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 genomics. Zach highlights the development of mycotools (https://github.com/xonq/mycotools) as a solution for analyzing fungal genomes and the importance of phylogenetics in understanding fungal pathogens like Candida auris.

The conversation also touches on the growing concern of antifungal resistance and the potential for next-generation sequencing to improve outbreak detection. Finally, Zach shares his passion for mushroom foraging, connecting his scientific interests with personal hobbies.

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 importance of both wet lab and dry lab skills, the role of KEMRI in global health, and the impact of COVID-19 on public health practices. Oteno also delves into the MPOX outbreak, the rapid sequencing technology used in Ebola outbreaks, and the future of genomic epidemiology in Africa, emphasizing the need for collaborative networks and equitable partnerships in global health efforts.

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 effective communication of scientific data to clinicians, and the future of diagnostics in veterinary medicine, emphasizing the shift towards sequencing technologies over traditional methods.

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 industry, and her current role in the microbiomics team at Zymo Research. Janina emphasizes the value of persistence and finding a fulfilling career path in the biotech industry.

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 master's program, and her experiences working in pathogen genomics during the COVID-19 pandemic. Amy emphasizes the importance of workflow management, containerization, and standardization in bioinformatics, particularly in the context of public health. She also reflects on her current work modernizing HIV pipelines and the collaborative efforts within the field.

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: https://pha4ge.org/

He discusses the importance of microbiology in understanding diseases, the impact of COVID-19 on public health practices, and the significance of the One Health approach in integrating animal and human health. Gültekin emphasizes the role of bioinformatics in pathogen surveillance and the need for collaboration within the scientific community to address global health challenges.

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 computational biology, and the evolution of bioinformatics tools. Tommy shares his experiences with learning Unix, the balance between remote work and in-person interactions, and the mindset of finding opportunities in crises. The conversation highlights the significance of humility, continuous learning, and the interconnectedness of roles within the scientific community.

Takeaways

Tommy started his blog to document his learning journey in bioinformatics.

Criticism can be a positive opportunity for growth and collaboration.

Journaling experiences helps in personal growth and reflection.

Unix skills are foundational for bioinformatics and computational biology.

The transition from wet lab to computational biology can be challenging but rewarding.

Understanding the data generation process is crucial for analysis.

In-person interactions enhance communication and collaboration.

The biotech startup environment fosters agility and innovation.

Mindset shifts can turn crises into opportunities.

The distinction between analysts and developers is becoming more pronounced in the field.

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 into the changing landscape of sequencing technologies, highlighting the emergence of new companies and the implications for biodiversity research. The discussion also touches on the future of sequencing, the challenges of cost reduction, and the potential for sequencing technologies to explore previously uncharted biological phenomena.

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 technology that have made metatranscriptomics more accessible and cost-effective. Dr. Vujicic also shares insights on building a successful biotech company, the future of diagnostics, and how to define a healthy microbiome based on biochemical reactions. In this conversation, Momo and Kevin delve into the complexities of gut health, particularly focusing on hydrogen sulfide production and its implications for overall health. They discuss the intricacies of personalized nutrition, the limitations of traditional health metrics, and the need for a paradigm shift in nutritional science towards preventive maintenance. The conversation emphasizes the importance of understanding individual microbiome profiles to create tailored dietary recommendations, moving away from one-size-fits-all approaches.

More info at https://www.viome.com/

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 prevention and control. They explore the transition from traditional methods to genomic surveillance, the challenges of operationalizing these technologies, and the ethical implications of transparency in patient care. The discussion also highlights the need for evidence-based practices, the importance of incentives for hospitals, and the potential for lowering barriers to entry for genomic technologies in healthcare settings. In this conversation, Alex Sundermann and Kevin Libuit discuss the critical role of genomic surveillance in infection prevention and control. They emphasize the need for actionable insights from genomic data, the importance of metadata, and the challenges of data sharing across institutions. Financial sustainability and legal implications of genomic practices are explored, alongside the necessity for community standards and equitable access to genomic technologies. The conversation concludes with a call for learning from outbreaks and the importance of publishing findings to improve patient safety.

Takeaways

Pathogen genomics enhances understanding of disease transmission in healthcare.

Genomic surveillance can significantly improve infection prevention efforts.

Public health has successfully utilized pathogen genomics for outbreak detection.

The evidence supporting genomic surveillance is compelling but underutilized in healthcare.

Operationalizing genomic surveillance requires collaboration between hospitals and payers.

Ethical considerations are crucial in the implementation of genomic technologies.

Incentives and regulations are needed to encourage hospitals to adopt genomic surveillance.

Lowering the barriers to entry can facilitate the adoption of genomic technologies.

Commercial partnerships can help hospitals access genomic sequencing services.

Methodological standards in genomics are essential for effective interpretation of results. Genomic data must be actionable for infection preventionists.

Metadata is crucial for effective genomic surveillance.

Data sharing across institutions is a significant challenge.

Financial sustainability is essential for genomic surveillance programs.

Legal liability may increase for hospitals not using genomic surveillance.

Community standards for genomic practices are needed.

Equitable access to genomic technologies is vital.

Learning from outbreaks can improve patient safety.

Publishing outbreak findings is essential for knowledge sharing.

Genomic surveillance can help identify misallocated resources.