: a bioinformatic software for single nucleotide polymorphism data acquisition and management.
    Wang L, Liu S, Niu T, Xu X
    BMC Bioinformatics. 2005 Mar 18;6:60.
  • novoSNP, a novel computational tool for sequence variation discovery.
    Weckx S, Del-Favero J, Rademakers R, Claes L, Cruts M, De Jonghe P, Van Broeckhoven C, De Rijk P
    Genome Res. 2005 Mar;15(3):436-42.