Independent transcriptional patterns reveal biological processes associated with disease-free survival in early colorectal cancer

Link to paper Knapen DG, Hone Lopez S, de Groot DJA, de Haan JJ, de Vries EGE, Dienstmann R, de Jong S, Bhattacharya A, Fehrmann RSN Abstract Background Bulk transcriptional profiles of early colorectal cancer (CRC) can fail to detect biological processes associated with disease-free survival (DFS) if the transcriptional patterns are subtle and/or obscured…

Exploring combinations of dimensionality reduction, transfer learning, and regularization methods for predicting binary phenotypes with transcriptomic data

Link to paper Oshternian SR, Loipfinger S, Bhattacharya A, Fehrmann RSN Abstract Background Numerous transcriptomic-based models have been developed to predict or understand the fundamental mechanisms driving biological phenotypes. However, few models have successfully transitioned into clinical practice due to challenges associated with generalizability and interpretability. To address these issues, researchers have turned to dimensionality…

Identification of new head and neck squamous cell carcinoma molecular imaging targets

Link to paper van Schaik JE, van der Vegt B, Slagter-Menkema L, van der Laan BFAM, Witjes MJH, Oosting SF, Fehrmann RSN, Plaat BEC ABSTRACTObjectives: Intraoperative fluorescence imaging (FI) of head and neck squamous cell carcinoma (HNSCC) is performed to identify tumour-positive surgical margins, currently using epidermal growth factor receptor (EGFR) as imaging target. EGFR,…

Total serum N-glycans associate with response to immune checkpoint inhibition therapy and survival in patients with advanced melanoma

Link to paper Visconti A, Rossi N, Deriš H, Lee KA, Hanić M, Trbojević-Akmačić I, Thomas AM, Bolte LA, Björk JR, Hooiveld-Noeken JS, Board R, Harland M, Newton-Bishop J, Harries M, Sacco JJ, Lorigan P, Shaw HM, Vries EGE de, Fehrmann RSN, Weersma RK, Spector TD, Nathan P, Hospers GAP, Sasieni P, Bataille V, Lauc…