MapMyCells: High-performance mapping of unlabeled cell-by-gene data to reference brain taxonomies https://www.biorxiv.org/content/10.64898/2026.03.06.710160v1

singIST: an R/Bioconductor library and Quarto dashboard for automated single-cell comparative transcriptomics analysis ofdisease models and humans https://www.biorxiv.org/content/10.64898/2026.03.03.709270v1

Inverse Protocol Prediction from Spheroid Microscopy Imaging via Morphology-Aware Structured Learning https://www.biorxiv.org/content/10.64898/2026.03.04.709682v1

Re-analysis of Transcriptomic and Proteomic Data Using Multi-Omics Approaches Identifies Biomarkers of Diabetes-Associated Complications in an INS Mutant Pig Model https://www.biorxiv.org/content/10.64898/2026.03.04.707880v1

Calibration improves estimation of linkage disequilibrium on low sample sizes https://www.biorxiv.org/content/10.64898/2026.03.05.709321v1

Deep-Palm：an integrated deep learning framework for structure-aware prediction of protein S-Palmitoylation https://www.biorxiv.org/content/10.64898/2026.03.05.709753v1

PROTOTYPE-BASED CONTINUAL LEARNING FOR SINGLE-CELL ANNOTATION https://www.biorxiv.org/content/10.64898/2026.03.05.709973v1

Deciphering Cell Cycle Dynamics and Cell States in Single-cell RNA-seq data with SPAE https://www.biorxiv.org/content/10.64898/2026.03.05.709782v1

MS-BCR-DB: an integrated BCR repertoire database to mine humoral multiple sclerosis signatures https://www.biorxiv.org/content/10.64898/2026.03.05.709606v1

Relationship Between Gene Expression and Drug Response in Triple-Negative Breast Cancer: Leveraging Single-Cell RNA Sequencing and Machine Learning to Identify Biomarker Profiles https://www.biorxiv.org/content/10.64898/2026.03.05.709737v1

HP2NET: Empowering Efficient Phylogenetic Network Analysis through High-Performance Computing https://www.biorxiv.org/content/10.64898/2026.03.05.709005v1

Perseus: Lineage-Aware Refinement of Kraken2 Taxonomic Classification for Long Read Metagenomes https://www.biorxiv.org/content/10.64898/2026.03.06.710148v1

REMAG: recovery of eukaryotic genomes from metagenomic data using contrastive learning https://www.biorxiv.org/content/10.64898/2026.03.05.709928v1

geneSTRUCTURE: A Modern Platform for Visualization of Gene Structures https://www.biorxiv.org/content/10.64898/2026.03.05.709980v1

Identifying genes associated with phenotypes using machine and deep learning https://www.biorxiv.org/content/10.64898/2026.03.05.709665v1

FourC: identifying significant and differential contacts in 1D chromatin conformation data https://www.biorxiv.org/content/10.64898/2026.03.05.709811v1

Multi-Target In Silico Investigation of Withaferin A as a Potential Antiviral Inhibitor Against Key Marburg Virus Proteins https://www.biorxiv.org/content/10.64898/2026.03.06.710011v1

SR2P: an efficient stacking method to predict protein abundance from gene expression in spatial transcriptomics data https://www.biorxiv.org/content/10.64898/2026.03.04.709692v1

Telomere-to-telomere assembly and haplotype analysis of tetraploid Dendrobium officinale illuminate Orchidaceae polyploid evolution and mycorrhizal symbiosis genes https://www.biorxiv.org/content/10.64898/2026.03.04.709700v1

Application of large language models to the annotation of cell lines and mouse strains in genomics data https://www.biorxiv.org/content/10.64898/2026.03.05.709906v1

Diffusion-ACP39: A Decoder-Adaptive Latent Diffusion Framework for Generative Anticancer Peptide Discovery https://www.biorxiv.org/content/10.64898/2026.03.04.709539v1

EasyPseudogene: an easy-to-use and multithreaded pipeline for pseudogene detection https://www.biorxiv.org/content/10.64898/2026.03.04.709571v1

Comprehensive Transcriptomic Analysis of Atopic Dermatitis Patients Documents the Spectrum of Molecular Abnormalities and the Response to Treatment https://www.biorxiv.org/content/10.64898/2026.03.04.709610v1

Phenotypic reversion and target prioritization for cellular inflammation via representation learning with foundation models https://www.biorxiv.org/content/10.64898/2026.03.04.709607v1

Using Variable Window Sizes for Phylogenomic Analyses of Whole Genome Alignments https://www.biorxiv.org/content/10.64898/2026.03.04.709403v1

Circular RNA identification using a genomic language model and a small number of authenticated examples https://www.biorxiv.org/content/10.64898/2026.03.04.709677v1

Minimal Amino Acid Alphabet for Protein Design https://www.biorxiv.org/content/10.64898/2026.03.06.710107v1

GWAS Summary Statistic Tool: A Meta-Analysis and Parsing Tool for Polygenic Risk Score Calculation https://www.biorxiv.org/content/10.64898/2026.03.04.709666v1

ProtNHF: Neural Hamiltonian Flows for Controllable Protein Sequence Generation https://www.biorxiv.org/content/10.64898/2026.03.04.709305v1

From variability to consensus: rescoring harmonizes peptide identification across diverse search engines and datasets https://www.biorxiv.org/content/10.64898/2026.03.04.709532v1

Single-Cell Genomics Decontamination with CellSweep https://www.biorxiv.org/content/10.64898/2026.03.04.709349v1

Unveiling Common Molecular Signatures and Pathways in Psychiatric Disorders and Alcohol Use Disorder through Integrated Transcriptome Analysis https://www.biorxiv.org/content/10.64898/2026.03.04.709553v1

ESGI: Efficient splitting of generic indices in single-cellsequencing data https://www.biorxiv.org/content/10.64898/2026.03.04.709594v1

A latent space thermodynamic model of cell differentiation https://www.biorxiv.org/content/10.64898/2026.03.04.709512v1

RNA-seq analysis in seconds using GPUs https://www.biorxiv.org/content/10.64898/2026.03.04.709526v1

Reliable prediction of short linear motifs in the human proteome https://www.biorxiv.org/content/10.64898/2026.03.04.709504v1

In silico drug repurposing and in vitro validation of cestode fatty acid binding proteins https://www.biorxiv.org/content/10.64898/2026.03.04.709508v1

What Do Biological Foundation Models Compute? Sparse Autoencoders from Feature Recovery to Mechanistic Interpretability https://www.biorxiv.org/content/10.64898/2026.03.04.709491v1

From expansion to consolidation: two decades ofGene Ontology evolution https://www.biorxiv.org/content/10.64898/2026.03.04.709507v1

TFBSpedia: a comprehensive human and mouse transcription factor binding sites database https://www.biorxiv.org/content/10.64898/2026.03.04.709638v1

bMAE: Masked Autoencoder Latent Representations for Bulk RNA-seq Tissues https://www.biorxiv.org/content/10.64898/2026.03.03.709470v1

Early Identification of At-Risk Patients: ProteomicSignature Predicts Progression to DecompensatedCirrhosis https://www.biorxiv.org/content/10.64898/2026.03.04.709475v1

An Energy Landscape Approach to Miniaturizing Enzymes using Protein Language Model Embeddings https://www.biorxiv.org/content/10.64898/2026.03.04.709378v1

Confidence Without Verification: Screening pLDDT Unreliability in AlphaFold2 Fold-Switching Predictions https://www.biorxiv.org/content/10.64898/2026.02.19.706878v1

A Quantum Lens on Molecular Design: A Machine-Learned Energy Function from Interacting Quantum Atoms. https://www.biorxiv.org/content/10.64898/2026.03.03.709242v1

waveome: a toolkit for longitudinal omics analysis using Gaussian processes https://www.biorxiv.org/content/10.64898/2026.03.03.709362v1

Gradient boosting regression and convolution improve deconvolution of bulk transcriptomes https://www.biorxiv.org/content/10.64898/2026.03.03.709368v1

Predicting how perturbations reshape cellular trajectories with PerturbGen https://www.biorxiv.org/content/10.64898/2026.03.04.709254v1

Genome-wide classification of tumor-derived reads from bulk long-read sequencing https://www.biorxiv.org/content/10.64898/2026.03.03.709085v1

FoldARE, an RNA secondary structure analysis and prediction tool via generative pseudo-SHAPE modeling https://www.biorxiv.org/content/10.64898/2026.03.04.709501v1