Can Cenik, [email protected] Curriculum Vitae

Can Cenik, PhD [email protected] Ph: +1-857-350-2187 Department of Molecular Biosciences, University of Texas at Austin

Education Stanford University, School of Medicine 2012-2018 Postdoctoral Fellow, . Advisor: Dr. Michael P. Snyder Harvard Medical School 2008-2011 PhD, Genetics. advisor: Dr. Frederick P. Roth Harvard College 2004-2008 BA, magna cum laude, highest honors, Applied Mathematics. Thesis Advisor: Dr. John Wakeley

Academic Positions University of Texas at Austin, Department of Molecular Biosciences 2018-present Assistant Professor University of Massachusetts Medical School and Howard Hughes Medical Institute 2009-2012 Graduate Researcher, Advisor: Dr. Melissa Moore /Cancer Research UK Cambridge University, England 2006 Undergraduate Researcher, Advisor: Dr. Julie Ahringer Harvard University Organismic and Evolutionary Biology Department 2004-2005 Undergraduate Researcher, Advisor: Dr. Kathleen Donohue Massachusetts Institute of Technology Mathematics Department 2003 Summer Internship, 20th Research Science Institute, Advisor: Dr. Fangyun Yang Hacettepe University Entomology Museum 2002-2003 Part-time Museum Curator, Advisor: Dr. Yusuf Durmus

Academic Awards and Honors Travel Award, 14th Human Proteome Organization World Congress 2015

Stanford Center for Computational, Evolutionary, and Human Genetics Fellowship (Declined) 2013

Steering committee member, Genetics and Program, Harvard Medical School 2011

Travel Award, EMBL conference: From Functional Genomics to Systems Biology 2010

Travel Award, 7th Cold Spring Harbor Meeting on Eukaryotic mRNA Processing 2009

Travel Award, 17th Annual International Conference, ISMB 2009

Thomas Temple Hoopes `19 Prize, for best undergraduate theses 2008

Harvard College Program for Research in Science and Engineering Award 2007

Herchel Smith Undergraduate Research Fellowship 2006

Weissman International Internship Program Fellowship (Declined) 2006

Harvard College Research Program Scholarship 2005

Admiral Rickover Medal and Best Research Paper, 20th Research Science Institute (RSI) at MIT 2003

Bronze medal, Turkish National Biology Olympiads 2001, 2002, 2003

Silver medal, 13th International Biology Olympiad in Riga, Latvia 2002 1

Can Cenik, [email protected] Curriculum Vitae

Research Funding Cancer Prevention & Research Institute of Texas 2018-2023 RR180042 (PI: Cenik) Recruitment Award, Tenure-Track Faculty Member NIH Pathway to Independence Award (K99/R00) 2016-2021 R00CA204522 (PI: Cenik) National Cancer Institute Pathway to Independence Award Lucille Packard Foundation for Children’s Health Postdoctoral Fellowship 2013 UL1TR000093 (PI: Cenik) Lucille Packard Foundation for Children’s Health Institute

Peer-reviewed Publications (>1350 citations, h-index 13) * Co-first authorship § Corresponding author 1. Han CM, Catoe D, Munro SA, Khnouf R, Snyder MP, Santiago JG, Salit ML, Cenik C§. Purification of RNA within a specific size range using on-chip isotachophoresis with ionic spacer for high-throughput sequencing. Lab Chip. 2019 Aug 21;19(16):2741-2749. doi: 10.1039/c9lc00311h. 2. Cenik ES, Meng X, Tang NH, Hall RN, Arribere JA, Cenik C, Jin Y, Fire A. Maternal Ribosomes Are Sufficient for Tissue Diversification during Embryonic Development in C. elegans. Developmental Cell. 2019, Mar 25;48(6):811-826.e6. doi: 10.1016/j.devcel.2019.01.019. 3. Cenik B*, Cenik C*, Snyder MP, Brown SE. Plasma sterols and depressive symptom severity in a population-based cohort. PLoS ONE. 2017, Sep 8; 12(9):e0184382. doi: 10.1371/journal.pone.0184382/ 4. Cenik C, Chua HN, Singh G, Akef A, Snyder MP, Palazzo AF, Moore MJ, Roth FP. A common class of transcripts with 5’-intron depletion, distinct early coding sequence features, and N1-methyladenosine modification. RNA. 2017 Mar; 23:270-283. doi: 10.1261/rna.059105.116. 5. Araya CL*, Cenik C*, Reuter JA, Kiss G, Pande VS, Snyder MP, Greenleaf WG. Systematic identification of significantly mutated regions across cancer types highlights a rich landscape of functional molecular alterations. Nature Genetics. 2016 Feb; 48(2):117-25. doi: 10.1038/ng.3471. 6. Cenik C, Cenik ES, Byeon GW, Grubert F, Candille S, Spacek D, Alsallakh B, Tilgner H, Araya CL, Tang H, Ricci E, Snyder MP. Integrative analysis of RNA, translation and protein levels reveals distinct regulatory variation across humans. Genome Research. 2015 Nov; 25(11):1610-21. doi: 10.1101/gr.193342.115. 7. Heyer EE, Ozadam H, Ricci EP, Cenik C, Moore MJ. An optimized kit-free method for making strand- specific deep sequencing libraries from RNA fragments. Nucleic Acids Research. 2015 Jan; 43(1):e2. doi:10.1093/nar/gku1235 8. Ricci EP, Kucukural A, Cenik C, Mercier BC, Singh G, Heyer EE, Ashar-Patel A, Peng L, Moore MJ. Staufen1 senses overall transcript secondary structure to regulate translation. Nature Structural & Molecular Biology. 2014 Jan; 21(1):26-35. doi: 10.1038/nsmb.2739. 9. Kucukural A, Ozadam H, Singh G, Moore MJ, Cenik C§. ASPeak: an abundance sensitive peak detection algorithm for RIP-Seq. Bioinformatics. 2013 Oct; 29(19):2485-6. doi: 10.1093/bioinformatics/btt428. 10. Mahadevan K, Zhang H, Akef A, Cui XA, Gueroussov S, Cenik C, Roth FP, Palazzo AF. RanBP2/Nup358 potentiates the translation of a subset of mRNAs encoding proteins destined for the secretory pathway. PLoS Biology. 2013; 11(4):e1001545. doi: 10.1371/journal.pbio.1001545. 11. Bicknell A*, Cenik, C*, Chua HN, Roth FP, Moore MJ. Introns in UTRs: Why we should stop ignoring them. Bioessays. 2012 Dec; 34(12):1025-34. doi: 10.1002/bies.201200073/ 12. Singh G*, Kucukural A*, Cenik C, Weng Z, Moore MJ. The cellular EJC interactome reveals higher- order mRNP structure and an EJC-SR protein nexus. Cell. 2012 Nov; 151(4):750-64. doi:10.1016/j.cell.2012.10.007. 13. Cenik C, Chua HN, Tarnawsky SP, Derti A, Tasan M, Moore MJ, Palazzo AF, Roth FP. Genome analysis reveals interplay between 5’UTR introns and nuclear mRNA export of secretory and mitochondrial genes. PLoS Genetics. 2011 7(4): e1001366. doi: 10.1371/journal.pgen.1001366.

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Can Cenik, [email protected] Curriculum Vitae

14. Sephton CF*, Cenik C*, Kucukural A, Dammer EB, Cenik B, Han Y, Dewey CM, Roth FP, Herz J, Peng J, Moore MJ, Yu G. Identification of neuronal RNA targets of TDP-43-containing ribonucleoprotein complexes. Journal of Biological Chemistry. 2011 Jan; 286(2):1204 –1215. Paper of the Week. doi: 10.1074/jbc.M110.190884. 15. Cenik C, Wakeley J. Pacific salmon and the coalescent effective population size. PLoS ONE. 2010 Sep; 5(9):e13019. doi: 10.1371/journal.pone.0013019. 16. Derti A, Cenik C, Kraft P, Roth FP. Absence of evidence for MHC-dependent mate selection within HapMap populations. PLoS Genetics. 2010 Apr; 6(4):e1000925. doi: 10.1371/journal.pgen.1000925. 17. Cenik C, Derti A, Mellor JC, Berriz GF, Roth FP. Genome-wide functional analysis of human 5'untranslated region introns. Genome Biology. 2010 Mar; 11(3):R29. doi: 10.1186/gb-2010-11-3-r29. 18. Berriz GF, Beaver JE, Cenik C, Tasan M, Roth FP. Next generation software for functional trend analysis. Bioinformatics. 2009 Nov; 25 (22): 3043-4. doi: 10.1093/bioinformatics/btp498.

Patents 1. Moore MJ, Heyer EE, Ricci EP, Ozadam H, Cenik C, Li X. Compositions and Methods for Constructing cDNA Libraries that Allow for Mapping the 5' and 3' Ends of RNAs. US9828600B2. Published on Apr 09, 2015. 2. Araya CL, Cenik C, Reuter JA, Snyder MP, Greenleaf WJ. A system for multi-scale, annotation- independent detection of functionally-diverse units of recurrent genomic alteration. US20160378915A1. Published on Dec 29, 2016.

Conference Presentations and Invited Talks Gordon Research Conference, Translation Machinery in Health and Disease, Vancouver, TX 2019

Columbia University, Department of Systems Biology, New York, NY 2018

University of Washington, Department of Bioengineering, Seattle, WA 2018

Washington University School of Medicine, Department of Genetics, St. Louis, MO 2018

Revolution Medicines, Redwood City, CA 2018

New York Genome Center, New York, NY 2018

University of California Los Angeles, Department of Human Genetics, Los Angeles, CA 2018

Baylor College of Medicine, The Therapeutic Innovation Center, Houston, TX 2018

University of Texas Southwestern Medical Center, Department of Pharmacology, Dallas, TX 2017

Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 2017

Centre for Genomic Regulation, Barcelona, Spain 2017

European Molecular Biology Laboratory Genome Biology Unit, Heidelberg, Germany 2017

Stanford Center for Computational, Evolutionary, and Human Genetics, Stanford, CA 2017

66th Annual Meeting of the American Society of Human Genetics, Vancouver, Canada 2016

Stanford Center for Computational, Evolutionary, and Human Genetics, Stanford, CA 2016

14th Human Proteome Organization World Congress, Vancouver, Canada 2015

Genotype-Tissue Expression Project Analysis Group Meeting, Washington, DC 2014

From Functional Genomics to Systems Biology, Heidelberg, Germany 2010

7th Cold Spring Harbor Meeting on Eukaryotic mRNA Processing, New York, NY 2009

17th Annual International Conference, ISMB, Stockholm/Sweden 2009

Center of Cancer Systems Biology, Dana Farber Cancer Institute, Boston, MA 2009

8th Annual Symposium for Undergraduate Research, Harvard University 2006

Institute of Applied Mathematics, Middle Eastern Technical University 2004

Mathematical Society of Southeastern Europe, International Congress, Borovets/Bulgaria 2003 3

Can Cenik, [email protected] Curriculum Vitae

Teaching

Stanford University, School of Medicine 2016, 2017 Guest lecturer, “Genetics 211: Genomics” (graduate-level class) Stanford University, School of Medicine 2012-Present Mentor, two Stanford undergraduates (>2 years, supervised senior theses), one high school student, three summer undergraduate students, and one graduate rotation student. Harvard Medical School 2010 Teaching assistant, “Biophysics 205: Computational and Functional Genomics” (graduate-level class) Harvard College 2005-2008 Undergraduate Peer Tutor, >10 students in introductory mathematics, and biology courses. Selected “Award Peer Tutor” and received weekly training on better tutoring practices.

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