My Bibliography

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Ntai I, Phelan VV, Bachmann BO. Phosphonopeptide K-26 biosynthetic intermediates in Astrosporangium hypotensionis. Chem Commun (Camb). 2006 Nov 21;(43):4518-20. doi: 10.1039/b611768f. PubMed PMID: 17283804.

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Hu Y, Phelan V, Ntai I, Farnet CM, Zazopoulos E, Bachmann BO. Benzodiazepine biosynthesis in Streptomyces refuineus. Chem Biol. 2007 Jun;14(6):691-701. doi: 10.1016/j.chembiol.2007.05.009. PubMed PMID: 17584616.

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Hu Y, Phelan VV, Farnet CM, Zazopoulos E, Bachmann BO. Reassembly of anthramycin biosynthetic gene cluster by using recombinogenic cassettes. Chembiochem. 2008 Jul 2;9(10):1603-8. doi: 10.1002/cbic.200800029. PubMed PMID: 18512205.

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Phelan VV, Du Y, McLean JA, Bachmann BO. Adenylation enzyme characterization using gamma -(18)O(4)-ATP pyrophosphate exchange. Chem Biol. 2009 May 29;16(5):473-8. doi: 10.1016/j.chembiol.2009.04.007. PubMed PMID: 19477411; PubMed Central PMCID: PMC2710614.

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Carter MD, Phelan VV, Sandlin RD, Bachmann BO, Wright DW. Lipophilic mediated assays for beta-hematin inhibitors. Comb Chem High Throughput Screen. 2010 Mar;13(3):285-92. doi: 10.2174/138620710790980496. PubMed PMID: 20230372; PubMed Central PMCID: PMC2901836.

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Panosian TD, Nannemann DP, Watkins GR, Phelan VV, McDonald WH, Wadzinski BE, Bachmann BO, Iverson TM. Bacillus cereus phosphopentomutase is an alkaline phosphatase family member that exhibits an altered entry point into the catalytic cycle. J Biol Chem. 2011 Mar 11;286(10):8043-8054. doi: 10.1074/jbc.M110.201350. Epub 2010 Dec 30. PubMed PMID: 21193409; PubMed Central PMCID: PMC3048691.

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Phelan VV, Liu WT, Pogliano K, Dorrestein PC. Microbial metabolic exchange--the chemotype-to-phenotype link. Nat Chem Biol. 2011 Dec 15;8(1):26-35. doi: 10.1038/nchembio.739. PubMed PMID: 22173357; PubMed Central PMCID: PMC3869239.

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Yang JY, Phelan VV, Simkovsky R, Watrous JD, Trial RM, Fleming TC, Wenter R, Moore BS, Golden SS, Pogliano K, Dorrestein PC. Primer on agar-based microbial imaging mass spectrometry. J Bacteriol. 2012 Nov;194(22):6023-8. doi: 10.1128/JB.00823-12. Epub 2012 Jul 20. Review. PubMed PMID: 22821974; PubMed Central PMCID: PMC3486372.

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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. doi: 10.1073/pnas.1206855109. Epub 2012 Aug 6. PubMed PMID: 22869730; PubMed Central PMCID: PMC3427086.

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Watrous JD, Phelan VV, Hsu CC, Moree WJ, Duggan BM, Alexandrov T, Dorrestein PC. Microbial metabolic exchange in 3D. ISME J. 2013 Apr;7(4):770-80. doi: 10.1038/ismej.2012.155. Epub 2013 Jan 3. PubMed PMID: 23283018; PubMed Central PMCID: PMC3603389.

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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 9;110(28):E2611-20. doi: 10.1073/pnas.1303471110. Epub 2013 Jun 24. PubMed PMID: 23798442; PubMed Central PMCID: PMC3710860.

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Phelan VV, Moree WJ, Aguilar J, Cornett DS, Koumoutsi A, Noble SM, Pogliano K, Guerrero CA, Dorrestein PC. Impact of a transposon insertion in phzF2 on the specialized metabolite production and interkingdom interactions of Pseudomonas aeruginosa. J Bacteriol. 2014 May;196(9):1683-93. doi: 10.1128/JB.01258-13. Epub 2014 Feb 14. PubMed PMID: 24532776; PubMed Central PMCID: PMC3993319.

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Phelan VV, Fang J, Dorrestein PC. Mass Spectrometry Analysis of Pseudomonas aeruginosa Treated with Azithromycin. J Am Soc Mass Spectrom. 2015 Jun;26(6):873-7. doi: 10.1007/s13361-015-1101-6. Epub 2015 Mar 24. PubMed PMID: 25801585; PubMed Central PMCID: PMC4425625.

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Quinn RA, Phelan VV, Whiteson KL, Garg N, Bailey BA, Lim YW, Conrad DJ, Dorrestein PC, Rohwer FL. Microbial, host and xenobiotic diversity in the cystic fibrosis sputum metabolome. ISME J. 2016 Jun;10(6):1483-98. doi: 10.1038/ismej.2015.207. Epub 2015 Dec 1. PubMed PMID: 26623545; PubMed Central PMCID: PMC5029181.

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Wang M, Carver JJ, Phelan VV, Sanchez LM, Garg N, Peng Y, Nguyen DD, Watrous J, Kapono CA, Luzzatto-Knaan T, Porto C, Bouslimani A, Melnik AV, Meehan MJ, Liu WT, Crüsemann M, Boudreau PD, Esquenazi E, Sandoval-Calderón M, Kersten RD, Pace LA, Quinn RA, Duncan KR, Hsu CC, Floros DJ, Gavilan RG, Kleigrewe K, Northen T, Dutton RJ, Parrot D, Carlson EE, Aigle B, Michelsen CF, Jelsbak L, Sohlenkamp C, Pevzner P, Edlund A, McLean J, Piel J, Murphy BT, Gerwick L, Liaw CC, Yang YL, Humpf HU, Maansson M, Keyzers RA, Sims AC, Johnson AR, Sidebottom AM, Sedio BE, Klitgaard A, Larson CB, P CAB, Torres-Mendoza D, Gonzalez DJ, Silva DB, Marques LM, Demarque DP, Pociute E, O'Neill EC, Briand E, Helfrich EJN, Granatosky EA, Glukhov E, Ryffel F, Houson H, Mohimani H, Kharbush JJ, Zeng Y, Vorholt JA, Kurita KL, Charusanti P, McPhail KL, Nielsen KF, Vuong L, Elfeki M, Traxler MF, Engene N, Koyama N, Vining OB, Baric R, Silva RR, Mascuch SJ, Tomasi S, Jenkins S, Macherla V, Hoffman T, Agarwal V, Williams PG, Dai J, Neupane R, Gurr J, Rodríguez AMC, Lamsa A, Zhang C, Dorrestein K, Duggan BM, Almaliti J, Allard PM, Phapale P, Nothias LF, Alexandrov T, Litaudon M, Wolfender JL, Kyle JE, Metz TO, Peryea T, Nguyen DT, VanLeer D, Shinn P, Jadhav A, Müller R, Waters KM, Shi W, Liu X, Zhang L, Knight R, Jensen PR, Palsson BO, Pogliano K, Linington RG, Gutiérrez M, Lopes NP, Gerwick WH, Moore BS, Dorrestein PC, Bandeira N. Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking. Nat Biotechnol. 2016 Aug 9;34(8):828-837. doi: 10.1038/nbt.3597. PubMed PMID: 27504778; PubMed Central PMCID: PMC5321674.

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Garg N, Luzzatto-Knaan T, Melnik AV, Caraballo-Rodríguez AM, Floros DJ, Petras D, Gregor R, Dorrestein PC, Phelan VV. Natural products as mediators of disease. Nat Prod Rep. 2017 Feb 1;34(2):194-219. doi: 10.1039/c6np00063k. Epub 2016 Nov 22. Review. PubMed PMID: 27874907; PubMed Central PMCID: PMC5299058.

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Shaffer M, Armstrong AJS, Phelan VV, Reisdorph N, Lozupone CA. Microbiome and metabolome data integration provides insight into health and disease. Transl Res. 2017 Nov;189:51-64. doi: 10.1016/j.trsl.2017.07.001. Epub 2017 Jul 14. Review. PubMed PMID: 28764956; PubMed Central PMCID: PMC5659916.

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Sanders JG, Nurk S, Salido RA, Minich J, Xu ZZ, Zhu Q, Martino C, Fedarko M, Arthur TD, Chen F, Boland BS, Humphrey GC, Brennan C, Sanders K, Gaffney J, Jepsen K, Khosroheidari M, Green C, Liyanage M, Dang JW, Phelan VV, Quinn RA, Bankevich A, Chang JT, Rana TM, Conrad DJ, Sandborn WJ, Smarr L, Dorrestein PC, Pevzner PA, Knight R. Optimizing sequencing protocols for leaderboard metagenomics by combining long and short reads. Genome Biol. 2019 Oct 31;20(1):226. doi: 10.1186/s13059-019-1834-9. PubMed PMID: 31672156; PubMed Central PMCID: PMC6822431.

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Kiggins C, Skinner A, Resendiz MJE. 7,8-Dihydro-8-oxoguanosine Lesions Inhibit the Theophylline Aptamer or Change Its Selectivity. Chembiochem. 2020 May 4;21(9):1347-1355. doi: 10.1002/cbic.201900684. Epub 2020 Jan 30. PubMed PMID: 31845489; PubMed Central PMCID: PMC7297664.

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Price CE, Brown DG, Limoli DH, Phelan VV, O'Toole GA. Exogenous Alginate Protects Staphylococcus aureus from Killing by Pseudomonas aeruginosa. J Bacteriol. 2020 Mar 26;202(8). doi: 10.1128/JB.00559-19. Print 2020 Mar 26. PubMed PMID: 31792010; PubMed Central PMCID: PMC7099135.

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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. Feature-based molecular networking in the GNPS analysis environment. Nat Methods. 2020 Sep;17(9):905-908. doi: 10.1038/s41592-020-0933-6. Epub 2020 Aug 24. PubMed PMID: 32839597; PubMed Central PMCID: PMC7885687.

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Phelan VV. Feature-Based Molecular Networking for Metabolite Annotation. Methods Mol Biol. 2020;2104:227-243. doi: 10.1007/978-1-0716-0239-3_13. PubMed PMID: 31953821.

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Neve RL, Carrillo BD, Phelan VV. Impact of Artificial Sputum Medium Formulation on Pseudomonas aeruginosa Secondary Metabolite Production. J Bacteriol. 2021 Oct 12;203(21):e0025021. doi: 10.1128/JB.00250-21. Epub 2021 Aug 16. PubMed PMID: 34398662; PubMed Central PMCID: PMC8508215.

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O'Toole GA, Crabbé A, Kümmerli R, LiPuma JJ, Bomberger JM, Davies JC, Limoli D, Phelan VV, Bliska JB, DePas WH, Dietrich LE, Hampton TH, Hunter R, Khursigara CM, Price-Whelan A, Ashare A, Cramer RA, Goldberg JB, Harrison F, Hogan DA, Henson MA, Madden DR, Mayers JR, Nadell C, Newman D, Prince A, Rivett DW, Schwartzman JD, Schultz D, Sheppard DC, Smyth AR, Spero MA, Stanton BA, Turner PE, van der Gast C, Whelan FJ, Whitaker R, Whiteson K. Model Systems to Study the Chronic, Polymicrobial Infections in Cystic Fibrosis: Current Approaches and Exploring Future Directions. mBio. 2021 Oct 26;12(5):e0176321. doi: 10.1128/mBio.01763-21. Epub 2021 Sep 21. PubMed PMID: 34544277; PubMed Central PMCID: PMC8546538.

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Petras D, Phelan VV, Acharya D, Allen AE, Aron AT, Bandeira N, Bowen BP, Belle-Oudry D, Boecker S, Cummings DA Jr, Deutsch JM, Fahy E, Garg N, Gregor R, Handelsman J, Navarro-Hoyos M, Jarmusch AK, Jarmusch SA, Louie K, Maloney KN, Marty MT, Meijler MM, Mizrahi I, Neve RL, Northen TR, Molina-Santiago C, Panitchpakdi M, Pullman B, Puri AW, Schmid R, Subramaniam S, Thukral M, Vasquez-Castro F, Dorrestein PC, Wang M. GNPS Dashboard: collaborative exploration of mass spectrometry data in the web browser. Nat Methods. 2022 Feb;19(2):134-136. doi: 10.1038/s41592-021-01339-5. PubMed PMID: 34862502; PubMed Central PMCID: PMC8831450.

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Jens JN, Breiner DJ, Phelan VV. Spray-Based Application of Matrix to Agar-Based Microbial Samples for Reproducible Sample Adherence in MALDI MSI. J Am Soc Mass Spectrom. 2022 Apr 6;33(4):731-734. doi: 10.1021/jasms.1c00208. Epub 2022 Feb 24. PubMed PMID: 35202541; PubMed Central PMCID: PMC9341124.

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Jens JN, Breiner DJ, Neve RL, Fiebig MM, Phelan VV. MBRA-2: a Modified Chemostat System to Culture Biofilms. Microbiol Spectr. 2023 Feb 14;11(1):e0292822. doi: 10.1128/spectrum.02928-22. Epub 2022 Dec 7. PubMed PMID: 36475832; PubMed Central PMCID: PMC9927502.

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Jenul C, Keim KC, Jens JN, Zeiler MJ, Schilcher K, Schurr MJ, Melander C, Phelan VV, Horswill AR. Pyochelin biotransformation by Staphylococcus aureus shapes bacterial competition with Pseudomonas aeruginosa in polymicrobial infections. Cell Rep. 2023 Jun 27;42(6):112540. doi: 10.1016/j.celrep.2023.112540. Epub 2023 May 24. PubMed PMID: 37227819; PubMed Central PMCID: PMC10592502.

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Neve RL, Giedraitis E, Akbari MS, Cohen S, Phelan VV. Secondary metabolite profiling of Pseudomonas aeruginosa isolates reveals rare genomic traits. mSystems. 2024 May 16;9(5):e0033924. doi: 10.1128/msystems.00339-24. Epub 2024 Apr 15. PubMed PMID: 38619244; PubMed Central PMCID: PMC11097636.

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Shahneh MRZ, Strobel M, Vitale GA, Geibel C, Abiead YE, Garg N, Wagner B, Forchhammer K, Aron A, Phelan VV, Petras D, Wang M. ModiFinder: Tandem Mass Spectral Alignment Enables Structural Modification Site Localization. J Am Soc Mass Spectrom. 2024 Nov 6;35(11):2564-2578. doi: 10.1021/jasms.4c00061. Epub 2024 Jun 3. PubMed PMID: 38830143; PubMed Central PMCID: PMC11540723.

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Wang X, Strobel M, Aron AT, Phelan VV, Acharya DD, Brown CJ, Clevenger K, Hu J, Kretsch A, Mahood EH, Menegatti C, Xiong Q, Wang M. Network Topology Evaluation and Transitive Alignments for Molecular Networking. J Am Soc Mass Spectrom. 2024 Sep 4;35(9):2165-2175. doi: 10.1021/jasms.4c00208. Epub 2024 Aug 12. PubMed PMID: 39133821; PubMed Central PMCID: PMC11516331.

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Wang X, Abiead YE, Acharya DD, Brown CJ, Clevenger K, Hu J, Kretsch A, Menegatti C, Xiong Q, Bittremieux W, Wang M. MS-RT: A Method for Evaluating MS/MS Clustering Performance for Metabolomics Data. J Proteome Res. 2025 Apr 4;24(4):1778-1790. doi: 10.1021/acs.jproteome.4c00881. Epub 2025 Mar 5. PubMed PMID: 40042915; PubMed Central PMCID: PMC12331128.

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Lau A, Wang X, Xu T, Schramm T, Abiead YE, Petras D, Phelan VV, Wang M. Multiple Spectrum Alignment for Molecular Networking Exploration and Discovery. J Am Soc Mass Spectrom. 2026 Jan 7;37(1):126-134. doi: 10.1021/jasms.5c00237. Epub 2025 Dec 2. PubMed PMID: 41328747; PubMed Central PMCID: PMC12724678.