Dereplication and De Novo Sequencing of Nonribosomal PeptidesNuno Bandeira, Julio Ng, Wei-Ting Liu, Roger Linington, Pieter Dorrestein, Pavel Pevzner (in revision after favorable reviews)
The interpretation of tandem mass spectra obtained from cyclic non-ribosomal peptides
Wei-Ting Liu, Julio Ng, Dario Meluzzi, Nuno Bandeira, Marcelino Gutierrez, Thomas Simmons, Andrew Schultz, Roger Linington, Bradley Moore, William Gerwick, Pavel Pevzner, Pieter Dorrestein
(in revision after favorable reviews)
Shared Peptides in Mass Spectrometry Based Protein Quantification
Banu Dost, Vineet Bafna, Nuno Bandeira, Xiangqian Li, Zhouxin Shen, Steve Briggs RECOMB 2009, 13th Annual International Conference on Research in Computational Molecular Biology
Spectral Profiles: A Novel Representation of Tandem Mass Spectra and its Applications for de Novo Peptide Sequencing and Identification
Sangtae Kim, Nuno Bandeira, Pavel Pevzner
Molecular and Cellular Proteomics (in press), PMID: 19254948
Automated de novo protein sequencing of monoclonal antibodies Nuno Bandeira, Victoria Pham, Pavel Pevzner, David Arnott, Jennie Lill
Nature Biotechnology 2008 Dec;26(12):1336-8, PMID: 19060866
Multi-Spectra Peptide Sequencing and its Applications to Multistage Mass Spectrometry Nuno Bandeira, Jesper Olsen, Matthias Mann, Pavel Pevzner
Bioinformatics, 2008 24(13):i416-i423 (ISMB 2008 special issue), PMID: 18785330
Spectral Dictionaries: Integrating De Novo Peptide Sequencing with Database Search of Tandem Mass Spectra
Sangtae Kim, Nitin Gupta, Nuno Bandeira, Pavel Pevzner
Molecular and Cellular Proteomics, 2009 Jan;8(1):53-69 (Epub 2008 Aug 14), PMID: 18703573
The Spectral Networks Approach to the Identification of Proteins and Post-translational Modifications Nuno Bandeira
Invited chapter, in The Bioanalytical Discovery of Post-translational Modifications
Research Sign Post series (in press), 2008
De Novo Sequencing of Nonribosomal Peptides Nuno Bandeira, Julio Ng, Dario Meluzzi, Roger Linington, Pieter Dorrestein, Pavel Pevzner RECOMB 2008, 12th Annual International Conference on Research in Computational Molecular Biology.
Clustering millions of tandem mass spectra
Ari Frank, Nuno Bandeira, Zhouxin Shen, Stephen Tanner, Steven Briggs, Richard Smith, Pavel Pevzner
J Proteome Res. Jan;7(1):113-22. Epub 2007 Dec 8., PMID: 18067247
Spectral networks: a new approach to de novo discovery of protein sequences and posttranslational modifications Nuno Bandeira
Biotechniques, 2007 Jun;42(6):687,
PMID: 17612289
Shotgun Protein Sequencing: Assembly of MS/MS Mass Spectra from Mixtures of Modified Proteins Nuno Bandeira, Karl Clauser, Pavel Pevzner
Molecular and Cellular Proteomics, 2007 Jul;6(7):1123-34. Epub 2007 Apr 19 (online version)PMID: 17446555
Protein identification by spectral networks analysis Nuno Bandeira, Dekel Tsur, Ari Frank, Pavel Pevzner
Proceedings of the National Academy of Sciences (PNAS), 2007 Apr 10;104(15):6140-5 (online version)PMID: 17404225
A new approach to protein identification Nuno Bandeira, Dekel Tsur, Ari Frank, Pavel Pevzner RECOMB 2006, 10th Annual International Conference on Research in Computational Molecular Biology.
Analysis of EEG of shooters Nuno Bandeira, Vitor Sousa Lobo, Fernando Moura-Pires Proceedings of the
International Conference on Mathematics and Engineering Techniques in Medicine and Biological Sciences METMBS'2000, 2000.
EEG/ECG data fusion using Self-Organising Maps Nuno Filipe
Cabrita Bandeira, Vitor Sousa Lobo, Fernando Moura-Pires Proceedings of
EuroFusion99, International Conference on Data Fusion, 1999, Joliver
Press, ISBN: 0-95337132-0-2 IEE/ISIF, Startford-upon-Avon, UK
Training a Self-Organizing Map distributed on a PVM network Nuno Filipe Cabrita Bandeira, Vitor Sousa Lobo, Fernando Moura-Pires
Proceedings of the International Joint Conference on Neural Networks
(IJCNN98 / WCCI98) IEEE, Alaska, USA
Distributed Kohonen Networks for Passive Sonar Based Classification Vitor Sousa Lobo, Nuno Filipe Cabrita Bandeira, Fernando Moura-Pires
Proceedings of the 1998 International Conference on
Multisource-Multisensor Information Fusion (FUSION98), Las Vegas, USA
Ship recognition using Distributed Self Organizing Maps Vitor
Sousa Lobo, Nuno Filipe Cabrita Bandeira, Fernando Moura-Pires Proceedings
of the 1998 International Conference on Engineering Applications of Neural
Networks (EANN98), Gibraltar
Tutorials and courses
Invited graduate course: Computational Approaches to Proteomics
Ph.D. program in Computational Biology
Gulbenkian Institute for the Sciences (IGC)
April 2009, Lisbon, Portugal
Invited graduate course: Computational Approaches to Proteomics
Ph.D. program in Computational Biology
Gulbenkian Institute for the Sciences (IGC)
March 2008, Lisbon, Portugal
Algorithmic Mass Spectrometry
Algorithmic Biology 2006, jointly with Stephen Tanner
Nov. 2006, University of California, San Diego, USA
Identification of Proteins and Post-translational Modifications via Spectral Networks Analysis
Computational Systems Bioinformatics (CSB'2006)
Aug. 2006, Stanford, USA
Invited talks
Beyond Edman Degradation: Automated de novo Protein Sequencing of Monoclonal Antibodies
Implementing the Next Generation of Antibodies
Cambridge Healthtech Institute (CHI) eighth annual PepTalk
Jan. 2009, San Diego, USA
Overlapping MS/MS Spectra and Disease Proteomics
Mass Spectrometry: Applications to the Clinical Lab
Nov. 2008, San Diego, USA
Multi-Spectra Peptide Sequencing and its Applications to Multi-stage Mass Spectrometry
Second workshop on Computational Proteomics
Mar. 2008, Dagstuhl, Germany
Spectral Alignment Approaches to the Blind Discovery of Post-translational Modifications
12th International Meeting of the Association of Biomolecular Resource Facilities: "ABRF 2008: Enabling Technologies in the Life Sciences"
Feb. 2008, Salt Lake City, USA
E Pluribus Unum: Enabling Discovery by Combining Tandem Mass Spectra from Overlapping Peptides
Mining the Plasma Proteome, Cambridge Healthtech Institute (CHI) seventh annual PepTalk
Jan. 2008, San Diego, USA
Spectral Networks: A New Approach to the Identification of Proteins and Post-translational Modifications
National Institutes of Health
Sep. 2007, Bethesda, USA
HUPO Young Investigator Award talk: Overlapping MS/MS spectra and disease proteomics
Human Proteome Organization 5th Annual World Congress (HUPO 2006)
Oct. 2006, Long Beach, USA
Shotgun Protein Sequencing of Novel Proteins by Assembly of MS/MS Spectra
Genentech Inc.
Aug. 2006, San Francisco, USA
Shotgun Protein Sequencing of Snake Venom Proteins
Southern California Bioinformatics Summer Institute
Jul. 2006, Los Angeles, USA
Spectral Networks for Identification of Proteins and Post-translational Modifications
University of Lisbon
Mar. 2006, Lisbon, Portugal
A New Approach to Protein Identification
Burnham Institute for Medical Research
Mar. 2006, San Diego, USA
Shotgun Protein Sequencing
Workshop on Computational Proteomics and Mass Spectrometry, Mathematical Biosciences Institute, Ohio State University
Jan. 2005, Columbus, USA
