定量方法
The multifactorial etiology of autism spectrum disorder (ASD) suggests that its study would benefit greatly from multimodal approaches that combine data from widely varying platforms, e.g., neuroimaging, genetics, and clinical…
The integration of sequencing data with clinical information is a widely accepted strategy in bioinformatics and health informatics. Despite advanced databases and sophisticated tools for processing omics data, challenges remain in handling…
Post-acute sequelae of SARS-CoV-2 (PASC) is an increasingly recognized yet incompletely understood public health concern. Several studies have examined various ways to phenotype PASC to better characterize this heterogeneous condition.…
The geometry of the blood vessel wall plays a regulatory role on the motion of red blood cells (RBCs). The overall topography of the vessel wall depends on many features, among which the endothelial lining of the endothelial surface layer…
Understanding the structure of supramolecular complexes provides insight into their functional capabilities and how they can be modulated in the context of disease. Super-resolution microscopy (SRM) excels in performing this task by…
Gene mining is an important topic in the field of life sciences, but traditional machine learning methods cannot consider the regulatory relationships between genes. Deep learning methods perform poorly in small sample sizes. This study…
A fundamental question in complex systems is how to relate interactions between individual components ("microscopic description") to the global properties of the system ("macroscopic description"). Another fundamental question is whether…
The rapid growth in the number of experimental and predicted protein structures and more complicated protein structures challenge users in computational biology for utilizing the structural information and protein surface property…
Because the attractors of biological networks reflect stable behaviors (e.g., cell phenotypes), identifying control interventions that can drive a system towards its attractors (attractor control) is of particular relevance when controlling…
Multiomics data fusion integrates diverse data modalities, ranging from transcriptomics to proteomics, to gain a comprehensive understanding of biological systems and enhance predictions on outcomes of interest related to disease phenotypes…
Pathogenic infections pose a significant threat to global health, affecting millions of people every year and presenting substantial challenges to healthcare systems worldwide. Efficient and timely testing plays a critical role in disease…
A hypercomplex representation of DNA is proposed to facilitate comparison of DNA sequences with fuzzy composition. Using hypercomplex number representation, conventional sequence analysis method, such as, dot matrix analysis, dynamic…
A statistical study of cis-regulatory modules (CRMs) is presented based on the estimation of similar-word set distribution. It is observed that CRMs tend to have a fat-tail distribution. A new statistical fat-tail test with two…
Different cell types aggregate and sort into hierarchical architectures during the formation of animal tissues. The resulting spatial organization depends (in part) on the strength of adhesion of one cell type to itself relative to other…
The biological roles of gene sets are used to group them into collections. These collections are often characterized by being high-dimensional, overlapping, and redundant families of sets, thus precluding a straightforward interpretation…
We present a whole-body model of human metabolism that utilizes a system of organs and blood vessels to simulate the enzymatic reactions. The model focuses on key organs, including the brain, heart and lungs, liver, gut, and kidney, as well…
Explainability for Deep Learning Models is especially important for clinical applications, where decisions of automated systems have far-reaching consequences. While various post-hoc explainable methods, such as attention visualization and…
The adaptive immune response relies on T cells that combine phenotypic specialization with diversity of T cell receptors (TCRs) to recognize a wide range of pathogens. TCRs are acquired and selected during T cell maturation in the thymus.…
The most recent and promising strategies for mitigating methane emissions in ruminants are reviewed highlighting the potential of reductive acetogenesis as a viable alternative to methanogenesis. The emergence of Clustered Regularly…
Molecular docking aims to predict the 3D pose of a small molecule in a protein binding site. Traditional docking methods predict ligand poses by minimizing a physics-inspired scoring function. Recently, a diffusion model has been proposed…