Curriculum Vitae of Giovanni Parmigiani
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COURSES AT HARVARD: • Methods for Comparative Effectiveness Research, Spring 2012 • Statistical Inference II, Spring 2015 • Freshman Seminar:My Genes and Cancer, Spring 2016, Fall 2016 • Data Analysis in Modern Biostatistics, Spring 2017 SHORT COURSES: * Utility and Decision Making, Universit` a di Pavia, May 1993. Bayesian Biostatistics: Applications to Clinical and Pharmaceutical Research. Houston, TX, Jan- uary 2001; * Gene Expression Data Analysis; Graduate Summer Institute of Epidemiology and Biostatistics, JHU, 2002. [Course Website] Gene Expression Data Analysis; Food and Drug Administration, Rockville, MD January 2004. Genomics Data Analysis and Clinical Trials; Food and Drug Administration, Rockville, MD July 2009.
Statistical Genomics, Summer School on Modern Methods in Biostatistics and Epidemiology, Cison di Valmarino-Treviso, Italy, June 2010 Bioinformatics, Istituto di Genetica Molecolare, CNR Pavia Italy, Co-taught with L. Marchionni, July 2014 Advising GRADUATE STUDENT ADVISING AT DUKE: PhD Theses . Student Year Title
Heather DeSimone 1996
Prediction Using Orthogonalized Model Mixing Fusheng Su 1996 Limit Theorems on Deviation Probabilities with Applications in Two-Armed Clinical Trials Heidi Ashih 2000 Joint Estimation of Mammographic Sensitivity and Tumor Growth Daniel Gudbjartsson 2000 Multipoint Linkage Analysis based on Allele Sharing Models Xi “Kathy” Zhou 2002
Classification of Missense Mutations of Disease Genes PhD Thesis committee member of Gabriel Huerta, Lurdes Inoue and Chengchang Li. Master Thesis supervisor of Richard Realbuto, Zhong Shen, Ying Su. Master and PhD Thesis external member of Kerem Harmanci, Department of Electrical and Com- puter Engineering. 42
GRADUATE STUDENT ADVISING AT JOHNS HOPKINS: PhD Theses . Student
Year Title
Natalie Blades 2002
Statistical Methods for Serial Analysis of Gene Expression Dongmei Liu 2005 Inference on functional classes using gene expression data Cristian Pattaro 2005
Haplotype block partitioning as a tool for dimensionality reduc- tion in complex disease modeling Valeria Edefonti 2006
Integrating Supervised and Unsupervised Learning in Genomics Applications Hormuzd Katki 2006
Extending Mendelian Models That Predict if One has a Disease- Causing Mutation Based on Family History of Disease Ainong Zhou 2006
Bayes factors comparing two multi-normal covariance matrices and their application to microarray data analysis Robert Scharpf 2007
Combining high-throughput genomic data: methods and utility Wenyi Wang 2007 Statistical Methods for Cancer Risk Assessment and Copy Num- ber Estimation YenYi Ho
2009 Gene Association Networks and Higher Order Interactions: Al- gorithms and Statistical Models Simina Boca 2011 Analysis of Cancer Genome Data MHS Thesis supervised or co-supervised, and areas Jian Wang Comparison of classification approaches for microarray data MPH Thesis supervised or co-supervised, and areas Rosemary Braun Searching for differentially expressed gene-pathway combinations PhD Thesis committee member for Majnu John, Mary Lin, Xiaogang Zhong (Applied Math- ematics and Statistics) Michelle Shardell, Rongheng Lin (Biostatistics) Sonja Berndt, Elizabeth Brown, Preeta Rajamaran, Reiko Sato (Epidemiology) Erica Breslau, Helen Meissner, Claire Snyder (Health Care Policy and Management), Micheal Zilliox (Molecular Microbiology and Immunology), Genevieve Weber (Neurosurgery), Xiao Liu, Matthew Pletcher and Nidhi Saran (Physiology). PhD Oral exam committee member for Majnu John, Xiaolin Wu (Applied Mathematics and Statis- tics) Hormuzd Katki (Biostatistics) Janine Genking, Elizabeth Brown, Preeta Rajamaran (Epi- demiology) Helen Meissner (Health Care Policy and Management) Xiao Liu, Matthew Pletcher (Physiology), Jerry Cai (Genetic Medicine) and Michael Zilliox (Molecular Microbiology and Im- munology). SKCCC Cancer in the Under-Privileged Indigent or Disadvantaged summer fellowship: Ije Abejoma. GRADUATE STUDENT ADVISING AT HARVARD: PhD Theses . 43 Student Year
Title Danielle Braun 2014 Statistical Methods to Adjust for Measurement Error in Risk Prediction Models and Observational Studies Yifan Zhang 2014 Bayesian Adaptive Clinical Trials Christina McIntosh In Progress Roberta DeVito In Progress Theodore Huang In Progress PhD Thesis committee member of Matthew Cefalu, Danielle Braun, David Zhou, Yifan Zhang, Alejandro Quiroz Zarate, Yuqing Zhang, Sarah Anoke, Christina McIntosh, Emma Schwager, Georgia Papadogeorgou, Boyu Ren. GRADUATE STUDENT AWARDS: Natalie Blades: 2003: Merrell Award for outstanding research by a PhD student. Johns Hopkins School of Public Health, Department of Biostatistics. Wenyi Wang: 2005 The June B. Culley Award for outstanding achievement in the second-year oral exam, Johns Hopkins School of Public Health Biostatistics. 2006 Travel Award for the International Genetic Epidemiology Society 15th Annual Meeting. 2006 Student Conference Fund Award at Johns Hopkins Bloomberg School of Health, The 15th Genetic Analysis Workshop. 2007: Travel Award for the 11th International Conference on Research in Computational Molecular Biology. 2008: Elected member of Phi Beta Kappa Society, Johns Hopkins University. 2008: Elected member of Delta Omega Honor Society, Alpha Chapter Johns Hopkins Bloomberg School of Public Health. 2008: The Jane and Steve Dykacz Award for outstanding student paper in medical statistics Johns Hopkins School of Public Health Department of Biostatistics. Hormuzd Katki: 2006: Merrell Award for outstanding research by a PhD student. Johns Hopkins School of Public Health, Department of Biostatistics. Dongmei Liu: ENAR travel award. Simina Boca: 2007: Glaxo SmithKline Award, for outstanding achievement on the Department of Biostatistics first-year exam. Rob Scharpf: 2007: Merrell Award for outstanding research by a PhD student. Johns Hopkins School of Public Health, Department of Biostatistics. Chi Wang: Distinguished Student Paper Awards. Biometric Society, ENAR. 44
Valeria Edefonti: 2008: Best Doctoral thesis in Statistics. Italian Statistical Society, 2008 45
POSTDOCTORAL FELLOWS MENTORING AT JOHNS HOPKINS: Fellow
Years Area
Sining Chen 2003-05
Risk prediction in familial cancer Qiushan Tao 2004-05 Networks in genomics Jianweng Zhang 2004-05
Genomics of resistance to chemotherapy Marcel Dettling 2004-06 Multivariate Differential Expression Luigi Marchionni 2005-07
Multi-study genomic data analysis YuChuan Tai 2005-07 Spatial modeling of cancer-causing mutations Suraj Peri 2005-07
miRNA analysis Betty Doan 2005— Colonoscopy screening modeling Sierra Min Li 2006-07
Bayesian Variable Selection Loris Mularoni 2008-11 Sequence Analysis Jeff Leek 2008-09
Microarray-based classification Corrie Joshu 2008-10 Colorectal Cancer Risk POSTDOCTORAL FELLOWS MENTORING AT HARVARD: 46
Fellow Years
Area Svitlana Tyekucheva 2008–11 Next Generation Sequencing Lorenzo Trippa 2009–11
Bayesian Modeling Victoria Wang 2010–11 Cross-Platform Genomic Integration Emanuele Mazzola 10–2012
Models for in situ breast carcinomas Jie Ding
2008–13 Modeling Signaling Pathways Cristian Tomasetti 2011–13
Mathematical modeling of cancer evolution, drug resis- tance, stem cell dynamics Levi Waldron 2011–13
Improving the reproducibility and robustness of conclu- sions drawn from high-dimensional genomic data, focus- ing on translational relevance Steffen Ventz 2012–15 Adaptive clinical trials, next generation sequencing methodology Reuma Admanit 2012–2015 Ovarian cancer prognosis, AIDS research Naim Rashid 2013–14
High dimensional data analysis, genomics, statistical ge- netics, next generation sequencing data analysis, classi- fication, variable selection in non-independent data Mehmet Samur 2013–15 Bioinformatics, Genomics and Computational Biology, Next generation sequencing and integrative data analy- sis, gene networks Danielle Braun 2014–
Cancer risk prediction, comparative effectiveness re- search, measurement error Alice Cleynen 2014–15
Statistical genetics; Decision theory, survival analysis, model selection David Mosen Ansorena 2015–16
Statistical analysis of high-throughput genomics; Ge- nomic copy number analysis in cancer; Algorithmics and optimization problems Anil Samur 2016– Alternative splicing, multiple myeloma genomics Prasad Patil 2016–
Personalized medicine, genomic biomarker development, prediction, study reproducibility/replicability, data visu- alization Nathanael Fillmore 2016– Machine
learning, medical
informatics, multiple
myeloma Boyu Ren
2017– Bayesian nonparametrics 47
SERVICE EDITORIAL WORK Associate Editor, Journal of the American Statistical Association — Theory and Methods, 1999– 2002.
Associate Editor, Journal of the American Statistical Association — Applications and Case Studies, 2003–2007. Associate Editor, Biometrics, 2000–2002. Editorial Board Member of Medical Decision Making, 1999–2005. Editorial Board Member of Source Code for Biology and Medicine, 2005–present. Book Series Editor, UseR!, Springer, 2004–present. Statistical Board of Reviewing Editors (SBoRE)Member, Science Magazine, 2014-2016 Referee for: American Journal of Epidemiology, American Journal of Human Genetics, Annals of Applied Statistics, Annals of Internal Medicine, Bioinformatics, Biometrics, Biometrika, Cancer Research, Clinical Chemistry, Computational Statistics and Data Analysis, Journal of Biomedical Informatics, Journal of the American Statistical Association, Journal of Econometrics, Journal of Statistical Computations and Graphics, Journal of Statistical Planning and Inference, Journal of the Royal Statistical Society B, Medical Decision Making, New England Journal of Medicine, Statistics in Medicine. Book reviewer for MIT Press, McMillan, Marcel Dekker, Springer, Wiley. GRANT REVIEWS Grant proposal reviewer for: National Science Foundation; Alberta Heritage Foundation for Medical Research; Department of Higher Education and Scientific Research, Italy; National Coordinating Center for Health Technology Assessment NIH Study Sessions: CA-99-013 ”Cancer Surveillance Modeling Network (CISNET)”, 1999 NIH “Genome” Study Section, Ad hoc member, 2003. NIH “Genomics, Computational Biology and Technology” Study Section, Ad hoc member, 2004.
NIH Special Emphasis Panel/Scientific Review Group 2007/01 ZCA1 RTRB-2. Ad hoc mem- ber, 2006. NIH Special Emphasis Panel/Scientific Review Group 2008/05 ZRG1 HOP-Z (29) ”Diversity Predoctoral Fellowship” Ad hoc member, 2008. NIH “Epidemiology of Cancer” Study Section, Ad hoc member, 2007. Charter member 2008– 2012.
48 NIH Site Visits: P01 ”Statistical Methods for Medical Studies”, Fred Hutchinson Cancer Research Center, 2000. PANELS, COMMITTEES AND ADVISORY BOARDS American Cancer Society’s Breast Cancer Risk Communication workshop and consensus statement, October 1999. Member. NIH-NIDDK mPSA Biomarkers Consortium External Advisory Panel. 2002–2005. The University of North Carolina-Chapel Hill Innovative Methods Program for Advancing Clinical Trials (IMPACT), External Advisory Committee, 2010-present The University of Texas M.D. Anderson Cancer Center External Advisory Board. 2010–present. Case Western University SPORE in Gastrointestinal Cancer External Advisory Board, 2009–present. Counsyl Scientific Advisory Board, 2010-present R01 “Personalizing NSCLC Therapy: Exploiting KRAS Activated Pathways”, External Advisory Board, 2011-present The Akbaraly Foundation, 4AWoman Project to Fight against Gynecological and Breast Cancer, Scientific Advisory Board, 2012-present National Brain Tumor Society Endpoints, Steering Committee, 2012-present Member, Committee on Applied and Theoretical Statistics (CATS), National Academies of Science, 2012-2015 Member, Active Surveillance P01, Johns Hopkins University, External Advisory Board, 2013-present Member, Intelligence Science and Technology Experts Group (ISTEG), The National Academies of Sciences, Engineering, and Medicine, 2015- Member, External Advisory Board, Pancreatic Cancer SPORE at UNC-Chapel Hill, 2016- PROFESSIONAL SOCIETIES Member of Sigma Xi, IMS, ISI, ASA, SMDM, AACR and Biometric Society. International Biometric Society / ENAR. Member of the ENAR Regional Advisory Board, 2000-2003. Member of the ENAR Education Advisory Committee 2004. American Statistical Association: Section on Risk Analysis. Charter Member, 1995. Publication Officer, 1998-1999. Chair, 2002. 49
International Society for Bayesian Analysis Member of the presidential nominating committee. 1995. CONFERENCES Promoter and organizer (with D. Draper and M. West) of the Workshop on Model Uncertainty and Model Robustness, Bath, England, June 30 and July 1, 1995. Program Committee member of the III-rd World Meeting of the International Society for Bayesian Analysis, Oaxaca, Mexico, 29-30 September 1995. Chair of the program committee and organizing committee of the Workshop on Stochastic Model Building and Variable Selection, Duke University, October 9 and 10, 1997. Member of the scientific committee of the International Workshop on Foundational Issues and Statistical Practice, October 14–16, 1999 Bibbiena, Italy. Co-organizer of the IMA Workshop on Statistical Methods for Gene Expression: Microarrays and Proteomics. Minneapolis, September 2003. Member of the scientific committee of the Genomic Signal Processing and Statistics (GENSIPS) workshop on “Computational Techniques for Genomic Regulatory Networks”, Baltimore, May 26- 28, 2004. Member of the scientific committee of the Third Annual AACR International Conference on Fron- tiers in Cancer Prevention Research, Seattle, October 16-20, 2004. Member of the scientific committee of the Second International IMS/ISBA Joint Meeting, Bormio, Italy, January 12-14, 2005. Session organizer. 1996 ENAR meetings. Richmond, VA. Invited session. 1996 Joint Statistical Meetings. Chicago, IL. Special contributed session. 1998 Joint Statistical Meetings. Dallas TX. Invited session. 1999 Joint Statistical Meetings. Baltimore MD. Invited session. AWARD COMMITTEES ASA, Risk Analysis Section. Best Contributed Paper Award, 1999—2003. ASA, Risk Analysis Section. Student Travel Award, 2001—2003. Myrto Lefkopoulou Lecture, 2000 Savage Award Committee, 2004—2007. SERVICE AT DUKE Committee for the revision of the ISDS PhD curriculum. 1991/92 and 1998/99. Committee for Ph.D. Exam, 1991/92 1992/93 and 1996/97. 50
Organizer of the ISDS Departmental Seminar. 1992/93 through 1994/95. Organizer of the ISDS Student/Faculty Workshop. 1992/93 through 1994/95. Committee for the Review of the ISDS PhD program. 1997-1998. SERVICE AT JOHNS HOPKINS Administration Director, Bioinformatics Shared Resource, Kimmel Cancer Center. 2004–present. Committees Organizer, Gene Expression Methodology Seminar Series, Department of Oncology, 1999–2001. Organizer, Grand Rounds, Department of Biostatistics, 2000–2002. Organizer, Genomics Working Group, Departments of Oncology and Biostatistics, 2001–2003. Chair, Search Committee for Oncology Biostatistics faculty position, Department of Oncology, 2001.
Member, Search Committee for Genetic Epidemiology faculty position, Department of Epidemiol- ogy, 2001. Member, Advisory Board for the JHMI Microarray Core Facility, School of Medicine. 2002— present.
Chair, Steering Committee for Genomics in Public Health, School of Public Health, 2002–present. Member, Ad hoc committee to evaluate the cancer prevention and control program, School of Medicine, 2002–2003. Ad hoc member, Appointment/Promotion Committee, School of Public Health, 3 associate pro- fessor cases. Member, Committee on information technology in research, Department of Oncology 2003–2004. Member, Shared Resources Committee, Department of Oncology, 2003–present. Member, Search Committee for Director of the Cancer Prevention and Control Program in the Cancer Center. 2003–2004. Member, Search Committee for Director of Information Technology in the Cancer Center. 2004– 2005. Chair, Joint Search Committee for Bioinformatics Faculty in Oncology, Biostatistics and MMI. 2004–2005 and 2005–2006. Member, Search Committee for Biostatistics Faculty in Oncology. 2007–2008. SERVICE AT HARVARD Member, Dana-Farber Cancer Institute, Executive Council on Research, 2009-present 51
Member, Committee of Comparative Effectiveness (CCE), Harvard Medical School. 2010–2011. Member, Subcommittee on the Degree of Doctor of Philosophy in Biostatistics, Harvard School of Public Health. 2010–2011, 2012-2014, 2014-2015. Member, Committee on Professional Conduct, 2010-present Member, External Advisory Board, Dana Farber Cancer Genetics, 2010 Member, Harvard University Milton Fund Committee, 2010-present Member, Dana-Farber/Harvard Cancer Center Center Scientific Council, 2010-present Member, Office for Faculty Development Advisory Committee, 2011-present Member, OnCore Faculty Advisory Committee, 2012-2013 Chair, Dana-Farber Cancer Institute Task Force on Research Computing, 2012. Member, Dana-Farber Faculty Database Steering Committee, 2012-present Member, Dana-Farber Cancer Institute Strategic Planning Research Computing Working Group, 2012-present Member, Internal Advisory Board for the Harvard Cancer Prevention Education and Career Devel- opment Program, 2013- Member, Claudia Adams Barr Review Committee, 2014-present Member, Genetics Search Committee, Dana-Farber Cancer Institute, 2014 Member, CCPM Search Committee, Dana-Farber Cancer Institute, 2013-2014 Member, Statistician Search Committee, Children’s Hospital, 2010, 2014 Member, Medical Oncology Search Committee, Dana-Farber Cancer Institute, 2013-2014, 2017- Member, Junior Faculty Search Committee, Harvard School of Public Health, 2009-2010. 2010- 2011, 2013-2014 Member, Senior Vice President of Research Administration Search Committee, Dana-Farber Cancer Institute, 2013-2014 Member, Research Backfill Task Force, Dana-Farber Cancer Institute, 2013-2014 Member, Senior Faculty Search Committee, Cancer Epidemiology and Cancer Prevention, Harvard School of Public Health, 2014 Member, Advisory Committee of the Harvard Office for Scholarly Communication, 2015- Member, Junior Faculty Search Committee, Dana-Farber and Harvard Medical School, 2017- 52 Document Outline
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