Schedule
- Session 2 (July 7 - 25, 2025)
- Synchronous time: Monday through Friday, 8 - 10 p.m. ET
Description
In this course we will examine the intersection of biology, computer science, and statistics, with special emphasis on the biological aspects. Advances in next-generation sequencing technologies have led to the production of large amounts of sequencing data and a growing need to develop researchers to analyze it. There are a variety of bioinformatics tools available for students to learn, enabling them to participate in authentic research. This course introduces these tools through hands-on training. The course will focus on using analytical methods to understand the features, functions, and evolution of genomics. Additionally, we will include a hands-on training module to learn Python coding and developing/applying the Python pipeline for high throughput data analysis. The overall aims of the course are for students to 1) learn the underlying theory behind bioinformatics tools for genomic analysis, 2) develop an understanding of how the analysis of sequence data informs the study of biology and 3) Develop expertise with Python coding and applications. Students will get an opportunity to work with biological datasets, perform authentic research and contribute to an ongoing research project.
Expected learning outcomes
- Be able to diagram/explain the various types of genome sequencing technologies and explain their strengths and weaknesses
- Gain facility with important general databases, focusing on those housed at the National Center for Biotechnology Information (NCBI)
- Students will also gain facility with the prokaryotic database at the Joint Genomic Institute (JGI)
- Be able to use web tools such as BLAST, MUSCLE, and MEGA to examine DNA and protein sequences and to explain in general terms how they work
- Be able to annotate genes in terms of both structure and function
- Be able to compare gene/protein sequences and draw inferences about evolutionary history
- Gain familiarity with Python coding and applications
- Gain facility in reading and interpreting primary literature
Program Director: Vinayak Mathur, PhD
Vinayak Mathur, PhD, is an assistant professor of biology at Cabrini University, with a faculty affiliation with the University of Pennsylvania. His current research focuses on microbial genomics and application of bioinformatics to answer questions of horizontal gene transfer between bacteria and bacteriophages.
He has a Bachelor of Engineering in biotechnology from the Manipal Institute of Technology in India. He received a doctorate in biology from the University of Pennsylvania, where he studied the effect of short-term adult plasticity on climatic adaptation of Drosophila melanogaster. He completed his postdoctoral training from Georgetown University, where he was involved in the Genome Solver Project.
Dr. Mathur is passionate about undergraduate biology education. He researches bioinformatics teaching tools and their implementation in the undergraduate classroom. His teaching style relies heavily on the CURE model (Course-Based Undergraduate Research Experience). In the classroom, his students work collaboratively to develop novel research projects and engage with the scientific process.
