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Babaei, S. (author), Akhtar, W. (author), De Jong, J. (author), Reinders, M.J.T. (author), De Ridder, J. (author)
Genomically distal mutations can contribute to the deregulation of cancer genes by engaging in chromatin interactions. To study this, we overlay viral cancer-causing insertions obtained in a murine retroviral insertional mutagenesis screen with genome-wide chromatin conformation capture data. Here we find that insertions tend to cluster in 3D...
journal article 2015
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De Jong, J. (author), Akhtar, W. (author), Badhai, J. (author), Rust, A.G. (author), Rad, R. (author), Hilkens, J. (author), Berns, A. (author), Van Lohuizen, M. (author), Wessels, L.F.A. (author), De Ridder, J. (author)
The ability of retroviruses and transposons to insert their genetic material into host DNA makes them widely used tools in molecular biology, cancer research and gene therapy. However, these systems have biases that may strongly affect research outcomes. To address this issue, we generated very large datasets consisting of to unselected...
journal article 2014
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De Jong, J. (author), De Ridder, J. (author), Van der Weyden, L. (author), Sun, N. (author), Van Uitert, M. (author), Berns, A. (author), Van Lohuizen, M. (author), Jonkers, J. (author), Adams, D.J. (author), Wessels, L.F.A. (author)
Insertional mutagenesis is a potent forward genetic screening technique used to identify candidate cancer genes in mouse model systems. An important, yet unresolved issue in the analysis of these screens, is the identification of the genes affected by the insertions. To address this, we developed Kernel Convolved Rule Based Mapping (KC-RBM). KC...
journal article 2011