Archive | October, 2019

New preprint and new video on how HIV evolves drug resistance

22 Oct

From my lab’s website.

The CoDE Lab

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:

We have previously made videos about related papers:

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Postdoc position open in the Code Lab at SFSU!

22 Oct

The CoDE Lab

IMG_20180907_144251 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:

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…

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Scientist Spotlight: Meet Dr Yee Mey Seah!

17 Oct

YeeMeySYee Mey is a postdoctoral researcher at the University of Washington Bothell in the lab of Dr Kristina Hillesland. A postdoctoral researcher is someone who has their PhD and works in research (so she is Dr Seah!).

Pleuni: Hi Yee Mey, thanks for answering some questions! When did you first learn to code?

Yee Mey: My first experience was through a required class on C++ programming in my pre-university program. I struggled to understand the material, and after the semester ended, I thought programming isn’t for me.

When I started grad school at Rutgers University, I was given a small programming project during a rotation in a protein design lab, and was advised to learn Python. Thanks to a peer mentor who taught me to first write pseudocode, and the fact that Python is so readable, and has many online learning resources and tutorials, made the learning experience a lot less intimidating. I actually started to enjoy coding! Even though I ultimately joined a different lab, I was hooked, and found reasons to code in Python, e.g., cleaning and formatting metadata of GenBank virus sequences.

Pleuni: What kind of work do you do?

Yee Mey: In both my last and current positions after grad school, I work with high-throughput whole genome and metagenomic sequencing data from microbes. Knowing Python (and bash) has been useful for me to set up workflows with different bioinformatic tools to batch process the GBs of sequencing data. I’m currently working on the genomics of experimentally co-evolving microbial mutualists, and I use the Snakemake program to manage my bioinformatics workflow.

Snakemake workflows are constructed using a Python-based language, so knowing Python is helping me manage the execution of my workflows. Coding in Python also allows me to explore my variant-calling data; I can compare and plot mutation frequencies in various genomic regions, across different replicates, evolution conditions, and variant-calling software.

Pleuni: How did learning Python impact your career?

Yee Mey: Learning Python gave me the confidence to explore other computational skills, thanks to the abundant resources and helpful communities like PyLadies and Software Carpentry.

Pleuni: You did your undergraduate degree at Penn State – how did you choose that school?

Yee Mey: I grew up in Malaysia, and was put in science classes in high school because I got good grades. After high school, I graduated with good enough scores in the national exams to be offered a STEM scholarship for college in the US. I did not know much about US colleges at the time, and had funding to apply to four schools. Penn State was the only one that accepted me, and so that’s where I went!

Pleuni: How did you end up working on evolution in microbes?

Yee Mey: I did a degree in Clinical Lab Science and got interested in microbiology during my coursework and hospital practicum, but it wasn’t until grad school that I started getting fascinated with virology and evolution when I rotated in Siobain Duffy’s lab. I love how viruses are a major influence in all branches of life, and though seemingly simple, have endless variety in form and processes, and often defy the rules and boxes that we like to impose on them.

Yee Mey’s Google Scholar website (it has links to her publications and her PhD thesis!):

Lab website:…

Yee Mey on twitter:

Pyladies website: