Sven Rahmann

TL;DR: Snakemake is a workflow engine that provides a readable Python-based workflow definition language and a powerful execution environment that scales from single-core workstations to compute clusters without modifying the workflow.

TL;DR: It is shown how the popular workflow management system Snakemake can be used to guarantee reproducibility, and how it enables an ergonomic, combined, unified representation of all steps involved in data analysis, ranging from raw data processing, to quality control and fine-grained, interactive exploration and plotting of final results.

TL;DR: Using exome sequencing, recurrent somatic mutations in EIF1AX and SF3B1 are identified occurring in uveal melanomas with disomy 3, which rarely metastasize and are associated with poor prognosis.

TL;DR: This work presents a visualization method that incorporates both emission and transition probabilities of the pHMM, thus extending sequence logos introduced by Schneider and Stephens, and demonstrates that HMM Logos can be a useful tool for the biologist.

TL;DR: The mutational burden significantly increased in relapsing tumors, accompanied by altered mutational signatures and reduced subclonal heterogeneity and global allele frequencies at relapse indicated clonal mutation selection during disease progression.