ITI HUMAN IMMUNE MONITORING TECHNOLOGY AND CONFERENCE – MARCH 30-31, 2018 Speakers Bios

Robert Michael Angelo, MD, PhD Mike Angelo is an assistant professor of Pathology and Member of the Child Heath Research Institute and Cancer Institute at Stanford. He received his BS in Physics at the University of Mississippi. From 2002-2010, he was enrolled at Duke University in the Medical Scientist Training Program where he completed an MD and a PhD with an emphasis in biochemistry and electrical engineering. His experience in systems development led to a broader interest in clinical diagnostics, and ultimately a residency in clinical pathology at University of California San Francisco (2010- 2013). During that time, he became interested in developing novel methods for immunohistochemical multiplexing using mass spectrometry, which led him to the Nolan Lab at Stanford University. He developed a completely new method for simultaneous imaging of up to 100 metal-labeled antibodies within a single tissue section using multiplexed ion beam imaging (MIBI). Dr. Angelo is interested in optimizing this and other mass reporter based technologies further with the goal of identifying new transcriptional and translational signatures in solid tissue malignancies that can be used to improve clinical diagnosis and treatment. https://med.stanford.edu/profiles/robert-angelo

Nima Aghaeepour, PhD Dr. Aghaeepour completed his undergraduate studies Computer Science at the University of Tehran were he helped create a soccer team of robots. His graduate research at University of British Columbia with Ryan Brinkman and Holger Hoos focused on bioinformatics analysis of single cell data. He established the first objective benchmark for evaluation of algorithms that could automatically identify cell-types (and, eventually, correlate them with clinical outcomes), namely the Flow Cytometry: Critical Assessment of Population Identification Methods (Flow- CAP). As a postdoc with Garry Nolan (Stanford), and now an independent faculty member, he is interested in the intersection of data sciences, , and clinical phenotyping. https://nalab.stanford.edu

Sean C. Bendall, PhD Sean C. Bendall is an Assistant Professor in the Department of Pathology at Stanford University, School of Medicine. His research specialty is the development and application of single-cell proteomic tools for the investigation of human systems. This includes pioneering single cell CyTOF mass cytometry and multiplexed ion beam imaging (MIBI). Sean’s work in mass cytometry analysis has gone on to provide an unparalleled granularity of understanding in multiple facets of human hematopoiesis and immunology. His lab work ranges from unravelling the nature of ‘healthy and dysfunctional’ human hematopoietic immune cell biology to investigating the phenotypic landscape of cognitive decline in the human brain using single cell proteomic analysis. His work has been recognized by numerous awards including the Damon Runyon Cancer Research Foundation “Breakthrough Scientist” Award, the International Society for the Advancement of Cytometry President’s Award of Excellence, and the NIH Common Fund “New Innovator” Award. https://profiles.stanford.edu/sean-bendall

Catherine Blish, MD, PhD Catherine Blish, MD, PhD, FIDSA is an Associate Professor of Medicine and Immunology at the Stanford University School of Medicine. As an undergraduate she studied biochemistry at the University of California, Davis, before completing her MD and PhD at the University of Washington. She completed residency in internal medicine and fellowship training in infectious diseases at the University of Washington and the Fred Hutchinson Cancer Research Center. She joined the Stanford faculty in in 2011, where her research is dedicated to learning how to harness the immune system to prevent and cure diseases. Her lab is perhaps best known for redefining our understanding of the diversity of human natural killer (NK) cells, a critical first line of defense against viruses and tumors. Her lab continues to explore how human natural killer cells sense and respond to a diverse array of pathogens, including HIV, dengue virus, and influenza. She divides her time between research, clinical practice in infectious diseases, teaching, and her role as an Associate Director of the Stanford Medical Scientist Training Program. She has received numerous awards for research and mentoring, including the Stanford Immunology Outstanding Faculty Mentor Award, the Beckman Young Investigator Award, the McCormick Faculty Award, the Baxter Faculty Scholar, the Doris Duke Charitable Foundation Clinical Scientist Development Award, the Tashia and John Morgridge Faculty Scholar in Pediatric Translational Medicine, the NIH Director’s New Innovator Award, and the NIDA Avant-Garde Award for HIV/AIDS Research. She is an elected a member of the American Society for Clinical Investigation and an Investigator of the Chan Zuckerberg Biohub. https://sites.stanford.edu/blishlab/

Scott D. Boyd, MD, PhD Dr. Boyd is an Associate Professor in the Department of Pathology at Stanford University. The Boyd laboratory develops high-throughput DNA sequencing and single-cell experiments together with data analysis methodology to study lymphocyte populations in human immune responses to infection and vaccination, as well as in immunological disorders such as food allergy and immunodeficiency. Many of the laboratory’s projects analyze the gene rearrangements encoding antibodies and T cell receptors that form the basis of immunological specificity and memory in health and disease. Dr. Boyd received bachelor's degrees in Biochemistry at the University of Manitoba, and English Literature at Oxford University, where he was a Rhodes Scholar. He obtained his M.D. from Harvard Medical School and Ph.D. from MIT, followed by pathology residency, a hematopathology fellowship, and postdoctoral research work, at Stanford University. http://med.stanford.edu/scottboydlab.html

Petter Brodin, MD, PhD Dr Brodin grew up in Stockholm, Sweden and graduated from a joint M.D and Ph.D program at the Karolinska Institute. After completing his clinical internship and pediatric residency at the Karolinska University Hospital, he joined the Mark Davis laboratory at Stanford University as a postdoctoral fellow. During this time the Davis lab was involved in several systems-immunology analyses in human cohort and Brodin contributed in particular to an analysis of immune system variation in healthy human twins in order to assess the influences of heritable and non-heritable factors. After this, Brodin was recruited back to the Karolinska Institute to lead his own research group, and also establish a Mass cytometry facility at the newly opened Science for life laboratory, a national center for life science technology funded by the Swedish government. Brodin now divides his time between clinical work at the Karolinska University Children’s Hospital with research aiming to understand human immune system variation in general, and the shaping of human immune systems early in life in particular. https://ki.se/en/people/pebrod

Atul Butte, MD, PhD Atul Butte, MD, PhD is the Priscilla Chan and Mark Zuckerberg Distinguished Professor and inaugural Director of the Institute for Computational Health Sciences (ichs.ucsf.edu) at the University of California, San Francisco (UCSF). Dr. Butte is also the Executive Director for Clinical Informatics across the six University of California Medical Schools and Medical Centers. Dr. Butte has authored over 200 publications, with research repeatedly featured in the New York Times, Wall Street Journal, and Wired Magazine. Dr. Butte was elected into the National Academy of Medicine in 2015, and in 2013, he was recognized by the Obama Administration as a White House Champion of Change in Open Science for promoting science through publicly available data. Other recent awards include the 2014 E. Mead Johnson Award for Research in Pediatrics, 2013 induction into the American Society for Clinical Investigation, and the 2011 National Human Genome Research Institute Genomic Advance of the Month. Dr. Butte is a principal investigator of three major programs: (1) the California Initiative to Advance Precision Medicine, implementing Governor Brown’s vision to promote precision medicine in California; (2) ImmPort, the clinical and molecular data repository for the National Institute of Allergy and Infectious Diseases; and (3) the California Precision Medicine Consortium, helping recruit tens of thousands of participants into President Obama's AllofUs Precision Medicine Initiative. Dr. Butte trained in Computer Science at Brown University, worked as a software engineer at Apple and Microsoft, received his MD at Brown University, trained in Pediatrics and Pediatric Endocrinology at Children's Hospital Boston, then received his PhD from Harvard Medical School and MIT. Dr. Butte is also a founder of three investor-backed data-driven companies: Personalis, providing medical genome sequencing services, Carmenta (acquired by Progenity), discovering diagnostics for pregnancy complications, and NuMedii, finding new uses for drugs through open molecular data. http://buttelab.ucsf.edu/

Arup K. Chakraborty, PhD Arup K. Chakraborty is the Robert T. Haslam Professor of Chemical Engineering, and Professor of Physics, Chemistry, and Biological Engineering at MIT. He was the founding Director of MIT’s Institute for Medical Engineering and Science from February 2012 to January 2018. He is also a founding steering committee member of the Ragon Institute of MIT, MGH, and Harvard, and an Associate Member of the Broad Institute of MIT & Harvard. After obtaining his PhD in chemical engineering and postdoctoral studies, he joined the faculty at the University of California at Berkeley in December 1988. He rose through the ranks, and ultimately served as the Warren and Katherine Schlinger Distinguished Professor and Chair of Chemical Engineering, Professor of Chemistry, and Professor of Biophysics at Berkeley. He was also Head of Theoretical and Computational Biology at Lawrence Berkeley National Laboratory. In September 2005, Chakraborty moved to MIT. His entire career has been focused on research at the intersection of disciplines. After an early career in guiding the engineering of polymers and catalysts using quantum mechanical calculations, since 2000, Chakraborty’s work has focused on bringing together immunology and the physical and engineering sciences; more specifically, the intersection of statistical mechanics and immunology. His interests span T cell signaling, T cell development and repertoire, and a mechanistic understanding of HIV evolution, antibody evolution, and vaccine design. Chakraborty’s work at the intersection of disciplines has been recognized by numerous honors, including the NIH Director’s Pioneer Award, the E.O. Lawrence Medal for Life Sciences from the US DOE, the Allan P. Colburn and Professional Progress awards from the AIChE, a Dreyfus Teacher-Scholar award, and a National Young investigator award. Chakraborty was elected a member of the National Academy of Sciences

and the National Academy of Engineering for completely different bodies of work. He is also a member of the National Academy of Medicine, making him one of 21 individuals who are members of all three branches of the US National Academies. He is a Fellow of the American Academy of Arts & Sciences and the American Association for the Advancement of Science, and serves on the US Defense Science Board. Chakraborty has received four teaching awards at Berkeley and MIT. http://web.mit.edu/akcgroup/

Mark M. Davis, PhD Mark M. Davis is the Director of the Stanford Institute for Immunology, Transplantation and Infection (ITI), a Professor of Microbiology and Immunology, and a Howard Hughes Medical Institute Investigator. He received a B.A. from Johns Hopkins University and a Ph.D. from the California Institute of Technology. He later was a postdoctoral and staff fellow at the Laboratory of Immunology at NIH and then became a faculty member in the Department of Microbiology and Immunology at Stanford University School of Medicine, where he remains today. Dr. Davis is well known for identifying many of the T-cell receptor genes, which are responsible for the ability of these cells to recognize a diverse repertoire of antigens. Current research interests involve understanding the molecular interactions that underlie T cell recognition and the challenges of human immunology, specifically a “systems level” understanding of an immune response to vaccination or infection. http://med.stanford.edu/davislab.html

Jennifer Dionne, PhD Jennifer Dionne is an associate professor of Materials Science and Engineering at Stanford. Jen received her Ph. D. in Applied Physics at the California Institute of Technology, advised by Harry Atwater, and B.S. degrees in Physics and Systems & Electrical Engineering from Washington University in St. Louis. Prior to joining Stanford, she served as a postdoctoral researcher in Chemistry at Berkeley, advised by Paul Alivisatos. Jen’s research develops new optical materials and microscopies to observe chemical and biological processes as they unfold with nanometer scale resolution. She then uses these observations to help improve energy- relevant processes (such as photocatalysis and energy storage) and medical diagnostics and therapeutics. Her work has been recognized with a Moore Inventor Fellowship (2017), the Materials Research Society Young Investigator Award (2017), Adolph Lomb Medal (2016), Sloan Foundation Fellowship (2015), and the Presidential Early Career Award for Scientists and Engineers (2014), and was recently featured on Oprah’s list of “50 Things that will make you say ‘Wow’!”. Web: dionne.stanford.edu https://profiles.stanford.edu/jennifer-dionne

Jim Heath, PhD Dr. Heath received his Ph.D. from Rice University in 1988 and was a Miller Postdoctoral fellow at UC Berkeley from 1988-91. He was a research staff member at IBM Watson Labs until joining the chemistry department at UCLA as an assistant professor in 1994, where he was promoted to Assoc Prof in 1996 and Prof in 1997. In 2003 he moved to Caltech as the Elizabeth Gilloon Professor of Chemistry. In 2018 took on the position of President and Professor at the Institute for Systems Biology in Seattle, WA. He also holds a Professorship within the UCLA Geffen School of Medicine. https://www.systemsbiology.org/

Susan Holmes, PhD Professor Holmes completed her undergraduate and PhD degrees in mathematics and statistics at University of Montpellier, France where she specialized in the French School of Data Analysis (Analyse des Données) in the 1980’s, specializing in exploring and visualizing complex

biological data. After being a Senior Researcher at INRA, Montpellier, she was an Associate Professor at Cornell, a visiting Professor at MIT and Harvard. She moved to Stanford in 1998 and is currently Professor of Statistics. Her research is focused on statistical methods for integrating the information provided by phylogenetic trees, community interaction graphs and metabolic networks with single cell data and clinical covariates. She uses computational statistics, in particular, nonparametric computer intensive methods such as the bootstrap and MCMC to draw inferences about many complex biological phenomena, interactions between the immune system and cancer, resilience and biomarker detection in the human microbiome and drug resistance in HIV. She teaches a popular statistics class called Modern Statistics for Modern Biology using R and BioConductor. She is currently a 2017-2018 fellow at the Center for for the Advanced Study of the Behavioral Sciences at Stanford. http://www-stat.stanford.edu/~susan/

Darrell Irvine, PhD Dr. Irvine obtained an Honors Bachelor’s degree in Engineering Physics from the University of Pittsburgh. As a National Science Foundation graduate fellow he then studied Polymer Science at the Massachusetts Institute of Technology. Following completion of his Ph.D., he was a Damon Runyon-Walter Winchell postdoctoral fellow in immunology at the Beckman Center for Molecular and Genetic Medicine. He is presently a Professor at the Massachusetts Institute of Technology and an Investigator of the Howard Hughes Medical Institute. He is an Associate Director for the Koch Institute for Integrative Cancer Research at MIT and serves on the steering committee of the Ragon Institute of MGH, MIT, and Harvard. http://irvine-lab.mit.edu/

Purvesh Khatri, PhD Dr. Khatri completed undergraduate coursework in Electronics and Communications Engineering at BVM Engineering College in India, and received his MS and PhD in computer science from Wayne State University in Detroit, Michigan. After graduate school, he was a postdoctoral fellow in the Department of Pediatrics at Stanford University School of Medicine. He is presently an assistant professor in Stanford Institute for Immunity, Transplantation and Infection and Division for Biomedical Informatics Research in Department of Medicine at Stanford University. Http://khatrilab.stanford.edu

J. Christopher Love, PhD J. Christopher Love is an associate professor in chemical engineering and member of the Koch Institute for Integrative Cancer Research at MIT. In addition, Chris is an associate member at the Eli and Edythe L. Broad Institute, and at the Ragon Institute of MGH, MIT, and Harvard. Dr. Love received his Ph.D. in 2004 in physical chemistry at Harvard University. He extended his research into immunology at Harvard Medical School from 2004-2005, and at the Immune Disease Institute from 2005-2007. His research centers on using simple microsystems to monitor cells from clinical samples in chronic human diseases, and on developing new approaches to manufacturing biologic drugs efficiently and affordably. Dr. Love was named a Dana Scholar for Human Immunology and a Keck Distinguished Young Scholar in Medical Research in 2009, as well as one of Popular Science’s Brilliant 10 in 2010. Chris is also a Camille Dreyfus Teacher-Scholar. https://love-lab.mit.edu/

Holden T. Maecker, PhD Dr. Maecker received a BS in Microbiology from Purdue University and a PhD in Cancer Biology from Stanford University. He did postdoctoral work with Ronald and Shoshana Levy at Stanford,

and was an Assistant Professor of Biology at Loyola University Chicago, as well as a Senior Scientist at BD Biosciences, San Jose, CA. He is currently a Professor of Microbiology and Immunology, and Director of the Human Immune Monitoring Center, at Stanford University. His research focuses on measuring immune competence, as well as how specific cellular immune responses correlate with immune protection. https://profiles.stanford.edu/holden-maecker

Garry Nolan, PhD Dr. Nolan is the Rachford and Carlota A. Harris Professor in the Department of Microbiology and Immunology at Stanford University School of Medicine. He trained with Leonard Herzenberg (for his Ph.D.) and Nobelist Dr. David Baltimore (for postdoctoral work for the first cloning/characterization of NF-?B p65/ RelA and the development of rapid retroviral production systems). He has published over 220 research articles and is the holder of 20 US patents, and has been honored as one of the top 25 inventors at Stanford University. Dr. Nolan is the first recipient of the Teal Innovator Award (2012) from the Department of Defense (a $3.3 million grant for advanced studies in ovarian cancer), the first recipient of an FDA BAAA, for "Bio-agent protection" grant, $3million, from the FDA for a "Cross-Species Immune System Reference", and received the award for "Outstanding Research Achievement in 2011" from the Nature Publishing Group for his development of CyTOF applications in the immune system. Dr. Nolan has new efforts in the study of Ebola, having developed instrument platforms to deploy in the field in Africa to study Ebola samples safely with the need to transport them to overseas labs (funded by a new $3.5 million grant from the FDA). Dr. Nolan is an outspoken proponent of translating public investment in basic research to serve public welfare. Dr. Nolan was the founder of Rigel Inc. (NASDAQ: RIGL, BINA (a genomics computational infrastructure company sold to Roche Diagnostics), and serves on the Boards of Directors of several companies as well as consults for other biotechnology companies. DVS Sciences, on which he was Chair of the Scientific Advisory Board, sold to Fluidigm for $207 million dollars (2014) on an investment of $14 million. His areas of research include hematopoiesis, cancer and leukemia, autoimmunity and inflammation, and computational approaches for network and systems immunology. Dr. Nolan's recent efforts are focused on a single cell analysis advance using a mass spectrometry- flow cytometry hybrid device (CyTOF) and nanoscale imaging with the "Multiparameter Ion Beam Imager" (MIBI). The approaches use an advanced ion plasma source to determine the levels of tagged reagents bound to cells - enabling a vast increase in the number of parameters that can be measured per cell - either as flow cytometry devices (CyTOF) or imaging platforms for cancer (MIBI). Further developments in imaging are enabled by CODEX—a system that inexpensively converts fluorescence scopes into high dimensional imaging platforms. Dr. Nolan's efforts are to enable a deeper understanding not only of normal immune function, trauma, pathogen infection, and other inflammatory events but also detailed substructures of leukemias and solid cancers to enable new understandings that will enable better management of disease and clinical outcomes. http://web.stanford.edu/group/nolan/

Bali Pulendran, PhD Professor Bali Pulendran is the Violetta L. Horton Professor at the Stanford University School of Medicine, and a member of the Institute for Immunology, Transplantation and Infection, and the Departments of Pathology and Microbiology & Immunology at Stanford University. He is also an adjunct professor at the Yerkes National Primate Center at Emory University, and director of the NIH U19 Center for Systems Vaccinology, at Emory University in Atlanta. He received his undergraduate degree from Cambridge University, and his Ph.D from the Walter & Eliza Hall Institute in Melbourne, Australia, under the supervision of Sir Gustav Nossal. He then did his

post-doctoral work at Immunex Corporation in Seattle. Dr. Pulendran is a world leader on understanding the mechanisms by which the innate immune system regulates adaptive immunity and harnessing such mechanisms in the design of novel vaccines. More recently, his laboratory pioneered the use of systems biological approaches to predicting the efficacy of vaccines, and deciphering new correlates of protection against infectious diseases. Dr. Pulendran’s research is published in front line journals such as Nature, Science, Cell, Nature Medicine, and Nature Immunology. Furthermore, Dr. Pulendran is the recipient of numerous grants from the National Institutes of Health, and from The Bill and Melinda Gates Foundation, serves on many editorial boards, and is the recipient of two concurrent MERIT awards from the National Institutes of Health, as well as the 2011 Albert. E. Levy Award, 2011 Paper of the year award by the International Society for Vaccines.

Lluis Quintana-Murci, PhD Dr Quintana-Murci earned his Ph.D. in Population Genetics at the University of Pavia (Italy), and his MSc in Biology at the University of Barcelona (Spain). After short training periods in the Universities of Arizona (Tucson) and Oxford (UK), he completed two years of postdoctoral training in human genetics at Institut Pasteur (Paris). He is presently a Director of Research of CNRS and Professor at the Institut Pasteur. He heads the Unit of Human Evolutionary Genetics at the Institut Pasteur since 2007, and has been Scientific Director of the Institut during 2016- 2017. He is a population geneticist whose research focuses on how pathogens have exerted selective pressures on the human genome, particularly at innate immunity genes. His research is also focused on the study of the genetic and non-genetic factors driving variation in human immune responses, as this helps to lay the foundations of precision medicine related to infectious and immune-related disorders and vaccine treatment. His laboratory combines molecular and population genetics approaches, with computational modelling and development of new statistical frameworks.

William H. Robinson, MD, PhD The Robinson laboratory works in the fields of B cell biology, autoimmunity and inflammation. Dr. Robinson pioneered development of protein arrays, lipid arrays, and high-throughput sequencing approaches to identify the targets of antibody responses, investigate mechanisms underlying disease, and to develop novel therapeutic approaches. Dr. Robinson co-founded the Stanford Human Immune Monitoring Center, serves on the editorial boards of several journals, and serves on the Board of Directors of the American College of Rheumatology. He is an inventor on 23 patent applications, and technologies developed in his Stanford and VA laboratories have been licensed to nine companies in the biotechnology industry. Dr. Robinson was elected to the American Society for Clinical Investigation and the Henry Kunkel Society. Dr. Robinson received his MD and PhD degrees from Stanford University, and completed his clinical training in internal medicine at UCSF. http://robinsonlab.stanford.edu

Alex K. Shalek, PhD Alex K. Shalek is currently the Pfizer-Laubach Career Development Assistant Professor at MIT, as well as a Core Member of the Institute for Medical Engineering and Science (IMES) and an Assistant Professor of Chemistry. He is also an Associate Member of the Ragon and Broad Institutes, an Assistant in Immunology at MGH, and an Instructor in Health Sciences and Technology at HMS. His research is directed towards the development and application of new technologies that facilitate understanding of how cells collectively perform systems-level functions in healthy and diseased states. Dr. Shalek received his bachelor's degree summa cum

laude from Columbia University and his Ph.D. from Harvard University in chemical physics under the guidance of Hongkun Park, and performed postdoctoral training under Hongkun Park and Aviv Regev (Broad/MIT). To date, his interdisciplinary research has focused on realizing and utilizing nanoscale manipulation and measurement technologies to examine how small components (molecules, cells) drive systems of vast complexity (cellular responses, population behaviors).http://www.shaleklab.com

Lynda Stuart, MD, PhD Dr. Lynda Stuart leads the Vaccine and Host Pathogen Biology domain of Discovery and Translational Sciences. This group works across all infectious diseases of interest to the foundation and aims to source novel approaches and accelerate the discovery, development and translation of new passive and active immunization strategies for foundation priority diseases. Prior to joining the foundation in 2016, Dr.Stuart was a member of the faculty at the Massachusetts General Hospital and Harvard Medical School where she was co-director of the Laboratory of Developmental Immunology; a member of the Center for Computational and Integrative Biology, an affiliate of the Broad Institute of Harvard and MIT; and served on the Massachusetts General Hospital Executive Committee for Research. She remains actively involved in basic research. Dr. Stuart earned an MD from the University of Cambridge and the University of London and a PhD from the University of Edinburgh. She completed residency training in Internal Medicine in the United Kingdom. https://www.gatesfoundation.org/What-We- Do/Global-Health/Discovery-and-Translational-Sciences/Strategy-Leadership/Lynda-Stuart

Alice Ting, PhD Dr. Ting completed undergraduate coursework in chemistry at Harvard University, and received her Ph.D. in chemistry from the University of California Berkeley. After graduate school, she completed her post-doctoral training with Roger Tsien at the University of California San Diego. In 2002, Alice started her independent laboratory in the Department of Chemistry at MIT. In 2016, she relocated with her laboratory to Stanford University, Departments of Genetics, Biology, and Chemistry. Her research is on the development of molecular technologies for probing and manipulating protein networks and cellular networks. http://www.tinglab.org