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K. Van den Berge · SciRah

Researcher profile · Semantic Scholar

K. Van den Berge

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K. Van den Berge — researcher profile on SciRah

h-index: 18
Works: 51
Citations: 2,855

Most-cited papers

Trajectory-based differential expression analysis for single-cell sequencing data
K. Van den Berge, Hector Roux de Bézieux, Kelly Street, Wouter Saelens +4 more
2019Nature Communications723 citations Open access
Semantic Scholar
A multimodal cell census and atlas of the mammalian primary motor cortex
E. Callaway, Hong-wei Dong, J. Ecker, Mike Hawrylycz +254 more
2020Nature465 citations Open access
Semantic Scholar
Non-neuronal expression of SARS-CoV-2 entry genes in the olfactory system suggests mechanisms underlying COVID-19-associated anosmia
D. Brann, Tatsuya Tsukahara, Caleb Weinreb, M. Lipovsek +21 more
2020Science Advances353 citations Open access
Semantic Scholar
A transcriptomic and epigenomic cell atlas of the mouse primary motor cortex
Z. Yao, Hanqing Liu, Fang-Ming Xie, Stephan Fischer +79 more
2021Nature332 citations Open access
Semantic Scholar
Observation weights unlock bulk RNA-seq tools for zero inflation and single-cell applications
K. Van den Berge, Fanny Perraudeau, C. Soneson, M. Love +5 more
2018Genome Biology193 citations Open access
Semantic Scholar
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, Mark D. Robinson, Lieven Clement
2017Genome Biology133 citations Open access
Semantic Scholar
RNA Sequencing Data: Hitchhiker's Guide to Expression Analysis
K. Van den Berge, Katharina M. Hembach, C. Soneson, S. Tiberi +4 more
2018Annual Review of Biomedical Data Science118 citations Open access
Semantic Scholar
Hierarchical Community Detection by Recursive Partitioning
Tianxi Li, Li-Hua Lei, Sharmodeep Bhattacharyya, K. Van den Berge +3 more
2018Journal of the American Statistical Association93 citations Open access
Semantic Scholar
An integrated transcriptomic and epigenomic atlas of mouse primary motor cortex cell types
Z. Yao, Hanqing Liu, Fang-Ming Xie, Stephan Fischer +79 more
2020bioRxiv68 citations Open access
Semantic Scholar
A sex-inducing pheromone triggers cell cycle arrest and mate attraction in the diatom Seminavis robusta
Sara Moeys, Johannes Frenkel, Christine Lembke, Jeroen T. F. Gillard +15 more
2016Scientific Reports66 citations Open access
Semantic Scholar
Trajectory inference across multiple conditions with condiments
Hector Roux de Bézieux, K. Van den Berge, Kelly Street, S. Dudoit
2021bioRxiv44 citations Open access
Semantic Scholar
Distinctive Growth and Transcriptional Changes of the Diatom Seminavis robusta in Response to Quorum Sensing Related Compounds
Frederike Stock, G. Bilcke, S. De Decker, C. M. Osuna-Cruz +6 more
2020Frontiers in Microbiology35 citations Open access
Semantic Scholar
satuRn: Scalable analysis of differential transcript usage for bulk and single-cell RNA-sequencing applications
Jeroen Gilis, K. Vitting-Seerup, K. Van den Berge, Lieven Clement
2021bioRxiv33 citations Open access
Semantic Scholar
A guide to trajectory inference and RNA velocity
P. Weiler, K. Van den Berge, Kelly Street, S. Tiberi
2021bioRxiv28 citations Open access
Semantic Scholar
Strain-specific transcriptional responses overshadow salinity effects in a marine diatom sampled along the Baltic Sea salinity cline
Eveline Pinseel, Teofil Nakov, K. Van den Berge, K. Downey +8 more
2022The ISME Journal25 citations Open access
Semantic Scholar
Polar lake microbiomes have distinct evolutionary histories
B. Tytgat, E. Verleyen, M. Sweetlove, K. Van den Berge +7 more
2023Science Advances22 citations Open access
Semantic Scholar
Mating type specific transcriptomic response to sex inducing pheromone in the pennate diatom Seminavis robusta
G. Bilcke, K. Van den Berge, S. De Decker, Elias Bonneure +11 more
2020The ISME Journal21 citations Open access
Semantic Scholar
zingeR: unlocking RNA-seq tools for zero-inflation and single cell applications
K. Van den Berge, C. Soneson, M. Love, Mark D. Robinson +1 more
2017bioRxiv19 citations Open access
Semantic Scholar
Normalization benchmark of ATAC-seq datasets shows the importance of accounting for GC-content effects
K. Van den Berge, Hsin-Jung Chou, Hector Roux de Bézieux, Kelly Street +3 more
2021bioRxiv18 citations Open access
Semantic Scholar
Structure learning for zero-inflated counts with an application to single-cell RNA sequencing data
T. Nguyen, K. Van den Berge, M. Chiogna, D. Risso
2020Annals of Applied Statistics9 citations Open access
Semantic Scholar
Immune signaling mediates stromal changes to support epithelial reprogramming in Celiac duodenum
Dylan J. Richards, Klebea Sohn, Shrikanth Chomanahalli Basavarajappa, D. Horowitz +10 more
2025bioRxiv8 citations Open access
Semantic Scholar
Differential detection workflows for multi-sample single-cell RNA-seq data
Jeroen Gilis, Laura Perin, Milan Malfait, K. Van den Berge +4 more
2023bioRxiv7 citations Open access
Semantic Scholar
Altering the Sex Pheromone Cyclo(l-Pro-l-Pro) of the Diatom Seminavis robusta towards a Chemical Probe
Elias Bonneure, Amber De Baets, S. De Decker, K. Van den Berge +3 more
2021International Journal of Molecular Sciences7 citations Open access
Semantic Scholar
Genotype-specific transcriptional responses overshadow salinity effects in a marine diatom sampled along the Baltic Sea salinity cline
Eveline Pinseel, Teofil Nakov, K. Van den Berge, K. Downey +8 more
2021bioRxiv7 citations Open access
Semantic Scholar
AAV-HBV mouse model replicates the intrahepatic immune landscape of chronic HBV patients at single-cell level
Nádia Conceição-Neto, Wim Pierson, Qing-Zeng Han, Zhi-Yuan Yao +13 more
2025Frontiers in Immunology5 citations Open access
Semantic Scholar
Datasets associated with the publication of the "satuRn" R package
Jeroen Gilis, K. Vitting-Seerup, K. Van den Berge, Lieven Clement
20215 citations
Semantic Scholar
Neurogenomic Profiling Reveals Distinct Gene Expression Profiles Between Brain Parts That Are Consistent in Ophthalmotilapia Cichlids
S. Derycke, L. Kéver, Koen Herten, K. Van den Berge +6 more
2018Frontiers in Neuroscience5 citations Open access
Semantic Scholar
Conserved genetic markers reveal widespread diatom sexual reproduction in the global ocean
G. Bilcke, Lucia Campese, Rossella Annunziata, Luz Amadei Martínez +10 more
2025Nature Communications4 citations Open access
Semantic Scholar
Assessing differential cell composition in single-cell studies using voomCLR
A. Assefa, Bie Verbist, K. Van den Berge
2024bioRxiv3 citations Open access
Semantic Scholar
Improving replicability in single-cell RNA-Seq cell type discovery with Dune
Hector Roux de Bézieux, Kelly Street, Stephan Fischer, K. Van den Berge +6 more
2020bioRxiv3 citations Open access
Semantic Scholar
Multiomic characterisation of the clinical efficacy of guselkumab induction therapy in ulcerative colitis
A. Hart, S. Sridhar, Swati Venkat, Tae-Hyong Lee +20 more
2026BMJ Open Gastroenterology2 citations Open access
Semantic Scholar
Strategies for addressing pseudoreplication in multi-patient scRNA-seq data
Milan Malfait, Jeroen Gilis, K. Van den Berge, A. Assefa +2 more
2024bioRxiv2 citations Open access
Semantic Scholar
A latent activated olfactory stem cell state revealed by single-cell transcriptomic and epigenomic profiling
K. Van den Berge, Dana Bakalar, Hsin-Jung Chou, Divya Kunda +6 more
2023bioRxiv2 citations Open access
Semantic Scholar
Year(s) of the wolf: no doubt about it!
K. Van den Berge
20182 citations
Semantic Scholar
A general and powerful stage-wise testing procedure for differential expression and differential transcript usage
K. Van den Berge, C. Soneson, Mark D. Robinson, Lieven Clement
2017bioRxiv2 citations Open access
Semantic Scholar
Longitudinal mechanisms of response, resistance and relapse to teclistamab in multiple myeloma: results from MajesTEC-1.
D. Vishwamitra, Sheri Skerget, D. Cortés-Selva, T. Perova +19 more
2026Haematologica1 citations Open access
Semantic Scholar
transfactor: Transcription factor activity estimation via probabilistic gene expression deconvolution
K. Van den Berge, Peter J. Bickel, Sandrine Dudoit
2025bioRxiv1 citations Open access
Semantic Scholar
Differential detection workflows for multi-sample single-cell RNA-seq data
Jeroen Gilis, Laura Perin, Milan Malfait, Helena L. Crowell +5 more
2025BMC Genomics1 citations Open access
Semantic Scholar
AAV-HBV mouse model replicates immune exhaustion patterns of chronic HBV patients at single-cell level
Nádia Conceição-Neto, Qing-Zeng Han, Zhi-Yuan Yao, Wim Pierson +11 more
2023bioRxiv1 citations Open access
Semantic Scholar
The return of wolves to the Netherlands : a fact-finding study
H. Jansman, J. Mergeay, E. A. van der Grift, G. D. de Groot +7 more
20211 citations Open access
Semantic Scholar
Observation weights to unlock bulk RNA-seq tools for zero inflation and single-cell applications
K. Van den Berge, Fanny Perraudeau, C. Soneson, Michael I. Love +5 more
2018bioRxiv1 citations Open access
Semantic Scholar
Biogeography and macroevolution in the Arctic and Antarctic lacustrine microbiomes
M. Sweetlove, B. Tytgat, E. Verleyen, K. Van den Berge +9 more
20171 citations
Semantic Scholar
CD8 T cells with classical and NK-like cytotoxic gene expression programs mediate control of HBV replication and functional cure
E. Lattouf, M. Feuerherd, L. Bartsch, Hannah K. Drescher +37 more
2026bioRxiv0 citations Open access
Semantic Scholar
Removal of unwanted variation in pseudobulk analysis of single-cell RNA sequencing data and the leveraging of pseudoreplicates
Sofía Prieto León, Ewoud De Troyer, Helena Geys, K. Van den Berge +1 more
2025NAR Genomics and Bioinformatics0 citations Open access
Semantic Scholar
Intrahepatic characterization of virological and immunological markers in two distinct populations of chronic hepatitis B: baseline assessment of core liver and fine needle aspiration biopsies from the investigational INSIGHT study
P. Lampertico, T. Asselah, E. Gane, S. Fung +20 more
2023Journal of Hepatology0 citations
Semantic Scholar
Covid19 anosmia: pre- and post-processed objects for mouse scRNA-seq OE dataset.
K. Van den Berge
20200 citations
Semantic Scholar
Interpretation of single-cell RNA-seq trajectories using differential expression and differential progression analysis
K. Van den Berge
20200 citations Open access
Semantic Scholar
Statistical methods for differential expression analysis in bulk and single-cell RNA-sequencing applications
K. Van den Berge
20190 citations
Semantic Scholar
Molecular regulation of mating in the pennate diatom Seminavis robusta
Sara Moeys, Jeroen T. F. Gillard, B. Bouillon, K. Van den Berge +5 more
20150 citations
Semantic Scholar
Quantifying expression divergence of duplicated genes with microarrays
K. Van den Berge, Riet de Smet, Y. Van de Peer, Lieven Clement
20150 citations
Semantic Scholar

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