定量方法
Cryo-EM is a transformational paradigm in molecular biology where computational methods are used to infer 3D molecular structure at atomic resolution from extremely noisy 2D electron microscope images. At the forefront of research is how to…
Factor analysis is a well-known statistical method to describe the variability of observed variables in terms of a smaller number of unobserved latent variables called factors. Even though latent factors are conceptually independent of each…
Retrieving homologous protein sequences is essential for a broad range of protein modeling tasks such as fitness prediction, protein design, structure modeling, and protein-protein interactions. Traditional workflows have relied on a…
Caco-2 permeability serves as a critical in vitro indicator for predicting the oral absorption of drug candidates during early-stage drug discovery. To enhance the accuracy and efficiency of computational predictions, we systematically…
Nutrients are critical to the functioning of the human body and their imbalance can result in detrimental health concerns. The majority of nutritional literature focuses on macronutrients, often ignoring the more critical nuances of…
Continuous Wavelet Transform (CWT) is frequently used for waveform analysis. For example, in the field of neuroscience research, CWT is performed to analyze electroencephalograms (EEG) and calculate the index of brain activity. Recent…
The mechanisms underlying the formation of post-infection sequelae are complex and remain controversial. This hypothesis integrates Bystryn's antibody feedback phenomenon and Imbiakha's immune cost theory, proposing for the first time a…
Quantitative Systems Pharmacology (QSP) promises to accelerate drug development, enable personalized medicine, and improve the predictability of clinical outcomes. Realizing this potential requires effectively managing the complexity of…
Gene silencing via small interfering RNA (siRNA) represents a transformative tool in cancer therapy, offering specificity and reduced off-target effects compared to conventional treatments. A crucial step in siRNA-based therapies is…
Motivation: A major challenge in metabolomics is annotation: assigning molecular structures to mass spectral fragmentation patterns. Despite recent advances in molecule-to-spectra and in spectra-to-molecular fingerprint prediction (FP),…
Recent successes in virtual screening have been made possible by large models and extensive chemical libraries. However, combining these elements is challenging: the larger the model, the more expensive it is to run, making ultra-large…
We propose a simple dynamic model of cancer development that captures carcinogenesis and subsequent cancer progression. A central idea of the model is to include the immune system as an extinction threshold, similar to the strong Allee…
Distinguishing one person from another (what biometricians call recognition) is extremely relevant for different aspects of life. Traditional biometric modalities (fingerprint, face, iris, voice) rely on unique, stable features that…
The emergent dynamics of complex gene regulatory networks govern various cellular processes. However, understanding these dynamics is challenging due to the difficulty of parameterizing the computational models for these networks,…
Medical data range from genomic sequences and retinal photographs to structured laboratory results and unstructured clinical narratives. Although these modalities appear disparate, many encode convergent information about a single…
Pulmonary hypertension (PH), defined by a mean pulmonary arterial pressure (mPAP) $>$ 20 mmHg, is characterized by increased pulmonary vascular resistance and decreased pulmonary arterial compliance. There are few measurable biomarkers of…
Postoperative stroke remains a critical complication in elderly surgical intensive care unit (SICU) patients, contributing to prolonged hospitalization, elevated healthcare costs, and increased mortality. Accurate early risk stratification…
Computational approaches which emulate in-vivo nervous system are needed to investigate mechanisms of the brain to orchestrate behavior. Such approaches must integrate a series of biophysical models encompassing the nervous system, muscles,…
Building a virtual cell capable of accurately simulating cellular behaviors in silico has long been a dream in computational biology. We introduce CellFlux, an image-generative model that simulates cellular morphology changes induced by…
Quantitative Susceptibility Mapping (QSM) is a technique for measuring magnetic susceptibility of tissues, aiding in the detection of pathologies like traumatic brain injury and multiple sclerosis by analyzing variations in substances such…