bioRxiv

Showing 3611 to 3620 of 5001 articles

DLRNA-BERTa: A transformer approach for RNA-drug binding affinity prediction

bioRxiv Jan 1, 2025
RNA-based therapies are a rapidly expanding field, offering treatments for a wide range of diseases, including many rare conditions. To date, 24 RNA therapeutics have received FDA approval, with 131 more in clinical trials, underscoring RNA’s growing...
View on bioRxiv DOI

Machine learning–driven decoding of maternal immune signatures in repeated pregnancy loss

bioRxiv Jan 1, 2025
Repeated pregnancy loss (RPL) is a multifactorial condition in which the underlying immunological mechanisms remain incompletely understood. Although immune tolerance at the maternal–fetal interface is critical for successful pregnancy, the immune di...
View on bioRxiv DOI

Understanding Foundation Models in Digital Pathology: Performance, Trade-offs, and Model-Selection Recommendations

bioRxiv Jan 1, 2025
The rapid proliferation of digital pathology foundation models (FMs), spanning widely in architectural scales and pre-training datasets, poses a significant challenge in selecting the optimal model for a specific clinical application. To systematical...
View on bioRxiv DOI

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

bioRxiv Jan 1, 2025
Avian influenza remains a serious risk to human health via zoonotic transmission, as well as a feasible pandemic threat. Although limited zoonotic cases have resulted from the current epizootic outbreak, the wide diversity of influenza viruses in avi...
View on bioRxiv DOI

Functional autophagy gene set signature and state classification reveal a link between autophagy induction, lysosomal activity, and poor prognosis in glioblastoma

bioRxiv Jan 1, 2025
Autophagy is an essential mechanism for maintaining cell homeostasis and, when dysregulated, is related to various pathologies. In cancer, it functions as a double-edged sword, either as a tumor suppressor or as a tumor promoter. Elevated GFP-LC3 pun...
View on bioRxiv DOI

Capturing the Mutational Dynamics of SARS-CoV-2 with Graphs

bioRxiv Jan 1, 2025
The rapid evolution of SARS-CoV-2 presents significant challenges for modeling viral dynamics, driven by lineage diversification and region-specific mutation patterns. While phylogenetic trees are traditionally used for evolutionary inference, the ma...
View on bioRxiv DOI

Modeling protein-small molecule conformational ensembles with PLACER

bioRxiv Jan 1, 2025
Modeling the conformational heterogeneity of protein-small molecule interactions is important for understanding natural systems and evaluating designed systems, but remains an outstanding challenge. We reasoned that while residue level descriptions o...
View on bioRxiv DOI

Deep Generative Optimization of mRNA Codon Sequences for Enhanced mRNA Translation and Therapeutic Efficacy

bioRxiv Jan 1, 2025
Messenger RNA (mRNA) therapeutics show immense promise, but their efficacy is limited by suboptimal protein expression. Here, we present RiboDecode, a deep learning framework that generates mRNA codon sequences for enhanced mRNA translation. RiboDeco...
View on bioRxiv DOI

AFMnanoSALQ: An Accurate Detection Framework for Semi-Automatic Labeling and Quantitative Analysis of α-Hemolysin Nanopores Using Intensity-Height Cues in HS-AFM Data

bioRxiv Jan 1, 2025
High-Speed Atomic Force Microscopy (HS-AFM) enables imaging of biological structures and dynamics with nanometer spatial and millisecond temporal resolution. AFM images contain three-dimensional (3D) surface information, comprising two-dimensional (2...
View on bioRxiv DOI

Tricked by Edge Cases: Can Current Approaches Lead to Accurate Prediction of T-Cell Specificity with Machine Learning?

bioRxiv Jan 1, 2025
The ability to predict T cell receptor (TCR) specificity from sequence could transform immunotherapy, vaccine development, and our understanding of immune recognition. While machine learning approaches have shown promise, progress is limited by the q...
View on bioRxiv DOI
Popular Topics
Popular Journals