PocketGNN: A Cross-Modal Framework Unifying Local 3D Pocket Geometry and Global Sequence Semantics for Enzyme Kinetic Prediction https://www.biorxiv.org/content/10.64898/2026.01.19.700244v1

VAETracer: Mutation-Guided Lineage Reconstruction and Generational State Inference from scRNA-seq https://www.biorxiv.org/content/10.64898/2026.01.19.700238v1

SPSID: A single-parameter shrinkage inverse-diffusion for denoising gene regulatory networks https://www.biorxiv.org/content/10.64898/2026.01.19.700249v1

Cardiac GLP1R gene Expression: A Cross-Species Single-Cell Transcriptomic Analysis https://www.biorxiv.org/content/10.64898/2026.01.18.700176v1

Zero-shot ecological annotation of microbial genomes with myLLannotator accelerates scientific discovery https://www.biorxiv.org/content/10.64898/2026.01.18.700140v1

Ancestral sequence reconstruction using generative models https://www.biorxiv.org/content/10.64898/2026.01.18.700141v1

Predicting Enzyme pH Optima from Structure Using Equivariant Graph Neural Networks https://www.biorxiv.org/content/10.64898/2026.01.18.700076v1

Optimizing broadly neutralizing antibodies via all-atom interaction modeling and pre-trained language models https://www.biorxiv.org/content/10.64898/2026.01.20.700456v1

Nevermore: Target-Conditioned Protein-Ligand Representation Learning for Multi-Objective Lead Optimization with Database-Grounded Retrieval https://www.biorxiv.org/content/10.64898/2026.01.20.700610v1

On the correctness of gene tree tagging and the consistency of ASTRAL-pro under a unified model of gene duplication, loss, and coalescence https://www.biorxiv.org/content/10.64898/2026.01.20.700722v1

Searching the Druggable Genome using Large Language Models https://www.biorxiv.org/content/10.64898/2026.01.18.700012v1

TPCAV: Interpreting deep learning genomics models via concept attribution https://www.biorxiv.org/content/10.64898/2026.01.20.700723v1

Integrative Whole-Genome Analysis reveals Genomic Signatures of Innate Immunity in Indicine Cattle. https://www.biorxiv.org/content/10.64898/2026.01.21.700751v1

RAGulate: Retrieval-Augmented Generation for Post-hoc Literature-Grounded Regulatory Assessment https://www.biorxiv.org/content/10.64898/2026.01.20.700704v1

dna-parser: a Python library written in Rust for fast encoding of DNA and RNA sequences https://www.biorxiv.org/content/10.64898/2026.01.20.700656v1

SigFormer: an Attention-Based Framework for Robust Single-Sample Mutational Signature Decomposition https://www.biorxiv.org/content/10.64898/2026.01.20.700228v1

A Scalable Framework for Pan-Cancer Tumor Evolution Analysis Enables Transfer of Progression Mechanisms Across Tumor Entities https://www.biorxiv.org/content/10.64898/2026.01.20.700556v1

Distinct Repeat Architecture Landscapes in the Proteomes of Protozoan Parasites https://www.biorxiv.org/content/10.64898/2026.01.20.700692v1

MoDPA: Inferring Modification-dependent Protein Associations from Uniformly Reprocessed Mass Spectrometry https://www.biorxiv.org/content/10.64898/2026.01.20.700550v1

MANTIS: Analytics toolkit for spatial metabolomics with matching spatial transcriptomics data https://www.biorxiv.org/content/10.64898/2026.01.20.700581v1

Point-Cloud Enhancement and Structural Interpretation Framework for Cryo-EM Maps https://www.biorxiv.org/content/10.64898/2026.01.17.700079v1

orthogene: a Bioconductor package to easily map genes within and across hundreds of species https://www.biorxiv.org/content/10.64898/2026.01.17.700094v1

Rice Annotation Project Database (RAP-DB): literature-curated gene annotation and integrated omics resources for rice functional genomics and molecular breeding https://www.biorxiv.org/content/10.64898/2026.01.16.699882v1

BiOmics: A Foundational Agent for Grounded and Autonomous Multi-omics Interpretation https://www.biorxiv.org/content/10.64898/2026.01.17.699830v1

Comparison of Deep Learning Approaches for Extreme Low-SNR Image Restoration https://www.biorxiv.org/content/10.64898/2026.01.16.700026v1

PersonaAI: An Interactive Agentic-AI Framework for Autonomous Hypothesis Generation and Validation in Aging https://www.biorxiv.org/content/10.64898/2026.01.16.699755v1

CellFluxV2: An Image Generative Foundation Model for Virtual Cell Modeling https://www.biorxiv.org/content/10.64898/2026.01.19.696785v1

Benchmarking Next-Generation Sequencing Platforms: A Comprehensive Comparison Of Single-Cell RNA-Seq from Ultima UG 100 vs. Illumina NovaSeq X Plus https://www.biorxiv.org/content/10.64898/2026.01.16.699571v1

Medea: An omics AI agent for therapeutic discovery https://www.biorxiv.org/content/10.64898/2026.01.16.696667v1

eTRex Reveals Oncogenic Transcriptional Regulatory Programs Across Human Cancers https://www.biorxiv.org/content/10.64898/2026.01.16.699950v1

Dynamics-aware Evolutionary Profiling Uncouples Structural Rigidity from Functional Motion to Enable Enhanced Variant Interpretation https://www.biorxiv.org/content/10.64898/2026.01.16.699945v1

High-PepBinder: A pLM-Guided Latent Diffusion Framework for Affinity-Aware Target-Specific Peptide Design https://www.biorxiv.org/content/10.64898/2026.01.12.698988v1

dgiLIT: A Method for Prioritization and AI Curation of Drug-Gene Interactions https://www.biorxiv.org/content/10.64898/2026.01.16.699733v1

SE3Bind: SE(3)-equivariant model for antibody-antigen binding affinity prediction https://www.biorxiv.org/content/10.64898/2026.01.17.700115v1

Structural alphabets approach performance of structural alignment in remote homology detection https://www.biorxiv.org/content/10.64898/2026.01.16.699908v1

AFsample3: Generating and selecting multipleconformational states with Alphafold3 https://www.biorxiv.org/content/10.64898/2026.01.16.699904v1

NetCrafter: Ontology-derived gene network modeling and interpretation https://www.biorxiv.org/content/10.64898/2026.01.16.699831v1

Mitigating Bias in Spatial Transcriptomic Pipelines via Human Feedback https://www.biorxiv.org/content/10.64898/2026.01.15.699786v1

TcrDesign: De novo design of epitope specific full-length T cell receptors https://www.biorxiv.org/content/10.64898/2026.01.15.699824v1

GARD: Genomic Data based Drug Repurposing in Head and Neck Cancer with Large Language Model Validation https://www.biorxiv.org/content/10.64898/2026.01.15.699561v1

PathDiffusion: modeling protein folding pathway using evolution-guided diffusion https://www.biorxiv.org/content/10.64898/2026.01.16.699856v1

TomoSegNet: Augmented membrane segmentation for cryo-electron tomography by simulating the cellular context https://www.biorxiv.org/content/10.64898/2026.01.15.699326v1

Leveraging Unified Sequence-Structure Representations for Enhanced Protein Stability Prediction https://www.biorxiv.org/content/10.64898/2026.01.15.699740v1

mtDNA-Network: a web tool to explore mitochondrial variant profiles in complex diseases https://www.biorxiv.org/content/10.64898/2026.01.15.699732v1

Signal Strength Aware Latent Spaces Reveal Molecularly Distinct Substructures within Human Kidney Tissue https://www.biorxiv.org/content/10.64898/2026.01.15.699686v1

AtlasMap: enabling low-cost, map-style exploration of million-cell single-cell atlases https://www.biorxiv.org/content/10.64898/2026.01.14.699595v1

RAREsim2: Flexible simulation of rare variant genetic data using real haplotypes https://www.biorxiv.org/content/10.64898/2026.01.14.694480v1

Label-free detection of individual virus-infected cells using deep learning https://www.biorxiv.org/content/10.64898/2026.01.15.699499v1

Enhancing volumetric microscopy with blind computational correction of spatially variant aberrations using neural field representation https://www.biorxiv.org/content/10.64898/2026.01.15.699665v1

DeepSpaceDB 2.0: an interactive spatial transcriptomics database for large-scale Xenium data exploration https://www.biorxiv.org/content/10.64898/2026.01.15.699623v1