Publications

Below is a list of selected publications and preprints. For a full list, please visit my Google Scholar page. My work has mostly focussed on differential expression analysis of high-throughput sequencing datasets.

* denotes shared first authorship and † denotes shared corresponding authors.

(Applied) statistical methodology

• Gillis J., Vitting-Seerup K., Van den Berge K.†, Clement L.†. satuRn: Scalable Analysis of differential Transcript Usage for bulk and single-cell RNA-sequencing applications. F1000Research (in open review).
• Nguyen K., Van den Berge K., Chiogna M., Risso D. (2020). Structure learning for zero-inflated counts, with an application to single-cell RNA sequencing data. arXiv
• Li T., Lei L., Bhattacharyya S., Van den Berge K., Sarkar P., Bickel P.J., Levina E. (2020). Hierarchical community detection by recursive partitioning. Journal of the American Statistical Association (in print).
• Van den Berge K., Roux de B’ezieux H., Street K., Saelens W., Cannoodt R., Saeys Y., Dudoit S.†, Clement L.† (2020). Trajectory-based differential expression analysis for single-cell sequencing data. Nature Communications 11:1201.
• Van den Berge K.*, Hembach K.M.*, Soneson C.*, Tiberi S.*, Clement L.†, Love M.I.†, Patro R.†, Robinson M.D.† (2019) RNA Sequencing Data: Hitchhiker’s Guide to Expression Analysis. Annual Review of Biomedical Data Science 2:139-173.
• Van den Berge K.*, Perraudeau F.*, Soneson C., Love M.I., Risso D., Vert J.P., Robinson M.D., Dudoit S., Clement L. (2018). Observation weights unlock bulk RNA-seq tools for zero inflation and single-cell applications. Genome Biology 19:24.
• Van den Berge K., Soneson C., Robinson M.D., Clement L. (2017). stageR: a general stage-wise method for controlling the gene-level false discovery rate in differential expression and differential transcript usage. Genome Biology 18:151.

Collaborative papers

• Bilcke G.*, Van den Berge K.*, De Decker S., Bonneure E., Poulsen N., Bulankova P., Osuna-Cruz C., Dickenson J., Sabbe K., Pohnert G., Vandepoele K., Mangelinckx S., Clement L., De Veylder L., Vyverman W. (2020). Mating type specific transcriptomic response to sex inducing pheromone in the pennate diatom Seminavis robusta. The ISME Journal 15(2): 562-576.
• Brann D.*, Tsukahara T.*, Weinreb C.*, Lipovsek M., Van den Berge K., Gong B., Chance R., Macaulay I., Chou H., Fletcher R., Das D., Street K., Roux de Bezieux H., Gi Choi Y., Risso D., Dudoit S., Purdom E., Mill J., Abi Hachem R., Matsunami H., Logan D., Goldstein B., Grubb M., Ngai J., Datta S. (2020). Non-neuronal expression of SARS-CoV-2 entry genes in the olfactory system suggests mechanisms underlying COVID-19-associated anosmia. Science Advances 6: eabc5801.
• Derycke S., Kéver L., Herten K., Van den Berge K., Van Steenberge M., Van Houdt M., Clement L., Poncin P., Parmentier E., Verheyen E. (2018). Neurogenomic profiling reveals distinct gene expression profiles between brain parts that are consistent in Ophthalmotilapia cichlids. Frontiers in Neuroscience 12:136.
• Moeys S., Frenkel J., Lembke C., Gillard J., Devos V., Van den Berge K., Bouillon B., Huysman M., De Decker S., Scharf J., Bones A., Brembu T., Winge P., Sabbe K., Vuylsteke M., Clement L., De Veylder L., Pohnert G., Vyverman W. (2016). A sex-inducing pheromone triggers cell cycle arrest and mate attraction in the diatom Seminavis robusta. Scientific Reports 6:19252.