Biological discovery and experimentation at scale is now the norm. Plummeting sequencing costs mean that genomic analysis is starting to enter clinical settings and guide medical decisions, CRISPR and other similar technologies have opened up new avenues for interrogating and manipulating genetic and transcriptomic data, and cloud-based platforms are democratizing access to the powerful computational engines and storage required to analyze all of this information. It’s an exciting time for the field. Here are some of the projects I’ve worked on in this space:
Review article on the genomics of response to checkpoint immunotherapy for cancer: https://genomemedicine.biomedcentral.com/articles/10.1186/s13073-018-0605-7
DeconstructSigs in Python: https://github.com/vanallenlab/deconstruct_sigs_py
MAF File Set Operations: https://github.com/vanallenlab/maf_set_ops