Quantitative Biology
Dabas et al. in Science 2025 report that approximately 117 human kinases directly phosphorylate the C-terminal domain (CTD) of RNA polymerase II (Pol II), proposing an extensive, direct biochemical bridge between signal transduction and…
Bantele and colleagues recently reported that repair of a single CRISPR/Cas9-induced DNA double-strand break (DSB) in the c-MYC topologically associated domain leads to a persistent depletion of chromatin interactions and long-term…
Effective analysis in neuroscience benefits significantly from robust conceptual frameworks. Traditional metrics of interbrain synchrony in social neuroscience typically depend on fixed, correlation-based approaches, restricting their…
Simulating the long-timescale dynamics of biomolecules is a central challenge in computational science. While enhanced sampling methods can accelerate these simulations, they rely on pre-defined collective variables that are often difficult…
Bacteria possess diverse mechanisms to regulate their motility in response to environmental and physiological signals, enabling them to navigate complex habitats and adapt their behavior. Among these mechanisms, interspecies recognition…
Zero-one biochemical reaction networks are widely recognized for their importance in analyzing signal transduction and cellular decision-making processes. Degenerate networks reveal non-standard behaviors and mark the boundary where…
Accurately predicting gene mutations, mutation subtypes and their exons in lung cancer is critical for personalized treatment planning and prognostic assessment. Faced with regional disparities in medical resources and the high cost of…
Resting-state EEG offers a non-invasive view of spontaneous brain activity, yet the extraction of meaningful patterns is often constrained by limited availability of high-quality data, and heavy reliance on manually engineered EEG features.…
Ribonucleic acid (RNA) plays fundamental roles in biological systems, from carrying genetic information to performing enzymatic function. Understanding and designing RNA can enable novel therapeutic application and biotechnological…
Protein language models (pLMs) have demonstrated success at generating functional proteins across vast sequence spaces but lack the ability to design high-fitness variants on demand. Here, we iteratively guide pLMs toward user-defined…
In this article we demonstrate a general protocol for constructing systematically experimental steady-state bifurcation diagrams for electrophysiologically active cells. We perform our experiments on entorhinal cortex neurons, both…
Collective cell flows are a hallmark of tissue dynamics in development, wound healing, and various diseases. Here, we perform experiments on epithelial MDCK cell monolayers, over tens of hours without jamming, on millimeter-scale…
We present an automated approach for identifying and annotating motifs and domains in protein sequences, using pretrained Protein Language Models (PLMs) and Concept Activation Vectors (CAVs), adapted from interpretability research in…
How does the brain know what is out there and what is not? Living organisms cannot rely solely on sensory signals for perception because they are noisy and ambiguous. To transform sensory signals into stable percepts, the brain uses its…
Mechanistic models are essential tools across ecology, epidemiology, and the life sciences, but parameter inference remains challenging when likelihood functions are intractable. Approximate Bayesian Computation with Sequential Monte Carlo…
We considered a model for an infectious disease outbreak, when the depletion of susceptible individuals is negligible, and assumed that individuals adapt their behavior according to the information they receive about new cases. In line with…
Criticality describes a regime between order and chaos that supports flexible yet stable information processing. Here we examine whether neural dynamics can be volitionally shifted toward criticality through the self-regulation of…
Classical models of cancer focus on tumour-intrinsic genetic aberrations and immune dynamics and often overlook how the metabolic environment of healthy tissues shapes tumour development and immune efficacy. Here, we propose that…
Brain-computer interfaces (BCIs) are evolving from research prototypes into clinical, assistive, and performance enhancement technologies. Despite the rapid rise and promise of implantable technologies, there is a need for better and more…
Inferring who infected whom in an outbreak is essential for characterising transmission dynamics and guiding public health interventions. However, this task is challenging due to limited surveillance data and the complexity of immunological…