Showing posts with label Jacobs Scholars. Show all posts
Showing posts with label Jacobs Scholars. Show all posts

Wednesday, January 13, 2021

Undergraduate Bioinformatics Student Teams Up With CS Professor on Nature Paper

Bonnie Huang ’21 had the opportunity to work with computer science Professor Melissa Gymrek on a paper published Jan. 13 that find tandem repeats, which are also associated with Huntington’s disease, may contribute to Autism Spectrum Disorder 

Why did you choose bioinformatics as a major?

Entering college, I was interested in human health and all areas of STEM, from biology and chemistry to math and computer science. I decided to major in bioinformatics due to its interdisciplinary nature and figured it would be fascinating to be able to apply computer science to solve biological problems in a variety of fields.

Why did you attend UC San Diego?
One of the main factors that drew me to UC San Diego was the Jacobs Scholarship, which gave me the opportunity to pursue my interests and focus on academics and extracurricular activities (such as research and community service) without worrying about the financial burden of college. Another important factor was the top-notch bioengineering/bioinformatics faculty/curriculum as well as the abundant research opportunities available at UC San Diego.

How did you get in touch with Professor Gymrek and become an undergraduate researcher in her lab?

My sophomore year, I took a class with Professor Gymrek (CSE 185 – Advanced Bioinformatics Laboratory) and learned about her lab’s work on the development of computational tools to analyze repetitive DNA regions in the human genome. I found her research extremely interesting, especially since I’ve always wanted to learn more about human genetics and find a way to combine my interests in computer science and biology. We set up a meeting to discuss research opportunities, and I’ve been fortunate to be a part of her lab ever since.

What was it like to be part of her lab and become a coauthor on a paper published in Nature?

Being a part of the Gymrek Lab has been an amazing experience. Professor Gymrek is a fantastic and extremely supportive mentor, and I’ve truly enjoyed working with everyone in the lab. Over the past year, I’ve been developing a novel software tool called SISTR to score short tandem repeat mutations in the human genome based on how likely they are to cause disease. In one part of the paper, we use SISTR to analyze short tandem repeat mutations in individuals with autism and predict which mutations are most likely to be harmful. Overall, I’ve learned a lot from working on SISTR and applying the skills I’ve gained from my computer science, biology, and bioinformatics courses to contribute to medical research.

What are your plans for after graduation? 

I plan to go to medical school and pursue a career in academic medicine, where I would be able to combine my interests in research, teaching and patient care. In the future, my goal is to both treat patients and use my background in bioinformatics to help solve medical problems and improve patient care through the development of new diagnostic tools and personalized treatments.

What would your advice be to an incoming freshman who wants to do research?

One way to find a lab to join is to explore different research groups’ websites/papers and email professors whose research you find interesting. It can also be helpful to go to office hours to talk with professors about their research and ask them questions about your field of interest. Another way to gain experience is through summer research programs, so keep an eye out for applications to those as well.


Paper: Patterns of de novo tandem repeat mutations and their role in autism


Related story:

Study finds neglected mutations may play an important role in Autism Spectrum Disorder


Thursday, June 19, 2014

Q&A with UC San Diego outstanding senior award winner and bioengineering major Damini Tandon

 Damini Tandon, a bioengineering major, who plans to attend medical school, won this year's outstanding senior award at the UC San Diego All Campus Graduation Celebration. In this Q&A, she talks about the research she conducted, the professors who mentored her and some of her favorite classes here at the Jacobs School of Engineering.
- What made you decide to attend UC San Diego and major in bioengineering?
1a. Upon being accepted to UC San Diego, I was offered the Jacobs Scholarship, a full-ride scholarship for selected engineering school admits. That was a big factor in my decision because the scholarship would (and did) allow me to devote my time to my academics and extracurriculars. This scholarship would (and did) give me the freedom to explore my interests and develop new passions without worrying about how I would pay for my education.
1b. Another reason that I chose UC San Diego was because I was intent on studying bioengineering, and UC San Diego has faculty that are pioneers in the field, has a well rounded curriculum, and is the center of some of the most groundbreaking bioengineering research in the nation. 
2. My decision to major in bioengineering was the natural choice given that I had interest in biology/medicine and a strong aptitude in mathematics, biology, physics and chemistry. Also, I realized that a) bioengineers learn how to think critically and become excellent problem solvers and b) are working on the cutting edge therapies and devices that expand the potential of medicine. This sealed the deal.

- How do you feel the Jacobs School has helped you be prepared for medical school and becoming a surgeon?

As I mentioned above, bioengineering has really helped me to become an excellent problem solver. My learning theory was always to master basic concepts and apply them to problems, and the curriculum at UC San Diego was very much in line with that--this meant that I was able to get ample practice and that too with extremely interesting bioengineering problems. The ability to problem solve and think critically is crucial in the field of medicine and surgery, so the development of this skill has surely helped me to prepare for my future career.
As a bioengineer, I also have a unique perspective because of the nature of the problems we solve. In one class, 186A Introduction to Biomaterials, we learned about different biomaterials, the types of responses they elicit when contacting the body, and how they can be applied to solve different bioengineering problems. At the end of this course, we were asked to design a biomaterial application and that task really helped me to apply what I had learned in the class to help address a need that we found emergent/interesting. My group worked to develop a nanoparticle treatment of glioblastoma multiforme (GBM), in which we used supraparamagnetic iron nano particles encapsulating a chemotherapy drug, functionalized with GBM targeting ligands, and encapsulated in a degrading injectable gel to treat the malignant brain cancer. The experience of understanding the disease in that depth and developing a therapy for it has given me a new look into medicine-when I practice medicine, I will be primed to look for and address needs with creative solutions. This means that in the position of physician, I can work to collaborate with bioengineering to more effectively bring in new therapies to the bedside/operating room.
I feel that the environment of the Jacobs School is one of collaboration and not competition and I think that has primed me to succeed in a career in medicine (and my peers to succeed in their field of choice). The key to success is surrounding yourself with individuals who are motivated and brilliant and working with them to learn from what they do better (improve yourself) and teach them what you do better (help them improve). In medical school, that will mean working with other intelligent students to develop as much understanding of the body (healthy and diseased). In residency, that will mean working with other physicians to improve both their and your own practice. When you are working toward the common goal of improving patient health, the point is not to compete to see who does it better but instead to collaborate and help achieve a combined greater good.

- What were your favorite classes here at UC San Diego?

My favorite classes were surely the ones that required us to apply our knowledge of concepts and facts to real-world problems, because these brought an additional excitement to the assigned tasks--these projects very well mimicked what we could go on to do in industry and showed that we as students had the ability to contribute and actually solve complex, real problems. Here are a few:
BENG 187 Design Series: We designed a device to prevent entrance of environmental toxins into the lactiferous ducts. 
BENG 125 Computational Bioengineering: We created a simplified system of equations to model the transmission of HIV/ADIS in a population (based on tweaking/simplifying existing models) and applied our qualitative understanding of differential equations to analyze and understand the behavior of the unique system.
BENG 186A Introduction to Biomaterials: As described above, we developed a targeted nanoparticle therapy of glioblastoma multiform by functionalizing the drug containing nanoparticles with GBM specific ligands and encapsulating the particles in an injectable, biodegradable gel.

- Are there any faculty members/staff members that you consider your mentors, and if yes, whom?

All bioengineering professors that I have interacted with have made themselves available for questions and to clear any doubts about the taught material. All of the professors that I have conducted research with have made sure to connect with me regularly and offer my advice/pointers/direction. 
A few: 
Professor Cabrales was the professor for the design sequence. He met with my team regularly to check in on our project progress (a few times per quarters) and made an effort to help us resolve any issues and helped to direct us to resources.
Professor Schmid-Schonbein cotaught the Mass Transfer class for bioengineers (BENG 103B) and served as advisor for my design project. He met with us weekly and helped my team to understand the need we were addressing, develop a background knowledge in the field, develop and evaluate our designs, and take the project to the next level as entrepreneurs. He advised us at every step and always made himself available for questions.
Dr. Sonia Ramamoorthy is my research mentor at Moores Cancer center. She has allowed me to shadow her in clinic and the OR to help develop a background understanding of colorectal cancer and its treatment. She then fostered my interest in clinical research by helping me to develop various projects, understand and master the IRB process, and work on data analysis. 
Dr. Adam Engler was my research mentor in my bioengineering lab research. When I was a freshman, Dr. Engler gave me the opportunity to volunteer in his lab and develop mastery of basic lab techniques. He then helped me to develop an independent project, which I was able to pursue with financial support from the CALIT2 program scholarship. He helped to to troubleshoot throughout the process (as did the graduate student who I worked with, Andrew Holle!). 

- Any engineering student organizations that you feel helped you stay connected to the campus?

The Jacobs Scholars Society is the engineering organization that I am a part of, that helps me stay connected to the campus. I, and a few other Jacobs Scholars, helped to conceive the society as a way to provide an organized way for scholars to plan social events that promote the JSS community, professional development events to help prepare the scholars, and service opportunities to allow the fortunate scholars to give back to the community. I served as VP Internal of the organization.

- Feel free to add any other thoughts about your engineering experience here at UC San Diego.

Overall, I have only good things to say about my time at UCSD and within the Jacobs School. I strongly believe that coming here is the best choice I made! I have been surrounded by motivated, intelligent individuals, eager to help brilliant advisors, and have gotten to experience a thorough curriculum focused on development of essential problem solving skills--this has helped to sculpt me into the person I am and I am sure that all that I have learned will help me in the future.