9100 D Regents Road Matan Hofree La Jolla, CA 92037 Phone: (310)913-7320 [email protected] Linked-in Website Research brief Precision medicine is poised to have tremendous impact on health and society in the coming decade. A key challenge to realizing this vision is the complexity of linking genotype to phenotype. Due to the combinatorial nature of this problem it will not be resolved by merely collecting ever larger datasets via high-throughput measurement techniques. To address this challenge, I am conducting research at the confluence of basic biology and medicine, using techniques from machine learning, statistics and network biology. My research focuses on two related fronts: (1) improving prediction and modeling of human disease through use of prior biological knowledge, and (2) understanding the role of rare mutation in cancer and the limitations of current methodology for identifying these. Education 2014 Ph.D. in Computer Science University of California, San Diego, CA 2007 B.Sc. in Computer Science and Computational Biology Hebrew University of Jerusalem, Jerusalem, Israel Magna cum laude Research Experience 2014 – Present Ideker Lab, Departments of Medicine and Bioengineering University of California, San Diego, CA Postdoctoral research fellow Advisor: Trey Ideker 2009 – 2014 Ideker Lab, Departments of Medicine and Bioengineering University of California, San Diego, CA Graduate student Thesis topic: Analysis of Genomic Variants via Gene Networks. Thesis advisor: Trey Ideker Summer 2007 Segal Lab of Computational Biology, Department of Computer Science Weizmann Institute of Science, Rehovot, Israel The Emma and Oscar Getz Summer Science Program for Israeli Students Visiting summer scholar Advisor: Eran Segal 2006 – 2007 Margalit Computational Molecular Biology Lab, Hebrew University of Jerusalem, Jerusalem, Israel Undergraduate researcher Advisor: Hanah Margalit Matan Hofree CV, Page 2 Peer-reviewed Journal Publications 13. Hofree M, Engin BH, Carter H, Kreisberg JF, Bandyopadhyay S, Mischel PS, Friend S, Ideker T. (2015). The role of rare and combinatorial mutations in cancer (in submission) 12. Jaeger PA, Lucin KM, Britschgi M, Vardarajan B, Huang RP, Kirby L, Abbey R, Boeve BF, Boxer AL, Farrer LA, Finch N, Graff-Radford N, Hofree M, Huang R, Johns H, Karydas A, Knopman DS, Loboda A, Mayeux R, Narasimhan R, Petersen RC, Podtelezhikov A, Pradhan S, Rademakers R, St George-Hyslop P, Sun CH, Younkin S, Miller BL, Ideker T, & Wyss-Coray T. (2015). Network-driven plasma proteomics expose molecular changes in the Alzheimer’s brain. (in submission) 11. Roosing S, Hofree M, Kim S, Scott E, Copeland B, Romani M, Silhavy JL, Rosti RO, Schroth J, Mazza T, Miccinilli E, Zaki MS, Swoboda KJ, Milisa-Drautz J, Dobyns WB, Mikati M, Incecik F, Azam M, Borgatti R, Romaniello R, Boustany RM, Clericuzio CL, D'Arrigo S, Stromme P, Boltshauser E, Stanzial F, Mirabelli-Badenier M, Moroni I, Bertini E, Emma F, Steinlin M, Hildebrandt F, Johnson CA, Freilinger M, Vaux KK, Gabriel SB, Aza-Blanc P, Heynen-Genel S, Ideker T, Dynlacht BD, Lee JE, Valente EM, Kim J & Gleeson JG. (2015). Functional genome-wide siRNA screen identifies as mutated in Joubert syndrome. eLife 4, doi:10.7554/eLife.06602. 10. Engin HB, Hofree M, Carter H. (2014). Identifying mutation specific cancer pathways using a structurally resolved protein interaction network. Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing 20, 84-95 9. The Cancer Genome Atlas Research Network. (2014). Integrated Genomic Characterization of Papillary Thyroid Carcinoma. Cell 159(3):676-690. 8. Novarino G*, Fenstermaker AG*, Zaki MS*, Hofree M, Silhavy JL, Heiberg AD, Abdellateef M, Rosti B, Scott E, Mansour L, Masri A, Kayserili H, Al-Aama JY, Abdel- Salam GM, Karminejad A, Kara M, Kara B, Bozorgmehri B, Ben-Omran T, Mojahedi F, Mahmoud IG, Bouslam N, Bouhouche A, Benomar A, Hanein S, Raymond L, Forlani S, Mascaro M, Selim L, Shehata N, Al-Allawi N, Bindu PS, Azam M, Gunel M, Caglayan A, Bilguvar K, Tolun A, Issa MY, Schroth J, Spencer EG, Rosti RO, Akizu N, Vaux KK, Johansen A, Koh AA, Megahed H, Durr A, Brice A, Stevanin G, Gabriel SB, Ideker T, & Gleeson JG (2014) Exome sequencing links corticospinal motor neuron disease to common neurodegenerative disorders. Science 343(6170):506-511. -- Ranked by Altmetrics in the top 3% of articles from the journal Science. Cited 78 times since Jan. 2014 5. Gross AM, Orosco RK, Shen JP, Egloff AM, Carter H, Hofree M, Choueiri M, Coffey CS, Lippman SM, Hayes DN, Cohen EE, Grandis JR, Nguyen QT, & Ideker T. (2014). Multi- tiered genomic analysis of head and neck cancer ties TP53 mutation to 3p loss. Nature genetics 46(9):939-943. 4. Zhang EY, Cristofanilli M, Robertson F, Reuben JM, Mu Z, Beavis RC, Im H, Snyder M, Hofree M, Ideker T, Omenn GS, Fanayan S, Jeong SK, Paik YK, Zhang AF, Wu SL, & Hancock WS. (2013). Genome wide proteomics of ERBB2 and EGFR and other oncogenic pathways in inflammatory breast cancer. Journal of proteome research 12(6):2805-2817. Matan Hofree CV, Page 3 3. Hofree M, Shen JP, Carter H, Gross A, & Ideker T. (2013). Network-based stratification of tumor mutations. Nature methods 10(11):1108-1115. -- Ranked by Altmetrics in the top 5% of articles tracked. Cited 82 times since Sept. 2013. 2. Potts MB, Kim HS, Fisher KW, Hu Y, Carrasco YP, Bulut GB, Ou YH, Herrera-Herrera ML, Cubillos F, Mendiratta S, Xiao G, Hofree M, Ideker T, Xie Y, Huang LJ, Lewis RE, MacMillan JB, & White MA. (2013). Using functional signature ontology (FUSION) to identify mechanisms of action for natural products. Science signaling 6(297):ra90. 1. Elefant N, Berger A, Shein H, Hofree M, Margalit H, & Altuvia Y. (2011). RepTar: a database of predicted cellular targets of host and viral miRNAs. Nucleic acids research 39(Database issue):D188-194. * Co-authored Reviews, Book Chapters and Invited Publications 2. Carter H, Hofree M, & Ideker T. (2013). Genotype to phenotype via network analysis. Current opinion in genetics & development 23(6):611-621. 1. Chuang HY*, Hofree M*, & Ideker T (2010) A decade of systems biology. Annual review of cell and developmental biology 26:721-744. * Co-authored Patents and Reports of Invention 2013 Personalizing Chemotherapy Using Network-based Stratification of Tumors Tech ID: 23065 / UC Case 2013-085-0 (licensed) U.S. Patent Pending International Conference Presentations Jul. 2014 22nd Annual Conference on Intelligent Systems for Molecular Biology, Boston, MA. Network-Based Stratification of Tumor Mutations Feb. 2014 The Second Annual Q-bio meeting, Waikoloa, HI Network-Based Stratification of Tumor Mutations Jul. 2013 21st Annual International Conference on Intelligent Systems for Molecular Biology/12th European Conference on Computational Biology, Berlin, Germany Network-Based Stratification of Tumor Mutations Mar. 2013 Joint Summit on Translational Bioinformatics, San Francisco, CA. Network-Based Stratification of Tumor Mutations Nov. 2012 TCGA Second Annual Scientific Symposium, Crystal City, VA. Network-Based Stratification of Tumor Mutations (video: goo.gl/lT1xkc) Aug. 2012 The 13th International Conference on Systems Biology, Toronto, Canada Network-Based Stratification of Tumor Mutations Matan Hofree CV, Page 4 Selected Poster Presentations May 2014 TCGA Third Annual Scientific Symposium, Bethesda, MD Network-Based Stratification Thyroid Cancer Apr. 2014 American Association for Cancer Research Annual Meeting, San Diego, CA. Network-Based Stratification of Thyroid Cancer Aug. 2012 The 13th International Conference on Systems Biology, Toronto, Canada Inferring sparse multivariate models to predict disease phenotype from genotype. Awards and Honors 2013 ISMB/ECCB 2013 Student Travel Award 2008 – 2011 UCSD Jacobs Fellow. A 3 year award to exceptional incoming PhDs in the Jacobs School of Engineering. 2008 Weizmann Institute, Emma and Oscar Getz Summer Scholars program 2007 Hebrew University Bioinformatics Program student scholarship 2006 Hebrew University, Faculty of Mathematics and Sciences Dean’s List Professional Affiliations 2014 – Present American Association for Cancer Research (AACR) 2012 – Present International Society for Computational Biology (ISCB) Teaching Experience Summer 2013 Instructor – Advanced data structures University of California, San Diego, CA A 6 week summer course of ~90 students, managing a supporting TA staff of five. The course was an upper division required class on advanced data structures and related algorithms, and included topics at the core of software development. I introduced the use of peer instruction into the curriculum for this class in UCSD. Winter 2011 Teaching Assistant – Introduction to Algorithms University of California, San Diego, CA I was a teaching assistant for the upper division algorithms class; a required core class taken by all CS and related majors. As part of my TA responsibilities I taught a weekly discussion section and held office hours. I helped write exam, midterms, weekly quiz and homework assignments, and managed the course website. I developed a novel Travelling Salesman problem with a remote testing paradigm in Python which allowed us to asses performance of ~150 students. 2004 - 2006 Ankori Ltd., Tel-Aviv, Israel Psychometric Instructor I worked as an instructor for a Psychometric exam (SAT equivalent) preparation company. The position involved all aspects of preparing groups of 20-35 students for the Israeli Psychometric examination. Each course spanned 2-3 months. Matan Hofree CV, Page 5 Non-academic Work Experience 2007 – 2008 Imperva