the bioinformatics lab

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.

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 policies. They share personal experiences and insights on how remote work has transformed their professional lives, the impact of commuting on quality of life, and the necessity of fostering communication and connection in a virtual environment. Takeaways Remote work allows hiring the best talent globally. Quality of life improves with reduced commuting time. In-person interactions enhance team dynamics and relationships. Informal conversations are crucial for problem-solving. Virtual communication lacks the nuances of face-to-face interactions. Creating informal communication spaces is essential in remote work. Return to office policies are a complex issue. Isolation can negatively impact mental health in remote work. Intentionality is key in fostering workplace culture remotely. Balancing remote work with in-person meetings is vital.

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 of bioinformatics. The conversation emphasizes the need for a multidisciplinary approach to software development and troubleshooting. Takeaways A lot of software lacks proper engineering and testing. User errors often stem from simple mistakes like formatting. Debugging requires careful attention to detail. New line endings can cause compatibility issues across systems. User documentation is crucial for effective troubleshooting. Understanding user needs can prevent software errors. Software engineers sometimes create unnecessary complexities. Output formats should be user-friendly and compatible. A multidisciplinary approach enhances software development. Effective communication between users and developers is essential.

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 epidemiologists and bioinformaticians, the importance of communication and collaboration, and the need for bi-directional learning to enhance public health practices. The conversation emphasizes the significance of building relationships and understanding each other's fields to effectively turn sequencing data into actionable insights for disease control. Takeaways Epidemiologists work on the front lines of public health. Genomic data can help build and confirm hypotheses in investigations. Integrating genetic data with epidemiological data enhances disease surveillance. Surveillance systems must be designed to drive public health action. Communication between labs and epidemiologists is crucial for effective data use. Bi-directional learning is essential for both epidemiologists and bioinformaticians. Genomic epidemiologists can bridge the gap between bioinformatics and epidemiology. Building relationships is the first step towards effective collaboration. Training opportunities should be available for both sides to learn from each other. Collaboration is key to successfully integrating bioinformatics into public health.

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 conversation also touches on the importance of trademark considerations and the potential pitfalls of naming conflicts in the bioinformatics community. Takeaways Naming bioinformatics tools is crucial for usability. A good name should be unique and memorable. Backronyms are a common naming strategy. Consistency in naming is important for software development. Names can be inspired by personal experiences or local culture. Trademark issues can arise with popular names. Creative themes can enhance the identity of tools. Names should be easy to Google and not offensive. Developers should consider the implications of their chosen names. A well-thought-out name can aid in communication and collaboration.

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 of genomic surveillance in understanding and combating the virus. The conversation highlights the rapid advancements in vaccine development and the need for ongoing monitoring to prevent future outbreaks. Takeaways H5N1 is a highly pathogenic avian influenza affecting poultry and cattle. Influenza viruses are adept at recombining, posing pandemic risks. The current H5N1 outbreak has significant economic impacts on U.S. agriculture. Mammalian spillover from birds to cattle raises public health concerns. Surveillance data is crucial for understanding the spread of H5N1. Genomic sequencing aids in vaccine development and monitoring mutations. Pasteurization is vital in preventing the spread of H5N1 through dairy products. The economic impact of H5N1 in the U.S. is already over a billion dollars. Public health risks from H5N1 remain low but could increase with mutations. Collaboration between public health labs and tech communities is essential for effective response.

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 curated reference database for public health pathogenomics. They explore the importance of high-quality genomic data, the implications of mobile genetic elements, and the various applications of the database in public health. The conversation highlights the collaborative efforts of experts in the field and the significance of reliable data in making informed public health decisions. Takeaways The Kalamari database is a curated resource for public health. High-quality genomic data is essential for accurate pathogen identification. Public health decisions rely on the accuracy of genomic data. Mobile genetic elements complicate species typing in bioinformatics. The collaboration of experts enhances the quality of the database. The database allows for effective quality control in laboratories. Understanding plasmids is crucial for outbreak investigations. The CDC's involvement underscores the importance of public health infrastructure. The database is accessible and user-friendly for public health applications. This initiative represents a significant advancement in pathogen genomics.

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 the role of online platforms like LinkedIn and GitHub in identifying and attracting talent. The conversation emphasizes the significance of having a strong digital footprint and the strategies that can help candidates stand out in a competitive job market. Takeaways Successful hires often come from personal networks. Recommendations from trusted colleagues add value. Passion for bioinformatics is crucial in candidates. Being findable on LinkedIn is essential for job seekers. A strong digital presence reduces friction in recruitment. Effective communication skills are vital for collaboration. Separating personal and professional online identities is advisable. Engagement in technical communities can highlight talent. GitHub profiles serve as portfolios for developers. A clear digital footprint enhances job application success.

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 through academia and social interactions. The conversation highlights actionable advice for job seekers, including leveraging social media and engaging with the community to build a robust professional network. Takeaways All jobs can stem from knowing the right people. Building a professional network is essential for career growth. Genuine curiosity and kindness can lead to unexpected opportunities. Networking should be organic, not forced or transactional. Social media platforms are valuable tools for connecting with others. Engaging in community discussions can enhance visibility and opportunities. Conferences provide a great avenue for networking and learning. It's important to have a clear online presence, like LinkedIn. Networking is about mutual interest, not just self-promotion. Being helpful and interested in others can pay off in the long run.

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 analysis, and the importance of public health responses, including vaccination efforts. The conversation highlights the need for updated tools and resources to effectively monitor and respond to MPXV outbreaks globally. Takeaways Viruses require different types of treatment and analysis. MPXV is a larger virus compared to SARS-CoV-2. Amplicon dropout is a significant concern in sequencing. Public health responses can effectively contain outbreaks. Genomic surveillance is crucial for monitoring MPXV. Different variants of MPXV require updated reference genomes. Vaccination efforts can limit the spread of M-Pox. The availability of hosts affects the outbreak dynamics. Bioinformatics tools need to be adaptable for different viruses. Collaboration among international labs enhances genomic analysis.

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 Spanish-language episode. They discuss their journeys in bioinformatics, the importance of collaboration in science, and their experiences at a hackathon. The conversation highlights the barriers of language in accessing scientific resources and the significance of community in learning and sharing knowledge. Takeaways The podcast aims to provide resources in Spanish for the scientific community. Julian's journey began in Argentina, focusing on bioinformatics and data fusion. Olento's background includes mathematical modeling and pharmacokinetics. Collaboration is key in scientific research and development. Hackathons provide excellent opportunities for networking and learning. Cultural exchange enriches the scientific community. Free online resources like Coursera are valuable for learning. The importance of community in overcoming learning barriers. Experiences at hackathons can lead to significant collaborations. Creating resources in Spanish is essential for inclusivity in science.

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 virus typing compared to bacteria. The conversation emphasizes the neglected status of dengue as a pathogen and the urgent need for improved methodologies in public health. Takeaways Dengue is a small but significant virus affecting warmer climates. Current mathematical tools for dengue analysis are inadequate. Open-source tools are essential for sustainable dengue typing. Phylogenetic placement is crucial for understanding circulating strains. Different countries have unique circulating dengue types. Amplicon sequencing is a viable method for dengue analysis. Data sharing in the viral world is significantly limited. The viral taxonomy system is less organized than that of bacteria. There is a pressing need for better tools and methods for dengue research. The conversation around dengue needs to be expanded and prioritized.