Bahman Afsari Contact Instructor (Tenure Track) j Information Sidney Kimmel Comprehensive Cancer Center j Cell: +1-443-786-5668 The Johns Hopkins University j E-mail: [email protected] 550 N. Broadway Suite 1101 j Baltimore, MD 21205, USA j Education Postdoctoral Fellow, Johns Hopkins University, 2017 Division of Bioinformatics-Biostatistics, Department of Oncology • Metnor: Cristian Tomasetti • Co-mentor: B. Vogelstein Analyzing mutation rates using machine learning and statistical methods and their relationship with age Postdoctoral Fellow, Johns Hopkins University, 2016 Division of Bioinformatics-Biostatistics, Department of Oncology • Mentor: Elana J. Fertig Analyzed high dimensional genomics data (microarray, RNA-seq) using machine learning and statistical methods PhD, Johns Hopkins University, 2013 Electrical and Computer Engineering • Adviser: Donald Geman • GPA: 3.94/4.00 • Dissertation : Modeling Cancer Phenotypes with Order Statistics of Transcript Data Predictors, distributions and biologically meaningful classification rules were pro- posed based on the ordering of a subset of gene expression levels. MSE, Johns Hopkins University, 2012 Applied Mathematics and Statistics • GPA: 4.00/4.00 • Area of Study: Statistics MSc, University of Tehran, 2006 Electrical and Computer Engineering • Advider: Ashkan R. Kian • GPA: 18.94/20 (with Honors in Control Engineering Major) • Thesis :Developing a Heuristic Method for Solving Nonlinear Games A heuristic-stochastic method was proposed to solve a special class of non-linear games useful in studying Wireless Mesh-Networks. BS, University of Tehran, 2004 Electrical and Computer Engineering • GPA: 16.93/20 (Top Student in Control Engineering Major) Honors and Awards • DREAM Challenge winner with Stochastic Chaos Team, Conference On Regulatory and Systems Genomics with DREAM Challenge, Toronto, Ontario, Canada, 2013 • ICMLA Competition Award: \Micro-array Classification Challenge," San Diego, CA, 2008 1 of 8 • Ranked 2nd among 17th MS students in Control Engineering and 3rd among more than 60 MS students in Electrical Engineering Department, University of Tehran, 2006 • Ranked 1st among undergraduate Control Engineering students, University of Tehran, 2004 • Member of the winning team of the \Easy Rob" (line tracking robot) contest, Uni- versity of Tehran, 2002 Research Interests • Computational Genomics • Machine Learning for High Dimensional Data • Robust Biomarkers • Gene Set Analysis • Alternative Splice Detection • Multi-variable Control Research and Professional • Instructor (Tenure Track), Sidney Kimmel Comprehensive Cancer Center, Johns Experience Hopkins University, 2017-present • Developed, contributed, implemented CancerSEEK, a cancer diagnosis test from ctDNA and Protein levels in blood • Postdoctoral Fellow, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, 2013-2017 • Developed and implemented (as the main contributor) the winning strategy for target efficacy prediction and gene interaction dynamics from time-course pro- teomics data in DREAM challenge (2013) • Developed a robust multivariate gene set analysis method using variability anal- ysis and customized and optimized the algorithm for multitude number of gene sets • Developed an algorithm which detects genes with aberrant alternative splicing and/or expression pattern change in cancer and collaborated with biologists to confirm the identified alternative splicing genes • Developed an algorithm for biomarker discovery to determine patients' survival from gene expression data • Prepared a proposal (R03) for splice variance analysis under Dr. Fertig supervi- sion • Analyzed and predicted the efficacy of anti-cancer agents in cell lines and collab- orated with biologists for further application • Analyzed statistical properties of the machine learning techniques for phenotype prediction and improved their efficiency using statistical theory • Implemented algorithms in R, made them freely available and prepared the ap- plication note papers • Research Assistant, Department of Electrical and Computer Engineering, Johns Hopkins University, Fall 2007-2013 • Implemented the winning strategy for ICMLA challenge for the cancer prediction from gene expression data (2008) • Developed algorithms for robust biomarker discovery and phenotype prediction 2 of 8 • Participated in improving and simplification of Mammaprint (a utilized clinical biomarker for recurrence of Breast cancer) and its implementation in R as a package • Developed an algorithm to discover mechanistic micro-RNA and mRNA biomark- ers • Participated in preparation of a grant proposal for hardwiring biological mecha- nisms into the biomarkers (R01) (under Dr. Marchionni and Prof. Geman) • Implemented bioinformatics algorithms in MATLAB and C/C++ • Developed ranked-based generative models to model gene expression and study their mathematical properties • Control Engineer, Foundation Field Bus Group, Farineh Technology Company, Tehran, Spring 2005-Fall 2007 • Modeled industrial plants, built model plants and implemented controllers. • Programmer, Sepanta Network Solution, Tehran, Spring 2002-Spring 2003 • Developed an automated phone credit check for Voice over Internet Protocol (VoIP) users. • Member of the Robotic Group, Robotic Lab, University of Tehran, 2001-2002 • Constructed a line tracker and a object collector robot. Academic ´ Experience • Visiting Student, CMLA, Ecole Normale Sup´erieure,France, Winter 2012 • Summer School, \Machine Learning Summer School," University of Chicago, Sum- mer 2009 Travel Grant • \Systems Biology: Global Regulation of Gene Expression Conference," Cold Spring National Harbor Laboratory, 2015 • CMLA, Ecole´ Normale Sup´erieure,France, Winter 2012 • \Machine Learning Summer School," University of Chicago, 2009 Advisees • Cameron Rudd (an Intern from Sarah Lawrence College), Johns Hopkins University, Summer 2014 Teaching Experience Instructor (Johns Hopkins University): • C/C++ Programming, Winter 2015 Instructor (Tehran Markaz Azad University): • Linear Control Systems, Spring 2007 designed and lecture a course for total 120 students in two sessions Teaching Assistant (Ecole´ Normale Sup´erieure): • Topics in Stochastic Molecular Biology, Winter 2012 Teaching Assistant (University of Tehran): • Stochastic Systems, Fall 2006, Fall 2005 • Linear Algebra, Fall 2004 • Linear Control Lab, Spring 2005 • Telecommunications I, Fall 2003-Fall 2004 3 of 8 Related • Computational Biology: Computational Functional Genomics, Principles of Com- Graduate plex Networked Systems, Topics in Bioinformatics Courses • Control Theory: Feedback control in biological signaling pathways, Modern Con- trol, Optimal Control, Stochastic Control, System Identification, Multi-variable Con- trol, Adaptive Control, Seminar on Control in Systems Biology • Probability and Statistics: Machine Learning, Monte Carlo Simulations, Infor- mation Theory, Graphical Models, Random Signal Analysis, Data Mining, Statistical Theory, Statistical Pattern Recognition, Random Process, Probability Theory • Miscellaneous: Heuristic Optimization, Game Theory, Commodities and Com- modity Derivatives, Advanced Topics in C++, Artificial Intelligence Languages • Farsi (native), English, Arabic (fluent), French, German (elementary) Computer Languages • C/C++, MATLAB, R, Python R Packages • \Top Scoring Triplet package," with D. Naiman, X. Lin, 2009 https : ==jshare:johnshopkins:edu=dnaiman1=public html=rxa= • \Switch-box," with Luigi Marchionni, 2014 Accepted in Bioconductor Also available in: http : ==luigimarchionni:org=software:html • \GS-Reg," with Elana J. Fertig, 2014 Accepted in Bioconductor • \GS-Benchmark," with Elana J. Fertig, 2014 Accepted in Bioconductor Professional Activities • Reviewer of Nucleic Acid Research, Bioinformatics, BMC Bioinformatics, PLOS ONE, Iranian Student's Conference on Electrical Engineering, PLOS Computational Biology, IEEE/ACM Transaction Computational Biology and Bioinformatics, Jour- nal of Medical and Biological Engineering Extracurricular Activities • Member of editorial board of Bargh Sharif (journal of Sharif University on electrical engineering), Sharif University, Tehran, 2002 • Deputy of the Scientific Committee of the 4th Iranian Student Conference on Elec- trical Engineering, University of Tehran, Summer 2001 • Students' Educational Representative, Department of Electrical Engineering, Uni- versity of Tehran, 2001-2003 (Head of the Students' Educational Council, 2003) Membership • Member of Institute of Electrical and Electronics Engineers • Member of American Association for Cancer Research • Member of American Statistical Association 4 of 8 Talks • \Variation Analysis to Detect Pathway Dysregulation in Cancer," Center for Cancer Research, National Institute for Cancer, Bethesda, MD, 2016 (Invited Talk) • \Splice Expression Variation Analysis (SEVA): A Variability Analysis to Detect Differential Isoform Usage in Cancer," Department of Bioinformatics and Computa- tional Biology, Genentech Research and Development, Genentech, CA, 2016 (Invited Talk) • \Anomaly Detection in Diseases using Variability Analysis of Measurement Order- ing," National Institutes of Health- National Heart, Lung, and Blood Institute, Bethesda, MD, 2016 (Invited Talk) • \Expression Variation Analysis (EVA) for Anomaly Detection in Cancer," University of Massachusetts, MA, 2016 (Invited Talk) • \Feature Selection for Ranked-based Classifiers Applied to Cancer Biomarker Dis- covery," International Biometric Society, Eastern North American Region Meeting, MD, 2014