Shows
The Bioinformatics and Beyond PodcastDr. Justin Siegel: Enzyme Design, Large-scale Mutant Generation, and Cloud LabsDr. 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 lea...2021-10-2322 minThe Bioinformatics and Beyond PodcastDr. Justin Siegel: Lab Automation, Cloud Labs, and the Future of the Wet LabDr. 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 d...2021-10-0933 minThe Bioinformatics and Beyond PodcastDr. Afshin Beheshti: MicroRNAs and COVID-19Dr. 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 discusses h...2021-09-1129 min
The Bioinformatics and Beyond PodcastDr. Afshin Beheshti: The Hazards and Molecular Features of SpaceflightThis 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, hostile and closed environment, and distance from Ea...2021-08-2848 minThe Bioinformatics and Beyond PodcastDr. Tejaswini Mishra: Wearables Detect Pre-symptomatic COVID-19This 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 data. Dr. Mishra also discusses the many...2021-08-1428 minThe Bioinformatics and Beyond PodcastDr. Tejaswini Mishra: The NASA Twins StudyThis 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...2021-07-3129 minThe Bioinformatics and Beyond PodcastWet Lab / Dry Lab Transitioning with Dr. Willian da SilveiraFor 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 subreddit on...2021-07-171h 02The Bioinformatics and Beyond PodcastDr. Willian da Silveira: The Mitochondria as a Central Hub for Spaceflight ImpactIn 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...2021-07-0347 minThe Bioinformatics and Beyond PodcastDr. Hayden Metsky: ADAPT for Large-scale Viral DetectionDr. 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 components.
Dr. Metsky goes on to talk about h...2021-06-1937 minThe Bioinformatics and Beyond PodcastDr. Hayden Metsky: Computational Methods for Viral Diagnostics, CRISPR-based Tests, CATCH, and MoreDr. 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 example, a more traditional qPCR approach. The discussion then moves...2021-06-0533 minThe Bioinformatics and Beyond PodcastEnvironmental Applications of Synthetic BiologyIn this episode we focus on the applications side of synthetic biology for the environmental sciences and environmental microbiology with Dr. Ilenne Del Valle and Emm Fulk. To start, we walk through the more classical omics approaches for understanding environmental microbiology, setting us up for newer synthetic biology approaches. We then discuss the main questions in environmental microbiology that synbio is well suited to help answer. We discuss a few specific problems such as quorum sensing. We learn about what quorum sensing is and how synthetic biology can be used to help understand it.
Next we discuss...2021-05-2230 minThe Bioinformatics and Beyond PodcastSynthetic Biology Intro and BiosensorsDr. Ilenne Del Valle and Emm Fulk introduce the topic of synthetic biology in this episode. I start by asking, "What is synthetic biology?" We then begin digging into some of the intricacies of synthetic biology by learning about biosensors; biosensors are a fundamental component of synthetic biology for translating environmental inputs and outputs. We next talk about all the different molecules that biosensors can sense that we could use for various applications.
Our conversation continues with introductions to many additional aspects of synthetic biology. We introduce and discuss synthetic biology circuit diagrams, which is another interesting a...2021-05-0840 minThe Bioinformatics and Beyond PodcastDr. Kyle Frischkorn: Transcriptomics vs. ProteomicsDr. Kyle Frischkorn explains the interplay between different sample analysis methods such as transcriptomics and proteomics. He starts by explaining some of the basics of both transcriptomics and proteomics and gives a refresher on the central dogma. This explanation covers aspects of these methods such as a high level description of what they are, how they work, and what data you get from them. He also mentions more detailed considerations such as difficulties with mapping RNA back to genomes, the power of transcriptomes and metatranscriptomes, and different types of RNA sequencing that can be performed.
We then m...2021-04-2433 minThe Bioinformatics and Beyond PodcastDr. Kyle Frischkorn: How to Publish in NatureIn this episode, we attempt to take a look behind the machine of science with Nature Communications senior editor Dr. Kyle Frischkorn. We begin by simply asking the question, "How do you publish in Nature?" Dr. Frischkorn breaks down several of the main hurdles to getting published in Nature. These include having striking findings in the actual research and picking the right venue from within the Nature portfolio. We learn about different aspects that could potentially help or hurt your chances and where they fit into the publishing process. Topics include having a relationship with an editor, writing a...2021-04-1728 minThe Bioinformatics and Beyond PodcastDr. Leor Weinberger: Overcoming the HIV Therapy MismatchDr. Leor Weinberger begins this episode by talking about his motivation for developing a novel therapy for HIV. He explains the fundamental mismatch between the mutation and transmission of the disease and how our therapies work, which inspired him to take a novel approach to try and combat the disease.
We discuss topics such as the potential for scientists to give up on an HIV vaccine and why it seems like there are no good general antiviral drugs. To lead up to discussing Dr. Weinberger's new therapy, we hear a bit about the history of HIV therapeutics. A...2021-04-1027 minThe Bioinformatics and Beyond PodcastDr. Leor Weinberger: HIV vs. COVID VaccinationThis episode begins by asking the question, "Why is it that we don't have an HIV vaccine after 40 years, but we do have a COVID-19 vaccine after one year?" Dr. Leor Weinberger explains that the answer to this question is primarily due to the existence (or lack thereof) of natural convalescents and whether the immune system is able to beat the virus. Dr. Weinberger further explains that there have only been two "recovered" people who had HIV. These two recoveries happened through bone marrow transplants, which themselves have 50 percent survival rates. Next, Dr. Weinberger gives a history of HIV...2021-04-0335 minThe Bioinformatics and Beyond PodcastDr. Sabrina Green: Clinical Use of PhagesIn this episode, Dr. Sabrina Green discusses the clinical aspects of phage use. We start by going back to one of the first ever uses of phage for a bacterial infection before discussing how phages are used now. Dr. Green explains a wide range of details related to clinical phage use. Topics discussed include cases today where phages are used, the safety of phages for clinical use, regulatory considerations for phage therapies, the pros and cons of phages, how specific phages are matched to specific patients, and phage affordability. Dr. Green describes potential hurdles for widespread adoption such as...2021-03-2729 minThe Bioinformatics and Beyond PodcastDr. Sabrina Green: Phages and Phage DiscoveryDr. Sabrina Green introduces the concepts of phages and phage therapy. She describes what phages are and gives us a bit of history on phage therapy, describing reasons why antibiotics were widely adopted despite phages being discovered first. She also discusses why phages have become so important in the light of emerging antibiotic resistant pathogens. Dr. Green explains the mechanisms of how phages work and how these mechanisms lend themselves well to, for instance, scaling to different types of infections and getting cleared from a person’s system. Finally, we discuss how phages are discovered, such as through evolving phages an...2021-03-2026 minThe Bioinformatics and Beyond PodcastPredicting COVID-19 with WearablesDr. Zahi Fayad and Dr. Robert Hirten return to continue their discussion on wearable technology. This episode revolves around the study Dr. Fayad and Dr. Hirten performed to find out if wearable devices can identify and predict COVID-19. They discuss some of the struggles they had being “largely restricted in the data they could collect”. Their findings have the potential to be ground-breaking and showed “there are significant changes in your heart rate variability over 24 hours, which allows us to diagnose someone 7 days before a nasal swab”. To finish the episode, they discuss the potential to expand the study in the f...2021-03-1327 minThe Bioinformatics and Beyond PodcastWearables with Dr. Zahi Fayad and Dr. Robert HirtenDr. Zahi Fayad and Dr. Robert Hirten discuss all things wearable technology. Throughout the episode we learn about the exciting potential of this technology for conducting health studies and for the general wellbeing of the population. Dr. Fayad and Dr. Hirten explain what wearables do for athletes and for the general health of the public, even predicting “there is a market for the future for scaling it up and making it bespoke”. Dr. Fayad explains why he utilises many different wearables all at once, stating “I am competing against myself, it helps me stay motivated and helps me compete agains...2021-03-0626 minThe Bioinformatics and Beyond PodcastMatthew Schechter: Metagenomics History Part 2In 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...2021-02-2722 minThe Bioinformatics and Beyond PodcastMatthew Schechter: Metagenomics History Part 1In 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...2021-02-2028 minThe Bioinformatics and Beyond PodcastDr. Heer Mehta: How Bacteria Become Resistant to AntibioticsDr. 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...2021-02-1326 minThe Bioinformatics and Beyond PodcastDr. Heer Mehta: Antibiotic Resistance and Experimental EvolutionDr. 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 ca...2021-02-0630 minThe Bioinformatics and Beyond PodcastDr. Dinler Antunes: Cancer ImmunotherapyWe 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...2021-01-3043 minThe Bioinformatics and Beyond PodcastDr. Dinler Antunes: Protein Folding, AlphaFold 2, Molecular DockingDr. 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...2021-01-2332 minThe Bioinformatics and Beyond PodcastDr. Lauren Stadler: Environmental Monitoring and MicrobiologyDr. 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. 2021-01-1629 minThe Bioinformatics and Beyond PodcastDr. Lauren Stadler: SARS-CoV-2 Wastewater MonitoringWhat 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...2021-01-0924 minThe Bioinformatics and Beyond PodcastDr. Luay Nakhleh: How to Effectively Communicate, Market, Listen, Read, and MoreIn 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. Nakh...2021-01-0240 minThe Bioinformatics and Beyond PodcastDr. Luay Nakhleh: The Expanded Scientific SkillsetIn 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 t...2020-12-2643 minThe Bioinformatics and Beyond PodcastDr. Kathryn Kundrod: Developing Low-Cost, Accessible Tests with LAMPDr. 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...2020-12-1942 minThe Bioinformatics and Beyond PodcastDr. Kathryn Kundrod: The State of COVID-19 Diagnostic Testing; How We Got Here, Types of Tests, and Emerging TechnologiesIn 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 h...2020-12-1237 minThe Bioinformatics and Beyond PodcastDr. Tomer Altman: Searching 5 Petabytes of Sequence Data with SerratusDr. 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/10.1101/2020.08.07.241729v12020-12-0533 minThe Bioinformatics and Beyond PodcastDr. Tomer Altman: Primer Design for SARS-CoV-2 DiagnosticsDr. 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.html2020-11-2843 minThe Bioinformatics and Beyond PodcastDr. Melissa Haendel: Ontologies, Phenotypes, and Disease DiagnosticsDr. 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.2020-11-2137 minThe Bioinformatics and Beyond PodcastDr. Melissa Haendel: COVID-19 Clinical InformaticsDr. 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.2020-11-1434 minThe Bioinformatics and Beyond PodcastDr. Fritz Sedlazeck: Sequencing and Detecting Structural Variants in SARS-CoV-2Dr. 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.2020-11-0731 minThe Bioinformatics and Beyond PodcastDr. Fritz Sedlazeck: Detecting and Interpreting Structural Variants in GenomesDr. 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.2020-10-3128 minThe Bioinformatics and Beyond PodcastDr. Todd Treangen: Fall 2020 Bioinformatics RoundupDr. 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.2020-10-2448 minThe Bioinformatics and Beyond PodcastDr. Todd Treangen: The Hidden Diversity of SARS-CoV-2A 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.2020-10-1750 minThe Bioinformatics and Beyond PodcastDr. Krista Ternus: Scientific Career PathsFor 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.2020-10-1129 minThe Bioinformatics and Beyond PodcastDr. Krista Ternus: Metagenomics, Biosecurity, and Clinical Applications; "What's in my sample?"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.2020-10-1016 minThe Bioinformatics and Beyond PodcastDr. Krista Ternus: Analyzing SARS-CoV-2 Sequence DataAs 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.2020-10-0329 minThe Bioinformatics and Beyond PodcastConvalescent Plasma Therapy (with Dr. Michael Joyner and Dr. Rickey Carter)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.2020-09-2653 minThe Bioinformatics and Beyond PodcastAdrianne Gladden-Young: Sequencing Previous OutbreaksAdrianne 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?2020-09-2617 minThe Bioinformatics and Beyond PodcastAdrianne Gladden-Young: Sequencing and Analyzing the SARS-CoV-2 GenomeAdrianne 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.2020-09-2630 minThe Bioinformatics and Beyond PodcastDr. Luay Nakhleh: Modeling Evolution (Complexities, Cancer, The Role of Evolution in Bioinformatics)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.2020-09-2625 minThe Bioinformatics and Beyond PodcastDr. Luay Nakhleh: What is Bioinformatics?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?2020-09-2630 min
Data Science and Machine Learning in Oil and GasRichard Copsey, Open Innovation Manager (Part 2)In part 2, we further discuss the role of the gig economy via the crowd in data science and machine learning, now and in the future.2020-01-0620 minData Science and Machine Learning in Oil and GasRichard Copsey, Open Innovation Manager (Part 1)Richard Copsey introduces the idea of looking "beyond the walls" for data science and machine learning solutions. New approaches like crowdsourcing can bring data science work in from a wide, external talent pool. We also discuss three specific oil and gas problems that were solved in part by the crowd.2020-01-0631 minData Science and Machine Learning in Oil and GasJenny Johnson, Emerging Technologies Incubation Manager (Part 2)In part 2, we get tips from Jenny for how to be a successful entrepreneur in the startup space of data science and machine learning. For instance, we cover the dos and don'ts of navigating a tech showcase as a startup.2020-01-0219 minData Science and Machine Learning in Oil and GasJenny Johnson, Emerging Technologies Incubation Manager (Part 1)Jenny Johnson discuss how to work with emerging technologies in data science and machine learning. In particular, she walks through working with startups, and more generally the startup ecosystem, to solve business pain points requiring new data science and machine learning solutions.2020-01-0214 minData Science and Machine Learning in Oil and GasMatt Morris, Project Geophysical Advisor (Part 2)How does a machine learning skeptic turn into a machine learning advocate? In Part 2, Matt recounts his data science and machine learning journey from his initial introduction and skepticism to his acceptance and forward looking thoughts on where these methods will proceed from here in oil and gas.2019-12-3119 minData Science and Machine Learning in Oil and GasMatt Morris, Project Geophysical Advisor (Part 1)As a senior geoscientist who has been involved in many data science and machine learning projects, Matt Morris discusses where these fields fit into the work of a geoscientist in oil and gas. He describes what problems are well suited for data science or machine learning and the qualities of the solutions that can make them more useful.2019-12-3115 minData Science and Machine Learning in Oil and GasDilshad Akkam Veettil, Data Scientist (Part 2)In part two, we find out what led Dilshad to pursue science and how his career took some unexpected turns along the path to becoming a data scientist.2019-12-3119 minData Science and Machine Learning in Oil and GasDilshad Akkam Veettil, Data Scientist (Part 1)Still new to being a data scientist, Dilshad tells us about his latest work on Geosteering and reveals how an afternoon at a loud cupcake cafe helped with a messy data problem.2019-12-3120 minData Science and Machine Learning in Oil and GasIngrid Tobar, Manager Data Science and Advanced Analytics (Part 2)In the second half of Ingrid Tobar's interview, she shares with us her love for Environmental Science and how that evolved into working in the Oil and Gas industry.2019-12-1813 minData Science and Machine Learning in Oil and GasIngrid Tobar, Manager Data Science and Advanced Analytics (Part 1)Data Scientist Ingrid Tobar walks us through one of her most interesting projects, Rapid Basin Evaluation. She discusses this project for shortening the timeline for a basin evaluation and how the team was able to accomplish that goal.2019-12-1813 minData Science and Machine Learning in Oil and GasAlex Bayeh, Data Science Technology Advancement Manager (Part 2)In the second half, we ask Alex about his journey into data science and his recommendations for someone interested in adding data science to their career path.2019-12-1818 minData Science and Machine Learning in Oil and GasAlex Bayeh, Data Science Technology Advancement Manager (Part 1)Alex Bayeh walks us through his current projects, highlighting a project called the Tops Propagation Tool. He shares with us how the project began, their approach, and what examining brain waves from a zebrafish has to do with Well Logs.2019-12-1724 minData Science and Machine Learning in Oil and GasVincent LeMoine, Data Engineering Manager (Part 2)After discussing the topic of data science and machine learning in part 1, we dig deeper into the oil and gas industry in part 2 of our interview. In part 2, Data Engineering Manager Vincent LeMoine gives his thoughts on how data science and machine learning can play a role in oil and gas specific problems, as well as some ideas on their place in the industry as a whole.2019-12-1530 minData Science and Machine Learning in Oil and GasVincent LeMoine, Data Engineering Manager (Part 1)Data Engineering Manager Vincent LeMoine gives a fantastic introduction to the high-level topics of data science, machine learning, and oil and gas. He shares with us his take on what data science is and what skill sets are required to work in this area. After discussing the topic of data science and machine learning, we dig deeper into the oil and gas industry in part 2 of our interview.2019-12-1511 min