UCSD Systems Biology / Bioinformatics Expert in Science

Bioengineering professor Bernhard Palsson is quoted in a story in the careers section of Science Magazine called, "Systems Biology and Bioinformatics: Something for Everyone."

Below is an excerpt from the Science story by Chris Tachibana:

The list of specific areas within systems biology is almost comically long, and includes everything from cutting-edge computer science to traditional life sciences. Fortunately, in this field, collaboration is the name of the game. Galetti Professor of Bioengineering at the University of California, San Diego (UCSD) Bernhard Palsson says systems biology includes "an understanding of networks, biological systems and linear algebra, genomics and genetics, the biochemistry of gene products, and how everything fits into the three-dimensional architecture of the cell." Hlatky says that attacking the complex, nonlinear nature of biology requires "a team of individuals collectively versed in the traditional biological as well as the quantitative sciences, from cell and molecular biology to physics, chemistry, computer science, and mathematics."

Palsson leads the Systems Biology Research Group within the Department of Bioengineering in the UC San Diego Jacobs School of Engineernig.

Jacobs School at the La Jolla Research and Innovation Summit

A number of different engineering faculty from the Jacobs School presented this week at the La Jolla Research and Innovation Summit. According to the event organizers, the summit is:

"...an invitation only program where San Diego’s leading scientists and engineers describe their innovative research to more than 100 venture capitalists in a closed meeting was developed to bring together our leading scientists with active venture capitalists from across the U.S. In this unique setting, VCs have the opportunity to learn from and build relationships with researchers working
on advances five and ten years into the future."

Jacobs School professors who presented are below:

Joseph Ford, Professor, Electrical and Computer Engineering, UC San Diego (Bruce Lieberman from Xconomy included Ford's solar concentrator technology in Xconomy summit his write up. Graduate student Jason Karp will present related solar concentrator work on April 15 at the Jacobs School of Engineering Research Expo 2010. It's THE place to connect with the engineering innovators and leaders of today (and tomorrow).

William Gerwick, Professor, Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, UC San Diego and Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego (Computer science professor Pavel Pevzner works with Gerwick on related projects. Read more about the collaboration aimed at discovering drug targets from natural compounds here.)

The High Tech/IT Panel Presentation was a Jacobs School sweep:

Sadik Esner, Professor, Department of Electrical and Computer Engineering, UC San Diego

Rajesh Gupta, Professor and Qualcomm Endowed Chair, Department of Computer Science and Engineering, UC San Diego

Stefan Savage, Associate Professor, Department of Computer Science and Engineering, UC San

(Graduate students from the labs of Esner, Gupta and Savage are all presenting at Research Expo 2010.)

The afteroon session included a political scientist from UC San Diego who is affiliated with Calit2...yes, you guessed the name right: James Fowler, Author, Connected; Associate Professor, Center for Wireless and Population Health Systems, CALIT2, and Department of Political Science, UC San Diego.

New Drugs from Natural Compounds

Congratulations to Julio Ng (front) and Nuno Bandeira (back), the UC San Diego researchers and co-lead authors on a Nature Methods paper describing computational and experimental advances that enable researchers to quickly and inexpensively determine whether natural compounds collected in oceans and forests are new -- or if these pharmaceutically promising compounds have already been described and are therefore not patentable.

The UC San Diego web-based tools for sequencing nonribosomal peptides (at no cost to researchers at nonprofit organizations) are available at: bix.ucsd.edu/nrp

This research appeared this week on a number of media outlets, including:

Scientific American (story by Brendan Borrell)
http://www.scientificamerican.com/article.cfm?id=new-algorithm-antibiotic-hunt

Genetic Engineering News
ttp://www.genengnews.com/news/bnitem.aspx?name=58159197

Natural Products Industry Insider http://www.naturalproductsinsider.com/news/2009/07/new-drugs-faster-from-natural-compounds.aspx

Genome Web Daily News
http://www.genomeweb.com/proteomics/ucsd-team-develops-de-novo-sequencing-dereplication-method-decipher-nonribosomal

Algorithms answer "Hot or Not?" question for natural compounds

Hot or Not? New or Not? Discovery or Not? Hot Pharmaceutical Prospect or Not?

A researcher isolates a natural compound with promising antimicrobial properties from ocean water. But is it a discovery? Or has the compound already been described and patented? University of California, San Diego researchers have invented computational tools that enable researchers to rapidly and economically answer the ‘is it new or not?’ question for promising drug targets.

Scientists will finally be able to rapidly identify and characterize ring-shaped nonribosomal peptides (NRPs)—a class of natural compounds of intense interest due to their potential to yield or inspire new pharmaceuticals. This advance should speed the discovery of natural compounds produced by organisms such as blue-green algae that could lead to new drugs.

This new work will be published online on July 13 in the journal Nature Methods.

Full press release is on the Jacobs School of Engineering web site:
http://www.jacobsschool.ucsd.edu/news/news_releases/release.sfe?id=866

More photos:

caption for above photo:
Nuno Bandeira (left) and Julio Ng (right) are UC San Diego researchers and co-lead authors on a Nature Methods paper describing computational and experimental advances that enable researchers to quickly and inexpensively determine whether natural compounds collected in oceans and forests are new -- or if these pharmaceutically promising compounds have already been described and are therefore not patentable.

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credit for photo above:
Scripps Institution of Oceanography, UC San Diego/ Cameron Coates

caption for photo above:
William Gerwick collects natural compounds in search of new pharmaceuticals. Gerwick is an author on the new Nature Methods paper and a professor with the UC San Diego Scripps Institution of Oceanography Center for Marine Biotechnology and Biomedicine and the UCSD Skaggs School of Pharmacy and Pharmaceutical Sciences. Read about Gerwick’s work to discover drugs and protect Panama’s natural and cultural resources at:
http://explorations.ucsd.edu/Features/2009/Discovering_Diversity/images/07_2009_Feature.pdf