Integrative Clinical-Molecular Modeling Identifies LRRN4CL as a Determinant of Structural and Functional Myocardial Improvement https://www.biorxiv.org/content/10.64898/2026.04.21.720029v1

Multi-Modal Deep Learning Integrates Spatial Topologies and Sequential Motifs to Identify Class I HDAC Inhibitors as Pan-Cancer Therapeutics https://www.biorxiv.org/content/10.64898/2026.04.22.720196v1

PP-MAPS: dynamic pharmacophore signatures of protein-peptide interfaces from molecular dynamics trajectories https://www.biorxiv.org/content/10.64898/2026.04.22.720140v1

Are Current AI Virtual Cell Models Useful for Scientific Discovery? https://www.biorxiv.org/content/10.64898/2026.04.23.719015v1

Graph Neural Networks (GNNs) for Protein-Ligand Interaction Prediction https://www.biorxiv.org/content/10.64898/2026.04.23.720519v1

Housekeeping Gene Expression Normalization in Transcriptomics Mitigates Data Leakage in Machine Learning Models https://www.biorxiv.org/content/10.64898/2026.04.24.720637v1

MVCBench: A Multimodal Benchmark for Drug-induced Virtual Cell Phenotypes https://www.biorxiv.org/content/10.64898/2026.04.22.720110v1

Structural variation shapes regulatory and evolutionary diversity at the HLA locus https://www.biorxiv.org/content/10.64898/2026.04.23.720469v1

Additive baselines furnish no evidence for epistasis learning by MULTI-evolve https://www.biorxiv.org/content/10.64898/2026.04.23.719915v1

PanVariants: Best Practice for Pangenome-based Variant Calling Pipeline and Framework https://www.biorxiv.org/content/10.64898/2026.04.22.720142v1

GenNA: Conditional generation of nucleotide sequences guided by natural-language annotations https://www.biorxiv.org/content/10.64898/2026.04.22.720063v1

SpatialQuery: scalable discovery and molecular characterization of multicellular motifs from spatial omics data https://www.biorxiv.org/content/10.64898/2026.04.22.720136v1

MSAgent: An Evidence Grounded Agentic Framework for LLM-driven Scientific Exploration in Mass Spectrometry-based Metabolomics https://www.biorxiv.org/content/10.64898/2026.04.22.720103v1

A Systematic Evaluation of Single-Cell Batch Integration Metrics and sBEE: A Robust New Metric https://www.biorxiv.org/content/10.64898/2026.04.22.720135v1

Small Area Estimation of Forest Volume Using Mixed Effects Random Forests and Multi-Source Remote Sensing Data https://www.biorxiv.org/content/10.64898/2026.04.22.720077v1

CellPulse: A Foundation Model of Coordinated Gene Dynamics Simulating Viral Infectious Diseases https://www.biorxiv.org/content/10.64898/2026.04.22.720078v1

Turep: Detecting cross-cancer tumor-reactive T cells in single-cell and spatial transcriptomics data https://www.biorxiv.org/content/10.64898/2026.04.21.719961v1

Genomic dialects: How amino acid properties and the second codon base shape the informational accents of life https://www.biorxiv.org/content/10.64898/2026.04.21.720023v1

H2O: A Foundation Model Bridging Histopathology to Spatial Multi-Omics Profiling https://www.biorxiv.org/content/10.64898/2026.04.21.717342v1

Systematic Evaluation of AlphaFold2 and OpenFold3 on Protein-Peptide Complexes https://www.biorxiv.org/content/10.64898/2026.04.21.720042v1

Verticall: A fast and robust tool for recombination detection in large-scale bacterial genomic datasets https://www.biorxiv.org/content/10.64898/2026.04.21.719734v1

Efficient and scalable modelling of cotranscriptional RNA folding with deterministic and iterative RNA structure sampling https://www.biorxiv.org/content/10.64898/2026.04.21.720041v1

Probabilistic coupling of cellular and microenvironmental heterogeneity by masked self-supervised learning https://www.biorxiv.org/content/10.64898/2026.04.21.719876v1

scConcept enables concept-level exploration of single-cell transcriptomic data https://www.biorxiv.org/content/10.64898/2026.04.21.719959v1

Quantifying data reuse in proteomics using PRIDE downloads statistics and a semi-supervised LLM-based framework https://www.biorxiv.org/content/10.64898/2026.04.16.718670v1

AutoRNAseq: Automated Bulk RNA-seq Analysis Pipeline https://www.biorxiv.org/content/10.64898/2026.04.21.719844v1

Hierarchical Breakdown of RNA Structure Prediction in CASP16: From Reliable Local Features to Speculative Multimer Assembly https://www.biorxiv.org/content/10.64898/2026.04.22.720187v1

An autonomous LLM agent platform for computational binder design and conjugation-aware prioritization of antibody drug conjugates https://www.biorxiv.org/content/10.64898/2026.04.21.719907v1

Aiki-XP: leakage-controlled multimodal prediction of within-species relative protein expression at pan-bacterial scale https://www.biorxiv.org/content/10.64898/2026.04.21.719525v1

Cross-Attention Over RNA And Protein Sequences Enables Generalizable Interaction Prediction https://www.biorxiv.org/content/10.64898/2026.04.22.720174v1

Improving AlphaFold3 by Engineering MSA and Template Inputs https://www.biorxiv.org/content/10.64898/2026.04.22.720119v1

EpiRanha: Hunting for Epitope Similarity with a Structure- and Residue-Aware Graph Neural Network https://www.biorxiv.org/content/10.64898/2026.04.21.719830v1

Tensor-Derived Similarity Networks for Characterising Spatial Patterns in Colorectal Cancer https://www.biorxiv.org/content/10.64898/2026.04.20.719742v1

Back to BERT in 2026: ModernGENA as a Strong, Efficient Baseline for DNA Foundation Models https://www.biorxiv.org/content/10.64898/2026.04.21.719816v1

Metaxa: A Transformer-Based Deep Learning Model for Taxonomic Classification of Long Nanopore Reads https://www.biorxiv.org/content/10.64898/2026.04.20.719780v1

Large Language Model Agent Enables Autonomous Machine Learning Model Building for Biomedicine https://www.biorxiv.org/content/10.64898/2026.04.20.719735v1

Continual Learning for Emerging Epitope Landscapes in TCR peptide Binding Prediction https://www.biorxiv.org/content/10.64898/2026.04.20.719750v1

Proteome-anchored multi-omics propagation of recurrent somatic alterations defines tumour states in cervical cancer and enables state-guided drug repurposing https://www.biorxiv.org/content/10.64898/2026.04.21.719801v1

Detection and evaluation of copy number variation using both linked-read and short-read sequencing in New Zealand dairy cattle https://www.biorxiv.org/content/10.64898/2026.04.20.718595v1

RVQ-Alpha: Bridging Single-Cell Transcriptomics and Large Language Models via Discrete Tokenization and Verifiable Reinforcement Learning https://www.biorxiv.org/content/10.64898/2026.04.20.719773v1

An Embeddings Fusion Approach Predicts Disease State from Microbiome Features https://www.biorxiv.org/content/10.64898/2026.04.20.719747v1

Attracting Cavities 3.0: Faster and More Versatile Molecular Docking for the SwissDock Webserver https://www.biorxiv.org/content/10.64898/2026.04.21.719847v1

scTrends: automated classification and strength quantification of gene expression trends along pseudotime in single-cell RNA-seq https://www.biorxiv.org/content/10.64898/2026.04.21.719599v1

High Purity Differential Expression of Genes across Spatial Domains https://www.biorxiv.org/content/10.64898/2026.04.20.719761v1

Proximity-Aware Graph Attention Networks for Spatially Resolved Cell-Cell Inference https://www.biorxiv.org/content/10.64898/2026.04.20.719753v1

SpaceBender: Denoising Spatial Transcriptomics Data to Enhance Biological Signals https://www.biorxiv.org/content/10.64898/2026.04.20.719715v1

AlphaInterp: Probing AlphaFold 3's Internal Representations Reveals Evolutionary Determinants of Predicted Structure and Confidence https://www.biorxiv.org/content/10.64898/2026.04.22.720175v1

scVIP: personalized modeling of single-cell transcriptomes for developmental and disease phenotypes https://www.biorxiv.org/content/10.64898/2026.04.20.717759v1

Signal, Bounds, and Baselines: Principles for Rigorous Evaluation of High-Dimensional Biological Perturbation Prediction https://www.biorxiv.org/content/10.64898/2026.04.20.719650v1

CD8scape: an accessible, command-line tool for predicting viral escape from the CD8+ T cell response https://www.biorxiv.org/content/10.64898/2026.04.20.719634v1