Quantitative Biology
Protein structural ensembles from NMR spectroscopy capture biologically important conformational heterogeneity, but it remains difficult to determine whether observed variation reflects coordinated motion or noise-like artifacts. We…
High-resolution brain imaging can now capture not just synapse locations but their molecular composition, with the cost of such mapping falling exponentially. Yet such ultrastructural data has so far told us little about local neuronal…
Short tandem repeats (STRs) are low-entropy regions in the genome, consisting of a short (1-6 bp) unit that is consecutively repeated multiple times. They are known for high mutational instability, due to so-called stutter-mutations, in…
If the universe follows a specific design, then a central question is which cost function is optimized by the observed forces. This is the problem of inverse optimal control, or inverse reinforcement learning, in which a reward function is…
What substrate features allow life? We exhaustively classify all 262,144 outer-totalistic binary cellular automata rules with Moore neighbourhood for self-replication and produce phase diagrams in the $(\lambda, F)$ plane, where $\lambda$…
Plasticity is a fundamental property of complex systems, such as the brain or an organism. Yet it typically remains a descriptive concept inferred retrospectively from observed outcomes, such as modifications in activity or morphology.…
When designing control strategies for an infectious disease it is critical to identify the key pathways of transmission. Data on infected hosts - when they were born, where they lived and with whom they interacted - can help infer sources…
Dynamic functional connectivity (dFC) derived from resting-state functional magnetic resonance imaging (fMRI) has been extensively utilized in brain science research. The sliding window correlation (SWC) method is a widely used approach for…
Accurate prediction of protein function is essential for elucidating molecular mechanisms and advancing biological and therapeutic discovery. Yet experimental annotation lags far behind the rapid growth of protein sequence data.…
Diffusion models offer a powerful means of capturing the manifold of realistic protein structures, enabling rapid design for protein engineering tasks. However, existing approaches observe critical failure modes when precise constraints are…
In attitude theory, formal theoretical predictions come largely from the simulation of computational models. We argue that to push attitude theory further, we should employ mathematical analysis/analytic methods alongside of computational…
Patients with rare types of melanoma such as acral, mucosal, or uveal melanoma, have lower survival rates than patients with cutaneous melanoma; these lower survival rates reflect the lower objective response rates to immunotherapy compared…
Transcriptomic foundation models pretrained with masked language modeling can achieve low pretraining loss yet produce poor cell representations for downstream tasks. We introduce whole-cell expression decoding (WCED), where models…
One of the fundamental questions in population dynamics is how biological populations respond to environmental perturbations. In population dynamics, the mean fitness and the fraction of a trait in the steady state are important because…
We propose a new microscopy simulation system that can depict atomistic models in a micrograph visual style, similar to results of physical electron microscopy imaging. This system is scalable, able to represent simulation of electron…
Cryo-Electron Tomography (cryo-ET) is a new 3D imaging technique with unprecedented potential for resolving submicron structural detail. Existing volume visualization methods, however, cannot cope with its very low signal-to-noise ratio. In…
We derive a Riemannian metric on three-dimensional color space from the Fisher information of neural population codes in the visual pathway. Photoreceptor adaptation, retinal opponent channels, and cortical population encoding each map onto…
Our subjective experience of color is typically described by abstract properties such as hue, saturation, and brightness that do not directly correspond to sensory signals arising from cones in the retina. Along the hue dimension, certain…
A major barrier to decentralized, near-patient diagnostics is the lack of a signal transduction modality that is both analytically precise and accessible at the point of care. Optical readouts remain instrument-dependent and difficult to…
The accurate prediction of protein-RNA binding affinity remains an unsolved problem in structural biology, limiting opportunities in understanding gene regulation and designing RNA-targeting therapeutics. A central obstacle is the…