HIV/AIDS

From Images to Detection: Machine Learning for Blood Pattern Classification

Bloodstain Pattern Analysis (BPA) helps us understand how bloodstains form, with a focus on their size, shape, and distribution. This aids in crime scene reconstruction and provides insight into victim positions and crime investigation. One challenge in BPA is distinguishing between different types of bloodstains, such as those from firearms, impacts, or other mechanisms. Our study focuses on di...

PG-SAG: Parallel Gaussian Splatting for Fine-Grained Large-Scale Urban Buildings Reconstruction via Semantic-Aware Grouping

3D Gaussian Splatting (3DGS) has emerged as a transformative method in the field of real-time novel synthesis. Based on 3DGS, recent advancements cope with large-scale scenes via spatial-based partition strategy to reduce video memory and optimization time costs. In this work, we introduce a parallel Gaussian splatting method, termed PG-SAG, which fully exploits semantic cues for both partitioni...

Learned Geometry, Predicted Binding: Structurally-Based Prediction of Peptide:MHC Binding Using AlphaFold 3 Enables CD4 T Cell Epitope Prediction

The accurate prediction of T cell epitope peptides within proteins of interest has a wide range of applications, but is complicated by the multiple de...

KIMMDY: a biomolecular reaction emulator

Molecular simulations have become indispensable in biological research. Their accuracy continues to improve, but directly modelling biochemical reacti...

A Deep Learning-based Method for Drug Molecule Representation and Property Prediction

Accurately and robustly representing drug molecule features, prediction of drug-target biomacromolecule interactions, and determining drug molecule ph...

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 ...

DeepPROTECTNeo: A Deep learning-based Personalized and RV-guided Optimization tool leveraging TCR Epitope interaction using Context-aware Transformers

The development of personalized cancer vaccines relies heavily on accurately identifying neoepitopes capable of eliciting strong immune responses. T c...

Variant effect prediction with reliability estimation across priority viruses

Viruses pose a significant threat to global health due to their rapid evolution, adaptability, and increasing potential for cross-species transmission...

Temporal adaptation aids object recognition in deep convolutional neural networks in suboptimal viewing scenario’s

The primate visual system excels in recognizing objects under challenging viewing scenario’s. A neural mechanism that is thought to play a key role in...

BRAVE: a highly accurate method for predicting HIV-1 antibody resistance using large language models for proteins

Broadly neutralizing antibodies (bNAbs) that target the envelope glycoprotein (Env) of human immunodeficiency virus-1 (HIV-1) have been utilized in cl...

Peripheral immune patterns enable robust cross-platform prediction of ALS onset and progression

Amyotrophic lateral sclerosis (ALS) progression rates vary dramatically between patients, yet the basis of this heterogeneity remains elusive, with no...

Predicting antifolate resistance in the unculturable fungal pathogen Pneumocystis jirovecii

Pneumocystis jirovecii is a fungal pathogen causing Pneumocystis pneumonia in humans, mainly in immunocompromised individuals. Infections by P. jirove...

A structure-informed evolutionary model for predicting viral immune escape and evolution

Persistent emergence of viral variants capable of evading host immunity constitutes a significant threat to public health. This antigenic evolution fr...

ppIRIS: deep learning for proteome-wide prediction of bacterial protein-protein interactions

Protein–protein interactions (PPIs) are central to cellular processes and host–pathogen dynamics, yet bacterial interactomes remain poorly mapped, esp...

Geno2pheno[bNAbs]: Interpretable and accurate HIV antibody resistance prediction

Antiretroviral therapy (ART) is a life saving option for people living with HIV-1 (PLWH) and is effective against many viral strains. The most common ...

Improved sensory representations as a result of temporal adaptation

Human perception is robust under challenging conditions, for example when sensory inputs change over time. Temporal adaptation in the form of reduced ...

Application and Characterization of the Multiple Instance Learning Framework in Flow Cytometry

For decades, flow cytometry has allowed for single-cell profiling based on selected biomarkers and is widely used in both clinical and research settin...

Structurally Informed Fitness Landscapes for Surveillance of Emerging PRRSV Variants

Antibodies play a central role in neutralizing pathogens through direct interference with viral entry and recruitment of effector immune cells. Howeve...

Lipid Nanoparticles with Aptamers Enable Targeted mRNA Delivery to CD4+ T Cells

In vivo genetic engineering of T cells could overcome the logistical, biological, and safety challenges of ex vivo modification, but effective and saf...

omicML: An Integrative Bioinformatics and Machine Learning Framework for Transcriptomic Biomarker Identification

Transcriptomic biomarker discovery has been a challenge due to variation in datasets and platforms, complexity in statistical and computational method...