Quantitative Biology
Spatial environmental variation can either amplify or suppress the fixation of beneficial mutants in structured populations, yet the interplay of ecological factors and spatial structure in determining which outcome occurs remains…
Cognitive neuroscience is fragmented into specialized models, each tailored to specific experimental paradigms, hence preventing a unified model of cognition in the human brain. Here, we introduce TRIBE v2, a tri-modal (video, audio and…
Antivirals are uniquely positioned to be deployed quickly during a new outbreak, especially when repurposed from approved drugs. Yet there are no FDA-approved antivirals for the majority of viral families with pandemic potential. Here we…
The free energy principle casts perception as variational inference, but its biological implementation remains underspecified. In particular, the generalized-coordinate formalism should not be read as a literal claim that neurons compute…
Ancestral sequence reconstruction (ASR) aims to infer extinct protein sequences at internal nodes of a phylogenetic tree. Classical ASR methods are typically based on continuous-time Markov substitution models, but they treat sites largely…
We introduce and discuss a kinetic framework describing the time evolution of the statistical distributions of a population divided into the compartments of susceptible, infectious, recovered, and resistant in the presence of a microbial…
Despite remarkable advances, today's AI systems remain narrow in scope, falling short of the flexible, adaptive, and multisensory intelligence that characterizes human capabilities. This gap has fueled longstanding debates about whether AI…
Haplotype phasing, the process of resolving parental allele inheritance patterns in diploid genomes, is critical for precision medicine and population genetics, yet the underlying optimization is NP-hard, posing a scalability challenge. To…
The COVID-19 pandemic has profoundly affected global health, driven by the remarkable transmissibility and mutational adaptability of the SARS-CoV-2 virus. Although five variants of concern, Alpha, Beta, Gamma, Delta, and Omicron, have been…
Polymerase chain reaction (PCR) underpins modern molecular biology, yet its deployment in emerging domains such as DNA data storage and distributed diagnostics remains constrained by bulky thermocyclers, complex thermal hardware, and…
We propose that consciousness arises from a single control agent, the Modelerschema. It monitors the brain's Modeler as that system constructs and updates the internal World Model. As part of that monitoring, the Modelerschema generates…
Scalable assessments of mental illness remain a critical roadblock toward accessible and equitable care. Here, we show that everyday human-computer interactions encode mental health with biomarker accuracy. We introduce MAILA, a…
Theoretical ecologists have long leveraged empirical data in various forms to advance ecology. Recently increased volumes and access to ecological data present an expanding set of opportunities for theoreticians to inform model development,…
We introduce a scalar reduction method for forced or coupled systems with nonlinearities in both heterogeneity and coupling strength. Heterogeneity is formulated as a relatively weak but nonlinear alteration of the vector field(s). The…
Scoring functions remain the principal bottleneck in molecular docking: they routinely fail to rank near-native poses above decoys, and their composite single-score design obscures the physicochemical basis of each ranking error. We present…
Bacterial chemotaxis has long been viewed as operating near the physical limits of sensing, as originally articulated by Berg and Purcell. Recent information-theoretic analyses challenge this view, suggesting that Escherichia coli uses only…
Boltzmann Machines trained on evolutionary sequence data have emerged as a powerful paradigm for the data-driven design of artificial proteins. However, the relationship between model architecture, specifically parameter density, and…
Identity by descent (IBD) tracts and runs of homozygosity (ROH) are related concepts that refer to the autozygosity in chromosome segments. However the formal relationship between their length distributions remains to be established. Here…
We present A-CODE, a fully atomic unified one-stage protein co-design model that simultaneously refines discrete atom types and continuous atom coordinates. Unlike predominant two-stage methods that cascade structure design with amino…
Donor-level disease classification from single-cell RNA sequencing (scRNA-seq) requires strict donor-aware cross-validation: naive pipelines that split cells randomly conflate training and test donors, inflating reported performance through…