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

UC San Diego at RoboCup 2017

Darren Chen, a Ph.D. student in computer science at UC San Diego, had just landed in Japan when he saw ads in the subway for the competition he was going to take part in. "I realized it was a big deal," he said. He might even have panicked a little, he admitted.
In fact, the competition, called the RoboCup, brought more than 10,000 spectators and competitors to Nagoya, Japan at the end of July. The event, which is broadcast on Japanese TV, was celebrating its 20th anniversary. 
Chen was part of a team of Ph.D. students from the Contextual Robotics Institute here at the Jacobs School that was taking part in the event's RoboCup @ Home challenge. It was UC San Diego's first time taking part in the competition.
In the @ Home challenge, 10 universities from around the world compete to complete a series of tasks by programming and training a Toyota Human Support Robot. The UC San Diego team had to sort groceries and help a person carry grocery items.
 In addition, they faced a task to qualify. On the fly, they had to program the Toyota robot to autonomously navigate and map out a room without bumping into people and objects. The robot also had to be able to obey verbal commands in a noisy environment.
But the team's worst foe turned out to be the venue's WiFi. When 10,000 people were using the same radio band, it became difficult for the robot to communicate with other computers quickly.
The researchers enjoyed the experience of participating in the competition, and look forward to continuing to build assistive robots in the future.
In addition to Chen, the team working on the RoboCup @ Home challenge included   Angelique Taylor, Priyam Parashar  and Ruffin White as well master's student Jaskaran Virdi from the research groups of computer science professors Laurel Riek and Henrik Christensen. Christensen is the director of the Contextual Robotics Institute.
More info: http://jacobsschool.ucsd.edu/news/news_releases/release.sfe?id=2268

Two of the UC San Diego Ph.D. students taking part in the competition, as seen by the Toyota robot.

Darren Chen, center, and Angelique Taylor, right, are two Ph.D. students in the research group of Professor Laurel Riek. 

Taylor has some fun with the robots on exhibit at RoboCup.

UC San Diego Engineering Student Wins First Place Overall at Target Team Hackathon

August 18-20, 2016, Target hosted a three-day Diversity Leadership Symposium, inviting undergraduate students across the nation to collaborate and devise strategies to address diversity and inclusion in the retail industry. Tony Melano-Gonzales, a transfer student and senior computer science major at UC San Diego, was invited to apply after a recruiter saw his profile on Piazza.

Gonzales learned about engineering careers in merchandising as well as advancements in finance and technology. In addition to panels, networking sessions, and workshops, he participated in Target’s case study hackathon and won first place with his team of four.

Target’s hackathon challenged competitors to develop an application that engages guests both inside and outside the store. The teams had to complete their hack within a three-hour time frame. In particular, the participants were to focus on the millennial market, including styling and baby products.

Gonzales and his teammates created Wishbone, a native Facebook chatbot that transforms ordinary situations into consumer products.

Gonzales explains, “Sometimes you go to Target and you know exactly what you want - shoes, Advil, a new backpack - but other times, you just want to stop by on the way to the beach, the movies, etc. With Wishbone, users can ask ‘What do I need for the beach?’ or say ‘I'm throwing a baby shower’ and the application connects them with real relevant products.”

Users may browse the recommended list, add their desired products to their cart, and check out on Target’s website — all with the chatbot Wishbone.

The first-place application garnered Gonzales $2000 in rewards to continue his journey here at the Jacobs School of Engineering. Many congratulations to Gonzales!

Engineers turn out in force for Triton 5K

Jacobs School of Engineering students, alumni, faculty and staff achieved an elusive trifecta at this year's Triton 5K race.  The Department of Computer Science and Engineering fielded the largest overall team--226 strong. The team also raised the most funds: $6,334. It's named Race Condition--a play on words on a computer science term that means a behavior that happens when a device or system tries to perform two or more operations at the same time, but can't because of its very nature. Some members of the team flew from as far as New York. Meanwhile, the Department of Electrical and Computer Engineering fielded the largest campus team-- 82 strong.

The Triton 5K raises funds for scholarships for UC San Diego students. This year, in addition to the race run on campus, teams also ran in China, Taiwan and the United Kingdom. The event is sponsored by a number of organizations and alumni.

It wasn't just departments that turned out. Global TIES fielded an all-female team. Photo above: from left: Jamie Bradley Steck, alumnus of Global TIES and computer science (master's), now a lecturer for Global TIES; Global TIES Program Director Mandy Bratton; Chonlada "Pam" Woointranon a senior majoring in management science and computer science; Regina Caluya, a chemical engineering senior; Christina Aguila, chemical engineering senior and Brooke Ryan, a computer science junior. The latter four are undergraduate project advisors for Global TIES.

Here is a snapshot of some members of Race Condition:

And some snapshots from the Department of Electrical and Computer Engineering, including Chancellor Pradeep K. Khosla:

#ILookLikeAnEngineer: Akanksha Kevalramani

Here is the next profile of our campaign! Akanksha is an international student at UC San Diego, with a focus on coding and a passion for equal representation STEM.

Name: Akanksha Kevalramani

Major: Computer Science

Estimated graduation date: June, 2018

Why did you choose engineering at UC San Diego?

I chose engineering at UC San Diego because I was really impressed by how far this university had come in such a short time, and I could see this university growing a lot in the years to come in terms of education, infrastructure and research opportunities. Other factors that mattered to me and impressed me were the attitude and enthusiasm of the student body, the living conditions, the location and the weather.

What are your career goals?

I want to be involved in something that really makes a difference in the field of Computer Science, and in the process of doing that, I'd also love to be able to affect the way women are represented in STEM fields.

Do you have a favorite quote or mantra?

This is a tough question because there are so many, but out of hundreds of quotes that I like and also believe in, one of my favorites is ‘Live & Let Live.’

What are three things that make you your own individual?

1. I'm always the quiet one in the group who's usually listening and observing.
2. I'm kind of a perfectionist and always prefer having things done my way.
3. I try my best to not be hesitant and to stand up for any unfair treatment I see around me.

What does this campaign mean to you?

I've been really lucky to be surrounded by people who've always supported and believed in me, but I've seen so many people being told what they can and cannot do based on their gender, body shape, skin color and race, among other things. I truly believe that everyone deserves an opportunity to prove that there’s more than what meets the eye. I believe that no one should be judged or mistreated based on another’s assumptions. I believe this campaign is an excellent way to raise awareness about that, and the fact that people here care about things like these makes me even more proud of UC San Diego.

Computer science teaching professor featured in Labor Day news story

Congratulations to computer science teaching professor Mia Minnes, who is featured in the Labor Day issue of UT San Diego!
Minnes was hired this year after serving as a postdoctoral visiting assistant professor in the Department of Mathematics at UC San Diego from 2010 to 2014. In addition to teaching many introductory and advanced undergraduate classes in the department, she works on outreach and research projects, including the five-week residential Summer Program for Incoming Students, which she co-developed. She's also the faculty sponsor for the Summer Internship Symposium for the Department of Computer Science and Engineering.
Read the full story here.

Don't drink and drone: Jacobs School alumns launch Kickstarter to create drone pilot flight school

"Don't drink and drone!" That's the advice in this fun video produced by SparkAerial, a start-up co-founded by Jacobs School computer science alums Radley Angelo, Kurt Selander and Austin Hill. The company bills itself as a full-service UAV shop and offers for example custom-built quadcopters and other flying UAVs and aerial cinematography services.

The team got their start in the Engineers for Exploration program here at the Jacobs School. Their got to accompany researcher Albert Lin on his expedition to find Genghis Khan's tomb in Mongolia. Since then, their work has been featured on CNN, Good Morning America and the National Geographic Channel, among many others.

They have recently launched a Kickstarter to create a drone pilot school. So far, with 26 days to go, backers have pledged $3,115 of a $5,000 goal. The money would go to creating an aerial cinematography video training series and an online resource center for aspiring drone pilots.
According to their Kickstarter page:

Our goal here is simple; we want to teach the world how to have fun, fly safe, and capture amazing content. The series covers everything from the basics, like choosing a copter and taking off for the first time, to more advanced piloting maneuvers that will make your video the talk of the town.

CSE-Related Research and Researchers Dominate USENIX Security Forum

Here's an alert to graduate students in CSE who want to attend the 23rd annual USENIX Security Symposium that will take place August 20-22 at the Manchester Grand Hyatt San Diego. The conference has extended the deadline for students to apply for travel, accommodations and/or registration grants to attend this year's event. The new deadline is Monday, July 14, and applications must be submitted online (see link below).

USENIX Security is one of the "big three" conferences in computer security, and this year's meeting is going to showcase the work of current faculty and grad students, but also the work of UC San Diego CSE alumni. CSE Prof. Hovav Shacham (pictured at right) is the senior author of a paper, "On the Practical Exploitability of Dual EC in TLS Implementations," co-authored with colleagues including grad student Jake Maskiewicz and CSE alumni Stephen Checkoway (now at Johns Hopkins) and Tom Ristenpart (University of Wisconsin-Madison). Shacham is also senior author on another paper with co-authors from UC San Diego and the University of Michigan. CSE Ph.D. student Neha Chachra(at left during previous internship at Google), advised by Geoffrey Voelker and Stefan Savage in the Systems and Networking group, is one of the co-authors on a paper titled, "Hulk: Eliciting Malicious Behavior in Browser Extensions." In addition to Chachra, the co-authors on the Hulk paper hail from two other University of California campuses -- three co-authors from UC Santa Barbara, and two from UC Berkeley and the International Computer Science Institute, including senior author Vern Paxson.

In addition to the paper above, CSE alumnus Tom Ristenpart (Ph.D. '10) has three other papers on the USENIX Security program. Both Ristenpart and Georgia Tech professor Alexandra (Sasha) Boldyreva (Ph.D. '04) studied under CSE Prof. Mihir Bellare, and Boldyreva also has a paper at USENIX Security this year. Another CSE alumnus, Stephen Checkoway (Ph.D. '12), had four papers accepted (two of them co-authored with UC San Diego researchers). A fourth CSE alumnus, Chris Kanich (Ph.D. '12) -- now an assistant professor at the University of Illinois at Chicago -- also has a paper ("The Long 'Taile' of Typosquatting Domain Names"). Pictured above (l-r): CSE alumni Ristenpart, Checkoway, Boldyreva and Kanich.

According to Center for Networked Systems director Stefan Savage, CSE's intellectual imprint on USENIX Security 2014 goes beyond the individual papers. "There are two sessions whose purpose is driven by our past work," said Savage. "There is a session on return-oriented programming (ROP) that is driven entirely by Hovav Shacham's seminal work on ROP. On top of that, roughly 75 percent of the side-channel session is motivated by the work Tom Ristenpart did here at UC San Diego on cross-VM attacks in the cloud."

Deciphering CSE's Upcoming Presence at Crypto 2014

CSE professors Mihir Bellare and Daniele Micciancio will be in Santa Barbara August 17-21 for the 34th International Cryptology Conference at UC Santa Barbara. The conference is sponsored by the International Association for Cryptologic Research (IACR), and the general chair of the conference is CSE alumna Alexandra (Sasha) Boldyreva (Ph.D. ’04), who worked in Bellare’s lab and is now an associate professor in Georgia Tech’s Information Security Center.

This year’s IACR Distinguished Lecture will be given by UC San Diego’s Bellare (pictured at left). The title of his talk: “Caught in between theory and practice.”  “This talk explores the culture and motivations of the cryptographic research community,” explains Bellare. “I examine the tension between theory and practice through the lens of my own experience in moving between them. I examine the peer-review process through the lens of psychology and sociology. In both cases the aim is to go from critique to understanding and, eventually, change.”

Bellare also has two other papers at Crypto 2014. In the August 18 opening session, he and colleagues Kenneth G. Paterson (University of London) and Phillip Rogaway (UC Davis) have a paper on "Security of Symmetric Encryption against Mass Surveillance." According to its authors, the research was “motivated by revelations concerning population-wide surveillance of encrypted communications.” In the paper, Bellare and colleagues formalize and investigate the resistance of symmetric encryption schemes to mass surveillance. The research abstract notes that, “We assume that the goal of ‘Big Brother’ is undetectable subversion,” going on to spell out a way to defend against so-called algorithm-substitution attacks (ASAs), which aim to replace a real encryption algorithm with a subverted encryption algorithm.

Separately, Bellare and his postdoc (Viet Tung Hoang), and Ph.D. student Sriram Keelveedhi teamed on a paper called, "Cryptography from Compression Functions: The UCE Bridge to the ROM." UCE stands for Universal Computational Extractor, and ROM is the Random Oracle Model.

Then on August 19, in a session on lattices, Micciancio (at right) and his French postdoc Léo Ducas have a paper on “Improved Short Lattice Signatures in the Standard Model.” They will present “a signature scheme provably secure in the standard model (no random oracles) based on the worst-case complexity of approximating the Shortest Vector Problem in ideal lattices within polynomial factors” – achieving short signatures (consisting of a single lattice vector), and “relatively short” public keys.

Lead architect of IBM's 1 million neuron neuromorphic chip is a Jacobs School alum

Huge congratulations to Jacobs School alumnus Dharmendra Modha, the principal investigator on the DARPA SyNAPSE project, which announced last week that it had built a one-million-cores neuromorphic chip and published its results in the journal Science.

The chip, called True North, was developed at IBM Research, where Modha leads the company's Cognitive Computing Group. It's "a synaptic supercomputer in your palm," Modha writes on his blog.
It also consumes dramatically less power than a supercomputer--70 milliwatts, or what it takes to power a hearing aid, according to The New York Times.

Also on the blog, Modha also writes:

The architecture can solve a wide class of problems from vision, audition, and multi–sensory fusion, and has the potential to revolutionize the computer industry by integrating brain–like capability into devices where computation is constrained by power and speed. These systems can efficiently process high–dimensional, noisy sensory data in real time, while consuming orders of magnitude less power than conventional computer architectures.

Modha also wrote a related article on the IBM Research website:

Introducing a Brain-inspired Computer 
TrueNorth's neurons to revolutionize system architecture

Modha earned a Ph.D. in electrical engineering in 1996, under now-retired professor Elias Masry and Robert Hecht-Nielsen, now an adjunct professor in ECE.
When we asked him back in 2009 what he had learned here at the Jacobs School, he said:

I owe a great debt to UCSD, and to my many wonderful professors from the Jacobs School, especially Elias Masry and Robert Hecht-Nielsen, for their priceless gift of education," says Modha, who recently returned to the Jacobs School for a visit. "Fundamental training persists. Professors change lives when they teach thinking, when they teach students how to approach any problem - how to rigorously break down any problem and deal with it," says Modha.

"Now, as a proud UC San Diego alumnus, I am staying connected and working with our university to raise the visibility of the accomplished students, faculty and alumni who add value to our degrees every day."

Computer scientists in the spotlight on the Torrey Pines Mesa

Several Jacobs School computer scientists and their work are highlighted in a UT San Diego story about the history of the scientific institutions on the Torrey Pines Mesa.

Under the major science accomplishments section:

•Computer scientist Kenneth Bowles and his students modified the Pascal programming language, allowing a program to be moved around from machine to machine, a technique now widely used to build mobile applications.

 •George Varghese and Stefan Savage developed the first automated method for automatically identifying worm and virus attacks across the Internet and other high-speed networks almost as soon as the outbreaks occur. Cisco acquired the technology.

We also spotted computer scientists Ryan Kastner and Mia Minnes in the video accompanying the story:

Cybersecurity experts call for better automotive cyber safety, echoing Jacobs School research findings

A group of cybersecurity experts has announced a Five Start Automotive Cyber Safety Program at the annual Defcon conference in Las Vegas this week to prevent cars from being hacked, a threat that was first pointed out by a team of computer scientists here at UC San Diego and at the University of Washington back in 2010.

The group, called I am the Cavalry, breaks down the five stars as follows:
Safety by Design
Third Party Collaboration
Evidence Capture
Security Updates
Segmentation and Isolation

Savage and colleagues explain the threat in the video below (courtesy of Motherboard):



More on the research here. 

Q&A with Janis Jimenez, intern at ViaSat

Janis Jimenez, a computer science major at the Jacobs School of Engineering at UC San Diego, is participating in ViaSat Inc.’s internship program this summer. The internship program selects student interns every summer from the best universities to work at ViaSat and contribute to real projects. For example, these projects include assisting in test and development of ViaSat satellite communications systems. Janis is working at the company’s Carlsbad office with the Architecture-based Enterprise Systems Engineering (AESE) department. In this Q&A (courtesy of ViaSat) she talked about her experiences.

 Q: What is the focus of your internship project?

A: Our department is AESE.  We are working on a web application that combines business metrics for the company along with security.  That was our project summary when we were hired. Things have stayed pretty vague because they have let us have some input.

Q: Why did you want to intern at ViaSat?

A: I heard from other people that I would be working with a team of interns. I have only been a single intern on a team of full time employees before. So it was something new to try out.

 Q: What is the best part about working with your team? Or supervisor?

A: The best part is that we are all in the same room, so we get to communicate a lot. If we get stuck we can just ask each other for help or we come up with better ideas by brainstorming on the whiteboard.

Q: What is the one thing you are hoping to accomplish during your internship?

A: I am hoping to pick up several new technologies, which I have already started doing. Specifically new languages and software.

Q: What has been your favorite meal at ViaSat so far?

A: I really like the meal at the most recent Tech Talk. It had two different types of pastas, bread, and a dessert. It was great.

Q: Favorite place to work on the Carlsbad campus?

A: I like to stay in the office. We have an office with a window and it is pretty nice in there.

Q: What is one word that describes your internship experience?

A: Collaborative

Q: After the internship ends, what is one thing you will take with you?

A: Experience of the office atmosphere, especially working with a team in a full time job.

Q: One fun fact about yourself!

A: I played the piano and clarinet. 

Robot and computer scientists featured on Innovate 8 TV show

MiP, the robot created by the UCSD Coordinated Robotics Lab and WowWee and ThoughtSTEM, a company founded by two Jacobs School computer science grad students were recently featured on Innovate 8, a program produced by CBS News 8 in partnership with UC San Diego and the San Diego County Office of Education. 
Watch below:

Google Tango Project / New video game from UC San Diego alumni

Last week, the UC San Diego computer science alumni behind Limbic Software announced a new game at the Google I/O Conference called Zombie Gunship Reality.

The game is slated to be one of the first generation to take advantage of the precise localization provided by Project Tango hardware and incorporate that into the game. The “history” paragraph on the game’s press website provides some context:

“As children, we often pretended to fly airplanes around the house, dropping bombs on flowerpots and landing on couches. With the 3D-positioning technology Project Tango makes available to us, we are able to turn that dream into reality. Players can now "become the gunship" and interact with the game world as never before, climbing onto chairs for a high vantage point, or getting down close to the ground for short-range shooting. A totally immersive new experience is now possible with Zombie Gunship Reality.”

Pretty cool.

Below is the boiler plate for Limbic.

Limbic Software, Inc. (www.limbic.com) is an independent entertainment company and Google Play Top Developer founded in 2008 by Arash Keshmirian, Iman Mostafavi, and Volker Schönefeld. Limbic's award-winning debut title, TowerMadness, launched in 2009. Their subsequent hit mobile games Nuts! and Zombie Gunship have helped them amass over thirty million downloads across their portfolio of original games. Craftsmanship and a commitment to creating the best gaming experience have won them legions of dedicated fans across the world.

(In March of this year, Keshmirian ('05, M.S. '08) spoke at a UC San Diego alumni gathering in Silicon Valley. His talk: “Sheep, Zombies,Squirrels, Aliens and Gunships: Five Years Climbing the App Store.”) Thanks for giving the talk, Arash!

Computer science Ph.D. student quoted in The New York Times about getting girls interested in programming

We are very excited to see that Jacobs School Ph.D. student Stephen Foster quoted in an opinion piece in The New York Times about getting girls interested in programming.
Forster is a co-founder, with fellow Ph.D. students Sarah Foster and Lindsey Handley, of ThoughtSTEM, a nonprofit organization that teaches children how to code here in San Diego. He talked to the author of the New York Times piece, Nitasha Tiku, the editor of Valleyway, Gawker's blog about the tech industry:

“Students kept walking in asking to learn how to code wearing Minecraft T-shirts,’” said Stephen Foster, a founder of the San Diego-based organization ThoughtSTEM, which teaches kids ages 8 to 18 to code in after-school programs and summer camps. “Once it happened the 20th time, we started to realize, ‘Oh, hey, maybe these kids know something that we don’t.’ ”

So ThoughtSTEM started offering Minecraft 101 classes at UC San Diego Extension. The organization also makes a special effort to enroll girls.  Foster told The New York Times:

A hundred students were on ThoughtSTEM’s waiting list for its first Minecraft class two months ago. “I would say that the girls are actually outperforming the boys, at least in my class,” Mr. Foster said. “And it’s very good to see, because as computer scientists, we definitely recognize that there’s a big gender disparity in our field.” He added, “There are just so many girls who play Minecraft who, as far as I’m concerned, are all people who can be swayed to pursue coding — they just don’t realize it yet.”

"ThoughtSTEM is a proud supporter of getting more girls and women into computing," Esper said. "With a majority of female co-founders, we are so excited to be featured as a company making headway, not just in computer science education, but in engaging a more diverse group with curriculum and programs that attract students of all kinds."