Molecular & Cell Biology · Life Sciences
Molecular Networks
The newest papers in Molecular Networks that ReadSearch has read, newest first. Each links to its own page, with its authors, date, where it was published and the original.
42 papers, from 31 August 2026 to 4 November 2026: 27 OpenAlex records and 15 arXiv preprints.
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Can a self-sustaining chemical network emerge due to just a few catalysts?
Understanding how self-sustaining chemical reaction networks can emerge from simple molecules is an important question in chemical approaches to the origin of life.Modeling Gene Expression Noise: From Transcriptional Dynamics to Cell Growth and Division
Gene expression is inherently noisy, leading to substantial cell-to-cell variation in mRNA and protein levels.GINsim 3.1: Qualitative modelling and dynamical analysis of logical regulatory networks
GINsim is a software for the definition and dynamical analysis of qualitative (Boolean and multi-valued) models of biological regulatory networks.Substrate hypergraph cycles: unique steady states and persistence for every enzyme assignment; oscillations enabled by enzyme sharing
We associate a directed substrate hypergraph with an enzymatic reaction system.Transmission and filtering of stochastic rhythms in bursty gene expression
How stochastic rhythms in upstream regulatory signals are transmitted to downstream gene expression is a fundamental question in systems biology.Generative discovery of chemical reaction networks
Chemical kinetics determines molecular stability, reaction selectivity and the evolution of reacting mixtures, but discovering the underlying reaction networks remains challenging.Spontaneous Spirals in Spatial Systems
Several chemical and biological systems produce spontaneous spirals in their dynamical behavior, such as the Belousov-Zhabotinsky reaction in chemistry and the slime mold Dictyostelium in biology.Bistability with equal and independent removal in small bimolecular networks
We classify two-species mass-action networks with at most three internal directed reactions on $\{X,Y,2X,X+Y,2Y\}$, positive inflows, and linear removal of both species.Global Convergence of Detailed Balanced Mass Action Systems
We give a self-contained proof that, for a finite detailed balanced mass-action system with positive rate constants, each positive stoichiometric compatibility class contains exactly one positive…Kinetic Proofreading Activation Times Beyond the Weibull Limit
T cells can detect a few foreign peptide-major histocompatibility complexes (pMHCs) among a far larger number of self pMHCs.Generic finiteness of solutions to parametrized systems of generalized polynomial inequalities
We study parametrized systems of $\mathit{generalized}$ polynomial inequalities, $(c \circ x^B) \in C$, for a positive variable vector $x \in \mathbb{R}^n_>$, a $\mathit{real}$ exponent matrix $B…System-evolutionary view of RNA presence in living cells
Our guiding question for this article was: How did RNA adjust its life when the RNA world era came to an end?Beyond Action Entropy: Quotient-Space Exploration for Genome-Scale Metabolic Model Repair
Repairing scientific models from functional observations differs fundamentally from supervised prediction: feedback may certify a solution without revealing which structural correction is responsible.Predictable Accuracy of Martini 3 Absolute Protein-Ligand Binding Free Energies across 15 Targets
Alchemical free-energy calculations predict protein-ligand binding affinities with close-to-experimental accuracy, but their cost restricts them to small sets of ligands.Effective Resistance and Graph Neural Network Reliability in Tissue-Specific Interactomes
Protein function annotation needs to know which predictions to distrust, not only what a model predicts.Towards Accurate Prediction of Mutation-Induced Changes in Protein Structure
Proteins can possess numerous mutations relative to their wild-type amino acid sequences with minimal impact to their structure and function.PlainMap: a lightweight, restartable mapping pipeline for ancient and modern DNA
Mapping sequencing reads to a reference genome requires preprocessing and alignment choices that can vary with library type, fragment length, sequencing platform, and reference genome.ProLiVis 2.0: Literature-Centric Visualization of Protein--Protein Interaction Networks, with a Citation-Trust Model for Interaction Evidence
Protein-protein interaction databases record evidence without weighing it.Are You Learning Biological Signal or Shortcuts? Auditing and Mitigating Bias in Protein-Protein Interaction Datasets
Protein-protein interaction (PPI) databases do not faithfully reflect biological realities.Quantum-accurate atomistic modeling of enzyme catalysis using a machine learned potential
Electronic rearrangements associated with bond forming/breaking in catalytic enzymes require quantum mechanical (QM) treatment beyond classical molecular mechanics (MM).