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Koen Van den Berge
Koen Van den Berge
J&J Innovative Medicine
Adresse e-mail validée de berkeley.edu
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Non-neuronal expression of SARS-CoV-2 entry genes in the olfactory system suggests mechanisms underlying COVID-19-associated anosmia
DH Brann, T Tsukahara, C Weinreb, M Lipovsek, K Van den Berge, ...
Science Advances, eabc5801, 2020
11582020
Trajectory-based differential expression analysis for single-cell sequencing data
K Van den Berge, H Roux de Bézieux, K Street, W Saelens, R Cannoodt, ...
Nature communications 11 (1), 1201, 2020
4282020
A multimodal cell census and atlas of the mammalian primary motor cortex
Principal manuscript editors, Analysis coordination, ...
Nature 598 (7879), 86-102, 2021
2532021
A transcriptomic and epigenomic cell atlas of the mouse primary motor cortex
Z Yao, H Liu, F Xie, S Fischer, RS Adkins, AI Aldridge, SA Ament, ...
Nature 598 (7879), 103-110, 2021
234*2021
Observation weights unlock bulk RNA-seq tools for zero inflation and single-cell applications
K Van den Berge, F Perraudeau, C Soneson, MI Love, D Risso, JP Vert, ...
Genome Biology 19 (24), 250126, 2018
2012018
RNA sequencing data: hitchhiker's guide to expression analysis
K Van Den Berge, KM Hembach, C Soneson, S Tiberi, L Clement, ...
Annual Review of Biomedical Data Science 2, 2019
1342019
stageR: a general stage-wise method for controlling the gene-level false discovery rate in differential expression and differential transcript usage
K Van den Berge, C Soneson, MD Robinson, L Clement
Genome biology 18 (1), 151, 2017
972017
A sex-inducing pheromone triggers cell cycle arrest and mate attraction in the diatom Seminavis robusta
S Moeys, J Frenkel, C Lembke, JTF Gillard, V Devos, K Van den Berge, ...
Scientific Reports 6 (1), 19252, 2016
752016
Hierarchical community detection by recursive partitioning
T Li, L Lei, S Bhattacharyya, K Van den Berge, P Sarkar, PJ Bickel, ...
Journal of the American Statistical Association 117 (538), 951-968, 2022
702022
Distinctive growth and transcriptional changes of the diatom Seminavis robusta in response to quorum sensing related compounds
F Stock, G Bilcke, S De Decker, CM Osuna-Cruz, K Van den Berge, ...
Frontiers in Microbiology 11, 511653, 2020
252020
A multimodal cell census and atlas of the mammalian primary motor cortex
BRAIN Initiative Cell Census Network (BICCN), RS Adkins, AI Aldridge, ...
Biorxiv, 2020.10. 19.343129, 2020
222020
Strain-specific transcriptional responses overshadow salinity effects in a marine diatom sampled along the Baltic Sea salinity cline
E Pinseel, T Nakov, K Van den Berge, KM Downey, KJ Judy, ...
The ISME Journal 16 (7), 1776-1787, 2022
212022
Mating type specific transcriptomic response to sex inducing pheromone in the pennate diatom Seminavis robusta
G Bilcke, K Van den Berge, S De Decker, E Bonneure, N Poulsen, ...
The ISME Journal 15 (2), 562-576, 2021
212021
satuRn: Scalable analysis of differential transcript usage for bulk and single-cell RNA-sequencing applications
J Gilis, K Vitting-Seerup, K Van den Berge, L Clement
F1000Research 10, 2021
202021
A guide to trajectory inference and RNA velocity
P Weiler, K Van den Berge, K Street, S Tiberi
Single Cell Transcriptomics: Methods and Protocols, 269-292, 2022
122022
Trajectory inference across multiple conditions with condiments: differential topology, progression, differentiation, and expression
HR de Bézieux, K Van den Berge, K Street, S Dudoit
BioRxiv, 2021.03. 09.433671, 2021
122021
Effect of management and age of ploughed out grass–clover on forage maize yield and residual soil nitrogen
M Cougnon, K Van Den Berge, T D'Hose, L Clement, D Reheul
The Journal of Agricultural Science 156 (6), 748-757, 2018
82018
Normalization benchmark of ATAC-seq datasets shows the importance of accounting for GC-content effects
K Van den Berge, HJ Chou, HR de Bézieux, K Street, D Risso, J Ngai, ...
Cell Reports Methods 2 (11), 2022
72022
Altering the Sex Pheromone Cyclo(l-Pro-l-Pro) of the Diatom Seminavis robusta towards a Chemical Probe
E Bonneure, A De Baets, S De Decker, K Van den Berge, L Clement, ...
International Journal of Molecular Sciences 22 (3), 1037, 2021
72021
Neurogenomic profiling reveals distinct gene expression profiles between brain parts that are consistent in Ophthalmotilapia cichlids
S Derycke, L Kéver, K Van den Berge, E Parmentier, E Verheyen
Frontiers in Neuroscience 12, 302361, 2018
72018
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