Nuno Bandeira

19 papers in the catalog · USA, La Jolla

Nuno Bandeira: 19 papers in the catalog · USA, La Jolla · University of California San Diego, University of California San Diego · Works on AI proteomics perspective, Automated mAb de novo (Bandeira SPS), Loxosceles intermedia venom proteome

Affiliations

University of California San Diego
University of California San Diego · Center for Computational Mass Spectrometry, Department of Computer Science and Engineering
University of California San Diego · Department of Computer Science and Engineering
University of California San Diego · Skaggs School of Pharmacy and Pharmaceutical Sciences
University of California System

Elsewhere

ORCID 0000-0001-8385-3655 · OpenAlex

Papers

AI proteomics: from protein identification to virtual cells (2026, Nature Methods)
A multi-protease, multi-dissociation, bottom-up-to-top-down proteomic view of the Loxosceles intermedia venom (2017, Scientific Data)
De Novo MS/MS Sequencing of Native Human Antibodies (2017, Journal of Proteome Research)
Neutron-encoded Signatures Enable Product Ion Annotation From Tandem Mass Spectra (2013, Molecular & Cellular Proteomics)
Sequencing-Grade De novo Analysis of MS/MS Triplets (CID/HCD/ETD) From Overlapping Peptides (2013, Journal of Proteome Research)
Shotgun Protein Sequencing with Meta-contig Assembly (2012, Molecular & Cellular Proteomics)
The spectral networks paradigm in high throughput mass spectrometry (2012, Molecular BioSystems)
Gapped Spectral Dictionaries and Their Applications for Database Searches of Tandem Mass Spectra (2011, Molecular & Cellular Proteomics)
Gapped Spectral Dictionaries and Their Applications for Database Searches of Tandem Mass Spectra (2010, Lecture Notes in Computer Science)
Dereplication and de novo sequencing of nonribosomal peptides (2009, Nature Methods)
Spectral Profiles, a Novel Representation of Tandem Mass Spectra and Their Applications for de Novo Peptide Sequencing and Identification (2009, Molecular & Cellular Proteomics)
Spectral Dictionaries: Integrating de novo Peptide Sequencing with Database Search of Tandem Mass Spectra (2009, Molecular & Cellular Proteomics)
Automated de novo protein sequencing of monoclonal antibodies (2008, Nature Biotechnology)
Multi-spectra peptide sequencing and its applications to multistage mass spectrometry (2008, Bioinformatics)
De Novo Sequencing of Nonribosomal Peptides (2008, Lecture Notes in Computer Science)
Shotgun Protein Sequencing: Assembly of Peptide Tandem Mass Spectra from Mixtures of Modified Proteins (2007, Molecular & Cellular Proteomics)
Spectral Networks: A New Approach to De Novo Discovery of Protein Sequences and Posttranslational Modifications (2007, BioTechniques)
Protein identification by spectral networks analysis (2007, Proceedings of the National Academy of Sciences)
Shotgun Protein Sequencing by Tandem Mass Spectra Assembly (2004, Analytical Chemistry)

Methods and tools

AI proteomics perspective, Automated mAb de novo (Bandeira SPS), Loxosceles intermedia venom proteome, MS-Dictionary, MS-Profile, MS/MS Triplets, Meta-SPS, Multistage MS multi-spectra sequencing, NRP dereplication and sequencing, Native antibody de novo MS/MS, NeuCode y-ion annotation, Shotgun Protein Sequencing, Spectral networks paradigm review

Co-authors (103)

Ranked by Newman fractional collaboration strength, so a pair on a two-author paper counts for more than a pair on a 50-author consortium paper.

Pavel A. Pevzner strength 3.58, 11 shared
Adrian Guthals strength 1.56, 6 shared
Sangtae Kim strength 1.50, 4 shared
Karl R. Clauser strength 1.33, 3 shared
Ari Frank strength 0.67, 2 shared
Kyowon Jeong strength 0.67, 2 shared
Pieter C. Dorrestein strength 0.66, 3 shared
Jennie R. Lill strength 0.38, 2 shared
Haixu Tang strength 0.35, 2 shared
Matthias Mann strength 0.35, 2 shared
Dekel Tsur strength 0.33, 1 shared
Jeramie D Watrous strength 0.33, 1 shared
Jesper V. Olsen strength 0.33, 1 shared
Nitin Gupta strength 0.33, 1 shared
Vineet Bafna strength 0.33, 1 shared
Julio Ng strength 0.33, 2 shared
Roger Linington strength 0.33, 2 shared
David Arnott strength 0.25, 1 shared
Vineet Pham strength 0.25, 1 shared
Dario Meluzzi strength 0.20, 1 shared
Alicia L. Richards strength 0.17, 1 shared
Catherine E. Vincent strength 0.17, 1 shared
Christopher M. Rose strength 0.17, 1 shared
Joshua J. Coon strength 0.17, 1 shared
Michael S. Westphall strength 0.17, 1 shared
Gerald Nakamura strength 0.12, 1 shared
Jeremy Stinson strength 0.12, 1 shared
Laura Murray strength 0.12, 1 shared
Majid Ghassemian strength 0.12, 1 shared
Thomas L Simmons strength 0.12, 1 shared
Wei-Ting Liu strength 0.12, 1 shared
Wendy Sandoval strength 0.12, 1 shared
William H Gerwick strength 0.12, 1 shared
Yongmei Chen strength 0.12, 1 shared
Yutian Gan strength 0.12, 1 shared
Aline V. Bednaski strength 0.10, 1 shared
Andrea Senff-Ribeiro strength 0.10, 1 shared
Dilza Trevisan-Silva strength 0.10, 1 shared
Fabricio K. Marchini strength 0.10, 1 shared
Felipe V. Leprevost strength 0.10, 1 shared

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