Bioinformatics Research at Drexel Biomed
Wednesday, February 24, 2021
4:00 PM-5:30 PM
BIOMED Seminar
Title:
Bioinformatics Research at Drexel Biomed
Speakers:
Ming Xiao, PhD
Associate Professor
School of Biomedical Engineering, Science and Health Systems
Drexel University
Ahmet Sacan, PhD
Associate Teaching Professor
School of Biomedical Engineering, Science and Health Systems
Drexel University
Andres Kriete, PhD
Teaching Professor
Associate Dean for Academic Affairs
School of Biomedical Engineering, Science and Health Systems
Drexel University
Details:
Talk #1 – Ming Xiao, PhD
Nano-genomics: Micro/Nano-technologies for Genome Research - The overall goal of the nano-genomics lab is to develop the micro/nano-technologies for genome research and apply these technologies to understand genomic structures and variations in the human genome. Dr. Xiao will discuss the recent research activities in his lab, including technology development and applications based on these technologies. He will also explain how bioinformatics plays a key role in his research.
Talk #2 – Ahmet Sacan, PhD
Dr. Ahmet Sacan will provide an overview of the graduate level bioinformatics and machine learning courses he is offering, followed by a discussion of the research projects he is currently involved in, including the use of circulating micro-RNAs for diagnosing Chronic Regional Pain Syndrome (CRPS) and the use of olfactory tests for diagnosing COVID-19.
Micro-RNAs are short RNA molecules that target mRNAs and negatively regulate their translation. Aberrant changes in the levels of micro-RNAs can cause de-regulation of their target genes and such changes have been implicated in many diseases, including CRPS. CRPS is a debilitating pain syndrome with heterogeneous etiology and is difficult to diagnose. We have shown that circulating micro-RNAs, which are packaged in small extracellular vesicles (sEVs) and remain stable in blood, can be used as biomarkers for CRPS. We have developed a machine learning model to classify CRPS patients vs. healthy controls with 95% accuracy. We have also demonstrated that the miRNA profiles of patients can be used to predict their response to ketamine treatment.
Coronavirus disease (COVID-19) continues to negatively impact the health and well-being of many around the world. Among the symptoms of COVID-19 is a sudden loss of smell function, making the assessment of such dysfunction an early disease biomarker. In a pilot study, we have administered a smell test containing 40 odorants to 138 COVID-19 PCR-positive and 132 COVID PCR-negative individuals. Using AdaBoost, an ensemble machine learning method that combines multiple decision trees, we developed a predictive model that achieved greater than 93% in accuracy, specificity, and sensitivity in classifying COVID-19 patients vs. health controls. Our current work involves validation of model independent centers and development of more concise odor sets to facilitate the adoption of smell tests as an additional early diagnostic tool for COVID-19.
Talk #3 – Andres Kriete, PhD
The focus of my research is on the systems biology of aging, taking an integrative view of a biological process that disturbs a broad range of cellular and physiological functions in a complex and global fashion. We explore concepts from engineering (complex systems, robustness, control theory) to decipher the mechanisms of aging at the intersection of experimental, computational, and theoretical biology.
Biosketches:
Ming Xiao, PhD, is an associate professor at Drexel University's School of Biomedical Engineering, Science, and Health Systems. The overall goal of Dr. Xiao's research is to develop the micro/nano-technologies for genome research and apply these technologies to understand human genomic structures and variations.
Ahmet Sacan, PhD, is currently an Associate Teaching Professor at Drexel University, School of Biomedical Engineering, Science and Health Systems. Dr. Sacan received his BSc degrees in Computer Science and in Cellular and Molecular Biology from University of Michigan, Ann Arbor (2001); and his PhD from the Computer Engineering Department of the Middle East Technical University (Turkey, 2008). He spent several years as a visiting scholar and Post-Doctoral Researcher at the Ohio State University (2006-2008), before joining Drexel University.
Andres Kriete, PhD, joined the School of Biomedical Engineering, Science and Health Systems at Drexel University, Philadelphia, as Associate Professor in 2003. He held adjunct appointments at the Center for Complex Systems and Visualization at the University of Bremen, Germany, the Bioengineering Department at the University of Pittsburgh, the Coriell Institute for Medical Research in Camden, and the Monell Institute for Chemical Senses in Philadelphia, before he was appointed Associate Dean for Academic Affairs at the School. He teaches students in computational bioengineering, biostatistics, and imaging. Dr. Kriete develops systems approaches to aging by combining theory, experimental data, and computational modeling. He is part of the Cell2Society Aging Research Initiative at Drexel University.
Contact Information
Lisa Williams
ltw22@drexel.edu