Hear from the leading experts in bioinformatics and other closely related fields. Topics discussed include computational biology, biotechnology, computer science, genetics, synthetic biology, math, statistics, and more. You can also find discussions on topics related to the scientific career field. For example, exploring career path options in science, or highlighting important skill sets such as writing and public speaking.
In this second part of our history of metagenomics with Matthew Schechter, we start with a description of what a metagenome contains and how you analyze this type of data. Matt explains a few high level concepts such as metagenome assembly, metagenomic assembled genomes, contigs, contig binning, and genome completeness. Matt explains how metagenomics can help answer previously unanswered questions and even generate new hypotheses like in the example of the Candidate Phyla Radiation. Matt further explains how metagenomics is unbiased when compared to 16S sequencing and what his vision is for “Metagenomics 3.0.” Further topics discussed include pangenomics, further ways metagenomics can generate new hypotheses, and metapangenomics. Read Matt's full article of the history of metagenomics at https://merenlab.org/2020/07/27/history-of-metagenomics/
In this episode we begin our history of metagenomics with Matthew Schechter. Beginning with highlights like the initial ability to see microbes with a microscope and growing microbial colonies, we work our way through the history of metagenomics leading to modern day sequencing. Matt describes a discrepancy between culturing and what is present in a sample, and how sequencing began to overcome this discrepancy. Matt covers what 16S sequencing is and where it fits in the history of metagenomics. We end with a discussion of a seminal work on reconstructing genomes from sequenced metagenomes. Read Matt's full article of the history of metagenomics at https://merenlab.org/2020/07/27/history-of-metagenomics/
Dr. Heer Mehta starts by going over several of the ways that bacteria become resistant to antibiotics. Dr. Mehta explains the connection between specific antibiotics and specific drugs, and how she uses this information to know what to look for when studying the outcomes of experimental evolution studies. She explains how her group can isolate individual mutations that arise as a pathogen becomes resistant, and determine the difference in the protein structure caused by the mutation. We then discuss specifics of how Dr. Mehta and her group have studied the mechanisms for resistance used by individual pathogens, including a potential biosecurity threat. This discussion includes an example of a pathogen evolving resistance to two antibiotics in a single experimental evolution experiment. Finally, we discuss the potential uses for this type of research to translate to clinical usefulness.
Dr. Heer Mehta first goes over some basics of what antibiotic resistance is, why it is a global concern, and some related history. Dr. Mehta explains how bacteria are able to evolve to become resistant to antibiotics. She goes on further to explain how experimental evolution is one way scientists can understand this process and potentially use as a weapon in humanity’s battle against antibiotic resistant pathogens. She explains additional tools we can use such as microscopy and genome sequencing. We walk through how experimental evolution is setup, how the full experiment proceeds, and the final results that can be obtained. Additional topics discussed include pharmacodynamics and hypermutation.
We begin this episode by having Dr. Dinler Antunes explain what cancer immunotherapy is. Dr. Antunes gives an extremely thorough, clear explanation of what cancer immunotherapy is, how it works, and the many concepts involved. These concepts include how the human immune system works and how peptides are displayed on the outside of cancer cells. Further topics include how cancer cells can be differentiated from normal cells and the different types of immunotherapy possibilities that arise as a result. We then learn about some of Dr. Antunes own work, such as the HLA-Arena software package (see more at https://dinlerantunes.com/). Finally, we discuss the future promise and potential hurdles of cancer immunotherapy.
Dr. Dinler Antunes explains what the protein folding problem is and gives a bit of history on the problem. Dr. Antunes describes the types of methods for solving the problem computationally. He then discusses the rise of AlphaFold 2 for protein folding and gives his thoughts on its impact. Our discussion then shifts to the molecular docking and related problems, where the problem becomes to predict how molecules interact with each other. Dr. Antunes discusses how this problem shows up in the real world, for instance when a drug interacts with a protein. He explains the computational aspect of molecular docking and molecular dynamics. Finally, we learn about related work in relation to finding potential treatments for SARS-CoV-2.
Dr. Lauren Stadler describes the connection between environmental microbiology and bioinformatics. We start with an explanation of wastewater monitoring including how it is collected, cleaned, gotten rid of, monitored, and studied. Dr. Stadler defines and gives a bit of history on wastewater-based epidemiology. Dr. Stadler discusses how SARS-CoV-2 environmental monitoring could be widened and further developed to monitor other pathogens such as influenza. We then discuss the technical aspects of wastewater and environmental monitoring. Final topics include environmental monitoring after hurricane Harvey and engineering our drinking water.
What if we could know how widespread COVID-19 is in our communities, in a low-cost way, that everyone automatically opts in to, with no additional effort? In this episode, Dr. Lauren Stadler tells us how her lab shifted from studying microbial communities in wastewater to monitoring levels of the SARS-CoV-2 virus in wastewater. Dr. Stadler explains how SARS-CoV-2 ends up in wastewater and how it can be used to track COVID-19 positivity rates. She discusses the incredible power and potential of this new form of community testing. For instance, she describes how the government is catching on to its power, the cost compared to individual testing, and how sequencing wastewater could give us additional information on how the virus is being transmitted.
In this episode we revisit the “expanded” scientific skillset, discussing skills such as written and oral communication, marketing, people skills, listening, reading, networking, and literature search. Dr. Luay Nakhleh teaches us how to improve each of these skills. He explains how he continually asks himself, “How did I do?” He also explains how we can use this question to improve ourselves, in addition to feedback from others. Dr. Nakhleh then elaborates on further ways to improve skills. For instance, describing how our writing skills can be improved through a more mindful analysis of what we read. For each skill, Dr. Nakhleh attempts to define what it looks like to do that skill well. For instance, he addresses what it means to be a good listener and a good reader. Additional topics discussed include the role of social media in science and how to become an effective communicator when english is not your first language.
In this episode, we introduce and explore the “expanded” scientific skillset. Dr. Luay Nakhleh, who was recently named Dean of Engineering at Rice University, describes how communication is a requirement for leadership. He tells us the story of when he decided to grow his own communication skills, how he began improving, and the rewards of being an effective communicator. Additional skills such as marketing are discussed. For instance, Dr. Nakhleh explains how skillful marketing can help scientists spread their work and increase their impact. Further skills discussed include writing, listening, reading, people skills, networking, and literature review. For each of these skills, we attempt to highlight how they complement traditional career skills in STEM, why they are important, and how this importance can change depending on a person’s career goals.
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.
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 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 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 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 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 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 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 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.
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.
For those considering a scientific career, Dr. Krista Ternus explains the wide array of scientific career paths in depth, from academia to companies to government labs to non profits and more. We also discuss leading a lab and winning scientific funding outside of academia. Finally, Dr. Ternus shares tips on writing successful grants and how to handle failure as a scientist.
Dr. Krista Ternus explains how studying metagenomics leads to being able to answer what is in an unknown sample, and describes the multiple applications of metagenomics. Dr. Ternus also explains applications of bioinformatics in synthetic biology and biosecurity.
As more sequence data becomes available from the SARS-CoV-2 outbreak, there are a number of considerations to make when analyzing read datasets coming from genome sequencers. Dr. Krista Ternus explains common steps to take when analyzing these data sets, potential pitfalls, and interesting scientific questions that can be answered using this type of data.
What is Convalescent Plasma Therapy and how can it be used as a treatment for COVID-19? In this episode, Dr. Michael Joyner and Dr. Rickey Carter give us a lesson on the past, present, and future of convalescent plasma therapy. From its origins to its role in the fight against the ongoing COVID-19 pandemic. We get a glimpse of both the clinical side, as well as the informatics side, of studying treatments for COVID-19, as well as the role of both clinicians and bioinformaticians in the future.
Adrianne Gladden-Young has been involved in the sequencing and surveillance of past outbreaks of emerging pathogens for many years. She discusses, for instance, her previous involvement in outbreaks such as Ebola and Zika. How can we be better prepared for future outbreaks?
Adrianne Gladden-Young tells us about her work in sequencing the very first SARS-CoV-2 genome in Massachusetts. She explains the full bioinformatics process of sequencing and analyzing SARS-CoV-2 genomes, starting from collecting a sample from someone who is sick, and ending with computational analyses leading to a better understanding of how COVID-19 spreads.
One of Darwin's original drawings of an evolutionary tree had "I think" written next to it. Dr. Luay Nakhleh explains how evolution underlies much, or perhaps all, of bioinformatics analyses. This includes his own research where he computationally models the evolutionary process, with a focus on cases where evolution violates Darwin's original assumption that evolution mirrors the shape of a tree. Dr. Nakhleh explains how he tackles the problem of modeling these complex evolutionary processes, including in cancer genomics.
What is Bioinformatics? What is the Bioinformatics and Beyond Podcast? What is the difference between Bioinformatics and Computational Biology? What skill sets are required to become a Bioinformatician? How would someone take their first step into the world of Bioinformatics? What career options are out there for Bioinformaticians?