A Two's Complement Array Multiplier Using True Values of the Operands. - Nuno Bandeira; Ken Vaccaro; James A. Howard (IEEE Trans. Computers, 1983)

A New Approach to Protein Identification. - Nuno Bandeira; Dekel Tsur; Ari Frank; Pavel A. Pevzner (RECOMB, 2006)

Protein identification by spectral networks analysis. - Nuno Bandeira; Dekel Tsur; Ari Frank; Pavel A. Pevzner (Proc. Natl. Acad. Sci. USA, 2007)

Multi-spectra peptide sequencing and its applications to multistage mass spectrometry. - Nuno Bandeira; Jesper V. Olsen; Matthias Mann 002; Pavel A. Pevzner (ISMB, 2008)

De Novo Sequencing of Nonribosomal Peptides. - Nuno Bandeira; Julio Ng; Dario Meluzzi; Roger G. Linington; Pieter C. Dorrestein; Pavel A. Pevzner (RECOMB, 2008)

Shared Peptides in Mass Spectrometry Based Protein Quantification. - Banu Dost; Nuno Bandeira; Xiangqian Li; Zhouxin Shen; Steve Briggs; Vineet Bafna (RECOMB, 2009)

Gapped Spectral Dictionaries and Their Applications for Database Searches of Tandem Mass Spectra. - Kyowon Jeong 001; Sangtae Kim; Nuno Bandeira; Pavel A. Pevzner (RECOMB, 2010)

NeuroPedia: neuropeptide database and spectral library. - Yoona Kim; Steven Bark; Vivian Hook; Nuno Bandeira (Bioinform., 2011)

False discovery rates in spectral identification. - Kyowon Jeong 001; Sangtae Kim; Nuno Bandeira (BMC Bioinform., 2012)

Accurate Mass Spectrometry Based Protein Quantification via Shared Peptides. - Banu Dost; Nuno Bandeira; Xiangqian Li; Zhouxin Shen; Steve Briggs; Vineet Bafna (J. Comput. Biol., 2012)

Spectral Library Generating Function for Assessing Spectrum-Spectrum Match Significance. - Mingxun Wang 001; Nuno Bandeira (RECOMB, 2013)

The Generating Function Approach for Peptide Identification in Spectral Networks. - Adrian Guthals; Christina Boucher 001; Nuno Bandeira (J. Comput. Biol., 2015)

On the Privacy Risks of Sharing Clinical Proteomics Data. - Sujun Li; Nuno Bandeira; XiaoFeng Wang 001; Haixu Tang (CRI, 2016)

Revealing deep proteome diversity with community-scale proteomics big data. - Nuno Bandeira (CSBio, 2017)

The ProteomeXchange consortium in 2017: supporting the cultural change in proteomics public data deposition. - Eric W. Deutsch; Attila Csordas; Zhi Sun; Andrew F. Jarnuczak; Yasset Pérez-Riverol; Tobias Ternent; David S. Campbell; Manuel Bernal Llinares; Shujiro Okuda; Shin Kawano; Robert L. Moritz; Jeremy Carver; et al. (Nucleic Acids Res., 2017)

Computational Proteomics (Dagstuhl Seminar 19351). - Nuno Bandeira; Lennart Martens (Dagstuhl Reports, 2019)

The ProteomeXchange consortium in 2020: enabling 'big data' approaches in proteomics. - Eric W. Deutsch; Nuno Bandeira; Vagisha Sharma; Yasset Pérez-Riverol; Jeremy Carver; Deepti Jaiswal Kundu; David García-Seisdedos; Andrew F. Jarnuczak; Suresh Hewapathirana; Benjamin S. Pullman; Julie Wertz; Zhi Sun; et al. (Nucleic Acids Res., 2020)

Index-based, High-dimensional, Cosine Threshold Querying with Optimality Guarantees. - Yuliang Li 001; Jianguo Wang 001; Benjamin S. Pullman; Nuno Bandeira; Yannis Papakonstantinou (Theory Comput. Syst., 2021)

P-Massive: A Real-Time Search Engine for a Multi-Terabyte Mass Spectrometry Database. - Narangerelt Batsoyol; Benjamin S. Pullman; Mingxun Wang 001; Nuno Bandeira; Steven Swanson (SC, 2022)

The ProteomeXchange consortium at 10 years: 2023 update. - Eric W. Deutsch; Nuno Bandeira; Yasset Pérez-Riverol; Vagisha Sharma; Jeremy Carver; Luis Mendoza; Deepti Jaiswal Kundu; Shengbo Wang; Chakradhar Bandla; Selvakumar Kamatchinathan; Suresh Hewapathirana; Benjamin S. Pullman; et al. (Nucleic Acids Res., 2023)

Strategic priorities for transformative progress in advancing biology with proteomics and artificial intelligence. - Yingying Sun; Jun A; Zhiwei Liu; Rui Sun; Liujia Qian; Samuel H. Payne; Wout Bittremieux; Markus Ralser; Chen Li 021; Yi Chen; Zhen Dong; Yasset Pérez-Riverol; et al. (CoRR, 2025)