定量生物学
By unifying three foundational principles of modern biology, we develop a mathematical framework to analyze the growing tree of life. Contrary to the static case, where the analogy between phylogenetic trees and the tree that grows in soil…
Distinguishing the rare "driver" mutations that fuel cancer progression from the vast background of "passenger" mutations in the non-coding genome is a fundamental challenge in cancer biology. A primary mechanism that non-coding driver…
Chronic critical illness (CCI) is a disease state in which, following an initial insult, a patient neither recovers nor dies but instead remains in a state of critical illness. CCI is characterized by prolonged organ dysfunction, weight…
Single-cell and single-nucleus RNA sequencing (scRNA-seq /snRNA-seq) are widely used to reveal heterogeneity in cells, showing a growing potential for precision and personalized medicine. Nonetheless, sustainable drug discovery must be…
This study develops and analyzes an extended Susceptible, Infected, Hospitalized and Recovered (SIHR) model incorporating time dependent control functions to capture preventive measures (e.g., distancing, mask use) and resource limited…
Gene enhancers control when and where genes switch on, yet their sequence diversity and tissue specificity make them hard to pinpoint in colorectal cancer. We take a sequence-only route and fine-tune DNABERT-2, a transformer genomic…
Machine learning has markedly advanced de novo peptide sequencing (DNS) for mass spectrometry-based proteomics. DNS tools offer a reliable way to identify peptides without relying on reference databases, extending proteomic analysis and…
In metapopulations, genetic variation of local populations is influenced by the genetic content of the founders, and of migrants following establishment. We analyse the effect of multiple paternity on genetic diversity using a model in…
Evolutionary branching is analysed in a stochastic, individual-based population model under mutation and selection. In such models, the common assumption is that individual reproduction and life career are characterised by values of a…
We analyse sequential Markov coalescent algorithms for populations with demographic structure: for a bottleneck model, a population-divergence model, and for a two-island model with migration. The sequential Markov coalescent method is an…
We suggest a simple deterministic approximation for the growth of the favoured-allele frequency during a selective sweep. Using this approximation we introduce an accurate model for genetic hitch-hiking. Only when Ns < 10 (N is the…
Selective interleukin-23 receptor antagonists (IL-23RA) show promise for treating moderate to severe ulcerative colitis (UC) but their efficacy and safety are not fully understood. We performed a systematic review and meta-analysis of…
In recent decades, European forests have faced an increased incidence of fire disturbances. This phenomenon is likely to persist, given the rising frequency of extreme events expected in the future. Estimating canopy recovery time after…
Recordings of brain activity, such as functional MRI (fMRI), provide low-dimensional, indirect observations of neural dynamics evolving in high-dimensional, unobservable spaces. Embedding observed brain dynamics into a higher-dimensional…
We present Brain Harmony (BrainHarmonix), the first multimodal brain foundation model that unifies structural morphology and functional dynamics into compact 1D token representations. The model was pretrained on two of the largest…
The human auditory cortex is topographically organized. Neurons with similar response properties are spatially clustered, forming smooth maps for acoustic features such as frequency in early auditory areas, and modular regions selective for…
13C-based metabolic flux analysis (13C-MFA) is a cornerstone of quantitative systems biology, yet its increasing data complexity and methodological diversity place high demands on simulation software. We introduce 13CFLUX(v3), a…
Large language models (LLMs) have shown strong ability in generating rich representations across domains such as natural language processing and generation, computer vision, and multimodal learning. However, their application in biomedical…
Despite the general assumption that completely locked-in state (CLIS) patients remain conscious and aware of their environment, the effectiveness of brain-computer interfaces (BCIs) in facilitating communication has been limited, as…
Social communication fundamentally involves at least two interacting brains, creating a unique modeling problem. We present the first application of Contrastive Embedding for Behavioral and Neural Analysis (CEBRA) to dyadic EEG…