About This Course
In this course, you will follow in the footsteps of the bioinformaticians investigating the COVID-19 outbreak by assembling the SARS-CoV-2 genome. Whether you’re new to the world of computational biology, or you’re a bioinformatics expert seeking to learn about its applications in the COVID-19 pandemic, or somewhere in between, this course is for you! As you go through this journey, we will introduce and explain genomic concepts and give you many opportunities to practice your skills, and we will provide a series of problems with gradually increasing complexity. This first course will only discuss the assembly of the SARS-CoV-2 genome, but future courses in this series will explore follow-up bioinformatics analyses used in the COVID-19 pandemic.
Course Staff
Niema Moshiri
Niema Moshiri (Ph.D.'19 UC San Diego) is an Assistant Teaching Professor in the Computer Science & Engineering (CSE) department at the University of California, San Diego. His educational background is in Bioinformatics, which spans Computer Science (with a focus on Algorithm Design) and Biology (with a focus on Molecular Biology). His research focus is in the development of computational methods for the study of viral phylogenetics and epidemiology.
Pavel Pevzner
Pavel Pevzner is a Professor of Computer Science & Engineering (CSE) at the University of California, San Diego (UCSD), where he holds the Ronald R. Taylor Chair and has taught a Bioinformatics Algorithms course for the last 12 years. In 2006, he was named a Howard Hughes Medical Institute Professor. In 2011, he founded the Algorithmic Biology Laboratory in St. Petersburg, Russia, which develops the online bioinformatics platform Rosalind. His research concerns the creation of bioinformatics algorithms for analyzing genome rearrangements, DNA sequencing, and computational proteomics. He authored Computational Molecular Biology (The MIT Press, 2000), co-authored (jointly with Neil Jones) An Introduction to Bioinformatics Algorithms (The MIT Press, 2004), and co-edited (with Ron Shamir) Bioinformatics for Biologists (Cambridge University Press, 2011). For his research, he has been named a Fellow of both the Association for Computing Machinery (ACM) and the International Society for Computational Biology (ISCB).
Mike Rayko
Mike Rayko is a senior researcher in the Center for Algorithmic Biotechnology, Saint Petersburg State University. He received his Ph.D. in Biology from Komarov Botanical Institute. His research interests include comparative genomics and evolution of the extrachromosomal DNA, including plasmids and viruses. He teaches molecular phylogenetics and applied bioinformatics, and has contributed to several MOOCs. He enjoys raising his child and volunteering in social programs.
Vikram Sirupurapu
Vikram Sirupurapu is an M.S. student in the Computer Science & Engineering (CSE) department at the University of California, San Diego (UCSD). His area of interests includes bioinformatics algorithms, population genetics and computer networks. His current research focus is in studying immunoglobulin loci of mammalian species.
Sabeel Mansuri
Sabeel Mansuri (B.S.'20 UC San Diego) is a Bioinformatician and Software Engineer with a special interest in education technology. His work includes building pedagogical material, research in computational biology, and, most recently, full-stack web development at leading technology companies such as Bravado and Amazon.