Journal Club

We will discuss about “Detecting and quantifying causal associations in large nonlinear time series datasets”, Runge et al., Science Advances, 2019 Identifying causal relationships and quantifying their strength from observational …

We will discuss about “Solving Singular Control Problems in Mathematical Biology, Using PASA”, Atkins et al., arXiv, 2020 In this paper, we will demonstrate how to use a nonlinear polyhedral …

We will discuss about “A Random Matrix Theory Approach to Denoise Single-Cell Data”, Aparicio et al., Patterns, 2020 Single-cell technologies provide the opportunity to identify new cellular states. However, a …

We will discuss about “Stiff-PINN: Physics-Informed Neural Network for Stiff Chemical Kinetics”, Ji et al., The Journal of Physical Chemistry A, 2020 The recently developed physics-informed neural network (PINN) has …

We will discuss about "Information Integration and Energy Expenditure in Gene Regulation", Estrada et al., Cell, 2016 Abstract: The quantitative concepts used to reason about gene regulation largely derive from …

We will discuss about "The Generalized Multiset Sampler", Kim and MacEachern, The Journal of Computation and Graphical Statistics, 2021 Abstract: The multiset sampler, an MCMC algorithm recently proposed by Leman …

We will discuss about "Fundamental limits on the suppression of molecular fluctuations", Lestas et al, Nature, 2010 Abstract: Negative feedback is common in biological processes and can increase a system’s …

We will discuss about "Quasi-Entropy Closure: A Fast and Reliable Approach to Close the Moment Equations of the Chemical Master Equation", Wagner et al, bioRxiv, 2021 Motivation: The Chemical Master …

We will discuss about "Network design principle for robust oscillatory behaviors with respect to biological noise", Qiao et al, bioRxiv, 2021 Oscillatory behaviors, which are ubiquitous in transcriptional regulatory networks, …

We will discuss about "Mechanisms for the generation of robust circadian oscillations through ultrasensitivity and differential binding affinity", Behera, Junco, and Vaikuntanathan, The Journal of Physical Chemistry B, 2021 Biochemical …

We will discuss about "Phiclust: a clusterability measure for single-cell transcriptomics reveals phenotypic subpopulations", Mircea et al., 2022, Genome Biology The ability to discover new cell phenotypes by unsupervised clustering …

We will discuss about "A Deficiency-Based Approach to Parametrizing Positive Equilibria of Biochemical Reaction Systems", Johnston, Müller, and Pantea, Bulletin of Mathematical Biology, 2019 We present conditions which guarantee a …