定量生物学
Enabling natural communication through brain-computer interfaces (BCIs) remains one of the most profound challenges in neuroscience and neurotechnology. While existing frameworks offer partial solutions, they are constrained by…
The spatial structure of populations may promote the emergence and maintenance of cooperation. Cooperation in the prisoner's dilemma is favored under specific update rules in evolutionary graph theory models with one individual per node of…
Each T cell typically carries a specific T-cell receptor (TCR) that determines its specificity against an epitope presented by the HLA complex on a target cell. Antigenic challenge triggers the expansion of reactive cells within a diverse…
Identifying the effects of mechanical ventilation strategies and protocols in critical care requires analyzing data from heterogeneous patient-ventilator systems within the context of the clinical decision-making environment. This research…
Diffusion MRI (dMRI) tractography is currently the only method for in vivo mapping of the brain's white matter (WM) connections. Tractometry is an advanced tractography analysis technique for along-tract profiling to investigate the…
Tumor growth is constrained by spatial, mechanical, and metabolic factors whose alignment progressively breaks down across cellular, mesoscopic, and tissue scales as tumors expand. We hypothesize that this misalignment drives tumors toward…
Promoters and enhancers are cis-regulatory elements (CREs), DNA sequences that bind transcription factor (TF) proteins to up- or down-regulate target genes. Decades-long efforts yielded TF-DNA interaction models that predict how strongly an…
Molecular representation learning aims to learn vector embeddings that capture molecular structure and geometry, thereby enabling property prediction and downstream scientific applications. In many AI for science tasks, labeled data are…
Designing enzymes with substrate-binding pockets is a critical challenge in protein engineering, as catalytic activity depends on the precise interaction between pockets and substrates. Currently, generative models dominate functional…
Visual illusions provide a window into the mechanisms underlying visual processing, and dynamical neural circuit models offer a natural framework for proposing and testing theories of their emergence. We propose and analyze a delay-coupled…
There are few, if any, algorithms in statistical phylogenetics which are used more heavily than Felsenstein's 1973 pruning method for computing the likelihood of a tree. We present LvD, (Likelihood via Decomposition), an alternative to…
Vehicle movements, including vehicle cabs and trailers, play a role in disseminating disease in swine production. However, there are many information gaps about vehicle movements patterns that increase the probability of disease…
Global biodiversity loss is accelerating, prompting international efforts such as the Kunming-Montreal Global Biodiversity Framework (GBF) and the United Nations Sustainable Development Goals to direct resources toward halting species…
Diseases originating from wildlife pose a significant threat to global health, causing human and economic losses each year. The transmission of disease from animals to humans occurs at the interface between humans, livestock, and wildlife…
Exposure to psychoactive substances during pregnancy, such as cannabis, can disrupt neurodevelopment and alter large-scale brain networks, yet identifying their neural signatures remains challenging. We introduced KOCOBrain: KuramotO…
Lattice-based random walk models are widely used to study populations of migrating cells with motility bias and proliferation. Crowding is typically represented by volume exclusion, where each lattice site can be occupied by at most one…
The ethical and legal imperative to share research data without causing harm requires careful attention to privacy risks. While mounting evidence demonstrates that data sharing benefits science, legitimate concerns persist regarding the…
A central idea in understanding brains and building artificial intelligence is that structure determines function. Yet, how the brain's complex structure arises from a limited set of genetic instructions remains a key question. The ultra…
On broadly Copernican grounds, we are entitled to assume that apparently behaviorally sophisticated extraterrestrial entities ("aliens") would be conscious. Otherwise, we humans would be inexplicably, implausibly lucky to have…
Mathematical modeling allows us to better understand myeloproliferative neoplasms (MPN), a group of blood cancers, emergence and development. We test different mathematical models on an initial cohort to determine the emergence and…