Community change and resident needs: Designing a Participatory Action Research study in Metropolitan Boston.

The health implications of urban development, particularly in rapidly changing, low-income urban neighborhoods, are poorly understood. We describe the Healthy Neighborhoods Study (HNS), a Participatory Action Research study examining the relationship between neighborhood change and population health in nine Massachusetts neighborhoods. Baseline data from the HNS survey show that social factors, specifically income insecurity, food insecurity, social support, experiencing discrimination, expecting to move, connectedness to the neighborhood, and local housing construction that participants believed would improve their lives, identified by a network of 45 Resident Researchers exhibited robust associations with self-rated and mental health.

Computational Pipeline for the PGV-001 Neoantigen Vaccine Trial.

This paper describes the sequencing protocol and computational pipeline for the PGV-001 personalized vaccine trial. PGV-001 is a therapeutic peptide vaccine targeting neoantigens identified from patient tumor samples. Peptides are selected by a computational pipeline that identifies mutations from tumor/normal exome sequencing and ranks mutant sequences by a combination of predicted Class I MHC affinity and abundance estimated from tumor RNA.

pileup.js: a JavaScript library for interactive and in-browser visualization of genomic data.

Unlabelled: P: ileup.js is a new browser-based genome viewer. It is designed to facilitate the investigation of evidence for genomic variants within larger web applications.