Tag Archives: SFSU

Postdoc position open in the Code Lab at SFSU!

22 Oct

Come join us in San Francisco!

Position Type:

NIH funded postdoc position at San Francisco State University to work with Dr Pleuni Pennings in the CoDE Lab on viral evolution in macaques. The project is in collaboration with Dr Zandrea Ambrose and Dr Philana Lin from the University of Pittsburgh.

CoDE Lab website: https://pleunipennings.wordpress.com/

Position Description:

I am looking for a postdoc to work on a project funded by NIH, in collaboration with Dr Zandrea Ambrose and Dr Philana Lin from the University of Pittsburgh. We study how SIV, TB and the immune system affect each other within the host. The work in SF will mostly be focused on analyzing the viral sequences. I am looking for someone who is interested in doing the programming, the statistics and the writing.

I have worked with Zandrea Ambrose previously which has let to this paper in Plos Pathogens by Alison Feder et al.  Philana Lin has done very cool work on TB evolution within macaques using barcoded TB.

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 (next-gen sequencing data) 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.

I’d be very happy to see applications from people who have left academia and are interested to come back.

I need someone who can start soon (Dec or Jan 1st at the latest).

Why this is a great opportunity:

It’s a cool project in a productive lab. You can expect to get several first-author papers out of this postdoc.

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 and that could help us understand why TB and HIV are such a dangerous combination.

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

You will get the opportunity to work with people at the University of Pittsburgh.

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 three years. Appointment will be for one year initially, but will be extended for up to three years if expectations are met. The starting salary is $57,000 per year.

How to apply:

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


I will start looking at applications from Nov 1st, 2019 and hope to hire as soon as possible after that.

Fitness cost paper on bioRxiv

27 Jun

A little while ago we published a new manuscript on fitness costs on the bioRxiv. I’m very excited about this paper, because it is on a new topic for me (fitness costs) and we found some exciting results (for example, I never expected to find that CpG sites were so costly for HIV).

I am also excited about the paper because it is the first paper from my lab at SFSU and it is the first paper that resulted from our collaboration with Adi Stern in Tel Aviv.

The work was done by Marion Hartl (SFSU), Kristof Theys (University of Leuven and SFSU), Alison Feder (Stanford), Maoz Gelbart (University of Tel Aviv), Adi Stern (University of Tel Aviv) and myself.


Fig 2 from the manuscript. Selection coefficients for transitions at every nucleotide site in the pol sequence show that CpG-forming mutations are more costly than non-CpG-forming mutations and that mutations that involve a drastic amino acid change are more costly than mutations that do not.
Selection coefficients were estimated using a generalized linear model and sequence data from 160 HIV-infected patients. Shown are predicted selection coefficients for synonymous (left) and non-synonymous (right) mutations that do not involve a drastic amino acid change and either create CpG sites (green) or do not (orange). For non-synonymous mutations, predictions are also shown for mutations that do involve drastic amino acid changes and either create CpG sites (pink) or do not (blue).



eLife paper and video on how HIV treatments affect selective sweeps

15 Feb

Very happy to announce that we have a new paper out and an accompanying video! The paper is about how effective treatments lead to (few) hard selective sweeps and bad treatments lead to soft selective sweeps.

The paper can be found here on the eLife website, but I suggest starting with the video that Alison Feder made.


Paper details

Title: More effective drugs lead to harder selective sweeps in the evolution of drug resistance in HIV-1.

Authors: Alison F Feder, Soo-Yon Rhee, Susan P Holmes, Robert W Shafer, Dmitri A Petrov, Pleuni S Pennings

DOI: http://dx.doi.org/10.7554/eLife.10670

Abstract: In the early days of HIV treatment, drug resistance occurred rapidly and predictably in all patients, but under modern treatments, resistance arises slowly, if at all. The probability of resistance should be controlled by the rate of generation of resistance mutations. If many adaptive mutations arise simultaneously, then adaptation proceeds by soft selective sweeps in which multiple adaptive mutations spread concomitantly, but if adaptive mutations occur rarely in the population, then a single adaptive mutation should spread alone in a hard selective sweep. Here, we use 6717 HIV-1 consensus sequences from patients treated with first-line therapies between 1989 and 2013 to confirm that the transition from fast to slow evolution of drug resistance was indeed accompanied with the expected transition from soft to hard selective sweeps. This suggests more generally that evolution proceeds via hard sweeps if resistance is unlikely and via soft sweeps if it is likely.


New paper, new videos!

31 Dec

With Ben Wilson, Nandita Garud, Alison Feder and Zoe Assaf, I wrote a review paper about population genetics and drug resistance. It was a lot of fun to write this paper and I feel like I learned a lot during the process.

We wrote about drug resistance in influenza, malaria, TB, MRSA and HIV. It turns out that each of these case studies have something unique to teach us about evolution.

The paper is now out in Molecular Ecology. You can also download it here: 2015Wilson_et_al-Molecular_Ecology.

We made five short movies about the paper. Have a look at the one you are most interested in!

Nandita Garud on using genome scans to find resistance loci in malaria

MolEcolNandita from Pleuni Pennings on Vimeo.

Ben Wilson on the role of epistasis in resistance in Influenza

BenMolEcol from Pleuni Pennings on Vimeo.

Pleuni Pennings on standing genetic variation in HIV

MolEcol from Pleuni Pennings on Vimeo.

Alison Feder on clonal interference in TB

MolEcolAlison from Pleuni Pennings on Vimeo.

Zoe Assaf on the origins of the SCCmec element that causes methicillin resistance

MolEcolZoe from Pleuni Pennings on Vimeo.

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