Raunaq Malhotra

TL;DR: An extensive immunogenomic analysis of more than 10,000 tumors comprising 33 diverse cancer types by utilizing data compiled by TCGA identifies six immune subtypes that encompass multiple cancer types and are hypothesized to define immune response patterns impacting prognosis.

TL;DR: The Seven Bridges Cancer Genomics Cloud (CGC) enables researchers to rapidly access and collaborate on massive public cancer genomic datasets, including The Cancer Genome Atlas, and enables scalable, reproducible analyses.

TL;DR: The analysis of 1000 Genomes Project Data (KGP) reveals numerous differences among the five KGP super-populations in the prevalence of individual and co-occurring HERV-K proviruses; a visualization tool is provided to easily depict the proportion of the KGP populations with any combination of polymorphic HERVs, and an integrated and computationally robust approach is presented that uses whole genome short read data to determine the occupation status at all sites reported to contain a HERV.

TL;DR: QuagmiR, the first cloud-based tool to analyze isomiRs from next generation sequencing data is presented, using a novel and flexible searching algorithm designed for the detection and annotation of heterogeneous isomiR.

TL;DR: MLEHaplo limits the over-estimation to 3 times the size of true viral haplotypes, reconstructs the full phylogeny in the HCV to greater than 99% sequencing identity and captures more sequencing variation for the HIV-1 strains dataset compared to their known consensus sequences.