I'm an Assistant Professor of Genetics in the Computational Medicine Program and Lineberger Cancer Center at the University of North Carolina - Chapel Hill.

I help run the Personalized Immunotherapy Research Lab at UNC where we work on T-cell epitope discovery, cancer genomics, machine learning for immunology, and making personalized cancer vaccines which actually do something useful.

Previously: researcher in Mount Sinai's OpenVax group and Hammer Lab.

Blogs

Personalized Immunotherapy Research Lab
My research lab at UNC Chapel Hill with posts about computational immunology, genomics, and machine learning
OpenVax Blog
Open source software for personalized cancer vaccines
Hammer Lab Blog
Former research lab: cancer genomics, immunotheray, machine learning, and bioinformatics
explain my data
Machine learning and data analysis
φ-node
My previous research life: translating programs into faster programs.

Writing & Presentations

Clinical Trials

I helped start and run the PGV (personalized genomic vaccine) series of therapeutic cancer vaccine at Mount Sinai: I am now at UNC helping create the next generation of personalized cancer vaccines at UNC:

Art

punch.card.collective
Ongoing collaboration working on generative fiber arts and proto-computational pattern crafts
Weave
Early experiments in generating textile patterns and weaving drafts
Texture Synthesis
An implementation of Efros & Leung's texture synthesis algorithm in Matlab, and some aesthetically pleasing outputs.

Projects

Vaxrank
Computational prediction and ranking of synthetic long peptides for personalized therapeutic cancer vaccines
Isovar
Python library for determining mutant protein sequences from somatic variants and tumor RNA sequencing
Topiary
Python library and commandline tool for predicting cancer epitopes from mutation and RNA expression data
MHCflurry
Neural network Class I MHC binding predictors
MHCdouble
Convolutional neural network Class II MHC binding predictors
MHCtools
Python API which wraps messy commandline peptide-MHC binding tools like NetMHC
PyEnsembl
Python interface to the Ensembl gene annotation database
Varcode
Library for analyzing and inferring effects of genomic variants in Python
PepData
Python interface to immunology and bioinformatics datasets
Parakeet
An optimizing just-in-time compiler for an array-oriented subset of Python
CudaTree
GPU Random Forest library for Python
GenePool
A basic framework for implementing genetic algorithms in OCaml.
ocaml_llvm
A toy compiler for a mini-language implemented with OCaml and LLVM
Falcon
A faster register-based virtual machine for Python (primarily by Russell Power)
TreeLearn
Decision tree learning algorithms for Python.
Yasper
simple single-header reference counting smart pointer for C++
Parsnip
packrat parser combinator library for C++