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This paper introduces EvoBind-multimer, a deep learning framework for designing molecular glues from protein sequences, demonstrating its ability to recruit E3 ligases to oncoproteins and showing context-dependent functionality.

The paper maps pathogenicity patterns in GLUT transporters by analyzing missense mutations and their structural impact across the family.

BindCORE improves prediction of interaction sites in intrinsically disordered regions by integrating biophysical ensemble features, outperforming sequence-based methods.

GaugeFixer is a Python package that efficiently fixes gauge freedoms in sequence-function models, enabling faster and more scalable analysis of large parameter sets.

The paper introduces methods to scale up the Human Reference Atlas by aligning tissue datasets across reference systems and using millitomes for bulk registration.

Protal provides ultra-fast, strain-resolved metagenomic profiling with high precision, outperforming existing tools in both species and strain-level analysis.

The paper introduces a method to perform set operations on k-mers using compacted representations, achieving efficient memory usage and high throughput.

The paper develops a workflow combining XGBoost rank aggregation and SVM-RFECV to identify compact, interpretable biomarker panels from small-sample microarray datasets.

FusedFCR identifies marker genes associated with developmental transitions in time-course scRNA-seq data by combining lasso and fusion penalties for interpretable gene selection.

This study evaluates IUPAC consensus references for improving variant detection in challenging genomic regions using a stratified benchmarking framework called BurdenBench.

VIProDesign is a computational tool that designs viral protein panels to balance diversity and size, enabling better evaluation of immune responses and identification of broadly neutralizing antibodies.

The paper introduces a matrix framework to map directional entropy transfer in proteins by incorporating continuous distance-dependent weighting into the Kirchhoff matrix, applied to KRAS to identify allosteric communication pathways.

The paper identifies dysregulated pathways and candidate driver genes in skeletal muscle from individuals with type 2 diabetes using co-expression networks and single-nucleus RNA-seq data.

The paper introduces arteMIS, a framework for optimizing molecular network parameters in metabolomics, showing improved network quality over default settings.

RIFT-VAE improves RNA inverse folding by combining grammar-conditioned pretraining with latent-space optimization, achieving high structural recovery on benchmark datasets.

IsoAtlas provides an interactive database for visualizing and interpreting transcript isoforms using long-read RNA-seq data from humans and mice.

The paper evaluates LLM-generated phenotype-genotype associations using external validation, finding 74.19% match genomic knowledge bases with varying support levels.

The paper presents a pipeline for longitudinal plant disease phenotyping using time-series imaging, enabling objective quantification of disease progression in wheat rusts.

LongOmicsTraj provides a topology-based framework to represent and query longitudinal omics trajectories, identifying corticosteroid response genes with temporal patterns across treatment groups.