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RiboGRAM learns multi-scale non-coding RNA grammar for structural and regulatory inference

The paper introduces RiboGRAM, a model that learns non-coding RNA sequence grammar for structural and regulatory inference across multiple organisms.

DIMPLE: A Tree-Guided Divide-and-Conquer Framework for ILS-Aware Phylogenetic Network Inference on Large-Scale Data

DIMPLE infers phylogenetic networks from large-scale data using a divide-and-conquer approach, achieving accurate merging and improved reticulation recovery over existing methods.

Pan-cancer nucleosome landscapes reveal tumor heterogeneity and inform cell-free DNA-based detection

The paper characterizes nucleosome organization across 23 cancer types using ATAC-seq and shows its utility for cancer classification and detection using cell-free DNA.

Latent-Factor Stability Is Not Sufficient: Evaluating SABLE-MO in Simulated and Cancer Multi-Omics Data

The paper evaluates SABLE-MO's performance in identifying shared factors in multi-omics data, finding that stricter retention reduces errors but does not eliminate them.

Relation-Aware Graph-Hypergraph Networks for Antibody Sequence-Structure Co-Design

This paper introduces RA-GHN, a framework for antibody sequence-structure co-design that captures multi-body interactions and structural constraints, outperforming existing methods.

PlasmoRhythm: A comprehensive database for malaria-associated rhythmic transcripts, proteins, and metabolites

PlasmoRhythm integrates time-resolved omics data from malaria parasites, hosts, and vectors to enable comparative analysis of rhythmic molecular profiles.

Metalink: Joint taxonomic and functional profiling of metagenomes and metatranscriptomes across resolution scales

Metalink integrates taxonomic and functional profiling across resolution scales in metagenomes and metatranscriptomes, improving accuracy and enabling mechanistic insights.

Distance-AF Multimer: A Multi-Step Approach for Protein Complex Structure Modeling with User-Defined Distance Constraints

Distance-AF Multimer improves protein complex structure prediction by incorporating user-defined residue distance constraints, achieving competitive or better performance than existing methods.

CAPO: Compute-Aware Automated Protein-Model Optimization

CAPO automates and selects protein-model adaptations by measuring feasibility and cost before training, improving performance while reducing compute usage and failures.

DeepD enables efficient genome modeling and controllable long-context sequence generation across domains of life

DeepD is a genome foundation model that enables accurate sequence-to-function prediction and controllable genome-scale sequence generation across domains of life.

Scalable Enzyme Reaction Retrieval Enables Metagenomic Biocatalyst Discovery

EzHit retrieves enzyme-reaction associations efficiently, outperforming baselines and enabling large-scale metagenomic biocatalyst discovery.

Hierarchical distribution matching enables comprehensive characterization of common and condition-specific cell niches in spatial omics data

This paper introduces Harmonics, a framework for identifying common and condition-specific cell niches in spatial omics data, demonstrating its effectiveness across diverse datasets and diseases.

An integrated database of ion channels

The paper introduces IDIC, a database integrating information on human ion channels and their disease associations, providing annotations and cross-references to biological resources.

MetaDome 2027: a comprehensively updated resource for aggregating missense variant evidence across homologous human protein domains

MetaDome now supports GRCh38 alongside GRCh37, adds coordinate lookup, and identifies 52,463 GRCh38 ClinVar missense variants of uncertain significance with uncontradicted pathogenic evidence at homologous Pfam-domain positions.

LigRNA: High-accuracy prediction of RNA-ligand binding sites via dynamic chemical complementarity and language model encoding

LigRNA predicts RNA-ligand binding sites using a graph neural network that combines language model embeddings and physicochemical features, achieving improved performance over existing methods.

Order Matters: Ambient RNA correction confounds doublet detection in single-cell RNA sequencing

This study shows that ambient RNA correction can reduce doublet detection accuracy and recommends detecting doublets before correction, except when using CellBender.

SubcellPert: Benchmarking Subcellular Perturbation Prediction

SubcellPert benchmarks subcellular perturbation prediction using imaging data, showing Gaussian transport achieves low spatial error in out-of-distribution datasets.

PATHNet: A Thermodynamic Path-Integral-Inspired Neural Network for Protein-Ligand Interaction Prediction

PATHNet improves protein-ligand interaction prediction by combining physics-inspired modeling with neural networks, achieving high accuracy across multiple targets.

Warmth shifts rather than speeds transcriptomic ageing in the malaria mosquito Anopheles gambiae

The paper shows that warming shifts the transcriptomic age of Anopheles gambiae mosquitoes to an older state without accelerating their ageing pace.

Scale-resolved correlation functions unify spatial omics across platforms and resolutions

SCOTE quantifies spatial relationships across all length scales in spatial omics data, revealing biological insights while distinguishing platform artifacts.