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The paper investigates how fluoxetine treatment affects ADAR editing and transcriptome regulation in Arid1b +/- mice, showing site-specific editing changes and impacts on miRNA-mRNA interactions.

ResolVI improves spatial transcriptomics by correcting molecule misassignment and batch effects, enhancing cell state distinction and cross-dataset integration.

The paper evaluates multi-omics prognostic models across TCGA-BRCA and METABRIC, finding limited incremental performance and highlighting issues with model transportability and feature stability.

This paper introduces nCycle-Forge, a computational method for designing cyclic peptides that outperforms existing approaches in hit rate and potency against two targets.

CardioChrom reconstructs chromatin accessibility and histone modifications from single-nucleus RNA data in human heart failure, improving prediction accuracy and identifying regulatory changes in endothelial cells.

The paper detects putative Cyclospora cayetanensis in wastewater metagenomic data using 31-mers, finding 3.5% of runs positive and seasonal patterns matching cyclosporiasis.

EPIC challenges teams to predict transcription initiation from DNA sequence in non-model metazoans, aiming to assess generalizability beyond human and model species.

MOTLAB improves breast cancer outcome prediction in underrepresented Black women by integrating multi-omics data with transfer learning and weighting strategies.

MoTRUST integrates mosaic single-cell multi-omics data and recovers missing molecular information, achieving top performance in integration and recovery tasks.

singIST compares disease model scRNA-seq data to human references to assess recapitulation at superpathway, cell type, and gene levels.

Minerva extracts RNA base-pairing, protein-contact and repeat maps from a genome language model without alignments, flagging unannotated structured loci and a phage ncRNA array reverse-transcribed into short cDNAs.

NeoToxPred improves toxicity classification by using a protein language model with carefully curated negative controls, outperforming existing methods on both internal and external benchmarks.

PICARD-seq enables rapid, affordable whole-plasmid sequencing using nanopore technology, improving accuracy and resolving repetitive regions in synthetic constructs.

FedEdgeR enables federated differential gene expression analysis while preserving privacy, outperforming meta-analysis methods and matching pooled edgeR results.

ASOFormer predicts ASO efficacy using sequence, structure, and modification features, outperforming existing methods in accuracy and candidate prioritization.

The paper presents a physics-based method to predict single mutation effects on protein-protein binding affinity using MMPBSA calculations and evaluates its performance on SARS-CoV-2 and Armadillo-repeat systems.

Boltz2-Notebook provides an accessible Colab interface for using the Boltz2 model to predict biomolecular structures and binding affinities, with benchmarking of its performance on protein-ligand pairs.

ARSA generates evidence-based target shortlists for Alzheimer's disease and related dementias by integrating natural language research interests with molecular data and cross-cohort evidence.

sRNAMap is a browser-based tool for analyzing and visualizing small RNA sequencing data, offering alignment, coverage, and feature quantification with high concordance to existing methods.