OK-INBRE Core Facilities

Bioinformatics Core

David Dyer, Ph.D.
Professor
Microbial Pathogenesis and Microbial Genomics
University of Oklahoma Health Sciences Center
Biomedical Research Center, room 362
975 NE 10th Street
Oklahoma City, OK 73104
405.271.1201 x1
David-dyer@ouhsc.edu
Dyer2

Biomedical research has evolved into an increasingly technology-driven endeavor and like the rest of society, has become critically dependent on computational tools and methods for data analysis, archiving and retrieval. This is particularly true as NIH moves into the era of Big Data. The OK-INBRE Bioinformatics Core supports this continuing evolution within the state of Oklahoma, by providing bioinformatics support for both the Oklahoma research and educational enterprises. Collectively, these efforts will enhance the competitiveness of Oklahoma investigators for local, state and national funding, and increase the pool of skilled young biomedical research scientists in Oklahoma.

Research Support. Our mission is to enhance Oklahoma research expertise and infrastructure by providing state-of-the-art bioinformatics support to investigators performing biomedical research on the campuses that participate in the Oklahoma IDeA Network. We currently provide bioinformatics research support for over 150 investigators in the state, enriching many scientific disciplines including cancer biology, cell and developmental biology, diabetes and microbial pathogenesis. This breadth demonstrates the wide-ranging power of bioinformatics to advance biomedical research. Our services include DNA sequence data cleanup and analysis of DNA sequence-based experiments including microbial genome sequencing and annotation, RNA-seq and ChIP-seq analysis, 16S rRNA-based microbiomics. Where possible, we will train laboratory personnel in the analysis of these data using commercial software that exploits a graphical user interface, to avoid the necessity of working on the command line to analyze this data. We also provide access to the Ingenuity Pathway Analysis (IPA) software suite, which is essential for exploring whole transcriptome data obtained from eukaryotic cells. If you need access to the IPA software for your project, please contact Dr. Dyer at the email address above to arrange for a user account. In all your studies, we strongly suggest that you contact us before you begin experiments that will require bioinformatics support, so that we can advise on your experimental design. A well-organized experiment is crucial for obtaining a statistically robust outcome for many of these experiments. In addition to these services, we have experience in protein structure modeling, including the analysis of protein interactions with small molecules for drug and inhibitory design. Support for other custom bioinformatics applications is available as needed. Please contact us for more details. As needed, we also will partner with the newly established OK-INBRE Proteomics Core to support your discovery and targeted proteomics experiments.

Educational Support. We provide support for bioinformatics education at Oklahoma IDeA Network Primarily Undergraduate Institutions (PUI) and Community Colleges (CC), by offering didactic coursework and hands-on computing laboratories, such as laboratory exercises in DNA Barcoding and 16S rRNA-based Microbial Ecology. These classes have enriched the educational experiences of undergraduate students, graduate students and high school science teachers in the state. We also provide custom lecture material on other topics such as structural bioinformatics and phylogenetic analysis. Beginning in 2020, we will offer a new course on the OUHSC campus, MI6401 Introduction to Bioinformatics. Holding this course in the summer session will eliminate potential overlap with existing coursework, making the scheduling more flexible and available to a wider selection of graduate students on the OUHSC campus, postdoctoral fellows and OUHSC faculty. This course will not be designed to teach attendees to write code and work extensively on the command line; rather, this is planned as a survey course intended to ensure that students, trainees, and faculty will gain familiarity with the basic tools and databases that are available to researchers for these types of studies.We will make use, where possible, of GUI-based commercial software such as CLC Genomics Workbench.The availability of GUI-driven bioinformatics software greatly enhances the ability of novice researchers to rapidly engage the full power of bioinformatics tools and their capabilities.We have in the planning stages a more formal instruction in writing code (R, Python, etc.) for solving problems in data management and analysis using a more advanced bioinformatics methods. Scheduling MI6401 in the summer also will ease the participation by OK-INBRE PUI and CC faculty; in fact, we plan to develop an on-line version of this course that will be available to PUI and CC faculty. This class will increase faculty familiarity with bioinformatics, and aid in incorporating these materials into coursework on the PUI and CC campuses. It is possible that this course could be included as part of the support offered to PUI and CC faculty who receive OK-INBRE funding for curriculum development. In sum, these bioinformatics educational efforts will stimulate the movement of promising students into the post-graduate education pipeline, foster the career development of young biomedical scientists at all stages of their training, and enable the use of state-of-the-art bioinformatics tools by Oklahoma investigators.

Proteomics Core

Kinter
Michael Kinter, Ph.D.

OK-INBRE Proteomics Core Director
Oklahoma Medical Research Foundation
825 NE 13th Street
Oklahoma City, OK 73104
mike-kinter@omrf.org

Fall 2022 Bioinformatics for Proteomics Workshop

Proteomics Core Goals

The goal of the OK-INBRE Proteomics Core is to provide researchers in Oklahoma and in all IDeA-eligible states access to state-of-the-art instrumentation and expertise for advanced mass spectrometry (MS). The core is equipped with the instrumentation and expertise required to make discovery proteomics and targeted quantitative proteomics experiments available to researchers in Oklahoma. The discovery proteomics experiments will use data dependent analyses to acquire high resolution survey scans to determine peptide mass with high accuracy and collision induced dissociation (CID) spectra to determine the amino acid sequence. Database searches then identify the proteins and find posttranslational modifications. The targeted quantitative proteomics experiments will use selected reaction monitoring (SRM) and parallel reaction monitoring (PRM) to selectively detect and quantify proteins based on peptides formed by trypsin digestion.

To ensure statewide awareness of the core’s capabilities and access to these methods, the OKINBRE Proteomics Core laboratory will, i) continue to offer educational workshops and develop on-line materials to describe our methods and educate potential users and ii) provide vouchers to defray costs associated with pilot projects to enhance utilization of the OK-INBRE Proteomics Core.

Finally, the OK-INBRE Proteomics Core will continue to function as the Targeted Quantitative Proteomics component of the IDeA National Resource for Proteomics that provides access to advanced proteomics methods and education for Core Directors, trainees, and researchers from all IDeA-eligible states.