Discover, rate, and discuss biology preprints.

Pixel2Gene improves spatial gene expression reconstruction and prediction by integrating histology images with spatial transcriptomics data.

The paper assesses peptide proteotypicity in-house for targeted proteomics by synthesizing and verifying peptides from three plasma proteins.

The paper analyzes the secretome of Zymoseptoria passerinii to show that conserved protein folds support functional diversification of effector-like proteins through local physicochemical variation.

The paper develops a scalable workflow to reclassify variants of uncertain significance using experimental and predictive evidence, resolving 75% of VUS in 40 genes.

REMAP reconstructs spatial tissue architecture from scRNA-seq using deep learning and ST references, revealing microenvironmental features and cancer subtypes.

The paper introduces CLADES, a contrastive learning method for differential splicing prediction using orthologous positive pairs, achieving strong performance in classification and regression tasks.

This study identifies new regulators of heat hormesis in C. elegans through transcriptomic and chromatin accessibility analysis, revealing tissue-specific responses and conserved factors involved in stress resilience and longevity.

This study uses a simulation framework to analyze how Neanderthal ancestry gradients in Europe were shaped by population expansions and interactions between Neanderthals, hunter-gatherers, and farmers.

This study develops a computational model of aneuploid karyotype dynamics in budding yeast, revealing that reversion mechanisms vary by chromosome and can involve coupled nondisjunction and recombination.

The paper validates a method to generate genome-wide polymorphism datasets from individual hookworm larvae, showing that accurate variant calling is possible with sufficient DNA input and strict filtering.

The paper traces the evolutionary history of Xanthomonas oryzae pv. oryzae in Africa, showing its adaptation to African rice and how the introduction of Asian rice shaped its population structure.

This study benchmarks donor-specific assemblies for improved detection of somatic structural variants in a melanoma cell line, finding they identify more variants, especially in repeat-rich regions.

The paper identifies ultra-conserved CpGs associated with ageing-related methylation changes and developmental pathways in the brain.

This study uses FFPE-compatible Hi-C to detect enhancer-hijacking rearrangements in lymphoid cancers, identifying clinically relevant drivers missed by standard methods.

This paper improves eccDNA enrichment and amplification methods, achieving >50% overlap in technical replicates compared to <1% previously observed.

This paper introduces an NLP-based method to predict RBP binding motifs, contexts, and interactions, identifying novel motifs and RBP-RBP interactions in HepG2 and K562 cells.

Portello improves variant calling accuracy in rare-disease whole genome sequencing by aligning de novo assembly contigs to a reference genome, reducing basecall errors and enabling better interpretation of complex loci.

APEX infers cancer gene expression from plasma cfChIP-seq data, outperforming existing methods and enabling subtype classification and biomarker identification.

OncoBERT models somatic mutations in cancer to identify patient-specific subtypes and improve prediction of treatment response by integrating mutational context with clinical biomarkers.