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Nuno Bandeira

Title(s)Associate Professor, School of Pharmacy And Pharmaceutical Science
SchoolHealth Sciences
Phone858-534-8666
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    Collapse Research 
    Collapse Research Activities and Funding
    MassIVE.quant: a curated and scalable community resource for quantitative proteomics
    NIH/NLM R01LM013115Jun 1, 2019 - May 31, 2023
    Role: Principal Investigator
    Center for Computational Mass Spectrometry
    NIH/NIGMS P41GM103484Sep 20, 2008 - Jun 30, 2019
    Role: Principal Investigator

    Collapse Bibliographic 
    Collapse Publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help.
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    1. Wang M, Jarmusch AK, Vargas F, Aksenov AA, Gauglitz JM, Weldon K, Petras D, da Silva R, Quinn R, Melnik AV, van der Hooft JJJ, Caraballo-Rodríguez AM, Nothias LF, Aceves CM, Panitchpakdi M, Brown E, Di Ottavio F, Sikora N, Elijah EO, Labarta-Bajo L, Gentry EC, Shalapour S, Kyle KE, Puckett SP, Watrous JD, Carpenter CS, Bouslimani A, Ernst M, Swafford AD, Zúñiga EI, Balunas MJ, Klassen JL, Loomba R, Knight R, Bandeira N, Dorrestein PC. Mass spectrometry searches using MASST. Nat Biotechnol. 2020 Jan; 38(1):23-26. PMID: 31894142.
      View in: PubMed
    2. Melnik AV, Vázquez-Baeza Y, Aksenov AA, Hyde E, McAvoy AC, Wang M, da Silva RR, Protsyuk I, Wu JV, Bouslimani A, Lim YW, Luzzatto-Knaan T, Comstock W, Quinn RA, Wong R, Humphrey G, Ackermann G, Spivey T, Brouha SS, Bandeira N, Lin GY, Rohwer F, Conrad DJ, Alexandrov T, Knight R, Dorrestein PC, Garg N. Molecular and Microbial Microenvironments in Chronically Diseased Lungs Associated with Cystic Fibrosis. mSystems. 2019 Sep 24; 4(5). PMID: 31551401.
      View in: PubMed
    3. Gauglitz JM, Aceves CM, Aksenov AA, Aleti G, Almaliti J, Bouslimani A, Brown EA, Campeau A, Caraballo-Rodríguez AM, Chaar R, da Silva RR, Demko AM, Di Ottavio F, Elijah E, Ernst M, Ferguson LP, Holmes X, Jarmusch AK, Jiang L, Kang KB, Koester I, Kwan B, Li J, Li Y, Melnik AV, Molina-Santiago C, Ni B, Oom AL, Panitchpakdi MW, Petras D, Quinn R, Sikora N, Spengler K, Teke B, Tripathi A, Ul-Hasan S, van der Hooft JJJ, Vargas F, Vrbanac A, Vu AQ, Wang SC, Weldon K, Wilson K, Wozniak JM, Yoon M, Bandeira N, Dorrestein PC. Untargeted mass spectrometry-based metabolomics approach unveils molecular changes in raw and processed foods and beverages. Food Chem. 2020 Jan 01; 302:125290. PMID: 31404873.
      View in: PubMed
    4. Quinn RA, Adem S, Mills RH, Comstock W, DeRight Goldasich L, Humphrey G, Aksenov AA, Melnik AV, da Silva R, Ackermann G, Bandeira N, Gonzalez DJ, Conrad D, O'Donoghue AJ, Knight R, Dorrestein PC. Neutrophilic proteolysis in the cystic fibrosis lung correlates with a pathogenic microbiome. Microbiome. 2019 02 13; 7(1):23. PMID: 30760325.
      View in: PubMed
    5. Wang M, Wang J, Carver J, Pullman BS, Cha SW, Bandeira N. Assembling the Community-Scale Discoverable Human Proteome. Cell Syst. 2018 10 24; 7(4):412-421.e5. PMID: 30172843.
      View in: PubMed
    6. Garg N, Wang M, Hyde E, da Silva RR, Melnik AV, Protsyuk I, Bouslimani A, Lim YW, Wong R, Humphrey G, Ackermann G, Spivey T, Brouha SS, Bandeira N, Lin GY, Rohwer F, Conrad DJ, Alexandrov T, Knight R, Dorrestein PC. Three-Dimensional Microbiome and Metabolome Cartography of a Diseased Human Lung. Cell Host Microbe. 2017 Nov 08; 22(5):705-716.e4. PMID: 29056429.
      View in: PubMed
    7. Luzzatto-Knaan T, Garg N, Wang M, Glukhov E, Peng Y, Ackermann G, Amir A, Duggan BM, Ryazanov S, Gerwick L, Knight R, Alexandrov T, Bandeira N, Gerwick WH, Dorrestein PC. Digitizing mass spectrometry data to explore the chemical diversity and distribution of marine cyanobacteria and algae. Elife. 2017 05 11; 6. PMID: 28492366.
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    8. Bouslimani A, Melnik AV, Xu Z, Amir A, da Silva RR, Wang M, Bandeira N, Alexandrov T, Knight R, Dorrestein PC. Lifestyle chemistries from phones for individual profiling. Proc Natl Acad Sci U S A. 2016 11 29; 113(48):E7645-E7654. PMID: 27849584.
      View in: PubMed
    9. Petras D, Nothias LF, Quinn RA, Alexandrov T, Bandeira N, Bouslimani A, Castro-Falcón G, Chen L, Dang T, Floros DJ, Hook V, Garg N, Hoffner N, Jiang Y, Kapono CA, Koester I, Knight R, Leber CA, Ling TJ, Luzzatto-Knaan T, McCall LI, McGrath AP, Meehan MJ, Merritt JK, Mills RH, Morton J, Podvin S, Protsyuk I, Purdy T, Satterfield K, Searles S, Shah S, Shires S, Steffen D, White M, Todoric J, Tuttle R, Wojnicz A, Sapp V, Vargas F, Yang J, Zhang C, Dorrestein PC. Mass Spectrometry-Based Visualization of Molecules Associated with Human Habitats. Anal Chem. 2016 11 15; 88(22):10775-10784. PMID: 27732780.
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    10. Na S, Payne SH, Bandeira N. Multi-species Identification of Polymorphic Peptide Variants via Propagation in Spectral Networks. Mol Cell Proteomics. 2016 11; 15(11):3501-3512. PMID: 27609420.
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    11. Wang J, Tucholska M, Knight JD, Lambert JP, Tate S, Larsen B, Gingras AC, Bandeira N. MSPLIT-DIA: sensitive peptide identification for data-independent acquisition. Nat Methods. 2015 Dec; 12(12):1106-8. PMID: 26550773.
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    12. Hook V, Bandeira N. Neuropeptidomics Mass Spectrometry Reveals Signaling Networks Generated by Distinct Protease Pathways in Human Systems. J Am Soc Mass Spectrom. 2015 Dec; 26(12):1970-80. PMID: 26483184.
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    13. Duncan KR, Crüsemann M, Lechner A, Sarkar A, Li J, Ziemert N, Wang M, Bandeira N, Moore BS, Dorrestein PC, Jensen PR. Molecular networking and pattern-based genome mining improves discovery of biosynthetic gene clusters and their products from Salinispora species. Chem Biol. 2015 Apr 23; 22(4):460-471. PMID: 25865308.
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    14. Guthals A, Boucher C, Bandeira N. The generating function approach for Peptide identification in spectral networks. J Comput Biol. 2015 May; 22(5):353-66. PMID: 25423621.
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    15. Wang J, Bourne PE, Bandeira N. MixGF: spectral probabilities for mixture spectra from more than one peptide. Mol Cell Proteomics. 2014 Dec; 13(12):3688-97. PMID: 25225354.
      View in: PubMed
    16. Mohimani H, Kersten RD, Liu WT, Wang M, Purvine SO, Wu S, Brewer HM, Pasa-Tolic L, Bandeira N, Moore BS, Pevzner PA, Dorrestein PC. Automated genome mining of ribosomal peptide natural products. ACS Chem Biol. 2014 Jul 18; 9(7):1545-51. PMID: 24802639.
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    17. Wang J, Anania VG, Knott J, Rush J, Lill JR, Bourne PE, Bandeira N. Combinatorial approach for large-scale identification of linked peptides from tandem mass spectrometry spectra. Mol Cell Proteomics. 2014 Apr; 13(4):1128-36. PMID: 24493012.
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    18. Wang J, Anania VG, Knott J, Rush J, Lill JR, Bourne PE, Bandeira N. A turn-key approach for large-scale identification of complex posttranslational modifications. J Proteome Res. 2014 Mar 07; 13(3):1190-9. PMID: 24437954.
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    19. Meyer JG, Kim S, Maltby DA, Ghassemian M, Bandeira N, Komives EA. Expanding proteome coverage with orthogonal-specificity a-lytic proteases. Mol Cell Proteomics. 2014 Mar; 13(3):823-35. PMID: 24425750.
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    20. Wang M, Bandeira N. Spectral library generating function for assessing spectrum-spectrum match significance. J Proteome Res. 2013 Sep 06; 12(9):3944-51. PMID: 23808827.
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    21. Nguyen DD, Wu CH, Moree WJ, Lamsa A, Medema MH, Zhao X, Gavilan RG, Aparicio M, Atencio L, Jackson C, Ballesteros J, Sanchez J, Watrous JD, Phelan VV, van de Wiel C, Kersten RD, Mehnaz S, De Mot R, Shank EA, Charusanti P, Nagarajan H, Duggan BM, Moore BS, Bandeira N, Palsson BØ, Pogliano K, Gutiérrez M, Dorrestein PC. MS/MS networking guided analysis of molecule and gene cluster families. Proc Natl Acad Sci U S A. 2013 Jul 09; 110(28):E2611-20. PMID: 23798442.
      View in: PubMed
    22. Guthals A, Clauser KR, Frank AM, Bandeira N. Sequencing-grade de novo analysis of MS/MS triplets (CID/HCD/ETD) from overlapping peptides. J Proteome Res. 2013 Jun 07; 12(6):2846-57. PMID: 23679345.
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    23. Jeong K, Kim S, Bandeira N. False discovery rates in spectral identification. BMC Bioinformatics. 2012; 13 Suppl 16:S2. PMID: 23176207.
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    24. Guthals A, Watrous JD, Dorrestein PC, Bandeira N. The spectral networks paradigm in high throughput mass spectrometry. Mol Biosyst. 2012 Oct; 8(10):2535-44. PMID: 22610447.
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    25. Moree WJ, Phelan VV, Wu CH, Bandeira N, Cornett DS, Duggan BM, Dorrestein PC. Interkingdom metabolic transformations captured by microbial imaging mass spectrometry. Proc Natl Acad Sci U S A. 2012 Aug 21; 109(34):13811-6. PMID: 22869730.
      View in: PubMed
    26. Guthals A, Clauser KR, Bandeira N. Shotgun protein sequencing with meta-contig assembly. Mol Cell Proteomics. 2012 Oct; 11(10):1084-96. PMID: 22798278.
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    27. Guthals A, Bandeira N. Peptide identification by tandem mass spectrometry with alternate fragmentation modes. Mol Cell Proteomics. 2012 Sep; 11(9):550-7. PMID: 22595789.
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    28. Watrous J, Roach P, Alexandrov T, Heath BS, Yang JY, Kersten RD, van der Voort M, Pogliano K, Gross H, Raaijmakers JM, Moore BS, Laskin J, Bandeira N, Dorrestein PC. Mass spectral molecular networking of living microbial colonies. Proc Natl Acad Sci U S A. 2012 Jun 26; 109(26):E1743-52. PMID: 22586093.
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    29. Dost B, Bandeira N, Li X, Shen Z, Briggs SP, Bafna V. Accurate mass spectrometry based protein quantification via shared peptides. J Comput Biol. 2012 Apr; 19(4):337-48. PMID: 22414154.
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    30. Wang J, Bourne PE, Bandeira N. Peptide identification by database search of mixture tandem mass spectra. Mol Cell Proteomics. 2011 Dec; 10(12):M111.010017. PMID: 21862760.
      View in: PubMed
    31. Kim Y, Bark S, Hook V, Bandeira N. NeuroPedia: neuropeptide database and spectral library. Bioinformatics. 2011 Oct 01; 27(19):2772-3. PMID: 21821666.
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    32. Frank AM, Monroe ME, Shah AR, Carver JJ, Bandeira N, Moore RJ, Anderson GA, Smith RD, Pevzner PA. Spectral archives: extending spectral libraries to analyze both identified and unidentified spectra. Nat Methods. 2011 May 15; 8(7):587-91. PMID: 21572408.
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    33. Yang YL, Xu Y, Kersten RD, Liu WT, Meehan MJ, Moore BS, Bandeira N, Dorrestein PC. Connecting chemotypes and phenotypes of cultured marine microbial assemblages by imaging mass spectrometry. Angew Chem Int Ed Engl. 2011 Jun 20; 50(26):5839-42. PMID: 21574228.
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    34. Gupta N, Bandeira N, Keich U, Pevzner PA. Target-decoy approach and false discovery rate: when things may go wrong. J Am Soc Mass Spectrom. 2011 Jul; 22(7):1111-20. PMID: 21953092.
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    35. Jeong K, Kim S, Bandeira N, Pevzner PA. Gapped spectral dictionaries and their applications for database searches of tandem mass spectra. Mol Cell Proteomics. 2011 Jun; 10(6):M110.002220. PMID: 21444829.
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    36. Bandeira N. Protein identification by spectral networks analysis. Methods Mol Biol. 2011; 694:151-68. PMID: 21082434.
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    37. Kim S, Mischerikow N, Bandeira N, Navarro JD, Wich L, Mohammed S, Heck AJ, Pevzner PA. The generating function of CID, ETD, and CID/ETD pairs of tandem mass spectra: applications to database search. Mol Cell Proteomics. 2010 Dec; 9(12):2840-52. PMID: 20829449.
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    38. Hook V, Bark S, Gupta N, Lortie M, Lu WD, Bandeira N, Funkelstein L, Wegrzyn J, O'Connor DT, Pevzner P. Neuropeptidomic components generated by proteomic functions in secretory vesicles for cell-cell communication. AAPS J. 2010 Dec; 12(4):635-45. PMID: 20734175.
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    39. Gonzalez DJ, Lee SW, Hensler ME, Markley AL, Dahesh S, Mitchell DA, Bandeira N, Nizet V, Dixon JE, Dorrestein PC. Clostridiolysin S, a post-translationally modified biotoxin from Clostridium botulinum. J Biol Chem. 2010 Sep 03; 285(36):28220-8. PMID: 20581111.
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    40. Wang J, Pérez-Santiago J, Katz JE, Mallick P, Bandeira N. Peptide identification from mixture tandem mass spectra. Mol Cell Proteomics. 2010 Jul; 9(7):1476-85. PMID: 20348588.
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    41. Ng J, Bandeira N, Liu WT, Ghassemian M, Simmons TL, Gerwick WH, Linington R, Dorrestein PC, Pevzner PA. Dereplication and de novo sequencing of nonribosomal peptides. Nat Methods. 2009 Aug; 6(8):596-9. PMID: 19597502.
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    42. Liu WT, Ng J, Meluzzi D, Bandeira N, Gutierrez M, Simmons TL, Schultz AW, Linington RG, Moore BS, Gerwick WH, Pevzner PA, Dorrestein PC. Interpretation of tandem mass spectra obtained from cyclic nonribosomal peptides. Anal Chem. 2009 Jun 01; 81(11):4200-9. PMID: 19413302.
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    43. Kim S, Bandeira N, Pevzner PA. Spectral profiles, a novel representation of tandem mass spectra and their applications for de novo peptide sequencing and identification. Mol Cell Proteomics. 2009 Jun; 8(6):1391-400. PMID: 19254948.
      View in: PubMed
    44. Kim S, Gupta N, Bandeira N, Pevzner PA. Spectral dictionaries: Integrating de novo peptide sequencing with database search of tandem mass spectra. Mol Cell Proteomics. 2009 Jan; 8(1):53-69. PMID: 18703573.
      View in: PubMed
    45. Bandeira N, Olsen JV, Mann JV, Mann M, Pevzner PA. Multi-spectra peptide sequencing and its applications to multistage mass spectrometry. Bioinformatics. 2008 Jul 01; 24(13):i416-23. PMID: 18785330.
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    46. Frank AM, Bandeira N, Shen Z, Tanner S, Briggs SP, Smith RD, Pevzner PA. Clustering millions of tandem mass spectra. J Proteome Res. 2008 Jan; 7(1):113-22. PMID: 18067247.
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    47. Bandeira N. Spectral networks: a new approach to de novo discovery of protein sequences and posttranslational modifications. Biotechniques. 2007 Jun; 42(6):687, 689, 691 passim. PMID: 17612289.
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    48. Bandeira N, Clauser KR, Pevzner PA. Shotgun protein sequencing: assembly of peptide tandem mass spectra from mixtures of modified proteins. Mol Cell Proteomics. 2007 Jul; 6(7):1123-34. PMID: 17446555.
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    49. Bandeira N, Tsur D, Frank A, Pevzner PA. Protein identification by spectral networks analysis. Proc Natl Acad Sci U S A. 2007 Apr 10; 104(15):6140-5. PMID: 17404225.
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    50. Bandeira N, Tang H, Bafna V, Pevzner P. Shotgun protein sequencing by tandem mass spectra assembly. Anal Chem. 2004 Dec 15; 76(24):7221-33. PMID: 15595863.
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