We will discuss about “A statistical framework for differential pseudotime analysis with multiple single-cell RNA-seq samples ”, Nature communications 14.1 (2023): 7286.   Abstract Pseudotime analysis with single-cell RNA-sequencing (scRNA-seq) data has been widely used to study dynamic gene regulatory programs along continuous biological processes. While many methods have been developed to infer the pseudotemporal trajectories …

We will discuss about "Reduced model for female endocrine dynamics: Validation and functional variations." Mathematical Biosciences 358 (2023): 108979. Abstract A normally functioning menstrual cycle requires significant crosstalk between hormones originating in ovarian and brain tissues. Reproductive hormone dysregulation may cause abnormal function and sometimes infertility. The inherent complexity in this endocrine system is a challenge to identifying mechanisms of cycle …

We will discuss about “Transcriptome-wide analysis of cell cycle-dependent bursty gene expression from single-cell RNA-seq data using mechanistic model-based inference”, bioRxiv (2024) Abstract Bursty gene expression is quantified by two intuitive parameters: the burst frequency and the burst size. While these parameters are known to be cell-cycle dependent for some genes, a transcriptome-wide picture remains …

We will discuss about "Anti-Windup Protection Circuits for Biomolecular Integral Controllers", bioRxiv (2023).   Abstract Robust Perfect Adaptation (RPA) is a desired property of biological systems wherein a system’s output perfectly adapts to a steady state, irrespective of a broad class of perturbations. Achieving RPA typically requires the deployment of integral controllers, which continually adjust …

We will discuss about "Phenotypic switching in gene regulatory networks", PNAS (2014).   Abstract Noise in gene expression can lead to reversible phenotypic switching. Several experimental studies have shown that the abundance distributions of proteins in a population of isogenic cells may display multiple distinct maxima. Each of these maxima may be associated with a …

We will discuss about "An improved rhythmicity analysis method using Gaussian Processes detects cell-density dependent circadian oscillations in stem cells", ArXiv (2023).   Abstract Detecting oscillations in time series remains a challenging problem even after decades of research. In chronobiology, rhythms in time series (for instance gene expression, eclosion, egg-laying and feeding) datasets tend to …