Stephen M. Mount

Qombucha infers unobserved progenitor methylation profiles in GBM, revealing subtype-specific developmental programs and improved subtype classification.

The paper identifies sequence features associated with recursive splicing and develops a classifier to detect these features.

The paper introduces FveOCRs, a database that predicts open chromatin regions in wild strawberry using a large language model, and allows predictions for any plant species.

This paper introduces FALAFL, a fair feature selection algorithm for single-cell methylation data, identifying universally tumor lineage-informative CpG sites in colorectal cancer.

The paper applies a kinetic proofreading model to elucidate how transient U2AF binding leads to high fidelity splice site selection.

This paper applies Latent Dirichlet Allocation to nucleotide sequences to identify motifs and subtypes, showing its utility in characterizing heterogeneous signals and discovering regulatory factors.

scCensus evaluates off-target scRNA-seq reads and shows they contain valuable information about chromatin structure, antisense transcription, and cell clustering.

The paper evaluates splicing prediction methods on 56 clinically validated variants, finding some methods match or exceed SpliceAI's performance but highlighting ongoing challenges in accuracy.

This paper introduces Sgootr, a method to infer tumor lineage trees from single-cell methylation data, revealing metastatic progression models and identifying lineage-informative CpG sites.

This paper presents the first draft genome assembly and annotation of the red raspberry Rubus idaeus, providing a valuable resource for research and breeding.

Yanagi segments transcriptomes to enable fast and interpretable analysis of alternative splicing and gene-level expression using pseudo-alignment.