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Nuno Bandeira

Title(s)Associate Professor, School of Pharmacy and Pharmaceutical Science
SchoolVc-health Sciences-schools
Address9500 Gilman Drive #
La Jolla CA 92093
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    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

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    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. to make corrections and additions.
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    Altmetrics Details PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. Feature-based molecular networking in the GNPS analysis environment. Nat Methods. 2020 Sep; 17(9):905-908. Nothias LF, Petras D, Schmid R, Dührkop K, Rainer J, Sarvepalli A, Protsyuk I, Ernst M, Tsugawa H, Fleischauer M, Aicheler F, Aksenov AA, Alka O, Allard PM, Barsch A, Cachet X, Caraballo-Rodriguez AM, Da Silva RR, Dang T, Garg N, Gauglitz JM, Gurevich A, Isaac G, Jarmusch AK, Kameník Z, Kang KB, Kessler N, Koester I, Korf A, Le Gouellec A, Ludwig M, Martin H C, McCall LI, McSayles J, Meyer SW, Mohimani H, Morsy M, Moyne O, Neumann S, Neuweger H, Nguyen NH, Nothias-Esposito M, Paolini J, Phelan VV, Pluskal T, Quinn RA, Rogers S, Shrestha B, Tripathi A, van der Hooft JJJ, Vargas F, Weldon KC, Witting M, Yang H, Zhang Z, Zubeil F, Kohlbacher O, Böcker S, Alexandrov T, Bandeira N, Wang M, Dorrestein PC. PMID: 32839597.
      View in: PubMed   Mentions: 4     Fields:    
    2. ReDU: a framework to find and reanalyze public mass spectrometry data. Nat Methods. 2020 Aug 17. Jarmusch AK, Wang M, Aceves CM, Advani RS, Aguirre S, Aksenov AA, Aleti G, Aron AT, Bauermeister A, Bolleddu S, Bouslimani A, Caraballo Rodriguez AM, Chaar R, Coras R, Elijah EO, Ernst M, Gauglitz JM, Gentry EC, Husband M, Jarmusch SA, Jones KL, Kamenik Z, Le Gouellec A, Lu A, McCall LI, McPhail KL, Meehan MJ, Melnik AV, Menezes RC, Montoya Giraldo YA, Nguyen NH, Nothias LF, Nothias-Esposito M, Panitchpakdi M, Petras D, Quinn RA, Sikora N, van der Hooft JJJ, Vargas F, Vrbanac A, Weldon KC, Knight R, Bandeira N, Dorrestein PC. PMID: 32807955.
      View in: PubMed   Mentions:    Fields:    
    3. Reproducible molecular networking of untargeted mass spectrometry data using GNPS. Nat Protoc. 2020 06; 15(6):1954-1991. Aron AT, Gentry EC, McPhail KL, Nothias LF, Nothias-Esposito M, Bouslimani A, Petras D, Gauglitz JM, Sikora N, Vargas F, van der Hooft JJJ, Ernst M, Kang KB, Aceves CM, Caraballo-Rodríguez AM, Koester I, Weldon KC, Bertrand S, Roullier C, Sun K, Tehan RM, Boya P CA, Christian MH, Gutiérrez M, Ulloa AM, Tejeda Mora JA, Mojica-Flores R, Lakey-Beitia J, Vásquez-Chaves V, Zhang Y, Calderón AI, Tayler N, Keyzers RA, Tugizimana F, Ndlovu N, Aksenov AA, Jarmusch AK, Schmid R, Truman AW, Bandeira N, Wang M, Dorrestein PC. PMID: 32405051.
      View in: PubMed   Mentions:    Fields:    Translation:HumansAnimals
    4. Mass spectrometry searches using MASST. Nat Biotechnol. 2020 01; 38(1):23-26. 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. PMID: 31894142.
      View in: PubMed   Mentions: 8     Fields:    
    5. Molecular and Microbial Microenvironments in Chronically Diseased Lungs Associated with Cystic Fibrosis. mSystems. 2019 Sep 24; 4(5). 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. PMID: 31551401.
      View in: PubMed   Mentions:
    6. Untargeted mass spectrometry-based metabolomics approach unveils molecular changes in raw and processed foods and beverages. Food Chem. 2020 Jan 01; 302:125290. 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. PMID: 31404873.
      View in: PubMed   Mentions: 4     Fields:    Translation:Cells
    7. Neutrophilic proteolysis in the cystic fibrosis lung correlates with a pathogenic microbiome. Microbiome. 2019 02 13; 7(1):23. 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. PMID: 30760325.
      View in: PubMed   Mentions: 8     Fields:    Translation:HumansCells
    8. Assembling the Community-Scale Discoverable Human Proteome. Cell Syst. 2018 10 24; 7(4):412-421.e5. Wang M, Wang J, Carver J, Pullman BS, Cha SW, Bandeira N. PMID: 30172843.
      View in: PubMed   Mentions: 7     Fields:    Translation:Humans
    9. Three-Dimensional Microbiome and Metabolome Cartography of a Diseased Human Lung. Cell Host Microbe. 2017 Nov 08; 22(5):705-716.e4. 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. PMID: 29056429.
      View in: PubMed   Mentions:
    10. Digitizing mass spectrometry data to explore the chemical diversity and distribution of marine cyanobacteria and algae. Elife. 2017 05 11; 6. 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. PMID: 28492366.
      View in: PubMed   Mentions: 5     Fields:    Translation:Cells
    11. Lifestyle chemistries from phones for individual profiling. Proc Natl Acad Sci U S A. 2016 11 29; 113(48):E7645-E7654. Bouslimani A, Melnik AV, Xu Z, Amir A, da Silva RR, Wang M, Bandeira N, Alexandrov T, Knight R, Dorrestein PC. PMID: 27849584.
      View in: PubMed   Mentions: 7     Fields:    Translation:Humans
    12. Mass Spectrometry-Based Visualization of Molecules Associated with Human Habitats. Anal Chem. 2016 11 15; 88(22):10775-10784. 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. PMID: 27732780.
      View in: PubMed   Mentions: 10     Fields:    Translation:Humans
    13. Multi-species Identification of Polymorphic Peptide Variants via Propagation in Spectral Networks. Mol Cell Proteomics. 2016 11; 15(11):3501-3512. Na S, Payne SH, Bandeira N. PMID: 27609420.
      View in: PubMed   Mentions: 4     Fields:    Translation:Cells
    14. MSPLIT-DIA: sensitive peptide identification for data-independent acquisition. Nat Methods. 2015 Dec; 12(12):1106-8. Wang J, Tucholska M, Knight JD, Lambert JP, Tate S, Larsen B, Gingras AC, Bandeira N. PMID: 26550773.
      View in: PubMed   Mentions: 22     Fields:    
    15. 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. Hook V, Bandeira N. PMID: 26483184.
      View in: PubMed   Mentions: 9     Fields:    Translation:HumansCells
    16. 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. Duncan KR, Crüsemann M, Lechner A, Sarkar A, Li J, Ziemert N, Wang M, Bandeira N, Moore BS, Dorrestein PC, Jensen PR. PMID: 25865308.
      View in: PubMed   Mentions: 38     Fields:    Translation:Cells
    17. The generating function approach for Peptide identification in spectral networks. J Comput Biol. 2015 May; 22(5):353-66. Guthals A, Boucher C, Bandeira N. PMID: 25423621.
      View in: PubMed   Mentions: 3     Fields:    Translation:HumansCells
    18. MixGF: spectral probabilities for mixture spectra from more than one peptide. Mol Cell Proteomics. 2014 Dec; 13(12):3688-97. Wang J, Bourne PE, Bandeira N. PMID: 25225354.
      View in: PubMed   Mentions: 7     Fields:    Translation:HumansAnimals
    19. Automated genome mining of ribosomal peptide natural products. ACS Chem Biol. 2014 Jul 18; 9(7):1545-51. 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. PMID: 24802639.
      View in: PubMed   Mentions: 40     Fields:    Translation:Cells
    20. Combinatorial approach for large-scale identification of linked peptides from tandem mass spectrometry spectra. Mol Cell Proteomics. 2014 Apr; 13(4):1128-36. Wang J, Anania VG, Knott J, Rush J, Lill JR, Bourne PE, Bandeira N. PMID: 24493012.
      View in: PubMed   Mentions: 8     Fields:    Translation:HumansAnimalsCells
    21. A turn-key approach for large-scale identification of complex posttranslational modifications. J Proteome Res. 2014 Mar 07; 13(3):1190-9. Wang J, Anania VG, Knott J, Rush J, Lill JR, Bourne PE, Bandeira N. PMID: 24437954.
      View in: PubMed   Mentions: 2     Fields:    Translation:HumansAnimalsCells
    22. Expanding proteome coverage with orthogonal-specificity a-lytic proteases. Mol Cell Proteomics. 2014 Mar; 13(3):823-35. Meyer JG, Kim S, Maltby DA, Ghassemian M, Bandeira N, Komives EA. PMID: 24425750.
      View in: PubMed   Mentions: 17     Fields:    Translation:AnimalsCells
    23. Spectral library generating function for assessing spectrum-spectrum match significance. J Proteome Res. 2013 Sep 06; 12(9):3944-51. Wang M, Bandeira N. PMID: 23808827.
      View in: PubMed   Mentions: 2     Fields:    Translation:HumansCells
    24. 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. 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. PMID: 23798442.
      View in: PubMed   Mentions: 93     Fields:    Translation:Cells
    25. 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. Guthals A, Clauser KR, Frank AM, Bandeira N. PMID: 23679345.
      View in: PubMed   Mentions: 19     Fields:    Translation:HumansAnimalsCells
    26. False discovery rates in spectral identification. BMC Bioinformatics. 2012; 13 Suppl 16:S2. Jeong K, Kim S, Bandeira N. PMID: 23176207.
      View in: PubMed   Mentions: 33     Fields:    
    27. The spectral networks paradigm in high throughput mass spectrometry. Mol Biosyst. 2012 Oct; 8(10):2535-44. Guthals A, Watrous JD, Dorrestein PC, Bandeira N. PMID: 22610447.
      View in: PubMed   Mentions: 29     Fields:    Translation:HumansCells
    28. Interkingdom metabolic transformations captured by microbial imaging mass spectrometry. Proc Natl Acad Sci U S A. 2012 Aug 21; 109(34):13811-6. Moree WJ, Phelan VV, Wu CH, Bandeira N, Cornett DS, Duggan BM, Dorrestein PC. PMID: 22869730.
      View in: PubMed   Mentions: 78     Fields:    Translation:HumansAnimalsCells
    29. Shotgun protein sequencing with meta-contig assembly. Mol Cell Proteomics. 2012 Oct; 11(10):1084-96. Guthals A, Clauser KR, Bandeira N. PMID: 22798278.
      View in: PubMed   Mentions: 12     Fields:    Translation:HumansAnimalsCells
    30. Peptide identification by tandem mass spectrometry with alternate fragmentation modes. Mol Cell Proteomics. 2012 Sep; 11(9):550-7. Guthals A, Bandeira N. PMID: 22595789.
      View in: PubMed   Mentions: 15     Fields:    Translation:Cells
    31. Mass spectral molecular networking of living microbial colonies. Proc Natl Acad Sci U S A. 2012 Jun 26; 109(26):E1743-52. 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. PMID: 22586093.
      View in: PubMed   Mentions: 224     Fields:    Translation:Cells
    32. Accurate mass spectrometry based protein quantification via shared peptides. J Comput Biol. 2012 Apr; 19(4):337-48. Dost B, Bandeira N, Li X, Shen Z, Briggs SP, Bafna V. PMID: 22414154.
      View in: PubMed   Mentions: 16     Fields:    Translation:AnimalsCells
    33. Peptide identification by database search of mixture tandem mass spectra. Mol Cell Proteomics. 2011 Dec; 10(12):M111.010017. Wang J, Bourne PE, Bandeira N. PMID: 21862760.
      View in: PubMed   Mentions: 10     Fields:    Translation:Cells
    34. NeuroPedia: neuropeptide database and spectral library. Bioinformatics. 2011 Oct 01; 27(19):2772-3. Kim Y, Bark S, Hook V, Bandeira N. PMID: 21821666.
      View in: PubMed   Mentions: 15     Fields:    Translation:HumansAnimalsCells
    35. Spectral archives: extending spectral libraries to analyze both identified and unidentified spectra. Nat Methods. 2011 May 15; 8(7):587-91. Frank AM, Monroe ME, Shah AR, Carver JJ, Bandeira N, Moore RJ, Anderson GA, Smith RD, Pevzner PA. PMID: 21572408.
      View in: PubMed   Mentions: 24     Fields:    
    36. 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. Yang YL, Xu Y, Kersten RD, Liu WT, Meehan MJ, Moore BS, Bandeira N, Dorrestein PC. PMID: 21574228.
      View in: PubMed   Mentions: 21     Fields:    Translation:Cells
    37. Target-decoy approach and false discovery rate: when things may go wrong. J Am Soc Mass Spectrom. 2011 Jul; 22(7):1111-20. Gupta N, Bandeira N, Keich U, Pevzner PA. PMID: 21953092.
      View in: PubMed   Mentions: 47     Fields:    Translation:Humans
    38. Gapped spectral dictionaries and their applications for database searches of tandem mass spectra. Mol Cell Proteomics. 2011 Jun; 10(6):M110.002220. Jeong K, Kim S, Bandeira N, Pevzner PA. PMID: 21444829.
      View in: PubMed   Mentions: 11     Fields:    Translation:HumansCells
    39. Protein identification by spectral networks analysis. Methods Mol Biol. 2011; 694:151-68. Bandeira N. PMID: 21082434.
      View in: PubMed   Mentions: 2     Fields:    Translation:AnimalsCells
    40. 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. Kim S, Mischerikow N, Bandeira N, Navarro JD, Wich L, Mohammed S, Heck AJ, Pevzner PA. PMID: 20829449.
      View in: PubMed   Mentions: 92     Fields:    Translation:HumansCells
    41. Neuropeptidomic components generated by proteomic functions in secretory vesicles for cell-cell communication. AAPS J. 2010 Dec; 12(4):635-45. Hook V, Bark S, Gupta N, Lortie M, Lu WD, Bandeira N, Funkelstein L, Wegrzyn J, O'Connor DT, Pevzner P. PMID: 20734175.
      View in: PubMed   Mentions: 14     Fields:    Translation:HumansCells
    42. Clostridiolysin S, a post-translationally modified biotoxin from Clostridium botulinum. J Biol Chem. 2010 Sep 03; 285(36):28220-8. Gonzalez DJ, Lee SW, Hensler ME, Markley AL, Dahesh S, Mitchell DA, Bandeira N, Nizet V, Dixon JE, Dorrestein PC. PMID: 20581111.
      View in: PubMed   Mentions: 33     Fields:    Translation:HumansCells
    43. Peptide identification from mixture tandem mass spectra. Mol Cell Proteomics. 2010 Jul; 9(7):1476-85. Wang J, Pérez-Santiago J, Katz JE, Mallick P, Bandeira N. PMID: 20348588.
      View in: PubMed   Mentions: 22     Fields:    Translation:AnimalsCells
    44. Dereplication and de novo sequencing of nonribosomal peptides. Nat Methods. 2009 Aug; 6(8):596-9. Ng J, Bandeira N, Liu WT, Ghassemian M, Simmons TL, Gerwick WH, Linington R, Dorrestein PC, Pevzner PA. PMID: 19597502.
      View in: PubMed   Mentions: 36     Fields:    Translation:Cells
    45. Interpretation of tandem mass spectra obtained from cyclic nonribosomal peptides. Anal Chem. 2009 Jun 01; 81(11):4200-9. Liu WT, Ng J, Meluzzi D, Bandeira N, Gutierrez M, Simmons TL, Schultz AW, Linington RG, Moore BS, Gerwick WH, Pevzner PA, Dorrestein PC. PMID: 19413302.
      View in: PubMed   Mentions: 31     Fields:    Translation:Cells
    46. 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. Kim S, Bandeira N, Pevzner PA. PMID: 19254948.
      View in: PubMed   Mentions: 12     Fields:    Translation:Cells
    47. Spectral dictionaries: Integrating de novo peptide sequencing with database search of tandem mass spectra. Mol Cell Proteomics. 2009 Jan; 8(1):53-69. Kim S, Gupta N, Bandeira N, Pevzner PA. PMID: 18703573.
      View in: PubMed   Mentions: 36     Fields:    Translation:HumansCells
    48. Multi-spectra peptide sequencing and its applications to multistage mass spectrometry. Bioinformatics. 2008 Jul 01; 24(13):i416-23. Bandeira N, Olsen JV, Mann JV, Mann M, Pevzner PA. PMID: 18785330.
      View in: PubMed   Mentions: 12     Fields:    Translation:Animals
    49. Clustering millions of tandem mass spectra. J Proteome Res. 2008 Jan; 7(1):113-22. Frank AM, Bandeira N, Shen Z, Tanner S, Briggs SP, Smith RD, Pevzner PA. PMID: 18067247.
      View in: PubMed   Mentions: 73     Fields:    Translation:Cells
    50. Spectral networks: a new approach to de novo discovery of protein sequences and posttranslational modifications. Biotechniques. 2007 Jun; 42(6):687, 689, 691 passim. Bandeira N. PMID: 17612289.
      View in: PubMed   Mentions: 11     Fields:    Translation:Cells
    51. Shotgun protein sequencing: assembly of peptide tandem mass spectra from mixtures of modified proteins. Mol Cell Proteomics. 2007 Jul; 6(7):1123-34. Bandeira N, Clauser KR, Pevzner PA. PMID: 17446555.
      View in: PubMed   Mentions: 22     Fields:    Translation:AnimalsCells
    52. Protein identification by spectral networks analysis. Proc Natl Acad Sci U S A. 2007 Apr 10; 104(15):6140-5. Bandeira N, Tsur D, Frank A, Pevzner PA. PMID: 17404225.
      View in: PubMed   Mentions: 68     Fields:    Translation:Cells
    53. Shotgun protein sequencing by tandem mass spectra assembly. Anal Chem. 2004 Dec 15; 76(24):7221-33. Bandeira N, Tang H, Bafna V, Pevzner P. PMID: 15595863.
      View in: PubMed   Mentions: 16     Fields:    Translation:Cells
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