Ph.D., University of California, Berkeley, Physics, 2001.
M.A., University of California, Berkeley, Physics, 1997.
A.B., Harvard University, Physics, 1995.
My research is computationally based and focuses on the adaptive immune system and its response to viral infection, with HIV a particular area of interest. Taking advantage of new high-throughput sequencing technology, in collaboration with experimental groups, we are isolating and sequencing millions of t-cell receptor VDJ rearrangements from different clonotypes. With this new technology, we can attempt a comprehensive description of the t-cell repertoire and ask what how this repertoire is modified during an immune response.
2006-2011, Assistant Member, Computational Biology, Public Health Sciences, Fred Hutchinson Cancer Research Center
2002-2006, Post-doctoral fellow, Institute for Advanced Study, Princeton, NJ
2001-2002, Post-doctoral fellow, Weizmann Institute of Science, Particle Theory Group
Clonal expansion of CD8 T cells in the systemic circulation precedes development of ipilimumab-induced toxicities.. Proceedings of the National Academy of Sciences of the United States of America. 113(42):11919-11924.. 2016.
TCR Sequencing Can Identify and Track Glioma-Infiltrating T Cells after DC Vaccination.. Cancer immunology research. 4(5):412-8.. 2016.
Discovery of T-Cell Receptor Beta Motifs Specific to HLA-B27(+) Ankylosing Spondylitis by Deep Repertoire Sequence Analysis.. Arthritis & rheumatology (Hoboken, N.J.).. 2016.
Tissue distribution and clonal diversity of the T and B cell repertoire in type 1 diabetes.. JCI insight. 1(20):e88242.. 2016.
A Public Database of Memory and Naive B-Cell Receptor Sequences.. PloS one. 11(8):e0160853.. 2016.
Targeted single molecule mutation detection with massively parallel sequencing.. Nucleic acids research.. 2015.
TCR sequencing facilitates diagnosis and identifies mature T cells as the cell of origin in CTCL.. Science translational medicine. 7(308):308ra158.. 2015.
PACCMIT/PACCMIT-CDS: identifying microRNA targets in 3' UTRs and coding sequences.. Nucleic acids research.. 2015.
High-throughput pairing of T cell receptor α and β sequences.. Science translational medicine. 7(301):301ra131.. 2015.
Dynamics of the cytotoxic T cell response to a model of acute viral infection.. Journal of virology. 89(8):4517-26.. 2015.
Annotation of pseudogenic gene segments by massively parallel sequencing of rearranged lymphocyte receptor loci.. Genome medicine. 7(1):123.. 2015.
Intramuscular Therapeutic Vaccination Targeting HPV16 Induces T Cell Responses That Localize in Mucosal Lesions.. Science translational medicine. 6(221):221ra13.. 2014.
CTLA4 blockade broadens the peripheral T cell receptor repertoire.. Clinical cancer research : an official journal of the American Association for Cancer Research.. 2014.
Role of Deletion of Donor-Reactive T Cells in Long-Term Human Allograft Tolerance Achieved Via Combined Kidney and Bone Marrow Transplantation (CKBMT).. American Journal of Transplantation. 14:221-222.. 2014.
Digital genomic quantification of tumor-infiltrating lymphocytes.. Science translational medicine. 5(214):214ra169.. 2013.
Ultra-deep T cell receptor sequencing reveals the complexity and intratumour heterogeneity of T cell clones in renal cell carcinomas.. The Journal of pathology. 231(4):424-32.. 2013.
Shaping of Human Germline IgH Repertoires Revealed by Deep Sequencing.. Journal of immunology (Baltimore, Md. : 1950). 189(6):3221-30.. 2012.
Ultra-sensitive detection of rare T cell clones.. Journal of immunological methods. 375(1-2):14-19.. 2012.
Palindromic nucleotide analysis in human T cell receptor rearrangements.. PloS one. 7(12):e52250.. 2012.
Deep sequencing of the human TCRγ and TCRβ repertoires suggests that TCRβ rearranges after αβ and γδ T cell commitment.. Science translational medicine. 3(90):90ra61.. 2011.
Detecting and monitoring lymphoma with high-throughput sequencing.. Oncotarget. 2(4):287-8.. 2011.