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, January 7, 2021

Triton Robosub: making progress in a pandemic

By Melissa Hernandez

The Triton Robosub team makes progress on their underwater 
autonomous vehicle design via Zoom.

Like so many student organizations in 2020, the Triton Robosub team at UC San Diego was forced to pivot from a hands-on, aquatic robotics competition to a fully online format where the team was judged on their technical designs, team video, and website. Fresh off their Blue Robotics Sponsor Award win for creatively integrating sponsored parts into their designs, the Triton Robosub team took the COVID-19-mandated distancing as an opportunity to find a way to work while following CDC guidelines, as well as improve their organization as a whole.

“That six-month remote period gave us a lot of time to critically think about our designs, really think about our software, and just overall improve a lot of aspects of the team,” said Patrick Paxson, Triton Robosub founder and computer science student. “As a group of officers, we had a clearer vision of what we wanted to work towards. This quarter we have made a lot of progress towards getting better at underwater engineering and improving a lot of aspects in terms of our robot’s hardware and software.”

Through the pandemic, Triton Robosub has been able to both continue progress on ongoing projects like FishSense, and collaborate with other engineering organizations on campus on new projects. FishSense is a handheld camera and data acquisition project done in collaboration with fellow student group Engineers for Exploration. Despite the circumstances, both organizations have been able to attend weekly meetings, maintain constant communication with each other, and will begin the device prototyping in winter quarter.

“[FishSense] is essentially a project where we develop a handheld recreational diver data acquisition system in order to measure fish length, biomass information, and species information for ocean ecosystem monitoring,” Paxson said. “We want to create a one-handed device that takes advantage of the commercially available Intel RealSense D455, a depth camera.”

With the FishSense project, both organizations contribute to the monitoring of ocean ecosystems and their maintenance. Their design testing has continued throughout fall quarter, and they plan to continue with prototyping FishSense through the winter.

Getting some pool tests in while masked.
Another project that Triton Robosub has been able to complete during this period is AI Tracks at Sea. This challenge, issued by the US Navy's Naval Information Warfare Center Pacific, was to track the longitude and latitude of boats from a provided dataset gathered from a single camera sitting at a dock that monitored boats passing by. The students had to create a computer vision algorithm capable of tracking the boats’  locations with the data provided by the Navy. 

“This was a fairly challenging project mainly because of the limitations in the hardware. Computer vision is hard to do, especially for accurately measuring things like longitude and latitude,” said Paxson. “The dataset was somewhat limited because it was hard to pick out the boat we were looking for from some of the background boats, so we had to train a custom algorithm to identify their particular boat. Another thing was that the lens was fisheye, so it was different from the human eye. The final thing is, estimating distances becomes infinitely easier when you have two cameras, similar to the way the human eye works. Unfortunately, their system is limited to one camera so we did our best. We submitted the final version on December 1st.”

The AI Tracks at Sea is a competition with monetary prizes. With a $200,000 total prize pool, Triton Robosub could place in the top seven teams and walk away with a cash prize. If they do earn a top-seven spot,  hey intend to use their earnings to fund their prototyping work for winter quarter.

Robosub has been able to stay connected to their members, sponsors and supporters through social media, but recently they also began to live stream their progress on Twitch. The team showcases the work they have been able to do, and keeps everyone updated through their live testing of the AUVs. Aside from updates, the business team has been able to set up workshops with representatives from local companies BrainCorp and Teledyne Marine to hold a resume workshop and discuss workplace expectations. The team would like to continue with these types of workshops, as well as use online platforms like Twitch and Zoom to incorporate other types of events.

“Details aren’t ironed out, but we want to have software workshops and also a high school outreach,” said Brian Chen, Triton Robosub’s social media and public relations manager. “Essentially we’re going to get members from each subteam to reach out to their old high schools’ robotics or computer science clubs to potentially work with us.”

Despite the setbacks that the pandemic has put on Triton Robosub, they have adapted to their new normal. Instead of taking the easy route of shelving projects indefinitely, the Robosub team has been hard at work with FishSense, they wrapped up work with AI Tracks @ Sea, and have plans to move forward with their original plans from past spring during spring 2021.

“We want to showcase the cool projects that we’re doing,” Chen said, “and showcase that the quarantine is not going to stop us from being productive.”

To stay connected with Triton Robosub, follow their Instagram, Facebook and website.

Friday, December 18, 2020

MAE3 Robot Competition: Animal Crossing

The annual MAE3 robot competition— part of the mechanical and aerospace engineering Introduction to Engineering Graphics and Design course— was held on Zoom for the fall 2020 class. 

This quarter's project was inspired by the popular Animal Crossing game. Students worked in teams of two or three to design and build a robot that can pick up as many "fruits" as possible and deliver them to a basket within a minute. These robots were built with the materials in a hardware kit shipped to the students, including cardboard, foam core, precut acrylic components, motors and more.

Congratulations to Andrew Hallett, Jason Howard and Parker Knopf from the winning Team 28! 

Learn more about the course and this year's teams:

Friday, November 6, 2020

Graduate students honored as mentors, leaders


Two Jacobs School of Engineering graduate students were honored with Community Awards from the UC San Diego Graduate Student Association for their contributions to graduate student life. The Community Awards celebrate faculty, staff and students who go out of their way to make being a graduate student at UC San Diego a little bit easier.

Structural engineering PhD student Adrielly Hokama Razzini was selected as the Peer Mentorship award recipient, and computer science PhD student Maryam Pourebadi was recognized with the Graduate Student Leader award. Learn more about both students below.

Adrielly Hokama Razzini

Razzini, a structural engineering PhD student, was recognized with the Peer Mentorship award for her work with graduate, undergraduate and even high school students. In addition to her role as a teaching assistant, she’s volunteered as a mentor for the Jacobs Undergraduate Mentoring Program through the IDEA Center, and has also mentored students through summer programs including Research Experience for Undergraduates and Enlace. Razzini also mentors undergraduates and a masters student in her research lab.

“In an informal capacity, I try to help my peers navigate school bureaucracy, chat about their research projects, and advise them based on my previous experiences as an international grad student,” she said.

“I've had really good mentors during my undergraduate and graduate studies, and also in industry. They've shared their knowledge and skills and helped me become a better person and professional. Being a mentor is a way of sharing my knowledge and giving back to the community, in hopes of enhancing the experience of my colleagues at UC San Diego.”

Razzini’s PhD research is in the area of structural health monitoring—the process of implementing damage detection and a characterization strategy for various structures. Her goal is to be able to monitor the wings of an airplane and assess its structural integrity in real time, using an optimal sensor placement and data interrogation process. This involves a lot of finite element modeling, signal processing, and machine learning.

“This award honors a graduate student at UC San Diego for their outstanding peer mentorship, and I feel extremely grateful to receive it. It is very nice to know that I had a positive impact on other people's lives,” she said.

She encourages any student who wants to take a more active role as a mentor to get involved in the IDEA Center’s JUMP or TEAM programs, and ask about additional opportunities within their departments.


Maryam Pourebadi

Computer science PhD student Maryam Pourebadi received the Graduate Student Leader award, given to a graduate student who has tirelessly advocated on behalf of graduate students, significantly improving their lives at UC San Diego.

She served as a leader in both the Graduate Women In Computing (GradWIC) group, and the Computer Science andEngineering Department’s diversity, equity and inclusion community.

For the past three years, I was actively involved in creating an inclusive community for masters and PhD students in the CSE department, and providing services to them.”

Pourebadi has been a member of the student admissions committee, helping review graduate student applications, and has also helped organize the PhD orientation panel for new CSE graduate students to help them get acclimated to life at UC San Diego. She also co-organized a workshop on Imposter Syndrome to make students aware of this phenomenon, and provide them with resources to combat it. Also at the department level, Pourebadi led several CSE social events, including the inaugural and second annual Waffle Social Hour, which drew more than 100 computer science students, faculty and staff.

 Through GradWIC, Pourebadi was elected as the coordinator of the group’s mentorship program, managing a group of mentors serving over 110 mentees. She also led GradWIC’s K-12 outreach program, which brought UC San Diego computer science students and staff to the Girls in STEAM Symposium at St. Margaret’s Episcopal School to share their research and experience in computer science.

 “I not only dedicated my time and energy to support my graduate fellows, but also worked toward identifying K-12 students from underrepresented minorities and encourage them to pursue their education in the STEM fields.”

 To that end, Pourebadi volunteers as an IEEE fellow judge for the SumoBot competition at UC San Diego, and as a judge for the VEX Robotics Competition; she helped open this opportunity up to other computer science graduate students as well.

 “It gives me great joy and happiness to help others and see them happy, to raise self-awareness and social-awareness, to significantly increase others' involvement in these activities, and to give back to the community by providing leadership and services in promoting equity, diversity, and inclusion in this department in a similar way that this community supported me once,” she said.

 Her PhD research focuses on building physical robots and virtual avatars that can realistically express human-like expressions and neurological impairments. This would enable platform-independent expression synthesis methods for robotic systems, and yields new modalities for interaction. Her work also has the potential to provide a realistic training tool for clinical students to better understand the expressions of patients and interact with them appropriately, which has the potential to significantly reduce the impact of patient harm.

 Her advice for students who want to take a more active leadership role?

“Think good, say good, and do good. Wherever you are and whatever your role is, do good deeds as little or as big as you can. And believe that putting all those good deeds together makes the world a better place.”


Monday, October 26, 2020

Home workspace tour: Ariane Nazemi

Electrical engineering undergraduate student Ariane Nazemi is a maker at heart. He enjoys designing, printing and painting miniature models; dabbles in printed circuit board modeling; and he even makes his own mechanical keyboards! 

As a student supervisor in the Electrical and Computer Engineering Makerspace, Nazemi had access to all the space and tools needed for these hobbies-- from 3D printers to laser cutters, soldering irons, and more. With the closure of this workspace and many campus spaces due to the COVID-19 pandemic, Nazemi decided to rearrange and spruce up his home work area.

Here's a tour of his space, featuring some of his creations. 

Wednesday, October 7, 2020

Digitizing the genome

by Cam Lamoureux, UC San Diego bioengineering PhD candidate 

The genome has historically been known as life’s instruction manual. Indeed, the genome sequence of any organism contains all of the information needed to specify its form and function, from the simplest single-celled bacterium to complex organisms such as humans. But with rapidly developing sequencing technology, the genome is taking the stage as a new type of hard drive, nature’s way of storing information.

Understanding exactly how the genome represents an organism’s information remains a challenge for scientists. Any given DNA base (A, T, C or G) in the genome sequence can be involved in multiple different functions. As part of a gene, for example, a DNA base codes for a particular building block, known as an amino acid, of the protein that the gene specifies. That amino acid, in turn, may be part of a particular shape in the final protein. The DNA base may also be part of a sequence on the opposite side of the DNA double helix that is involved in controlling another gene’s activity. With so many different functions, information encoded by the genome sequence is convoluted and overlapping, yet it is critical to understanding an organism’s behavior.

Our work in bioengineering professor Bernhard Palsson’s Systems Biology Research Group at UC San Diego addresses this challenge. We introduce a completely new way of representing this information. For every DNA base, we can answer a simple yes/no question about every type of information the sequence can encode: does this DNA base encode that information? Borrowing from computer science, we realized that the answer to this question can be thought of as a “bit,” a binary digit. By doing so, we can scan across the entire genome of any organism, ask this question, and tabulate the answer as 1 for “yes” and 0 for “no.”

With this approach, we can construct a clean, quantitative record of the bits of information that an entire genome encodes. We call this method of genome annotation the “Bitome.”

We envision that the Bitome will serve as a key foundational tool for genome engineering, with applications in the sustainable production of industrial and medical compounds. For example, bioprocess engineers who reprogram bacterial genomes to sustainably produce chemical compounds can use our method to quickly assess which parts of an organism’s genome sequence are important for their application, and which are less important. They can make predictions about how proposed changes to the genome sequence will affect the organism.

While the Bitome’s capability mirrors traditional genome browsers, our approach provides far more utility and flexibility. Because we have digitized genome information, we can perform computations on those bits of information.

As a test case, we studied the E. coli genome and showed that DNA bases that contain fewer bits of information are more likely to be mutated during adaptive evolution. Because this observation is based on information that can be encoded by any genome sequence—not just E. coli—it could be used to predict genes that are more likely to mutate in cancerous tissues, for example.

The Bitome’s digitized representation facilitates prediction with machine learning. In part of our study, we applied machine learning to pinpoint the use of a particular stop codon as a predictor of mutability. This result is significant because it provides a deeper understanding of how genes mutated during adaptive evolution, a key tool for genome engineering. We also used machine learning to predict gene essentiality directly from the genome, another key capability for engineering genomes.

We are excited by the potential future applications of the Bitome as a way of analyzing genome sequences. This concept is inherently extensible to any organism’s genome and will undoubtedly serve useful both for deeply understanding the information encoded in a genome and for predicting behavior based on that information. With this work, we hope to further bridge the gap between the genome sequence information and the complex, critical functions that it encodes.

Publication: Lamoureux, C. et al (2020) The Bitome: digitized genomic features reveal fundamental genome organization. Nucleic Acids Res.

Tuesday, September 15, 2020

Summer 2020: a virtual NASA internship

The summer of 2020 was a far-out one for many people, but for Ferrill Rushton, a 2020 electrical engineering alumnus of the Jacobs School, it was really, really far-out; to deep space, to be exact. Rushton, who is returning to UC San Diego this fall to work towards his master’s degree in photonics, was an intern at NASA’s Space Communication and Navigation (SCaN) Internship Project, analyzing photon counting methods that affect deep space communications.
The internship was designed to be an in-person research experience, but Rushton and the NASA team quickly transitioned to create a meaningful remote internship when the COVID-19 pandemic forced many plans to change.
Rushton's at-home setup for his remote
NASA internship

When electromagnetic radiation from certain deep space communications or low-power systems in low-Earth orbit gets to a receiver on Earth, there is so little incoming light that the photons actually need to be counted. Rushton’s job this summer was to quantify the inefficiency in photon counting methods in situations where a ground station is detecting incoming light from these photon-depraved situations. The results from his project—Finding the Modes of Arbitrary 2D Geometries Using Finite Difference Techniques—will be incorporated into existing NASA frameworks.
“I don’t feel like I was given work just so there could be an internship, they had all this real work for us,” Rushton said.
The internship allows students to perform hands-on training with real mission scenarios, gain exposure and analyze powerful space communication systems, utilize networks software tools and effectively communicate their findings in a final presentation to NASA management. Each student is paired with an experienced and multidisciplinary mentor who counsels the student with his/her work, and also engages with career planning.
Rushton speaking with former NASA astronaut
Alvin Drew during his virtual 2020 NASA internship. 
At UC San Diego, Rushton was involved with SPIE—the International Society of Optics and Photonics—serving as treasurer of the UC San Diego branch last year. He is also involved in Engineers for Exploration, on the Maya Archaeology team.
His advice to current and future students?
“If there's something that you want, there's no reason not to apply for it. Never be afraid to put yourself out there.”