biomeStat: Using Agentic AI for Scalable Genomic Epidemiology Demonstrated Through End-to-End Analysis of 1,000 Asian Dengue Virus Genomes https://www.biorxiv.org/content/10.64898/2026.06.10.731380v1

Few-Shot Classification of C. elegans Developmental Stages via Explainable Hierarchical Hyperbolic Graph Embeddings https://www.biorxiv.org/content/10.64898/2026.06.21.733631v1

EMAlign: accurate alignment of cryo-EM maps through main-chain probability using deep learning https://www.biorxiv.org/content/10.64898/2026.06.21.733642v1

PanRes: A database of latent and acquired antimicrobial resistance allowing 3D-based protein homology search https://www.biorxiv.org/content/10.64898/2026.06.22.733705v1

Drug-Prot: A query system for statistical inference of drug effects and interactions in dynamic proteomic networks https://www.biorxiv.org/content/10.64898/2026.06.17.732914v1

HTS-Oracle X: AI-Guided Prospective Discovery of Small Molecule Immune Checkpoint Binders https://www.biorxiv.org/content/10.64898/2026.06.17.732853v1

Multivariate Random Forests for Cross-Modal Multi-Omics Integration https://www.biorxiv.org/content/10.64898/2026.06.17.732933v1

Dynamic balance of sparse flux vectors for efficient simulation of culture dynamics and metabolic network reduction https://www.biorxiv.org/content/10.64898/2026.06.17.733012v1

PhaseWY: A pipeline for haplotype phasing, sex chromosome identification and extraction of sex-limited sequences https://www.biorxiv.org/content/10.64898/2026.06.17.732863v1

When Less Is Not More: DICEPro Mitigates the Impact of Incomplete Reference Matrices on Cellular Frequency Deconvolution. https://www.biorxiv.org/content/10.64898/2026.06.17.732876v1

Benchmarking cell type annotation in spatial transcriptomics: resolving cellular hierarchies, biological fidelity, and dynamic cell states https://www.biorxiv.org/content/10.64898/2026.06.16.732716v1

CellTosg2Sequence: A Unified Text-Omics-Signaling-Graph Large Language Model for Single-Cell Analysis https://www.biorxiv.org/content/10.64898/2026.06.16.732397v1

Complex-valued representations of time-series gene expression profiles for network analysis https://www.biorxiv.org/content/10.64898/2026.06.16.732574v1

EventHorizon: A Foundation Model for Clinical Flow Cytometry https://www.biorxiv.org/content/10.64898/2026.06.18.733197v1

From hotspot dependence to distributed robustness in resistance-aware lead optimization https://www.biorxiv.org/content/10.64898/2026.06.16.732538v1

Reference-guided immune recovery matching prioritizes traditional Chinese medicine ingredients https://www.biorxiv.org/content/10.64898/2026.06.16.732528v1

ReSeT: a taxonomy-aware reference genome selection tool https://www.biorxiv.org/content/10.64898/2026.06.17.732946v1

Machine learning evaluation of gene expression-based ALS subtypes across brain and blood tissues https://www.biorxiv.org/content/10.64898/2026.06.19.733362v1

Expanding the GUSome: Structure-guided identification and characterization of gut microbial β-glucuronidases https://www.biorxiv.org/content/10.64898/2026.06.20.733316v1

DeepCDS: Ab initio coding sequence prediction in prokaryotic short reads https://www.biorxiv.org/content/10.64898/2026.06.17.732633v1

SPA-C: an hybrid tool to accurately scaffold genomes using Hi-C and Deep-Learning https://www.biorxiv.org/content/10.64898/2026.06.16.732382v1

OracleScreen-LILRB4: Machine Learning-Guided Discovery of Myeloid Immune Checkpoint Binders Validated in Patient-Derived Cells https://www.biorxiv.org/content/10.64898/2026.06.17.732859v1

GENATATORs: ab initio Gene Annotation With DNA Language Models https://www.biorxiv.org/content/10.64898/2026.06.17.732686v1

Antibody-Antigen Affinity Prediction with Chain-Aware Protein Language Modeling https://www.biorxiv.org/content/10.64898/2026.06.19.733375v1

Seed variation impacts clustering stability in Single-Cell RNA-Seq and can be mitigated by StAbility-BasEd-Reassignment (SABER) https://www.biorxiv.org/content/10.64898/2026.06.16.732539v1

Systematic Evaluation of Feature Representations for Cancer-Associated sORF Prediction in Non-coding RNA https://www.biorxiv.org/content/10.64898/2026.06.16.732659v1

RNAStabFormer: Region-Aware Multi-Task Hybrid Learning for RNA Stability Prediction from Pulse-Chase Transcriptomics https://www.biorxiv.org/content/10.64898/2026.06.19.733389v1

Evaluation of Trypanosoma brucei Phosphofructokinase Allosteric Inhibition: An In-Silico Study https://www.biorxiv.org/content/10.64898/2026.06.16.732740v1

MIRATS framework: Normative multiscale characterization of brain regulatory systems across sex and age using multimodal MRI https://www.biorxiv.org/content/10.64898/2026.06.15.732296v1

SAbDab2: The structural antibody database in the age of machine learning https://www.biorxiv.org/content/10.64898/2026.06.16.732554v1

A network approach to DNA methylation clocks https://www.biorxiv.org/content/10.64898/2026.06.18.733218v1

Ribosomes are covered by a coat of flexible protein fragments https://www.biorxiv.org/content/10.64898/2026.06.18.733196v1

The recount3 Python package for programmatic access to uniformly processed RNA-seq data https://www.biorxiv.org/content/10.64898/2026.06.17.732943v1

Morpho-FM: spatial molecular reconstruction from routine H&E histology using transcriptomic foundation-model priors https://www.biorxiv.org/content/10.64898/2026.06.15.732498v1

Evaluation of analysis modes for RNA coexpression in single-cell and bulk tissue https://www.biorxiv.org/content/10.64898/2026.06.17.731965v1

Identification of Altered Potassium Channels for Drug Repurposing in Long COVID Patients https://www.biorxiv.org/content/10.64898/2026.06.18.733062v1

Sanjeevani: A manually curated anti-cancerous phytochemical database integrated with downstream analysis tools. https://www.biorxiv.org/content/10.64898/2026.06.15.732344v1

Tox21mer, A transformer foundation model for Tox21 high-throughput concentration-response curves data https://www.biorxiv.org/content/10.64898/2026.06.15.732308v1

Geometric Deep Learning Reveals Ligandable and Cryptic RNA Binding Small Molecule Pockets (SMARTPocket) https://www.biorxiv.org/content/10.64898/2026.06.18.732920v1

Accurate detection of tumor clonality and ongoing expansion mode from genomic data https://www.biorxiv.org/content/10.64898/2026.06.15.732415v1

HTS-Oracle v2: Prospective AI-Guided Discovery and Experimental Validation of Small Molecule Modulators Across Multiple Targets https://www.biorxiv.org/content/10.64898/2026.06.15.732399v1

Children's DNA Methylation and Family Dynamics in a Congo Basin Subsistence Community: Links with Parental Conflict and Fathers' Caregiving https://www.biorxiv.org/content/10.64898/2026.06.15.732362v1

FeatureMSEA: Metabolic Feature-based Metabolite Set Enrichment Analysis https://www.biorxiv.org/content/10.64898/2026.06.15.732313v1

Perturbation Curve models continuous transcriptional response trajectories and improves prediction of genetic modulations https://www.biorxiv.org/content/10.64898/2026.06.16.732192v1

ContinuumCellAgent: A Framework-Guided Agent for Long-Horizon Scientific Research https://www.biorxiv.org/content/10.64898/2026.06.15.732409v1

Nickel-Driven Dynamics of Urease in Sporosarcina pasteurii: Integrated Computational and Experimental Insights https://www.biorxiv.org/content/10.64898/2026.06.15.732323v1

StickForStats: automated statistical assumption validation for reproducible computational biology https://www.biorxiv.org/content/10.64898/2026.06.15.732278v1

SteerAF: Distogram-based Steering of AlphaFold2 toward Alternative Conformations https://www.biorxiv.org/content/10.64898/2026.06.19.733296v1

OmniPath Metabo: chemical structures, interactions and mechanisms to study the metabolome https://www.biorxiv.org/content/10.64898/2026.06.18.733117v1

Simulation-based Bayesian deep learning enables uncertainty-aware tumor fraction estimation in cell-free DNA https://www.biorxiv.org/content/10.64898/2026.06.15.732265v1