Michael Fletcher

Jan 15, 2025 | nature.com | Michael Fletcher

Machine learning models have recently generated excitement for their potential in a broad range of domain applications, including genomics. However, owing to their complexity, they are prohibitively expensive to train for the large genomic contexts of DNA language models, resulting in limited receptive fields and/or n-mer sequence tokenization. Nguyen et al.

Dec 9, 2024 | nature.com | Michael Fletcher

Aspects of single-cell RNA sequencing (scRNA-seq) data, such as its sparsity and high cell–cell variability, have made it hard to apply statistical approaches developed for bulk RNA-seq analyses, such as differential gene expression Kim et al.

Nov 8, 2024 | nature.com | Michael Fletcher

Genome sequencing of large cohorts has identified many protein-coding missense variants, the functional consequences of which remain difficult to predict computationally. Lacoste et al. use a new high-throughput screening approach to characterize the effects of known pathogenic variants on protein localization.

Jul 15, 2024 | nature.com | Michael Fletcher

Tumor somatic mutational signatures offer insights into disease etiology, and such analyses may identify exposures underlying differential cancer incidence between countries. Past work on esophageal cancer did not find major mutational differences, in contrast with a new study by Senkin et al. on clear cell renal carcinoma. Whole-genome sequencing was carried out on 962 clear cell renal carcinomas from 11 countries, mostly European but covering 4 continents.

Jun 13, 2024 | nature.com | Michael Fletcher

Spatial transcriptomic methods are increasingly available for a growing user group. Given the technical similarities between spatial transcriptomics and single-cell RNA sequencing (scRNA-seq), such as measurement sparsity, many spatial transcriptomic bioinformatic approaches have been adopted from those developed for scRNA-seq. However, new technologies often present their own unique issues and pitfalls. Bhuva et al.