Reinforcement learning for adaptive control of phenotypically heterogeneous bacterial populations https://www.biorxiv.org/content/10.1101/2025.11.21.689767v1

InfluenceNet: Encoding Motif Influence for Interpretable Modeling of Cis-Regulatory Syntax https://www.biorxiv.org/content/10.1101/2025.11.20.689553v1

LongPhase-S: purity estimation and variant recalibration with somatic haplotying for long-read sequencing https://www.biorxiv.org/content/10.1101/2025.11.20.689492v1

Transcriptomic module fingerprint reveals heterogeneity of whole blood transcriptome in type 1 diabetic patients https://www.biorxiv.org/content/10.1101/2025.11.19.689306v1

Determining gene specificity from multivariate single-cell RNA sequencing data https://www.biorxiv.org/content/10.1101/2025.11.21.689845v1

Mapping the AI Life Sciences Landscape in Greece: A National Survey and Bibliometric Comparison with Global Trends https://www.biorxiv.org/content/10.1101/2025.11.19.689212v1

MAGIC: Methylation Analysis with Genomic Inferred Contexts https://www.biorxiv.org/content/10.1101/2025.11.19.689248v1

Accurate Reconstruction of Circular RNAs from Complex Rolling Circular Long Reads with CircPlex https://www.biorxiv.org/content/10.1101/2025.11.21.689841v1

Selector: A General Python Library for Diverse Subset Selection https://www.biorxiv.org/content/10.1101/2025.11.21.689756v1

AlterNet: Alternative splicing-aware gene regulatory networkinference https://www.biorxiv.org/content/10.1101/2025.11.21.689745v1

Billi: Provably Accurate and Scalable Bubble Detection in Pangenome Graphs https://www.biorxiv.org/content/10.1101/2025.11.21.689636v1

CCK* (Convex Closure K*): A Suite of Algorithms for the De Novo Design of L- and D-peptide Binders https://www.biorxiv.org/content/10.1101/2025.11.21.689740v1

Comparative genomics and interactions of vector thysanopterans and transmitted viruses https://www.biorxiv.org/content/10.1101/2025.11.21.689785v1

Bias in genome-wide association test statistics due to omitted interactions https://www.biorxiv.org/content/10.1101/2025.11.21.689603v1

GBoost-CTL: A novel method in multi-tissue transcriptome-wide associations studies in cross-tissue learner incorporating GWAS information https://www.biorxiv.org/content/10.1101/2025.11.22.689782v1

Quantum and Classical Graph Convolutional Neural Networks for Protein Ligand Dissociation Constant Prediction https://www.biorxiv.org/content/10.1101/2025.11.20.689635v1

Minimizer Density revisited: Models and Multiminimizers https://www.biorxiv.org/content/10.1101/2025.11.21.689688v1

Compressed inverted indexes for scalable sequence similarity https://www.biorxiv.org/content/10.1101/2025.11.21.689685v1

ASVNet: Inferring microbes from 16S rRNA amplicon sequencing data https://www.biorxiv.org/content/10.1101/2025.11.21.689717v1

The Human-In-the-Loop Drug Design Framework with Equivariant Rectified Flow https://www.biorxiv.org/content/10.1101/2025.11.20.689585v1

biocentral: embedding-based protein predictions https://www.biorxiv.org/content/10.1101/2025.11.21.689449v1

Snail plots are badges of genome assembly quality https://www.biorxiv.org/content/10.1101/2025.11.20.689594v1

Transforming Biological Foundation Model Representations for Out-of-Distribution Data https://www.biorxiv.org/content/10.1101/2025.11.20.689462v1

Continuous Motility Fingerprints from Gaussian Mixture Models Reveal Hidden Sperm Heterogeneity https://www.biorxiv.org/content/10.1101/2025.11.20.689493v1

Causality-oriented regulatory inference and rational transcriptomic reprogramming design with CASCADE https://www.biorxiv.org/content/10.1101/2025.11.20.689377v1

Orchestrating Spatial Transcriptomics Analysis with Bioconductor https://www.biorxiv.org/content/10.1101/2025.11.20.688607v1

Decrypting cellular engagement and recruitment from spatially resolved transcriptomics https://www.biorxiv.org/content/10.1101/2025.11.20.689581v1

scDock: Streamlining drug discovery targeting cell-cell communication via scRNA-seq analy-sis and molecular docking https://www.biorxiv.org/content/10.1101/2025.11.20.689638v1

PertAdapt: Unlocking Single-Cell Foundation Models for Genetic Perturbation Prediction via Condition-Sensitive Adaptation https://www.biorxiv.org/content/10.1101/2025.11.21.689655v1

cpiVAE: Robust and Interpretable Cross-Platform Proteomics Imputation https://www.biorxiv.org/content/10.1101/2025.11.20.689433v1

On the Comparison of LGT networks and Tree-based Networks https://www.biorxiv.org/content/10.1101/2025.11.20.689557v1

ARCADIA Reveals Spatially Dependent Transcriptional Programs through Integration of scRNA-seq and Spatial Proteomics https://www.biorxiv.org/content/10.1101/2025.11.20.689521v1

SpaTRACE: Spatiotemporal recurrent auto-encoder for reconstructing signaling and regulatory networks from spatiotemporal transcriptomics data https://www.biorxiv.org/content/10.1101/2025.11.20.689569v1

Diffusion-based Representation Integration for Foundation Models Improves Spatial Transcriptomics Analysis https://www.biorxiv.org/content/10.1101/2025.11.20.689624v1

Inferring and Evaluating Network Medicine-Based Disease Modules with Nextflow https://www.biorxiv.org/content/10.1101/2025.11.20.687681v1

Analyzing the Performance of Deep Learning Splice Prediction Algorithms https://www.biorxiv.org/content/10.1101/2025.11.20.689501v1

A frameshift mutation in the methyltransferase rlmN is associated with increased linezolid resistance in Mycobacterium tuberculosis https://www.biorxiv.org/content/10.1101/2025.11.20.689544v1

CAcnesDB: A database of Cutibacterium acnes with Integrated Functional Insights derived from Multi-modal Genome Annotation https://www.biorxiv.org/content/10.1101/2025.11.20.689451v1

Generating Hybrid Proteins with the MSA-Transformer https://www.biorxiv.org/content/10.1101/2025.11.20.689447v1

A Global Discovery of Antimicrobial Peptides in Deep-Sea Microbiomes Driven by an ESM-2 and Transformer-based Dual-Engine Framework https://www.biorxiv.org/content/10.1101/2025.11.20.689422v1

IRCAS: a novel end-to-end approach to identify, rectify and classify comprehensive alternative splicing events in a transcriptome without genome reference https://www.biorxiv.org/content/10.1101/2025.11.20.689457v1

ybyra: Y-chromosome haplogroup calling using a tree-based scoring method https://www.biorxiv.org/content/10.1101/2025.11.20.689455v1

Zygosity-Aware DNA Language Modeling Improves Ancestry and Gene Expression Prediction https://www.biorxiv.org/content/10.1101/2025.11.19.689326v1

Systematic evaluation of peptide property predictors with explainable AI technique SHAP https://www.biorxiv.org/content/10.1101/2025.11.19.689259v1

Semantic-Aware Graph Embedding Approach Uncovers LC-61, a Potent Anti-Leishmania infantum Compound https://www.biorxiv.org/content/10.1101/2025.11.19.687645v1

Puget predicts gene expression across cell types using sequence and 3D chromatin organization data https://www.biorxiv.org/content/10.1101/2025.11.19.689320v1

The Rayleigh Quotient and Principal Component Analysis I https://www.biorxiv.org/content/10.1101/2025.11.19.689125v1

sc4D: spatio-temporal single-cell transcriptomics analysis through embedded optimal transport identifies joint glial response to Alzheimer's disease pathology https://www.biorxiv.org/content/10.1101/2025.11.19.689166v1

SHEST: Single-cell-level artificial intelligence from haematoxylin and eosin morphology for cell type prediction and spatial transcriptomics reconstruction https://www.biorxiv.org/content/10.1101/2025.11.19.689364v1

Pseudotimecascade visualizes gene expression cascade in pseudotime analysis https://www.biorxiv.org/content/10.1101/2025.11.19.689263v1