定量生物学
Phylogenetic trees are the primary framework for conveying evolutionary relationships. While many tools exist for visualizing phylogenetic trees, most are limited to static graphics, require coding expertise, or are developed for a specific…
Background: Short sequence substrings of a fixed length k, called k-mers, are a ubiquitous computational primitive in bioinformatics, used across sequence indexing, read mapping, genome assembly, metagenomic classification, and comparative…
In a context of growing agricultural demand and new challenges related to food security and accessibility, boosting agricultural productivity is more important than ever. Reducing the damage caused by invasive insect species is a crucial…
Why do some physical systems possess consciousness, while others do not? Is this a question of physics? Or is it a question of the theory of causation? Physics and the theory of causation serve different descriptive purposes, and in this…
Neural synchronization is central to cognition However, incomplete synchronization often produces chimera states where coherent and incoherent dynamics coexist. While previous studies have explored such patterns using networks of coupled…
The brain transforms visual inputs into high-dimensional cortical representations that support diverse cognitive and behavioral goals. Characterizing how this information is organized and routed across the human brain is essential for…
Procrastination represents one of the most prevalent behavioral problems associated with individual health and societal productivity. Despite its high prevalence and substantial impact on daily functioning, its underlying neurocognitive…
We answer several fundamental geometric questions about reaction networks with power-law kinetics, on topics such as generic finiteness of the number of steady states, robustness, and nondegenerate multistationarity. In particular, we give…
RNA viruses form genetically diverse populations structured as mutant spectra, or quasispecies, whose internal organization influences their evolutionary and adaptive dynamics. While genetic diversity has been extensively characterized, the…
Endocrine-disrupting chemicals (EDCs) threaten human health, ecosystems, and biodiversity by interfering with hormonal signaling pathways conserved across vertebrates. Traditional in vivo assays are costly and time-consuming, limiting their…
The orientation of cell division is a major determinant of three-dimensional plant morphogenesis. Whether and how a simple division orientation rule explains the establishment of symmetric body plans is a fundamental question. Testing such…
Biological systems perform complex multi-step processes in a reproducible way despite underlying stochasticity. The standard explanation is micromanagement by molecular machinery that recognizes and corrects specific errors. Here we study…
Closed-loop brain-computer interfaces often require both a forecast of upcoming neural population activity and a readout of the animal's behavioral state. A single Mamba forecaster, trained only on next-step spike counts at Neuropixels…
Neural population models, which predict the joint firing of many simultaneously recorded neurons forward in time, are typically evaluated by a single aggregate Pearson correlation $r$ between predicted and actual spike counts, a number that…
Individual contributions to the spread of an epidemic vary widely due to an individual's location in a social network and their intrinsic ability to spread or contract diseases. While the effect of heterogeneous population structure and…
The ability to predict the future is of great value for biological and artificial cognitive systems alike. However, successfully predicting the future typically requires maintaining a memory of the recent past. It is currently unclear how…
The perceptual representations supporting our ability to recognize faces remain a computational mystery. Deep neural networks offer mechanistic hypotheses for human face perception, but theoretically distinct models often make…
Some conscious contents disappear after access; others return repeatedly, long after their triggering conditions have ceased. We propose Canxianization as the process by which a perturbation becomes closure-resistant self-relevant…
The Free Energy Principle (FEP) is a leading framework for mathematically modeling self-organization and learning, while Integrated Information Theory (IIT) is a computational ontology of consciousness oriented around irreducible cause and…
Qualitative models provide crucial instruments for modelling complex biological systems. While advances in automated reasoning and symbolic encodings have enabled rigorous inference of these models from data, the process remains highly…