Dr. Justin Siegel: Enzyme Design, Large-scale Mutant Generation, and Cloud Labs
The Bioinformatics and Beyond Podcast
by Leo Elworth
1y ago
Dr. Justin Siegel begins this episode by explaining what enzymes are, how they have evolved, and why Dr. Siegel is motivated to try to engineer enzymes to perform functions tailored to help humanity instead of to perform functions based on how they evolved in nature. He explains the primary goal of the work discussed and relating enzyme sequence to function. Dr. Siegel also explains how his work was the first of its kind by scaling up enzyme design to hundreds of mutants instead of dozens.  We then dig into the details of Dr. Siegel’s work. We learn details of his study such as why his te ..read more
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Dr. Justin Siegel: Lab Automation, Cloud Labs, and the Future of the Wet Lab
The Bioinformatics and Beyond Podcast
by Leo Elworth
1y ago
Dr. Justin Siegel explains the past, present, and future of wet lab work and wet lab automation. We start by hearing a description of what it is like to work in a wet lab, covering the contrast between the excitement of seeing life changing results and the countless hours of monotony that is often involved to produce these results.  We then begin discussing where automation will fit in to help alleviate the burden of long term monotonous work in the wet lab. We learn about the challenges of implementing automation in a lab, and hear about the dream that exists from the promise of automati ..read more
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Dr. Afshin Beheshti: MicroRNAs and COVID-19
The Bioinformatics and Beyond Podcast
by Leo Elworth
1y ago
Dr. Afshin Beheshti begins this episode by explaining what microRNAs are and why they are emerging as an important area of biological research. He then explains how microRNAs relate to viruses, which is a recently developing area of research in this already young field of study. Dr. Beheshti then tells the story of how he started to discover that microRNAs could be a driver of COVID-19 infections.  His story begins by using microRNA analysis tools to analyze COVID-19 infected patients from China which predicted a handful of microRNAs that could be involved in COVID-19 infection. He discus ..read more
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Dr. Afshin Beheshti: The Hazards and Molecular Features of Spaceflight
The Bioinformatics and Beyond Podcast
by Leo Elworth
1y ago
This episode concludes the podcast’s series of episodes focused on space biology and space omics. NASA scientist Dr. Afshin Beheshti discusses the many high level hazards and corresponding molecular features of spaceflight throughout this episode. For instance, we begin with a discussion of the hazards of radiation and microgravity. Dr. Beheshti spends time explaining a high level view of what each hazard is, why it is a concern for spaceflight, and educates us on many useful and interesting pieces of information for each hazard. Further hazards discussed include confinement and isolation, hos ..read more
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Dr. Tejaswini Mishra: Wearables Detect Pre-symptomatic COVID-19
The Bioinformatics and Beyond Podcast
by Leo Elworth
1y ago
This episode discusses Dr. Tejaswini Mishra’s recent publication in Nature Biomedical Engineering: https://www.nature.com/articles/s41551-020-00640-6 Dr. Mishra begins the episode by explaining the origin story of this work and how the idea for this paper came to be. She then explains how this study enrolled thousands of participants and used the participants’ smartwatch or wearable device data to detect COVID-19 infections.  After explaining how this study began, Dr. Mishra discusses how she and her team came up with two main algorithms for detecting COVID-19 infections from wearables da ..read more
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Dr. Tejaswini Mishra: The NASA Twins Study
The Bioinformatics and Beyond Podcast
by Leo Elworth
1y ago
This episode continues our series of episodes on space biology and #SpaceOmics with Dr. Tejaswini Mishra. Dr. Mishra introduces The NASA Twins Study, a cornerstone scientific work where two twin astronauts were monitored, with one twin traveling to space, and one staying on earth. Dr. Mishra explains the importance of studying long term spaceflight missions, how The NASA Twins Study was set up in a particularly great way to study spaceflight impact, the many different types of data collected and analyzed, and some of the results found by the study. During the episode, Dr. Mishra explains many ..read more
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Wet Lab / Dry Lab Transitioning with Dr. Willian da Silveira
The Bioinformatics and Beyond Podcast
by Leo Elworth
1y ago
For people who work in the life sciences, a very common occurrence is for folks who work on the "wet" side of research, largely doing bench work, to become interested in or start wanting to transition to doing more "dry" research, like computational research in bioinformatics. In this special episode, dedicated to those thinking about transitioning from "wet" lab work to doing more "dry" lab type work, my guest Dr. Willian da Silveira explains his own transition from a full bench scientist to a full time bioinformatician. Dr. da Silveira also answers many questions from the bioinformatics subr ..read more
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Dr. Willian da Silveira: The Mitochondria as a Central Hub for Spaceflight Impact
The Bioinformatics and Beyond Podcast
by Leo Elworth
1y ago
In this episode we begin discussing the biology of spaceflight with Dr. Willian da Silveira. We start by hearing the story of how Dr. da Silveira's recent high profile space omics paper (https://www.cell.com/cell/pdf/S0092-8674(20)31461-6.pdf) came to be. He first describes the NASA GeneLab and how he got involved, and how his story of this paper began with an analysis of some liver transcriptomics data. We hear about all the different types of data used in this study, including epigenetics and metabolomics data. Dr. da Silveira discusses how to try to incorporate and work with this many types ..read more
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Dr. Hayden Metsky: ADAPT for Large-scale Viral Detection
The Bioinformatics and Beyond Podcast
by Leo Elworth
1y ago
Dr. Hayden Metsky begins by introducing the ADAPT method for doing large-scale detection of viruses. ADAPT is a computational method that aids the design of CRISPR-based viral testing. He then discusses the motivation for ADAPT and how it relates to his previous works like CATCH. In comparing ADAPT to other work, Dr. Metsky discusses, for instance, differences between CRISPR-based testing and more traditional testing like qPCR. In discussing the challenges of designing diagnostic tests and detection assays, Dr. Metsky then describes how he breaks these challenges into three different component ..read more
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Dr. Hayden Metsky: Computational Methods for Viral Diagnostics, CRISPR-based Tests, CATCH, and More
The Bioinformatics and Beyond Podcast
by Leo Elworth
1y ago
Dr. Hayden Metsky begins the episode by describing his goal of being able to harness sequenced viral genomes to computationally design diagnostics, therapies, and vaccines. He discusses the value of having methods available that can handle all available genomic data for diverse species for diagnostics and therapies. Next, we learn how CRISPR can be used in a diagnostics setting. Dr. Metsky explains how collateral cleavage broadens the use of CRISPR beyond simply being a tool for genome editing. Advantages and disadvantages of CRISPR-based diagnostics techniques are discussed versus, for exampl ..read more
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