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! 

sfsu

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!

Paper on sweeps in HIV in PLoS Genetics

24 Jan

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

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Interview published on The Molecular Ecologist

21 Jan

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).

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Gordon Research Seminar Microbial Population Biology 2015 approved

18 Nov

Update (Dec 19th 2013): just got news that “The Microbial Population Biology Gordon Research Seminar (GRS) has been scheduled to take place July 18-19, 2015 at Proctor Academy, Andover, NH. The Microbial Population Biology GRC will take place July 19-24, 2015 at the same location.” 

Many Gordon Research Conferences now start with a Gordon Research Seminar. The GRSeminar is a smaller meeting only for the graduate students and postdocs who will attend the GRConference. Last summer I went to the Microbial Population Biology GRConference and the GRSeminar that occurred before it.

I thought the GRSeminar was a really nice way to start the week, because there were fewer people and no famous professors (except two invited speakers) so the graduate students and postdocs could focus on getting to know each other. Although the GRSeminar only lasted for about 24 hours, I still think it had a very positive effect on the rest of the week.

At the end of the GRConference I was asked to be the chair of the next GRSeminar on Microbial Population Biology that will accompany the GRConference on the same topic in 2015. Three people offered to help me with organizing the next GRSeminar (Krishna Swamy, Elizabeth Jerison and Helena Mendes-Soares) so we’ll be working as a team. Michael Travisano is the chair of the 2015 GRConference. Last week we heard that the GRC organization approved our request to have another GRSeminar, so I’ll be traveling to LA in January to learn all I need to know to be a good GRSeminar chair.

Editorial published in Journal of Infectious Disease

2 Nov

An editorial I wrote with Bob Shafer and Susan Holmes (both Stanford) got published this week in Journal of Infectious Disease. See here.

The editorial is about a recent paper by Joel Wertheim and colleagues who analyze 80,000 HIV sequences to characterize the worldwide HIV epidemic.

I wrote a blog post about it here.

A short review on F1000 said: “This is an editorial commentary that provides an excellent summary of the use and limitations of HIV viral phylogenetics to understand transmission and sexual networks.”

Paper on sweeps in HIV accepted by PLoS Genetics

29 Oct

Last week, we got news that our paper on “Loss and recovery of genetic variation in adapting HIV populations” is accepted for publication in PLoS Genetics! My coauthors on this paper are Sergey Kryazhimskiy and John Wakeley. You can find an earlier version of the paper on the arXiv, and a related blog post on Haldane’s Sieve.

In a nutshell, this is what the paper is about: we analyze longitudinal data on 30 patients in which the virus evolves to become drug resistant. We see that

1. known resistance mutations mostly fix one at a time,

2. these fixations are associated with a reduction in genetic diversity due to hitchhiking,

3. the fixations involve both soft and hard sweeps (see pictures), and

4. recovery of genetic diversity is slow for synonymous sites and faster for non-synonymous sites.

Soft selective sweep in HIV. The K103N substitution is caused by an A to T or A to C mutation. In this patient both alleles are present. A clear example of a "multiple-origin soft sweep".

Soft selective sweep in HIV. The K103N substitution is caused by an A to T or A to C mutation. In this patient both alleles are present. A clear example of a “multiple-origin soft sweep”.

Selective sweep in HIV. An NNRTI drug resistance mutation (K103N) goes to fixation in patient virus. The mutation (A to T) apparently occurred on one haplotype (genetic background) and as it went to fixation, genetic variation on was lost. Not all sweeps in HIV are hard sweeps, see next figure.

Selective sweep in HIV. An NNRTI drug resistance mutation (K103N) goes to fixation in patient virus. The mutation (A to T) apparently occurred on one haplotype (genetic background) and as it went to fixation, genetic variation on was lost.

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