定量生物学
Data-Independent Acquisition (DIA) was introduced to improve sensitivity to cover all peptides in a range rather than only sampling high-intensity peaks as in Data-Dependent Acquisition (DDA) mass spectrometry. However, it is not very clear…
A central feature of complex systems is the relevance and entanglement of different levels of description. For instance, the dynamics of ecosystems can be alternatively described in terms of large ecological processes and classes of…
A fundamental question in the field of molecular computation is what computational tasks a biochemical system can carry out. In this work, we focus on the problem of finding the maximum likelihood estimate (MLE) for log-affine models. We…
Background: The existence of different basal cell carcinoma (BCC) clinical criteria cannot be objectively validated. An adequate ground-truth is needed to train an artificial intelligence (AI) tool that explains the BCC diagnosis by…
Bioinformatics tools are essential for complex computational biology tasks, yet their integration with emerging AI-agent frameworks is hindered by incompatible interfaces, heterogeneous input-output formats, and inconsistent parameter…
Automated semantic segmentation of whole-slide images (WSIs) stained with hematoxylin and eosin (H&E) is essential for large-scale artificial intelligence-based biomarker analysis in breast cancer. However, existing public datasets for…
Understanding how subjective experience arises from information processing remains a central challenge in neuroscience, cognitive science, and AI research. The Modular Consciousness Theory (MCT) proposes a biologically grounded and…
Chronic upper extremity (UE) impairment is common after stroke. This study evaluated Boost, a novel wheelchair-mounted rehabilitation device designed to assist individuals in UE motor recovery during inpatient rehabilitation. Thirty-five…
Effective recognition of foreign antigens by the adaptive immune system relies on T cells being activated by antigen-presenting cells (APCs) in lymph nodes. Here, diffusing T cells may encounter cognate APCs that present matching antigen…
Chikungunya (CHIK) is a viral disease transmitted to humans through the bites of {\it Aedes} mosquitoes infected with the chikungunya virus (CHIKV). CHIKV has been imported annually to Florida in the last decade due to Miami's crucial…
We study a bi-virus susceptible-infected-susceptible (SIS) epidemic model in which individuals are either susceptible or infected with one of two virus strains, and consider mutation-driven transitions between strains. The general case of…
The integration of artificial intelligence (AI) in early-stage drug discovery offers unprecedented opportunities for exploring chemical space and accelerating hit-to-lead optimization. However, docking optimization in generative approaches…
Recent advances in large language models (LLMs) and biomedical foundation models (BioFMs) have achieved strong results in biological text reasoning, molecular modeling, and single-cell analysis, yet they remain siloed in disjoint embedding…
Malaria remains a major public health concern in Ethiopia, particularly in the Amhara Region, where seasonal and unpredictable transmission patterns make prevention and control challenging. Accurately forecasting malaria outbreaks is…
Accurate cell nuclei segmentation is critical for downstream tasks in kidney pathology and remains a major challenge due to the morphological diversity and imaging variability of renal tissues. While our prior work has evaluated…
Remote photoplethysmography (rPPG) aims to extract non-contact physiological signals from facial videos and has shown great potential. However, existing rPPG approaches struggle to bridge the gap between source and target domains. Recent…
Recent advances in structure-based protein design have accelerated de novo binder generation, yet interfaces on large domains or spanning multiple domains remain challenging due to high computational cost and declining success with…
Predicting the 3D conformation of small molecules within protein binding sites is a key challenge in drug design. When a crystallized reference ligand (template) is available, it provides geometric priors that can guide 3D pose prediction.…
Single-cell RNA sequencing (scRNA-seq) reveals cell heterogeneity, with cell clustering playing a key role in identifying cell types and marker genes. Recent advances, especially graph neural networks (GNNs)-based methods, have…
Much of our mechanistic understanding of the functions of biological macromolecules is based on static structural experiments, which can be modelled either as single structures or conformational ensembles. While these provide us with…