Boosting the speed and accuracy of protein quantification algorithms in mass spectrometry-based proteomics https://www.biorxiv.org/content/10.1101/2025.10.06.680769v1

Accelerating scRNA-seq analysis: automated cell type annotation using representation learning and vector search https://www.biorxiv.org/content/10.1101/2025.10.06.680787v1

GOFlowLLM - Curating miRNA literature with Large Language Models and flowcharts https://www.biorxiv.org/content/10.1101/2025.10.07.680945v1

SpaDiff: Denoising for Sequence-based Spatial Transcriptomics via Diffusion Process https://www.biorxiv.org/content/10.1101/2025.10.07.681011v1

Citizen science gamers enable automated flow cytometry gating through machine learning https://www.biorxiv.org/content/10.1101/2025.10.07.679685v1

Protein Language Models are Accidental Taxonomists https://www.biorxiv.org/content/10.1101/2025.10.07.681002v1

Nanoscale spatial-omics via contrastive embedding of single-molecule localisation data https://www.biorxiv.org/content/10.1101/2025.10.07.679170v1

Temporal Expression Prediction by Integrating Genome Dynamics via Spatio-temporal GNNs https://www.biorxiv.org/content/10.1101/2025.10.07.678022v1

An improved epigenetic age estimation with TFMethyl Clock reveals DNA methylation changes during aging in transcription factor binding sites https://www.biorxiv.org/content/10.1101/2025.10.07.680024v1

Sharing Patterns Between Proteins and Exploring Possible Drug Interactions https://www.biorxiv.org/content/10.1101/2025.10.07.680866v1

Evaluation and Aggregation of Active Module Identification Algorithms https://www.biorxiv.org/content/10.1101/2025.10.06.680790v1

Boolean Logic Coupled with Overrepresentation Analysis Reveals Activation of the Platelet-derived Growth Factor Receptor Beta Pathway in a Model of Oliguric Acute Kidney Injury; Implications for Transition to Chronic Kidney Disease https://www.biorxiv.org/content/10.1101/2025.10.06.680804v1

Evolutionary and geometric signatures reveal ligand-binding sites across proteomes https://www.biorxiv.org/content/10.1101/2025.10.07.680847v1

CellMAPS: A no-code model-based customisable multiplex image analysis workflow https://www.biorxiv.org/content/10.1101/2025.10.07.680848v1

CardioWAS Pathway-Based RNA-Seq and Genome Integration Platform for CVD Omics-Wide Associations https://www.biorxiv.org/content/10.1101/2025.10.06.679779v1

Identification of Diverse Cellulose Binding Domains using in silico Prioritisation and High-Throughput Screening https://www.biorxiv.org/content/10.1101/2025.10.06.677802v1

ComplexMatrixComb: Predicting Drug Combination IC50 Doses via Complex Numbers and Matrix Factorization https://www.biorxiv.org/content/10.1101/2025.10.06.680642v1

Mango: Unearthing Patterns in Large-Scale Biological Data Through Interactive Correlation Analysis https://www.biorxiv.org/content/10.1101/2025.10.06.680608v1

PymolFold: A PyMOL Plugin for API-driven Structure Prediction and Quality Assessment https://www.biorxiv.org/content/10.1101/2025.10.03.680230v1

Learning Protein Representations with Conformational Dynamics https://www.biorxiv.org/content/10.1101/2025.10.06.680789v1

ceQTL: A co-expression QTL model to detect a variant that affects transcription factor binding and its target regulation https://www.biorxiv.org/content/10.1101/2025.10.06.680553v1

A Fully Automated, Data-Driven Approach for Dimensionality Reduction and Clustering in Single-Cell RNA-seq Analysis https://www.biorxiv.org/content/10.1101/2025.10.06.680609v1

Addressing multiple facets of ligand-receptor network inference including single-cell proteomics https://www.biorxiv.org/content/10.1101/2025.10.05.680519v1

Uncertainty-aware transcription factor activity and perturbation inference without additional training https://www.biorxiv.org/content/10.1101/2025.10.05.680506v1

Multimodal AI agents for capturing and sharing laboratory practice https://www.biorxiv.org/content/10.1101/2025.10.05.680425v1

Optimal transport modeling uncovers spatial domain dynamics in spatiotemporal transcriptomics studies https://www.biorxiv.org/content/10.1101/2025.10.06.680672v1

Aardvark: Sifting through differences in a mound of variants https://www.biorxiv.org/content/10.1101/2025.10.03.680257v1

MS2extract: an R Package for a Scalable LC-MS/MS Library Creation https://www.biorxiv.org/content/10.1101/2025.10.05.680545v1

SpaGene: A Deep Adversarial Framework for Spatial Gene Imputation https://www.biorxiv.org/content/10.1101/2025.10.03.680242v1

SLAE: Strictly Local All-atom Environment for Protein Representation https://www.biorxiv.org/content/10.1101/2025.10.03.680398v1

Paraplume: A fast and accurate paratope prediction method provides insights into repertoire-scale binding dynamics https://www.biorxiv.org/content/10.1101/2025.10.04.680432v1

VirTrack: A Framework for Inferring Viral Influence on Disease-Associated Transcriptomes -- Clinical Type-Specific Epstein-Barr Virus Pathogenesis in Multiple Sclerosis https://www.biorxiv.org/content/10.1101/2025.10.05.680499v1

Epigenetic characterization of pseudogenes across human tissues https://www.biorxiv.org/content/10.1101/2025.10.05.680540v1

Beyond P-values: A Multi-Metric Framework for Robust Feature Selection and Predictive Modeling https://www.biorxiv.org/content/10.1101/2025.10.05.680380v1

Non-invasive estrous cycle classification in mice using convolutional neural networks https://www.biorxiv.org/content/10.1101/2025.10.03.680273v1

A Convolutional Deep Learning Approach to identify DNA Sequences for Gene Prediction https://www.biorxiv.org/content/10.1101/2025.10.03.680292v1

Probe-Based Identification of Metal-Binding Sites Using Deep Learning Representations https://www.biorxiv.org/content/10.1101/2025.10.04.680417v1

Discovering Condition-specific Cell Populations via Integrative Clustering of Single-cell Data https://www.biorxiv.org/content/10.1101/2025.10.03.680413v1

Locus-specific transcriptional regulation of transposable elements by p53 https://www.biorxiv.org/content/10.1101/2025.10.01.679811v1

SCREAM: Single-cell Clustering using Representation Autoencoder of Multiomics https://www.biorxiv.org/content/10.1101/2025.10.03.680290v1

Pan-cancer analysis of patient-specific gene regulatory landscapes identifies recurrent PD-1 pathway dysregulation linked to outcome https://www.biorxiv.org/content/10.1101/2025.10.03.680219v1

Gradient-aware modeling advances AI-driven prediction of genetic perturbation effects https://www.biorxiv.org/content/10.1101/2025.10.03.680360v1

Facial photographs as proxies for inflammatory aging https://www.biorxiv.org/content/10.1101/2025.10.02.680162v1

Towards functional annotation with latent protein languagemodel features https://www.biorxiv.org/content/10.1101/2025.10.02.680154v1

De Novo Design of Anti-Aging Peptides https://www.biorxiv.org/content/10.1101/2025.10.04.680435v1

Improving the benchmark of variant calling in clonal bacteria using more realistic in silico genomes, the case of Mycobacterium tuberculosis https://www.biorxiv.org/content/10.1101/2025.10.04.680280v1

Helical Reconstruction of Amyloids in cryoSPARC https://www.biorxiv.org/content/10.1101/2025.10.03.680389v1

AstraPTM2: A Context-Aware Transformer for Broad-Spectrum PTM Prediction https://www.biorxiv.org/content/10.1101/2025.10.03.680341v1

GECSI: Large-scale chromatin state imputation from gene expression https://www.biorxiv.org/content/10.1101/2025.10.02.679828v1

Towards Human Inverse Dynamics from Real Images: A Dataset and Benchmark for Joint Torque Estimation https://www.biorxiv.org/content/10.1101/2025.10.03.679772v1