Code Lab on zoom

Stuart Castaneda, Pleuni Pennings, Saul Gamboa, Ryan Fergusson, Caroline Solis, Kohinoor Joshi, Anjani Pradhananga, Kaho Tisthammer, Geo Pineda, Naoko Fujito, Ryan Winstead and Candace Clark. Missing: Lorena Benitez Rivera and Rochelle Reyes.

Code Lab presents at Bay Area Pop Gen Fall 2019

From left to right: Emily Fryer (lab alum, now works at the Carnegie Institute at Stanford), Dr Kaho Tisthammer (gave a talk about fitness costs in Hep C Virus), Pleuni Pennings, Anjani Pradhananga (Master’s student), Stuart Castaneda (Master’s student, presented a poster on fitness costs of mutations in HIV).

Thanks to Aaron Stern and CTEG at UC Berkeley for hosting BAPG!

 

Postdoc position open in the Code Lab at SFSU!

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.

Appointment:

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!

Deadline:

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

New preprint and new video on how HIV evolves drug resistance

Together with Alison Feder (UC Berkeley) and Kristin Harper (freelance medical writer) I have written a manuscript on HIV drug resistance evolution on triple-drug therapies.

Triple-drug therapies were introduced in the 1990s to stop the evolution of drug resistance, but especially in the first years after their introduction, drug resistance evolution still happened often in patients on these treatments. How could this be? Have a look at our video and preprint!

The video was made by Dr Sarah Engelhard. Contact her if you would like to create a video for your paper!

Preprint link: https://www.biorxiv.org/content/10.1101/807560v1

 

 

We have previously made videos about related papers:

 

 

Lab News Summer 2019

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.

Gabriella

 

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

Geo

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.

 

Emily

 

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. 

 

Olivia

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: https://ab-hiv-coevolution.github.io/HIV_AB_CoEvo/ and the paper here on biorxiv. 

 

Victoria

 

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!

 

Sarina

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!

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.

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: 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.

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.

Appointment:

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 pennings@sfsu.edu. Only pdf’s please!

Deadline:

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

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

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

https://www.biorxiv.org/content/10.1101/548198v1

Abtract

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

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

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.