PROFILE:
Marshall Bern
Marshall Bern specializes in algorithm design, with 25 years of experience in such diverse areas as signal and image processing, computer graphics, combinatorial optimization, and bioinformatics. He is currently working in the area of proteomics, developing algorithms and software for peptide and protein identification by mass spectrometry.
Marshall has published about 100 scientific papers, including influential papers on mesh generation, surface reconstruction, and the mathematics of origami. He has taught courses at U.C. Berkeley, U.C. Santa Cruz, and Carnegie Mellon University. Marshall received his B.A. in Mathematics from Yale University, his M.A. in Applied Mathematics and Statistics from the University of Texas at Austin, and his Ph.D. in Computer Science from the University of California at Berkeley.
He started Yale as an art major, and has been involved in art shows and the PARC artist-in-residence program since 1992.
PARC publications
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2013
2012
Handheld flow cytometer for rapid pathogen characterization in water
2012 Materials Research Society Fall Meeting
25 November 2012
Micro-fluidic based detection platform for rapid pathogen characterization in water
Frontiers in Optics 2012 and Laser Science XXVIII
14 October 2012
Opto-fluidic detection system enabling sophisticated point-of-care diagnostics
Invited Seminar, Stanford Optical Society, Stanford University
5 April 2012
Opto-fluidic detection system enabling sophisticated point-of-care diagnostics
First Annual SLAS (Society for Laboratory Automation and Screening) Conference and Exhibition
4 February 2012
2011
Two-dimensional target decoy strategy for shotgun proteomics
Journal of Proteome Research
20 October 2011
Opto-fluidic detection system enabling sophisticated point-of-care diagnostics
IEEE/Photonics Society Winter Topicals 2011
10 October 2011
Ubiquitous meeting facilitator with playful real-time user interface
IEEE Conference on Ubiquitous Intelligence and Computing
2 September 2011
Recent developments in quantitative proteomics
Mutation Research - Genetic Toxicology and Environmental Mutagenesis
17 June 2011
Preview: a program for surveying shotgun proteomics tandem mass spectrometry data
Analytical Chemistry
28 May 2011
On-the-flow pathogen detection in water
SPIE Defense, Security and Sensing Symposium 2011
25 April 2011
Constrained de novo sequencing of peptides with applications to conotoxins
Research in Computational Molecular Biology (RECOMB 2011)
28 March 2011
Comment on “Unbiased statistical analysis for multi-stage proteomic search strategies”
Journal of Proteome Research
February 2011
2010
Conversion of methionine to homocysteic acid in heavily oxidized proteomics samples
Rapid Communications in Mass Spectrometry
30 March 2010
2009
Molecular & Cellular Proteomics
2009
2008
Journal of the American Society of Mass Spectrometry
November 2008
Spectrum fusion: using multiple mass spectra for de novo peptide sequencing
Research in Computational Molecular Biology
30 March 2008
2007
Automated N-glycopeptide identification using a combination of single- and tandem-MS
Journal of Proteome Research
October 2007
Improved ranking functions for protein and modification-site identifications
International Conference on Research in Computational Molecular Biology (RECOMB 2007)
21 April 2007
Analytical Chemistry
23 January 2007
2006
Automatic determination of O-glycan structure from fragmentation spectra
Journal of Proteome Research
1 June 2006
De novo analysis of peptide tandem mass spectra by spectral graph partitioning
Journal of Computational Biology
March 2006
2005
Automatic selection of representative proteins for bacterial phylogeny
BMC Evolutionary Biology
May 2005
EigenMS: de novo analysis of peptide tandem mass spectra by spectral graph partitioning
RECOMB 2005
14 May 2005
2004
Automatic quality assessment of peptide tandem mass spectra
Twelfth International Conference on Intelligent Systems for Molecular Biology (ISMB 2004)
31 July 2004
Automatic classification of protein crystallization images using a curve tracking algorithm
Journal of Applied Crystallography
April 2004
Model-based particle picking for cryo-electron microscopy
Journal of Structural Biology
January 2004
2002
An image signature for any kind of image
IEEE International Conference on Image Processing (ICIP 2002)
22 September 2002
A global approach to automatic solution of jigsaw puzzles
Proceedings of the 18th Annual ACM Symposium on Computational Geometry
5 June 2002
2001
Document image matching and annotation lifting
Sixth International Conference on Document Analysis and Recognition
10 September 2001
Secure notarization of paper text documents
Twelfth Annual ACM-SIAM Symposium on Discrete Algorithms
7 January 2001
2000
Model-based document image improvement
Proceedings of the 2000 International Conference on Image Processing
10 September 2000
1999
1998
Crust and the beta-skeleton: combinatorial curve reconstruction
Graphical Models and Image Processing
2 March 1998
1997
Optimal point placement for mesh smoothing
Eighth Annual ACM-SIAM Symposium on Discrete Algorithms
20 January 1997
1995
Linear-size nonobtuse triangulation of polygons
Discrete and Computational Geometry.
13 November 1995
contact
related competencies
- bioinformatics
in the news
view all 
Twisted structure preserved dinosaur proteins
14 June 2011 | Nature
Dinosaur Study Backs Controversial Find
31 July 2009 | AAAS ScienceNOW [sub required]
Reanalysis of T. rex Spectra Confirms Findings of 2007 Study
30 July 2009 | Genome Web - ProteoMonitor
events
view all
Handheld Flow Cytometer for Rapid Pathogen Characterization in Water
25 November 2012
Micro-fluidic based detection platform for rapid pathogen characterization in water
14 October 2012 | Rochester, NY
The Mathematics of Origami
4 October 2011 | Santa Clara, CA