Journal Club

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 …

We will discuss about "Modeling polypharmacy side effects with graph convolutional networks", Zitnik, Agrawal, and Leskovec, Bioinformatics, 2018 Motivation The use of drug combinations, termed polypharmacy, is common to treat …

Abstract: Genetic feedback loops can be used by cells as a means to regulate internal processes or keep track of time. It is often thought that, for a genetic circuit …