Archive by Author

Appalled by Trump actions

28 Jan

I am appalled by what is happening in the US since Trump, Pence and the Republican Party are in charge. I believe that women should have access to safe abortions and birth control. I believe everyone has the right to affordable medical insurance. I believe refugees should be welcomed in this country. (Soon, we may need other countries to welcome refugees from the United States!) I believe scientists who work for the government should be free to speak their minds and share their findings with the world. I believe no one should be banned from this country based on their religion. I belief that Black Lives Matter.

I will do everything I can to provide a safe space in my classrooms and my lab for everyone, regardless of their race, religion, gender, sexual orientation, immigration status or physical abilities.



In defense of science

28 Jan

I (Pleuni Pennings) endorse the following, which was drafted by Graham Coop (UC Davis), Michael Eisen (UC Berkeley) and Molly Przeworski (Columbia):

We are deeply concerned by the Trump administration’s move to gag scientists working at various governmental agencies. The US government employs scientists working on medicine, public health, agriculture, energy, space, clean water and air, weather, the climate and many other important areas. Their job is to produce data to inform decisions by policymakers, businesses and individuals. We are all best served by allowing these scientists to discuss their findings openly and without the intrusion of politics. Any attack on their ability to do so is an attack on our ability to make informed decisions as individuals, as communities and as a nation.

If you are a government scientist who is blocked from discussing their work, we will share it on your behalf, publicly or with the appropriate recipients. You can email us at

If you use this email address, here is a PGP public key for PGP encryption:

More women at French mathematical biology conference this year (200% increase)

24 Jan

Two years ago, I was annoyed about a conference (Mathematical and Computation Evolutionary Biology Meeting) on an island near Marseille that had never had more than one female invited speaker.

This year, I noticed that the number of women at the conference has gone up from 1 (in the past) to 3 this year! That is an increase of 200%, and they now have >40% women among invited speakers (3 of 7). 


Here are links to the women’s websites.


Compiling a list of REU opportunities for my students

3 Dec

I started looking into opportunities for undergrad students who are interested in biology and bioinformatics / computer science. The list is far from complete. I will add when I have more time!

What is an REU? 

NSF funds a large number of research opportunities for undergraduate students through its REU Sites program. An REU Site consists of a group of ten or so undergraduates who work in the research programs of the host institution.

Auburn University NSF REU Site in Computational Biology

Deadline: March 1st, 2017

Integrated Science For Society Boston College

February 1st, 2017

BRITE REU Boston University


Feb 17th, 2017


Unclear if open this year (2017)

City College New York

Unclear if open this year (2017)

From Genomes to Phenomes — Exploring Function Across Scales

February 5, 2017

NSF REU in Bioinformatics and Computational Neuroscience, Cold Spring Harbor

Unclear if open this year (2017)

Computational Genomics Undergraduate Research Experience, Charleston

February 15, 2017

REU at the Intersection of Mathematics and Biology, Florida

Unclear if open this year (2017)

Undergraduate Research Experience in Genomics, Proteomics and Bioinformatics Florida A&M University

Please submit Application Forms before March 21, 2016.

Genetics and genomics research, Jackson Labs

Thursday, February 2 – Application deadline

Note to self: Continue searching here:

American Museum of Natural History

The American Museum of Natural History hosts two summer National Science Foundation Research Experience for Undergraduate Site grants – Research in Biology: Evolution and Systematics and research in Physical Sciences: Earth Sciences and Astrophysics. 

This year’s REU program will run from May 30 to August 4, 2017

The Research Experiences for Undergraduates (REU) program, funded by the National Science Foundation (NSF), offers paid summer internships for qualified undergraduate students to conduct research projects with AMNH scientists in either evolutionary biology or physical sciences. Students receive a generous stipend and living and transportation expenses; housing is provided at nearby Columbia University. In addition to hands-on research, students participate in a series of weekly meetings at which they discuss their research, present informal progress reports, and engage in discussions and seminars regarding scientific research, graduate school, and research career opportunities. At the conclusion, they deliver oral presentations of their work and prepare publication quality research papers.

All REU students must be U.S. citizens, U.S. nationals or permanent residents of the U.S. Students must be entering or continuing in an Associates or Baccalaureate degree program following this summer internship. As part of the National Science Foundation’s commitment to broadening participation in STEM fields, we especially encourage students who come from community colleges, undergraduate-only institutions, and minority-serving institutions to apply. 

Students may apply directly at our website: 

The application deadline is February 6 2017 for both programs.

Genome Sciences U Washington

Love Trumps Hate

9 Nov
Today in the biology department at SF State.

Today in the biology department at SF State, our students and my colleagues reminded me that Love Trumps Hate. 

Canvassing in Nevada

24 Oct

Last weekend I went to Reno, Nevada, to canvass for the Democrats.

Ready to canvass in Reno, Nevada!

Ready to canvass in Reno, Nevada!

We drove to Reno on Saturday morning, then spent the afternoon knocking on doors and talking to people, went out for a simple dinner and checked into our hotel. On Sunday morning, we drove back and made a little detour to drink coffee on the shore of Lake Tahoe. It was a fun road trip!

How does canvassing work?

As expected, we found the campaign to be well organized. After we arrived at one of the campaign headquarters in Reno, they explained to us what we were going to do. They gave us a list of addresses with names of people who lived there. Our list contained 87 addresses. It took us almost four hours to knock on all the doors! To everyone who wanted to talk to us, we asked then whether they were planning to vote for Clinton, for Catherine Cortez Masto (she could become the first Latina in the Senate) and Chip Evans (Congress). We then asked if they knew when and where they planned to vote and we explained how easy it is to do early voting in Nevada. In Reno (Washoe County), you have from Oct 22 to Nov 4th to go to any early voting location in the county, and there are many such polling stations, for example, in the library or the supermarket. Finally, if people were supportive of the Democratic candidates, we’d ask them whether they’d be interested to volunteer.

Who did we talk to?

I had never really thought of how canvassing is done, but I somehow assumed that it would consist of convincing people to vote for Clinton and not Trump. However, I had only one conversation on Saturday where I explained why I support Hillary, and Trump was hardly mentioned at all (what a relief!) Instead, we were mostly talking to people who were known to be supportive of Democrats, but who may or may not actually vote. Our main goal was therefore to encourage people to go and vote and to use the opportunity of early voting in Nevada. That’s why it was probably most important for us to be able to say: “Do you know that you can vote today in the supermarket down the road until 6PM? And tomorrow they’re open from 11 till 4.”

Would I do it again?

Yes, absolutely. It was fun (and tiring). Most people were happy to talk to us. I may have convinced a few people to go and vote and I may have encouraged someone to volunteer for the campaign. Plus, the weather was nice and I walked 5 miles. Highly recommended!

Ready to canvass in Reno, Nevada.

Ready to canvass in Reno, Nevada.





How you can help the Clinton campaign from California and why you should

15 Oct


I would like to convince you to join me in helping the Clinton campaign.

Why help the campaign?

First of all: does the campaign still need help? It seems like a sure win at this point!

1. Things can change quickly. Chances of Trump winning are small, but if it does happen it would be a major disaster for the country and the world, so I want to do my part to prevent it.

2. The senate is not a sure win, and right next door, in Nevada, is one of the tightest races for a senate seat. A democratic majority in the senate is within reach and would make a huge difference.

What to do?

For the longest time, I didn’t realize how I could help the Clinton campaign. Now I do, and I thought I share it with you!

1. Send money.

2. Volunteer for a two hour shift at one of the SF phone banks.

3. Drive or fly to Nevada (Reno or Las Vegas) in one of the next weekends to get out the vote right where it matters most.

To sign up for a phone bank or to go to Nevada, go to:

Is it hard?

I did a two-hour shift at the phone bank last week and it was easy. I was calling people who were known Hillary supporters to ask if they wanted to go to Nevada to get out the vote. It was a simple question with a simple yes/no answer. I was not supposed to try and convince people of something they didn’t want.