CoDE Lab visits Seven Bridges Genomics

After the Summer CoDE Program ended, we had the opportunity to visit Seven Bridges Genomics (https://www.sbgenomics.com/) 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

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 (Ancestry.com, 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

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

Fitness cost paper on bioRxiv

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

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:

http://news.feinberg.northwestern.edu/2016/06/new-gene-shown-to-cause-parkinsons-disease/

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

http://www.nature.com/ng/journal/vaop/ncurrent/full/ng.3589.html

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!

End-of-semester CoDE lab update

A lot is happening in the CoDE lab! Here are some updates on what everyone has been up to this spring and what we are planning for the summer!

Marion Hartl

This semester, Marion spent seven weeks in Tel Aviv to work in the lab of our collaborator Adi Stern on improving accuracy of sequencing methods for HIV patient samples. She very much enjoyed being in a country where being a vegetarian is the norm rather than the exception.

Melissa Luk

Melissa is graduating this semester with a Major in Cell and Molecular Biology and a Minor in Chemistry. She is very excited to move to UC Davis next semester to start a Master’s Degree in Forensic Science concentrating on DNA track. She enjoys spending time with her nephew, Gabriel.

Farheen Ghiasuddin

Farheen is graduating this spring with honors as a Physiology Major and a Chemistry Minor. She is planning to take her MCAT soon and then apply for med school in New York. This semester Farheen enjoyed watching The Flash!

Dwayne Evans

Dwayne presented a poster about his graduate research at the CoSE Showcase. He made a lot of progress with his R coding skills this semester. He is preparing to teach a hiphop class soon.

Patricia Kabeja

Patricia is graduating this spring with honors as a Physiology Major and a Chemistry Minor. She is planning to take her MCAT soon and then apply for med school on the East Coast. This summer Patricia is going on a medical mission in Jamaica. Patricia’s favorite character in Game of Thrones is Khaleesi.

Julia Pyko

Julia spent most of this semester interviewing at various medical schools across the country. She received many offers but has not yet selected where she will spend the next 4 years. Her current interests are neurology and OB/GYN. She is getting married this summer and is excited to have all her dogs under one roof again!

Olivia Pham

Olivia will start a Master’s in the fall (in the CoDE lab!) and she got accepted in the prestigious RISE program. Olivia presented a poster at the CoSE Showcase on the work she did as part of the Microbial Genomics class this semester. Olivia plans to learn to play the drums this summer.

Kadie Williams

Kadie presented her research at the CoSE Showcase, and won 4th place in the Graduate Life Science category! Congrats Kadie!! She is the co-founder and president of the Biology Student Council.  Currently enjoying her time working on her prospectus and research.

Dasha Fedorova

Dasha is the president of the MEDLIFE chapter at San Francisco State. She has planned a trip, along with her chapter, to go volunteer in Lima, Peru in June. On this trip, she will be setting up health clinics for low-income communities, as well as helping with various developmental projects. She is graduating Fall 2016, and will be taking the MCAT and applying to medical school shortly after.

Sidra Tufon

Sidra is graduating this summer as a Physiology Major and a Chemistry Minor. This is her last year of having the title of a fundraising officer for SFSU’s MEDLIFE chapter. She is planning to take her MCAT next April and then applying to med schools for the next cycle. She will also work as a medical assistant while gaining clinical exposure in medical offices this fall. This summer she plans travel to Cabo and Miami with her friends and family as a graduation treat.

Austin Lim

Austin left the lab early during the spring semester because he found a full time job in a microbiology lab! Congrats Austin!

PINC! New CS program for Bio majors at SFSU

The Biology and Computer Science departments at SF State are excited to announce a new program: Promoting Inclusivity in Computing (PINC) with the goal of attracting and supporting more Biology students to Computer Science.

A few faculty members from the Biology department have joined forces with the Computer Science department to design a program that lowers the barriers that Biology students experience in learning computer science skills. This program will expose students to basic computing topics such as web design, mobile app development, data structures, and algorithms. All classes in the PINC program are new and especially designed for biologists.

In the PINC program, biology majors will complete 15 units of computer science course work (5 courses spread over 4 semesters) that will allow the students to earn an “Emphasis in Computer Science”.

For more information about PINC, see pincsfsu.com !