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MOFI reveals dynamic multi-omics coordination during cell fate progression

MOFI reconstructs continuous cell fate transitions from paired multi-omics snapshots across time, revealing coordinated changes in transcriptomic, chromatin, and protein layers.

Antigen-aware TCR embeddings reveal conserved immune patterns for personalized immune monitoring

TCRmeta integrates antigen specificity with TCR repertoires to enable cross-individual and longitudinal immune monitoring by revealing conserved patterns and technical variation robustness.

Biopsy-aware phylogenetic reconstruction from longitudinal single-cell copy number profiles

This paper introduces biopsy-guided methods for phylogenetic reconstruction from longitudinal single-cell copy number profiles, showing improved accuracy over pooled methods in simulated data and demonstrating feasibility in patient-derived data.

NeoOmni Atlas: an integrated database for pan-cancer neoantigen derived from proteogenomics analysis

NeoOmni Atlas integrates proteogenomic data to catalog tumor neoantigens across 26 cancer types, identifying novel ligands and epitopes for immunotherapy.

The Evolving Bileome: A Pan-Repository Landscape of Expanded Bile Acid and Related Steroidal Signatures

The paper expands a bile acid and steroidal MS/MS spectral library across three repositories, capturing diverse structures and providing a resource for classifying unknown spectra.

IsoMatch enables population-scale transcript integration and reveals reference-dependent isoform novelty

IsoMatch integrates transcript models across references, showing how reference choice affects estimates of transcript novelty.

Efficient and precise discovery of LTR-retrotransposon families using HiRepEat

The paper introduces HiRepEat, a method for efficiently discovering and clustering LTR-retrotransposon families across genomes, showing results on vertebrate and Drosophila genomes.

Constructed Negatives Shape the Evaluation of Sequence-Based Protein--Protein Interaction Models

The paper evaluates how different constructed negative examples affect sequence-based protein-protein interaction models, showing significant variability in performance metrics based on negative construction methods.

Optimization of Search and Acquisition Strategies for DSSO Crosslinking Mass Spectrometry using Protein Prospector and Touchstone.

The paper evaluates DSSO crosslinking strategies using Protein Prospector and Touchstone, finding that DSSO's advantage comes from backbone fragmentation, not diagnostic ions, and that MS3 is better for proteome-scale samples.

Hidden introns and repeated gains shape the heavily interrupted tRNA genes of Asgard archaea

The paper identifies and corrects missed introns in tRNA genes of Asgard archaea, revealing repeated intron gains and their splicing motif preferences.

DIPLER: rapid k-mer-based locus identification

DIPLER identifies structurally complex loci using k-mer analysis and de novo assembly from low-coverage sequencing data.

A Benchmark of Unsupervised Circadian Phase Inference Methods for Bulk Transcriptomic Data

This study benchmarks unsupervised circadian phase inference methods on bulk transcriptomic data, finding CHIRAL performs best with lower error than other methods.

Non-exonic read content reorganises lncRNA co-expression networks in renal and other cancers

The paper shows that non-exonic read fractions reorganize lncRNA co-expression networks in renal and other cancers, with varying impacts across cancer types.

DUMMEST: A simpler and faster model for frameshift-aware alignment of a DNA sequence to a protein family

DUMMEST improves frameshift-aware alignment of DNA sequences to protein families by combining simplicity and speed, outperforming existing methods in sensitivity and specificity.

Deciphering Spatial Cellular Organization through RNA-Anchored Multi-Omics Deconvolution

SMODER deconvolves spatial multi-omics data by prioritizing RNA for cell-type identification and integrating other modalities, improving accuracy and spatial coherence.

Cellular proximity and conditional coordination in the colorectal and pancreatic tumor microenvironment: a patient-level analysis of multiplexed imaging

The paper analyzes spatial organization of immune and epithelial cells in colorectal and pancreatic cancers using multiplexed imaging, finding differences in conditional coordination and proximity between disease subtypes.

Alpha Spatial: Language-guided prediction of single-cell spatial gene expression from histology

Alpha Spatial predicts single-cell gene expression from histology using language-guided models, improving accuracy with matched biological context and outperforming existing methods in breast cancer analysis.

A spatial topology atlas of type I myofibers in porcine skeletal muscle reveals local slow-oxidative niches associated with meat quality traits

Systematic evaluation of transcript normalization methods and quantification pipelines across long-read sequencing platforms

The paper evaluates normalization methods and quantification pipelines for long-read RNA sequencing across PacBio and ONT platforms, showing platform-specific impacts on accuracy.

ExpertTwins: Auditable Long Horizon Scientific Panels through Grounded Expertise

ExpertTwins is a framework for auditable scientific deliberation using evidence-based roles, showing high quotation grounding and differentiated reasoning across models and tasks.