bioRxiv Bioinfo

SingleRust: A High-Performance Toolkit for Single-Cell Data Analysis at Scale https://www.biorxiv.org/content/10.1101/2025.08.04.668429v1

Python-based automation of INDIGO webserver using Selenium: A high throughput analysis of Sanger sequence data to detect allelic variations created by CRISPR/Cas9-mediated genome editing of crop plants https://www.biorxiv.org/content/10.1101/2025.08.04.668409v1

In silico pharmacological analysis of Tinospora cordifolia compounds targeting African swine fever virus B175L https://www.biorxiv.org/content/10.1101/2025.08.03.668349v1

scMomer: A modality-aware pretraining framework for single-cell multi-omics modeling under missing modality conditions https://www.biorxiv.org/content/10.1101/2025.08.04.668374v1

Reengineering the antigen optimization process for superior neoantigen vaccine design https://www.biorxiv.org/content/10.1101/2025.08.03.668363v1

A mathematical model for inflammation and demyelination in multiple sclerosis https://www.biorxiv.org/content/10.1101/2025.07.31.667831v1

Defining the molecular determinants of titin kinase by analysing distantly evolved fish orthologues https://www.biorxiv.org/content/10.1101/2025.08.04.668337v1

Mechanism of Tethered Agonist Binding to an Adhesion G-Protein-Coupled Receptor https://www.biorxiv.org/content/10.1101/2025.08.04.668378v1

Interpreting the Effects of DNA Polymerase Variants at the Structural Level https://www.biorxiv.org/content/10.1101/2025.08.04.653638v1

OmniCellAgent: Towards AI Co-Scientists for Scientific Discovery in Precision Medicine https://www.biorxiv.org/content/10.1101/2025.07.31.667797v1

Snappy: de novo identification of DNA methylation sites based on Oxford Nanopore reads https://www.biorxiv.org/content/10.1101/2025.08.03.668330v1

GeneTerrain-GMM Unmasks a Coordinated Neuroinflammatory and Cell Death Network Perturbed by Dasatinib in a Human Neuronal Model of Alzheimer's Disease https://www.biorxiv.org/content/10.1101/2025.08.03.667745v1

Learning from B Cell Evolution: Adaptive Multi-Expert Diffusion for AntibodyDesign via Online Optimization https://www.biorxiv.org/content/10.1101/2025.08.02.668313v1

MicrobioRel: A Set of Datasets for Microbiome Relation Extraction https://www.biorxiv.org/content/10.1101/2025.08.03.666357v1

Comparative Analysis of De Novo Assemblers and Quantification Software for RNA-sequencing Data in Non-Model Arthropods https://www.biorxiv.org/content/10.1101/2025.08.01.668104v1

ProteomeLM: A proteome-scale language model allowing fast prediction of protein-protein interactions and gene essentiality across taxa https://www.biorxiv.org/content/10.1101/2025.08.01.668221v1

In-Silico Evaluation of Silk Fibroin-Conjugated Doxycycline for Sustained Drug Delivery https://www.biorxiv.org/content/10.1101/2025.07.31.668034v1

Adaptive trade-offs between niche-driven defence system selection and horizontal gene transfer suggests clinical success in Acinetobacter spp. https://www.biorxiv.org/content/10.1101/2025.08.01.668115v1

ET-Pfam: Ensemble transfer learning for protein family prediction https://www.biorxiv.org/content/10.1101/2025.08.02.668111v1

spOT-NMF: Optimal Transport-Based Matrix Factorization for Accurate Deconvolution of Spatial Transcriptomics https://www.biorxiv.org/content/10.1101/2025.08.02.668292v1

Aggregation-Prone Region Mapping in Olfactomedin Domain of Myocilin through Classical and Enhanced Sampling Molecular Dynamics Simulations https://www.biorxiv.org/content/10.1101/2025.08.02.668245v1

Interpretable spatial multi-omics data integration and dimension reduction with SpaMV https://www.biorxiv.org/content/10.1101/2025.08.02.668264v1

HPInet: Interpretable prediction of Host-Pathogen protein-protein Interactions using a transformer-based neural network https://www.biorxiv.org/content/10.1101/2025.08.02.668281v1

Federated Knowledge Retrieval Elevates Large Language Model Performance on Biomedical Benchmarks https://www.biorxiv.org/content/10.1101/2025.08.01.668022v1

Measuring Dependencies between Biological Signals with Temporal Self-supervision, and its Limitations https://www.biorxiv.org/content/10.1101/2025.08.02.668286v1

Benchmarking RNA velocity methods across 17 independent studies https://www.biorxiv.org/content/10.1101/2025.08.02.668272v1

LeukGenePipeline: Modular Workflow for Genomic Datasets https://www.biorxiv.org/content/10.1101/2025.08.01.668175v1

quick analysis of sedimentary ancient DNA using quicksand https://www.biorxiv.org/content/10.1101/2025.08.01.668088v1

A benchmarking workflow for assessing the reliability of batch correction methods https://www.biorxiv.org/content/10.1101/2025.08.01.668073v1

scDIAGRAM: Detecting Chromatin Compartments from Individual Single-Cell Hi-C Matrix without Imputation or Reference Features https://www.biorxiv.org/content/10.1101/2025.08.01.668129v1