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)
If you’re interested to know what the paper is about, check out the video abstract:
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 MelodyLoops.com.
Selective sweeps in HIV from Pleuni Pennings on Vimeo.
I submitted the video to the Nescent Evolution Video Contest 2014.
The video is an abstract for this paper: 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
The data are on Figshare: figshare.com/articles/LossAndRecoveryHIV/703928
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!
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
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 that Martin Sikora blogged about.
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.
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!
The paper I wrote with Sergey Kryazhimskiy and John Wakeley (both at Harvard) came out this week in PLoS Genetics. In the paper we describe how genetic diversity is lost and recovered in HIV populations that evolve and become drug resistant. This was possible because of a dataset that was collected in the late 1990s. This dataset is unique because it has multiple sequences of the protease and reverse transcriptase regions at multiple time points for many patients. We found evidence for soft and hard sweeps.
Meredith Carpenter (Stanford) wrote a very nice blog post about the paper.
Download the paper with the supplementary materials here: 2014PennKryWakeleyPGeneticsWSupplMat
The Molecular Ecologist is a blog written by a group of authors and linked to the journals Molecular Ecology and Molecular Ecology Resources.
Today The Molecular Ecologist published an interview with me. I am honored to be only the fourth person featured in their “People behind the science” series, after Loren Riesenberg (editor in chief for Molecular Ecology), Ruth Shaw (editor in chief for Evolution) and Richard Lenski. The interview series is the work of John Stanton-Geddes (his website is worth a look, especially if you like open science).
