Code Lab walks to Fort Funston

23 Oct

Our campus is close to the ocean, but we are usually too busy to take advantage of that.

Last week we took the afternoon off to walk to Fort Funston.


Members of the Code Lab at Fort Funston. 

How you can help the Clinton campaign from California and why you should

15 Oct

Being A Better Scientist


I would like to convince you to join me in helping the Clinton campaign.

Why help the campaign?

First of all: does the campaign still need help? It seems like a sure win at this point!

1. Things can change quickly. Chances of Trump winning are small, but if it does happen it would be a major disaster for the country and the world, so I want to do my part to prevent it.

2. The senate is not a sure win, and right next door, in Nevada, is one of the tightest races for a senate seat. A democratic majority in the senate is within reach and would make a huge difference.

What to do?

For the longest time, I didn’t realize how I could help the Clinton campaign. Now I do, and I thought I share it with you!

1. Send money.

2. Volunteer for a…

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CoDE Lab visits Seven Bridges Genomics

26 Sep

After the Summer CoDE Program ended, we had the opportunity to visit Seven Bridges Genomics ( here in San Francisco for an academic tour. It was a great experience seeing how bioinformatics is used in the industry!

Seven Bridges is a cloud-based company that offers different apps they have created to store, analyze, and interpret bioinformatic data. Some examples of the apps they offer are: RNA-Seq alignments (TopHat), whole genome analysis, ChimeraScan and more.

At Seven Bridges, we met a few of their bioinformaticians and they showed us what they have been working on and how we as students can use their apps and tools in our projects. Marion, Kadie, and Olivia each gave a brief presentation on their research and the summer students Kayla, Gabriella, and Abdul presented their posters on questions they were interested in using R to analyze data.

A special thanks to :

Zeynep Onder
Rohit Reja
Jing Zhao
Luke Chan
Anurag Sethi

Kayla presenting her work on Facebook Birthday data


Abdul presenting his work on Facebook Friend Count based on gender


Gabriella presenting her work on sugar consumption around the world


The Code Lab and Bioinformaticians at Seven Bridges




BAPGXIV meeting at SF State

18 Sep

Yesterday we hosted the 14th Bay Area Population Genomics meeting. It was the first time this meeting was held at SF State. A big thanks to all the speakers, poster presenters, lunch-career session volunteers and our sponsors (, the College of Science and Engineering and the Biology Department). Plus, a really big thanks to all the student volunteers who did an amazing job to make this meeting run smoothly! Many of them are on the picture below.


Bay Area Population Genomics at SF State

9 Sep

We are proud to host the Bay Area Population Genomics meeting at SF State!


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).



CoDE Summer Program 2016 Update

21 Jun

Hi Everyone!

Here’s an update about the summer Code Program! Now in week 3, I think everyone is feeling a little bit more comfortable with coding.

In week 1, we worked on a problem set that included vectors, plotting, and rbind/cbind and in week 2, we went through a HIV problem set. This week we’ll be working on some data about ant colonies (Click here to read more about the data: small scale spatial structure of ants of the species Temnothorax longispinosus)!

Also, it has been very nice having socials with Rori’s and Scott’s lab (the other computational labs on campus). We have tried to get together for lunches more and we just had our second social with snacks!

Last Wednesday in the first session ….

We read this press release chosen by one of our students, Christine:

Then we followed up on the press release with the primary article:

We talked about Figure 1 and the use of DNA sequences versus amino acid sequences and the pros and cons how using either in analysis. Then we broke up into two groups and the students worked on the methods section… one group was to explain what Whole exome sequencing was and the other what RT-PCR was.

You can see the picture attached of the two post-it poster🙂


After lunch…


DJ did a mini lecture following up on ‘for loops’ from the day before and the ability of writing your own functions in R. Stuff that we have learned and seen in the R book!


Now we are all just working independently! I think the students are learning a lot and are open to asking questions when they need help.


Here is a picture of some of the students in the program!

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