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Active Learning framework for Antibody Binding Affinity Prediction

This paper benchmarks a Gaussian process active learning framework for antibody-antigen binding affinity prediction, showing significant improvements over random selection.

Computational Profiling and Pathogenicity Assessment of VHL Missense Mutations

This study assesses the pathogenicity of VHL missense mutations using AlphaMissense, protein stability simulations, and molecular dynamics to identify critical regions and mutation effects.

msallsearchpy: Universal Search Engine with Enhanced Performance for High-Flow Quantitative LC-MS Proteomics

The paper introduces msallsearchpy, a search engine for high-flow quantitative LC-MS proteomics, showing improved identification and quantification performance over existing methods.

How AlphaFold 3 helps with multiscale drug discovery

This study benchmarks AlphaFold 3's interaction scores against BANDOCK+ for drug discovery, showing AF3's slightly better performance in disease ranking but BANDOCK+'s broader coverage.

NuFold RNA Structure Database: Large-Scale RNA Tertiary Structure Prediction with Confidence Metrics

The paper introduces NuFold, a tool for large-scale RNA tertiary structure prediction, and provides a database with precomputed structures and confidence metrics.

General Purpose AI for Public Data Analysis and Experimental Hypothesis Generation

The paper demonstrates how general-purpose AI can analyze public molecular datasets to generate hypotheses and identify biological relationships, though not all findings were validated experimentally.

Pose: a pure-NumPy, chirality-aware, structural engine for building and manipulating the molecular structures of proteins, nucleic acids, and small organic molecules

Pose is a Python library for molecular structure manipulation that handles chirality and matches existing tools in energy and docking accuracy.

LiverHomo: An Integrated and Interactive Human Liver Single-Cell Atlas with Protein Interaction and Cell-Cell Communication Networks

LiverHomo integrates human liver scRNA-seq data with PPI and cell-cell communication networks to provide an interactive resource for exploring liver health and disease.

A prediction-interval framework for identifying outlier control cohorts in lifespan studies

The paper develops a prediction-interval framework to identify outlier control cohorts in lifespan studies using data from the National Institute on Aging Interventions Testing Program.

Using Arabian Sea Coastal Water as a Model to Study Plasmid-mediated AMR Dissemination driven by Anthropogenic Impacts

The paper studies AMR dissemination in Arabian Sea coastal waters, identifying diverse plasmid replicons and clinically relevant antibiotic resistance genes linked to anthropogenic stressors.

MutaStruct: Revisiting Benchmarks for Single-Site Mutation-Induced Structural Change Prediction

The paper introduces MutaStruct, a curated benchmark for evaluating mutation-induced structural changes, showing that overall structural fidelity does not guarantee accurate modeling of mutation effects.

SpacePath enables pathway and molecular-family analysis beyond annotation ambiguity in spatial metabolomics and lipidomics

SpacePath improves spatial metabolomics analysis by handling molecular ambiguity and identifying novel lipid families in spatial datasets.

MorphoDeep enables fast 3D cell instance segmentation by learning cell interfaces and junctions

MorphoDeep improves 3D cell segmentation by learning cell interfaces and junctions, achieving higher accuracy and speed than existing methods.

EG-BINN: Parameter-Efficient Ensembling of Gated Biologically Informed Neural Networks for Epigenetic Age Estimation

EG-BINN improves epigenetic age estimation by combining parameter-efficient ensembling of biologically informed neural networks with sample-specific gating, achieving lower error rates than existing methods.

Decoding Cell-level Circadian Phase and Rhythm-state Remodeling in Single-cell Transcriptomes With scRhythmBayes

scRhythmBayes infers cell-level circadian phase and rhythm-state remodeling in single-cell transcriptomes, revealing distinct temporal patterns in liver zonation and heart disease.

Cell-level integration of gene expression and B cell receptor data captures complementary B cell information

The paper integrates gene expression and B cell receptor data to capture complementary B cell information, revealing substructure supported by both transcriptional and receptor features.

Optimizing Cognitive Phenotyping for Genetic Discovery in Alzheimer's Disease: A Simulation-Based Evaluation of Mini-Mental State Examination-Based Decline Measures

The paper evaluates cognitive decline measures for genetic studies in Alzheimer's disease using simulations, finding that simpler measures like Slope and dMMSE/dt are more powerful.

GeoSinkhorn Flow: Geometry-Aware Flow Matching for Perturbation-Conditioned Dynamics in Single cell Data Phenoscapes

GeoSinkhorn Flow converts static phenoscapes into dynamic ones by learning perturbation-conditioned transport trajectories that respect the phenoscape's geometry and generalize to unseen conditions.

Benchmarking Molecular Methods of Protein Engineering and Surveying Protein Search Space to Bolster Artificial Intelligence-Based Designs

The paper benchmarks molecular methods for protein engineering and evaluates AI-based designs by comparing mutagenesis and phenotypic screening of a fluorophore.

Towards a Unified Framework for Protein Interaction Site Prediction Using Hierarchical Protein Representations

PRIME-ISP predicts interaction sites across diverse biomolecular interactions using a hierarchical structural framework, outperforming sequence-based methods and matching specialized approaches without task-specific features.