We will discuss about “Comparison of transformations for single-cell RNA-seq data”,Ahlmann-Eltze, Constantin, and Wolfgang Huber, Nature Methods (2023): 1-8. Abstract The count table, a numeric matrix of genes × cells, is the basic input data structure in the analysis of single-cell RNA-sequencing data. A common preprocessing step is to adjust the counts for variable sampling efficiency and …

We will discuss about “Improving gene regulatory network inference and assessment: The importance of using network structure”, Escorcia-Rodríguez, Juan M., et al., bioRxiv (2023): 2023-01. Abstract Gene regulatory networks are graph models representing cellular transcription events. Networks are far from complete due to time and resource consumption for experimental validation and curation of the interactions. Previous …

We will discuss about “Inference and uncertainty quantification of stochastic gene expression via synthetic models”, Öcal et al., J. R. Soc. Interface. Abstract Estimating uncertainty in model predictions is a central task in quantitativebiology. Biological models at the single-cell level are intrinsically stochastic and nonlinear, creating formidable challenges for their statistical estimation which inevitably has …

We will discuss about “A multi-scale model explains oscillatory slowing and neuronal hyperactivity in Alzheimer’s disease”, Alexandersen, Christoffer G., et al., Journal of the Royal Society Interface 20.198 (2023): 20220607. Abstract Alzheimer’s disease is the most common cause of dementia and is linked to the spreading of pathological amyloid-β and tau proteins throughout the brain. Recent studies …