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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.

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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.

 

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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

Caroline

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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.

 

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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

 

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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

 

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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

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!

 

 

 

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

CoDE Lab visits Seven Bridges Genomics

26 Sep

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
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Kayla presenting her work on Facebook Birthday data

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Abdul presenting his work on Facebook Friend Count based on gender

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Gabriella presenting her work on sugar consumption around the world

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The Code Lab and Bioinformaticians at Seven Bridges

 

 

 

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 🙂

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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!

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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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The CoDE Lab presents a summer coding program 2016

5 Apr

The CoDE Lab is very excited to announce a summer coding program that aims to promote more opportunities for undergraduate students to participate in ongoing research!

We have designed a free two-month program that will expose undergraduates not only to research in a lab but also to learn the basics of coding, reading scientific journal articles, and participate in lab meetings. The main goal is for students to learn new skills in the coding language R and be able to apply computational analysis to biological problems.

Program Details

This program will begin June 7, 2016 and run through August 4, 2016.

Our weekly meetings will consist of coding with learning programs such as Udacity, Code Academy, and worksheets provided by the facilitators, reading journal articles related to drug resistance and other topics of research students may be interested in, and lab meetings. Also, we are hoping to go on field trips to various places where coding in biology is applicable!

Each week will look roughy like this:

Course Outline

Who is behind this summer program?

There is four of us organizing the program. We are here to guide and mentor students. Please contact us (phamorrific@gmail.com) if you have any questions. We’d love to hear from you.

Olivia Pham (graduate student in the CoDE lab)

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Dwayne Evans (graduate student in the CoDE lab)

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Kadie Williams (graduate student in the CoDE lab)

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Marion Hartl (Post-doc in the CoDE lab)

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Who is this program for?

This program is for SF State Undergraduates in biology, whom are interested in learning about computational biology, HIV, evolution and/or drug resistance.

Previous experience with programming is not required.

The only requirement for this program is enthusiasm and willingness to work hard. Also, being nice is a plus…! However, we do ask that students who are interested be able to commit at least 6 hours/week during the days that we meet.

If you are not a biology student at SF State but are interested, please contact us and we’ll see what we can do.

How much does the summer program cost?

This program is free for students, there is no fee to apply!

When and where will this summer program be held?

The program will be held in the CoDE Lab at SF State Hensil Hall 520. This program will begin June 7, 2016 and run through August 4, 2016

How to apply?

The deadline to apply is May 6th, 2016.

Please fill out the application at: http://goo.gl/forms/7vGrWC4Mtc

 

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