PRX Life

A mathematical framework reveals how morphogenesis mediates morphogen transport and compartmentalization, formalizes cell-cell interaction ranges in dynamic tissues, and provides new nondimensional numbers to assess when tissue deformation affects patterning.

Inferring division-induced force dipoles from tissue strain fields quantifies mechanical forces of cell division and their impact on tissue mechanics.

This review article on quantum computing applications in genomics highlights its realistic potential for the field, theoretical limitations, and the conditions that a problem and an algorithm must satisfy to benefit from quantum speedup.

Hierarchical cell identity emerges from the dynamic interplay between competition among enhancers for the recruitment of epigenetic readers and cooperation among enhancers in activating shared transcriptional programs.

A graph-based generative model designed to capture long-range chromatin interaction patterns from Hi-C data reveals a latent structure of chromatin interactions in the GM12878 lymphoblastoid cell line that strongly align with known biological annotations.

Chemotactic cells working together balance sensing and signal modulation, showing how shared information speeds and stabilizes collective search for targets.

Networks of stochastically spiking neurons can be reduced to combinatorial threshold-linear networks, representing a new tool for analyzing neural networks with clustered connectivity.

Scaling theories differ for spike response models of in vitro and in vivo circuits — representing different universality classes that both exhibit anomalous scaling at a critical balance of inhibition and excitation.

The study examines noise contributions from random cell division times, extending beyond the effects of gene expression and partitioning noise, and presents the resulting analytical cyclo-stationary distributions of mRNA and protein counts.

An eco-evolutionary framework including evolution in infectiousness and antigenic features reveals that mildly infectious viruses might be more likely to become endemic that those with higher infectiousness.

Using single-cell sequencing data, cell-cell interactions in ascidian embryonic development are identified, revealing collective gene expression patterns.

By using information-theoretic quantities as cost functions, this study solves nonlinear stochastic control problems efficiently, enabling optimal strategies across a range of biological problems.

When mice correctly detect visual targets, the primary visual cortex shows stronger scale-invariant structure than during passive or non-natural viewing.

Using manifold learning, this study shows that CryoSBI representations form smooth low-dimensional manifolds linked to molecular properties, and provide a workflow for interpreting cryo-EM heterogeneity and enhancing simulation-based inference.

This model uses AlphaFold2-like architecture to perform flexible docking of small molecules into protein targets, predicting both structure and affinity.