MLDAAPP: machine learning data acquisition for assessing population phenotypes https://academic.oup.com/g3journal/article/doi/10.1093/g3journal/jkaf173/8220571

Genomic and hyperspectral imaging-based prediction blending enables selection for reduced deoxynivalenol content in wheat grains https://academic.oup.com/g3journal/article/doi/10.1093/g3journal/jkaf176/8223452

MyESL: A Software for Evolutionary Sparse Learning in Molecular Phylogenetics and Genomics https://academic.oup.com/mbe/article/doi/10.1093/molbev/msaf224/8254024

Interpreting Supervised Machine Learning Inferences in Population Genomics Using Haplotype Matrix Permutations https://academic.oup.com/mbe/article/doi/10.1093/molbev/msaf250/8276164

Modelling transcription with explainable AI uncovers context-specific epigenetic gene regulation at promoters and gene bodies https://journals.plos.org/plosgenetics/article

Screening of Oyster Peptides for Anti-Muscle Atrophy Based on Machine Learning and Computer Simulation: Guided by Antioxidant Pathways https://www.biorxiv.org/content/10.1101/2025.10.28.685008v1

DCBK: A Fragment-Based Hybrid Simulation and Machine Learning Framework for Predicting Ligand Dissociation Kinetics https://www.biorxiv.org/content/10.1101/2025.11.01.685950v1

Oyster: a neural network for modelling genomic sequences that enables exact position-specific k-mer contributions https://www.biorxiv.org/content/10.1101/2025.11.01.686014v1

PRSformer: Disease Prediction from Million-Scale Individual Genotypes https://www.biorxiv.org/content/10.1101/2025.10.26.684578v1

Genomic Prediction and SNP Importance Analysis for Agronomic Traits in Two Coffea canephora Populations https://www.biorxiv.org/content/10.1101/2025.10.31.685932v1

A spatiotemporal analysis of the effect of urbanization on birdsong https://www.biorxiv.org/content/10.1101/2025.10.30.685579v1

Generative models for antimicrobial peptide design: auto-encoders and beyond https://www.biorxiv.org/content/10.1101/2025.10.29.685317v1

ProteinSight: A Volumetric Deep Learning Model for Carotenoid-Binding Site Prediction https://www.biorxiv.org/content/10.1101/2025.10.30.685633v1

ProAffinity++ https://www.biorxiv.org/content/10.1101/2025.10.31.685718v1

LINKER-Pred: A Public Web Server for Accurate Prediction of Disordered Flexible Linkers in Proteins https://www.biorxiv.org/content/10.1101/2025.10.29.685455v1

iDeepLC: chemical structure information yields improved retention time prediction of peptides with unseen modifications https://www.biorxiv.org/content/10.1101/2025.10.31.685771v1

Clair-Mosaic: A deep-learning method for long-read mosaic small variant calling https://www.biorxiv.org/content/10.1101/2025.10.31.685831v1

An Application for Automated Drosophila Locomotor Assay with Integrated Device Design and Computer Vision Tracking https://www.biorxiv.org/content/10.1101/2025.10.31.685789v1

Limitations of current machine learning models in predicting enzymatic functions for uncharacterized proteins https://academic.oup.com/g3journal/article/doi/10.1093/g3journal/jkaf169/8211502

MLDAAPP: machine learning data acquisition for assessing population phenotypes https://academic.oup.com/g3journal/article/doi/10.1093/g3journal/jkaf173/8220571

Genomic and hyperspectral imaging-based prediction blending enables selection for reduced deoxynivalenol content in wheat grains https://academic.oup.com/g3journal/article/doi/10.1093/g3journal/jkaf176/8223452

Fast and Memory-Efficient Dynamic Programming Approach for Large-Scale EHH-Based Selection Scans https://academic.oup.com/mbe/advance-article/doi/10.1093/molbev/msaf275/8303545

MyESL: A Software for Evolutionary Sparse Learning in Molecular Phylogenetics and Genomics https://academic.oup.com/mbe/article/doi/10.1093/molbev/msaf224/8254024

Interpreting Supervised Machine Learning Inferences in Population Genomics Using Haplotype Matrix Permutations https://academic.oup.com/mbe/article/doi/10.1093/molbev/msaf250/8276164

Modelling transcription with explainable AI uncovers context-specific epigenetic gene regulation at promoters and gene bodies https://journals.plos.org/plosgenetics/article

IRIS: A Machine Learning-Based Pose Re-Ranking Tool for RNA-Ligand Docking https://www.biorxiv.org/content/10.1101/2025.10.24.684232v1

Quantifying the impact of genetic mutations on enhancer dynamics https://www.biorxiv.org/content/10.1101/2025.10.21.683558v1

Bibliometric Insights into Medical Data Science Applications in Genomics: Evidence from Kaggle and Dimensions Datasets https://www.biorxiv.org/content/10.1101/2025.10.24.684317v1

Cross-Species Insights from ART-D to Uncover Evolutionarily Conserved Oncogenic Mechanisms https://www.biorxiv.org/content/10.1101/2025.10.20.683390v1

Benchmarking Perturbation Tools for the Noncoding Genome https://www.biorxiv.org/content/10.1101/2025.10.21.683665v1

Gradient-based Optimization for mRNA Sequence Design https://www.biorxiv.org/content/10.1101/2025.10.22.683691v1

Accurate protein structure determination from cryo-EM maps using deep learning and structure prediction https://www.biorxiv.org/content/10.1101/2025.10.23.684082v1

Histology-informed spatial domain identification through multi-view graph convolutional networks https://www.biorxiv.org/content/10.1101/2025.10.23.683862v1

A novel attention mechanism for noise-adaptive and robust segmentation of microtubules in microscopy images https://www.biorxiv.org/content/10.1101/2025.10.23.684152v1

M-DeepAssembly2: A Web Server for Predicting Multiple Conformations of Multi-domain Proteins Using Deep Learning https://www.biorxiv.org/content/10.1101/2025.10.23.684122v1

Universal super-resolution for subcellular fluorescence imaging https://www.biorxiv.org/content/10.1101/2025.10.26.683961v1

Limitations of current machine learning models in predicting enzymatic functions for uncharacterized proteins https://academic.oup.com/g3journal/article/doi/10.1093/g3journal/jkaf169/8211502

MLDAAPP: machine learning data acquisition for assessing population phenotypes https://academic.oup.com/g3journal/article/doi/10.1093/g3journal/jkaf173/8220571

Genomic and hyperspectral imaging-based prediction blending enables selection for reduced deoxynivalenol content in wheat grains https://academic.oup.com/g3journal/article/doi/10.1093/g3journal/jkaf176/8223452

MyESL: A Software for Evolutionary Sparse Learning in Molecular Phylogenetics and Genomics https://academic.oup.com/mbe/article/doi/10.1093/molbev/msaf224/8254024

New proteomic biomarkers identified in plasma extracellular vesicles in sarcoidosis: a case-control matched study https://www.biorxiv.org/content/10.1101/2025.10.14.682425v1

Lectin Microarray-based Glycomics and Machine Learning Identify Shared Osteoarthritis Biomarkers in Humans, Dogs, and Horses https://www.biorxiv.org/content/10.1101/2025.10.16.682971v1

Integrative metabolome-genome analysis reveals the genetic architecture of metabolic diversity in sorghum grain https://www.biorxiv.org/content/10.1101/2025.10.14.682411v1

Building an epigenetic clock: Utilizing whole genome DNA methylation patterns to predict age in haddock, Melanogrammus aeglefinus https://www.biorxiv.org/content/10.1101/2025.10.16.682892v1

Neural network-based cross-species chromatin annotation goes beyond sequence conservation https://www.biorxiv.org/content/10.1101/2025.10.16.682871v1

Mechanistic Genome Folding at Scale through the Differentiable Loop Extrusion Model https://www.biorxiv.org/content/10.1101/2025.10.17.682904v1

Robust footprinting with sample-specific Tn5 bias correction for bulk and single cell ATAC-seq https://www.biorxiv.org/content/10.1101/2025.10.17.683160v1

MAP-PRS: Multi-Ancestry Portfolio-Based Polygenic Risk Scores https://www.biorxiv.org/content/10.1101/2025.10.15.682516v1

Deep learning the dynamic regulatory sequence code of cardiac organoid differentiation https://www.biorxiv.org/content/10.1101/2025.10.15.680997v1

The persistence and loss of hard selective sweeps amid ancient human admixture https://www.biorxiv.org/content/10.1101/2025.10.14.682443v1