People

Faculty

Adam's Headshot - updated 2015
Adam Margolin, Ph.D.
Director, Computational Biology Program
Professor, Biomedical Engineering

Dr. Margolin was appointed as the director of computational biology in the OHSU School of Medicine in January of 2014. Dr. Margolin was hired with the charge of leading the institution's investment in the capacity for computational biology across the basic and clinical sciences. Prior to coming to OHSU Dr. Margolin was the director of computational biology and co-leader of strategy at Sage Biometrics, a biomedical research institute in Seattle, with a joint appointment at the Fred Hutchinson Cancer Research Center. He received his B.S. in economics from the Wharton School of Business at the University of Pennsylvania in 2002, his M.S. in computer information technology from the University of Pennsylvania in 2002 and his Ph.D. in biomedical informatics from Columbia University in 2007. His thesis was entitled, "Computational Inference of Genetic Regulatory Networks in Human Cancer Cells" and was subsequently developed into a book with the same title.

Ozgun Babur
Ozgun Babur, Ph.D.
Research Assistant Professor, Molecular & Medical Genetics

Dr. Babur is currently focusing on all aspects of biological pathways: modeling, integrating, visualization, and their use in genomics/proteomics/metabolomics analyses. Dr. Babur is working on understanding the cell at the system-level by integrating knowledge, developing statistical methods, and building software tools. He received his B.S. degree in Molecular Biology and Genetics, and M.S. and Ph.D. degrees in Computer Engineering at Bilkent University.

Young-Hwan  Chang, Ph.D

Young-Hwan Chang, Ph.D.
Assistant Professor, Biomedical Engineering

Dr. Chang's research is focused on data-driven system identification, control theory, quantitative image analysis and machine learning. He received his Ph.D in Mechanical Engineering from University of California, Berkeley under the supervision of Professor Claire J. Tomlin. He then worked as a postdoctoral researcher at Hybrid Systems Laboratory in the department of electrical engineering and computer sciences, UC Berkeley. He has also held appointments at Cognitive Robotics Research Center, Korea Institute of Science and Technology (KIST) and Hyundai-Kia R&D Center.

Emek Demir Ph.D

Emek Demir, Ph.D.
Assistant Professor, Molecular & Medical Genetics

Dr. Demir is working to discover novel methods of incorporating pathway information to predict tumor response to drug interventions. He received his B.S. and M.S. degrees in Molecular Biology and Genetics, and his Ph.D. in Computer Engineering at Bilkent University. He completed his postdoctoral fellowship at Memorial Sloan Kettering Cancer Center in Computational Biology in 2008.

Kyle Ellrott

Kyle Ellrott, Ph.D.
Assistant Professor, Biomedical Engineering

Dr. Ellrott specializes in computational biology and scientific computing. His work focuses on big data, reproducible compute, large scale compute and analysis in the field of cancer biology. He has worked on large cancer consortium projects including the ICGC and TCGA PanCancer projects. He received his B.S. in Computer Science from University of California, Riverside and his Ph.D. in Life Sciences at University of Tennessee.

Jeremy Goecks

Jeremy Goecks, Ph.D.
Assistant Professor, Biomedical Engineering

Dr. Goecks is an Assistant Professor in the Department of Biomedical Engineering where he leads a [biomedical computing research laboratory]and is a primary contributor to cancer informatics research across OHSU. He has published papers in many areas of biomedical computing, including novel analysis methods for genomics and proteomics, new visual analytics tools for making sense of large datasets, and computational infrastructure for biomedical data science. Dr. Goecks is a lead investigator for the [Galaxy Project], a Web-based biomedical data analysis platform that is used throughout the world. He received his Ph.D. in Computer Science from the Georgia Institute of Technology (Georgia Tech) and did postdoctoral research in genomics at Emory University.

Abhinav Nellore

Abhinav Nellore, Ph.D.
Assistant Professor, Biomedical Engineering
Assistant Professor, Department of Surgery

Dr. Nellore focuses on building software for integrative analysis of many high-throughput sequencing samples to improve usability and utility of archived data. His tools of choice are in the Hadoop ecosystem, and his flagship product is Rail-RNA, which scales to analyze thousands of RNA sequencing (RNA-seq) samples on Amazon Elastic MapReduce. With collaborators at Johns Hopkins University, he has used Rail-RNA to reanalyze over 70,000 human RNA-seq samples, including publicly available samples on the Sequence Read Archive (SRA) as well as controlled-access samples from The Cancer Genome Atlas (TCGA) and the Genotype-Tissue Expression (GTEx) project. Check out his papers: the largest study of transcriptomic variation to date and recount, a resource that facilitates reuse of existing RNA-seq data. Dr. Nellore received his B.S. in Physics at University of Maryland, College Park, and his Ph.D. in Physics at Princeton University.

Kemal Sonmez
Kemal Sonmez, Ph.D.
Associate Professor, Center for Spoken Language and Computer Science
Associate Professor, Computer Science & Electrical Engineering

Dr. Sonmez is currently the technical lead and liaison between OHSU and Intel on the Collaborative Cancer Cloud (CCC) Project. His work focuses on computational genomics and systems biology with applications broadly in precision medicine targeting cancer, retinopathy of immaturity, addiction, and onset of puberty. In addition to playing a key role in the CCC Project, Dr. Sonmez also teaches Computational Sequence Analysis and ASR with Hidden Markov Models courses for the Computer Science and Electrical Engineering degree program, and organizes the OHSU-Intel Data Jamborees.

Reid Thompson

Reid Thompson, Ph.D., M.D.
Assistant Professor, Radiation Medicine
Staff Physician, VA Portland Health Care System

Dr. Thompson joined the faculty at OHSU and the Portland VA in August 2016 and is actively engaged in both patient care and genomics research. He is a native of New Jersey but, along with his husband and two cats, is very proud to call Portland home. He completed his MD and PhD in molecular genetics at the Albert Einstein College of Medicine in 2011, and his internship and Radiation Oncology residency at the University of Pennsylvania in 2016.

Zheng Xia, Ph.D

Zheng Xia, Ph.D.
Assistant Professor, Molecular Microbiology & Immunology

Dr. Xia's research interest is in developing and applying bioinformatics tools and machine learning algorithms for large-scale genomics data analysis to unravel the underlying mechanisms in immunology and cancer biology. Dr. Xia received his B.S. degree in Automation and Ph.D. degree in Pattern Recognition and Intelligent Systems at Zhejiang University. Before joining OHSU, he was an Instructor at Baylor College of Medicine.

Staff

Alex Buchanan

Alex Buchanan, B.S.
Research Software Engineer

Alex joined the Computational Biology Program in Oct. 2016 as a Research Software Engineer. He received a B.S. in Computer Science from Oregon State University. Alex has dabbled in many areas of software development, spending much of his career building websites and making the dreams of marketing teams come true. Following his interests into a computational biology lab at OSU, he lent his skills to the study of RNA-seq expression data and alternative splicing in plants and bacteria. At OHSU, he works on improving the tools scientists work with daily, including making it easier to run workflows on clusters of computers. He’s known as the “traveler guy” because he’s been to a few countries and climbed a few mountains.

Allison Creason - Headshot

Allison Creason, Ph.D. 
Computational Biologist

Dr. Creason joined the Computational Biology Program in May 2016 as a computational biologist. Creason is primarily interested in patient-driven analysis of genomics and transcriptomics data. She is currently working on the SMC-RNA Challenge, which utilizes crowd-sourced benchmarking and cloud computing to improve and standardize methods for analyzing RNA-seq data. In addition, Creason works on multiple components of SMMART including development of genomic workflows and analysis of genomic/transcriptomic data derived from patients. After completing her Ph.D. in Molecular and Cellular Biology at Oregon State University, she worked as a postdoctoral researcher at the Knight Diagnostic Laboratories at OHSU.

Funda Durupinar Babur

Funda Durupinar-Babur, Ph.D.
Research Software Engineer

Dr. Durupinar-Babur joined the Computational Biology Program at OHSU in February 2016 as a software engineer. She is currently working on DARPA's Communicating with Computers program with a focus on biocuration. She received her B.S. from Middle East Technical University and her M.S. and Ph.D degrees from Bilkent University, all in computer engineering. After completing her Ph.D, she worked as a postdoctoral researcher at the Center for Human Modeling and Simulation, University of Pennsylvania, and as a software engineer at the Computational Biology Department, Memorial Sloan Kettering Cancer Center.

Joseph Estabrook - Headshot

Joey Estabrook
Computational Biologist 

Joey joined the Computational Biology program in July 2017 as a computational biologist. He received his M.S degree in Bioinformatics from the University of Oregon. While completing his internship at MIT, Joey's research for his Master's degree focused on the analysis of high-throughput RNA sequencing data derived from myotonic dystrophy (DM) tissue samples. Joey’s research focused on studying the pathogenesis of micro satellite repeat diseases, RNA processing and localization, and combining insights made in both these areas to develop treatments for people with these diseases. As a member of the Pathways and Omits group, Joey will help in the development of methods to predict tumor vulnerabilities and drug responses.

Michal Grzadkowski, S.M.

Michal Grzadkowski, M.S.
Research Software Engineer

Michal earned his BMath in Combinatorics and Optimization from the University of Waterloo in 2013. As part of his degree, he completed co-op terms in the Petronis Lab at the Centre for Addiction and Mental Health and in the Boutros Lab at the Ontario Institute for Cancer Research, both located in Toronto. He went on to obtain an SM from the Electrical Engineering and Computer Science Department at MIT in 2016, investigating transregulatory networks in the Kellis Lab. Michal joined the Pathway Team at OHSU in June 2016, working under Emek Demir to discover novel methods of incorporating pathway information to predict tumour response to drug interventions.

Burcu Gurun-Demir

Burcu Gurun-Demir, M.A.
Research Associate

Burcu joined the Computational Biology Program at OHSU in April 2016. She is interested in implementing statistical approaches to find quantitative insights in medical data, which provides evidence-based strategies to improve patient care. Burcu holds a BSc in Statistics from Middle East Technical University, and an M.A. degree in Statistics from Columbia University. Upon graduating she worked at the United Nations, New York, and at Nielsen as a statistical modeling analyst, as well as at Cornell Medical College and Columbia University Hospital as a biostatistical researcher. She was also teaching statistics at the New Jersey Institute of Technology before joining OHSU.

Severin Leonard

Sev Leonard, M.S.
Research Software Engineer

Sev is a Research Software Engineer with a B.S. and M.S. in Electrical Engineering from The Ohio State University. Originally from Eastern Pennsylvania, Sev was attracted to Portland by a large blue object named Intel, where he worked on the Core i7 microprocessor design team and went on to develop software for overclocking, user experience prototypes, and custom hardware interfaces. Prior to joining OHSU, Sev worked directly with clients to develop machine learning and software solutions, technical training, and writing. Sev likes the outdoors, furry animals, and grilling.

Patrick Leyshock

Patrick Leyshock, Ph.D.
Sr. Systems Engineer

Dr. Leyshock is a Research Systems Engineer for the Computational Biology Program, leading data integration projects for several OHSU labs.  Leyshock's analytic skills and diverse work experience make him a valuable asset to the Program.  A Reed College graduate, Leyshock has earned both an M.A. from Arizona State University and a PhD in Computer Science from Portland State University.  His doctoral dissertation research focused on tools and methods for analyzing array-structured scientific data.

Georgia Mayfield
Georgia Mayfield, M.S. 
Research Software Engineer

Georgia works for the SMMART division of Computational Biology. Her projects include multiplex immunohistochemistry imaging data management in the Labkey database, creation and management of the SMMART variant store database, and normalization and expansion of the Genotype to Phenotype (g2p) evidence database. Prior to integration with SMMART, Mayfield worked on various aspects of the Collaborative Cancer Cloud (CCC) project of Computational Biology, most recently the translocation of the ICGC data portal to OHSU and the accompanying Euler project as well as the data sharing partnership between Computational Biology and the Beat AML group. She has a Masters in Biology and Bioinformatics from the University of Oregon.

Olga Nikolova

Olga Nikolova, Ph.D.
Sr. Research Associate

Dr. Nikolava is a senior research associate with the Computational Biology group at OHSU and visiting scientist at Fred Hutchinson Cancer Research Center in Seattle. Currently, working on the Cancer Target Discovery and Development project with Chris Kemp, Eddie Mendez, VK Gadi, Mehmet Gonen and Adam Margolin. Her focus in working on predictive models for cancer biology integrating cell line panels and patient tumor data. In addition she assists with the development of an analytical pipeline to analyze, annotate, and visualize all experimental data generated by our collaborators (high-throughput siRNA screens with and without compounds, patient sample compound screens, various omics data). Olga completed her Ph.D. in Bioinformatics and Computational Biology in the High Performance Computational Biology group under the supervision of Srinivas Aluru (now at Georgia Tech) and Patrick Schnable (ISU).

Janice Patterson - Headshot

 Janice Patterson, M.S.
Computational Biologist

Janice joined the Computational Biology Program in July 2016 as a computational biologist. She received her Bachelor's degree in Chemistry from Portland State University and a M.S. in Biomedical Informatics and Computational Biology.  She then worked as a researcher at the Portland VA Research Center studying gastrointestinal stromal tumors and mast cell diseases. Her focus is on developing analysis pipeline for the Serial Measurements of Molecular and Architectural Responses to Therapy (SMMART) patient trials and providing analysis that is accessible and understandable to physicians and scientific collaborators.

Carl Pelz
Carl Pelz, B.A.  
Computational Biologist

Carl received his B.A. in Physics from Reed College in 1987.  He started his career as a software developer in the life sciences developing user friendly research software to automatically read DNA sequencing films for both Windows and Mac personal computers.  He subsequently worked in the telecom industry as a server side developer responsible for interfaces to telecom hardware.  Carl joined OHSU in 2004 when Affymetrix microarrays were popular and provided multiple labs with microarray processing, analysis, and visualization support, including the development of normalization and gene signature predictive algorithms.  When high throughput sequencing was replacing microarray technology, Carl joined the Oregon Stem Cell Center at OHSU where he developed a set of analysis pipelines using a combination of custom developed C++ utilities and statistical tools in R (as they became available) to support RNA-Seq, ChIP-Seq and DNA methylation studies.  Carl continues to support projects for the Stem Cell Center in addition to high throughput RNA sequencing analysis for the Brenden Collson Center for Pancreatic Care and, most recently, has joined the Computational Biology Department at OHSU as part of the LabKey team developing data management systems for translational research.  One of the goals of this team is to integrate processing, analysis, and visualization of RNA-Seq and other OMICs data with data management systems (LabKey and others).

David Servillo

David Servillo, M.S.
Research Software Engineer

With a background of biology which David acquired while studying in Sup'Biotech, the engineering school of biotechnology in Paris (France), David specialized himself in computational biology in the Paris Diderot University where he was graduated with a master's degree in bioinformatics. He integrated to OHSU in May 2016 as software engineer in the Computational Biology Program with the mission to track causative genes and discover pathways involved in diseases. Currently David is developing new ways to help biologists to curate biological pathways, especially those related to cancer.

Ryan Spangler

Ryan Spangler, M.S.
Research Software Engineer

Ryan is a lifetime creator and explorer of mysteries of all kinds. His passion for biology and biological problems goes back to the moment he first considered his own existence. Ryan started coding at age 6 when his dad brought home a Commodore 64;he has been learning and building things ever since. While getting his Masters in Systems Science from PSU, he began exploring the intersection between code and biology –seeking all the ways the two disciplines can contribute to each other.

Adam Struck

Adam Struck, M.S.
Scientific Programmer

Adam joined the Computational Biology program in September 2015 as a scientific programmer. He received his B.S. and M.S. degrees in Biochemistry from the University of Oregon. Adam's research for his Master's degree focused on the analysis of high-throughput, RNA sequencing data derived from the tissues of patients with myotonic dystrophy type 1 to gain insight into disease mechanisms, discover biomarkers, and study the regulation of alternative pre-mRNA splicing. His current work focuses on the development of containerized bioinformatics workflows using community standard descriptor languages (CWL/WDL) and distributed machine learning for the Collaborative Cancer Cloud (CCC) project.

Matt Viehdorfer

Matt Viehdorfer, M.S.
Research Software Engineer

Matt is a Research Software Engineer for the Computational Biology program with a B.S. and M.S. in Computer Science from Oregon State University. His research focused on designing and developing virtual reality and web-based applications and data integration processes designed to enhance teaching complex anatomy using 2D and 3D data generated from CT images. Matt’s past work experience similarly involved developing interactive visualizations, applications, and mobile apps to explore and make sense of datasets.

Brian Walsh

Brian Walsh
Sr. Research Software Engineer

Brian has extensive software engineering and project management experience in high technology companies.  He has proven expertise in strategic and tactical aspects of software development in leadership positions.  Customer focused with business acumen. Brian is an effective communicator with extensive written and verbal skills.  Results driven and team oriented.  His technical leadership with business focuses in: working with customers, product management, and executive management to achieve clear engineering product and release requirements. He provides engineering leadership and project management grounded in an understanding of business goals for the team.

Brian has over 20 years of experience as an architect and engineer with broad experience in Internet applications, web services, object-oriented systems, client-server computing, interfaces, numerical modeling, simulation, and high-performance computing. In addition he is proficient developer with most common programming languages and contributes to all aspects of the software development process.

Visiting Scientists

Elin Nyman

Elin Nyman, Ph.D.

Dr. Nyman focuses on protein signaling networks and the mechanisms of deregulation of these networks in disease. In her graduate studies at Linköping University, Sweden, she developed mathematical models to study insulin resistance mechanisms in adipocytes from diabetic patients. This work led up to a postdoctoral collaboration with AstraZeneca on drugs for diabetes and obesity that target signaling pathways in adipocytes. Dr. Nyman is now a visiting scientist in the group of Dr. Demir to broaden her knowledge towards oncogenic signaling networks and data driven analysis of the response to combination therapy in canner.

Post-Doctoral Researchers

Vahid Jalili

Vahid Jalili, Ph.D.

Dr. Jalili joined the computational biology program in January 2017 as a postdoctoral scholar. He was awarded his PhD in Information Technology (with cum laude) from Politecnico di Milano. He joined Goecks lab in September 2016 at George Washington University, as a core developer team member for Galaxy project, a web-based biomedical data analysis platform. Then he moved to Taylor's lab at Johns Hopkins University, another Galaxy lab, as a visiting researcher. Currently his research is focused on cloud bursting, and database federation for Galaxy project. 

Duan Chen Sun - Headshot

Duan Chen Sun, Ph.D.

Duanchen Sun is a postdoctoral research scholar, studying cancer genomics in the Computational Biology Program at OHSU. He received his Ph.D. degrees in operations research (applied mathematics) from the Academy of Mathematics and Systems Science, Chinese Academy of Sciences. Duanchen joined Dr. Xia’s group in July, 2017. His research field mainly focuses on the mathematical modeling and novel algorithm design in the field of bioinformatics, system biology and computational biology. Such as designing novel network-based biomarker identification algorithms, building high-dimensional data analysis tools for single cell sequencing, and executing semi-supervised prediction for drug response, etc.

Graduate Students

Julianne David - Headshot

Julianne David

Julianne is a PhD student in the Biomedical Engineering Department, working with Drs. Abhi Nellore and Reid Thompson.  She has previously worked on molecular dynamics modeling of hairpin DNA, and computational Bohmian quantum mechanics; her publications develop novel methods for integrating the quantum hydrodynamic equations of motion.  She holds a BA in Computational Chemistry and an MS in Chemistry from Northwestern University.

 

Elliot Gray - Headship

Elliot Gray

Elliot is a PhD student in the Biomedical Engineering Department.  He is interested in using computational methods to rigorously and automatically analyze tissue imaging and genomic data to address fundamental questions about how the heterogeneity of cellular genotype and phenotype impacts the response of a tumor to drug treatment.  In particular, he focuses on analyzing the contribution of immune cell populations to tumor evolution and survival.  Elliot received his B.S. in Physics and Mathematics from Montana State University in Bozeman.

 

Research Interns

Chris Anderson

Chris Anderson

Chris is a University of Oregon Bioinformatics master’s student and intern working under Abhinav Nellore. Internship experience in bioinformatics and time as a private sector software developer have led him to the computational biology department at OHSU, and he is excited to work on tools and methods that make a difference for both research and health outcomes. He is currently working on similarity search for RNA-sequencing data and as well as additional pipeline development projects.

Erik Burlingame

Erik Burlingame

Erik is an OHSU Computational Biology intern working toward an M.S. in Biology with an emphasis on Bioinformatics from the University of Oregon. He received a B.S. in Biochemistry from the University of Oregon while conducting molecular neurobiology research in the lab of Dr. Phil Washbourne. He is currently working with Dr. Young-Hwan Chang to leverage techniques from the domains of quantitative image analysis and machine learning to improve the clinical management of melanoma.

Hannah Manning

Hannah Manning

Hannah is completing an internship with OHSU's Computational Biology team while working towards a master's degree from the University of Oregon's Bioinformatics and Genomics program. She holds a bachelor's degree in Behavioral Neuroscience with a minor in Chemistry from Western Washington University. As a member of the Pathways and Omics group, Hannah is dipping her toes into the development of methods to predict tumor vulnerabilities and drug responses with the ultimate goal of improving precision medicine for better patient outcomes.

Sam Sivagnam

Sam Sivagnanam

Sam is an intern in the Computational Biology department working on medical image analysis, data processing and visualization of multiplex IHC oncogenic tissue samples.  She studied molecular bioscience at the University of Kansas and worked on spectral karyotyping and basic cell biology research at the Stowers Institute in Kansas City, MO before attending the Bioinformatics and Genomics Master's program at the University of Oregon. She is now combining her passion for biology, art and code to extract meaning from biological images, provide quantitative analysis for physicians, and develop predictive models for cancer treatment outcome.

Mary Wood

Mary Wood

Mary is an intern from the University of Oregon’s Applied Bioinformatics and Genomics Master’s program. She completed her undergraduate degree in Biology with an emphasis in cellular, molecular, and developmental biology at the University of Oregon in 2014. Continuing her undergraduate research interests in the evolution of blood feeding in the pitcher plant mosquito, she began working towards a Master’s degree in Biology with a focus on evolution and ecology at the University of Oregon before developing an interest in Computational Biology and changing programs to pursue that focus.

Administrative Staff

Holly Chung
Holly Chung
Program Administrator
(503)494-9726
RJH 4514
Mailcode L333
JoAnn Takabayashi
JoAnn Takabayashi
Program Technician
Assistant to Dr. Adam Margolin
RJH 4517
Mailcode L333
Merri LeClerc
Ozzy Garcia
Ozzy Garcia
Project Coordinator
MSB 700/RJH 6522
Mailcode ITG07
Jake Redmond
Jake Redmond
Human Resources Coordinator
(503)494-2469
RJH 4359
Raj Shah
Grants & Contracts Coordinator - Pre-award
(503)494-8632
RJH 7385