Archive | January, 2018

Summer opportunities for undergraduate students at SFSU

3 Jan

REU programs (paid research for undergrads during the summer)

The National Science Foundation funds a large number of research opportunities for undergraduate students through its REU Sites program. An REU Site consists of a group of around ten undergraduates who work in the research programs of the host institution. The programs usually provide travel money, room and board and some stipend. There is also an REU program at SFSU, but most spots in this program go to non-SFSU students.

The deadlines for these summer programs are early February to early March.

MARC program / SEO office fellowships (paid research for undergrads during the summer and academic year)

Science students at SFSU can apply for fellowships through the SEO office. The MARC fellowship description says:
“Purpose: To prepare students from underrepresented groups (African-American, Native American, Hispanic American and Pacific Islanders) and students with disabilities for biomedical careers by providing academic support and a stimulating research experience. The goal of the program is to prepare each participant for entrance into a competitive graduate program and successful completion of a PhD in the biomedical or physical sciences.”

A MARC fellowship provides mentoring, research experience and financial support ($12,588/year and partial tuition for the junior and senior years). If you are unsure if you are eligible, consider applying nevertheless!

Deadline: March 16th!

PINC summer program (not paid, coding and research)

The exact form of the 2018 PINC summer program is not yet clear. In 2017, 15 undergraduate students were part of the program, and together with 4 graduate students, they learned coding skills in R or python, they read research papers and they performed a small research project. The students spent 8 hours per week on the program for 9 weeks. In terms of coding skills, some students were absolute beginners, whereas others had taken a CS class before.

We will open op the program for applications in April of 2018.

Research (mostly volunteer, possibly for credit / paid)

If you are interested in getting research experience during the summer, you can see if any professor is looking for students to join their lab in the summer. Start with the professors you know or whose research you are particularly interested in. Some professors post opportunities on posters in the hallways of Hensill Hall, but many don’t and so you will just need to go and ask – by email or in person during their office hours. Almost everyone on this list does research and gets help from volunteer undergraduate students. Some students get credit for doing research (fairly common) and some get paid (not so common, but not impossible).

In the biology newsletter that you get by email every week, there are often opportunities posted, for example from labs at UCSF. If you are looking for a volunteer or paid research opportunity, make sure you read the newsletter!

Letters of recommendation

Many times you need a letter of recommendation from a professor when you apply for a fellowship or other opportunity. For us, professors, writing such letters is part of our job. Some professors only write letters for students they know well (for example, because they come to office hours often or because they volunteer in the lab of the professor). Other professors are happy to write a letter for anyone who has taken their class (that’s me!). Either way, don’t be afraid to ask! The worst that can happen is that they say no.
If a professor has agreed to write a letter for you, make sure that you email them all the materials that you also use to apply to the opportunity (e.g., unofficial transcript, essay, resume). Having those materials at hand makes it much easier for us to write a good letter! Plus, if you send them early enough, you may get some useful feedback. Once a professor has written one letter for you, they are usually happy to send that letter to as many programs as necessary. So if you want to apply to 20 different REU sites, go ahead! Our letter can go to all of these places, and really, we don’t mind. It’s our job.


Students in the 2017 PINC summer program.


New plans and new HIV stories

3 Jan

I love making plans and I love the beginning of the new year and the new semester. I actually think that the yearly rhythm of semesters and breaks is a huge benefit of being in academia.

Today I spent some time thinking about the writing I plan to do in the coming semester and the talks I will be giving in the near future. The first talk that’s coming up is an invited talk at Stanford. I am very honored to be an invited speaker at the CEHG symposium alongside Anne Stone (ASU) and Graham Coop (UC Davis). I want to try and use the opportunity of the talk to think about what stories I want to tell and I plan to write the story up for publication in addition to talking about it at Stanford.

So what are the stories I want to tell? There are many! But here are some thoughts:

“The evolution of HIV evolution.”

Recently I’ve given seminars in which the overarching storyline was “The evolution of HIV evolution.” I focused on the evolution of drug resistance within patients and explained how drug resistance evolution used to be very fast, but became slower over time. When people were treated with a single drug (AZT) in the late 80s and early 90s, the virus would evolve drug resistance very quickly and the treatment would quickly become useless. Freddy Mercury probably died because of a very fast evolving virus. Over time, treatments improved (using combinations of drugs and using better drugs) such that it became harder for the virus to evolve and nowadays, drug resistance evolution is so slow in patients on treatment, that it is no longer a big worry, and people can stay on the same drugs for many years.

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A slide from a talk I gave at SMBE and ESEB in the summer of 2017.

“HIV does it all”

Here is another storyline. Any field in science needs some systems that are looked at in detail. In evolutionary genetics, these systems are fruitflies, yeast, humans, mice etc. HIV is a great system as well in part because we know so much about it and data is abundant. One of the things we have learned in recent years, thanks to work by people like Richard Neher and Kathryna Lythgoe, is that HIV evolution can surprise us again and again. For example, HIV evolution, even in absence of drugs, can be fast within patients and slow at the epidemic level. It can be happening with a lot of recombination, or showing clonal interference (unpublished, Kadie-Ann Williams and PSP), and sweeps can be hard or soft. Within host populations can be panmictic or structured. So if everything can happen, how can we make sense of this all?

“Drugs to prevent HIV”

I like the story of how drugs were and are used to prevent HIV infection. In the 90s and well into the 2000s, drugs were used to prevent mother-to-child-transmission of the virus during child birth. In fact, this was one of the big successes in the world of HIV before treatment was really working to keep infected people alive. Nowadays, drugs are available for HIV-negative people who are at increased risk of HIV infection. Pre-exposure-prophylaxis (Prep, marketed as Truvada) is probably contributing to the shrinking of the HIV epidemic in San Francisco as many of the HIV-negative gay men in the city are taking Prep. When drugs were used to save babies, they were uncontroversial, but when they are used to save gay men, they continue to be controversial and there are many places where Prep is not available (for example, in my home country, The Netherlands).

How is this story linked to evolutionary genetics? When someone is taking drugs to prevent HIV, but they end up getting infected anyways, there may be a high risk of drug resistance evolution (this happened in the babies, in their already infected mothers, and it is happening occasionally in Prep users). Also, at an epidemic level, if a large part of the population is on Prep, this may lead to sub-epidemics of drug-resistant viral strains. There is some interesting modeling work by Sally Blower on these questions.


OK, that’s enough brainstorming for today. I’ll develop one of these stories into a presentation for CEHG and for an article to be published somewhere. If you have any questions or suggestions, let me know!