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Manuscript on HIV sweeps and clonal interference posted on BioRxiv

13 Feb

Kadie-Ann Williams and I posted a new manuscript on the BioRiv. It is 30 pages with 28 figures and a supplement of 118 figures! I guess we could call it an HIV drug resistance evolution picture book!


Muller plot showing clonal interference in patient 89.

Nowadays, drug resistance evolution is quite rare, but in the late 1990s, HIV populations within patients on treatment were undergoing soft sweeps, hard sweeps, clonal interference and other things. If you like sequence data, you’ll enjoy looking at our pictures!

Title: Drug resistance evolution in HIV in the late 1990s: hard sweeps, soft sweeps, clonal interference and the accumulation of drug resistance mutations


The goal of this paper is to provide examples of evolutionary dynamics of HIV within patients who are treated with antiretrovirals. We hope that the figures in this paper will be used in evolution and population genetics classes. We show a wide variety of patterns, specifically: soft sweeps, hard sweeps, softening sweeps and hardening sweeps, simultaneous sweeps, accumulation of mutations and clonal interference.


Kadie-Ann Williams, SFSU BSc 2014, MSc 2017

Download the paper 2019WilliamsPennings2019_Feb

Download the supplemental figures 2019WilliamsPennings2019_Supplement118Patients



Fall semester lab update

21 Sep

The fall is here and we are all working hard on classes (as students, teachers, mentors and TAs) and our research.

We have some new folks who joined in the summer. Kaho Tisthammer joined as a postdoc, Anjani Pradhananga and Stuart Castaneda joined as a grad students, Caroline Solis and Chris Cabasal came as REU students and stayed as undergrad research students.

Some of us will be on the road presenting and learning! Emily Fryer will be presenting at SACNAS, Anjani Pradhananga and Gabriella Tenorio are going to present at ABRCMS. Ryan Fergusson will be traveling to Berlin to take a class on GWAS studies.




New video about soft sweeps

12 Jul

I made a new video about why soft sweeps are more common than you may think!

This is a second video about a paper I published in 2017 with Joachim Hermisson.

I hope that these videos make it easy to understand some of the main conclusions from our paper!


It’s the sequel to this one:


Hermisson, J. and Pennings, P.S. 2017, Soft sweeps and beyond: understanding the patterns and probabilities of selection footprints under rapid adaptation. Methods Ecol Evol, 8: 700–716. 2017Hermisson_Pennings_Methods_in_Ecology_and_Evolution.

Lab News Spring 2018

13 May

This past month, a lot of great things have happened in the lab! Time to share with the world:


Dwayne Evans

Dwayne Evans, our grad student who works on Prep and drug resistance, is finishing up his Master’s as quick as he can so that he can move to Boston this summer to start a PhD at Harvard!


Ryan Fergusson

Ryan Fergusson, who joined the lab this semester as a grad student, won an NIH-RISE fellowship, which will support him for the next 4 semesters as he works on his Master’s thesis and prepares for PhD applications.



Gabriella Tenorio

Gabriella Tenorio, one of our undergrad researchers will spend the summer at the Jackson Labs in Maine as an REU student, and when she comes back she will be supported by an NIH-MARC fellowship.



Ryan Winstead

The other Ryan in the lab, undergrad researcher Ryan Winstead, who is part of our CpG team, won an NIH-RISE fellowship that will support him starting this summer. He also won an honorable mention at the Cose Poster Showcase for his desktop app on cell imaging.


Sarina Qin

Sarina Qin, another undergrad research on the CpG team, will graduate this semester with a BS in Cell and Molecular Biology. Sarina will take some time after graduation to decide on her next steps.



Deshawn Hopson

Deshawn Hopson, an undergrad researcher who works on the interactions between drugs and their resistance mutations will graduate with a BS in physiology. Deshawn plans to apply for medical school.


Emily Fryer

Emily Fryer, Gabriella Tenorio, Ryan Winstead and Stuart Castenada (future grad student in the lab) will all complete the 5 CS classes that make up the PINC program, which will allow them to graduate with a minor in Computer Applications in addition to their major in Biology.

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!

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