定量生物学
Since early 2020, several theories have suggested that a distribution of restriction endonuclease recognition sites in the SARS-CoV-2 genome indicates a synthetic origin. The most influential of these, a 2022 preprint by Bruttel et al.…
Sequencing of PCR amplicons generated using degenerate primers (typically targeting a region of the 16S ribosomal gene) is widely used in metagenomics to profile the taxonomic composition of complex microbial samples. To reduce taxonomic…
Determining mechanistic models of gene regulation, especially underlying phenotypic variation, is a central goal of both mathematical biology and modern evolutionary biology. However, several challenges, involving both common…
Over the past two decades, considerable strides have been made in advancing neuroscientific techniques, yet challenges remain in attributing causality to observed associations. This review addresses a fundamental issue in observational…
Deep generative models provide a promising approach to de novo 3D peptide design. Most of them jointly model the distributions of peptide's position, orientation, and conformation, attempting to simultaneously converge to the target pocket.…
Recent progress in artificial intelligence (AI) has been driven by insights from physics and neuroscience, particularly through the development of artificial neural networks (ANNs) capable of complex cognitive tasks such as vision and…
We develop a model the dynamics of human mesenchymal stem cells (hMSCs) and chondrocytes evolving in a nonwoven polyethylene terephtalate (PET) scaffold impregnated with hyaluron and supplied with a differentiation medium. The scaffold and…
Gliomas are primary brain tumors with a high invasive potential and infiltrative spread. Among them, glioblastoma multiforme (GBM) exhibits microvascular hyperplasia and pronounced necrosis triggered by hypoxia. Histological samples showing…
Simplified stochastic models are widely used in the study of frequency-resolved noise propagation in biochemical reaction networks, a common measure being the coherence between random fluctuations in molecule number trajectories. Such…
DNA helicases undergo conformational changes; however, their structural dynamics are poorly understood. Here, we study single molecules of superfamily 1A DNA helicase Rep, which undergo conformational transitions during bacterial DNA…
Neural dynamics underlie behaviors from memory to sleep, yet identifying mechanisms for higher-order phenomena (e.g., social interaction) is experimentally challenging. Existing whole-brain models often fail to scale to single-neuron…
Aquaculture is pivotal for global food security but faces significant challenges from infectious diseases, particularly those caused by Streptococcus species such as Streptococcus iniae and Streptococcus agalactiae. These pathogens induce…
We model sensory streams as observations from high-dimensional stochastic dynamical systems and conceptualize sensory neurons as self-supervised learners of compact representations of such dynamics. From prior experience, neurons learn…
By stabilizing weak and transient protein-protein interactions (PPIs), molecular glues address the challenge of targeting proteins previously considered undruggable. Rapamycin and WDB002 are molecular glues that bind to FK506-binding…
Auditory sensory overload affects 50-70% of individuals with Autism Spectrum Disorder (ASD), yet existing approaches, such as mechanistic models (Hodgkin Huxley type, Wilson Cowan, excitation inhibition balance), clinical tools (EEG/MEG,…
UK woodlands, forests, and urban treescapes are under threat from invasive species, exacerbated by climate change, trade, and transport. Invasive tree pests debilitate their host and disrupt forest ecosystems, thus it is imperative to…
Bright-field microscopy, a cost-effective solution for live-cell culture, is often the only resource available, along with standard CPUs, for many low-budget labs. The inherent challenges of bright-field images -- their noisiness, low…
Many people suffer from mental health problems but not everyone seeks professional help or has access to mental health care. AI chatbots have increasingly become a go-to for individuals who either have mental disorders or simply want…
Single-cell sequencing technology maps cells to a high-dimensional space encoding their internal activity. Recently-proposed virtual cell models extend this concept, enriching cells' representations based on patterns learned from…
Chaos is ubiquitous in high-dimensional neural dynamics. A strong chaotic fluctuation may be harmful to information processing. A traditional way to mitigate this issue is to introduce Hebbian plasticity, which can stabilize the dynamics.…