Infection control / Modes of transmission

ESMDynamic: Fast and Accurate Prediction of Protein Dynamic Contact Maps from Single Sequences

Understanding conformational dynamics is essential for elucidating protein function, yet most deep learning models in structural biology predict only static structures. Here, we introduce ESMDynamic, a deep learning model that predicts dynamic residue-residue contact probability maps directly from protein sequence. Built on the ESMFold architecture, ESMDynamic is trained on contact fluctuations fr...

Hi-Cformer enables multi-scale chromatin contact map modeling for single-cell Hi-C data analysis

Single-cell Hi-C captures the three-dimensional organization of chromatin in individual cells and provides insights into fundamental genomic processes such as gene regulation and transcription. While analyses of bulk Hi-C data have revealed multi-scale chromatin structures like A/B compartments and topologically associating domains, single-cell Hi-C data remain challenging to analyze due to sparsi...

Organelle bridges and nanodomain partitioning govern targeting of membrane-embedded proteins to lipid droplets

Numerous metabolic enzymes translocate from the ER membrane bilayer to the lipid droplet (LD) monolayer, where they perform essential functions. Mislo...

Novel Machine Learning-based Approach to Identify Viral Biomarkers of Human Respiratory Emissions from Oral and Nasal Metagenomes

Humans spend approximately 90% of their lives in built environments, making virus transmission indoors a key determinant of health. Environmental samp...

Synthetic community Hi-C benchmarking provides a baseline for virus-host inferences

Microbiomes influence diverse ecosystems, and viruses increasingly appear to impose key constraints. While viromics has expanded genomic catalogs, hos...

Mesoscopic analysis of GABAergic marker expression in acetylcholine neurons in the whole mouse brain

In the central nervous system, acetylcholine (ACh) neurons coordinate neural network activity required for higher brain functions, such as attention, ...

Rapid and Interpretable Protein Contact Map Prediction Using a Pattern-Matching Strategy

Protein sequence determines the structure, function, and dynamics of a protein. In recent years, enormous progress has been made in translating sequen...

An AI for an AI: identifying zoonotic potential of avian influenza viruses via genomic machine learning

Avian influenza remains a serious risk to human health via zoonotic transmission, as well as a feasible pandemic threat. Although limited zoonotic cas...

Artificial intelligence-enabled automated analysis of transmission electron micrographs to evaluate chemotherapy impact on mitochondrial morphology in triple negative breast cancer

Advancements in transmission electron microscopy (TEM) have enabled in-depth studies of biological specimens, offering new avenues to large-scale imag...

Highly Adaptive Conductive Polymer Electronics Enhance Neural Data and Learning Accuracy

Human skin, the body’s largest organ, plays a vital role in sensing and transmitting neuronal, mechanical, and biochemical signals, making it an essen...

Evolutionary Reasoning Does Not Arise in Standard Usage of Protein Language Models

Protein language models (PLMs) are often assumed to capture evolutionary information by training on large protein sequence datasets. Yet it remains un...

Hybrid Epidemic–Neuronal Dynamics: A SEIR–FitzHugh–Nagumo Model for Information Flow in Complex Neural Networks

Information transfer in neural systems is often modeled through diffusive or synaptic mechanisms that fail to capture the contagion-like propagation o...

Normalized Raman Imaging for Studies of Tissue Physiology of the Kidney

Histology is the cornerstone of clinical pathology and an essential tool for many areas of medicine. Nevertheless, conventional histological methods, ...

Mapping high resolution, multidimensional phase diagrams of physiological protein condensates

Biomolecular condensates are membraneless compartments, crucial for organising and regulating diverse cellular processes. Current approaches to study ...

Deep Learning Enables Automated Segmentation and Quantification of Ultrastructure from Transmission Electron Microscopy Images

The widths of kidney glomerular basement membrane (GBM) and podocyte foot processes (FP) are essential ultrastructural markers for assessing kidney fu...

Ultrahigh throughput screening to train generative protein models for engineering specificity into unspecific peroxygenases

Enzyme engineering is central to developing biocatalysts with improved activity and specificity, yet traditional approaches are often limited by the s...

Extending digital biology: bacterial survival and morphological heterogeneity under antibiotic stress

The morphology of bacteria is modified by antibiotic stress while also serving to survive the antibiotic. However associating morphological descriptor...

SpecLig: Energy-Guided Hierarchical Model for Target-Specific 3D Ligand Design

Structure-based generative models often optimize single-target affinity with ignorance of specificity, resulting in the generation of high-affinity ca...

The Dominance of Geometric Graph Models in Animal Social Networks

Detecting patterns in animal social behaviour and movement is complicated by the diversity of ecological, evolutionary, environmental, and biological ...

Closing the Sim-to-Real Gap: An End-to-End Robotic Ultrasound System Leveraging In Vivo Reinforcement Learning and 3D-Prior Guided Hybrid Control

Abdominal ultrasound is a crucial first-line diagnostic tool, yet its efficacy is inherently constrained by a strong dependency on operator skill, lea...