พอดคาสท์ Bioinformatics ชั้นนำ (2024)

1
#70 Prioritizing drug target genes with Marie Sadler 52:20

4M ago52:20

52:20

In this episode, Marie Sadler talksabout her recent Cell Genomics paper, Multi-layered genetic approaches toidentify approved drug targets. Previous studies have found that the drugs that target a gene linked to thedisease are more likely to be approved. Yet there are many ways to define whatit means for a gene to be linked to the disease. Perhaps …

1
Mo Jain - novel technologies for biomarker discovery 37:04

6M ago37:04

37:04

Mo Jain, Founder and CEO of Sapient, discusses the importance of small molecule biomarkers and his approach to biomarker discovery research. 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/…

1
#69 Suffix arrays in optimal compressed space and δ-SA with Tomasz Kociumaka and Dominik Kempa 56:46

7M ago56:46

56:46

Today on the podcast we have Tomasz Kociumaka and Dominik Kempa,the authors of the preprintCollapsing the Hierarchy of Compressed Data Structures: Suffix Arrays in Optimal Compressed Space. The suffix array is one of the foundational data structures in bioinformatics,serving as an index that allows fast substring searches in a large text.However, i…

1
Evan Floden - Nextflow and Reproducibility in Science 38:05

7M ago38:05

38:05

Evan Floden, CEO and Co-founder of Seqera Labs, discusses Nextflow, the push for reproducibility in scientific workflows, and his experience as a scientist with a start-up. 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:/…

1
#68 Phylogenetic inference from raw reads and Read2Tree with David Dylus 49:11

8M ago49:11

49:11

In this episode,David Dylus talks aboutRead2Tree,a tool that builds alignment matrices and phylogenetic trees from rawsequencing reads.By leveraging the database of orthologous genes called OMA, Read2Tree bypasses traditional, time-consuming steps such as genome assembly, annotation and all-versus-all sequence comparisons. Links: Inference of phylo…

1
#67 AlphaFold and variant effect prediction with Amelie Stein 35:25

9M ago35:25

35:25

This is the third and final episode in the AlphaFold series, originally recorded on February 23, 2022,with Amelie Stein, now an associate professor at the University of Copenhagen. In the episode, Amelie explains what 𝛥𝛥G is, how it informs uswhether a particular protein mutation affects its stability, and how AlphaFold 2helps in this analysis. A n…

1
#66 AlphaFold and shape-mers with Janani Durairaj 20:51

9M ago20:51

20:51

This is the second episode in the AlphaFold series, originally recorded on February 14, 2022,with Janani Durairaj, a postdoctoralresearcher at the University of Basel. Janani talks about how she used shape-mers and topic modelling to discoverclasses of proteins assembled by AlphaFold 2 that were absent from the ProteinData Bank (PDB). The bioinform…

1
#65 AlphaFold and protein interactions with Pedro Beltrao 52:23

10M ago52:23

52:23

In this episode, originally recorded on February 9, 2022,Roman talks to Pedro Beltraoabout AlphaFold, the software developed by DeepMind that predicts a protein’s3D structure from its amino acid sequence. Pedro is an associate professor at ETH Zurich and the coordinator ofthe structural biology community assessment of AlphaFold2 applications projec…

1
Linnea Fletcher - Training Technicians for the Biotechnology Industry 37:13

10M ago37:13

37:13

Linnea Fletcher, Biotechnology Department chair at Austin Community College and Director of the InnovATEBIO National Biotechnology Education Center, discusses training technicians to tackle real world challenges in the biotechnology industry. The Bioinformatics CRO is a fully distributed contract research company that serves the computational biolo…

1
Yuri Deigin - Partial Reprogramming Drug Development for Aging 54:17

1y ago54:17

54:17

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…

1
Adam Freund - targeting cells to treat disease 38:15

1+ y ago38:15

38:15

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…

1
Alfredo Andere - connecting biologists and bioinformaticians 38:46

1+ y ago38:46

38:46

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…

1
Joshua Hare - cell-based therapies for aging 35:22

2y ago35:22

35:22

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…

1
Alex Shalek - new technology for systems biology 38:48

2y ago38:48

38:48

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…

1
Jamie Smyth - heart disease and viral infection 31:06

2+ y ago31:06

31:06

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://…

1
#64 Enformer: predicting gene expression from sequence with Žiga Avsec 59:41

2+ y ago59:41

59:41

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…

1
Amar Gajjar - pediatric brain cancer 26:57

2+ y ago26:57

26:57

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…

1
Dr. Justin Siegel: Enzyme Design, Large-scale Mutant Generation, and Cloud Labs 22:01

2+ y ago22:01

22:01

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…

1
Dr. Justin Siegel: Lab Automation, Cloud Labs, and the Future of the Wet Lab 33:25

2+ y ago33:25

33:25

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…

1
Jill Reckless & Jon Heal - outsourcing drug development 33:06

2+ y ago33:06

33:06

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…

1
#63 Bioinformatics Contest 2021 with Maksym Kovalchuk and James Matthew Holt 1:00:47

2+ y ago1:00:47

1:00:47

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:…

1
Adam Siepel - evolutionary genomics 35:11

2+ y ago35:11

35:11

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…

1
Erich Jarvis - genomics of vocal learning 45:40

2+ y ago45:40

45:40

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…

1
Dr. Afshin Beheshti: MicroRNAs and COVID-19 29:21

2+ y ago29:21

29:21

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…

1
Mauro Calabrese - long non-coding RNA 28:02

2+ y ago28:02

28:02

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 …

1
Damian Kao - cat genetics 30:38

2+ y ago30:38

30:38

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.…

1
Dr. Afshin Beheshti: The Hazards and Molecular Features of Spaceflight 48:51

2+ y ago48:51

48:51

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…

1
Nicholas Heaton - influenza & SARS-CoV-2 30:26

2+ y ago30:26

30:26

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…

1
Becca Chodroff Foran - consumer genetics for dogs 44:57

2+ y ago44:57

44:57

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:…

1
Dr. Tejaswini Mishra: Wearables Detect Pre-symptomatic COVID-19 28:54

2+ y ago28:54

28:54

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…

1
Stacy Horner - flaviviruses and SARS-CoV-2 35:26

2+ y ago35:26

35:26

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…

1
Jason Arnold - microbiome core facilities 45:37

2+ y ago45:37

45:37

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…

1
Dr. Tejaswini Mishra: The NASA Twins Study 29:12

2+ y ago29:12

29:12

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…

1
#62 Steady states of metabolic networks and Dingo with Apostolos Chalkis 38:25

2+ y ago38:25

38:25

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…

1
Bettina Hein - managing chronic illness with AI 36:28

2+ y ago36:28

36:28

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…

1
Bharath Ramsundar - applications of AI 37:49

2+ y ago37:49

37:49

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…

1
Wet Lab / Dry Lab Transitioning with Dr. Willian da Silveira 1:02:04

3y ago1:02:04

1:02:04

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…

1
Saroja Voruganti - nutrition and genetics 28:16

3y ago28:16

28:16

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…

1
Jon Chee - equipment leasing for life sciences 29:51

3y ago29:51

29:51

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/…

1
Dr. Willian da Silveira: The Mitochondria as a Central Hub for Spaceflight Impact 47:19

3y ago47:19

47:19

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…

1
Ian Carroll - the intestinal microbiota 38:49

3y ago38:49

38:49

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…

1
#61 3D genome organization and GRiNCH with Da-Inn Erika Lee 1:09:41

3y ago1:09:41

1:09:41

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…

1
Mark Kotter - stem cell programming 34:50

3y ago34:50

34:50

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/…

1
Dr. Hayden Metsky: ADAPT for Large-scale Viral Detection 37:08

3y ago37:08

37:08

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,…

1
Matthias Gromeier - viral cancer therapeutics 42:04

3y ago42:04

42:04

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…

1
Carolyn Coyne - immunity in the placenta 34:31

3y ago34:31

34:31

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. …

1
Dr. Hayden Metsky: Computational Methods for Viral Diagnostics, CRISPR-based Tests, CATCH, and More 33:38

3y ago33:38

33:38

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…

1
Bryan Cullen - viral genetics 40:29

3y ago40:29

40:29

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…

1
Micah Luftig - Epstein-Barr virus and cancer 51:25

3y ago51:25

51:25

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…

1
Environmental Applications of Synthetic Biology 30:45

3y ago30:45

30:45

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…

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