Journal Club

We will discuss about “The ups and downs of biological oscillators: A comparison of time-delayed negative feedback mechanisms”,Rombouts, Jan, Sarah Verplaetse, and Lendert Gelens., bioRxiv (2023) Abstract Many biochemical oscillators are driven by the periodic rise and fall of protein concentrations or activities. A negative feedback loop underlies such oscillations. The feedback can act on …

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 …