定量方法
The aerial flocking of birds, or murmurations, has fascinated observers while presenting many challenges to behavioral study and simulation. We examine how the periphery of murmurations remain well bounded and cohesive. We also investigate…
Protein design often begins with the knowledge of a desired function from a motif which motif-scaffolding aims to construct a functional protein around. Recently, generative models have achieved breakthrough success in designing scaffolds…
Homeostasis occurs in a biological system when a chosen output variable remains approximately constant despite changes in an input variable. In this work we specifically focus on biological systems which may be represented as chemical…
The random motion of molecules in living cells has consistently been reported to deviate from standard Brownian motion, a behavior coined as ``anomalous diffusion''. Fluorescence Correlation Spectroscopy (FCS) is a powerful method to…
With the advances in artificial intelligence (AI), data-driven algorithms are becoming increasingly popular in the medical domain. However, due to the nonlinear and complex behavior of many of these algorithms, decision-making by such…
Small molecule protonation is an important part of the preparation of small molecules for many types of computational chemistry protocols. For this, a correct estimation of the pKa values of the protonation sites of molecules is required.…
From flocking birds to schooling fish, organisms interact to form collective dynamics across the natural world. Self-organization is present at smaller scales as well: cells interact and move during development to produce patterns in fish…
The recent rise of generative artificial intelligence (GenAI) capable of creating scientific images presents a challenge in the fight against academic fraud. This study evaluates the efficacy of three free web-based AI detectors in…
\textbf{Background}: Identifying differentially methylated regions (DMRs) is a basic task in DNA methylation analysis. However, due to the different strategies adopted, different DMR sets will be predicted on the same dataset, which poses a…
The Dynamical Graph Grammar (DGG) formalism can describe complex system dynamics with graphs that are mapped into a master equation. An exact stochastic simulation algorithm may be used, but it is slow for large systems. To overcome this…
We focus on connectivity methods used to understand and predict how landscapes and habitats facilitate or impede the movement and dispersal of species. Our objective is to compare the implication of methodological choices at three stages of…
The explosion in known microbial diversity in the last two decades has made it abundantly clear that microbes in the environment do not exist in isolation; they are members of communities. Accordingly, omics approaches such as metagenomics…
Systems biology models are useful models of complex biological systems that may require a large amount of experimental data to fit each model's parameters or to approximate a likelihood function. These models range from a few to thousands…
The spatial location of cells within tissues and organs is crucial for the manifestation of their specific functions.Spatial transcriptomics technology enables comprehensive measurement of the gene expression patterns in tissues while…
The SIR model is one of the most prototypical compartmental models in epidemiology. Generalizing this ordinary differential equation (ODE) framework into a spatially distributed partial differential equation (PDE) model is a considerable…
A distinct feature of pancreatic ductal adenocarcinoma (PDAC) is a prominent tumor microenvironment (TME) with remarkable cellular and spatial heterogeneity that meaningfully impacts disease biology and treatment resistance. The dynamic…
Cancer and its subtypes constitute approximately 30% of all causes of death globally and display a wide range of heterogeneity in terms of clinical and molecular responses to therapy. Molecular subtyping has enabled the use of precision…
Cryogenic Electron Tomography (CryoET) is a useful imaging technology in structural biology that is hindered by its need for manual annotations, especially in particle picking. Recent works have endeavored to remedy this issue with few-shot…
Dysregulation of the tumour suppressor gene Adenomatous Polyposis Coli (APC) is a canonical step in colorectal cancer development. Curiously, most colorectal tumours carry biallelic mutations that result in only partial loss of APC…
We introduce a unified Python package for the prediction of protein biophysical properties, streamlining previous tools developed by the Bio2Byte research group. This suite facilitates comprehensive assessments of protein characteristics,…