Bahman Afsari

Contact Instructor (Tenure Track) | Information Sidney Kimmel Comprehensive Cancer Center | Cell: +1-443-786-5668 The | E-mail: [email protected] 550 N. Broadway Suite 1101 | Baltimore, MD 21205, USA |

Education Postdoctoral Fellow, Johns Hopkins University, 2017 Division of -Biostatistics, Department of Oncology • Metnor: Cristian Tomasetti • Co-mentor: B. Vogelstein Analyzing mutation rates using 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 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 , 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 , 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 • “Ordering of the Features for Molecular Cancer Classification,” School of Electrical and Computer Engineering, University of Tehran, 2013 (Invited Talk) • “Microarray classification from several two-gene expression comparisons,” Interna- tional Conference on Machine Learning and Applications, CA, 2008

Refereed [1] E.F. Davis-Marcisak, P. Orugunta, G. Stein-O’Brien, SV Puram, ER Torres, A. Journal Hopkins, E.M. Jaffee, A.V. Favorov, B. Afsari, L. A. Goff, E.J. Fertig, “Expres- Publications sion variation analysis for tumor heterogeneity in single-cell RNA-sequencing data,” accepted to Cancer Research [2] M. Dal Molin, S. Springer, D. Massica, C. Douville, C. Thoburn, B. Afsari, ...,“A multi-modality test to guide the management of patients with pancreatic cysts,” accepted to Sci. Trans. Med. [3] Y. Wang, ... “Evaluation of liquid from the Papanicolaou test and other liquid biopsies for the detection of endometrial and ovarian cancers.” Sci. trans. med., 10(433), eaap8793, 2018. [4] S. Springer, ..., “Non-invasive detection of urothelial cancer through the analysis of driver gene mutations and aneuploidy,” eLife , e32143, 2018 [5] J. Cohen, L. Li, Y. Wang, C. Thoburn, B. Afsari,..., “Detection and localization of surgically resectable cancers with a multi-analyte blood test,” Science, 2018 [6] B. Afsari, T. Guo, ...., E. J. Fertig, “Splice Expression Variation Analysis (SEVA) for Inter-tumor Heterogeneity of Gene Isoform Usage in Cancer,” Bioinformatics, 2018 [7] D. Kelley,..., “Integrated analysis of whole-genome ChIP-Seq and RNA-Seq data of primary head and neck tumor samples associates HPV integration sites with open chromatin marks,”Cancer research, 2017 [8] T. Guo, S. Akihiro, B. Afsari, ..., “A novel functional splice variant of AKT3 defined by analysis of alternative splice expression in HPV-positive oropharyngeal cancers,” Cancer research, 2017 [9] M. G¨onen,...,“A Community Challenge for Inferring Genetic Predictors of Gene Essentialities through Analysis of a Functional Screen of Cancer Cell Lines,” Cell systems, 2017

5 of 8 [10] S. M. Hill, L. M. Heiser, ..., B. Afsari, ..., S. Mukherjee, “Empirical assessment of causal network inference through a community-based effort,” Nature Methods, 13, 2016 (as the main contributor of Stochastic Chaos team). [11] B. Afsari, D. Geman, E. J. Fertig, “Learning Dysregulated Pathways in Cancers from Differential Variability Analysis,” invited paper, Cancer informatics , 13 (S5) (2014), 61-67. [12] B. Afsari, E. J. Fertig, D. Geman, L. Marchionni, “switchBox: An R package for k-Top Scoring Pairs (kTSP) classifier development,” Bioinformatics, btu622 (2014).

[13] B. Afsari, U.M. Braga-Neto, D. Geman, “Rank discriminants for predicting phe- notypes from RNA expression,” Annals of Applied Statistics, 8, no (3), 2014. [14] Marchionni, L., Afsari, B., Geman, D., Leek, J. T., “A simple and reproducible breast cancer prognostic test,” BMC Genomics, 14, no. 1 (2013): 336. [15] X. Lin , B. Afsari, L. Marchionni, G. Parmigiani, L. Cope, D. Naiman, D. Ge- man, “The ordering of expression among a few genes can provide simple cancer biomarkers and signal BRCA1 mutations,” BMC Bioinformatics. 10:256, 2009.

Submitted and [16] B. Afsari, Y. Zhang, A. L. Lie, L. Danilova, V. Favarov, T. Rosenquist, P. Grollman, Working Papers K. W. Kinzler, B. Vogelestein, C. Tomassetti, “Supervised mutational signatures predict tissue-specific etiological factors in cancer,” to be submitted in Cell [17] B. Afsari, E.J.Fertig, A. V. Favorov, L. M.Cope, “REVA: a Rank-based Multi- dimensional Measure of Correlation,” in Bioarxiv

Conference [18] B. Afsari, T. Guo, M. Considine, ..., E. J. Fertig, “Splice Expression Variation Anal- Publications ysis (SEVA) for Inter-tumor Heterogeneity of Gene Isoform Usage in Cancer,” RECOMB-CBB , 2017 [19] B. Afsari, K. Mazdapour, B. Jedynak, “Ordinal-Contextual Dissimilarity for Anal- ysis of Heros in Tragedies,” Bridges Conference Proceedings, Baltimore, 2015 [20] F. Ahourai, M.Tabandeh, M. Jahed, B. Afsari, “A fair routing algorithm for wireless Mesh networks based on game theory,” 144-149, ICN 2009 [21] D.Geman, B.Afsari, A.C.Tan, D. Naiman, “Microarray classification from several two-gene expression comparisons,” Proceedings of ICMLA, San Diego, 2008 [22] V. S. Mansouri, B. Afsari, H. S. Mansouri, “A simple transport layer protocol for wireless sensor networks,” Proceedings of ISSNIP 2005

Posters [23] B. Afsari, T. Guo, M. Considine, ..., E. J. Fertig, “Splice Expression Variation Analysis (SEVA) for Differential Gene Isoform Usage in Cancer,” American As- sociation for Cancer Research, Washington, D.C., USA, 2017 [24] B. Afsari, D. Geman, E. J. Fertig, “Expression Variation Analysis (EVA) identifies alterations in the gene-gene interactions of pathways in human cancers,” Systems Biology: Global Regulation of Gene Expression Conference, Cold Spring National Harbor Laboratory meeting, San Juan, 2015 [25] B. Afsari, E. J. Fertig, L. Younes, D. Geman, and L. Marchionni, “Hardwiring Mechanism into Predicting Cancer Phenotypes by Computational Learning,” American Association for Cancer Research, San Diego, 2014

6 of 8 [26] B. Afsari, L. Marchianno, E. J. Fertig, U. Braga-Neto, D. Geman,“Feature Selection for Ranked-based Classifiers Applied to Cancer Biomarker Discovery,” Interna- tional Biometric Society, Eastern North American Region Meeting, Baltimore, 2014 [27] B. Afsari, E. J. Fertig, D. Geman, J. T. Leek, L. Marchionni, “Applying k-Top Scoring Pairs (kTSP) to Simplify Mammaprint using a new R Package,” Genetics Research Day, Maryland Genetics, Epidemiology, and Medicine, Baltimore, 2014 [28] B. Afsari, L. V. Danilova, A. V. Favorov, W. Lee, D. Taylor, Elana J. Fertig, “Prediction for Time-Course Proteomics In Vitro ,” RECOMB/ISCB Conference On Regulatory and Systems Genomics, with DREAM Challenge, Toronto, Ca, Nov. 2013 (invited poster and oral presentation, DREAM Challenge winner)

References Professor Donald Geman (PhD Adviser) Dept. of Applied Mathematics and Statistics Johns Hopkins University Clark Hall 302A 3400 N. Charles Street Baltimore, MD 21218 Email: [email protected] Phone: 410-516-7678

Dr. Elana J. Fertig (Postdoctoral Supervisor) Assistant Professor of Oncology Division of Biostatistics and Bioinformatics Johns Hopkins University 550 N Broadway, 1101 E Baltimore, MD 21205 Email: [email protected] Phone: 410 955 4268

Dr. Cristian Tomasetti (Postdoctoral Supervisor) Assistant Professor of Oncology and Biostatistics Johns Hopkins University 550 N Broadway, 1103 E Baltimore, MD 21205 Email: [email protected] Phone: 443 287 5683

Professor Daniel Naiman Dept. of Applied Mathematics and Statistics Johns Hopkins University, 202C Whitehead Hall, 3400 N. Charles Street, Baltimore, MD 21218 E-mail: [email protected] Phone: 410-516-7203

Dr. Bert Vogelestein Clayton Professor of Oncology and Pathology Johns Hopkins University Room 589, Cancer Research Bldg.

7 of 8 1650 Orleans Street, Baltimore, MD 21231 Baltimore, MD 21205 Email: [email protected] Phone: 410-955-8878

Dr. Luigi Marchionni Assistant Professor of Oncology Johns Hopkins University 1550 Orleans St., CRB2, Room 1M54 Baltimore, MD 21231 E-mail: [email protected] Phone: 410-502-8179

Dr. Bruno Jedynak Maseeh Associate Professor Dept. of Mathematics and Statistics Portland State University Neuberger Hall, Room 335 724 SW Harrison Street Portland, OR 97201 Email: [email protected] Phone: 503-725-8283

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