Affiliations

Research interests

News

Conferences

Nuno Bandeira, Ph.D. Associate Professor Dept. Computer Science and Engineering Skaggs School of Pharmacy and Pharmaceutical Sciences Executive director, NCRR/NIH Biomedical Technology Research Center for Computational Mass Spectrometry Email: bandeira.ucsd.edu (replace leftmost dot with @) Phone: 1-858-534-8666 Office: EBU3B 4210 (CSE building) Mailing address: Department of Computer Science and Engineering University of California, San Diego 9500 Gilman Drive, Mail Code 0404 La Jolla, CA 92093-0404, USA

Research interests

Broadly defined, my main research interests are in bioinformatics and computational biology, with a special focus on computational mass spectrometry. I am particularly interested in algorithmic and statistical problems in proteomics and on how mass spectrometry instruments can be used to identify and quantify proteins, post-translational modifications, protein structure features and protein-protein interactions.

A significant part of my recent work stems from the novel Spectral Networks paradigm introduced by our group - in a departure from previous approaches that interpret each spectrum in isolation, spectral networks algorithms derive consensus interpretations for groups of spectra from overlapping peptides. By focusing on the detection, assembly and consensus interpretation of multiple spectra from overlapping peptides it becomes possible to address new challenges such as: how to reconstruct a protein sequence given only MS/MS spectra of some of its subsequences? Find this answer and more right here!

	Spectral Networks: A New Approach to the Identification of Proteins and Post-translational Modifications Archived webcast courtesy of the Proteomics Interest Group (ProtIG), NIH
	Overlapping MS/MS Spectra and Disease Proteomics HUPO 2006 Young investigator Award (news release)

Some of our research has been covered in the news

• De novo Sequencing of Nonribosomal Peptides, in PepTalk 2010 podcast (Jan 2010)
  
  
• New drugs faster from natural compounds: A UC San Diego breakthrough, in Genetic Engineering & Biotechnology News (July 2009)
  
  
• UC San Diego and Genentech Scientists Develop Potentially Disruptive Antibody Sequencing Technology, in News release, Calit2:California Institute for Telecommunications and Information Technology, UCSD (December 2008)
  
  
• Genentech, UCSD Team Develop MS/MS-Based Method for De Novo Protein Sequencing, in ProteoMonitor, (December 2008)
  
  
• Put the Protein Pieces Together with Algorithms: Solving “the Mass Spec Data Mess” in News release, UCSD News Center (October 2008)
  
  
• Mass spectrometry technique may aid drug discovery, in Biophotonics News (May 2008)
  
  
• Researchers Eliminate Drug Discovery Bottleneck, in News release, Jacobs School of Engineering, UCSD (April 2008)
  
  
• From spectral networks to shotgun sequencing, in Nature Methods (June 2007)
  
  
• Identifying peptides without a database, in Journal of Proteome Research (May 2007)
  
  
• UCSD Computer Scientist Wins Young Investigator Award, in News release, Jacobs School of Engineering, UCSD (November 2006)
  
  
• UCSD Team Frees Protein Identification From Database Searching Via 'Spectral Networks', in bioInform (April 2006)
  
  

Conference organization

• RECOMB Satellite conference on Computational Mass Spectrometry (2009)
  Program committee chair (co-chaired with Oliver Kohlbacher)
• La Jolla Proteomics Conference (June 2008)
  Program committee chair
• Algorithmic Biology 2006, Co-organized with Pavel Pevzner
• RECOMB Satellite conference on Computational Proteomics (2006)
  Organizing committee member