Michele Busby

TL;DR: It is found that the RNase H method performed best for chemically fragmented, low-quality RNA, and was confirmed through analysis of actual degraded samples, and can even effectively replace oligo(dT)-based methods for standard RNA-seq.

TL;DR: A direct comparison of MEI and SNP diversity levels suggests a differential mobile element insertion rate among populations, and a comprehensive map of 7,380 MEI polymorphisms from the 1000 Genomes Project whole-genome sequencing data is presented.

TL;DR: This work exploits the modularity of a refactored Klebsiella oxytoca nitrogen fixation (nif) gene cluster to build genetic permutations that could not be achieved by starting from the wild-type cluster to provide a useful, fast tool for genetic optimization and hypothesis testing.

TL;DR: RNAtag-Seq, an approach to generate multiple RNA-seq libraries in a single reaction, lowers time and cost per sample, and it produces data on prokaryotic and eukaryotic samples that are comparable to those generated by traditional strand-specificRNA-seq approaches.

TL;DR: This work applies deep learning to a large HLA peptide and genomic dataset from various human tumors to create a computational model of antigen presentation for neoantigen prediction, and shows that this model, named EDGE, increases the positive predictive value of HLA antigen prediction by up to ninefold.