Archive by Author

Scientist spotlight: supervised and unsupervised methods for microbiome data analysis with Dr Nandita Garud 

7 Mar

I got to know Nandita Garud when she was a PhD student in the biology department at Stanford and I was a postdoc there. While we were in the same lab, we got to collaborate on two papers: one about population genetics and drug resistance evolution and one about rats in New York City. After finishing her PhD, Nandita worked at UCSF as a postdoc and then took a job as an assistant professor at UCLA. You can read more about her interesting work on the microbiome, fruit flies and other topics on her website. I asked her about a recent paper on using supervised and unsupervised methods to analyze microbiome data. 

Image: Headshot of Dr Nandita Garud, assistant professor UCLA
Headshot of Dr Nandita Garud, assistant professor UCLA

Pleuni: Hi Nandita! Thanks for taking the time to chat with me! Can you tell me in a few sentences what your job is?

Nandita: Hi Pleuni! Thank you so much for inviting me to chat about my work. I am an assistant professor in the Department of Ecology and Evolutionary Biology at UCLA. My research is on understanding the evolutionary dynamics of natural populations, currently with a focus on the human microbiome, but I also work on Drosophila and other organisms!  My research group (or, ‘lab’) consists of several PhD students that perform computational work to understand how natural populations evolve. 

Pleuni: So, you consider the community of microbes that live in my intestinal tract as a natural population, is that right? And they evolve? 

Nandita: That’s correct. I consider populations that live outside a test tube in the lab to be natural populations. Interestingly, gut microbiota can evolve on even 1-day timescales, even in the absence of a selective pressure like antibiotics!

Pleuni: I saw that you published a paper about supervised and unsupervised methods for background noise correction in human gut microbiome data. Could you explain what the human gut microbiome is? And why you need background noise correction for it?

Nandita: The human gut microbiome is a complex community that is composed of hundreds of microbial species coexisting and interacting with one another. The human microbiome is known to play an essential role in health, and changes in the microbiome are associated with numerous diseases like diabetes, obesity, and inflammatory bowel disease. Being able to predict disease status from the human microbiome is important for helping individuals diagnose any illnesses they may have. One major complication, however, is that technical variables, such as how the DNA was extracted from the sample, can introduce noise in the data, making it harder to predict human phenotypes. So, background noise correction is an important approach for addressing this data heterogeneity so that more reliable predictions can be made. 

Pleuni: Thanks! In the new paper from your lab, you compare supervised methods (which are currently standard for noise correction) and unsupervised methods (which have not been applied to microbiome data). What is the difference here between supervised and unsupervised methods?

Nandita: Supervised methods are ones where a machine is shown labeled data and is trained to understand the differences between data classes. Unsupervised methods are ones where the machine needs to figure out on its own what groupings are present in the data. We use an unsupervised approach because we don’t always know what sources of noise contribute to variation in the data. 

Pleuni: Okay, thanks! So, I imagine something like this: If microbial species A is always 2x as abundant in samples that were sequenced with machine X vs machine Y, then we can correct by changing the abundance of species A so that it matches between the two machines? Is that what’s happening? 

Nandita: Yes, but we aren’t explicitly adjusting the abundances, rather, throwing away variation due to noise. 

Pleuni: Does this mean that you do a dimension reduction method first and then throw away dimensions? 

Nandita: Exactly — we do PCA (principal component analysis) and then throw away the first PCs (principal components) because they usually are correlated with noise. We do run the risk of throwing away signal too, but that’s the tradeoff in an unsupervised approach. But when we compare this unsupervised approach to the standard supervised approaches, it can work just as well in many scenarios! And the good thing is that this way we can correct for unidentified confounders. 

Pleuni: Cool 😎 Thank you for explaining all of this, Nandita! 

I have one more question. What is something you like to do when you are not doing science? 

Nandita: I enjoy taking walks with my family and enjoying the outdoors in Los Angeles! 

Pleuni: Thank you Nandita! 

Here is a link to the paper:

The website of the Garud lab:

Dr Chris Davies’ PINC/GOLD/gSTAR Program 2022 Graduation Speech

16 Sep
Image of Dr Chris Davies giving his speech. On the right you see the slide with his name and title: Christopher Davies, PhD. Antibody Engineering Department. Genentech Early Research and Development (gRED). Genentech, Inc.

Chris Davies: “Today, we are here to recognize and celebrate these students who began, endured, and successfully completed the PINC, GOLD, or gSTAR certificate programs. I want to begin by saying congratulations and well done. Bringing together the fields of computing and data science with biology and chemistry is a pathway towards the future, that is now. The growth of technology to analyze large data sets, create applications, and the ability to code has never been more important in a generation than it is now. To the dreamers and organizers of these programs, I am happy to say your dream has come true amongst these students today.

For those of you that do not know me, my name is Chris Davies, and I am so honored to be here today speaking to you. My involvement in this celebration today arose from a vision that began with Joy Branford and Marlena Jackson at Genentech. A vision for change and opportunity. To change the face of STEM education, and to provide an opportunity to those that were not born into opportunity. My job at Genentech is to discover next generation medicines that change the lives of the patients that we serve. My job in life is to be Chris, a man that tries to make a difference in the lives of all the individuals that he encounters. I saw the gSTAR program as the opportunity that aligned perfectly with that job description. Alongside, my Genentech colleague, Chunwan, and SF State professor, Anagha, we envisioned a course that not only imparts knowledge to the students, but builds a bridge of life experiences that each student can walk across, allowing them to see and believe that they can achieve and aspire to similar or even greater levels. That vision became CSC 601, a seminar series course that outlined the drug discovery and drug development process from basic biology to post market approval, using current Genentech employees as guest speakers, whose jobs span the entire drug development process. Not only did the speakers talk about their job description and the role it plays in drug development, but also, each speaker outlined their life and career journey, emphasizing the successes, failures, and challenges that have led up to where they are at now.

The journey of a class and a scientist

Chunwan and I were the first “guest speakers.” We introduced the entire drug development process from start to finish. I have to say this was fun! Getting back into the classroom (albeit virtual) to engage with college students brought me back to my days in graduate school. We were able to set to tone and foundation for what was to come during the semester. Think about the timing and relevance of this course topic. We were and still are in the midst of the largest global health pandemic anyone has ever seen. The news was littered with information on the discovery and development of vaccines, followed by more information on vaccine and drug authorizations and approvals. What better way to engage with current events than to impart knowledge, but also make room for open discussion? Just like the rest of the speaker panel, we highlighted our life and career journey. A journey that included for me growing up in Kentucky to Sierra Leonean parents, who immigrated to the United States South in the embers of the Jim Crow era in 1973. A journey that included balancing life as a division I soccer player at Western Kentucky University with a chemistry major, mathematics minor, all while being heavily involved in undergraduate research. A journey that took me to Atlanta, GA for two summers for an internship at the Centers for Disease Control and Prevention (CDC), which opened the doors for me to pursue my doctoral degree at Purdue University in Indiana. A journey that led me to pack up my car to drive 2225.5 miles across the country to start a new life in Oakland, CA on a $39k postdoc salary at 26 years old.

As I sat through each class during the semester, I could see the level of engagement from the students and the impact each speaker was making as he or she described their journey and job. My favorite class of the semester was the last class, in which we held an in-person discussion session. I was blown away by the overwhelmingly positive responses and feedback from those that took 601. On behalf of all the guest speakers, I want to thank the 601 students for your willingness to allow us to take you along for the ride through our life and career journey.

The students of the gSTAR class that Dr Davies (on the far right) developed and taught with Dr Anagha Kulkarni (on the far left) and Dr Chun-Wan Yen (not pictured).

To the graduating students

That was a little bit about me, my involvement, and appreciation for the gSTAR partnership with SF State. For the second part of this speech, I would like to speak directly to you, students, because we are here to celebrate you and your achievement today. When I was asked to be the speaker at this celebration, I was overwhelmed with humility and honor that I would be entrusted with this responsibility. A responsibility to not only represent myself, Genentech, and the ones who were brave enough to ask me to talk and impart my ridiculousness, that some might call wisdom or encouragement. For those that know me, I love to talk, connect with people through stories, laughing, jokes, and through wrestling with life’s most challenging and deep topics. In order to collect my thoughts to ensure they were coherent, I first went to YouTube and searched for commencement speeches.  I listened to speeches from Barack Obama, Oprah Winfrey, Denzel Washington, and Chadwick Boseman. Even this past weekend, I heard former NBA champion, Dwayne Wade, give Marquette University’s commencement speech. Each speaker used their life’s journey to impart wisdom to the graduates, in hopes to inspire them as they embark on their next steps.  These individuals that I listened to need no introduction. These individuals have done extraordinary things in their lives that we continue to celebrate today, but let us not forget they all started out as people just like you and I. They had upbringings and experiences like many people in this room today, but what was it that separated them from the rest? Was it their talent, resilience, passion, desire, determination, hard work, belief, support system, opportunity, etc? The first thing I want to say to you is that you have to embrace your own journey, it isn’t about comparing yourself to other’s successes or failures, but try to take pieces of others experiences to help propel you on your own path.  

There are four things that I have learned along my journey through life that I hope will help inspire you along your own life journey.  I continue to live by and struggle through what these four things mean for me in each season of my life. This is an ever changing and ongoing process.

The 2022 GOLD, PINC and gSTAR graduates. The picture shows 18 students and a cake with candles.

#1: Explore what brings you excitement and try to do those things

In school, I always did well in math and science, and my dad was/is a chemist, therefore, he pushed my siblings and I towards majoring in chemistry in college. Doing chemistry and working in a lab did not fit for my brother and sister, even though they did it to please my father. For me, once I started doing undergraduate research my second semester of college, chemistry became real for me. I enjoyed it! I learned so much working alongside my professor. I enjoyed getting results and analyzing data, all in pursuit of telling a story of what we think is going on. Soon I realized that working in the lab enabled me to travel all over the United States to go to conferences to present my data, talk to people, and continue to learn even more. Being at a conference opened the door for me to get an internship at the CDC, which exposed me to the world of proteins, biochemistry, but most importantly, that getting a PhD was possible for me. Obtaining a PhD open doors for me to come out here to do a postdoc at UC Berkeley, and then, transition to Genentech. The main takeaway is that it started with my openness to trying something new that ending up being fun and exciting. I had no idea that saying yes back then would lead me to me standing here in front of you today. What I do know is that doing stuff that excited me helped me to navigate the challenging and difficult moments along the way.

#2: Seek balance in your life

Following on from my first point about doing things that you are excited about. I grew up playing soccer since age 5. I played on travel teams, high school varsity, I was a division I soccer player, and I even played for a semi-pro soccer team while pursing my PhD. A typical weekday during graduate school consisted of working in the lab from morning until 5pm, and then, I would leave campus to go to the sports club to coach kids for 2-3 hours, before having my team training for another 2 hours. After practice, we would go eat around 10:30-11PM, and then, I would shower and go to bed to do it all over again the next day. Weekends consisted of playing games locally, or traveling as far as 4-6 hours for away games. As crazy as this schedule was, it brought the perfect balance in my life.  When I was at school, I was focused on chemistry, when I left school, I was focused on coaching and playing. The main takeaway here is that seeking balance in your life is healthy and beneficial. I learned to be so much more efficient in my work, but also soccer gave me a release from school, and school gave me a release from soccer.

#3: Find mentors

This I believe is one of the most important things that I’ve learned along the way. Finding people that can help guide you along your path. You do not need people to give you step by step instructions, but you need a mix of people, a board of advisors, that you can lean on a times to help you navigate this journey called life. The key things about mentors are: (1) they do not have to look like you, (2) they do not have to be your friend, (3) they should be people who have your best interest in mind, (4) they should be individuals that challenge you to grow, and (5) they should be people who call you out equally as often as they praise and support you. These are people whose goal and desire is to see you reach your full potential, along your own journey. Sometimes these people are in your life for only a season, others across multiple seasons, but I encourage you to seek these people, be open to learning along the way, and continue to stay connected or in touch, even if it is only for a simple check-in or hello.

#4: Do not be afraid to be uncomfortable

I have found that growth and progress is uncomfortable. Some of my greatest successes and accomplishments stemmed from saying yes to stepping into, remaining in, and/or enduring uncomfortable situations and circumstances. The best example in my life was my decision to move out here. I was finishing my doctorate degree and I was still playing soccer, coaching, and I had a couple job opportunities, one in particular to work for my friend/mentor’s company. He painted the picture of learning directly from him in the area of pharmaceutical analysis, while continuing to play and coach soccer. He even proposed that I take over managing the soccer club. To put it simply, I thought this was my dream scenario to do science and soccer.  Everything was perfect, I knew the area, the people, and I would still learn and grow in my career, however, there was one thing that held me back from saying yes, this would have been comfortable. I had one opportunity, a postdoc at UC Berkeley, that paid me less, in an area that I knew nothing about, without friends and family, but would be an adventure, especially since I was 26 at the time. I chose to move out here to the unknown instead of staying for the known. I would rather come out here and it not work out, than to be too afraid to try.  It was uncomfortable adjusting to life in the Bay Area compared to the south and Midwest. It was uncomfortable having to start life all over again making new friends and learning new routines. It was uncomfortable paying $1100 for an apartment the exact same size as one that I only paid $500 for in Indiana. I had no idea at the time how my life would turn out, but that decision changed my life forever. Just think, I would not be standing before you here today. The main takeaway here is do not be afraid to be uncomfortable because you never know what can come out on the other side.

Dream big and do not be afraid

            In closing, I would like to encourage you to dream big and do not be afraid. Congratulations on completing these programs and good luck with the next steps in the journey. Thank you for your time and this opportunity to speak.” 

The SFSU and Genentech team responsible for creating and teaching the gSTAR program. Chris Davies is in the middle of the back row, the tallest of the group.

Matt Suntay’s jump into the PINC computing program

27 May

Matt Suntay is one of the students in the PINC program and also a research student in my lab in the E. coli / drug resistance / machine learning team. A few days ago he gave a speech at our PINC/GOLD/gSTAR graduation event. I thought it was a great speech and Matt was kind enough to let me share it here both as a video and the text for those of you who prefer reading.

“To those of you who may know me, you all know I’m pretty adventurous. For those of you who may not know me, first off, my name is Matthew Suntay, and I have jumped off planes, cliffs, and bridges – and each time was just as exhilarating as the last. But, let me tell you about my most favorite jump: the leap of faith I took for the PINC program.

I call it a leap of faith because when I first heard about the PINC program, and specifically CSC 306, I thought, “Ain’t no way this could be for me. I may be stupid because I can barely understand the English in o-chem and now I gotta understand the English in Python? Maaaan, English isn’t even my first language… But they said I don’t need any prior computer science knowledge, so why not? It’s Spring ‘21, new year, new me, right?”

And let me tell you, it definitely made me a new me. I went from printing “Hello World!” to finding genes in Salmonella to constructing machine-learning models to study Alzheimer’s Disease and antibiotic resistance in E. coli. These are some pretty big jumps–my favorite, right?–and they weren’t easy to make. However, I was never scared to make any one of those jumps because of the PINC program.

When I think PINC, I don’t only see lines of code across my screen or cameras turned off on Zoom. I see friends, colleagues, mentors, and teachers. I see a community.

I see a community willing to support me in my efforts to develop myself as a scientist. I see a community providing me the platform and opportunities to grow as a researcher. And most importantly, I see a community that shared hardships, tears, laughter, and success with me.

I can confidently say that the PINC program was, and still is, monumental to my journey through science. Thanks to the PINC program, many doors have been opened to me and one of those doors I’m always happy to walk through each time is the one in Hensill Hall, Room 406 – or the CoDE lab. It was here in this lab that I met some of the most amazing people who want to do nothing but help me reach new heights. I’m so grateful and lucky to have them. So thank you, Dr. Pennings, for believing in me and continuing to believe in me. Thank you to everyone in the CoDE lab for supporting me and laughing at my terrible jokes – and real talk, please keep doing so, I don’t know how to handle the embarrassment that comes after a bad joke.

If I haven’t said it enough already, thank you so much to the PINC program. If you were to ask the me from a year ago what his plans were for the future, he would tell you, “Slow down, dude, I don’t even know I’m trying to eat for breakfast tomorrow.” But now if you were to ask me what my plans for the future are, I’d still tell you I don’t know what I’m trying to eat for breakfast tomorrow because I’m too busy writing code to solve my most current research question, whatever it may be.

For many students, including myself, one of the biggest causes of an existential crisis is, “What am I gonna do after I graduate?” To be honest, I’m still thinking that same thought, but without the dread of an existential crisis. One of the coolest parts of the PINC program is the exposure to research and the biotechnology industry, and learning that research == me and not just != the stereotype of a scientist.

Dr. Yoon, thank you for taking the time and effort to push me and my teammates forward, because even though our projects were difficult, we learned a lot about machine-learning and ourselves, like who knew we had it in us this whole time? You definitely did and you helped us see that. Professor Kulkarni, you also helped us realize that we should give ourselves more credit. 601 and 602 showed us we can be competitive and that we’re worth so much more than we make ourselves out to be. Also, I would like to give a quick shoutout to Chris Davies and Chun-Wan Yan for the wonderful seminars because those talks gave me hope and inspiration for the future. Knowing that there’s something out there for me makes going into the future a lot less scary and a lot more exciting because who knows what awesome opportunity is waiting for me?

And one last honorable mention I would like to make is to Professor Milo Johnson. He was my CSC 306 professor, and I don’t know if he is here today, but he was an amazing teacher in more ways than one. He helped me turn my ideas into possibilities and I have him to thank for helping kick start my journey through PINC. When I thought “I couldn’t do it, this isn’t for me,” he said “Don’t worry, you got this.”

So, once again, to wrap things up, thank you to everyone who’s helped me out this far and continues to help me out. Thank you to all my friends, mentors, and teachers that I’ve met along the way. And thank you to the PINC program, the best jump I’ve ever made.

Matthew Suntay – PINC graduate 2022

Letter from Mila, 19 and very seriously ill with ME/CFS

4 May

This letter was written by Mila Hermisson, with the help of her parents, Joachim and Sabine Hermisson. Mila is extremely sick and has been in her bed in total darkness for well over a year now. Her letter was initially published in German on this Kudoboard.

ME/CFS is a very serious disease that can be caused by viral infections. Long Covid can also lead to ME/CFS, which means that the number of patients is expected to rise significantly. Time to learn about ME/CFS!

Picture of Mila Hermisson who is severely ill with ME/CFS in her bed with a mask. Smaller picture of Mila outside with her cat, from before she became bedridden.

My name is Mila. I am 19 years old and very seriously ill with ME/CFS. I know that people who are not affected themselves can hardly imagine what that means. That is why I would like to tell you about it here.

Since November 2020, more than 10,000 hours, I have been confined to my bed in total darkness as you can see me in the picture. I can barely move my arms and legs, can’t eat by myself, can’t sit for more than a minute, and haven’t been able to speak for half a year. If I want to communicate something (like here), I can only do it on good days, when I can write letters on my bedsheet with my finger.

But worst of all is the uncertainty, the fright and the total loneliness. Even my cat is too exhausting and can no longer be with me. My parents and nurses are only in the room for the most necessary tasks. Everything has to go quickly and as calmly as possible to avoid stimulus overload and further crashes. Outside, life goes on. My twin sister and my friends have graduated from high school, have been abroad, are starting their studies. I am trapped here, hour after hour, day after day, month after month, in solitary confinement, buried alive.

I was 15 years old when I did not recover after a viral flu in the fall of 2018. In the small picture, I’m already sick, even if you can’t see it. In the early years, with great effort, I still managed to finish 10th and 11th grade. Today, I know that it was not good for my health, but I had so many plans. I was used to not losing optimism and going my way despite difficulties. Today, after my severe crash, my only hope is that the disease will finally be recognized, that there will be research and, as soon as possible, a therapy.

ME/CFS is a terrible disease that takes away my youth and can completely destroy a life. There are so many people affected, the stories on this page are just examples. And it can strike anyone. Given this, it’s hard to believe that there is almost no medical care, appalling ignorance and ignorance among many doctors, and far too little research.

Please: Build up care structures at long last! Make postviral diseases a focus of research and medical education and training! Take the experiences of patients seriously and act! Thank you.

Written by Mila Hermisson, Mödling, Austria, 2021.

4 things you can do to support people with ME/CFS

If reading about Mila and her disease makes you want to take action, here are some suggestions.

  1. First, you can read about ME/CFS. This interview has a lot of info and also tells the story of an impressive young woman (Evelien van den Brink) who petitioned the EU to spend more on ME/CFS research.  .
    Here you can see part of the speech Evelien van den Brink gave in the EU parliament.
  2. Also, have a look at this video about the problem that we are not spending nearly enough research dollars on this disease.
  3. You can donate money for research here: – especially in May and June of 2022 when all donations will be doubled!
  4. Finally, please share this information so that more people will know about ME/CFS. 

Meet Christopher Davies, senior principal scientific researcher at Genentech.

1 Dec

Christopher has a BS in Chemistry from Western Kentucky University where he was also a very successful collegiate soccer player. As an undergrad he did an internship at the CDC. He then went to do a PhD at Purdue University. The title of his thesis was “Structural and Functional Characterization of the Endosome-associated Deubiquitinating Enzyme AMSH.” He published his results in peer-reviewed journals such as the Journal of Molecular Biology (link). He then applied for and got a postdoc fellowship from the National Institutes of Health to go to UC Berkeley to do a postdoc. From there he got a job at Genentech and now has been there for 6 years.

Christopher Davies’ LinkedIn Profile photo.
Image of one of the research articles Christopher published from his PhD work.

1. How did you decide to get a degree in biochemistry? What interested you in making this choice? What were the challenges (if any) and were your successes that drove you to achieve this degree?

My first experience working with proteins came during my summer internship at the Centers for Disease Control and Prevention (CDC) after my junior year in college. After that summer at the CDC, I returned for my senior year in college, took a biochemistry course and a nutrition course, and I thoroughly enjoyed how practical and applicable biochemistry is to all of us. From here, I knew I would pursue my graduate studies in biochemistry. The main challenge that I had going into graduate school was that I was a chemistry and mathematics major in undergrad, therefore, I had to spend a lot of time learning the basic biology concepts. Overall, my passion for learning the interface between chemistry and biology really drove me to successfully obtaining my doctorate degree in biochemistry.

2. Why are you interested in a career in Biotech? What inspires you about this work?

I am interested in biotech because this is an industry in which you can make a tangible and life-changing impact in the lives of patients. Coming out of my postdoc, I wanted to my work on real drug discovery, and learn about how basic research can be turned into drugs that make a difference. The ability to be involved in and around people who have discovered impactful medicines inspires me every day.  

3. What do you want to do in your future career? What are you aiming for?

In my future career, I want to learn about how the other parts of the organization, outside of early research, fit together to form an impactful organization that makes a difference in the lives of patients.

4. In your opinion, why should a student at SF State consider a career in Biotech?

An SF State student should consider a career in biotech because this is an industry in which you can make a broad, impactful difference in the lives of people, while also being at the center of innovation.

5. Can you share something interesting about yourself?

I played soccer my entire life since I was 5 years old. I played division I college soccer, semi-professionally while pursuing my doctorate degree, and I traveled to three European tournaments with the Genentech soccer team.

News story about Christopher Davies winning soccer and academic honors.
Image of Christopher Davies playing soccer.
Image of Christopher Davies playing soccer.

Short term postdoc position open at SFSU

15 Oct

The CoDE Lab

Come join us in San Francisco!

NIH / NSF funded postdoc position at San Francisco State University to work with Dr Pleuni Pennings in the CoDE Lab.

We are looking for a postdoc who can work on two different projects on viral evolution. One project is in collaboration with Dr Zandrea Ambrose and Dr Philana Lin from the University of Pittsburgh. The other project is in collaboration with Dr Adi Stern in Tel Aviv.

Both of the grants are nearing their end, which is why we are advertising only a short term opportunity (1 year of funding). This is a great opportunity though because there is great data available and there is a possibility of writing / contributing to two papers.

Preferred qualifications:

I am looking for someone with experience and interest in several of the following domains: evolution, virology, bioinformatics (next-gen sequencing data) and statistics. If you are interested…

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SCIP 2021 helped 130 bio/chem students improve their coding skills.

26 Aug

This past June and July, 130 participants improved their coding skills in the 2021 SCIP program at SF State University! I am so excited about this program and very grateful for the amazing team of people who ran SCIP 2021 (Rochelle Reyes, Ryan Fergusson, Olivia Pham).

I would like to share with you all how it went. The 130 participants were mostly biology and biochemistry students, but we also had some alums and staff who joined. Just over half of the participants were undergrads, and most had little or no coding experience.

Our participants were ethnically diverse and 63% identified as female, non-binary or gender non-conforming.

How was SCIP 2021 organized?

The participants were organized in teams of 5-7 people. This summer, we had 10 R teams, 11 Python teams and 2 ImageJ teams. For each team, we pick one member to be the team leader. Team leaders are chosen based on their leadership experience, not their coding experience.

MaryGracy Antony, an incoming SFSU Biology Master’s student was one of the team leaders – she had no coding experience at the beginning of the summer. Here is an image from one her zoom meetings. I asked MaryGracy how it went for her and she said: “I let my team know on the first day that I, like them, have no experience with Python and we will be helping each other out throughout our time in SCIP. It definitely worked. […] As the weeks went by, people who were further in the course were helping others and even me. It was a very fulfilling experience 🙂

Each team met 4 times a week for 2 hours during 6 weeks (48 hours total). All meetings had a similar structure with time to talk and time to work quietly. The “I” in SCIP stands for immersion, which means that the learning is done during the zoom meetings. We discourage working on the materials outside of the zoom meetings, to avoid getting stuck on a coding problem with no help nearby. If the teams got stuck, they could ask questions on the Slack forum, which was monitored by the SCIP admin team.

Once a week we held a webinar for one hour, with speakers who use coding in biology, chemistry or biochemistry. This year, we hosted a teacher, a PhD student, someone who worked in the biotech industry and many others. Many of our guests were SFSU and PINC alums.


One of the main goals for SCIP is to allow participants to learn coding skills in a non-threatening, ungraded environment. We think we are succeeding in this for most participants, but to make sure our environment is as non-threatening as possible, we don’t test their coding knowledge and we don’t keep track of attendance. Still, there are several indicators that show that participants are learning and finding a community in SCIP. First, 97% participants would recommend SCIP to others. Second, self-reported coding confidence goes up a lot. Third, almost 90% of participants expect that coding will be part of their future career – that is huge, given that most of our participants had no prior coding experience.

New materials received very well

Participants in SCIP all learn from freely available online coding classes that we pick out for them. While these coding classes from Udacity and EdX work quite well, there are also some issues with these classes. They are not made for science students and they are mostly taught by white men. The SCIP team therefore created new materials this year.

These new materials included a series of videos about R made by Ryan Fergusson and coding projects designed by all of the SCIP admin team members (see here More than 90% of the participants scored the new videos as a 4 or 5 (on a scale from 1 to 5) in terms of how helpful they were.  

The story behind SCIP

Last summer, in 2020, many of our bio/chem students were stuck at home, without a job or summer research experience. In the meantime, Dr Megumi Fuse, was looking for something that our research students could do during the summer, while they were funded to do research but the labs were closed. We designed a community-focused online coding program to make the most of the summer of 2020. It worked great! 160 people joined in 2020, and most of them loved it and learned new coding skills! To learn more about SCIP have a look at our website.

The people behind SCIP 2021

The most important people behind SCIP 2021 were Rochelle-Jan Reyes, Olivia Pham and Ryan Fergusson. Rochelle did most of the admin work, Olivia ran the webinar series and Ryan created videos for learning the R programming language. All three of them answered many technical questions on the Slack channel.


Funding for SCIP 2021 came from the NSF-funded Center for Cellular Construction (NSF grant DBI-1548297) and the NIH MBRS-RISE grant (#R25-GM059298). Some of the SCIP participants, especially those who had learned ImageJ spent the second half of their summer in the CCC research workshop. Many SCIP participants are now in the PINC or GOLD programs (link).

Scientist Spotlight: Berenice Chavez Rojas

28 May

Berenice Chavez Rojas graduated from SFSU in 2021 with a major in biology and a minor in computing applications. She is moving to Boston to work in a lab at Harvard’s Medical School.

Pleuni: Hi Berenice, congratulations on graduating this semester! 
I know that you are starting a job at Harvard soon. Would you mind telling me what you’ll be doing there and how you found that job? Did your coding skills help you land this job?

Berenice: I’ll be working as a research assistant in a wet lab. The model organism is C. elegans and the project will focus on apical-basal polarity in neurons and glia. I found this job on Twitter! Having a science Twitter is a great way to find research and job opportunities as well as learn new science from other scientists. While I won’t be using my computational skills as part of this job, the research experience I have been able to obtain with my coding skills did help me. 

“coding always seemed intimidating and unattainable”

Pleuni: When did you start to learn coding? 

Berenice: I started coding after I was accepted to the Big Data Summer Program two years ago [Note from Pleuni: this is now the PINC Summer Program]. This was also my first exposure to research and I’m grateful I was given this opportunity. This opportunity really changed my experience here at SFSU and it gave me many new opportunities that I don’t think I would have gotten had I not started coding. Following the Big Data Summer Program I started working in Dr. Rori Rohlfs’ computational biology lab. I also received a fellowship [] which allowed me to stop working my retail job, this gave me more time to focus on school and research. 

Pleuni: Did you always want to learn coding?

Berenice: Not at all, coding always seemed intimidating and unattainable. After my first exposure to coding, I still thought it was intimidating and I was slightly hesitant in taking CS classes. Once I started taking classes and the more I practiced everything began to make more sense. I also realized that Google and StackOverflow were great resources that I could access at any time. To this day, I still struggle and sometimes feel like I can’t make any progress on my code, but I remind myself that I’ve struggled many times before and I was able to persevere all those times. It just takes time!

The forensic genetics team at the Big Data Science Program in the summer of 2019. Berenice Chavez Rojas is in the middle.
The forensic genetics team at the Big Data Science Program in the summer of 2019. Berenice Chavez Rojas is in the middle.

“At the end of this project, I was able to see how much I had learned and accomplished”

Pleuni: You did the entire PINC program – which part did you like most? Which part was frustrating?

Berenice: My favorite part of the PINC program was working on a capstone project of our choice. At the end of this project, I was able to see how much I had learned and accomplished as part of the PINC program and it was a great, rewarding feeling. As with any project, our team goals changed as we made progress and as we faced new obstacles in our code. Despite taking many redirections, we made great progress and learned so much about coding, working in teams, time management, and writing scientific proposals/reports.

Link to a short video Berenice made about her capstone project:

Pleuni: Sometimes it looks like coding is something for only some kinds of people. There are a lot of stereotypes associated with coding. How do you feel about that? 

Berenice: I think computer science is seen as a male-dominated field and this makes it a lot more intimidating and may even push people away. The PINC program does a great job of creating a welcoming and accepting environment for everyone. As a minority myself, this type of environment made me feel safe and I felt like I actually belonged to a community. Programs like PINC that strive to get more students into coding are a great way to encourage students that might be nervous about taking CS classes due to stereotypes associated with such classes. 

“talking to classmates […] was really helpful”

Pleuni: Do you have any tips for students who are just starting out?

Berenice: You can do it! It is challenging to learn how to code and at times you will want to give up but you can absolutely do it. The PINC instructors and your classmates are always willing to help you. I found that talking to classmates and making a Slack channel where we could all communicate was really helpful. We would post any questions we had and anyone could help out and often times more than a few people had the same question. Since this past year was online, we would meet over Zoom if we were having trouble with homework and go over code together. Online resources such as W3Schools, YouTube tutorials and GeeksforGeeks helped me so much. Lastly, don’t bring yourself down when you’re struggling. You’ve come so far; you can and will accomplish many great things!

Pleuni: What’s your dog’s name and will it come with you to Boston?

Berenice: His name is Bowie and he’ll be staying with my family here in California. 

Pleuni: Final question. Python or R?

Berenice: I like Python, mostly because it’s the one I use the most. 

Pleuni: Thank you, Berenice! Please stay in touch!

SFSU bio and chem Master’s students do machine learning and scicomm

20 May

This semester (spring 2021) I taught a new class together with my colleagues Dax Ovid and Rori Rohlfs: Exploratory Data Science for Scientists. This class is part of our new GOLD program through which Master’s students can earn a certificate in Data Science for Biology and Chemistry (link). We were happily surprised when 38 students signed up for the class! 

In the last few weeks of the class I taught some machine learning and as their final project, students had to find their own images to do image classification with a convolutional neural network. Then they had to communicate their science to a wide audience through blog, video or twitter. Here are the results! I am very proud 🙂

If you are interested in the materials we used, let me know.


Two teams made videos about their final project: 

Anjum Gujral, Jan Mikhale Cajulao, Carlos Guzman and Cillian Variot classified flowers and trees. 

Ryan Acbay, Xavier Plasencia, Ramon Rodriguez and Amanda Verzosa looked at Asian and African elephants. 


Three teams decided to use Twitter to share their results. 

Jacob Gorneau, Pooneh Kalhori, Ariana Nagainis, Natassja Punak and Rachel Quock looked at male and female moths. 

Joshua Vargas Luna, Tatiana Marrone, Roberto (Jose) Rodrigues and Ale (Patricia) Castruita and Dacia Flores classified sand dollars. 

Jessica Magana, Casey Mitchell and Zachary Pope found cats and dogs. 


Finally, four teams wrote blogs about their projects

Adrian Barrera-Velasquez, Rudolph Cheong, Huy Do and Joel Martinez studied bagels and donuts. 

Jeremiah Ets-Hokin, Carmen Le, Saul Gamboa Peinada and Rebecca Salcedo were excited about dogs! 

Teagan Bullock, Joaquin Magana, Austin Sanchez and Michael Ward worked with memes. 

Musette Caldera, Lorenzo Mena and Ana Rodriguez Vega classified trees and flowers.

This week I learned about ME/CFS

12 Nov

This week I learned about ME/CFS when I sent a 2-line email to my PhD advisor Joachim Hermisson. Me: “Hope you & your family are well. Could you send me your recent Nature Reviews Genetics paper?” His reply came quick: “Sure, paper attached. We are not well. One of my daughters is very sick.”

In a few more back and forth emails, I learned that his daughter has very severe ME/CFS (myalgic encephalomyelitis/chronic fatigue syndrome). She is so sick that she is in bed in a dark room 24hours a day. She is a teenager.

Let me repeat that. This 18-year old girl is bedridden in a dark room for 24 hours a day.

When I last saw Joachim’s family in 2017 in Berkeley, she and her twin sister were healthy teenagers adjusting to school abroad.

It is thought that 20 million people worldwide have ME/CFS. It’s a chronic disease and there is no cure. Symptoms include extreme fatigue, post-exertional malaise (which means doing anything makes you more tired), severe headaches and light and sound sensitivity.

It’s thought that
20 million people have ME/CFS

Okay, you may think. Many diseases are bad. It’s always horrible when a young person gets so sick. But hey, we can’t do much about it.

But here’s the thing. According to CDC, this disease, while not exactly rare (probably 2 million people in the US and 2 million in Europe have it), is not even taught in most medical schools.

Also, ME/CFS gets almost no funding! This chart shows that almost all diseases get more research money than ME/CFS, despite its enormous impact in terms of lost “disability-adjusted life years”.

The funding situation for ME/CFS in Europe is probably worse, but nobody has the numbers.

If researchers have no money to work on this disease, no wonder that there is no diagnostic test and no FDA-approved medication.

Plus, ME/CFS is likely to get much more common with every COVID-19 wave because it is often triggered by a viral infection. Here is an article about the link between Covid-19 and ME/CFS.

After reading just a few things about ME/CFS I could see how difficult it must be to live with (or see a loved one live with) such a crippling disease that’s not even taken seriously by medical schools or funding agencies. So I asked Joachim “Is there anything I can do?” His answer was “Being informed is most important.” Later he added: “People can donate money or sign the EU petition”. Here’s a short list of action items:

4 things you can do to support people with ME/CFS

  1. First, you can read about ME/CFS. This interview has a lot of info and also tells the story of an impressive young woman (Evelien van den Brink) who petitioned the EU to spend more on ME/CFS research.

    Here you can see or read the speech Evelien van den Brink gave in the EU parliament (her speech starts at 2’10’’).
  2. Second, if you are an EU citizen, you can sign this petition to ask the EU to spend more money on ME/CFS research.
  3. Third, you can donate money for research here: or here
  4. Finally, please share this information so that more people will know about ME/CFS. 

Thanks for reading this thread / blogpost!

Note: I am sharing this story with Joachim’s permission.