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On The Bioinformatics CRO Podcast, we sit down with scientists to discuss interesting topics across biomedical research and to explore what made them who they are today.
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.
A podcast about computational biology, bioinformatics, and next generation sequencing.
This course covers fundamental algorithms for efficient analysis of biological sequences and for building evolutionary trees. This is an undergraduate course focusing on the ideas and concepts behind the most central algorithms in biological sequence analysis. Dynamic Programming, Alignment, Hidden Markov Models, Statistical Analysis are emphasized.
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The Bioinformatics CRO Podcast
Yuri Deigin, co-founder of YouthBio Therapeutics, discusses developing rejuvenation gene therapies based on partial reprogramming and his role reinvigorating investigations into the origins of SARS-CoV-2. The Bioinformatics CRO is a fully distributed contract research company that serves the computational biology needs of biotechnology companies, w…
Adam Freund, founder and CEO of Arda Therapeutics, discusses how targeted killing of pathogenic cells could be used to treat chronic disease and aging. The Bioinformatics CRO is a fully distributed contract research company that serves the computational biology needs of biotechnology companies, with a focus on genomics. https://www.bioinformaticscr…
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The Bioinformatics CRO Podcast
Alfredo Andere, co-founder and CEO of Latch Bio, discusses the unique challenges facing young entrepreneurs and the future of cloud computing in biology. The Bioinformatics CRO is a fully distributed contract research company that serves the computational biology needs of biotechnology companies, with a focus on genomics. https://www.bioinformatics…
Joshua Hare, Professor of Medicine at the University of Miami and co-founder of Longeveron, discusses the regenerative and reparative potential of MSCs and how cell therapies will revolutionize medicine. The Bioinformatics CRO is a fully distributed contract research company that serves the computational biology needs of biotechnology companies, wi…
Alex Shalek, Associate Professor of Chemistry at MIT, discusses new methods and technologies in systems biology that have enabled advances in the diagnosis and treatment of autoimmune diseases and cancer. The Bioinformatics CRO is a fully distributed contract research company that serves the computational biology needs of biotechnology companies, w…
Jamie Smyth, Associate Professor at Virginia Tech, discusses intercellular communication in the heart and how viral infection of cardiac cells can result in heart disease. The Bioinformatics CRO is a fully distributed contract research company that serves the computational biology needs of biotechnology companies, with a focus on genomics. https://…
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the bioinformatics chat
In this episode, Jacob Schreiber interviews Žiga Avsec abouta recently released model, Enformer. Their discussion begins with lifedifferences between academia and industry, specifically about how researchis conducted in the two settings. Then, they discuss the Enformer model,how it builds on previous work, and the potential that models like it have…
Amar Gajjar, world-renowned neuro-oncologist and chair of the Department of Pediatric Medicine at St. Jude Children's Research Hospital, discusses emerging treatments for pediatric brain tumors such as medulloblastoma. The Bioinformatics CRO is a fully distributed contract research company that serves the computational biology needs of biotechnolog…
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The Bioinformatics and Beyond Podcast
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…
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The Bioinformatics and Beyond Podcast
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 di…
Jill Reckless, CEO and co-founder of RxCelerate, and Jon Heal, Head of In Silico Designs at RxCelerate, discuss the virtual biotech industry, outsourcing drug development, and using bioinformatics for target optimization. The Bioinformatics CRO is a fully distributed contract research company that serves the computational biology needs of biotechno…
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the bioinformatics chat
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#63 Bioinformatics Contest 2021 with Maksym Kovalchuk and James Matthew Holt
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The Bioinformatics Contest is back this year, and we are back to discussit! This year’s contest winnersMaksym Kovalchuk (1st prize) andMatt Holt (2nd prize)talk about how they approachparticipating in the contest and what strategies have earned them the topscores. Timestamps and links for the individual problems: 00:10:36 Genotype Imputation 00:21:…
Adam Siepel, Professor of quantitative biology at Cold Spring Harbor Laboratory, discusses the applications of evolutionary genomics in anthropology, infectious disease, and cancer. The Bioinformatics CRO is a fully distributed contract research company that serves the computational biology needs of biotechnology companies, with a focus on genomics…
Erich Jarvis, Professor at The Rockefeller University and investigator at HHMI, explains how studying the neural and genetic mechanisms of vocal learning in songbirds gives insights into the development of spoken language in humans. The Bioinformatics CRO is a fully distributed contract research company that serves the computational biology needs o…
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 m…
Mauro Calabrese, Associate Professor at UNC Chapel Hill and Director of Graduate Studies in the Department of Pharmacology, discusses the future of RNA-based therapeutics and the role of lncRNA in gene transcription. The Bioinformatics CRO is a fully distributed contract research company that serves the computational biology needs of biotechnology …
Damian Kao, COO of Basepaws, discusses the challenges B2C science and the future of consumer genomics in cats, from microbiome to epigenetic testing. The Bioinformatics CRO is a fully distributed contract research company that serves the computational biology needs of biotechnology companies, with a focus on genomics. https://www.bioinformaticscro.…
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The Bioinformatics and Beyond Podcast
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 sp…
Nicholas Heaton, Assistant Professor of molecular genetics and microbiology at Duke University School of Medicine, talks about influenza, SARS-CoV-2, and potential future pandemics. The Bioinformatics CRO is a fully distributed contract research company that serves the computational biology needs of biotechnology companies, with a focus on genomics…
Becca Chodroff Foran, Head of R&D at Wisdom Panel, describes the recent advances in pet genomics and how we can use genetic data from dogs to guide research on human health. The Bioinformatics CRO is a fully distributed contract research company that serves the computational biology needs of biotechnology companies, with a focus on genomics. https:…
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The Bioinformatics and Beyond Podcast
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 p…
Stacy Horner, associate professor of molecular genetic and microbiology at Duke University Medical School, compares hepatitis C and dengue virus to SARS-CoV-2 and suggests policy changes to make academia more inclusive. The Bioinformatics CRO is a fully distributed contract research company that serves the computational biology needs of biotechnolo…
Jason Arnold, Technical Director of the Microbiome Core Facility at UNC Chapel Hill, describes methods of improving the scientific rigor of microbiota research and his experiences as a snake breeder. The Bioinformatics CRO is a fully distributed contract research company that serves the computational biology needs of biotechnology companies, with a…
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…
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In this episode, Apostolos Chalkis presents sampling steadystates of metabolic networks as an alternative to the widely used flux balanceanalysis (FBA). We also discuss dingo, aPython package written by Apostolos that employs geometric random walks tosample steady states. You can see dingo in actionhere. Links: Dingo on GitHub Searching for COVID-1…
Bettina Hein, CEO and founder of juli, is a serial tech entrepreneur, using artificial intelligence to help people manage symptoms of chronic illness. The Bioinformatics CRO is a fully distributed contract research company that serves the computational biology needs of biotechnology companies, with a focus on genomics. https://www.bioinformaticscro…
Bharath Ramsundar, founder and CEO of Deep Forest Sciences, described many applications of artificial intelligence in biotech, society, and the military. The Bioinformatics CRO is a fully distributed contract research company that serves the computational biology needs of biotechnology companies, with a focus on genomics. https://www.bioinformatics…
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The Bioinformatics and Beyond Podcast
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Wet Lab / Dry Lab Transitioning with Dr. Willian da Silveira
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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…
Saroja Voruganti, Associate Professor at UNC Chapel Hill, shares her passion for nutrition as she discusses the fields of nutrigenetics and nutrigenomics. The Bioinformatics CRO is a fully distributed contract research company that serves the computational biology needs of biotechnology companies, with a focus on genomics. https://www.bioinformatic…
Jon Chee, co-founder and CEO of Excedr, shares his experience founding a life sciences equipment leasing company before the latest biotech boom. The Bioinformatics CRO is a fully distributed contract research company that serves the computational biology needs of biotechnology companies, with a focus on genomics. https://www.bioinformaticscro.com/…
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The Bioinformatics and Beyond Podcast
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 b…
Ian Carroll, assistant professor of nutrition at the University of North Carolina, Chapel Hill, describes the relationship between the intestinal microbiota and eating disorders. The Bioinformatics CRO is a fully distributed contract research company that serves the computational biology needs of biotechnology companies, with a focus on genomics. h…
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#61 3D genome organization and GRiNCH with Da-Inn Erika Lee
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In this episode, Jacob Schreiber interviews Da-Inn Erika Lee aboutdata and computational methods for making sense of 3D genome structure. They begin their discussion by talking about 3D genome structure at a high level and the challenges in working with such data. Then, they discuss a method recently developed by Erika, named GRiNCH, that mines thi…
Mark Kotter, co-founder and CEO of Bit Bio, discusses the uses of reprogrammed human cells in research and drug development. The Bioinformatics CRO is a fully distributed contract research company that serves the computational biology needs of biotechnology companies, with a focus on genomics. https://www.bioinformaticscro.com/…
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The Bioinformatics and Beyond Podcast
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,…
Matthias Gromeier, professor of neurosurgery at Duke University, describes how his breakthrough therapeutic combines poliovirus and rhinovirus to eliminate brain cancers. The Bioinformatics CRO is a fully distributed contract research company that serves the computational biology needs of biotechnology companies, with a focus on genomics. https://w…
Carolyn Coyne, professor of Molecular Genetics and Microbiology at Duke University, discusses how pathogens can subvert cellular barriers in the placenta and gut to cause disease. The Bioinformatics CRO is a fully distributed contract research company that serves the computational biology needs of biotechnology companies, with a focus on genomics. …
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The Bioinformatics and Beyond Podcast
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Dr. Hayden Metsky: Computational Methods for Viral Diagnostics, CRISPR-based Tests, CATCH, and More
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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…
Bryan Cullen, director of Duke University’s Center for Virology, describes how viruses use microRNAs, epigenetics, and epitranscriptomics to regulate their biology. The Bioinformatics CRO is a fully distributed contract research company that serves the computational biology needs of biotechnology companies, with a focus on genomics. https://www.bio…
Micah Luftig, associate professor and vice-chair of Molecular Genetics and Microbiology at Duke University, explains how Epstein-Barr virus can induce tumorigenesis and how is father inspired him to become a virologist. The Bioinformatics CRO is a fully distributed contract research company that serves the computational biology needs of biotechnolo…
In 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…
Jim Ray, head of MD Anderson's Neurodegeneration Consortium, explains new perspectives in Alzheimer's disease research and shares his experience in biotech, pharma, and academia. The Bioinformatics CRO is a fully distributed contract research company that serves the computational biology needs of biotechnology companies, with a focus on genomics. h…
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the bioinformatics chat
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#60 Differential gene expression and DESeq2 with Michael Love
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In this episode, Michael Love joins us to talk about the differential geneexpression analysis from bulk RNA-Seq data. We talk about the history of Mike’s own differential expression package,DESeq2, as well as other packages in this space, like edgeR and limma, and thetheory they are based upon. Mike also shares his experience of being theauthor and…
Fernando Martinez, senior scientist at Fountain Therapeutics, uses AI and phenotypic screening to discover drugs that reduce the signs of aging. The Bioinformatics CRO is a fully distributed contract research company that serves the computational biology needs of biotechnology companies, with a focus on genomics. https://www.bioinformaticscro.com/…
Dr. 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…
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The Bioinformatics CRO Podcast
Jeremy Kamil, associate professor of microbiology at LSU Health Shreveport, discusses the genetics of SARS-CoV-2, variants, and vaccines with guest host Razib Khan. The Bioinformatics CRO is a fully distributed contract research company that serves the computational biology needs of biotechnology companies, with a focus on genomics. https://www.bio…
Adam Robertson, CSO of Hemispherian, talks about developing cancer therapeutics in an Oslo-based startup. The Bioinformatics CRO is a fully distributed contract research company that serves the computational biology needs of biotechnology companies, with a focus on genomics. https://www.bioinformaticscro.com/…
Dr. 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,…
In this episode, Lindsay Pino discusses thechallenges of making quantitative measurements in the field of proteomics.Specifically, she discusses the difficulties of comparing measurements acrossdifferent samples, potentially acquired in different labs, as well as a methodshe has developed recently for calibrating these measurements without the need…
Brett Abrahams, Executive VP of R&D at Magnolia Neurosciences, discusses his work on chemotherapy-induced peripheral neuropathy and other brain disorders. The Bioinformatics CRO is a fully distributed contract research company that serves the computational biology needs of biotechnology companies, with a focus on genomics. https://www.bioinformatic…
