Lab News Summer 2019

12 Jun

Summer is finally here! A lot has happened during the Spring semester and we would like to share some news:

Stuart & Anjani

Graduate students Anjani Pradhananga and Stuart Castaneda are currently visiting Dr. Amy Goldberg’s lab at Duke University for the summer! They will be doing research on the genetics of malaria resistance in Latin American populations.




Undergraduate student Gabriella Tenorio has graduated this semester with a Bachelor of Science in Microbiology and a Minor in Computing Applications. This summer she is a mentor in the Big Data Summer Program at SFSU. She is teaching the biology and economic students how to code in R. Their group is working with Dr. Luella Fu from the Mathematics Department at SFSU.



Ryan W.


Undergraduate student Ryan Winstead is participating in a Summer Research Internship at IBM Almaden in San Jose. He is using the computer science skills he has learned in the PINC program to do research in visual recognition at IBM.


Caroline Solis




Undergraduate students Caroline Solis and Geo Pineda are getting a lot of research experience this summer. Caroline is currently at UCLA in Dr Kirk Lohmueller’s lab and Geo is participating in the REU at SFSU.





Undergraduate student Emily Fryer has graduated this semester with a Bachelor of Science in Ecology and a Minor in Computing Applications. She is currently working and doing researching in Dr. Sue Rhee’s lab at the Carnegie Institution for Science – Department of Plant Biology at Stanford. Emily along with another lab member, Olivia Pham recently published a paper with collaborators at UCSF (Ryan Hernandez and Nicolas Strauli) on biorxiv




Graduate student Olivia Pham defended her thesis in March and has graduated this semester with a Master of Science in Cell and Molecular Biology. Along with Emily, they worked together with collaborators at UCSF to build an interactive website to display data involving genetic interaction between HIV and the antibody repertoire. The website can be found here: and the paper here on biorxiv





Graduate student Victoria Caudill has recently defended her thesis this month on polygenic adaptation and will be graduating this summer with a Master of Science in Evolution, Ecology, Conservation Biology. Next semester, she will be starting a PhD program at the University of Oregon!




After graduating last Spring 2018, Sarina Qin has continued to working on research on the CpG team. Next semester, she will be starting a PhD program at the UC Merced!





Emily, Gabriella. and Victoria at the Biology Recognition Ceremony!

NIH-funded postdoc position in the Code Lab!

11 Jun

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.

IMG_20190403_212845 copy

Philana Lin (Ling), Zandrea Ambrose, Pleuni Pennings are the PIs on the R01 grant “Influence of SIV replication on TB progression and immunity.” 

Lab website:

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.

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 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 $54,000 per year.

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 July 10th, 2019 and hope to hire as soon as possible after that.

Lab visit to Tel Aviv

10 Apr

In February of 2019, 10 of us visited Adi Stern’s lab at Tel Aviv University. A blog post about the trip is on my blog.


Lab trip to Tel Aviv University

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.

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