The Bioinformatics and Beyond Podcast

Latest Episodes:

Dr. Kathryn Kundrod: Developing Low-Cost, Accessible Tests with LAMP Dec 19, 2020

Show notes

Dr. Kathryn Kundrod explains how her work has focused on making quality testing available in more resource limited settings. She discusses the design decisions involved and the tradeoffs that can be made to balance the accuracy of a test against the accessibility and cost of a test. We learn about how resource constraints apply to all COVID-19 testing done in all countries of the world. We then dive into the technical details of designing a test with a technology like LAMP. She discusses further considerations that impact designing a new COVID-19 test, such as practical considerations like ease of regulatory approval and availability of reagents. We conclude by hearing about what the experience was like when Dr. Kundrod and her colleagues rolled out their newly designed test at Rice University.

Dr. Kathryn Kundrod: The State of COVID-19 Diagnostic Testing; How We Got Here, Types of Tests, and Emerging Technologies Dec 12, 2020

Show notes

In this episode, we explore the landscape of COVID-19 diagnostic testing with Dr. Kathryn Kundrod. Dr. Kundrod walks us through a bit of history on how we got to where we are at with COVID-19 diagnostic testing from the start of the pandemic to now. This history includes perspectives from both the technical and regulatory sides, as well as practical considerations such as shortages in test reagents. For those wondering about getting a test, Dr. Kundrod explains the different types of tests currently available. She discusses some of the early roadblocks to setting up widespread testing and thoughts on how things could have potentially gone more smoothly. Finally, we explore newer technologies and how close we are to getting to tests that can be used at home in a format as simple as a pregnancy test. Emerging technologies discussed include methods such as isothermal amplification with RPA and LAMP.

Dr. Tomer Altman: Searching 5 Petabytes of Sequence Data with Serratus Dec 05, 2020

Show notes

Dr. Tomer Altman describes the atypical origin of the Serratus project and explains why Serratus is such a big leap forward from doing a sequence search with something like BLAST. Dr. Altman dives into the nuts and bolts of how Serratus works and how it was used to find entirely new branches of the tree of life, filled in with previously uncharacterized coronaviruses. Dr. Altman also outlines potential future uses of systems like Serratus for things like biosurveillance and human health in relation to the human microbiome. Learn more about Serratus at https://www.biorxiv.org/content/10.1101/2020.08.07.241729v1

Dr. Tomer Altman: Primer Design for SARS-CoV-2 Diagnostics Nov 28, 2020

Show notes

Dr. Tomer Altman explains what primers and probes are in the context of PCR tests for detecting pathogens such as SARS-CoV-2 when someone is infected with COVID-19. He explains the issues he found in the original CDC primer and probe designs, as well as his thoughts on what may have caused the issues. He then walks us through how these sequences are designed, giving a very clear tutorial of the bioinformatic design of oligonucleotide sequences for diagnostics use. For more information, please see https://tomeraltman.net/2020/03/03/technical-problems-COVID-primers.html and https://tomeraltman.net/2020/03/11/COVID-19-candidate-primers-update.html

Dr. Melissa Haendel: Ontologies, Phenotypes, and Disease Diagnostics Nov 21, 2020

Show notes

Dr. Melissa Haendel explains what ontologies are and their usefulness in bioinformatics, genome phenome mapping, and diagnostics. We also discuss the relationship between ontologies and electronic health records.

Dr. Melissa Haendel: COVID-19 Clinical Informatics Nov 14, 2020

Show notes

Dr. Melissa Haendel discusses how the N3C organization she co-leads and co-founded has led the way in integrating COVID-19 clinical data to aid research efforts. She discusses how the creation of synthetic clinical data also has the potential to help COVID-19 researchers. Further topics include the current status of electronic health records in the United States and how her team overcomes heterogeneity and data quality concerns in electronic health records.

Dr. Fritz Sedlazeck: Sequencing and Detecting Structural Variants in SARS-CoV-2 Nov 07, 2020

Show notes

Dr. Fritz Sedlazeck discusses his own SARS-CoV-2 research works. He discusses a number of projects such as quantifying structural variants in the SARS-CoV-2 genome and converting a human sequencing center to a COVID-19 testing center. He also shares tips on how he analyzes genomic data sets.

Dr. Fritz Sedlazeck: Detecting and Interpreting Structural Variants in Genomes Oct 31, 2020

Show notes

Dr. Fritz Sedlazeck discusses detection and interpretation of structural variants within genomes. He begins by explaining the basics of what structural variants are and how they affect organisms' phenotypes. He also covers some of his own work, for instance, categorizing the effects of structural variants in tomatoes and yeast, including being able to edit the genome of a tomato to change its flavor. Finally, he explains how the methods for detecting structural variants have evolved over time.

Dr. Todd Treangen: Fall 2020 Bioinformatics Roundup Oct 24, 2020

Show notes

Dr. Todd Treangen gives us an update on what's been going on lately in the field of bioinformatics. We begin with a discussion on the best ways to stay current in bioinformatics. Dr. Treangen discusses the roles of the wide variety of sources of information such as conferences and journals. In particular, he expands on the role of social media sites like twitter in science. Finally, Dr. Treangen covers some of the current bioinformatics buzz, such as the integration of machine learning and the progress on a final, fully finished human genome sequence.

Dr. Todd Treangen: The Hidden Diversity of SARS-CoV-2 Oct 17, 2020

Show notes

A diverse population of the SARS-CoV-2 virus can exist inside of a single person who is infected with COVID-19. Dr. Todd Treangen explains how his background in analyzing microbial genomes set him up to investigate this "hidden" diversity. He also discusses related work in co-developing a COVID-19 diagnostic test and co-founding and co-leading the COV-IRT organization.