Directors: Jeffrey D. Parvin, MD, PhD; Philip R.O. Payne, PhD
Technical Director of BISR Computational Services: Gulcin Ozer, PhD
Technical Director of BISR Data Sharing Infrastructure Arm: Joshua Yoder, MBA
Scientific Advisor: Kun Huang, PhD
The Biomedical Informatics Shared Resource (BISR) analyzes high-throughput, high dimensional biological data and other biomedical data and information using state-of-the-art informatics tools and high-quality informatics analysis for OSUCCC – James investigators.
The BISR has two service arms: Computational Biology Services and Data Sharing Infrastructure.
BISR offers computational biology and bioinformatics consultative services that include:
- Analysis of next generation sequencing data including Exome-sequencing, RNA-sequencing, ChIP-sequencing and whole genome re-sequencing
- Analysis of microarray datasets, including mRNA (Affymetrix), SNP, and micro-RNA
- Analysis of nCounter NanoString data
- Analysis of publicly available datasets using search parameters defined by the OSUCCC client—for example, from the Gene Expression Omnibus (GEO) database of microarray results, The Cancer Genome Atlas (TCGA) and the International Cancer Genome Consortium (ICGC) data portals that allows access to results of thousands of deep sequencing projects
- Pathway analysis of results from microarray and sequencing data
- Image analysis, including the processing of images in order to reconstruct a three-dimensional tissue, or improvement of image quality using specialized computer programs
- Provide state-of-the-art computational biology service
- Provide access to readily adoptable, service-oriented technologies and platforms that facilitate use of data analytic pipelines
- Provide custom research data management, application development, deployment and support
The Biomedical Informatics Share Resource (BISR) leadership and staff provide OSUCCC investigators with state-of-the-art informatics tools, high-quality informatics analysis and expert computational biology consultative services. Below is a list of key staff who are currently available for collaboration/direct appoint/billable work:
- Co-director: Philip R.O. Payne, PhD
- Co-director: Jeffrey D. Parvin, MD, PhD
- Technical Director of Computational Biology Arm: Gulcin Ozer, PhD
- Technical Director of Data Sharing Infrastructure Arm: Joshua Yoder, MBA
- Scientific Advisor: Kun Huang, PhD
- Staff: Jie Zhang, PhD
- Staff: A. Selen Yilmaz, MS
- Staff: Keiko Akagi, PhD
- Staff: Sandya Liyanarachchi, MS
Jeffrey D. Parvin, MD, PhD, director for the BISR Computational Biology Services arm, is a Professor of the Department of Biomedical Informatics at The Ohio State University, he is associate dean for Graduate Studies at Ohio State’s College of Medicine, and he is co-director of the Biomedical Sciences Graduate Program, the umbrella graduate program of the College of Medicine. Dr. Parvin’s training included earning an MD and a PhD in microbiology for studies of the biochemistry of influenza virus expression and the regulation of oncogenic retroviruses. Dr. Parvin trained as a postdoctoral fellow at the MIT Center for Cancer Research (now called the Koch Institute for Integrative Cancer Research) and was supported there by fellowships from the Irvington Institute and a Special Fellow award from the Leukemia Society of America. He was an assistant and then associate professor of Pathology at Harvard Medical School, where he established a successful research program supported by multiple NIH and American Cancer Society Awards, with a major focus on BRCA1 and breast cancer. In addition, Dr. Parvin taught medical school pathology. He joined The Ohio State University Comprehensive Cancer Center (OSUCCC) and Department of Biomedical Informatics in 2007, where he now leads a research group focused on breast cancer with expertise that spans biochemistry to cell biology to systems biology. An interim chair of the Department of Biomedical Informatics, Dr. Parvin is Director of the OSUCCC Biomedical Informatics Shared Resource. He also leads two informatics cores, on a U01 studying pharmacogenomics and a P01 studying the breast cancer microenvironment.
Philip R.O. Payne, PhD, director for the BISR Data Sharing Infrastructure arm, is an associate professor and chair of the Department of Biomedical Informatics at The Ohio State University. He is also an adjunct associate professor of Health Services Management and Policy within Ohio State’s College of Public Health, associate director for Data Sciences in Ohio State’s Center for Clinical and Translational Science (CCTS), co-director of the OSUCCC BISR, and an executive-in-residence within Ohio State’s Office of Technology Commercialization and Knowledge Transfer. Dr. Payne is an internationally recognized leader in the field of clinical research informatics, and leads the Department of Biomedical Informatics Laboratory for Knowledge Based Applications and Systems Engineering (KBASE), overseeing a research portfolio that is actively supported by a combination of NCATS, NLM, and NCI awards and contracts. Dr. Payne received his PhD with distinction in Biomedical Informatics from Columbia University. Prior to pursuing his graduate training, Dr. Payne served in a number of technical and leadership roles at both the UCSD Shiley Eye Center and UCSD Moores Cancer Center. Dr. Payne’s leadership in the clinical and translational research informatics communities has been recognized through his appointment to numerous national steering and advisory committees as part of the American Medical Informatics Association (AMIA), Association for Computing Machinery (ACM), National Cancer Institute, National Library of Medicine, and the CTSA consortium, as well as his engagement as a consultant to academic health centers throughout the United States and the Institute of Medicine. Dr. Payne is the author of over 140 publications focusing on the intersection of biomedical informatics and the clinical and translational science domains, including several seminal reports that have served to define a new sub-domain of biomedical informatics theory and practice specifically focusing upon clinical research applications.
Gulcin Ozer, PhD, is a research scientist in Ohio State’s Department of Biomedical Informatics and technical director of the OSUCCC BISR. During her postdoctoral training at the OSUCCC BISR, Dr. Ozer has built up a robust expertise in analysis and integration of high-throughput high dimensional biological data including RNA-sequencing, exome-sequencing, ChIP-sequencing, whole genome re-sequencing, Microarray and NanoString data. As technical director of BISR, Dr. Ozer is responsible for comprehensive and systematic management of daily operations, as well as building and expanding research initiatives. Dr. Ozer has authored or coauthored 28 peer-reviewed publications.
Joshua Yoder, MBA, is the Technical Director for the Data Sharing Infrastructure Arm. He is a Senior Informatics Consultant within the department of Biomedical Informatics. He has extensive leadership experience within the research informatics services and technology space. He is currently leading the Research Informatics Services (RIS) team at The Ohio State University. He previously led the informatics operations for the Alliance for Clinical Trials in Oncology at Duke University. As the Director of RIS, Mr. Yoder oversees effort allocation for several Biomedical Informatics Shared Resource (BISR) staff as well as providing guidance and consultation to those requiring novel research-related informatics solutions.
Kun Huang, PhD, is an associate professor of the Department of Biomedical Informatics at The Ohio State University. Dr. Huang has extensive experience in collaborating with biomedical researchers in developing new hypothesis using computational and bioinformatics methods, as well as developing approaches and infrastructure for data sharing and management. Specifically, his research program focuses on developing bioinformatics tools for analyzing, visualizing and managing the large high throughput datasdets to enable systems biology and translational medical research. His lab has developed many methods for analyzing various types of high-throughput biomedical data including gene expression microarray, next generation sequencing (including ChIP-seq, RNA-seq, exome-seq, MDBCap-seq, genome re-sequencing), qRT-PCR, proteomics and microscopic imaging experiments. These methods have been successfully applied to biomedical studies in cancers (e.g., breast cancer, brain tumor, leukemia, oral cancer, colon cancer), pharmacogenomics, neurological diseases, brain development, wound healing, fibrosis and inflammatory bowel diseases. Specifically, from 2007 to 2013, Dr. Huang was the technical director of the OSUCCC Biomedical Informatics Shared Resource (BISR). He has led the services on data analysis and the development of the NGS data processing and analysis pipeline. In this CCSG grant, he will continue to serve as the scientific advisor to the BISR, focusing on identifying key technical issues and bridging the translational bioinformatics research in his lab and department and the needs in BISR.
Jie Zhang, PhD, is a research scientist who consults with OSUCCC biologists. During her postdoctoral training at the OSUCCC BISR, Dr. Zhang trained in downstream analysis of ChIP-sequencing, RNA-sequencing, Exome-sequencing and Microarray data. Dr. Zhang is an expert in gene network, gene co-expression network mining, and pathway analysis.
A. Selen Yilmaz, MS, is a bioinformatics specialist who consults with biologists on a variety of experimental results. Ms. Yilmaz has implemented and run best practice pipelines for the analysis of RNA-sequencing, ChIP-sequencing, Exome-sequencing and whole genome re-sequencing. She also helps design and implement custom workflows and integrate publicly available data to generate new hypotheses or draw new conclusions.
Keiko Akagi, PhD, has expertise is the analysis of genomic data from mouse and humans. She brings extensive experience in establishing an integrated database resource containing thousands of previously unreported mouse genomic “indel” (insertion and deletion) polymorphisms ranging from approximately 100 nt to 10 Kb in size. She has a strong informatics and statistical background and is currently assisting the OSUCCC Genomics Shared Resource in the development, evaluation and analysis of next-generation sequencing data.
Sandya Liyanarachchi, MSc, MAS, has a strong statistical and computational background and currently assists on several projects from multiple basic research labs. She has worked at OSU since 2001 and has worked on numerous research projects utilizing a variety of data analysis techniques. Her expertise in data analysis ranges from high throughput microarray and microRNA data analysis, linkage analysis, haplotype analysis, genotyping data analysis to the current next generation sequencing data analysis.
The BISR Computational Biology Service has conducted analyses for the following institutions:
- Harvard Medical School
- Johns Hopkins University
- Memorial Sloan-Kettering Cancer Institute
- Michigan State University
- Vanderbilt University
Biomedical Informatics Shared Resource
1800 Cannon Drive
Room 340C (Computational Biology Service)
Columbus, OH 43210
Phone: 614-366-1538 or 614-292-4778
Availability: Monday – Friday, 9 a.m. – 5 p.m., or by appointment