Journal Club

We will discuss about “Filtering and inference for stochastic oscillators with distributed delays”, Calderazzo et al., Bioinformatics, 2018 at the Journal Club Motivation The time evolution of molecular species involved in biochemical reaction networks often arises from complex stochastic processes involving many species and reaction events. Inference for such systems is profoundly challenged by the …

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 time series data are key problems in disciplines dealing with complex dynamical systems such as the Earth system or the human body. Data-driven causal inference …

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 constrained optimization solver called the Polyhedral Active Set Algorithm (PASA) for solving a general singular control problem. We present methods of discretizing a general optimal …

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 major obstacle to the identification of biological signals is noise in single-cell data. In addition, single-cell data are very sparse. We propose a new method …

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 …