Journal Club

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 achieved success in many science and engineering disciplines by encoding physics laws into the loss functions of the neural network such that the network not …

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 bacterial studies. We show that this bacterial paradigm cannot explain the sharp expression of a canonical developmental gene in response to a regulating transcription factor …

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 and coauthors, is an easy-to-implement algorithm which is especially well-suited to drawing samples from a multimodal distribution. We generalize the algorithm by redefining the multiset …

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 stability to internal and external perturbations. But at the molecular level, control loops always involve signalling steps with finite rates for random births and deaths …

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 Equation is the most comprehensive stochastic approach to describe the evolution of a (bio-)chemical reaction system. Its solution is a time-dependent probability distribution on all …

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, are often subject to inevitable biological noise. Thus a natural question is how transcriptional regulatory networks can robustly achieve accurate oscillation in the presence of …

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 circadian rhythm oscillations play an important role in many signaling mechanisms. In this work, we explore some of the biophysical mechanisms responsible for sustaining robust …

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 of single-cell transcriptomes has revolutionized biology. Currently, there is no principled way to decide whether a cluster of cells contains meaningful subpopulations that should be …

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 parametrization of the set of positive equilibria of a generalized mass-action system. Our main results state that (1) if the underlying generalized chemical reaction network …

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 patients with complex diseases or co-existing conditions. However, a major consequence of polypharmacy is a much higher risk of adverse side effects for the patient. …

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 to display self-sustained oscillations, a degree of cooperativity is needed in the binding and unbinding of actor species. This cooperativity is usually modeled using a …

Abstract: The discovery of governing equations from scientific data has the potential to transform data-rich fields that lack well-characterized quantitative descriptions. Advances in sparse regression are currently enabling the tractable identification of both the structure and parameters of a nonlinear dynamical system from data. The resulting models have the fewest terms necessary to describe the …