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Citing The Genomic HyperBrowser

If you use or extend The Genomic HyperBrowser in your published work, please cite the following publications:

  • Sandve GK, Gundersen S, Rydbeck H, Glad IK, Holden L, Holden M, Liestol K, Clancy T, Ferkingstad E, Johansen M, Nygaard V, Tostesen E, Frigessi A, Hovig E. The Genomic HyperBrowser: inferential genomics at the sequence level. Genome Biol. 2010 Dec 23;11(12):R121. PMID: 21182759.

  • Sandve GK, Gundersen S, Johansen M, Glad IK, Gunathasan K, Holden L, Holden M, Liestøl K, Nygård S, Nygaard V, Paulsen J, Rydbeck H, Trengereid K, Clancy T, Drabløs F, Ferkingstad E, Kalas M, Lien T, Rye MB, Frigessi A, Hovig E. The Genomic HyperBrowser: an analysis web server for genome-scale data. Nucleic Acids Res. 2013 Jul;41(Web Server issue):W133-41. PMID: 23632163.

  • Simovski B, Vodák D, Gundersen S, Domanska D, Azab A, Holden L, Holden M, Grytten I, Rand K, Drabløs F, Johansen M, Mora A, Lund-Andersen C, Fromm B, Eskeland R, Gabrielsen OS, Ferkingstad E, Nakken S, Bengtsen M, Nederbragt AJ, Thorarensen HS, Akse JA, Glad I, Hovig E, Sandve GK. GSuite HyperBrowser: integrative analysis of dataset collections across the genome and epigenome. bioRxiv (2016): 067561 [Preprint]

If you use or extend any of the following methodological additions of the Genomic HyperBrowser, please cite the corresponding publications:

The differential disease regulome
  • Sandve GK, Gundersen S, Rydbeck H, Glad IK, Holden L, Holden M, Liestøl K, Clancy T, Drabløs F, Ferkingstad E, Johansen M, Nygaard V, Tøstesen E, Frigessi A, Hovig E. The differential disease regulome. BMC Genomics. 2011 Jul 7;12:353.
MCFDR algorithm
  • Sandve GK, Ferkingstad E, Nygård S. Sequential Monte Carlo multiple testing. Bioinformatics. 2011 Dec 1;27(23):3235-41.
GTrack and track types
  • Gundersen S, Kalaš M, Abul O, Frigessi A, Hovig E, Sandve GK. Identifying elemental genomic track types and representing them uniformly. BMC Bioinformatics. 2011 Dec 30;12:494.
HiBrowse

  • Paulsen J, Lien TG, Sandve GK, Holden L, Borgan O, Glad IK, Hovig E. Handling realistic assumptions in hypothesis testing of 3D co-localization of genomic elements. Nucleic Acids Res. 2013 May 1;41(10):5164-74.

  • Paulsen J, Sandve GK, Gundersen S, Lien TG, Trengereid K, Hovig E. HiBrowse: multi-purpose statistical analysis of genome-wide chromatin 3D organization. Bioinformatics. 2014 Jun 1;30(11):1620-2.

ClusTrack
  • Rydbeck H, Sandve GK, Ferkingstad E, Simovski B, Rye M, Hovig E. ClusTrack: feature extraction and similarity measures for clustering of genome-wide data sets. PloS one. 2015 Apr 16;10(4):e0123261.