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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…

View original post 327 more words

Meet Hailey Garma, SFSU and PINC Alum and Scientific Researcher in Genentech’s Development Sciences Rotation Program (DSRP)

14 Oct

My biggest advice when pursuing an internship, career, degree, etc. is to be your authentic self, know you are good enough, and do what is best for your growth.

How did you decide to get a degree in biology? What interested you in making this choice?

My interest in science stems from wanting to understand how the human body works in order to have a better knowledge when understanding medical conditions my loved ones suffer from. When I was a child, my father had a stroke — my family’s frustrations from not fully understanding how my father was affected by this incident and the doctors not having all of the answers is what initially piqued my interest in studying science, I wanted to be able to understand and answer those questions.

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

Initially, I thought I wanted to pursue a career in medicine or healthcare; this seemed like the most obvious choice to use my biology degree to help others, more than just my loved ones. However, throughout my college experiences, I realized that I love benchwork, research, and working to answer biological questions. I am interested in a career in Biotech because I find this industry a perfect mesh between day-to-day scientific research and that research being directly related to drug development and impacting the advancement of medicine to help people.

The more I talk to others in this industry, the more I realize that my career journey does not have to be a linear path.

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

I don’t know. I used to have a set plan. Originally, my goal was to pursue a PhD in neuroscience, in honor of my dad, and then a permanent career in biotech. The further I get in my career, the more possibilities I discover. The more I talk to others in this industry, the more I realize that my career journey does not have to be a linear path.

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

Working in Biotech is a great opportunity to discover the potential for scientific research, how your work can impact the world and others, and what kind of research suits you based on your passions or interests, even if this results in a career shift to healthcare or academia. With the enthusiastic and collaborative community in this industry, there is the opportunity to be exposed to a wide variety of research projects and disease areas, whether you are participating in the project, attending seminars, or networking with other scientists. 

Can you tell us something interesting about yourself?

I debated between pursuing a degree in biology or in art. Those are my two greatest interests. Although I did not pursue an artistic degree or career, I still paint, take classes, go to museums, and indulge in it as much as I do with biology in my career now. Having a passion for science and research is important when pursuing a career in this field, but it definitely does not have to be your only interest!

Regarding the SFSU PINC program, are there coding classes you took for your current position? 

The coding classes I took in college for the PINC program do not directly relate to the current work I am doing now. However, because I have that coding background, there are more opportunities for me to integrate myself and my projects in the informatics space. 

How did you find the job at Genentech? Where did you find the announcement, what materials did you have to send, who helped you, how did the interview go. 

In a SFSU science newsletter, I found an announcement for Genentech’s Campus Engagement Day event in fall 2019. After attending this networking event, I searched for summer internships at Genentech through During this search for an internship, I stumbled across an application for DSRP, my current position. 

My biggest advice when seeking these types of opportunities is to always keep your eyes open, even if you are […] not exactly sure what you are looking for. My current position is what I was always searching for, without even knowing that a program like DSRP existed. When applying for this position, I was not entirely confident in what I was doing or how to apply, but I was confident in myself. My biggest advice when pursuing an internship, career, degree, etc. is to be your authentic self, know you are good enough, and do what is best for your growth. Keeping these key things in mind, I feel, is what made me successful during the interview process. 

Meet Faye Orcales – Genentech intern, PINC alum and CSC 508 Mentor.

21 Sep

Pleuni: Faye Orcales is a recent SFSU alum and I am lucky enough to be working with her this year thanks to an NSF supplement for post-bacc students. She is also a PINC alum and PINC mentor (for my class CSC 508: Machine Learning and Data Science for Personalized Medicine). This past summer, Faye was an intern at Genentech. We asked her to write about her experience!

My name is Faye and I’m a recent graduate from San Francisco State University. I obtained a bachelor’s degree in Cell and Molecular Biology with a minor in Computing Applications from the PINC Program.

I’m currently working under Daniel Le as a bioinformatics intern for Genentech’s Next Generation Sequencing Department.

Faye worked with Daniel Le at Genentech in the summer of 2021 (

In my junior year I got introduced to coding when I had to take a mandatory elective course. At first, I didn’t think I would like the subject. In contrast I found out that I had a genuine interest in coding, and mentioned it to a counselor. They told me about the PINC Program at SFSU, which is a coding program offered primarily to students majoring in biology, chemistry, or biochemistry. My interests aligned with the program, so I spent my last two years of university taking coding classes along with my regular biology courses.

I first obtained research and informatics experience under PINC’s Summer Program in 2020, where I worked with Dr. Rori Rohlfs and a group of other students. I went on to do more research with Dr. Pleuni Pennings in the CoDE Lab where I utilized machine learning to study impacts on fitness cost in Hepatitis C.

“I’ve known about Genentech ever since I was in middle school”

In senior year my PINC Program Director Dr. Nina Hosmane informed me about Genentech’s Summer Internship Program. I’ve known about Genentech ever since I was in middle school, so I’ve seen the scientific innovations that Genentech has built throughout the years. I decided to challenge myself and apply to the internship because I wanted to strengthen my coding skills and see what industry standard research looks like.

I was able to obtain the internship with much support from my connections in the PINC Program. They took the time to help me strengthen my resume and provide me interview resources. I highly recommend to anyone interested in applying to Genentech, or somewhere similar, to have their trusted peers or professors give them lots of feedback on their application materials.

My work ethic and inspiration to pursue higher learning came from my parents. My family came to the United States as immigrants when I was very young. I’ve seen my mom stay up long nights studying and my dad juggle three jobs all while raising two kids. My parents’ hard work allowed our family to survive in a new country, and taught me the importance of education and perseverance.  

“My scientific inspirations came from my middle school science teachers.”

My scientific inspirations came from my middle school science teachers. They were all women of color, so their representation had a big impact on me. Every lab I did in their classes were memorable. Their passion for science influenced my current curiosity for life and the universe.

In the future I would like to become a physician-scientist. At first, I only wanted to become a doctor. After my experience in the PINC Program and Genentech, I realized that I still wanted to continue doing research as a career. To have the best of both worlds, I hope to one day get accepted into an MD-PhD program to fulfill my biggest career goal.

Outside of research and science, I’m a big fan of food. Whenever I can, I love trying out new restaurants with friends. Luckily, I live in the bay area which is rich in cultural diversity.

The PINC Summer Program 2021 got 30 Bio/Chem Students into Coding and Research at the Same Time!

13 Sep

by Dr. Pleuni Pennings

One of our students said it best: 

“PSP led me through my first research project and allowed me to present on the summer project. PSP has given me confidence in my ability to do scientific research and analyze the results of the research. Most importantly, I had the opportunity to improve my public speaking through our research symposium at the end of the program.”

What is the PINC Summer Program? 

The PINC Summer Program is a part-time program where students work in teams with a peer-mentor. They learn coding skills as well as work on a research project with their mentor and a faculty advisor. At the end of the 9-week program, the teams give a talk about their work at a research symposium. 

We have run a similar program since 2017 and written about it here. Most importantly: (1) The program is part-time on purpose to allow students to join who have other obligations, like jobs and families; (2) the students work in teams and all work takes place during team meetings – this way there is always a friendly person nearby (on zoom these days) when you are stuck; and (3) the coding skills they learn are applied to biology or chemistry research immediately.   

Who participated in the 2021 PINC summer program? 

Many people are involved in the PINC Summer Program. 

First of all, there are about 30 student participants, more about them in the next paragraph. The 30 students were organized in 6 teams. Each team had a peer mentor and a faculty advisor. The peer mentors were Angela Lane (grad student and CC lecturer), Carmen Gonzalez, Elissa Vazquez, Liz Mathiasen, Jason Hernandez and Patra Holmes (all PINC students and GenPINC scholars). The faculty advisors this year were Drs Gretchen Lebuhn, Jaime Chavez, Rori Rohlfs, Jessica Weng, Nicole Adelstein and Derrick Groom. 

In addition to those groups, the staff consisted of Torey Jacques (mentor trainer), Dr Sophie Archambeault (weekly workshop organizer), Rochelle-Jan Reyes (all-around organizer). Pleuni Pennings, Nicole Adelstein and Rori Rohlfs were responsible for the entire program. 

More about the students

The PINC Summer Program reaches a diverse group of students, in terms of ethnicity, gender and majors (see image). 

In terms of prior experience, 6 students had prior research experience, while 24 didn’t. 5 students had previously taken a coding class at SFSU while 25 didn’t. The 5 students who had coding experience were all part of the PINC program. We placed them all in the same team. Out of the 25 students with no coding experience, 9 signed up for CSC 306 (intro to python) in the fall of 2021. 

How did it go?

Overall, the program worked well this summer, with a few hiccups. In one team, several students had to leave the program midway for personal reasons. We recruited one new student from another program (SCIP) to join the team that had gotten a little small. 

At the end of the summer all teams did a presentation in our end-of-summer research symposium. It was really fun to hear the students talk about their research! Almost all students spoke for at least a few minutes. 

Most students who did the post-program survey are expecting to use coding in their career. 

We got answers such as “I want to pursue a career in medicinal research, and I envision using my coding skills to analyze and communicate my research with other scientists who share my interest in study.” However, a few students didn’t see it this way: “No I don’t because programming is a little too hard for me. I don’t see myself doing it seriously but for fun and for educational purposes, yes.”

Here are a few other interesting quotes from the post-program survey: 

“PSP has really showed me how fun research and science can be if you’re in a group with people you get along with.”

“I think it was helpful because we were a small group with our mentor and advisor which made it more “relaxing”. We could easily ask questions, and reach to each other. It was a nice dynamic overall.”

“Relentlessly positive, but slightly chaotic”

What’s next?

During the program, we held a lab matchmaking event in order to help students meet faculty and see if their interests align with faculty labs from SFSU and UC Berkeley. At the end of the summer, several students joined a lab. Secondly, several signed up for a coding class. Some felt like they were too busy during the fall to do either coding or research. For a few students, we don’t know what their plans are. 


The PINC Summer Program 2021 was paid for by a grant from the Genentech Foundation (PI Dr Frank Bayliss). The budget was $60,000 (roughly $9,000 for support staff, $6000 for the directors, $17000 for the mentors and $22,000 for the faculty advisors). 

How learning to code is like learning to drive a car

31 Aug

Written by Pleuni Pennings

I was in my late thirties when I learned to drive a car. I grew up in The Netherlands, in an area with excellent bike and train infrastructure and I never felt the need to learn how to drive a car. Also, I didn’t want to spend money or time on learning to drive a car. But when I finally learned to drive a car, it turned out to be very useful! It gave me independence, and it gave me options I didn’t have before.

Recently, I added to my skillset. Two weeks ago, for the first time in my life, I drove a car over significant distances in The Netherlands. I thought driving in The Netherlands was scary – but when I finally did it, it wasn’t as scary as I thought!

Now, am I the best driver in The Netherlands? Surely not!
But it’s real nice to be able to borrow my dad’s car to visit my cousin who runs a lego workshop to rent some legos. It gives me independence. And it makes my son happy too (see picture below).

If you are learning to code, you should consider your coding journey as a journey towards independence. After one semester or one summer of coding, you are not a star coder (sorry to break it to you 😉 ). But you have started! You have learned new things. You have learned new jargon and new tools. And maybe you can now analyze a small dataset by yourself. Or you know enough about coding to be able to ask for help in a smarter way. And next semester or next summer, or when you have time, you will learn more. And one day you’ll be able to drive a car in The Netherlands!

4 ways learning to drive a car is like learning to code

  1. It gives you independence. Before I always had to ask my mom or my husband to drive if I needed to use a car, now I can do it myself. For coding tasks, you may depend on a lab mate or software like SPSS or SAS, but it’s just nicer if you can do it yourself.
  2. It is not about being the best driver or the best coder. I can drive, but I will never be the best driver in any group of people. But who cares? I get from A to B safely and that’s what matters. For coding, it’s the same thing. If you want to use coding in your studies or work, you don’t need to be the best coder. You just need to get from A to B (or from raw data to a nice plot).
  3. Practice is key. When I first got my license, I didn’t have access to a car and I didn’t drive for a few years. Clearly, that was not very good for my driving skills or confidence. Later, when I did have a car available, I would regularly take it to drive to a friend who lived just 5 miles away to have a coffee. These short trips helped me feel comfortable in the car. If you’ve learned some coding skills, try to find a way to keep using it, even if it is just for short 5-mile drives.
  4. It opens up jobs and opportunities. For many jobs, you need to be able to drive a car. Not just jobs such as taxi driver, but also jobs that are utterly unrelated to driving. For me, I got the job at SFSU when I lived in Menlo Park. Public transport from Menlo Park to SFSU is so bad, that I really couldn’t do the job if I wasn’t able to drive to the SFSU campus. With coding it can be the same thing. I am a biologist and I am interested in evolution of viruses and bacteria – yet I couldn’t do that research without coding skills.

Happy coding!