We welcome three new faculty members to the ML group: David Duvenaud, Sanja Fidler, and Roger Grosse.
Congratulations to Michael Wainberg, Victoria Dean and Omar Wagih on their summer projects, which used machine learning to understand the genetics of disease (3rd, 4th and 5th from left).
Checkout http://www.deepgenomics.com/ for more details.
Phylo* is a family of statistical methods that use nonparametric Bayesian tree priors to infer clonal evolution of tumors from whole genome sequencing data.
Amit G. Deshwar, Shankar Vembu, Christina K. Yung, Gun Ho Jang, Lincoln Stein, Quaid Morris. PhyloWGS: Reconstructing subclonal composition and evolution from whole genome sequencing of tumors. Genome Biology 16:35, 2015.
Amit G. Deshwar, Shankar Vembu, Quaid Morris. Comparing Nonparametric Bayesian Tree priors for clonal reconstruction of tumors. InProceedings of the Pacific Symposium on Biocomputing, 2015.
Wei Jiao, Shankar Vembu, Amit G. Deshwar, Lincoln Stein, Quaid Morris. Inferring clonal Evolution of tumors from single nucleotide Somatic Mutations. BMC Bioinformatics 15:35, 2014.
My new, faster, version of R, called pqR.
pqR is a new version of the R interpreter. It is based on R-2.15.0, distributed by the R Core Team, but improves on it in many ways, mostly ways that speed it up, but also by implementing some new features and fixing some bugs.
– Radford Neal
Together with Stephen Rumble (with contributions from Adrian Dalca, Marc Fiume, Vlad Yanovsky, and in a collaboration with Arend Sidow and his group) we developed SHRiMP — the SHort Read Mapping Program. SHRiMP can align short reads to a reference genome quickly and accurately, while allowing for insertions/deletions. It also comes with special color-space options to handle reads made by the AB SOLiD technology. More recently Matei David, Misko Dzamba, and others have worked on the second version of SHRiMP (SHRiMP2), which significantly speeds up mapping without sacrificing sensitivity.