The Clock that Breeds

Bioengineering professor Jeff Hasty recently published a Nature paper describing the first fast, robust genetic clock that works inside living E. coli cells.

Carl Zimmer wrote a nice piece of this research advance for Discover Magazine.

Technology Review's Emily Singer also covered this Nature paper here.

San Diego Wireless History

Going through piles of paper on my desk just now, I uncovered this great story from the Union Tribune from January 2008 by Jonathan Sidener and Kathryn Balint entitled,

Well-connected from the start

San Diego's bustling wireless industry can trace its roots to one local company

It's a great read.

BTW, Balint is no longer at the San Diego Union Tribune. According to her LinkedIn profile, she is President and CEO of CropMom Corporation, a digital scrapbooking site.

Bad Times a Good Time for Tech?

Microsoft's Craig Mundie visited UC San Diego on Friday Oct 10, in order to connect with Jacobs School students and faculty as well as univeristy administrators.

After Mundie's tech demo, he sat down with Alex Pham from the Los Angeles Times, which resulted in a Q&A. Read the full Q&A here. The final question is below.

Do you see a problem with the quality of American computer science graduates?

It is a serious problem, especially in the U.S. For us, our raw materials are smart people. Our culture for the last few decades does little to celebrate engineers and scientists and a lot to celebrate entertainers and athletes.

Parents in the U.S. also are just more decoupled from the academic interests of their kids. They are less demanding of their kids academically and perhaps even encouraging their kids into whatever the parents see as the quickest way to make a lot of money. Taken together, that is creating a somewhat acute shortage of American kids growing up with any passion for math and science.

There is a silver lining in this economic turmoil. Perhaps fewer of our best students will now go to Wall Street. Maybe some will even stay and build things. We need smart people to tackle the hard, long-term problems society faces. It can't be done by politicians and entertainers. It's going to be done by engineers and scientists.

Proteins...Putting them Back Together (Algorithmically)

UC San Diego computer scientists just received an NIH grant to help clean up "the mass spec data mess". (San Diego Untion Tribune clip here)

It's easy to blast apart proteins with mass spectrometers and generate huge amounts of data comprised of all the little protein pieces. It is much harder to put those pieces back together in order to figure out what proteins (and protein modifications) are present in biological samples such as blood and tumors.) UCSD engineers are doing just that...using computational tools, and they just secured an almost $5M NIH grant to keep up the good work and create the software and cyberinfrastructure to enable scientists around the world to take advantage of their algorithmic breakthroughs. More info below and at the links provided.


UC San Diego engineers and scientists have received a five-year $4.94M grant from the National Center for Research Resources (NCRR), a part of NIH, to develop algorithms and software for deciphering all the proteins that are present in biological samples. This “proteomics” work promises to revolutionize routine blood tests, vaccine development, cancer diagnostics, and many other
important biomedical challenges, says Pavel Pevzner, the UC San Diego Jacobs School of Engineering computer science professor leading the project. (Read the UCSD release here and the NIH press release here)

"Unanalyzed data from mass spectrometers is piling up in laboratories around the world. Our algorithms can turn much of these ‘dark’ data into the lists of modified proteins that researchers are looking for,” says Nuno Bandeira, the first executive director of the Center for Computational Mass Spectrometry at UCSD’s Jacobs School of Engineering.

Key collaborators on the new grant are Jacobs School of Engineering computer science professors Vineet Bafna and Ingolf Krueger as well as Steven Briggs, a professor of biology at UCSD’s Division of Biological Sciences.

Genetic Engineering News also picked up the story.

Nano-Bio-Electronics at the Jacobs School

Joseph Wang, an extremely prolific and influential engineer and chemist joined the Jacobs School faculty this summer. He joined our NanoEngineering Department which got its start in 2007.

Joseph Wang, was the most cited engineer from 1991 to 2001 and consistently one of the world’s most cited engineers and chemists.

Check out his lab webpage, or jump here for an idea of what nanobioelectronics is all about.

Structural Engineering Startup Grabs Venture Funding

AgileNano, a Jacobs School of Engineering structural engineering startup that is commercializing technology from the laboratories of Yu Qiao recently received funding from the Tech Coast Angels. Professor Qiao is the CTO and Jacobs School PhD Candidate Nicole Justis Truitt is the VP of Research and Development at Agile Nano.

I picked up this story from Xconomy San Diego. Thanks Bruce!

Nicole Justis Truitt was one of the co-founders of UCSD's Triton Innovation Network $50k Entrepreneurship Competition, which is currently called the UC San Diego Entrepreneurship Challenge.

Microsoft's Craig Mundie Came to UC San Diego

The students who came to see Craig Mundie were captivated by Microsoft Surface, a tabletop computing surface that allows several users to work independently or together without a mouse or a keyboard.

The grad students who showed off their posters and then participated in a roundtable with Mundie got to see into the inner workings of Microsoft Research that doesn't get covered in the fun demos.

Watch Calit2's Webcast here. See more photos from the event on Calit2's Flikr photostream.

Read the story on the Jacobs School Web site here.