Related papers: Automated generation of bacterial resource allocat…
Some organism-specific databases about regulation in bacteria have become larger, accelerated by high-throughput methodologies, while others are no longer updated or accessible. Each database homogenize its datasets, giving rise to…
The availability of fast to evaluate and reliable predictive models is highly relevant in multi-query scenarios where evaluating some quantities in real, or near-real-time becomes crucial. As a result, reduced-order modelling techniques…
Controlled branching processes are stochastic growth population models in which the number of individuals with reproductive capacity in each generation is controlled by a random control function. The purpose of this work is to examine the…
The analysis of non-equilibrium steady states of biochemical reaction networks relies on finding the configurations of fluxes and chemical potentials satisfying stoichiometric (mass balance) and thermodynamic (energy balance) constraints.…
ABCpy is a highly modular scientific library for Approximate Bayesian Computation (ABC) written in Python. The main contribution of this paper is to document a software engineering effort that enables domain scientists to easily apply ABC…
Bacteria are highly adaptive microorganisms that thrive in a wide range of growth conditions via changes in cell morphologies and macromolecular composition. How bacterial morphologies are regulated in diverse environmental conditions is a…
Reinforcement learning (RL) is a critical component of large language model (LLM) post-training. However, on-policy algorithms used for post-training are not naturally robust to a diversified content of experience replay buffers, which…
Motivation: An essential step in developing computational tools for the inference, optimization, and simulation of biochemical reaction networks is gauging tool performance against earlier efforts using an appropriate set of benchmarks.…
Robotic Process Automation (RPA) has emerged as a game-changing technology in data extraction, revolutionizing the way organizations process and analyze large volumes of documents such as invoices, purchase orders, and payment advices. This…
Despite major environmental and genetic differences, microbial metabolic networks are known to generate consistent physiological outcomes across vastly different organisms. This remarkable robustness suggests that, at least in bacteria,…
Understanding the organization of reaction fluxes in cellular metabolism from the stoichiometry and the topology of the underlying biochemical network is a central issue in systems biology. In this task, it is important to devise reasonable…
Assuming a steady-state condition within a cell, metabolic fluxes satisfy an under-determined linear system of stoichiometric equations. Characterizing the space of fluxes that satisfy such equations along with given bounds (and possibly…
Constraint-based stoichiometric models are ubiquitous in metabolic research, with Flux Balance Analysis (FBA) being the most widely used method to describe metabolic phenotypes of cells growing in steady-state. Of the many variants of…
Solving population balance equations, we derive analytical steady-state cell size distributions for single-lineage experiments, such as the mother machine. These experiments are fundamentally different from batch cultures where populations…
Mamba selective state space models (SSMs) provide linear-time sequence modeling but remain sensitive to selective-scan chunk scheduling. We present COREY, a \emph{concept-and-feasibility} runtime scheduler that maps fixed-bin activation…
A major theme in constraint-based modeling is unifying experimental data, such as biochemical information about the reactions that can occur in a system or the composition and localization of enzyme complexes, with highthroughput data…
New computational tools for solid-state synthesis recipe design are needed in order to accelerate the experimental realization of novel functional materials proposed by high-throughput materials discovery workflows. This work contributes a…
Metabolic models condense biochemical knowledge about organisms in a structured and standardised way. As large-scale network reconstructions are readily available for many organisms, genome-scale models are being widely used among modellers…
Motivation: NMR spectra are widely used in metabolomics to obtain metabolite profiles in complex biological mixtures. Common methods used to assign and estimate concentrations of metabolites involve either an expert manual peak fitting or…
We present a step towards the metabolome-wide computational inference of cellular metabolic reaction networks from metabolic profiling data, such as mass spectrometry. The reconstruction is based on identification of irreducible statistical…