Resume
Nurix Therapeutics
Machine Learning Scientist 1
May 2021 - Feb 2024
Optimization of ML models on DNA Encoded Libraries (DEL) for predicting binding affinity of small molecules to targets of interest with an interest in exploring new ML techniques for property predictions. Leader in data aggregation statistics for assay trackers and downstream analytics. Senior leadership in data science, bioinformatics (RNAseq/ATACseq), NLP models for T cell receptor informatics, and ML for cell therapy product design for ovarian and epithelial cancers.
DEL skills: DEL informatics, python, RDKit, AWS, Jira, Confluence, Git
Bioinformatics skills: Bioconductor, R, Matlab, PCA, UMAP, Nanostring, bulk-, ss-RNAseq/ATACseq
Data Science skills: Data curation, aggregation/analysis statistics
Carnegie Mellon University
Ph.D. Biomedical Engineering
Aug 2016 - Feb 2021
Doctoral Thesis: “Machine learning tools for smarter automation and diagnostics in the development of personalized medicine from size-limited datasets”
M.S. Biomedical Engineering
Aug 2016 - Feb 2021
Master’s Thesis: “Nano-bio interfaces: Towards the fabrication of graphene-graphite FETs for elucidating the electrical activity of excitable cells”
Awards and Fellowships:
The AAI Young Investigator Award - The American Association of Immunologists, June 2022
CMLH Fellow - Center for Machine Learning and Health, 2020-2021
B.A. Physics
B.A. Molecular Cell Biology
Aug 2008 - Dec 2012
University of California, Berkeley
Bone J, Childs CM, Menon A, Poczos B, Feinberg FW, LeDuc PR, Washburn NR. Hierarchical machine learning for high-fidelity 3D printed biopolymers. ACS Biomaterials. 2021.
Bone J, Guo Yuxin, Person C, Murthy P, Lotze MT, Washburn NR. Machine learning for monitoring renal cancer disease progression from patient immune repertoires. Manuscript in Preparation.
Mataev E, Rastogi SK, Madhusudan A, Bone J, Lamprinakos YP, Cohen-Karni T. Synthesis of group IV nanowires on graphene: the case of GE nanocrawlers. Nano Lett. 2016.
Myers FB, Henrikson RH, Bone J, Lee LP. A handheld point of care genomics diagnostic system. PLoS ONE 8(8) e70266, 2013.
Provisional Patent
Publications
Lucira Health (fka DiAssess)
Biomedical Engineer
May 2013 - Feb 2024
Start-up Experience
Founding Team Member
Feb 2013 - Aug 2013
Towards diagnostics, I developed a low-cost, disposable rapid RNA/DNA diagnostic device for infectious disease that would ultimately serve as the founding technology for Lucira Health’s OTC covid test. I further developed the genomics-based PCR assay pipeline for influenza A, with special attention to primer design that optimized for detection of infectious gene content in patient samples amid rapid mutation of the disease, non-specific binding, primer dimerization, and interference from raw patient samples. I led the transition of assay mixtures into lyophilized reagents, led the initiation of the first clinical trial for FDA approval, and led the start-up team for Series A funding before returning to graduate school for my PhD.
Laboratory skills: DNA/RNA extraction, qPCR, PCR, LAMP assay and primer design, on-chip optimization, microfluidic chip design, soft-lithography manufacturing, BSL2 sterile technique, CAD.