Thom Cuddihy

The paper identifies new protein-coding sequences in E. coli using transposon mutagenesis and translation reporters, revealing previously unannotated genes.

SCIFR is a single-file interactive reporting framework that improves efficiency and usability compared to existing tools in genomics analysis.

This paper benchmarks six microbial SNP calling pipelines using multiple datasets, highlighting the variability in performance and the need for standardized benchmarking.

ScrepYard is an online resource for identifying and characterizing SCREP sequences, revealing structural features of multivalent peptides and demonstrating its utility in virtual screening.