Revised 9/12/2019 CURRICULUM VITAE Ece D. (Gamsiz) Uzun, Phd

Revised 9/12/2019

CURRICULUM VITAE Ece D. (Gamsiz) Uzun, PhD

Business or Mailing Address: Department of Pathology Rhode Island Hospital 593 Eddy Street Providence, RI 02903 Business Telephone Number: 401-793-8190 Business Fax Number: 401-444-3109 Electronic Mail Address: [email protected]

EDUCATION Undergraduate Northeastern University, Boston, MA PhD in Chemical Engineering, 12/2009 Thesis title: Modeling the Influence of Drug Delivery Technologies on Oral Bioavailability of Low Solubility Drugs

Sabanci University, Istanbul, Turkey Master of Science in Biological Sciences and Bioengineering, 7/2003 Thesis Title: Cytotoxicity of Peroxynitrite and Nitric Oxide Induced Oxidative Stress on 3T3 Fibroblast Cell Line

Istanbul Technical University, Istanbul, Turkey Bachelor of Science in Chemical Engineering Graduated with honors, 6/2001

POSTGRADUATE TRAINING Fellowship Brown University, Providence, RI NIH Child T32 Postdoctoral Fellow, Dept. of Psychiatry and Human Behavior (Rhode Island Hospital) 9-2014 – Present

Translational Neurosciences Postdoctoral Fellow 9-2012 - 8-2014 Lifespan Research Institute the Lifespan division of Psychiatry, the Brown Institute for Brain Science and the Norman Prince Neurosciences Institute

Postdoctoral Fellow, Dept. of Molecular Biology, Cellular Biology and Biochemistry 1-2010 – 8-2012 Mentor: Dr. Eric Morrow 1

POSTGRADUATE HONORS AND AWARDS 2013 First Place in Department of Psychiatry and Human Behavior (DPHB) Research Day Postdoctoral Fellow Research Poster Competition

2012 First Place in Department of Psychiatry and Human Behavior (DPHB) Research Day Postdoctoral Fellow Research Poster Competition

Spring 2010 Fellowship from the Institute for Brain Science at Brown University, Center for Vision Research

Spring 2009 Fellowship from the Office of Provost at Northeastern University

2008 Research Assistantship from Simulations Plus, Inc., Lancaster, CA

2007 Northeastern University Outstanding Graduate Student Award in Teaching in Life Sciences, Physical Sciences and Engineering

2007 Northeastern University College of Engineering Outstanding Teaching Assistant Award

2007 Second Place in American Association of Pharmaceutical Scientists (AAPS), Northeast Regional Discussion Group Poster Competition

2007 First Place in International Society of Pharmaceutical Engineering (ISPE) New England Regional Poster Competition

2006-2008 Teaching Assistantship from Northeastern University

2004-2006 Research Assistantship from Pfizer Global Research and Development, Groton, CT

2003-2004 Teaching Assistant Accreditation, Northeastern University

2001-2003 Teaching Assistant from Sabanci University, Istanbul, Turkey

ACADEMIC APPOINTMENTS Assistant Professor April 2016 - Present Department of Pathology and Laboratory Medicine, Alpert Medical School of Brown University

HOSPITAL APPOINTMENTS Director of Clinical Bioinformatics March 2019 - Present Lifespan Academic Medical Center Rhode Island Hospital and Miriam Hospital

Bioinformatics Scientist April 2016 – March 2019 Lifespan Academic Medical Center Rhode Island Hospital and Miriam Hospital Molecular Pathology Lab

OTHER APPOINTMENTS Affiliate Faculty April 2016 - Present Center for Computational Molecular Biology, Brown University

HOSPITAL COMMITTEES Lifespan Research IT Council

UNIVERSITY COMMITTEES CCMB PHD Admissions Committee

EXTERNAL COMMITTEES Barrington School Advisory Committee for Diversity, Equity and Inclusivity

MEMBERSHIP IN SOCIETIES American Society of Human Genetics Association for Molecular Pathology

PUBLICATIONS LIST ORIGINAL PUBLICATIONS IN PEER-REVIEWED JOURNALS

Marinelli, NA, Rosenzweig, S, Joesch-Cohen, L, Hollingsworth, EW, Douglas, A, Maguire, AM, Cowen, MM, Schmidt, M, Schorl, C, Imitola, J, Morrow, EM, Gamsiz Uzun, ED* and Lizarraga, SB*, “Valproic acid effect on first trimester stem cell derived human neurons shows dysregulation of mitochondrial and chromatin regulatory pathways”, In progress *Equal corresponding author

Lizarraga, SB, Maguire AM, Ma L, van Dyck, LI, Wu, Q, Nagda, D, Livi, LL, Pescosolido, MF, Schmidt, M, Alabi, S, Cowen, MH, Brito-Vargas, P, Hoffman-Kim, D, Gamsiz Uzun, ED, Schlessinger, A, Jones, RN, Morrow, EM, “Human neurons from Christianson syndrome iPSCs reveal allele-specific responses to rescue strategies”, Submitted to Science Translational Medicine

Von Werra, L, Schongens, M, Gamsiz Uzun, ED, Eickhoff, C, “Generative adversarial networks in precision oncology”, ICTIR 2019 Meeting Proceedings, Short Paper

Xu, M, Ouyang, Q, Gong, J, Pescosolido, MF, Pruett, BS, Mishra, S, Schmidt, M, Jones, RN, Gamsiz Uzun, ED, Lizarraga, SB, Morrow, EM, “Mixed neurodevelopmental and neurodegenerative pathology in Nhe6-null mouse model of Christianson syndrome”, eNeuro 2017, 4(6).

PUBLICATIONS LIST - continued Harrison, AJ, Gamsiz, ED, Berkowitz, IC, Nagpal, S, Jerskey, BA, “Genetic Variation in the Oxytocin Receptor Gene is Associated with a Social Phenotype in Autism Spectrum Disorders, American Journal of Medical Genetics B: Neuropsychiatric Genetics 2015, 168(8). PMID: 26365303

Gamsiz, ED, Viscidi, EW, Nagpal, S, Sanders, SJ, Murtha, MT, Simons Simplex Collection Genetics Consortium, Istrail, S, Triche, EW, State, MW, Cook Jr, EH, Devlin, B Morrow, EM, “Intellectual Disability is Associated with Increased Runs of Homozygosity in Simplex Autism”, American Journal of Human Genetics 2013, 93(1):103-109. PMID: 23830515; PMC3710760

Pescosolido M, Schwede, M, Ashley, J, Schmidt, M, Gamsiz, ED, Phornphutkul, C, Morrow, EM, “Expansion of the Clinical Phenotype Associated with Mutations in Activity- Dependent Neuroprotective Protein”, Journal of Medical Genetics 2014, 51(9):587-9, PMID: 25057125; PMC4135390

Pescosolido, MF, Gamsiz ED, Nagpal, S, Morrow, EM, “Distribution of Disease- associated Copy Number Variants Across Distinct Disorders of Cognitive Development”. Journal of American Academy of Child and Adolescent Psychiatry 2013, 52(4):414-430. PMID: 23582872; PMC3774163

Gamsiz, ED, Thombre, A, Ahmed, I, Carrier, RL, “Model Predicting Impact of Complication with Cyclodextrins on Oral Absorption”. Biotechnology and Bioengineering 2013, 110(9);2536-47. PMID:23592239

Gamsiz, ED, Ouyang, Q, Schmidt, M, Nagpal, S, Morrow, EM, “Genome-wide Transcriptome Analysis in Murine Neural Retina Using High-throughput RNA Sequencing”, Genomics 2012, 99(1):44-51. PMID:22032952; PMC3392719

Gamsiz, ED, Thombre, A, Ahmed, I, Carrier, RL, “Drug Salts and Solubilization: Modeling the Influence of Cyclodextrins on Oral Absorption”, Annuals of Biomedical Engineering 2011, 39(1);455-68 PMID: 20960062

Gamsiz, ED, Ashtikar, M, Crison, J, Woltosz, W, Carrier, RL “Predicting the Effect of Fed State Intestinal Contents on Drug Dissolution”, Pharmaceutical Research 2010, 27(12):2646-56. PMID:20963629

Gamsiz, ED, Thombre, A, Miller, LA, Ahmed, I, Carrier, RL “Modeling the Influence of Cyclodextrins on Oral Absorption of Insoluble Drugs: 1. Model Development, Biotechnology and Bioengineering 2010, 105(2):409-420. PMID: 19725042

Gamsiz, ED, Thombre, A, Miller, LA, Ahmed, I Carrier, RL, “Modeling the Influence of Cyclodextrins on Oral Absorption of Insoluble Drugs: 2. Model Validation, Biotechnology and Bioengineering 2010, 105(2):421-430. PMID: 19725043

PUBLICATIONS LIST - continued Gamsiz, ED, Shah, L, Amiji, M, Carrier, RL, “A Model Predicting Delivery of Saquinavir in Nanoparticles to Human Monocyte/macrophage (Mo/Mac) cells”, Biotechnology and Bioengineering 2008, 101(5):1072-1082. PMID: 18553495

OTHER PEER-REVIEWED PUBLICATIONS Gamsiz, ED, Sciarra, LN, Maguire, AM, Pescosolido, MF, van Dyck, LI, Morrow, EM, “Discovery of Rare Mutations in Autism: Elucidating Neurodevelopmental Pathways”, Neurotherapeutics 2015, 12(3): 553-71, PMID: 26105128; PMC4489950

ABSTRACTS Nam, G, Hui, Y, Edmund, L, Lombardo, KA, Uzun, ED, Patel ,NR, Garcia-Moliner, ML, Lu, S, Wang L, “Immune Microenvironment Markers (PD-L1, WARS, IDO) and Clinical Outcomes in Mucinous Lung Adenocarcinomas” USCAP 2018 Annual Meeting, Vancouver, Canada

Edmund, L, Patel, NR, Uzun, ED, Lombardo, KA,Yakirevich, E, Mangray, S, Aswad, B, “STAT6 Expression in Adenofibroma of the Lung Supports Classification as Intrapulmonary Solitary Fibrous Tumor” USCAP 2018 Annual Meeting, Vancouver, Canada

He, X, Uzun, ED, Jackson, C, Pisharodi, L, Patel, NR, “Validation of Alternative Pre- Stained Cytology Specimens for a Clinical Next-Generation Sequencing Assay” USCAP 2018 Annual Meeting, Vancouver, Canada

Invited Speaker. Turkish Society of Medical Genetics. “Autism Genetics and Next Generation Sequencing Technologies” May 2015, Istanbul, Turkey

Gamsiz, ED Viscidi, EW, Frederick A, Schmidt, M, Nagpal, S, Morrow, EM, “Runs-of- Homozygosity are Associated with Intellectual Disability and Female Gender in Simplex Autism” Proceedings of 14th Internatinal Congress of Human Genetics 2013, Boston. MA

Gamsiz, ED, Viscidi, WE, Frederick, A, Morrow, EM “Intellectual Disability is Associated with Increased Runs of Homozygosity in Simplex Autism” Department of Psychiatry and Human Behavior (DPHB) Research Day 2013, Providence, RI

Pescosolido, MF, Gamsiz ED, Nagpal, S, Morrow, EM “Pathway Analysis of Highly Recurrent Copy Number Variants in Neurodevelopmental Disorders, Proceedings of Society for Neuroscience 2011, Washington, DC

Gamsiz, ED, Ouyang, Q, Schmidt, M, Nagpal, S, Morrow, EM, “Novel Features of Neural Retina Transcriptome Revealed by High-throughput RNA-Sequencing” Proceedings of 12th International Congress of Human Genetics 2011, Montreal, Canada

Gamsiz, ED, Miller, L, Thombre, A, Ahmed, I, Carrier, RL “Model Prediction of the Influence of Cyclodextrins on Oral Bioavailability of Incoluble Drugs. Proceedings of International Society of Pharmaceutical Engineers Annual Meeting 2007, Las Vegas, NV 5

Gamsiz, ED, Thombre, A, Miller, LA, Carrier, RL “Development of a Computer Program Predicting the Influence of Cyclodextrins on Oral Bioavailablity of Insoluble Drugs: From Modeling to in Vivo Comparison” Proceedings of American Institute of Chemical Engineers Annual Meeting 2007, Salt Lake City, UT

GRANTS Ongoing Research Support

Completed Research Support ADVANCE-CTR Pilot Project Grant Uzun (PI) 11/1/2017-5/30/2019 U54GM115677 Identification of Gene Pathway Involved in Phenotype Modification of Pompe Disease Role: PI

Pilot Project Grant Uzun (PI) 6/1/2017-5/31/2019 The William and Mary Oh-William and Elsa Zopfi Professorship at the Department of Pediatrics, Women and Infants Hospital Gene pathways involved in phenotype modification of Pompe Disease Role: PI

2T32 MH019927-2 (PI: Spirito) 9-2014 – 4-2016 Research Training in Child Mental Health Mentor: Dr. Eric Morrow This training prepares basic and behavioral scientists to conduct independent research in the area of child mental health as full-time University faculty members. It includes didactic work, participation in ongoing funded projects and independent research. Role: Postdoctoral Fellow/Trainee

Translational Neuroscience Fellowship 9-2012 – 9-2014 Lifespan Research Institute the Lifespan Division of Psychiatry, the Brown Institute for Brain Science and the Norman Prince Neurosciences Institute Mentor: Dr. Eric Morrow; Co-mentors: Dr. Rowland Barrett, Dr. Karyn Blane This is a postdoctoral fellowship to conduct translational research in the field of neuroscience. During the fellowship period, Dr. Gamsiz was introduced to the clinical setting of autism research in addition to her research on genetics and computational biology Role: Postdoctoral Fellow/PI

Withdrawn Grants K01 2016 1 K01 MH107656-01A1 Received a score (32) and withdrawn upon accepting the current clinical faculty position Role: PI

UNIVERSITY TEACHING, ADVISING and MENTORING ROLES

Graduate Students Qing Wu Computational Biology PhD student Co-advised by Dr. Eric Morrow

Jiaying Lai Computational Biology PhD student Rotation student in Fall 2018 Differentially Expressed lncRNAs in Autism

Shiyin Li Computer Science Master’s Student Co advised by Dr. Carsten Eickhoff at BCBI Literature Retrieval of Fusion Gene Information Using Machine Learning Algorithms

Undergraduate Students Amy Wang (September 2019- ) Co-mentored with Eric Morrow Comparison of fusion detection algorithms

David Wu (June 2018- ) -Received LINK Award (June 2019) Co-mentored by Dr. Carsten Eickhoff Literature Retrieval of Fusion Genes Using Machine Learning Algorithms -Funded by Oh-Zopfi Project (Sept 2018-May 2019) Gene Networks in Pompe Disorder -Co-mentored by Drs. Adam and Joanna Chodopski (June -August 2018) Funded by Department of Emergency Medicine Differentially Expressed Genes Associated with Brain Trauma

Shoshana Rosenzweig (September 2018-May 2019) Co-mentored by Dr. Eric Morrow Effect of Valproic Acid on Stem Cell Derived Human Neurons Won the Center for Computational Molecular Biology Honors Thesis Award

Lena Joesch-Cohen (June 2018- ) Co-mentored by Dr. Eric Morrow Gene Networks Associated with X-Linked Intellectual Disability Won the Biology Undergraduate Education Senior Biology Prize for Academic Excellence in the Biological Sciences

Ashley Chen (June - September 2018) Received LINK award in Summer 2018 Webtool for Clinical Significance of Somatic Mutations in Cancer

Helen Cho (June -September 2018)

Funded by Oh-Zopfi Pilot Project Grant Gene Networks in Pompe Disorder

Angie Kim (June -September 2018) Co-mentored by Dr. Carsten Eickhoff from Brown Center for Biomedical Informatics Literature Retrieval of Fusion Genes Using Machine Learning Algorithms

Thomas Collins, Computational Biology Concentration (June 2016-May 2018) Received LINK award in Summer 2016, UTRA in Summer 2017 (he had to turn it down to accept a fellowship from NSF/Johns Hopkins University) and summer fellowship from NSF/Johns Hopkins University for an internship at UC Davis. Received UTRA in Fall 2017 Runs of Homozygosity Carries the Most Deleterious Variants in Autism

Josephine Issenman (June 2017-May 2018 ) Received LINK award in Summer 2017. Funded by Oh-Zopfi Pilot Project Grant on Pompe Disease Project Gene Expression Changes under Runs of Homozygosity Blocks in Autism

Gur Agci, Chemical Engineering Concentration (June 2016-May 2018) Common Pathways in Autism and Glioblastoma

Teaching Experience Brown University, Department of Pathology (Spring 2019) Resident Lectures Lectured on Next Generation Sequencing and Bioinformatics for DNA-seq Next Generation Sequencing and Bioinformatics for RNA-seq

Brown University, Department of MCB (Spring 2018) BIOL 1545/2545: Human Genetics and Genomics Lectured on Cancer Genetics

Brown University, Department of Pathology (Fall 2017) Resident Lectures Lectured on Next Generation Sequencing and Bioinformatics

Brown University, Department of Pathology (Spring 2017) BIOL 1870: Techniques in Pathobiology Lectured on Next Generation Sequencing and Bioinformatics

Lifespan/ Rhode Island Hospital (Spring 2017) Continued Medical Education Lecture Series Lectured on Next Generation Sequencing and Bioinformatics

Brown University, Department of Pathology (Fall 2016) Resident Lectures Lectured on Next Generation Sequencing and Bioinformatics

Teaching Experience (During Graduate School) Northeastern University, Boston, MA 9-2003 – 1-2008 8

Teaching Assistant, Department of Chemical Engineering Lectured in Chemical Engineering Kinetics, Transport, Thermodynamics, Chemical Engineering Design Classes.

Sabanci University, Istanbul, Turkey 9-2001 – 7-2003 Teaching Assistant, Graduate Program in Biological Sciences and Bioengineering Lectured in Biology 101 and Calculus 101

EDITORIAL Academic Editor in PLOS One

AD-HOC REVIEWER JAMA Psychiatry Scientific Reports

CONFERENCE MODERATOR Session Moderator - ASHG Annual Meeting 2018 Session Moderator - ASHG Annual Meeting 2017

LEADERSHIP, COMMUNITY SERVICE AND EXTRACURRICULAR ACTIVITIES 2018- Mentor for Two Students from Barrington High School on their science fair project 2006-2007 President, Chemical Engineering Graduate Student Council, Northeastern University 2005-2006 Vice President, Chemical Engineering Graduate Student Council, Northeastern University 2005-2009 Mentor for High School Students, MIT Research Science Institute 2004-2009 Member, Teaching Assistant Leadership Board, Northeastern University

ADDITIONAL SKILLS AND INTERESTS Computer Programming languages: Perl, Matlab, Python, PHP, HTML, CSS Bioinformatics programs: Plink, BEDtools, SAMtools, Cufflinks, TopHat, Bowtie, Annovar, BWA, GATK, PennCNV, Nexus Pathway and network analysis: Ingenuity IPA, Cytoscape, GSEA Statistical Analysis: R, STATA, JMP, SPSS and Polymath Database: SQL Data visualization: IGV, Galaxy, UCSC Genome Browser, Circos Engineering: ASPEN, Latex

Laboratory Expertise in molecular biology techniques and materials characterization, Mammalian Cell Culturing, Gel Electrophoresis, PCR, HPLC, Fluorescence Microscopy, XRD, Diffusion Cell for drug delivery, Lyophilzation, LC-MS, Next Generation Sequencing