Meet Our Interns

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102Bijou Basu
Washington University in St. Louis, Class of 2018
Major: Neuroscience and Statistics
Mentors: Seth Ament and Jocelynn Pearl
Price Lab

Our understanding of bipolar disorder is limited by the lack of a consensus network that integrates transcription factor (TF) information with gene expression. I constructed a Transcriptional Regulatory Network (TRN) model with data from the Allen Brain Atlas, and integrated the model with GWAS, sequencing an expression datasets to detect TFs involved in bipolar disorder. I designed guide sites for these TFs of interest with hopes of knocking them out using the CRISPR model, a genome editing technique. We then performed a transfection and analyzed the results. Once we confirm gene editing through our CRISPR library, we can monitor gene expression regulated by the absence of the targeted TF and eventually observe other molecular phenotypes in more appropriate cell model systems, such as human neural stem cells.

Growing up, I often found people baffled by the fact that I was passionate about a lot of different things. There’s nothing I find more stimulating than when I’m working in a lab surrounded by brilliant minds bouncing around ideas. There’s no time I’m more at peace with myself than when I am in my studio listening to Jack Johnson and creating art. There’s never a time that I’m laughing more than when I’m entertaining others, whether it be through my YouTube videos or surrounded by my friends on a Saturday night. There’s no time I feel more passionate about issues that I care about than when I’m sitting in front of my computer, on my blog, typing away furiously.

However, I’ve recently learned that it’s not strange for me to be both a neuroscience major who’s learning programming in R and a watercolor portrait artist. I can love speaking in front of crowds of people and like quiet nights alone with my thoughts. These apparent dichotomies in my personality don’t make me two different people but rather one person who just really cares about a lot of things.

 

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Elizabeth Burns
Georgia Institute of Technology, Class of 2016
Major: Biology
Mentor: Ariel Abramov
Myler Lab

My research project was focused on determining the minimum sequence requirements for insertion of “base J,” a novel nucleotide modification, by the Leishmania parasite. I learned many new lab techniques, including plasmid prep and how to use “Geneious” software, but the most suprsing skill I gained was the ability to recognize the scent of E. coli from a mile away.

I love theater! I am a member of DramaTech Theatre, Georgia Tech’s student run theater. We are dedicated to creating diverse, professional quality productions and promoting participation in the arts at Georgia Tech. If you are ever in the Atlanta area, try to come see a show!

 


AaronGordonAaron Gordon
Washington University in St. Louis, Class of 2018
Major: Computer Science
Mentor: Kai Wang
Hood Lab

I worked to develop web-based pipelines for the analysis of small RNA-Seq and DNA microarray data. These web-based tools allow biologists without any programming experience to easily analyze high-throughput gene and miRNA expression data in order to identify differentially expressed genes. I am now working on analyzing time-course gene expression data in a study of patient recovery after surgery. My goal is to find patterns in gene expression responses and to integrate the analysis of mRNA and microRNA expression levels. This summer, I have learned a lot about how the analyze large quantities to data and seen how collaboration between computer scientists and biologists is so important to the research at ISB.

Hometown: Seattle, WA

 


bkBrendan King
University of Washington, Class of 2017
Major: Computer Science
Mentors: Vangelis Simeonidis & Matt Richards
Price Lab

My project involves implementing a function to take an existing metabolic model for one organism and output a working metabolic model for a close genetic relative. It’s been a great experience learning about the fundamentals of metabolic modeling, the math used to represent a metabolic model, and the different software tools available for working with these models. I learned valuable computational and interpersonal skills, as I learned to program in Python and work with scientists and programmers here at ISB and KBase developers around country. Working at ISB has been a wonderful experience learning research and collaboration between scientific disciplines. The collaborative nature of work at ISB makes it a very friendly, welcoming place to work.

Hometown: St. Louis, MO
In my spare time I like to hike, see concerts, and spend time with friends.

 

ZinaZina Kurian
Santa Clara University, Class of 2016
Major: Bioengineering
Mentor: Thurston Herricks
Aitchison Lab

My project was to determine the optimum parameters for fluorescent tagging of multiplexed yeast assays. Cell colonies were imaged to obtain maximal fluorescence within the threshold by changing the media and limiting expensive cell-based resources. This is a scaled version of my mentor’s larger project called ODELAY, a multiparameter growth rate analysis platform. I’ve enjoyed learning and tuning the instrumentation that was developed for this project, as well as understanding the novel software platform. In a macroscopic sense, systems biology has taught me that when you don’t have the tools you need, you create them.

I enjoy kayaking, hiking, and soaking up Seattle summers. After I graduate in June, I hope to work at a startup that utilizes informatics for digital health or medical devices. I’ve learned so much from being here at ISB, especially the leadership and guidance from my mentors about the nature of research, and I look forward to using these skills in my future professions.

 


KO headshot bwKareem Osman
Johns Hopkins University, Class of 2017
Major: Molecular and Cellular Biology & Neuroscience
Mentor:John Chevillet
Hood Lab

My intrigue with integrative science began a little over a year ago when I began to observe relationships and co-dependencies inherent in my neuroscience coursework. Getting tired of the stresses of bulimic learning in the fight to keep ahead of the curve, I decided it was time to quit the memorization and resume my education. One timely experience and a couple lucky emails later, and here I am!

This summer, I’ve attended lectures, sat in on seminars, gave a couple talks in conference, learned myriad protocols of science, worked and played with researchers and technicians, and heard the term ‘robust’ be used in more ways than I ever could have imagined. ISB has truly blinded me with science. And not any science, but systems science. My project focused on pipeline development for the characterization and functional analysis of novel small RNAs observed during NextGen sequencing. I didn’t know any of that stuff just a couple months ago. And I wouldn’t have learned much from leafing through wads of flashcards in that time I daresay. Systems Education – watch this space.
Thank you for the exemplary mentorship, John.

I hail from the far reach of the US’ ultralineamentum- Fort Lauderdale FL.
Comparing the East/West coast was a definite hobby of mine this summer.

 


louisa

Louisa Pendergast
Carnegie Mellon University, Class of 2016
Major: Biological Sciences
Mentor:Nina Arens and Sergey Stolar
Baliga Lab

I have been working on a project producing a biodegradable plastic, PHB, in the peroxisome of a genetically modified yeast strain. My portion of this project has been to introduce a plasmid into the yeast strain that will amplify the synthesis of Acetyl-CoA, which will hopefully amplify the production of PHB as a result. This project has spanned a realm of lab skills I’ve never experienced; ranging from developing custom primers, to transforming yeast genomes, to designing, executing, and analyzing a week long growth experiment with multiple components. I’ve loved working with my mentors, as they have both guided my understanding of the scientific process from the conceptual level to the minute details of experimental procedures. I could not have asked for a better research experience or better support system here at ISB.

I am from Snohomish, a small town north of Seattle. Since leaving Washington for Pittsburgh, I’ve wanted to come back to work in Seattle; partially for the scientific opportunities, partially for the mountains.

 


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Kevin Shi

University of Washington, Class of 2017
Major: Bioengineering
Mentor: Irit Rubin
Huang Lab

This summer I investigated the notion of a critical tipping point threshold for HL-60 acute myeloid leukemia tumor growth in vitro. Through my investigation, I learned about how systems biology can be applied to cancer research and provide novel perspectives for understanding cancer. Using dynamic gene regulatory network models, one can think of cancer as a stable attractor state among the standard differentiated cell type attractor states. Conducting the experiments rather than reading journal papers actually taught me the most about science: that scientific design is hard, pedantry is best avoided, communication is key, and that asking questions often can save a lot of stress. If I were given the opportunity to intern at ISB again, I would check in with my PI more often to ensure the experiments are on the right track.

I feel very grateful for the experience and thank my mentors Irit Rubin, Joseph Zhou, and Sui Huang as well as Jennifer Dougherty and the Institute for Systems Biology for giving me this opportunity!

 

 

IMG_2104(1)Katie Strehler
University of Washington, Class of 2015
Major: Molecular and Cellular Biology
Mentor: Fred Mast
Aitchison Lab

This summer I’ve had the privilege of working in John Aitchison’s lab to develop high throughput, optimized methods for the affinity capture of protein complexes.  Affinity capture is a powerful tool for discovering protein-protein interactions, and this fundamental data is used to build systems models of disease as interactions change between cell states. I have adapted affinity capture protocols to a liquid-handling robotic platform to increase speed and reproducibility. I have also used the robot to optimize the pull-down of different proteins using an iterative process of parameter manipulation.  In addition to pulling down previously-captured proteins, I have used my novel method to capture Pex3, a low abundance peroxisomal membrane protein that has never been captured before. This project would not have been possible without the guidance and collaboration of the brilliant scientists at ISB and the Center for Infectious Disease Research. I have been impressed by their interdisciplinary culture and tireless efforts to drive science, computation and technology forward.

I am originally from Juneau, Alaska. I got interested in biology as a kid playing in tide pools.


PortraitStuart Yandell
Middlebury College, Class of 2017
Major: Biohemistry & Computer Science
Mentor:Kristian Swearingen
Moritz Lab

I’ve been optimizing protocols for protein extraction and proteomic analysis in a mass spectrometer. Basically, a lot of pipetting clear liquids into and out of tiny little tubes. Other than that, I’ve spent a lot of time doing analysis of the data we (Kristian and I) gathered during the optimization process. I also wrote a program to streamline the process, mostly because it was just so repetitive that I didn’t feel like doing it.
What I’ve learned… Mostly, I learned about the process of becoming a research scientist and staying employed as one. It’s a lot of work, but also very rewarding. My work will be going towards a grant Kristian won recently to investigate possible applications of proteomics to malaria vaccines.

I grew up just north of San Francisco, in the small town of Ross. I’m a black belt in Shaolin Kempo and write a lot of short stories, mostly focused around problems in bioethics and the advancement of humanity in the scientific age. Other than that, I love to bake, hike, and program in my spare time.

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