定量生物学
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…
Usutu virus (USUV) is a flavivirus of the Japanese encephalitis complex transmitted between \textit{Culex} mosquitoes and birds, a transmission pattern similar to that of the West Nile virus (WNV). In Germany, the first case of USUV was…
Fitness landscapes provide a quantitative framework for understanding how natural selection shapes evolutionary trajectories. A central feature of these landscapes is their number of local optima, which determines whether fitness-increasing…
A fundamental problem in protobiological dynamics is to understand how chemically generated polymers can form persistent sequence distributions before the emergence of replication. We study deterministic polymer growth in which each finite…
Predicting complex human traits from genetic data is challenging because different genetic, clinical, and molecular data sources often contain different parts of the signal. Here, we present EFGPP, a reproducible framework for generating,…
Understanding the development of adolescent behavioral and mental health outcomes requires integrating genetic predisposition, environmental exposures, and neurobiological processes over time. Here, we present a unified quantitative…
Representing dynamical systems through data-driven universal spaces has proven effective; however, achieving this universality for human brain activity remains a significant challenge, further aggravated by diverse cognitive states and…
Brain-wide recordings of large-scale networks of neurons now provide an unprecedented view into how the brain drives behavior. However, brain activity contains both information directly related to behavior as well as the potential for many…
Autocatalysis is an important feature of metabolic networks, contributing crucially to the self-maintenance of organisms. Autocatalytic subsystems of chemical reaction networks (CRNs) are characterized in terms of algebraic conditions on…
The consciousness standing for artificial intelligence divides opinions across epistemological positions. Whether or not machines can be conscious, and whether we can ascertain the truth of such a proposition for any given case, has…
Synthetic data holds substantial potential to address practical challenges in epidemiology due to restricted data access and privacy concerns. However, many current methods suffer from limited quality, high computational demands, and…
Branch-specific substitution models are popular for detecting evolutionary change-points, such as shifts in selective pressure. However, applying such models typically requires prior knowledge of change-point locations on the phylogeny or…