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Shirlee Wohl joined WARN-ID and the Andersen lab in the fall of 2021 as a researcher, writer, trainer, and right hand to Kristian Andersen. But most recently, she added Scripps Research faculty to her CV in her new position as an Institute Investigator in the Department of Immunology and Microbiology. We chatted with Shirlee Wohl to get to know her, her background, the career path that led her to where she is today, and much more: 

Can you tell me a little bit about your academic and research background prior to joining Andersen Lab?*

I started down this path as an undergrad, where I studied molecular biophysics and biochemistry at Yale. Even as early as then, I really enjoyed doing biological sciences research, but I was always more drawn to the computational side of things. So I was always taking more math classes instead of, say, anatomy and physiology classes. About halfway through college, I happened to see a graduate-level class offered on bioinformatics. And I thought, “Oh! This seems really interesting.” That was my first introduction to sequencers and sequence aligners and things along those lines, which made me excited to learn more about bioinformatics, computational biology, and genomics. This inspired me to go to graduate school to learn more. I started my PhD in Systems Biology at Harvard in 2013, and I knew from the beginning that I wanted to work in Pardis Sabeti’s lab, which would allow me to apply my burgeoning interest in genomics and bioinformatics to infectious disease. The beginning of my time in the Sabeti lab coincided with the beginning of the Ebola outbreak, which launched my work applying genomic and bioinformatic techniques to ongoing outbreaks and global health. Soon after that, I analyzed genomic data from the Zika virus outbreak in the Americas in 2015 and, in my last couple years of graduate school, I had the opportunity to study a local mumps outbreak at Harvard and in Massachusetts. This was a really interesting opportunity to combine everything I learned to a pathogen circulating closer to home, where I had a little bit more access to epidemiological data that we could use to inform the genomic analysis. 

Having access to epidemiological data and realizing how critical it was to the correct interpretation of genomic data motivated me to pursue a postdoc at the intersection of genomics and  classical epidemiology. I found that opportunity working with Justin Lessler in the Epidemiology department of the Johns Hopkins Bloomberg School of Public Health. There, I focused my research on cholera — a pathogen that has been closely monitored by epidemiologists for decades, but for which genomic analysis for the purpose of understanding spread is still relatively new. Trying to make sense of sparse genomic data from cholera outbreaks spurred my recent research interest in sample size calculations for genomic studies. In other words,“How do we design genomic studies so we can ensure we are correctly interpreting the results?” 

During my time at Johns Hopkins, I had the opportunity to work closely with and train many African scientists on sequencing and genomic methods, which was one of the highlights of my post-doc. I wanted to continue my genomics-informed research as well as these sorts of academic collaborations as I continued in my research career, and I thought Andersen lab would be a great place to continue working with amazing people who care a lot about the capacity-building and education component of infectious disease genomics.

What have you found to be most motivating throughout the different stages of your career thus far? 

Definitely seeing other people learn how to do genomic analysis and bioinformatics! Just as I became completely fascinated with the field in college, I find that so motivating to see others find the same excitement, especially when the people I’m working with have an immediate need or application for genomics tools. It makes me really excited to continue in this field, and think about what the next tools that we can use to impact global health. 

What are some of the things you’ve learned over the past few years working as a Project Scientist? 

Of course, a huge portion of the past few years of my life has been affected by the COVID-19 pandemic, and that has highlighted both the importance of this kind of work and its incredible potential for growth. The pandemic has been really hard for a multitude of reasons, but a silver lining is that it has also accelerated the field of genomics a great deal. Now, every lab in the world wants to be performing sequencing and using genomic technology to track viruses, and there has been an enormous increase in the number of labs with this capacity. On the flip side, the pandemic has also accentuated how quickly misinformation can spread and how difficult it is to convey public health guidance given that science is inherently iterative. We are always trying to improve and disprove new hypotheses, and communicating this uncertainty to non-scientists is—and has always been—quite difficult. As a general rule, we as scientists need to be a lot better at communicating our science and presenting it in ways that can be used to generate positive impact without the information being misconstrued or misinterpreted. 

Has it been challenging to work as a Project Scientist remotely? 

Shirlee visiting the Andersen Lab in sunny San Diego in February 2022

I really appreciate that Andersen lab has welcomed me despite my distance from California. Establishing myself in this role required me to be deliberate about reaching out to people early on and building connections via Zoom, since I don’t have the opportunity for casual day-to-day interaction. But despite the challenges, I feel like I’ve really gotten to know the lab (visiting in person a few times has also helped!).

It also has been a relatively seamless transition because of the number of international collaborators that the lab already has – they relied on Zoom far before the pandemic!

What are you most proud of accomplishing while at Andersen Lab? 

I am most proud of the WARN-ID training workshop that we ran last spring. It was a huge combined effort from the Andersen lab, the Sabeti lab, and ACEGID, and we all came together to meet the urgent need for SARS-CoV-2 sequencing at the time. A lot of the trainees from that workshop are already thinking about how to apply what they’ve learned to other pathogens, so it’s been really cool to help lay the foundation for that and also, in many ways, build upon the foundation that the Broad Institute and Andersen lab have established over the course of many years. 

With this promotion to Institute Investigator, you will have more opportunities for self-directed research and the ability to explore new topics of inquiry. What are you most excited about in your new role? Are there any areas of research/ projects you’d like to pursue?

I’m really excited to come back to my post-doc work focusing on sample size calculations. Especially now that the field is transitioning from sequencing individual samples from infected patients to wastewater samples potentially containing pathogen DNA or RNA from a whole city or population of infected people, the question of, “How do we properly design studies that give us the answers we need?” remains critical and mostly unexplored. I think there are a lot of questions related to sample size calculations that are relevant specifically to SARS-CoV-2, but we’re also going to have similar questions about other pathogens, such as, “How many sequences of this pathogen do I need to definitively say that this pathogen is not here, or alternatively, that it is here?” I’m excited to continue this work in the context of all the other work that is going on at Scripps and Andersen Lab. It’s one thing to develop a theoretical method, and another thing entirely to apply it to a wide variety of settings. So, for example, we can try to apply these methods in San Diego, which has a very different genomic sequencing program than our collaborators in West Africa, and then work with collaborators to implement new methods abroad so we can compare the results. Thinking about the implementation of new methods is always really exciting for me. 

I am also excited to get the opportunity to do more teaching and mentoring. I think there’s so many smart scientists out there who, for some reason or another, haven’t learned about genomics yet, and I’m excited to hopefully work with them in the future. 

Can you tell me a bit about your work in cholera that you recently received a subcontract from the Gates Foundation for? 

The Gates Foundation is funding the establishment of a new consortium that is jointly led by Africa CDC and Johns Hopkins University. The idea is to build in genomics as part of cholera control. We’ve identified five countries on the African continent that are going to be pilot focuses of this consortium, where we’ll work with them to ensure they’re up to speed on cholera sequencing and bioinformatics, while using genomics to better understand the spread of cholera on the continent. I think cholera is an interesting pathogen because it’s been around for a long time, but we still don’t really understand local and regional patterns of spread. The hope is that by using genomics to identify which lineages are circulating where, and potentially where they’re coming from, we can use that information to help improve existing control programs. 

What is the advice you’d give to a current student or research scientist?

One thing I often say is that the people you work with matters more than almost anything else. There’s a lot of really exciting science out there, but finding the people you jive with— who you think are smart, who have similar working styles to you, that have a good mentorship style for you—is by far the most important thing. I’ve been so so fortunate to have amazing mentors and lab environments in the Sabeti Lab and in the Lessler lab, and now in the Andersen lab. These kinds of supportive environments have been critical to any success I’ve had so far. So my advice is to find good people: even if you don’t know exactly what project you want to work on, if you’re around good people who make you excited about science, you will find important questions to work on. 

When you look at the advances in research and capacity building across organizations in the WARN-ID network, what are some of the projects that make you most hopeful for the future? 

Looking forward, I’m really excited about the current focus on wastewater sequencing and how that will change infectious disease genomics on a global scale, in particular lowering the cost barriers to genomic epidemiology. And I’m personally excited to introduce bacterial genomics into the Andersen lab through my work on cholera. Bacterial genomics is a totally different beast since bacteria are much bigger than viruses and the technology to study them is different. I think the Andersen lab community can play an important role in applying the thinking and inroads we’ve made in genomics to cholera and other new pathogens that arise, whether they be viruses or bacteria. 

Excited about the work you read about above? Shirlee is hiring two Postdoctoral Associates to work in the Andersen Lab and lead projects focused in the areas of Bacterial Genomics and Viral Genomics. Read more about the positions here and here. 

*Interview conducted by Kyra Benowitz on December 20th, 2022.