| 2022 | SC | P-Massive: A Real-Time Search Engine for a Multi-Terabyte Mass Spectrometry Database. | Narangerelt Batsoyol, Benjamin S. Pullman, Mingxun Wang, Nuno Bandeira, Steven Swanson |
| 2019 | ICDT | Index-Based, High-Dimensional, Cosine Threshold Querying with Optimality Guarantees. | Yuliang Li, Jianguo Wang, Benjamin S. Pullman, Nuno Bandeira, Yannis Papakonstantinou |
| 2014 | RECOMB | The Generating Function Approach for Peptide Identification in Spectral Networks. | Adrian Guthals, Christina Boucher, Nuno Bandeira |
| 2013 | RECOMB | Spectral Library Generating Function for Assessing Spectrum-Spectrum Match Significance. | Mingxun Wang, Nuno Bandeira |
| 2010 | RECOMB | Gapped Spectral Dictionaries and Their Applications for Database Searches of Tandem Mass Spectra. | Kyowon Jeong, Sangtae Kim, Nuno Bandeira, Pavel A. Pevzner |
| 2009 | RECOMB | Shared Peptides in Mass Spectrometry Based Protein Quantification. | Banu Dost, Nuno Bandeira, Xiangqian Li, Zhouxin Shen, Steve Briggs, Vineet Bafna |
| 2008 | ISMB | Multi-spectra peptide sequencing and its applications to multistage mass spectrometry. | Nuno Bandeira, Jesper V. Olsen, Matthias Mann, Pavel A. Pevzner |
| 2008 | RECOMB | De Novo Sequencing of Nonribosomal Peptides. | Nuno Bandeira, Julio Ng, Dario Meluzzi, Roger G. Linington, Pieter C. Dorrestein, Pavel A. Pevzner |
| 2006 | RECOMB | A New Approach to Protein Identification. | Nuno Bandeira, Dekel Tsur, Ari Frank, Pavel A. Pevzner |