Advertise on podcast: A Coffee with CompBio

Networking is really just talking, but doing it well in bioinformatics takes strategy. Join Dina and Saba as they break down how to make meaningful connections at conferences, local events, and online, plus some unconventional tips and how to keep your network alive through career transitions. Whether you're a grad student or job hunting, you'll leave with practical steps you can use this week. Links: Season 1 Archive Thanks to Amulya Shastry and Yaseswini Neelamraju for editing and management support, Dina Issakova for the cover art and Valisha Shah and Elyse Loveman for social media support. Follow us on LinkedIn: https://www.linkedin.com/in/saba-nafees/ and https://www.linkedin.com/in/sharvarinarendra/

Academia or Industry? Join us as we talk to two scholars in academia and two scientists in industry. They share a day in their life, what they would redo and how they navigated one of the biggest career forks a PhD in computational biology faces. Explore both worlds and the various career paths in both sectors. A must listen if you have a PhD or are a current PhD student. Deciding between academia and industry is a hard question, hear from lived experiences in both fields. Links: Season 1 Archive Thanks to Amulya Shastry and Yaseswini Neelamraju for editing and management support, Dina Issakova for the cover art and Valisha Shah and Elyse Loveman for social media support. Follow us on LinkedIn: https://www.linkedin.com/in/saba-nafees/ and https://www.linkedin.com/in/sharvarinarendra/

Bioinformatics is a field built on collaboration and some of the most meaningful work happens beyond the lab and workplace. In our latest podcast episode, we chat with our two wonderful guests Ryan Yordanoff from Cambridge biotech club and Aaron Blotnick from Bits in Bio and SynbioBeta. Together, we explore the people and communities working to make science more accessible, inclusive, and impactful. From creating opportunities for students and early-career researchers to building supportive communities, these organizations play an important role in shaping the future of bioinformatics. Tune in as we talk about the impact of volunteering, community building, and giving back to the bioinformatics community. Because science isn't just about the work we do, it's also about the communities we build along the way! Links: Season 1 Archive Thanks to Amulya Shastry and Yaseswini Neelamraju for editing and management support, Dina Issakova for the cover art and Valisha Shah and Elyse Loveman for social media support. Follow us on LinkedIn: https://www.linkedin.com/in/saba-nafees/ and https://www.linkedin.com/in/sharvarinarendra/

In this episode of A Coffee with CompBio, we sit down with Lorena Pantano - a bioinformatician with about two decades of experience, founder of Boston Women+ in Bioinformatics, and co-founder of the Health Integrity project. We talk about her journey through computational biology, how the field has shifted (AI included), and the work she's done to build community and open doors for others along the way. Fittingly for Pride month, we also dig into what allyship looks like in science. A conversation about the work, the why, and what comes next. Links: Season 1 Archive Thanks to Amulya Shastry and Yaseswini Neelamraju for editing and management support, Dina Issakova for the cover art and Valisha Shah and Elyse Loveman for social media support. Follow us on LinkedIn: https://www.linkedin.com/in/saba-nafees/ and https://www.linkedin.com/in/sharvarinarendra/

May is mental health awareness month and we're highlighting neurodiversity with an open and insightful conversation centered on lived experience and understanding. In this episode, our co-host Dina Issakova sits down with two guests Isabella Chawrun and Lorena Pantano who share their experiences with ADHD and autism. Together, they discuss challenges, strengths, misconceptions, diagnosis journeys, and what neurodiversity looks like in everyday life and Bioinformatics. 5086ef111f0a90bedc0162713250a713eaf7538e Sharvari Narendra: Co-host & Co-chair Saba Nafees : Co-host & Co-chair Amulya Shastry : Co-host & Production Manager Dina Issakova : Co-host & Creative Director Yaseswini Neelamraju: Co-editor If you enjoyed the episode, please subscribe and leave us a review. Subscribe here:

What does it really take to land a bioinformatics role? In this episode, we sit down with Lauren Fitch, the Head of Computational Biology at ArkeaBio and Kaye Guerard-Hatziioannou, HR Business Partner at ArkeaBio, to break down how a Bioinformatics Software Engineer position actually gets filled — from resume screening to interview rounds, and the things hiring managers wish candidates knew. Whether you're early-career or mid-career, this one's full of practical, behind-the-scenes advice you won't find in a job description. Thanks to Amulya Shastry for editing and management support, Dina Issakova for cover art and Valisha Shah for social media support. Follow us on LinkedIn: Saba Nafees and Sharvari Narendra Go through all the podcast episodes on the Boston Women in Bioinformatics website: boston-wib.org

Claude code has taken over the tech world like a storm. But how good is Claude code when it comes to Bioinformatics and Computational Biology? In this episode of A Coffee with Compbio, Saba and Amulya take on the task of testing claude code on a simple task of performing QC on a Peripheral Blood Mononuclear Cells (PBMC) single cell dataset. They find out the dos and don’t with a tool like claude code while comparing it to how a real bioinformatician would analyze these results. Tune into this episode to learn more about Claude code for Bioinformatics. Bonus - We share all the results, markdown files and the single cell RNA QC skills markdown file that you can try on your own! Links: All files related to this episodeJournalMatch: A vibe-coded tool for finding the right match for your publication by Amulya Sharvari Narendra: Co-host & Co-chair \ Saba Nafees : Co-host & Co-chair \ Amulya Shastry : Co-host & Production Manager \ Dina Issakova : Co-host & Creative Director \ Valisha Shah : Marketing Lead \ If you enjoyed the episode, please subscribe and leave us a review. Subscribe here:

Hackathons are not just for coders anymore — computational biologists have made it their own with data, models, and insights! Hackathons can be a great way to understand the trends in your field, meet new people, and network. Do you want to try and participate in a hackathon this year and feel like a true hacker? The wait is over — in this episode we give you all the tea about hackathons, over a cup of coffee! Tune into our latest episode of "A Coffee with CompBio" where Sharvari Narendra and Saba Nafees talk about hackathons and more! If you think you know some more hackathon-related resources, let us know in the comments and we will give you a shoutout in the next episode! Links: Season 1 ArchiveBioHackathonsnf-core Hackathon Eventsnf-core Hackathon March 2026How I Organized a Hackathon at HarvardBIO-IT World FAIR Data HackathonOpenHackathonsMLH 2026 EventsCodeDayDevpostNCBI Codeathons Thanks to Amulya Shastry for editing and management support and Dina Issakova for social media support and the cover art! Follow us on LinkedIn: Saba Nafees and Sharvari Narendra

New year, new episode, new comp-bio goals and new hosts. But first, we wish you a very Happy New Year! Most new year's resolutions fail due to lack of clarity, so to make it easier, we begin our first episode of the season with a list that hopefully inspires you. From using AI tools to make your life easier to documenting your own code better, we are bringing resolutions every computational biologist needs this new year. Tune into the latest episode of "A Coffee with CompBio" where Sharvari Narendra and Saba Nafees present 12 awesome resolutions for the new year. If you think you have a better one, let us know in the comments and we will give you a shoutout in the next episode! Links: Season 1 Archive Thanks to Amulya Shastry for editing and management support and Dina Issakova for social media support and the cover art!. Follow us on LinkedIn: https://www.linkedin.com/in/saba-nafees/ and https://www.linkedin.com/in/sharvarinarendra/

As our first season comes to an end, we would like to wish all of our listeners a very happy holiday season. But wait! We also have some presents for our listeners. In this episode of “A Coffee with Compbio”, Lorena Pantano and Alex Bartlett present 12 cool things in bioinformatics.  From a tool that will rescue you out of Python dependency hell to the one that can generate a functional genome, they discuss some really innovative tools that have been rolled out this year. Tune in to listen to these 12 tools and how you might use them!  And find out about the exciting announcement we have at the end! Send us your comments, questions, and suggestions using this form 📁: https://forms.gle/ncwo6HZeN4uA9gPg7 Thanks to Amulya Shastryfor editing and management support. Follow us on LinkedIn: https://www.linkedin.com/in/lpantano/ and https://www.linkedin.com/in/alexandra-bartlett-926b32109/ If you enjoyed the episode, please subscribe and leave us a review. Subscribe here: https://podcast.ausha.co/a-coffee-with-compbio?s=1 Hosted on Ausha. See ausha.co/privacy-policy for more information.

What really happens when a wet lab scientist and a computational biologist sit down to plan an experiment? Spoiler: it's not always smooth sailing. In this episode of 'A Coffee with Compbio,' Lorena Pantano and Alex Bartlett chat with Amulya about the real talk nobody tells you about scientific collaborations. They break down the three make-or-break moments of any project: that first meeting where you're figuring out if single-cell sequencing on mouse eyes is actually the move (hint: maybe start simpler), the data processing stage where quality issues rear their ugly head, and those uncomfortable conversations when results don't pan out. What you'll learn: How to redirect overambitious project plans without shutting people down Smart ways to communicate technology limitations early What to say when pilot data quality is... not great Why being adaptable beats being rigid every single time If you want to level up your collaboration game and avoid common pitfalls, grab your coffee and tune in. Thanks to Amulya Shastryfor editing and management support. Follow us on LinkedIn: https://www.linkedin.com/in/lpantano/ and https://www.linkedin.com/in/alexandra-bartlett-926b32109/ If you enjoyed the episode, please subscribe and leave us a review. Subscribe here:https://podcast.ausha.co/a-coffee-with-compbio?s=1 Hosted on Ausha. See ausha.co/privacy-policy for more information.

In this episode of A Coffee with Comp Bio, hosts Alex Bartlett and Lorena Pantano sit down with Saranya Canchi, a computational biologist specializing in neuroscience. Together, they explore how to thrive as a self-directed learner in bioinformatics—tackling early challenges, learning through projects, and building problem-solving resilience. Saranya shares her journey as a self-taught bioinformatician, highlighting the importance of mastering the field’s unique language and embracing failure as part of growth. Whether you’re just starting out or looking to strengthen your learning approach, this conversation offers practical insights and inspiration for your bioinformatics journey. https://s-canchi.github.io/ Thanks to Amulya Shastry for editing and management support. Send us your comments, questions, and suggestions using this form 📁: https://forms.gle/ncwo6HZeN4uA9gPg7 Please get in touch if you or your business would like to help support this podcast. Follow us on LinkedIn: https://www.linkedin.com/in/lpantano/ and https://www.linkedin.com/in/alexandra-bartlett-926b32109/ If you enjoyed the episode, please subscribe and leave us a review. Subscribe here: https://podcast.ausha.co/a-coffee-with-compbio?s=1 Hosted on Ausha. See ausha.co/privacy-policy for more information.

Grab your coffee and join us for another episode of Coffee with CompBio!  This time, we kick things off with Amulya, a PhD student at Boston University and co-chair of Boston Women in Bioinformatics, who introduces us to llmr — a new Tidyverse-friendly tool for connecting with LLMs like ChatGPT, Gemini, and more. Think structured outputs, agent workflows, and even building your own chatbot in R. Then we sit down with Lina Faller, a veteran in bioinformatics with nearly two decades of experience bridging software engineering, research, and pharma. Lina shares why she started blogging about sustainable data systems, leadership in tech, and the very human side of computational biology. We dive into one of her favorite topics: why computational biologists should keep lab notebooks (yes, even if your “lab” is just a laptop). From reproducibility to institutional memory to the art of “forensic bioinformatics,” Lina brings stories and advice that will be useful to anyone working with data. If you’ve ever forgotten what you coded six months ago (we’ve all been there), or wondered how AI might fit into documentation and knowledge-sharing, this episode is for you. Send us your comments, questions, and suggestions using this form 📁: https://forms.gle/ncwo6HZeN4uA9gPg7 https://ellmer.tidyverse.org/articles/ellmer.html https://lfaller.github.io/ Thanks to Amulya Shastry for editing and management support. Follow us on LinkedIn: https://www.linkedin.com/in/lpantano/ and https://www.linkedin.com/in/alexandra-bartlett-926b32109/ If you enjoyed the episode, please subscribe and leave us a review. Subscribe here: https://podcast.ausha.co/a-coffee-with-compbio?s=1 Hosted on Ausha. See ausha.co/privacy-policy for more information.

In this episode, Alex and Lorena tackle the computational challenges of spatial transcriptomics. Learn how BPCells can help you work with millions of cells without needing terabytes of RAM, discover how Banksy's neighborhood-aware clustering reveals tissue architecture, and explore RCTD's approach to cell type deconvolution in spatially-resolved data. Plus, Lorena reviews Positron, the new R-friendly IDE that's catching attention in the bioinformatics community. https://github.com/bnprks/BPCells https://github.com/prabhakarlab/Banksy https://github.com/dmcable/spacexr https://github.com/bcbio/spatial-reports https://github.com/seandavi/awesome-single-cell https://positron.posit.co/ Send us your comments, questions, and suggestions using this form 📁: https://forms.gle/ncwo6HZeN4uA9gPg7 Follow us on LinkedIn: https://www.linkedin.com/in/lpantano/ and https://www.linkedin.com/in/alexandra-bartlett-926b32109/ Thanks to Amulya Shastry for editing and management support. If you enjoyed the episode, please subscribe and leave us a review. Subscribe here: https://podcast.ausha.co/a-coffee-with-compbio?s=1 Hosted on Ausha. See ausha.co/privacy-policy for more information.

Alex Barlett and Lorena Pantano welcome Katie Hughes, their first guest, to discuss her career transition from bioinformatics to product management. Katie shares her journey from studying genetics, working in wet labs, and discovering a passion for bioinformatics, to eventually earning a master's degree in the field. She details her experience at various biotech companies, including Harvard Medical School, Moderna, Sonata Therapeutics, and Generate Biomedicines. Katie emphasizes the importance of curiosity, adaptability, and soft skills in making career transitions. She explains what a product manager does, differentiates it from similar roles, and outlines the skills and experiences that helped her succeed. The discussion also covers the day-to-day responsibilities of a product manager, the collaborative nature of the role, and advice for those interested in making a similar career shift. Marty Cagan  How I AI podcast Send us your comments, questions, and suggestions using this form 📁: https://forms.gle/ncwo6HZeN4uA9gPg7 Please get in touch if you or your business would like to help support this podcast. Hosted on Ausha. See ausha.co/privacy-policy for more information.