SoluProtMut: Siamese Deep Learning for Predicting Solubility Effects of Protein Mutations with Experimental Validation [new] Siamese DNN predicts mutation impact on protein solubility via deep mutational scanning data.

Identification of KKL-35 as a novel carnosine dipeptidase 2 (CNDP2) inhibitor by in silico screening [new] KKL-35: CNDP2 inhibitor (cancer), favorable drug properties.

Fusing Sequence Motifs and Pan-Genomic Features: Antimicrobial Resistance Prediction using an Explainable Lightweight 1D CNN - XGBoost Ensemble [new]

Augmented prediction of multi-species protein--RNA interactions using evolutionary conservation of RNA-binding proteins [new] DL predicts cross-species RBP-RNA interact., enabling variant effect quant. w/ conservation & label smooth.

multiDEGGs: a multi-omic differential network analysis package for biomarker discovery and predictive modeling [new] Analyzes multi-omic data via differential networks for biomarker discovery, visualization, & predictive modeling.

Modeling protein-small molecule conformational ensembles with PLACER [updated] Models protein-ligand interactions at the atomic level using a graph neural network, enabling rapid generation of conformational ensembles.

BindFlow: a free, user-friendly pipeline for absolute binding free energy calculations using free energy perturbation or MM(PB/GB)SA [new]

The AlphaFold Database Ages [updated] AlphaFold DB: ...needs updating as entries conflict with newer UniProt releases, showing bioinformatics databases' rapid obsolescence.

P-KNN: Maximizing variant classification evidence through joint calibration of multiple pathogenicity prediction tools [new] Jointly calibrating tools maximizes classification evidence, enabling flexible use.

SOFT METROPOLIS-HASTINGS CORRECTION FOR GENERATIVE MODEL SAMPLING [new] MH correction addresses biases in molecular diffusion models. It uses continuous interpolation for smoother, chemically-valid structure generation.

It is Not Always Crystal Clear: In-Pocket Analysis for Understanding Binding Site Microenvironment Properties [new] QM optimizes protein-ligand binding, fixes structural ambiguities, improves model quality.

LoFT-TCR: A LoRA-based Fine-tuning Framework for TCR-Antigen Binding Prediction [new] TCR-antigen binding via LoRA, seq+struct data & graph learning.

Fine-tuning sequence to function deep learning models on large-scale proteomic data improves the accuracy of variant effect prediction [new]

Interpretable deep generative ensemble learning for single-cell omics with Hydra [updated] DL enables robust single-cell omics analysis.

Small Molecule Approach to RNA Targeting Binder Discovery (SMARTBind) Using Deep Learning Without Structural Input [new] Deep learning + contrastive learning predicts RNA-binding molecules from seq only, no structure needed.

Predicting Protein Crystal Solvent Content from Patterson Maps Using Machine Learning [new] ML predicts solvent content using Patterson Maps; novel structure ID clustering shown.

Bridging Evolution and Design: Mapping the Diversity of LOV Photosensors [new] LOV domain photodynamics across evolution reveal kinetic diversity matching physiological roles. AI design expands the natural sensor catalog.

HRDPath: An Explainable Multi-Model Deep Learning Architecture for Predicting Homologous Recombination Deficiency from Histopathology Images [new]

VECTOR: A Framework to Identify and Quantify Structural Changes in Chromatin using Hi-C Data [new] Hi-C chromatin org. via Von Neumann entropy & spectral theory. Structural patterns for comparative analysis.

ProteinDJ: a high-performance and modular protein design pipeline [new] ProteinDJ: modular, scalable protein design pipeline for HPC; parallel deep learning yields high-throughput binders.

A molecular stabiliser of an inhibitory eIF2B-eIF2(αP) complex activates the Integrated Stress Response][new] Novel compound stabilizes eIF2B-eIF2(αP), allosterically inhibiting eIF2B, and activating ISR.

Ciprofloxacin resistance in Klebsiella pneumoniae: phenotype prediction from genotype and global distribution of resistance determinants [new]

Physics-Informed Neural Networks for Real-Time Deformation-Aware AR Surgical Tracking [new] Physics-informed NNs enhance AR surgery tracking using biomechanics for plausible deformation prediction.

Steering Vector Fields for Property-Controlled Molecular Generation with Chemical Language Models [new] Steering Vector Fields use global/state vectors in Chemical Language Models for molecule generation & property control.

A Novel MiRNA Detection System Combining TWJ-SDA,Multistep L-TEAM, and CRISPR-Cas3 [new] TWJ-SDA, L-TEAM, CRISPR-Cas3: sens., spec. miRNA detect. ML optimizes seq. design.

MechFind: A computational framework for de novo prediction of enzyme mechanisms [new] Predicts enzyme mechanisms from reaction stoichiometry alone. It identifies plausible, elementally-balanced step-by-step reaction pathways.

Sensitive, direct detection of non-coding off-target base editor unwinding and editing in primary cells [new] Direct seq. quantifies off-target base editor & DNA unwinding.

Detecting gene-environment interactions to guide personalized intervention: boosting distributional regression for polygenic scores [new] GxE model: variance-linked SNPs via boosting to personalize interventions.

Screen-VarCal: An Interpretable Probabilistic Framework for Recalibrating ACMG Rule-Based Variant Classification in Preventive Medicine [new]

Integrative Spatial Modelling of Cellular Plasticity using Graph Neural Networks and Geostatistics [new] GNNs & geostatistics predict cell state variation in spatial transcriptomics.

Pocket-based molecule generation with an SE(3)-equivariant language model leads to a potent and selective HPK1 inhibitor with in vivo efficacy [new]

Incorporating LLM Embeddings for Variation Across the Human Genome [new] LLM embeddings create variant-level representations of the entire human genome, capturing semantic descriptions for billions of variants.

A Genetic Algorithm for Navigating Synthesizable Molecular Spaces [new] Navigating Synthesizable Molecular Spaces: Genetic algorithm explores synthesis routes for analog search & property optimization, ensuring synthesizability.

Data-driven Neural Networks for Windkessel Parameter Calibration [new] Calibrates Windkessel parameters by training a neural network on simulated blood pressures. Assesses robustness against location uncertainty and noise.

SlideMamba: Entropy-Based Adaptive Fusion of GNN and Mamba for Enhanced Representation Learning in Digital Pathology [new] SlideMamba: Adaptive GNN+Mamba fusion for pathology. Uses entropy to capture local/global WSI dependencies, enhancing analysis.

Exploring Augmentation-Driven Invariances for Graph Self-supervised Learning in Spatial Omics [new] Graph SSL spatial omics: Augmentations impact embedding quality (un/supervised tasks).

DeepSpot2Cell: Predicting Virtual Single-Cell Spatial Transcriptomics from H&E images using Spot-Level Supervision [new] Pred. sc gene expr. via DeepSet & spot sup. for spatial transcriptomics.

CIRCE: a scalable Python package to predict cis-regulatory DNA interactions from single-cell chromatin accessibility data [new] CIRCE: Efficient cis-regulatory interaction prediction from scATAC-seq via improved Cicero.

The structural context of mutations in proteins predicts their effect on antibiotic resistance [new] Protein struct. predicts mut. effects on antibiotic resistance. Mut. clustering indicates resistance.

Simulation-Based Inference of Cell Migration Dynamics in Complex Spatial Environments [new] Cell migration analysis via Potts models & neural estimation.

Chromatin and gene-regulatory dynamics of human pulmogenesis by single cell multiomic sequencing [new] Pulmogenesis needs gene regulation. scATAC-seq & RNA-seq show clusters, elements, & links defining dynamic programs.

Domain-Invariant Feature Learning for Patient-Level Phenotype Prediction from Single-Cell Data [new] scRNA-seq disease prediction generalizes poorly; adversarial MIL learns robust representations.

Peptide molecular glues select between BET paralogues by exploiting allosteric sites and conformational dynamics [new] mRNA display gave cyclic peptides, highly selective for BRD2/4 via allosteric glue mech.

Genetically encoded RNA strand exchange circuits for programmable protein expression and computation in cells [new] Genetically encoded RNA circuits control protein expression in cells. Design principles transferable from in vitro.

BioBO: Biology-informed Bayesian Optimization for Perturbation Design [new] Uses gene embeddings and enrichment analysis within Bayesian optimization to guide perturbation design. Provides mechanistic insights.

How many crystal structures do you need to trust your docking results? [new] Accurate drug docking needs crystal struct. Template docking via mol. similarity helps w/ ltd. data.

A co-evolving agentic AI system for medical imaging analysis [new] Enables researchers to query, plan workflows, and refine results in real-time across imaging modalities. Continuously learns from expert feedback.

PGCLODA: Prompt-Guided Graph Contrastive Learning for Oligopeptide-Infectious Disease Association Prediction [new] Oligopeptide-disease assoc. via contrastive learning on tripartite graph.

ppIRIS: deep learning for proteome-wide prediction of bacterial protein-protein interactions [new] Leverages deep learning on sequence data to predict bacterial and cross-species protein-protein interactions proteome-wide.

Mapping Risk and Resilience Across Indo-Pacific Reefs with Shark Genomescapes [new] Uses shark genomes to assess population health, connectivity, and geographic origins. Enables traceability of illegally fished sharks.