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    Nuno Bandeira

    TitleAssociate Professor
    SchoolUniversity of California, San Diego
    DepartmentSchool of Pharmacy and Pharmaceutical Science
    Address9500 Gilman Drive #0404
    CA La Jolla 92093
    Phone858-534-8666
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      Collapse Research 
      Collapse Research Activities and Funding
      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. 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 Oct 17. PMID: 29056429.
        View in: PubMed
      2. 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 Nov 29; 113(48):E7645-E7654. PMID: 27849584.
        View in: PubMed
      3. 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 Nov 15; 88(22):10775-10784. PMID: 27732780.
        View in: PubMed
      4. Na S, Payne SH, Bandeira N. Multi-species Identification of Polymorphic Peptide Variants via Propagation in Spectral Networks. Mol Cell Proteomics. 2016 Nov; 15(11):3501-3512. PMID: 27609420.
        View in: PubMed
      5. 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; PMCID: PMC4857761.
      6. 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; PMCID: PMC4749436 [Available on 12/01/16].
      7. 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; PMCID: PMC4409930.
      8. 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; PMCID: PMC4425220.
      9. 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; PMCID: PMC4256515.
      10. 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; PMCID: PMC4215869.
      11. 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; PMCID: PMC3977190.
      12. 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; PMCID: PMC3993922.
      13. 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; PMCID: PMC3945911.
      14. 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; PMCID: PMC3766387.
      15. 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; PMCID: PMC3710860.
      16. 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; PMCID: PMC4591044.
      17. Jeong K, Kim S, Bandeira N. False discovery rates in spectral identification. BMC Bioinformatics. 2012; 13 Suppl 16:S2. PMID: 23176207; PMCID: PMC3489529.
      18. 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; PMCID: PMC3893064.
      19. 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; PMCID: PMC3427086.
      20. Guthals A, Clauser KR, Bandeira N. Shotgun protein sequencing with meta-contig assembly. Mol Cell Proteomics. 2012 Oct; 11(10):1084-96. PMID: 22798278; PMCID: PMC3494147.
      21. 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; PMCID: PMC3434779.
      22. 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; PMCID: PMC3387089.
      23. 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; PMCID: PMC3317402.
      24. 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; PMCID: PMC3237077.
      25. Kim Y, Bark S, Hook V, Bandeira N. NeuroPedia: neuropeptide database and spectral library. Bioinformatics. 2011 Oct 01; 27(19):2772-3. PMID: 21821666; PMCID: PMC3179654.
      26. 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; PMCID: PMC3128193.
      27. 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; PMCID: PMC3687529.
      28. 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; PMCID: PMC3220955.
      29. 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; PMCID: PMC3108828.
      30. Bandeira N. Protein identification by spectral networks analysis. Methods Mol Biol. 2011; 694:151-68. PMID: 21082434.
        View in: PubMed
      31. 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; PMCID: PMC3101864.
      32. 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; PMCID: PMC2976990.
      33. 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; PMCID: PMC2934687.
      34. 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; PMCID: PMC2938093.
      35. 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; PMCID: PMC2754211.
      36. 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; PMCID: PMC2765223.
      37. 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; PMCID: PMC2690493.
      38. 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; PMCID: PMC2621003.
      39. 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; PMCID: PMC2718660.
      40. 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; PMCID: PMC2533155.
      41. 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.
        View in: PubMed
      42. 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.
        View in: PubMed
      43. 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; PMCID: PMC1851064.
      44. 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.
        View in: PubMed
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