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 workflow managers and the evolution of bioinformatics tools, emphasizing the need for both technical and soft skills in the field. The conversation highlights the collaborative nature of bioinformatics and the future trends shaping careers in this domain.

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 sequencing is becoming increasingly important in identifying and controlling infections. Current outbreak detection methods in healthcare are often limited and retrospective. APIC 2024 highlighted the potential of genomic epidemiology in healthcare. Cost-effectiveness is a key factor in adopting genomic sequencing in hospitals. Challenges include financial investment and the need for bioinformatics expertise. Healthcare systems must learn from public health to implement genomic sequencing effectively. The ultimate goal is to prevent harm to patients through better infection control practices.

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 addressing antibiotic resistance and the need for effective communication within the medical team.

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 growth, the impact of experiences on career choices, and the value of stepping back to gain perspective on life and work.

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 from animal science into bioinformatics, profiling the gut microbiomes of indigenous village chickens using 16S and metagenomic sequencing, and how wrestling with messy real-world data led him into multi-omics integration and machine learning. Mxolisi explains concepts like feature engineering, neural networks, and ecological “tipping points” in soil ecosystems—showing how combining metagenomic, metabolomic, proteomic, and genomic layers can help predict when an environment is on the brink of collapse, with implications for agriculture, food security, and even disease research.

We also dig into the philosophical side of his work: why the explosion of public omics data makes it almost a moral obligation to use these tools for better outbreak prevention and environmental stewardship, how conferences like PHA4GE in Cape Town and the AI working group are quietly seeding a new generation of multi-omics scientists, and what it feels like to realize that the five-year-old kid obsessed with dirt grew up to do exactly what he was pretending to do—only now with HPC clusters, neural nets, and GitHub.

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.