Archive | August, 2016

The acknowledgement section of our NSF proposal

25 Aug

A few weeks ago two colleagues and I submitted an NSF proposal. We submitted on a Friday afternoon even though the deadline wasn’t until Tuesday! I am proud that we managed this almost without any deadline stress!

I had fun and we wrote a great proposal

I know that we may not end up getting funded by NSF, but until we get that message, I plan to be very optimistic. We wrote a really neat proposal for a great project. I can’t wait to get started! The ambitious goal of the project is to determine the fitness cost of every possible point mutation in the HIV genome in vivo.

I think nobody likes to write proposals when the success rate is only 5%, but I actually enjoyed working on this proposal and I learned a lot while writing it: both about the biology of our project and about the art of proposal writing. It’s important for me to commit that to paper (OK, screen) so that if NSF decides not to fund us, I will remember that writing the proposal was actually a good experience.

Writing with a newborn

In addition the many scientists and administrators who contributed to the proposal, I also want to mention how I could write a proposal with a newborn. We started working on the proposal two weeks before I gave birth and we submitted the proposal when our baby was just shy of seven weeks old. The hours that I spent on the proposal were made possible by my mom who flew in to help and by the fact that Facebook gives new parents four months paid paternity leave so that my husband was also at home during my maternity leave. It was fun to be home together with my husband and we took shifts working and taking care of Maya. Most days I worked on the proposal just two or three hours, so a large part of the work was done by others.


Me in my home office with baby, changing table, a laptop and a grant writing handbook.

It was a huge team effort

Many people were involved in writing the proposal. Many more than I ever expected to be. I want to list them here so that I remember who helped out and also to show that being a researcher doesn’t have to be a lonely affair.

Note that these people are only the people I am aware off. Others certainly helped my co-PI Adi Stern.

The main team that wrote the proposal consisted of four people:

  • co-PI Adi Stern (Tel Aviv)
  • postdoc Marion Hartl (SFSU)
  • professional grant writer Kristin Harper
  • myself

At SFSU, people from the Office for Research and Sponsored Programs helped:

  • Rowena Manalo
  • Raman Paul
  • Michael Scott
  • Jessica Mankus
  • Uschi Simonis (vice-dean for Research)

At Stanford there were

  • co-PI Bob Shafer
  • collaborator David Katzenstein
  • Elizabeth White (Katzenstein lab)
  • Holly Osborne (Office for Sponsored Research)

In Tel Aviv

  • Office for Sponsored Research
  • Adi Stern’s lab members brainstormed ideas
  • Maoz Gelbart help with ideas and figures

Colleagues who read earlier versions of the proposal

  • Sarah Cobey (U Chicago)
  • Sarah Cohen (SFSU)
  • Alison Feder (Stanford)
  • Nandita Garud (UCSF)
  • Arbel Harpak (Stanford)
  • Joachim Hermisson (U Vienna)
  • Claus Wilke (U Texas Austin)

A huge thank you to all these amazing people! I am lucky to be part of such a supportive community.


Is it a soft sweep or a hard sweep?

14 Aug

2016-08-14 11.49.34

As the summer and my maternity leave come to an end, I am starting to think about what I will do in the fall semester. One thing that is on my to do list is to write a review paper on soft sweeps together with Joachim Hermisson, who is spending the year at UC Berkeley. Joachim and I wrote three papers on soft sweeps ten years ago (H&P 2005, P&H 2006a and 2006b) and it’ll be fun to work together again.

One of the reasons that we are planning to write such a review paper is that in the last couple of years, some controversy has arisen surrounding soft sweeps. Put very simply, some people think that soft sweeps are ubiquitous and others think that they are nonsense.

Dmitri Petrov is a strong proponent of the view that soft sweeps are very common (Garud et al 2015, Messer and Petrov 2013). Jeffrey Jensen is probably the strongest critic of the concept of soft sweeps as evidenced by his paper entitled “On the unfounded enthusiasm for soft selective sweeps.” (Jensen 2014).

I look forward to writing a paper that makes the “It’s complicated” in the flowchart I made less complicated!


Garud, N. R., Messer, P. W., Buzbas, E. O., Petrov, D. A., Fay, J., Wyckoff, G., … Stephan, W. (2015). Recent Selective Sweeps in North American Drosophila melanogaster Show Signatures of Soft Sweeps. PLOS Genetics, 11(2), e1005004. doi:10.1371/journal.pgen.1005004

Hermisson, J., & Pennings, P. S. (2005). Soft sweeps: Molecular population genetics of adaptation from standing genetic variation. Genetics, 169(4), 2335–2352. doi:10.1534/genetics.104.036947

Jensen, J. D., (2014). On the unfounded enthusiasm for soft selective sweeps. Nature Communications, 5, 5281. doi:10.1038/ncomms6281

Messer, P. W., & Petrov, D. A. (2013). Population genomics of rapid adaptation by soft selective sweeps. Trends in Ecology & Evolution, 28(11), 659–669.

Pennings, P. S., & Hermisson, J. (2006a). Soft sweeps II-molecular population genetics of adaptation from recurrent mutation or migration. Molecular Biology and Evolution, 23(5), 1076–1084. doi:10.1093/molbev/msj117

Pennings, P. S., & Hermisson, J. (2006b). Soft sweeps III: The signature of positive selection from recurrent mutation. Plos Genetics, 2(12), 1998–2012. doi:10.1371/journal.pgen.0020186