Journal Club

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 …

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 …

Abstract: Consider a biomolecular reaction network that exhibits robust perfect adaptation to disturbances from several parallel sources. The well-known Internal Model Principle of control theory suggests that such systems must include a …

We will discuss about "Physics-informed learning of governing equations from scarce data", Chen et al., Nature Communications, 2021 Abstract: Extracting governing equations from data is a central challenge in many …

We will discuss about "RTransferEntropy — Quantifying information flow between different time series using effective transfer entropy", Behrendt et al., SoftwareX, 2019 Abstract: This paper shows how to quantify and …

We will discuss about "A topological data analysis based classifier", Kindelan et al., arXiv, 2022 Abstract: Topological Data Analysis is an emergent field that aims to discover the underlying dataset’s …

We will discuss about "An Efficient Characterization of Complex-Balanced, Detailed-Balanced, and Weakly Reversible Systems", Craciun et al., SIAM Journal on Applied Mathematics, 2020 Abstract: Very often, models in biology, chemistry, …

We will discuss about "Toroidal topology of population activity in grid cells", Gardner et al., Nature, 2021. Abstract: The medial entorhinal cortex is part of a neural system for mapping …