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





Sometimes complaining helps

24 May

Two years ago I learned about a conference at Stanford called “Big Data in Biomedicine.” I was interested to sign up, but then found out that there were 40 male speakers and 2 women: not even 5%!

OK, I must admit that I was not entirely surprised, because large parts of Stanford are very male biased. But this seemed extreme even for Stanford. So I sent an email to the organizers and later learned that several others had done the same thing.

Screen Shot 2016-05-24 at 8.31.07 PM

And? It helped. People involved in the meeting realized that there was a problem and several women were added to the speaker list last minute for the 2014 conference.

Now, I just got an email about the 2016 conference and so I was curious to look at the list of speakers. They currently have 48 confirmed speakers and 20 of them are female. That is 42%!! Also, there is a few people of color on the list of speakers. Certainly not yet enough, but more than I usually see at these kinds of meetings.

I’d like to say: congrats to the organizers for creating an (almost) gender-balanced line-up and congrats to those of us at Stanford who opened our mouths. Complaining is not fun, and it’s not going to help us make friends or get ahead in our careers, but it can lead to change!

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Five Reasons why you should attend the Annual SACNAS National Conference

27 Apr

Guest post by: Bridget Hansen, SFSU undergraduate researcher


First, who am I? What is SACNAS?

My name is Bridget Hansen and I am an undergraduate in Microbiology at San Francisco State University, doing research at the Romberg Tiburon Center for Environmental Studies. Over the summer, I participated in the Howard Hughes Medical Institute Excellent Research Opportunity Program (HHMI-ExROP) summer research and the AMGEN program at the University of California, Berkeley. I worked on a project that I then presented at the SACNAS Conference this past October.

SACNAS stands for the Society for Advancing Chicanos/Hispanics and Native Americans in Science. This society, made up of many successful Chicanos and Native Americans in science related careers, puts on a national conference once a year. The conference has opportunities for scientists at all levels, from undergraduates to professors and researchers. Many graduate school recruiters and other professional organizations come to this conference to recruit, providing a great platform for networking.

I used this opportunity to network for graduate schools! I will be attending a PhD program in the fall, in part, thanks to my interactions that I had at SACNAS.

What happens at the SACNAS National Conference?

Students from all over the country submit abstracts for the opportunity to present their work, either in the form of a poster or an oral presentation. The students had a scheduled time and room to present. Other than presentations, the meat of the conference was geared towards guest speakers and networking. The whole goal of the conference was to introduce young students to the world of research and science related careers! The best part is the graduate student recruiter booths where you have the opportunity to chat with recruiters, professors, and students from that university.

Five reasons why I recommend SACNAS

  1. The networking

There were hundreds of booths set up, all stocked with professors, recruiters, graduate students and pamphlets listing the reasons why you should come to their school. Nearly every research institution was in attendance, looking for the next round of graduate students to apply to their programs. They want you to apply to their programs but most importantly, they want to make sure their school lines up with your research interests. You can ask them about the programs, the application process, what it is like to live in that part of the United States and any funding opportunities. Exchanging business cards or information is very common and the badge that you are given upon arriving even has a scanner square that the recruiters can use to keep in touch with you (they scan your badge and your e-mail is logged with them).

I spoke to over a dozen booths about their programs and had all my questions answered. I was even recruited during my poster session presentation! Which brings me to my next point.

  1. The presentations

The presentations are great for two reasons: 1. You have an opportunity to talk about your work and receive feedback on your presentation skills and 2. Other schools can come by your presentation and see you as a researcher. This is fantastic! I am not the best on paper in some ways, so having other schools approach me based on my science, reassures me that I am more than just my GPA or my GRE scores. Not only that, I received written evaluations based on my presentation skills and my poster, which were all constructive and positive!

  1. The seminars

The guest speakers focus on their journeys as minorities in the sciences and how their transforming experiences have brought them to where they are today. They inspire us to continue to pursue our passions and create a sense of community, which I will get to in a minute. The seminars are also great opportunities for junior scientists, like myself, because they offer an opportunity to check out new areas of research, hear about different paths in science outside of academia and get insights into how to be successful. There are workshops on how to give a compelling interview, what to expect in graduate school and how to master networking. All of these skills are important ones that give you a competitive edge.

  1. The experience

The experience itself was wonderful. Surrounded by 3,600 other students, mentors and researchers, the conference felt grand. I say grand because the conference center was massive, the sheer number of attendees was at times, a bit overwhelming, and the hotel that we were assigned to left me in awe. The Gaylord National Conference Center in Washington D.C. was an incredible place to hold this conference this year. As apart of the conference fees, we were fed in a large hall, which also created a sense of community.

  1. The sense of community

The SACNAS conference creates a sense of community for young scientists; a community that they can be a part of throughout their careers in the sciences. The idea of having a supportive community that I can be part of is a great feeling, especially coming from a background that does not have any college graduates. It can be lonely sometimes, walking into a completely new field that no one you grew up around, has any experience in. So, when I attended the conference with other San Francisco State students who were also presenting, they immediately considered me one of the group, even though we had just met. Similarly, other students from other places also welcomed conversation with open arms. The inclusion that occurs at SACNAS is excellent.

Overall, I highly recommend attending a SACNAS national conference. It looks great on your CV, it is great for your future scientific career and definitely gives you an edge when applying for graduate school. Bring your own business cards!

If you have any questions about SACNAS, please refer to the SACNAS website: .

Hope to see you there next year! I will be attending as a graduate student!

Feel free to contact me with questions at: blhansen “at” or missbridgette4 “at” and indicate you read this blog so I know where the questions are coming from!



Shut up and write session in the CoDE lab

3 Mar

Today my graduate students held our first “Shut up and Write” session. Five students from my lab, two students from other labs and I participated. We met at 2 PM in the main room of the lab. Dwayne was in charge. At 2:05 he told us all to shut up and write. It worked! Everyone was silent. I cheated, because I had a bunch of reading to do, so I read, instead of writing, but I think that’s OK😉

At 2:25, Dwayne announced that it was time for a break. We all chatted a bit. I made a coffee for myself, a few people went to the bathroom. After 10 minutes, Dwayne told us to get back to writing and we did another 20 minutes of silent work. It was wonderful! Eighth people in the lab in complete (non-awkward) silence!

When we were done, I asked what everyone thought of the “Shut up and Write” session and it seemed that everyone agreed that it was surprisingly efficient. More work can fit into two times 20 minutes than we had thought. I was even thinking that for me it would be good to do this every day!

How to get started with R

1 Feb


I often get asked how to get started with learning R if there is not currently a class offered. Here is what I recommend:

1. Start with a free online Code School tutorial

First of all, check out this (free) online course:
No need to install anything, no need to pay. Students in my bioinformatics class liked this online Code School course a lot. It will not make you a master of R, but it’s a nice starting point.

2. Install R, Rstudio and swirl on your computer

Next, it is time to install R and Rstudio on your computer. Once you have that, install the swirl package. Instructions for installing R, Rstudio and swirl can be found here:
swirl is an R package that helps you learn R while you are in the Rstudio environment. I highly recommend using the Rstudio environment! The swirl tutorials teach you the basics of vectors, matrices, logical expressions, base graphics, apply functions and many other topics. Kind words included (“Almost! Try again. Or, type info() for more options.”)

3. Dive in with great Udacity class …

If you are ready to really dive in (and have some time to invest), try out this great Udacity class:–ud651 (no need to pay for it, you can do the free version). This class is taught by people from the Facebook data science team. They do a great job guiding you through a lot of R coding. Importantly, they always take the time to explain why you’d want to do something before they let you do it. A large part of the course is focused on using the ggplot2 package.

… or start reading The R Book

The R Book is a book by biologist and R hero Michael Crawley. The pdf of the book is available from many websites (for example: Make sure you also download the example data that come with the book (

The R Book is a great resource and very clearly written. The students in my lab enjoy reading from it and trying out the code. If you are a biologist, it’ll be fun to work with the biology examples in the R book.

4. Find others who are using R or learning R.

Learning R is hard. You will get frustrated sometimes. If you know someone who is learning with you or who could help you when you are stuck, things will be easier! If there is no one near you, try to find R minded people on Twitter or elsewhere online. Also, check out the R forum on Stack Overflow ( for many questions and answers on R.

Good luck!


Why I write my NSF preproposal by hand and to a lay audience

18 Jan


Susan Holmes suggests (here) that it’s best to write your first draft of anything on paper, with an old fashioned pen, rather than on your computer. She believes
that the process of writing by hand helps us clear our thoughts. l think she has a point. So, I am writing this blog post on paper.

I would like to add my own piece of advice for better writing: l like to write my first draft as if I am writing to a friend or family member. For me, this strategy helps to remedy some anxiety I have thinking about the colleagues who may ultimately read my manuscript or proposal, and who may be harsh and skeptical. Writing with a lay person in mind also helps me to use simple words and to get to he point faster.

Years ago, l was struggling with the introduction chapter of my PhD thesis. The audience for this chapter would be my advisor and the other committee members. They were all well established and accomplished researchers in the field of population genetics. I was completely writer’s blocked. What could l write that they didn’t already know? l guess the only real information they were going to get from this chapter was whether I had mastered the material, but I had no motivation at all to write the chapter as a test of my knowledge.
l don’t remember who or what gave me the idea, but I decided to write the chapter as if it was meant for a lay audience. I actually didn’t think that my committee cared about the chapter much anyways, so I imagined an audience of friendly lay-people and students who were interested to enter the field., and I started to write for them.

This change of perspective made a huge difference to my writing. Suddenly, I was eager to write and I enjoyed the process. I had no more fear and a clear goal. (If you’re interested, you can download the introduction of my thesis here:  2007_Pennings_Pleuni_ThesisIntroduction).

This week, I am working on an NSF proposal. This is just as daunting and possibly nearly as futile as writing an intro chapter to my thesis (OK, not really). I therefore decided to try the same trick. I will write my first draft as if I’m writing to a friendly lay person, not the NSF committee that will ultimately read and judge my work. In addition to writing to a lay person, I will write my first draft on paper, following Susan Holmes’ advice. Clear thoughts and sentences, here I come!



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