Marching for science with colleagues and students

14 Apr



Over 22,000 Participants Enrolled in PrEP Trials

24 Mar

Overview of eleven different PrEP Trials divided into treatment arms. Trials are organized by total number of participants.

Link to Larger Figure

Pre-Exposure Prophylaxis, or PrEP, is a medication that prevents HIV infection. It is intended to be used together with safer sex practices (e.g., condoms). This stacked barplot shows the number of participants in 11 different PrEP studies. The earliest study in the plot is the West Africa trial, which was initiated in 2004. Each bar corresponds to its labeled trial. The different colored sections in each bar represent the “arms” or “cohorts” of the study. Most studies have a placebo cohort and a treatment cohort. The PROUD study only has the treatment arm. The VOICE study has three different treatment arms, while the Partners PrEP study has two different treatment arms.

The light blue color represents the Truvada (emtricitabine/tenfovir disoproxil fumarate combination) cohorts. The dark blue color represents the cohort only given TDF (tenofovir disoproxil fumarate), and the off-white color represents the placebo cohort. The light green and pink colors represent the 1% Tenofovir vaginal gel cohort and placebo vaginal gel cohorts, respectively. The blue pill icon over a graph indicates the study employed a daily oral pill to be used as PrEP. The green gel icon indicates the study employed a topical vaginal gel to be used as PreP. We can see that all of the individuals enrolled in the studies give a combined total of over 22,000 participants. Even though PrEP is a relatively new preventative, the plot shows that a large number of participants have already enrolled in PrEP trials and the prophylaxis is becoming well studied.

About the Author

Dwayne Evans is a graduate student at SFSU. He works on HIV drug resistance in relation to Pre-Exposure Prophylaxis (PrEP). He made a figure to show how many people participated in PrEP trials since 2004.


Dwayne Evans, SFSU


(Please click on the reference for a link to the study)


Marrazzo JM, Ramjee G, Chirenje ZM, et al. Tenofovir-Based Preexposure Prophylaxis for HIV Infection among African Women. N Engl J Med 2015; 372:509-518.

Partners PrEP Study

Baeten JM, Donnell D, Celum C, et al. Antiretroviral Prophylaxis for HIV Prevention in Heterosexual Men and Women. N Engl J Med 2012; 367:399-410

Donnell D, Baeten JM, Celum C, et al. HIV Protective Efficacy and Correlates of Tenofovir Blood Concentrations in a Clinical Trial of PrEP for HIV Prevention. J Acquir Immune Defic Syndr 2014; 66: 340-348

Ndase P, Celum C, Baeten JM, et al. Successful discontinuation of the placebo arm and provision of an effective HIV prevention product after a positive interim efficacy result: the partners PrEP study experience. J Acquir Immune Defic Syndr 2014; 66:206-12

iPrEx Study

Grant RM, Lama JR, Glidden DV, et al. Preexposure Chemoprophylaxis for HIV Prevention in Men Who Have Sex with Men. N Engl J Med 2010; 363:2587-99

Liegler T, Abdel-Mohsen M, Grant RM, et al. HIV-1 Drug Resistance in the iPrEx Preexposure Prophylaxis Trial. J Infect Dis 2014; 210:1217-27

Bangkok Tenofovir Study

Choopanya K, Martin M, Vanichseni S, et al. Antiretroviral prophylaxis for HIV infection in injecting drug users in Bangkok, Thailand (the Bangkok Tenofovir Study): a randomized, double-blind, placebo-controlled phase 3 trial. The Lancet 2013; 381:2083-90


Van Damme L, Corneli A, Taylor D, et al. Preexposure Prophylaxis for HIV Infection among African Women. N Engl J Med 2012; 367:411-422

TDF2 Study

Thigpen MC, Kebaabetswe PM, Brooks JT, et al. Antiretroviral Preexposure Prohpylaxis for Heterosexual HIV Transmission in Botswana. N Engl J Med 2012; 367:423-434

Chirwa LI, Johnson JA, Brooks JT, et al. CD4(+) cell count, viral load, and drug resistance patterns among heterosexual breakthrough HIV infections in a study of oral preexposure prophylaxis. AIDS 2014;28:223-6

West Africa Study

Peterson L, Taylor D, Cates W, et al. Tenofovir Disoproxil Fumarate for Prevention of HIV Infection in Women: A Phase 2, Double-Blind, Randomized, Placebo-Controlled Trial. PLoS Clin Trials 2007; 2:e27

CAPRISA 004 Trial

Mansoor LE, Abdool Karim Q, Yende-Zuma N, et al. Adherence in the CAPRISA 004 Tenofovir Gel Microbicide Trial. AIDS Behav 2014; 18:811


McCormack S, Dunn DT, Gill ON, et al. Pre-exposure prophylaxis to prevent the acquisition of HIV-1 infection (PROUD): effectiveness results from the pilot phase of a pragmatic open-label randomized trial. The Lancet 2015; 387:53-60


Molina JM, Capitant C, Delfraissy JF, et al. On Demand Preexposure Prophylaxis in Men at High Risk for HIV-1 Infection. N Engl J Med 2015;373:2237-2246

US MSM Trial

Liu A, Vittinghoff E, Buchbinder S, et al. Sexual risk behavior among HIV-uninfected men who have sex with men (MSM) participating in a tenofovir pre-exposure prophylaxis (PrEP) randomized trial in the United States. J Acquir Immune Defic Syndr 2013; 64:87-94

On executive orders and protest fatigue

5 Feb

Poster by Shephard Fairey / via Amplifier Foundation

This thoughtful post was written by my friend Arne Bakker who works at Stanford. He allowed me to post it here. Pleuni

So, I spent part of my night listening to legal experts of the Stanford Law School discussing the impact of 3 recent executive orders by President Trump. It was pretty impressive, with some of the top legal scholars of the country being present. I learned about Executive Order #1 (by Lincoln), and about an Executive Order actually describing what an Executive Order is (Chicken, meet Egg). And I learned a lot about how these orders are affecting thousands of people inside and outside the US, which brought tears to our eyes and fear in our hearts.

But I also learned from these pretty amazing people what they think we can (and should) do:

***First, there was the positive reminder that after 9/11 the courts allowed many laws impacting civil liberties to pass because of broad ‘national security’ concerns, but that today it looks like the courts are actually resisting the policy changes from the Trump administration. Keeping my fingers crossed for that one.

***Second, there was the heartfelt plea to not just rely on the courts, but to continue calling your representatives to resist these policies and remain active and vocal in your protests. It actually works, people! These top legal experts attributed the recent changes in allowing permanent residents to enter the country and backtracking on some other provisions purely to the quick and vocal response of thousands of people after the Executive Orders went into effect less than a week ago.

***Third, they cautioned for protest fatigue. There is a real agenda for controlling the news cycle with new shock after new shock to wear us out. As someone said, don’t fall for forgetting yesterday’s news because of today’s new shocker. Think hard about what issue you deeply care about and keep track of it, even when the news cycle has moved on. Keep reminding people, give them updates on policy changes, victories and losses where you can. And don’t be upset if someone else knows less about ‘your thing’ and is vocal about a different issue that they care deeply about. Learn from them, since they will keep track of those issues and can share their knowledge with you.


If you are interested to read more on the travel ban by Stanford professors, see here:


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