User profiles for K. Van den Berge

Koen Van den Berge

J&J Innovative Medicine
Verified email at berkeley.edu
Cited by 2885

RNA sequencing data: hitchhiker's guide to expression analysis

K Van den Berge, KM Hembach… - Annual Review of …, 2019 - annualreviews.org
… While very fast, these k-mer-based approaches do not retain the coherence of the k-mers
along a read, which can reduce specificity, and they cannot easily estimate certain aspects of …

Non-neuronal expression of SARS-CoV-2 entry genes in the olfactory system suggests mechanisms underlying COVID-19-associated anosmia

…, C Weinreb, M Lipovsek, K Van den Berge… - Science …, 2020 - science.org
Altered olfactory function is a common symptom of COVID-19, but its etiology is unknown. A
key question is whether SARS-CoV-2 (CoV-2) – the causal agent in COVID-19 – affects …

Cognitive diagnostic error in internal medicine

K van den Berge, S Mamede - European journal of internal medicine, 2013 - Elsevier
Medical error poses an important healthcare burden and a challenge for physicians and
policy makers worldwide. Diagnostic error accounts for a substantial fraction of all medical …

[HTML][HTML] Trajectory-based differential expression analysis for single-cell sequencing data

K Van den Berge, H Roux de Bézieux, K Street… - Nature …, 2020 - nature.com
… (K − 1) matrix, where each column corresponds to a contrast between two consecutive β glk
and β gl(k+1) and where we have K − 1 contrasts per lineage for a total of L (K − 1) contrasts. …

Effect of availability bias and reflective reasoning on diagnostic accuracy among internal medicine residents

SÝ Mamede, T van Gog, K van den Berge… - Jama, 2010 - jamanetwork.com
Context Diagnostic errors have been associated with bias in clinical reasoning. Empirical
evidence on the cognitive mechanisms underlying biases and effectiveness of educational …

[HTML][HTML] A transcriptomic and epigenomic cell atlas of the mouse primary motor cortex

…, SA Ament, A Bartlett, MM Behrens, K Van den Berge… - Nature, 2021 - nature.com
Single-cell transcriptomics can provide quantitative molecular signatures for large, unbiased
samples of the diverse cell types in the brain 1 , 2 – 3 . With the proliferation of multi-omics …

[HTML][HTML] Observation weights unlock bulk RNA-seq tools for zero inflation and single-cell applications

K Van den Berge, F Perraudeau, C Soneson, MI Love… - Genome biology, 2018 - Springer
… computed with the number of unknown covariates K=0, ie, no latent variables were inferred.
To cluster the real datasets, we inferred an optimal choice of K using the AIC (Additional file 1…

Polar lake microbiomes have distinct evolutionary histories

…, E Verleyen, M Sweetlove, K Van den Berge… - Science …, 2023 - science.org
Toward the poles, life on land is increasingly dominated by microorganisms, yet the evolutionary
origin of polar microbiomes remains poorly understood. Here, we use metabarcoding of …

[HTML][HTML] 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… - Genome biology, 2017 - Springer
RNA sequencing studies with complex designs and transcript-resolution analyses involve
multiple hypotheses per gene; however, conventional approaches fail to control the false …

Do patients' disruptive behaviours influence the accuracy of a doctor's diagnosis? A randomised experiment

…, T Van Gog, SCE Schuit, K Van den Berge… - BMJ quality & …, 2017 - qualitysafety.bmj.com
Background Literature suggests that patients who display disruptive behaviours in the
consulting room fuel negative emotions in doctors. These emotions, in turn, are said to cause …