Archive by Author

The CoDE lab is looking for a postdoc

13 Dec

Position Type:

NSF funded postdoc position at San Francisco State University to work with Dr Pleuni Pennings in the CoDE lab on fitness costs of mutations in HIV.


Lab website:

Position Description:

I am looking for a postdoc to work on a project funded by NSF, in collaboration with Dr Adi Stern (Tel Aviv University) and Dr Robert Shafer (Stanford University). The goal of the project is to estimate the fitness costs of mutations in HIV, which will help us understand how the virus evolves and which parts of the HIV genome are most important for the functioning of the virus. All wet lab work for this project will be carried out in Tel Aviv, so in San Francisco I am looking for someone who is interested in doing the programming, the statistics and the writing.

Requirements: PhD in Biology or related field.

Other preferred qualifications:

I am looking for someone with experience and interest in several of the following domains: evolution, virology, bioinformatics and statistics.

The preferred candidate will also have an interest in / experience with one or more of the following: teaching, working with students from groups who are traditionally underrepresented in research, outreach (e.g., writing, social media, video).

The preferred candidate will have experience with writing clear / understandable scientific prose as evidenced by a writing sample.

Why this is a great opportunity:

You will be part of an extremely diverse department of biology.

You will be working on an exciting project that bridges virology and evolutionary genetics.

You will be able to contribute to training of students of diverse backgrounds.

You will get the opportunity to work with people at Stanford and Tel Aviv University (including trip to Tel Aviv).

If you are interested to collaborate with people at Stanford, UCSF or UC Berkeley, I will encourage that and help set up contacts.

In the CoDE lab, you will work in a supportive environment where research is important, but papers are never more important than people.


Funding is available for at least three years. Appointment will be for one year initially, but will be extended for up to three years if expectations are met.

How to apply:

Send a 1-2 page cover letter, your CV, a recent paper (or draft) written by you, and names and email addresses for three references to Only pdf’s please!


I will start looking at applications from January 4th 2018 and hope to hire as soon as possible after that.

Bay Area Population Genomics 15 at Stanford

2 Nov

The 15th Bay Area Population Genomics meeting will take place at Stanford on November 4th, 2017 at Stanford in the Clark Center.

Hashtag: #BAPG15

Location: Clark Auditorium ( Note that parking is free on Saturdays at Stanford. Park in any A or C spots. Roth Way is a particularly good spot.

Sponsors: BAPG 15 is free thanks to generous support from Ancestry Inc., 23&me Inc, and Karius Inc.

9AM Coffee and pastries; poster set up.

**For the poster session, we will have 6’ tall tripod easels for use. There will be 40”x60” foam boards (and binder clips) available for you to clip your posters on to. Please plan accordingly.**

10-11:10 (4 talks, 15 min + 2min Q&A each)

1. Nandita Garud, UCSF, Characterizing the population genetic environment in the microbiome.

2. Zheng Hu, Stanford, Inferring timing of metastatic dissemination through spatial-temporal modeling.

3. Aaron Stern, Berkeley, Approximate full-likelihood inference of selective sweeps using ancestral recombination graphs

4. Russ Corbet, UC Santa Cruz, The effects of Hill-Robertson Interference on rates of adaptive molecular evolution.

11:10-11:40 Coffee 

11:40 – 12:50 (4 talks, 15 min + 2min Q&A each)

5. Michelle Stitzer, UC Davis, Transposable elements in Arabidopsis thaliana – population genetics of TE polymorphism

6. Geoff Fudenberg, UCSF, Chromatin features constrain structural variation across evolutionary timescale

7. Moises Exposito-Alonso, Max Planck Institute for Developmental Biology, Genomics and climatic adaptation in Arabidopsis thaliana

8. Markus Stetter, UC Davis, Dynamics of polygenic adaptation after sudden environmental changes

LUNCH – thanks to the generosity of Ancestry Inc., 23&me Inc, and Karius Inc.

13:50 – 14:40 (1 talk 15+2 minutes & 6 lightning talks 4+1 min each).

9. Nancy Chen, UC Davis, Tracking short-term evolution in a wild pedigreed population.

10. Jose R. de la Torre, SF State, Population Genomics of Thermophilic Archaea: Larval Stages

11. Bryan Thornlow, UCSC,  Transcription-Associated Mutagenesis drives variation patterns in tRNAs and flanking regions    

12. Mikhail Tikhonov, Stanford, Theoretical ecology without species

13. Dwayne Evans, SF State, HIV-1 Drug Resistance Mutations to Truvada and Rilpivirine Used as PrEP

14. Jonathan Kang, Stanford, Consanguinity rates predict long runs of homozygosity in Jewish populations

15. Liza Huijse, Karius Inc., Plasma NGS-test for pathogen detection

14:40 – 15:40 (poster session with drinks and snacks).

Questions? Please contact Dmitri Petrov ( or Pleuni Pennings (


Alison Feder won the Omenn Prize 2017

5 Sep

In August 2017, Alison Feder (Stanford, Dmitri Petrov’s lab) gave a talk at the ISEMPH conference to accept the Omenn Prize for the article judged best on evolution, medicine and public health in any journal! So proud to work with Alison on this and other projects!


I didn’t see her talk, but judging from other people’s opinions, she did a great job!

Screen Shot 2017-09-05 at 9.50.31 AM


R01 grant to work on SIV-TB coinfection

29 Jun

Earlier this week I received the wonderful news that I was awarded an R01 grant together with Zandrea Ambrose and Philana Lin from the university of Pittsburgh!!

Screen Shot 2017-06-27 at 2.02.45 PM.jpeg

Here is a 3 minute video on the kind of work we will be doing (video and paper by Alison Feder, Stanford): 


CoDE Lab students: good news all around!

14 Jun

Kadie-Ann Williams (graduate student in the CoDE lab) won a Graduate Distinguished Achievement Award!


Keith Bowman, Pleuni Pennings, Kadie Williams, Teaster Baird, Blake Riggs.

Christine Fu, Abdul Alrefaie and Danny Posadas graduated with a B.S. degree!

Danny got accepted in pre-med post-bacc certificate program at UCSF,  Christine is studying for the MCAT and Abdul got accepted in a Master’s Program in Biochemistry & Molecular Biology at Georgetown University.

Deshawn Hopson and Gabriella Tenorio accepted in NIH funded research programs.

Deshawn was accepted in the MARC program (Maximizing Access to Research Careers) and Gabriella was accepted into the REU program (Research Experience for Undergraduates). They will keep doing research with me.

Dwayne Evans and Olivia Pham supported by RISE and Genentech fellowships.

Dwayne and Olivia are planning to defend their Master’s one year from now. They both have funding for the coming academic year, which allows them to focus on their research.


Paper on SHIV in macaques published in PLOS Pathogens

26 May

A new paper that I was lucky enough to be involved in came out this week in PLOS Pathogens. In the paper we follow how drug resistance evolves in space and time in macaques infected with RT-SHIV. The first author of the paper (Alison Feder) made a beautiful short video to explain our main findings. Have a look!

Note on the use of primates for research

This is the first time I have been involved in work with primates and I know that many of you probably think that primates should not be used for research. I think that this specific type of research is important and may lead to better treatments and less suffering for people.

A spatio-temporal assessment of simian/human immunodeficiency virus (SHIV) evolution reveals a highly dynamic process within the host
Feder AF, Kline C, Polacino P, Cottrell M, Kashuba ADM, et al. (2017) A spatio-temporal assessment of simian/human immunodeficiency virus (SHIV) evolution reveals a highly dynamic process within the host. PLOS Pathogens 13(5): e1006358.

Anna-Sophie Fiston-Lavier visits Code Lab

26 Mar

My friend and former Stanford colleague Anna-Sophie Fiston-Lavier came to visit us at SFSU all the way from Montpellier in France. She met with students from the Code Lab and students from the PINC program and she gave a talk in our seminar series on detecting Transposable Elements (TEs) in genomes. Very exciting stuff!


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:


Correction to eLife paper published

24 Jan

We just published a correction to our 2016 eLife paper.

While we were preparing the code to share it on Github, we discovered an error in calling drug resistance mutations (DRMs) in the protease gene in 140 sequences in our dataset (out of 6,717 sequences). The mistake was related to how R reads in data using read.table(). Even though the error only affected 2% of the sequences, it affected all downstream analysis and multiple figures had to be updated to reflect this correction. The resulting changes are minor and do not substantially change the conclusions and in some cases make them stronger.

When the analysis is updated with new numbers for these 140 sequences, all of our conclusions hold qualitatively, although the points in some figures shift slightly quantitatively. In fact, updating to the correct DRM calling for these sequences results in estimates for two treatments that are more in line with the expectations laid out in our paper.

As an illustration of this effect, we show here a version of Figure 4, which appeared in the paper (although has been slightly altered here for readability), and the shift of the model coefficients after correcting the 140 sequences of DRM calling. As you can see, the shifts are minor in most cases, and only serve to strengthen our conclusions for two of the PI treatments (points in the middle of the figure in light blue).


Figure 4, from the paper (slightly altered here for readability) shows the shift of the model coefficients after correcting the 140 sequences of DRM calling. The shifts are minor in most cases, and only serve to strengthen our conclusions for two of the PI treatments (points in the middle of the figure in light blue).

After finding the original mistake, we spent a lot of time going through all of the code for the paper and found a few other small mistakes in the description of the analysis. In all cases, the mistakes were minor.

The eLife editors and staff were very helpful in the entire process.


Feder, Alison F., et al. “More effective drugs lead to harder selective sweeps in the evolution of drug resistance in HIV-1.” Elife 5 (2016): e10670. Link.



Happy holidays from the CoDE lab!

20 Dec


%d bloggers like this: