Paper on imperfect drug penetration and drug resistance out in PNAS

18 May

I am very excited to announce that our paper entitled: “Imperfect drug penetration leads to spatial monotherapy and rapid evolution of multidrug resistance” is out in PNAS.

Stefany Moreno-Gamez and Alison Hill are co-first authors on this paper. Both of them have contributed to every aspect of the paper.

Daniel Rosenbloom, Dmitri Petrov and Martin Nowak are the other co-authors on the paper.

Two-minute movie explains the main point of the paper

I made a short movie (2.5 minutes) to explain the main point of the paper:

Press info

A press release was posted on EurekAlert.

If you are interested to report on our paper, feel free to get in touch with one of the authors. Pleuni Pennings, Stefany Moreno and Daniel Rosenbloom are most available this week.

Pleuni Pennings is based in San Francisco (Pacific Time Zone, UTC-08:00).

My email address is

Phone number: +1 617 417 7311

Stefany Moreno-Gamez is based in Groningen, The Netherlands (Central European Time Zone, UTC+01:00)

Email address:

Daniel Rosenbloom is based in New York City (Eastern Time Zone, UTC-05:00)

Email address:

The story behind the paper

I wrote a blog post for Haldane’s Sieve about how we started the collaboration that let to the paper. Here is the link.

Paper on sweeps in HIV wins honorable mention Omenn prize

19 Mar

The Gilbert S. Omenn Prize is awarded by the International Society for Evolution, Medicine, and Public Health for best article published each year on a topic related to evolution in the context of medicine and public health. The prize committee consisted this year of Sarah Tishkoff, Joe Alcock, Noah Rosenberg, and Alison Galvani. The real prize for 2014 went to, “Escape from bacterial iron piracy through rapid evolution of transferrin” by Matthew Barber and Nels Elde from the University of Utah. But my paper together with John Wakeley and Sergey Kryazhimskiy won an honorable mention :-)

Look here for the paper and here for a 3 minute explanation of the results.

Pennings PS, Kryazhimskiy S, Wakeley J (2014) Loss and Recovery of Genetic Diversity in Adapting Populations of HIV. PLoS Genet 10(1): e1004000. doi:10.1371/journal.pgen.1004000

Paper on ant slaves accepted in Journal of Evolutionary Biology

17 Sep

In 2009 I made a trip to the USA to collect ants in New York and West Virginia to study their small scale population structure. Now, 5 years later, the paper is finally accepted for publication in the Journal of Evolutionary Biology!

The accepted version is also posted on the arXiv.

Stefan Suette, Pleuni Pennings, Susanne Foitzik, Tobias Pamminger, Andreas Mödlmeier (West Virginia 2009)

Stefan Suette, Pleuni Pennings, Susanne Foitzik, Tobias Pamminger, Andreas Mödlmeier (West Virginia 2009)

If you’re interested to know what the paper is about, check out the video abstract:

Teaching at SFSU in the fall

5 Jun

I’ll be teaching an exciting course in the fall at SFSU.



Short video about PLoS Genetics paper

3 Jun

I made a video about selective sweeps in HIV.

As always, it was a lot of fun to make the movie and it took much more time than I planned.

I used two apps to make the video, iMotionHD on my iPhone and iMotion remote, on a second iPhone. For editing and adding the voiceover I used iMovie and a simple headset with microphone. I bought music from

Selective sweeps in HIV from Pleuni Pennings on Vimeo.


Accepted assistant professorship at SFSU!

11 Apr

I have just signed the offer letter from San Francisco State University! The start date is not yet clear, but either in the fall or next spring, I will become an assistant professor in the biology department of SFSU! So excited! 


New outreach activities

21 Mar

Regular column in Bionieuws

I was recently asked to write a regular column for the newspaper (Bionieuws) of the Dutch Biology Institute (NIBI). I wrote the first one a couple of weeks ago and it came out last weekend. I had so much fun writing in my native language! The topic of the short article is the use of antiretrovirals by HIV positive and by HIV negative people for HIV prevention.

You can download the pdf of the column here: Column_Maart_2014. If you prefer English, have a look at the translation on my blog here.

My first column in Bionieuws

My first column in Bionieuws

The CEHG “community” blog

CEHG is the Stanford Center for Computational, Evolutionary and Human Genomics. I recently became responsible for all outreach activities of CEHG. Because I strongly believe in the power of writing and the power of community, I decided to start a community blog for CEHG. The blog posts are written by CEHG graduate students and CEHG postdocs. They usually write about a paper that was written by another CEHG researcher. We have several goals with the blog. First, we encourage interactions between researchers within CEHG by asking people to write about someone else’s work. Second, the blog showcases the science that is done in CEHG to others in the CEHG community, but also to the world outside of CEHG and Stanford.

The most popular post until now is a story written by graduate student Joe Davis about “Which genetic variants determine histone marks?” Joe wrote about a series of papers that came out in Science and Nature in November 2013, one of which came from Jonathan Pritchard’s lab. About this paper, Joe says: “This paper provides clear evidence that regulatory variation has very complex impacts affecting multiple and diverse molecular phenotypes at multiple regions simultaneously. ”

The second most popular post was written by postdoc Martin Sikora, who wrote about “Demographic inference from genomic data in nonmodel insect populations.” This blog post focused on a study by graduate student Rajiv McCoy, who works on  the butterfly Euphydryas gillettii. Martin says: “For me, this study is a great example of how next-generation sequencing and sophisticated statistical modeling can open up a new world of possibilities to researchers interested in the ecology and evolution of natural populations.”

Martin’s blog also got posted on The Molecular Ecologist blog.

Gillete’s Checkerspot (Euphydryas gillettii). Photo taken by Carol Boggs, co-advisor of Rajiv and one of the senior authors of the study.

Gillete’s Checkerspot (Euphydryas gillettii). Photo taken by Carol Boggs, co-advisor of Rajiv and one of the senior authors of the study that Martin Sikora blogged about.

Workshop on Quantitative Evolutionary Biology in Turkey

I will be teaching population genetics in Turkey this summer (Sep 14-21 Şirince, İzmir). I am very excited about this workshop. The organizers Mehmet Somel, Hannes Svardal and Murat Tuğrul have already done a great job bringing together a great team of speakers and getting funding (from ESEB and NESCent). I am sure it will be a great experience! The deadline for applications (to participate and for fellowships) is April 22nd.

Nerd Nite SF

I have been invited to give a talk at Nerd Nite SF in June!

“Nerd Nite is a monthly event held in more than 75 cities across the globe during which several folks give 18-21-minute fun-yet-informative presentations across all disciplines – while the audience drinks along.” From experience, I can say that Nerd Nite is fun even if you don’t drink!


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