Alumni faculty profile: Olivia Graeve

It’s no secret that UC San Diego’s reputation as a top-ranked university is a major draw for prospective students—but it’s also pulling many graduates back to campus to serve as members of the faculty. In classrooms and labs across the university, our alumni are leading new directions in research and helping to train the next generation of innovators.

“We’re proud to have so many talented graduates who return to campus as faculty members, bringing with them fresh thinking that enriches our academic community,” said Chancellor Pradeep K. Khosla. “UC San Diego is ranked the 15th best university in the world, a testament to our faculty and students.”

 Olivia Graeve is a professor of mechanical engineering at the Jacobs School of Engineering and a proud native of the San Diego-Tijuana region. She grew up in Tijuana and attended Southwestern Community College before transferring to UC San Diego to study structural engineering. As an undergraduate, she worked in the lab of Professor Joanna McKittrick and saw first-hand what it takes to run a research laboratory.

“The experience put me on an excellent path toward the professoriate,” she said.

Graeve is working on developing materials that can withstand extreme impacts and are faster and more cost-effective to manufacture. Earlier this year, her lab developed a record-breaking steel alloy—a material that could be used for everything from drill bits, to body armor for soldiers, to meteor-resistant casing for satellites.

Graeve held faculty positions at the University of Nevada, Reno and Alfred University in New York before joining the UC San Diego faculty. Reflecting on how the campus has changed since she was a student, Graeve says that UC San Diego is bigger and better, with more opportunities for students, staff and faculty.

Today, she’s doing her part to ensure the university continues on its upward trajectory. Graeve leads a number of outreach programs for underrepresented students on both sides of the border. She also serves as director of the CaliBaja Center for Resilient Materials and Systems, which brings together researchers across the San Diego-Tijuana region.

“The opportunity to serve my alma mater and the region in which I grew up is something that is very important to me,” said Graeve. “Coming back to UC San Diego was coming home. Who would not want to be home?”

Contextual Robotics Forum at UC San Diego on Oct 10, 2014

Attend UC San Diego’s International Forum on ContextualRobotics Technologies on OCTOBER 10, 2014

Ubiquitous Consumer Robotics
Join us at this one-day forum. Explore the future of ubiquitous consumer robotics and its potential to revolutionize medicine, agriculture, environmental monitoring, disaster response and more.

Meet the Robotics Community
This interactive event includes multiple networking sessions with speakers, UC San Diego faculty and attendees. Learn more about UC San Diego’s vision and plans for robotics research and technology development. 

FORUM SPEAKERS

Matt Grob
CTO, Qualcomm

Vijay Kumar
UPS Foundation Professor, U. of Pennsylvania

Chris Anderson
Co-Founder and CEO, 3D Robotics

Gill Pratt
Program Manager, DARPA

Brad Nelson
Professor of Robotics and Intelligent Systems, ETH-Zurich

Dean Kamen
Founder, DEKA Research
Founder, FIRST competitions

Daniela Rus
Director, the Computer Science and Artificial Intelligence Laboratory (CSAIL), MIT

Rodney Brooks
CTO, Rethink Robotics

REMARKS

Pradeep K. Khosla
Chancellor, UC San Diego

Albert P. Pisano, Dean
Jacobs School of Engineering

Ramesh R. Rao, Director
Qualcomm Institute

Krstic Wins Chestnut Textbook Prize

Miroslav Krstic, professor of mechanical and aerospace engineering and associate vice chancellor for research at UC San Diego, has received the triennial Chestnut Textbook Prize awarded by the International Federation of Automatic Control (IFAC).

His book, Boundary Control of PDEs, earned the following citation from the award committee: “This textbook makes the difficult subject of control of partial differential equations accessible to engineering students for the first time. It fills a decades-long need in control education. It covers, at an introductory level, a wide spectrum of physically relevant topics. The clarity and thoroughness of the presentation have already earned it a broad audience and its impact is already exceptional and will continue to grow within and beyond the field of control engineering.”

Krstic also serves as Director of the Cymer Center for Control Systems and Dynamics at the UC San Diego Jacobs School of Engineering. 

He received the award in Cape Town, South Africa, in late August. The award honors the memory of Harold Chestnut, the founding president of IFAC (1957), president of IEEE (1973), and member of National Academy of Engineering (1974).

IFAC, founded in 1957, is a multinational federation of national member organizations representing the engineering and scientific societies concerned with automatic control.

The federation promotes the science and technology of control systems.

Juan C. Lasheras Joins NIH MABS Study Section

Distinguished Professor Juan C. Lasheras from UC San Diego has accepted an invitation from the U.S. National Institutes of Health (NIH) to serve as a member of the Modeling and Analysis of Biological Systems Study Section, which reviews grant applications for scientific merit as a part of the NIH Center for Scientific Review.

The Modeling and Analysis of Biological Systems Study Section (MABS) reviews NIH grant applications concerned with the development of modeling / enabling technologies for understanding the complexity of biological systems. The scope of these systems ranges from molecular, to supra-molecular, to genes, to organelles, to cellular, to tissue and to organ level studies.

In March 2014, Lasheras and a team of biologists and engineers from UC San Diego published a paper in the Journal of Cell Biology (JCB) in which they reported their discovery that white blood cells move to inflamed sites by walking in a stepwise manner. The cells, the researchers found, periodically form and break adhesions mainly under two “feet,” and generate the traction forces that propel them forward by the coordinated action of contractile proteins.

Their discovery, which was highlighted on the cover of the March 17 issue of JCB, is an important advance toward developing new pharmacological strategies to treat chronic inflammatory diseases such as arthritis, irritable bowel syndrome, Type 1 diabetes, and multiple sclerosis.

The paper is titled “Both contractile axial and lateral traction force dynamics drive amoeboid cell motility” Read the UC San Diego press release here.

Modeling and Analysis of Biological Systems

Tools developed by grants funded by the NIH Modeling and Analysis of Biological Systems study section are characteristically applied to further understanding of interactions and integrations through levels and scales and the emergence of patterns that help to explain system behavior.

Members are selected on the basis of their demonstrated competence and achievement in their scientific discipline as evidenced by the quality of research accomplishments, publications in scientific journals, and other significant scientific activities, achievements and honors. 

Professor Lasheras, for example, holds the Stanford S. & Beverly P. Penner Professor in Engineering or Applied Science endowed chair at the UC San Diego Jacobs School of Engineering. A member of the National Academy of Engineering, Lasheras is a faculty member in the Department of Mechanical and Aerospace Engineering at the Jacobs School.

Professor Lashers serves as Director of the Center for Medical Devices and Technology, part of the Institute for Engineering in Medicine at UC San Diego. He is a Faculty Director of the Medical Device Engineering executive master’s degree program at the UC San Diego Jacobs School of Engineering.

Lasheras joins UC San Diego bioengineering professor Andrew McCulloch on the 16-person Modeling and Analysis of Biological Systems Study Section. UC San Diego is the only university with more than one professor on this NIH study section. 

Computer science department hires two faculty

In the face of heavy enrollment and strong demand for computer science education, the Computer Science and Engineering (CSE) department at the University of California, San Diego is expanding its faculty. CSE Chair Rajesh Gupta recently announced two more new faculty hires in the department, indicating that there will also likely be more announcements to come. Following the recent hiring of lecturer Mia Minnes, CSE has recruited two assistant professors who will join the faculty as of July 1, 2014: mathematician and computer scientist Daniel M. Kane, and datacenter and networked systems expert George Porter.

Porter is not a newcomer to CSE or UC San Diego (which may be why he opted to stay despite several competing offers). The former research scientist and associate director of the Center for Networked Systems (CNS) now becomes an assistant professor in the department, where he will continue his work at the intersection of computer networks and data-intensive computing. Porter will remain associate director of CNS. For most of his time at UCSD, Porter has also been a key player in the NSF-funded Center for Integrated Access Networks (CIAN). Since arriving on campus in 2009, Porter has been involved in a long series of industry grants as principal investigator or co-PI. These include projects funded by Cisco Systems, Google, Ericsson and NetApp (a faculty fellowship in 2011). Porter also designed and built the Scalable Energy Efficient Datacenter (SEED) testbed, and he was a co-PI on the Mordia project, which developed a microsecond optical research datacenter interconnect architecture (with primary funding from Google). A team of CSE graduate students and Porter achieved world records back-to-back in 2010 and ’11 in the SortBenchmark.org competition. In 2010 they broke two records for highly efficient sorting, and the following year they came out on top in five categories.

Going forward, Porter is PI on a major project funded by NSF through mid-2016. The large-scale Networking Technology and Systems (NeTS) research project on "Hybrid Circuit/Packet Networking" is developing a hybrid switching paradigm that spans the gap between traditional circuit switching and full-fledged packet switching. "The hybrid model will allow us to achieve a level of performance and scale not previously attainable," said Porter. "This will result in a hybrid switch whose optical switching capacity is orders of magnitude larger than the electrical packet switch, yet whose performance from an end-to-end perspective is largely indistinguishable from a giant (electrical) packet switch." If successful, Porter and his co-PIs (CSE's Alex Snoeren as well as ECE's George Papen and Joseph Ford) will produce a system that stands to dramatically improve data center networks by increasing energy efficiency and significantly reducing operating costs.

Daniel Kane is moving to San Diego from Palo Alto, where he has been a postdoctoral researcher in the Department of Mathematics at Stanford University on an NSF Postdoctoral Research Fellowship. Kane will be based in CSE, but with a dual appointment in the Department of Mathematics. Prior to Stanford, he attended graduate school in mathematics at Harvard University (Ph.D. '11, MS '08). Before that, with a perfect GPA, Kane received two BS degrees at MIT in 2007, one in mathematics with computer science, the other in physics.

Kane has diverse research interests in mathematics and theoretical computer science, though most of his work fits into the broad categories of number theory, complexity theory or combinatorics. "My mathematics work has tended to focus on analytic number theory," said Kane. "My computer science work has typically involved k-independence, polynomial threshold functions or derandomization." In 2013, he received the Best Paper award at the Conference on Computational Complexity, and a decade earlier Kane – as a member of the USA team – won a gold medal at the International Mathematical Olympiad in 2002 and again in 2003.

Both Kane and Porter are members of the Association for Computing Machinery. Kane is also a member of the American Mathematical Society and the Mathematical Association of America. "George and Daniel are wonderful additions to the Computer Science and Engineering faculty," says CSE chair Gupta. "We also owe a big thanks to our recruiting committee that continues to attract compelling talent to the department! And yes, I do look forward to repeating this sentence again this recruiting season!"

See Clean Tech and Energy Research Advances from UC San Diego Engineers at Research Expo 2014

With more than 1,700 engineering graduate students, 200 engineering professors and $158M is engineering research expenditures, the UC San Diego Jacobs School of Engineering is teeming with exciting projects and entrepreneurial engineers looking to transfer their advances to society in order to solve problems, advance technology and make the world a better place. A good sized chunk of the Jacobs School’s graduate students and professors are working on research that can be leveraged to address our global clean-technology and energy challenges.

At Research Expo 2014 on April 17, UC San Diego engineering graduate students will present about 35 posters that the students have specifically tagged as relevant for “clean technology / energy” applications. But no doubt, more of the 200 students presenting at Research Expo are working on engineering challenges that are relevant for emerging clean technology and energy applications.

Below are just a few of the official clean-tech and energy posters. Have a look at the entire list of poster titles here. When you register for Research Expo, you get access to the full abstracts of each poster.

In addition to the posters session, Research Expo includes six fast-paced faculty talks and a networking reception…all during the afternoon of April 17, here at UC San Diego.

Research Expo admission is $100. Half-price for UC San Diego alumni. Our Corporate Affiliates Program members receive 2-for-1 admission.

28. WORKLOAD SHAPING TO MITIGATE VARIABILITY IN RENEWABLE POWER USE BY DATA CENTERS
Student: Muhammad Abdullah Adnan
Professor: Rajesh Gupta
Industry Application Area: Energy/Clean technology

42. USING OPTICAL NETWORKS IN THE DATA CENTER FOR ENERGY EFFICIENCY
Students: Henrique Da Silva Rodrigues, Henrique Rodrigues
Professor: Tajana S. Rosing
Industry Application Areas: Electronics/Photonics | Energy/Clean technology | Internet, Networking, Systems

93. ONLINE OPTIMIZATION OF WAVE ENERGY CONVERTERS
Student: Daniele Cavaglieri
Professor: Thomas R. Bewley
Industry Application Areas: Control Systems | Energy/Clean technology

109. PREPARATION OF HEXABORIDE NANOCUBES FOR HYDROGEN STORAGE APPLICATIONS
Student: James Timothy Cahill
Professor: Olivia A. Graeve
Industry Application Areas: Aerospace, Defense, Security | Energy/Clean technology | Materials

112. POWERING THE FUTURE WITH SOLAR ENERGY: ASSESSMENT, FORECASTING AND INTEGRATION STRATEGY
Student: Dung Nguyen
Professor: Jan P. Kleissl
Industry Application Areas: Control Systems | Energy/Clean technology | Software, Analytics

120. DECENTRALIZED CHARGING CONTROL FOR ELECTRIC VEHICLES
Student(s): Andres Ivan Cortes 
Professor: Sonia Martinez Diaz
Industry Application Areas: Control Systems | Energy/Clean technology

165. STRETCHING AND CONFORMAL BONDING OF ORGANIC SOLAR CELLS TO HEMISPHERICAL SURFACES
Student: Timothy Francis Oconnor
Professor: Darren J. Lipomi
Industry Application Areas: Electronics/Photonics | Energy/Clean technology | Materials

San Diego Companies Looking for Engineering Talent: Attend Research Expo at UC San Diego

Find engineering talent at Research Expo on April 17

ResearchExpo is a great way to connect with the big ideas, graduate students and faculty of the Jacobs School of Engineering at UC San Diego.

  

The Top Five Reasons to Attend Research Expo on April 17:

5. Early Access to Ideas and Technologies
At the 200+ poster session, get an early look at big ideas and advances in engineering and information technology. Browse poster titles here. For access to poster abstracts before the event, register now. 

4. Lightning Talks from Engineering Faculty
Ten-minute talks from top faculty from all six engineering departments. Talks cover composite aircraft safety; robotics and education; trainingtomorrow's data scientists; 3D-modeling and healthcare; injectable biomaterials; and wearable sensors. 

3. Stretch your Mind...and your Legs
Enjoy a productive and interactive afternoon on campus. (The new networking app Whova from UC San Diego computer science prof. YY Zhou is in the mix.)

2. Make the Most of this World-Class Engineering Resource
You have a top-ranked, innovative engineering school in your own backyard. Make the most of the opportunities.

1. Connect with 200+ Graduate Students
At the poster session and networking reception, recruit top talent or spark a collaboration. 

Attend Research Expo at the Jacobs School of Engineering

When: Thursday, April 17 from 2:00-6:00 p.m.
Where: UC San Diego Price Center
Register Today: www.jacobsschool.ucsd.edu/re

Half-Price Admission for UC San Diego Alumni
2-for-1 Admission for members of the Corporate Affiliates Program

Faculty Speakers at Research Expo

Six professors from the Jacobs School of Engineering will speak at Research Expo on April 17. (One professor from each of the six departments.)

2:30 pm: Hyonny Kim (Structural Engineering)
2:50 pm: Thomas Bewley (Mechanical and Aerospace Engineering)

3:10 pm: Yoav Freund (Computer Science and Engineering)
3:30 pm: Truong Nguyen (Electrical and Computer Engineering)
3:50 pm: Karen Christman (Bioengineering)
4:10 pm: Joseph Wang (NanoEngineering)

Talk titles and abstracts to come. 

Faculty talks are just one aspect of Research Expo at the UC San Diego Jacobs School of Engineering. The half-day event also includes a 200+ graduate student poster session and a networking reception. 

Research Expo is Thursday April 17

On Friday, as I was describing Research Expo to someone here in San Diego, the person told me that Research Expo falls on the day BEFORE tax day this year...but that's not correct. Tax Day is Tuesday April 15 and Research Expo is Thursday April 17.

We all know the famous saying about death and taxes:

Our new Constitution is now established, and has an appearance that promises permanency; but in this world nothing can be said to be certain, except death and taxes.

—Benjamin Franklin, in a letter to Jean-Baptiste Leroy, 1789

...but it occurs to me that technological change is something else that is certain. Given the fact that technology is racing forward in many different directions -- with implications for so many different aspects of business -- it's important to stay abreast of this change. Research Expo is a great opportunity to do just this.

What happens at Research Expo?

Meet Potential Hires

At the poster session, meet 200+ Jacobs School of Engineering graduate students working with world-class faculty.

Dive Deep into Research

The 200+ research posters provide access to the Jacobs School’s world-renowned $158M/year research enterprise, all in one afternoon.

Ten-Minute Faculty Tech Talks

Enjoy fast-paced technical talks from six engineering professors.

Networking Reception

Connect with Jacobs School graduate students, faculty, alumni and industry partners.

Register Today

UC San Diego Alumni enjoy half-price admission.

Corporate Affiliates Program member companies receive 2-for-1 admission.

BeneFunder.org Goes Live

From the "how it works page" on Benefunder.org which is building a unique funding platform where individual donors can connect with the innovators of science. BeneFunder helps donors to engage in long-term giving to the researchers of their choice, to support the next innovations in our society. They are starting off at UC San Diego, and one of the co-founders is Gert Lanckriet, an electrical engineering professor here at the Jacobs School of Engineering.

Benefunder is a marketplace that allows donors to find, fund, and follow researchers and other university initiatives in a simple, efficient way.

Benefunder partners with top universities to gain access to top researchers and initiatives across all disciplines to ensure that your donations go to the intended use. Researchers create and manage their profiles on our site, which must be approved internally prior to getting published. This way you always get the most up to date information regarding their work and can rest assured knowing that all our causes are in fact vetted.

To search for causes you can browse our home page, click on a category, or click on "search" in the header and type in a term that matches your areas of interest. Click on a tile to learn more about the cause details and watch the videos from our researchers.

Once you have found the researcher and cause of interest to you, click the "Benefund it" link to make a donation. You will be asked for specific information to be able to process the transaction through our secure servers. You can rest at ease knowing Benefunder is backed by Blackbaud Merchant Services, the leader in non-profit payment processing currently serving thousands of non-profits. Benefunder provides you with a tax deductible receipt for your donations and passes the money you donated to the university as a gift earmarked for the cause or researcher of the donor's choosing. Benefunder receives 10% of every donation which funds its overhead and operating expenses.

When a researcher has updates, they post them and we pass that information along to you to see the impact your donation has made. We encourage you to interact with researchers through the Benefunder portal, continue to donate to one or more causes you find interesting as often as you'd like and share the things you find interesting with your friends!

We will constantly be improving the site with new features and functions, your feedback is very welcome!

Nanosponge Vaccine Research Featured in Technology Review

Research on nanosponges for vaccines against MRSA toxins and beyond are featured in an MIT Technology Review story by Mike Orcutt. The research is from the Liangfang Zhang lab in the NanoEngineering Department at the UC San Diego Jacobs School of Engineering. (Original press relesase from the Nature Nanotechnology paper is here.)

Congrats ECE Prof Sujit Dey / IEEE Fellow

Electrical engineering professor Sujit Dey

Congratulations to electrical engineering professor Sujit Dey, who is one of 62 IEEE Computer Society members and associates to be elevated to IEEE Fellow status in 2014 "for contributions to the design and testing of low-power systems and system-on-chips."

Dey leads the Mobile Systems Design Lab in the Electrical and Computer Engineering department at the UC San Diego Jacobs School of Engineering. He is faculty director of the von Liebig Entrepreneurism Center. The team in his lab is currently doing R&D in a field that could be the focus of future commercialization efforts: cloud-based mobile gaming.

Dey is also a longtime participant in the UC San Diego Division of Calit2, now known as the Qualcomm Institute. 

The IEEE Fellow honor recognizes unusual distinction in the profession. Dey was a co-PI (with PI Ramesh Rao) on the Ericsson- and UC Discovery Grant-funded Adaptive Systems project launched in 2002, prior to founding Ortiva Wireless in 2004. Ortiva was subsequently acquired by Israel-based Allot Communications in early 2012. 

Dey was awarded a proof-of-concept grant from the von Liebig Center in 2004 to create a prototype that became the core technology to launch Ortiva Wireless, which enables proactive management of mobile video and rich media content delivery. Dey said the von Liebig Center helped him get the funding he needed to hire students, develop an advanced prototype that could be presented to potential customers and investors, and to offer valuable advice in the business development and technology transfer process.

Nanosponge Vaccine Resarch from Liangfang Zhang in NanoEngineering

It has certainly been an exciting year for Liangfang Zhang and the other researchers in his Nanomaterials & Nanomedicine Laboratory over in NanoEngineering here at UC San Diego.

They published two "nanosponge" papers in Nature Nanotechnology (nanosponges as toxin grabbers, and nanosponges as experimental vaccines) Zhang was named one of Technology Review's 35 Innovators Under 35, and graduate student Ronnie Fang won top poster at Research Expo 2013. (And no doubt, this is the very abridged version.)

It will be very exciting to see how the nanosponge technology develops over the next year. Will any clinical studies get started? Will other researchers around the world publish exciting results based on the nanosponge platform?

This story in Chemistry World offers a couple of different perspectives on the research: "Caged toxin for safer, better bacterial vaccines" by Simon Hadlington, a science writer in the UK.

Bradley Fikes' story in UT San Diego spells out the mechanics of how the nanosponges are used to trigger immune-system protection from MRSA toxins.

Below is a video that describes the nanosponge for toxin removal paper.

'Rack-on-Chip’ Design Proposed to Meet Traffic Demands of Global Cloud Computing

In its Global Data Cloud Index released Oct. 15, Cisco forecasts that global cloud traffic will grow 4.5-fold, a 35 percent combined annual growth rate, by 2017. Today’s data centers in which rows of servers sprawl over hundreds of thousands of square feet already consume some 30 billion watts of electricity, The New York Times reported last year. 

And this is all the more reason to rethink data center design and size so they require a lot less power and space, said two University of California, San Diego researchers in the Oct. 11 issue of the journalScience. 

Cloud computing is the fastest growing segment of data center traffic, approximating 1.2 zettabytes of annual traffic in 2012, according to Cisco’s annual report.  Meanwhile, overall global data center traffic will grow threefold to 7.7 zettabytes by 2017. Cisco provides a little social math to illustrate just how much data traffic we’re talking about.  

“A zettabyte is one billion terabytes. For context, 7.7 zettabytes is the equivalent to: 

• 107 trillion hours of streaming music -- about 1.5 years of continuous music streaming for the world’s population in 2017.

• 19 trillion hours of business web conferencing -- about 14 hours of daily web conferencing for the world’s workforce in 2017.

• 8 trillion hours of online high-definition (HD) video streaming -- about 2.5 hours of daily streamed HD video for the world’s population in 2017.”

Graduate student Qing Gu at work in the Fainman lab in the ECE dept. at UC San Diego's Jacobs School of Engineering. 

In their commentary, electrical engineer Yeshaiahu (Shaya) Fainman and computer scientist George Porter proposed replacing the racks and racks of servers in today’s data centers into a single chip. “These ‘rack-on-chips’ will be networked, internally and externally, with both optical circuit switching to support large flows of data and electronic packet switching to support high-priority data flows,” Fainman and Porter write. 

Fainman is professor and chair of the Department of Electrical and Computer Engineering, and Porter is a research scientist in the Center for Networked Systems at UC San Diego Jacobs School of Engineering. 

Their proposed solution will require several significant technology advances. The most significant are how to network all the individual processors on a single chip as well as how to network multiple rack-on-chips to each other, said Porter. “To handle Big Data processing and data-intensive applications, you've got to have an enormous amount of network bandwidth, and we're developing new technologies to deliver that bandwidth cheaper, with less power and heat, and in a smaller form-factor than existing approaches,” Porter said. Fainman’s lab has been developing several aspects of the dense integration of electronics and photonics and nanophotonic technology required to achieve this vision in collaboration with several other universities as part of the Center for Integrated Access Networks. Fainman’s lab last year built thesmallest no-waste laser to date, a significant step needed to enable future computer chips with optical communications. Their breakthrough was reported in the journal Nature. 

Motherboard reported on Fainman and Porter’s idea for “nanoservers” this week: 

“But the meat and potatoes of Yeshaiahu Fainman and George Porter’s server-rack-on-a-chip vision is really about taking the existing framework for a server rack and recreating it at the nano-level. They say that miniaturizing all server components so that several servers can fit onto a computer chip would increase processing speed. Making circuit systems to support all these mini-components using advanced lithography is already feasible, but scientists have yet to realize nano-transceivers and circuit-switchers—the key components that transmit data. And while silicon chips are increasing being used to transmit data-carrying light waves in fiber optic networks, efficiently generating light on a silicon chip is still early in its development. The researchers offer some solutions, like including light generating nanolasers in the chip design.”

Upcoming talk: Probing cell metabolism using isotope tracers and metabolic flux analysis

Bioengineering professor Christian Metallo will be speaking next month at the Scripps Research Institute. His talk: “Probing cell metabolism using isotope tracers and metabolic flux analysis”. 

More info below.

The CENTER FOR METABOLOMICS AND MASS SPECTROMETRY presents: SAN DIEGO MASS ANALYSIS NETWORK (SANDMAN)

Thursday, October 17th from 5-7PM

The Scripps Research Institute Auditorium

A reception will follow the presentations.  All are welcome.

Eric C. Peters, Ph.D.

Genomics Institute of the Novartis Research Foundation

“The Increasing Role of MS-based Analyses in Research-Stage Biotherapeutic Construct Optimization”

Christian Metallo, Ph.D.
Dept of Bioengineering, UC San Diego Jacobs School of Engineering

“Probing cell metabolism using isotope tracers and metabolic flux analysis”

Host: Gary Siuzdak

Contact: Adam Schuyler (schuyler@scripps.edu)

  

For more information: http://sandman.scripps.edu/

Systems Biology Paper: Story in Process

I'm working on a story about the Nature Scientific Reports paper from the Subramaniam lab in the bioengineering department here at the UC San Diego Jacobs School of Engineering.

The paper, "Quantitative Transcriptomics using Designed Primer-based Amplification" is open access.

Here is a summary on the RNA-Seq blog.

Wave Frozen in Time / Have you seen the video?

In less than 48 hours, the video illustrating the "static pipeline wave" paper in the journal Experiments in Fluids already has more than 23,000 views. As an added bonus, the video gives you a chance to brush up on your spanish. Created by the Universidad Carlos III of Madrid (UC3M), the researchers are discussing their static wave in spanish...but video is video and there are great shots of the experimental setup, even if you don't understand any spanish at all.

The video goes along with this press release: Researchers Create a Wave Frozen in Time



UC San Diego MAE professor and interim dean of the Jacobs School of Engineering, Juan C. Lasheras, is one of the authors on the paper. The first author of the paper Pablo Martinez Legazpi is currently a post-doc in the Lasheras lab. Also author  Javier Rodriguez-Rodriguez served as a postdoc in the Lasheras lab years ago. More info here.

Albert Pisano Named Dean of UC San Diego Jacobs School of Engineering

UC San Diego has named professor Albert P. (Al) Pisano, a highly accomplished mechanical engineer from UC Berkeley, as the next dean of the UC San Diego Jacobs School of Engineering. Pisano’s appointment begins Sept. 1, 2013. The appointment follows an international search for a prominent research engineer to lead the Jacobs School of Engineering, which ranks 12th in the world according to theAcademic Ranking of World Universities.

An excerpt from the press release from the UC San Diego Jacobs School of Engineering:

“I am honored to be given the opportunity to serve as the dean of the Jacobs School of Engineering at UC San Diego. The campus is ranked number one in terms of the public good. This to me is a big deal. If a university is not serving the public good, then we are not doing our job correctly,” said Albert Pisano, referring to the fact that in 2012, for the third consecutive year, UC San Diego ranked first in the nation for positive impact on the country by Washington Monthly’s College Guide. The ranking is based on research, the social mobility of students, and commitment to service. 

One of Pisano’s new projects is development of an inexpensive yet rugged sensor system that will predict landslides in the Philippines, a country where landslides are a deadly, national problem. 

“My secret to making a very rugged sensor is miniaturizing it as much as you can because that gets you the shock resistance. You beat temperature and corrosion by using slightly exotic materials, which also means the devices need to be small in order to keep materials costs down,” Pisano explained. Using MEMS, Pisano and his colleagues can make the sensors sufficiently small and rugged.

Media outlets covering the announcement: 

San Diego Union Tribune online story, July 15.

San Diego Union Tribune print story, July 16.

San Diego Business Journal story, July 16.

San Diego Daily Transcript story, July 15.

Daily Californian story, July 16. 

Two Electrical Engineering Profs Land Awards from Yahoo! Labs

Two electrical engineering professors from the Jacobs School of Engineering, Gert Lanckriet and Nuno Vasconcelos, have won spots in the 2013 Yahoo! Faculty Research and Engagement Program (FREP). 

Check out the full list of awardees at the Yahoo! Labs Faculty Research and Engagement Program website.

This program funds help academics across the globe collaborate with Yahoo! research scientists on new, exciting internet research studies and experiments.

Lanckriet and Vasconcelos, from the Department of Electrical and Computer Engineering at UC San Diego, are two of 27 recipients from 24 universities in 7 countries were selected based on their areas of science and interest to Yahoo!.

A summary of Lanckriet’s project is below.

Machine Learning with Highly Unstructured Multimedia DataAn increasingly important aspect of information in today’s world is that it is highly unstructured and heterogeneous. For example, a search for “miss world 2013” yields fundamentally different modes of information about the topic via news articles, blogs, videos, pictures etc.  While there are some commonalities in the information provided in these modalities (i.e., they are about the beauty pageant), the nature of information differs widely amongst the modalities.

Videos and pictures are innately visual in nature, and differ from news articles and blogs which are textual in nature. Even within the textual sources, there exist differences: news articles are more factual in nature, while blogs are opinionated. In multimedia applications, such information is often available in a variety of unstructured formats: blogs may contain one or more pictures, or none, embedded videos, audio tracks, and/or tweets, or not, etc.

Ideally, an algorithm to make inferences from the data (e.g., whether or not the judges were fair in deciding the winner) would be given access to all available information sources, since each source may bring some unique information to the table. Machine learning with such unstructured, heterogeneous data is challenging and an active topic of research. Existing approaches assume a rigidly structured input format. They cannot accommodate missing modalities (incomplete information) or modalities with multiple instances (over-complete information).  In this project, we intend to design and develop principled approaches to learning from heterogeneous, unstructured multimedia data.

One of the problems that we are interested in is artist recommendation. Current approaches rely on either collaborative filtering methods (relying on the wisdom of the crowd to determine if two artists are similar), or content based methods (two artists are considered similar if the audio content of their songs are similar) to determine if two artists are similar.  We are interested in developing a multimodal artist similarity, based on heterogeneous unstructured social and multimedia data that relates to artists.  This can include band videos and pictures (which implicitly provide information about the “look-and-feel” of an artist), tweets, reviews, and blogs about the artists’ music (providing opinions and information about artists), lyrics, their social network of listeners, etc. We believe that combining all this information through a more accurate multimodal similarity measure will improve recommendation compared to using content or collaborative filtering only.