PODCAST · science
the bioinformatics lab
by The Bioinformatics Lab
Ramblings on all things bioinformatics.
Episodes
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EP 69: Honeybee Virology and Colony Collapse with Declan Schroeder
In this episode of the Bioinformatics Lab Podcast, host Kevin interviews Declan Schroeder, a prominent virologist specializing in honeybee populations. Declan shares his unconventional journey into biology, detailing his early experiences with sequencing technology and his transition from marine...
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EP 68: Bioinformatics Careers, Communication, and Workflow Managers with Cristina Guijarro-Clarke
Summary In this podcast episode, the host and guest Cristina Guijarro-Clarke discuss various aspects of bioinformatics, including the importance of communication, navigating career paths, the role of social media, and the transition from academia to industry. We delve into the significance of...
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EP 67: Pathogen Genomics for Infection Prevention and Control with Ellie Carter
Ellie's background in microbiology and public health shaped her career in infection prevention. Building a laboratory network in Indiana was a significant project that enhanced public health. Infection preventionists play a crucial role in managing outbreaks in healthcare settings. Genomic...
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EP 66: One Health, Genomic Epidemiology, and Antimicrobial Resistance with Anita Kasanga
Summary In this conversation, Anita shares her experiences in critical patient care, emphasizing the importance of timely clinical alerts and collaboration among healthcare professionals. She recounts a specific case involving a 12-year-old girl post-surgery, highlighting the urgency of…
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EP 65: Taking Time Off with Christie Rose Woodside
In this episode of the Bioinformatics Lab Podcast, Christie Rose Woodside shares her journey from academia to industry, her experiences during the COVID-19 pandemic, and her decision to walk El Camino with her father. The conversation explores the importance of taking time off for personal…
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EP 64: Machine Learning and Mutli-Omics Data with Mxolisi Nene
In this episode of the Bioinformatics Lab Podcast, Mxolisi Nene shares his journey from a curious kid “scanning soil” with a stick and a broken Pentium II in rural KwaZulu-Natal to a bioinformatician and PhD candidate at the Agricultural Research Council in Pretoria. He walks through his path…
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EP 63: Mycotic Bioinformatics with Zachary Konkel
In this episode of the Bioinformatics Lab Podcast, Zachary Konkel shares his journey from studying chemistry to specializing in mycology and bioinformatics. He discusses the significance of fungi in medicine, particularly in producing antimicrobial compounds, and the challenges faced in fungal...
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EP 62: Public Health Pathogen Genomics in Africa with James Otieno
Summary In this episode of the Bioinformatics Lab podcast, James Oteno shares his journey as a bioinformatician and genomic epidemiologist, discussing the intersection of bioinformatics and public health, particularly in the context of emerging pathogens in Africa. The conversation covers the...
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EP 61: MiDog Technical Deep Dive with Kaylie Zapanta
Summary In this engaging conversation, Kaylie Zapanta, a PhD in neurophysiology, discusses her journey from academia to her current role at MyDog, where she focuses on veterinary diagnostics through NGS data. The discussion highlights the complexities of microbial interactions, the importance of...
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EP 60: NGS for Veterinary Diagnostics with Janina Krumbeck (MiDog)
In this episode of the Bioinformatics Lab Podcast, Janina Krumbeck shares her unique journey from Germany to the United States, detailing her academic experiences and the challenges she faced during her PhD program. She discusses the importance of mentorship, the transition from academia to...
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EP 59: Navigating Bioinformatics and Public Health with Amy Gaskin
In this conversation, Amy Gaskin shares her journey into bioinformatics, detailing her transition from an ecological background to a career in public health. She discusses the pivotal moments that led her to discover her passion for bioinformatics, the essential skills she acquired during her...
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EP 58: From Veterinary Medicine to Pathogen Genomics with Gültekin Ünal
In this episode of the Bioinformatics Lab podcast, Gültekin Ünal shares his unique journey from veterinary medicine to bioinformatics, highlighting the pivotal moments that shaped his career. For more information about the PHA4GE organization discussed in this episode, please visit:...
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EP 57: Open Conversation with Tommy Tang
Tommy's Blog: https://divingintogeneticsandgenomics.com/ Summary In this conversation, Kevin Libuit and Tommy Tang explore the journey of communication in science, particularly in the field of bioinformatics. They discuss the importance of sharing knowledge, the transition from wet lab to...
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EP 56: Open Conversation with Keith Robison
Ketih's Blog, Omics Omics: https://omicsomics.blogspot.com/ Summary In this conversation, Keith Robison discusses the inception of his blog Omix, the evolution of social media in the scientific community, and the importance of feedback and community engagement in scientific writing. He delves…
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EP 55: Microbiome and Human Health with Momo Vuyisich
Summary In this conversation, Dr. Momo Vuyisich discusses the significance of metatranscriptomics in understanding the microbiome and its impact on human health. He emphasizes the importance of gene expression over gene content, the challenges of metabolomics, and the innovations in RNA…
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EP 54: Pathogen Genomics in Healthcare w/ Alex Sundermann
Pathogen genomics in healthcare: overcoming barriers to proactive surveillance: https://journals.asm.org/doi/10.1128/aac.01479-24 Summary In this conversation, Kevin Libuit and Alex Sundermann delve into the significance of pathogen genomics in healthcare, discussing its role in infection...
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EP 53: Remote Work
Summary In this episode of the Bioinformatics Lab podcast, Kevin Libuit and Andrew Page discuss the evolution of remote bioinformatics work, exploring the benefits and challenges of remote work, the importance of in-person interactions, and the ongoing debate surrounding the return to office...
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EP 51: Software Bugs
Summary In this episode, Kevin Libuit and Andrew Page discuss the complexities of software bugs, focusing on the distinction between user errors and software errors. They explore the importance of understanding user needs and the challenges of software compatibility, particularly in the context…
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EP 52: Genomic Epidemiology with Krisandra Allen
Summary In this episode of the Bioinformatics Lab podcast, Kevin Libuit and Krisandra Allen discuss the integration of bioinformatics and epidemiology, focusing on the challenges and solutions in utilizing genomic sequencing data for infectious disease surveillance. They explore the roles of...
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EP 50: Software Naming
Summary In this episode of the Bioinformatics Lab podcast, Kevin Libuit and Andrew Page discuss the art and challenges of naming bioinformatics tools. They explore various naming conventions, the significance of unique and memorable names, and the creative strategies employed by developers. The...
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EP 49: H5N1 Outbreak
Summary In this episode of the Bioinformatics Lab Podcast, Kevin Libuit and Andrew Page discuss the ongoing H5N1 outbreak, its implications for public health, and the economic impact on agriculture. They explore the nature of avian influenza, the risks of mammalian spillover, and the importance…
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EP 48: The Kalamari Database
Kalamari GitHub: https://github.com/lskatz/Kalamari & Public Health Announcement: https://journals.asm.org/doi/10.1128/mra.00963-24 Summary In this episode of the Bioinformatics Lab podcast, Kevin Libuit and Andrew Page discuss a public health announcement regarding the Kalamari database, a…
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EP 47: The Job Hunt Experience pt. 02
Summary In this episode of the Buy Informatics Lab podcast, Kevin Libuit and Andrew Page discuss the intricacies of the job market from a recruiter's perspective. They share insights on how to effectively navigate the recruitment process, the importance of leveraging professional networks, and…
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Ep. 46: The Job Hunt Experience pt. 01
Summary In this episode, Kevin Libuit and Andrew Page discuss their personal experiences with job hunting in the bioinformatics field, emphasizing the importance of professional networks and genuine relationships. They share anecdotes about how their careers were shaped by connections made…
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Ep 45: Pathogen Focus - MPXV
Summary In this episode of the Bioinformatics Lab Podcast, Kevin Libuit and Andrew Page discuss the complexities of analyzing MPXV genomes, particularly in light of recent outbreaks. They explore the differences between MPXV and other viruses, the challenges faced in genomic sequencing and...
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Ep 44: Career Focus:Julian Paganini & Olinto Linares-Perdomo
Note: This episode was recorded in Spanish. A video of this recording with AI-generated, English subtitles is available on YouTube: https://www.youtube.com/watch?v=FNjUbtcm9Z4 Summary In this episode of the Bioinformatics Lab Podcast, Kevin Libuit hosts Julian and Olinto in a special...
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Ep 43: Pathogen Focus: Dengue Virus
Summary In this episode of the Bioinformatics Lab Podcast, Kevin Libuit and Andrew Page discuss the challenges and limitations in analyzing dengue virus genomes using bioinformatics. They highlight the importance of open-source tools, the need for better data sharing, and the complexities of…
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Ep 42: GMI 14, Barcelona, Spain
Summary In this episode of the Bioinformatics Lab podcast, Kevin Libuit and Andrew Page discuss their experiences at the GMI 14 conference in Barcelona, reflecting on the importance of metadata in microbial bioinformatics, the role of AI in data sharing, and the significance of communicating the...
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Ep 41 Importance of Dev Environments
Summary In this episode, Kevin and Andrew discuss the importance of dev environments in bioinformatics and the adoption of software engineering practices. They highlight the need for separate environments for development, production, and staging, and the importance of stability and consistency in...
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Ep 40 Career Spotlight: Sharvari Narendra
Summary In this conversation, Sharvari Narendra shares her career journey in bioinformatics, which includes experiences in academia, industry, and a startup. She emphasizes the importance of exploring different career tracks and finding alignment with personal passions. Sharvari highlights the...
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Ep 39: Bioinformatics Hackathons
ASM NGS Hackathon Details: - Date: 10-12 October 2024 - Location: Washington DC, Venue TBD (within 30 minutes of the ASM NGS venue) - Registration form: https://lnkd.in/e8KTqZYQ - Admission: Free (Sponsored by Theiagen Genomics) Summary In this episode, Kevin and Andrew discuss hackathons and the...
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Ep 38: Workflow Infrastructure
Also available on YouTube: https://youtu.be/i9oT5ku11is Summary In this episode, Kevin and Andrew discuss different mechanisms to run and support bioinformatics pipelines. They explore the use of workflows, workflow managers, and graphic user interfaces for pipeline execution. They highlight...
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Ep 37: SRALite
YouTube: https://youtu.be/RybtspKHkgA Summary The conversation discusses the topic of SRA Lite, a data storage format for genomic information. SRA Lite is a compressed version of the original data, with the quality scores removed. The conversation highlights the challenges and controversies...
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Ep 36: Technical Career Tracks
Also available on YouTube: https://youtu.be/ZlKYKuOeGZc Summary In this episode, Kevin Libuit and Andrew Page discuss the different levels of a bioinformatics developer and the career track in the field. They explain that bioinformatics is a relatively new field and the levels have emerged over...
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Ep 35: Bioinformatics in the Cloud
Summary In this episode, Kevin and Andrew discuss cloud computing in the context of bioinformatics. They explore the different layers of cloud technology and how it can be implemented in laboratories. They highlight the benefits of cloud computing, such as quick access to resources, cost savings,...
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Ep 34: PHA4GE with Dr. Alan Christoffels
PHA4GE Website: https://pha4ge.org/ Summary Alan Christoffels, the principal investigator for the Public Health Alliance for Genomic Epidemiology (PHA4GE), discusses the challenges and future directions of the consortium. He shares his background as a scientist and director of a program leading...
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Ep 33: Communicating Results in Public Health
Summary In this episode, Kevin Libuit and Andrew Page discuss the challenges of communicating complex genomic information to different audiences in public health. They explore the need for tailored communication strategies for various stakeholders, including bioinformatics scientists,...
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Ep 32: Best Practices - Pipeline Development, Part Three
Summary This episode of the Bioinformatics Lab Podcast continues the conversation on public health pipeline best practices. The focus is on pipeline functionality, documentation for local install and remote access, and example usage. The hosts discuss the importance of clearly articulating the...
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Ep 32: Best Practices - Pipeline Development, Part Two
PHA4GE Ten Best Practices for Public Health Bioinformatics Pipelines: https://github.com/pha4ge/public-health-pipeline-best-practices/blob/main/docs/pipeline-best-practices.md Summary In this episode, Kevin Libuit and Andrew Page discuss the 10 best practices for public health pipeline…
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Ep 32: Best Practices - Pipeline Development, Part One
PHA4GE Ten Best Practices for Public Health Bioinformatics Pipelines: https://github.com/pha4ge/public-health-pipeline-best-practices/blob/main/docs/pipeline-best-practices.md Summary In this episode, Andrew Page and Kevin Libuit discuss best practices for public health bioinformatics pipelines....
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Ep31: AI-Generated Images
Summary In this episode, Kevin Libuit and Andrew Page discuss the use of AI-generated images in scientific publications. They start by addressing a recent retracted publication that featured images with anatomical inaccuracies and AI-generated labels. They highlight the failure of the peer review...
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Ep30 Part 2: Gut-Brain Axis with Kevin Bonham, Part Two
Manuscript Discussed: https://www.science.org/doi/10.1126/sciadv.adi0497 Summary This conversation discusses a study that explores the relationship between the gut microbiome and cognitive function. The study design involved collecting stool samples and cognitive function scores from a diverse...
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Ep30 Part One: Gut-Brain Axis with Kevin Bonham
Manuscript Discussed: https://www.science.org/doi/10.1126/sciadv.adi0497 Summary In this episode, Dr. Kevin Bonham discusses the relationship between the gut microbiome and brain development. He explains the concept of the gut-brain axis and provides evidence for the connection between the two.…
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Ep29 Career Spotlight: Kevin G. Libuit
In this episode, Kevin Libuit discusses his career in the world of public health, pathogen genomics, and bioinformatics. He shares his journey from studying biology with the intention of pursuing a medical career to discovering his passion for bioinformatics during his undergraduate research.…
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Ep28 Food Safety Research Network
Summary In this episode of the Bioinformatics Lab Podcast, Kevin Libuit and Andrew Page discuss the Food Safety Research Network and a recent conference they attended. The network brings together government, academia, and industry to focus on food safety research. The conference had an…
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Ep27 Science and Social Media with Emma Hodcroft
Dr. Emma Hodcroft discusses her experience with scientific communication, particularly on social media. She shares her background in infectious diseases and how she became involved in science communication. Dr. Hodcroft reflects on the influence of her father's involvement in a football club on…
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Ep 26 Utility of Open-Source Software
In this episode, Kevin Libuit and Andrew Page discuss the utility of open source software in the world of public health and pathogen genomics. They highlight the importance of reproducibility, cost-effectiveness, and community collaboration that open source software offers. The conversation also...
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Ep 25 Containerized Software
Ep 25 Containerized Software by The Bioinformatics Lab
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Ep 24 Reasons to (or not to) Pursue a PhD
Ep 24 Reasons to (or not to) Pursue a PhD by The Bioinformatics Lab
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Ep 23 Benefits of Cloud Computing for Bioinformatics
In this episode we discuss the shift from traditional High-Performance Computing (HPC) systems to cloud computing in bioinformatics. Key points of the conversation include: Transition to Cloud Computing: The discussion begins with the gradual adoption of cloud computing over the past 5-6 years in...
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ABOUT THIS SHOW
Ramblings on all things bioinformatics.
HOSTED BY
The Bioinformatics Lab
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Ramblings on all things bioinformatics.
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