Mingxun Wang

Title(s)Postdoctoral Scholar, School of Pharmacy and Pharmaceutical Science
SchoolVc-health Sciences-schools
Address9500 Gilman Drive #
La Jolla CA 92093
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    UCSDPhD05/2017Computer Science and Engineering

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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. GNPS Dashboard: collaborative exploration of mass spectrometry data in the web browser. Nat Methods. 2022 02; 19(2):134-136. Petras D, Phelan VV, Acharya D, Allen AE, Aron AT, Bandeira N, Bowen BP, Belle-Oudry D, Boecker S, Cummings DA, 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. PMID: 34862502; PMCID: PMC8831450.
      View in: PubMed   Mentions:
    2. Tandem Mass Spectrometry Molecular Networking as a Powerful and Efficient Tool for Drug Metabolism Studies. Anal Chem. 2022 01 18; 94(2):1456-1464. Yu JS, Nothias LF, Wang M, Kim DH, Dorrestein PC, Kang KB, Yoo HH. PMID: 34985284.
      View in: PubMed   Mentions:
    3. NPClassifier: A Deep Neural Network-Based Structural Classification Tool for Natural Products. J Nat Prod. 2021 11 26; 84(11):2795-2807. Kim HW, Wang M, Leber CA, Nothias LF, Reher R, Kang KB, van der Hooft JJJ, Dorrestein PC, Gerwick WH, Cottrell GW. PMID: 34662515; PMCID: PMC8631337.
      View in: PubMed   Mentions:    Fields:    
    4. A proteomics sample metadata representation for multiomics integration and big data analysis. Nat Commun. 2021 10 06; 12(1):5854. Dai C, Füllgrabe A, Pfeuffer J, Solovyeva EM, Deng J, Moreno P, Kamatchinathan S, Kundu DJ, George N, Fexova S, Grüning B, Föll MC, Griss J, Vaudel M, Audain E, Locard-Paulet M, Turewicz M, Eisenacher M, Uszkoreit J, Van Den Bossche T, Schwämmle V, Webel H, Schulze S, Bouyssié D, Jayaram S, Duggineni VK, Samaras P, Wilhelm M, Choi M, Wang M, Kohlbacher O, Brazma A, Papatheodorou I, Bandeira N, Deutsch EW, Vizcaíno JA, Bai M, Sachsenberg T, Levitsky LI, Perez-Riverol Y. PMID: 34615866; PMCID: PMC8494749.
      View in: PubMed   Mentions:
    5. Chemical Proportionality within Molecular Networks. Anal Chem. 2021 09 28; 93(38):12833-12839. Petras D, Caraballo-Rodríguez AM, Jarmusch AK, Molina-Santiago C, Gauglitz JM, Gentry EC, Belda-Ferre P, Romero D, Tsunoda SM, Dorrestein PC, Wang M. PMID: 34533933.
      View in: PubMed   Mentions:    Fields:    Translation:Humans
    6. Chemical Gradients of Plant Substrates in an Atta texana Fungus Garden. mSystems. 2021 Aug 31; 6(4):e0060121. Caraballo-Rodríguez AM, Puckett SP, Kyle KE, Petras D, da Silva R, Nothias LF, Ernst M, van der Hooft JJJ, Tripathi A, Wang M, Balunas MJ, Klassen JL, Dorrestein PC. PMID: 34342533; PMCID: PMC8409729.
      View in: PubMed   Mentions:
    7. Quick-start infrastructure for untargeted metabolomics analysis in GNPS. Nat Metab. 2021 07; 3(7):880-882. Leao TF, Clark CM, Bauermeister A, Elijah EO, Gentry EC, Husband M, Oliveira MF, Bandeira N, Wang M, Dorrestein PC. PMID: 34244695; PMCID: PMC8705952.
      View in: PubMed   Mentions: Translation:Humans
    8. Ion identity molecular networking for mass spectrometry-based metabolomics in the GNPS environment. Nat Commun. 2021 06 22; 12(1):3832. Schmid R, Petras D, Nothias LF, Wang M, Aron AT, Jagels A, Tsugawa H, Rainer J, Garcia-Aloy M, Dührkop K, Korf A, Pluskal T, Kameník Z, Jarmusch AK, Caraballo-Rodríguez AM, Weldon KC, Nothias-Esposito M, Aksenov AA, Bauermeister A, Albarracin Orio A, Grundmann CO, Vargas F, Koester I, Gauglitz JM, Gentry EC, Hövelmann Y, Kalinina SA, Pendergraft MA, Panitchpakdi M, Tehan R, Le Gouellec A, Aleti G, Mannochio Russo H, Arndt B, Hübner F, Hayen H, Zhi H, Raffatellu M, Prather KA, Aluwihare LI, Böcker S, McPhail KL, Humpf HU, Karst U, Dorrestein PC. PMID: 34158495; PMCID: PMC8219731.
      View in: PubMed   Mentions: 4     Fields:    Translation:AnimalsCells
    9. The prognostic value of sarcopenia combined with preoperative fibrinogen-albumin ratio in patients with intrahepatic cholangiocarcinoma after surgery: A multicenter, prospective study. Cancer Med. 2021 07; 10(14):4768-4780. Yu H, Wang M, Wang Y, Yang J, Deng L, Bao W, He B, Lin Z, Chen Z, Chen K, Zhang B, Liu F, Yu Z, Ye L, Jin B, Chen G. PMID: 34105304; PMCID: PMC8290250.
      View in: PubMed   Mentions:
    10. A community resource for paired genomic and metabolomic data mining. Nat Chem Biol. 2021 04; 17(4):363-368. Schorn MA, Verhoeven S, Ridder L, Huber F, Acharya DD, Aksenov AA, Aleti G, Moghaddam JA, Aron AT, Aziz S, Bauermeister A, Bauman KD, Baunach M, Beemelmanns C, Beman JM, Berlanga-Clavero MV, Blacutt AA, Bode HB, Boullie A, Brejnrod A, Bugni TS, Calteau A, Cao L, Carrión VJ, Castelo-Branco R, Chanana S, Chase AB, Chevrette MG, Costa-Lotufo LV, Crawford JM, Currie CR, Cuypers B, Dang T, de Rond T, Demko AM, Dittmann E, Du C, Drozd C, Dujardin JC, Dutton RJ, Edlund A, Fewer DP, Garg N, Gauglitz JM, Gentry EC, Gerwick L, Glukhov E, Gross H, Gugger M, Guillén Matus DG, Helfrich EJN, Hempel BF, Hur JS, Iorio M, Jensen PR, Kang KB, Kaysser L, Kelleher NL, Kim CS, Kim KH, Koester I, König GM, Leao T, Lee SR, Lee YY, Li X, Little JC, Maloney KN, Männle D, Martin H C, McAvoy AC, Metcalf WW, Mohimani H, Molina-Santiago C, Moore BS, Mullowney MW, Muskat M, Nothias LF, O'Neill EC, Parkinson EI, Petras D, Piel J, Pierce EC, Pires K, Reher R, Romero D, Roper MC, Rust M, Saad H, Saenz C, Sanchez LM, Sørensen SJ, Sosio M, Süssmuth RD, Sweeney D, Tahlan K, Thomson RJ, Tobias NJ, Trindade-Silva AE, van Wezel GP, Wang M, Weldon KC, Zhang F, Ziemert N, Duncan KR, Crüsemann M, Rogers S, Dorrestein PC, Medema MH, van der Hooft JJJ. PMID: 33589842; PMCID: PMC7987574.
      View in: PubMed   Mentions: 11     Fields:    
    11. A Multi-Omics Characterization of the Natural Product Potential of Tropical Filamentous Marine Cyanobacteria. Mar Drugs. 2021 Jan 06; 19(1). Leão T, Wang M, Moss N, da Silva R, Sanders J, Nurk S, Gurevich A, Humphrey G, Reher R, Zhu Q, Belda-Ferre P, Glukhov E, Whitner S, Alexander KL, Rex R, Pevzner P, Dorrestein PC, Knight R, Bandeira N, Gerwick WH, Gerwick L. PMID: 33418911; PMCID: PMC7825088.
      View in: PubMed   Mentions: 1     Fields:    Translation:Cells
    12. Reply to: Examining microbe-metabolite correlations by linear methods. Nat Methods. 2021 01; 18(1):40-41. Morton JT, McDonald D, Aksenov AA, Nothias LF, Foulds JR, Quinn RA, Badri MH, Swenson TL, Van Goethem MW, Northen TR, Vazquez-Baeza Y, Wang M, Bokulich NA, Watters A, Song SJ, Bonneau R, Dorrestein PC, Knight R. PMID: 33398188.
      View in: PubMed   Mentions: 1     Fields:    
    13. Non-targeted tandem mass spectrometry enables the visualization of organic matter chemotype shifts in coastal seawater. Chemosphere. 2021 May; 271:129450. Petras D, Minich JJ, Cancelada LB, Torres RR, Kunselman E, Wang M, White ME, Allen EE, Prather KA, Aluwihare LI, Dorrestein PC. PMID: 33460888; PMCID: PMC7969459.
      View in: PubMed   Mentions: 2     Fields:    
    14. Therapy for advanced cholangiocarcinoma: Current knowledge and future potential. J Cell Mol Med. 2021 01; 25(2):618-628. Wang M, Chen Z, Guo P, Wang Y, Chen G. PMID: 33277810; PMCID: PMC7812297.
      View in: PubMed   Mentions:
    15. Chemically informed analyses of metabolomics mass spectrometry data with Qemistree. Nat Chem Biol. 2021 02; 17(2):146-151. Tripathi A, Vázquez-Baeza Y, Gauglitz JM, Wang M, Dührkop K, Nothias-Esposito M, Acharya DD, Ernst M, van der Hooft JJJ, Zhu Q, McDonald D, Brejnrod AD, Gonzalez A, Handelsman J, Fleischauer M, Ludwig M, Böcker S, Nothias LF, Knight R, Dorrestein PC. PMID: 33199911; PMCID: PMC8189545.
      View in: PubMed   Mentions: 9     Fields:    
    16. Fungal-bacterial interaction selects for quorum sensing mutants with increased production of natural antifungal compounds. Commun Biol. 2020 11 12; 3(1):670. Albarracín Orio AG, Petras D, Tobares RA, Aksenov AA, Wang M, Juncosa F, Sayago P, Moyano AJ, Dorrestein PC, Smania AM. PMID: 33184402; PMCID: PMC7661731.
      View in: PubMed   Mentions: 2  Translation:AnimalsCellsPHPublic Health
    17. Auto-deconvolution and molecular networking of gas chromatography-mass spectrometry data. Nat Biotechnol. 2021 02; 39(2):169-173. Aksenov AA, Laponogov I, Zhang Z, Doran SLF, Belluomo I, Veselkov D, Bittremieux W, Nothias LF, Nothias-Esposito M, Maloney KN, Misra BB, Melnik AV, Smirnov A, Du X, Jones KL, Jones KL, Dorrestein K, Panitchpakdi M, Ernst M, van der Hooft JJJ, Gonzalez M, Carazzone C, Amézquita A, Callewaert C, Morton JT, Quinn RA, Bouslimani A, Orio AA, Petras D, Smania AM, Couvillion SP, Burnet MC, Nicora CD, Zink E, Metz TO, Artaev V, Humston-Fulmer E, Gregor R, Meijler MM, Mizrahi I, Eyal S, Anderson B, Dutton R, Lugan R, Boulch PL, Guitton Y, Prevost S, Poirier A, Dervilly G, Le Bizec B, Fait A, Persi NS, Song C, Gashu K, Coras R, Guma M, Manasson J, Scher JU, Barupal DK, Alseekh S, Fernie AR, Mirnezami R, Vasiliou V, Schmid R, Borisov RS, Kulikova LN, Knight R, Wang M, Hanna GB, Dorrestein PC, Veselkov K. PMID: 33169034; PMCID: PMC7971188.
      View in: PubMed   Mentions: 10     Fields:    Translation:HumansAnimals
    18. Feature-based molecular networking in the GNPS analysis environment. Nat Methods. 2020 09; 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; PMCID: PMC7885687.
      View in: PubMed   Mentions: 64     Fields:    
    19. ReDU: a framework to find and reanalyze public mass spectrometry data. Nat Methods. 2020 09; 17(9):901-904. 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, 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; PMCID: PMC7968862.
      View in: PubMed   Mentions: 10     Fields:    
    20. Protocol for community-created public MS/MS reference spectra within the Global Natural Products Social Molecular Networking infrastructure. Rapid Commun Mass Spectrom. 2020 May 30; 34(10):e8725. Vargas F, Weldon KC, Sikora N, Wang M, Zhang Z, Gentry EC, Panitchpakdi MW, Caraballo-Rodríguez AM, Dorrestein PC, Jarmusch AK. PMID: 31930757.
      View in: PubMed   Mentions: 2     Fields:    
    21. 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: 33     Fields:    Translation:HumansAnimals
    22. Global chemical effects of the microbiome include new bile-acid conjugations. Nature. 2020 03; 579(7797):123-129. Quinn RA, Melnik AV, Vrbanac A, Fu T, Patras KA, Christy MP, Bodai Z, Belda-Ferre P, Tripathi A, Chung LK, Downes M, Welch RD, Quinn M, Humphrey G, Panitchpakdi M, Weldon KC, Aksenov A, da Silva R, Avila-Pacheco J, Clish C, Bae S, Mallick H, Franzosa EA, Lloyd-Price J, Bussell R, Thron T, Nelson AT, Wang M, Leszczynski E, Vargas F, Gauglitz JM, Meehan MJ, Gentry E, Arthur TD, Komor AC, Poulsen O, Boland BS, Chang JT, Sandborn WJ, Lim M, Garg N, Lumeng JC, Xavier RJ, Kazmierczak BI, Jain R, Egan M, Rhee KE, Ferguson D, Raffatellu M, Vlamakis H, Haddad GG, Siegel D, Huttenhower C, Mazmanian SK, Evans RM, Nizet V, Knight R, Dorrestein PC. PMID: 32103176; PMCID: PMC7252668.
      View in: PubMed   Mentions: 57     Fields:    Translation:HumansAnimals
    23. A Convolutional Neural Network-Based Approach for the Rapid Annotation of Molecularly Diverse Natural Products. J Am Chem Soc. 2020 03 04; 142(9):4114-4120. Reher R, Kim HW, Zhang C, Mao HH, Wang M, Nothias LF, Caraballo-Rodriguez AM, Glukhov E, Teke B, Leao T, Alexander KL, Duggan BM, Van Everbroeck EL, Dorrestein PC, Cottrell GW, Gerwick WH. PMID: 32045230; PMCID: PMC7210566.
      View in: PubMed   Mentions: 20     Fields:    Translation:HumansCells
    24. 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; PMCID: PMC7236533.
      View in: PubMed   Mentions: 32     Fields:    
    25. Detection of Ovarian Cancer Using Samples Sourced from the Vaginal Microenvironment. J Proteome Res. 2020 01 03; 19(1):503-510. Galey MM, Young AN, Petukhova VZ, Wang M, Wang J, Salvi A, Russo A, Burdette JE, Sanchez LM. PMID: 31738564; PMCID: PMC7020100.
      View in: PubMed   Mentions:
    26. The Natural Products Atlas: An Open Access Knowledge Base for Microbial Natural Products Discovery. ACS Cent Sci. 2019 Nov 27; 5(11):1824-1833. van Santen JA, Jacob G, Singh AL, Aniebok V, Balunas MJ, Bunsko D, Neto FC, Castaño-Espriu L, Chang C, Clark TN, Cleary Little JL, Delgadillo DA, Dorrestein PC, Duncan KR, Egan JM, Galey MM, Haeckl FPJ, Hua A, Hughes AH, Iskakova D, Khadilkar A, Lee JH, Lee S, LeGrow N, Liu DY, Macho JM, McCaughey CS, Medema MH, Neupane RP, O'Donnell TJ, Paula JS, Sanchez LM, Shaikh AF, Soldatou S, Terlouw BR, Tran TA, Valentine M, van der Hooft JJJ, Vo DA, Wang M, Wilson D, Zink KE, Linington RG. PMID: 31807684; PMCID: PMC6891855.
      View in: PubMed   Mentions: 57  
    27. Learning representations of microbe-metabolite interactions. Nat Methods. 2019 12; 16(12):1306-1314. Morton JT, Aksenov AA, Nothias LF, Foulds JR, Quinn RA, Badri MH, Swenson TL, Van Goethem MW, Northen TR, Vazquez-Baeza Y, Wang M, Bokulich NA, Watters A, Song SJ, Bonneau R, Dorrestein PC, Knight R. PMID: 31686038; PMCID: PMC6884698.
      View in: PubMed   Mentions: 31     Fields:    Translation:AnimalsCells
    28. 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; PMCID: PMC6759567.
      View in: PubMed   Mentions: 7  
    29. Author Correction: Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nat Biotechnol. 2019 Sep; 37(9):1091. Bolyen E, Rideout JR, Dillon MR, Bokulich NA, Abnet CC, Al-Ghalith GA, Alexander H, Alm EJ, Arumugam M, Asnicar F, Bai Y, Bisanz JE, Bittinger K, Brejnrod A, Brislawn CJ, Brown CT, Callahan BJ, Caraballo-Rodríguez AM, Chase J, Cope EK, Da Silva R, Diener C, Dorrestein PC, Douglas GM, Durall DM, Duvallet C, Edwardson CF, Ernst M, Estaki M, Fouquier J, Gauglitz JM, Gibbons SM, Gibson DL, Gonzalez A, Gorlick K, Guo J, Hillmann B, Holmes S, Holste H, Huttenhower C, Huttley GA, Janssen S, Jarmusch AK, Jiang L, Kaehler BD, Kang KB, Keefe CR, Keim P, Kelley ST, Knights D, Koester I, Kosciolek T, Kreps J, Langille MGI, Lee J, Ley R, Liu YX, Loftfield E, Lozupone C, Maher M, Marotz C, Martin BD, McDonald D, McIver LJ, Melnik AV, Metcalf JL, Morgan SC, Morton JT, Naimey AT, Navas-Molina JA, Nothias LF, Orchanian SB, Pearson T, Peoples SL, Petras D, Preuss ML, Pruesse E, Rasmussen LB, Rivers A, Robeson MS, Rosenthal P, Segata N, Shaffer M, Shiffer A, Sinha R, Song SJ, Spear JR, Swafford AD, Thompson LR, Torres PJ, Trinh P, Tripathi A, Turnbaugh PJ, Ul-Hasan S, van der Hooft JJJ, Vargas F, Vázquez-Baeza Y, Vogtmann E, von Hippel M, Walters W, Wan Y, Wang M, Warren J, Weber KC, Williamson CHD, Willis AD, Xu ZZ, Zaneveld JR, Zhang Y, Zhu Q, Knight R, Caporaso JG. PMID: 31399723.
      View in: PubMed   Mentions: 49     Fields:    
    30. Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nat Biotechnol. 2019 08; 37(8):852-857. Bolyen E, Rideout JR, Dillon MR, Bokulich NA, Abnet CC, Al-Ghalith GA, Alexander H, Alm EJ, Arumugam M, Asnicar F, Bai Y, Bisanz JE, Bittinger K, Brejnrod A, Brislawn CJ, Brown CT, Callahan BJ, Caraballo-Rodríguez AM, Chase J, Cope EK, Da Silva R, Diener C, Dorrestein PC, Douglas GM, Durall DM, Duvallet C, Edwardson CF, Ernst M, Estaki M, Fouquier J, Gauglitz JM, Gibbons SM, Gibson DL, Gonzalez A, Gorlick K, Guo J, Hillmann B, Holmes S, Holste H, Huttenhower C, Huttley GA, Janssen S, Jarmusch AK, Jiang L, Kaehler BD, Kang KB, Keefe CR, Keim P, Kelley ST, Knights D, Koester I, Kosciolek T, Kreps J, Langille MGI, Lee J, Ley R, Liu YX, Loftfield E, Lozupone C, Maher M, Marotz C, Martin BD, McDonald D, McIver LJ, Melnik AV, Metcalf JL, Morgan SC, Morton JT, Naimey AT, Navas-Molina JA, Nothias LF, Orchanian SB, Pearson T, Peoples SL, Petras D, Preuss ML, Pruesse E, Rasmussen LB, Rivers A, Robeson MS, Rosenthal P, Segata N, Shaffer M, Shiffer A, Sinha R, Song SJ, Spear JR, Swafford AD, Thompson LR, Torres PJ, Trinh P, Tripathi A, Turnbaugh PJ, Ul-Hasan S, van der Hooft JJJ, Vargas F, Vázquez-Baeza Y, Vogtmann E, von Hippel M, Walters W, Wan Y, Wang M, Warren J, Weber KC, Williamson CHD, Willis AD, Xu ZZ, Zaneveld JR, Zhang Y, Zhu Q, Knight R, Caporaso JG. PMID: 31341288; PMCID: PMC7015180.
      View in: PubMed   Mentions: 1417     Fields:    Translation:Humans
    31. MolNetEnhancer: Enhanced Molecular Networks by Integrating Metabolome Mining and Annotation Tools. Metabolites. 2019 Jul 16; 9(7). Ernst M, Kang KB, Caraballo-Rodríguez AM, Nothias LF, Wandy J, Chen C, Wang M, Rogers S, Medema MH, Dorrestein PC, van der Hooft JJJ. PMID: 31315242; PMCID: PMC6680503.
      View in: PubMed   Mentions: 34  
    32. Initial Development toward Non-Invasive Drug Monitoring via Untargeted Mass Spectrometric Analysis of Human Skin. Anal Chem. 2019 07 02; 91(13):8062-8069. Jarmusch AK, Elijah EO, Vargas F, Bouslimani A, da Silva RR, Ernst M, Wang M, Del Rosario KK, Dorrestein PC, Tsunoda SM. PMID: 31074958.
      View in: PubMed   Mentions: 2     Fields:    Translation:Humans
    33. Whole Cell MALDI Fingerprinting Is a Robust Tool for Differential Profiling of Two-Component Mammalian Cell Mixtures. J Am Soc Mass Spectrom. 2019 Feb; 30(2):344-354. Petukhova VZ, Young AN, Wang J, Wang M, Ladanyi A, Kothari R, Burdette JE, Sanchez LM. PMID: 30353292; PMCID: PMC6347503.
      View in: PubMed   Mentions: 1     Fields:    Translation:HumansAnimalsCells
    34. Qiita: rapid, web-enabled microbiome meta-analysis. Nat Methods. 2018 10; 15(10):796-798. Gonzalez A, Navas-Molina JA, Kosciolek T, McDonald D, Vázquez-Baeza Y, Ackermann G, DeReus J, Janssen S, Swafford AD, Orchanian SB, Sanders JG, Shorenstein J, Holste H, Petrus S, Robbins-Pianka A, Brislawn CJ, Wang M, Rideout JR, Bolyen E, Dillon M, Caporaso JG, Dorrestein PC, Knight R. PMID: 30275573; PMCID: PMC6235622.
      View in: PubMed   Mentions: 111     Fields:    Translation:Humans
    35. 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; PMCID: PMC6279426.
      View in: PubMed   Mentions: 27     Fields:    Translation:Humans
    36. Propagating annotations of molecular networks using in silico fragmentation. PLoS Comput Biol. 2018 04; 14(4):e1006089. da Silva RR, Wang M, Nothias LF, van der Hooft JJJ, Caraballo-Rodríguez AM, Fox E, Balunas MJ, Klassen JL, Lopes NP, Dorrestein PC. PMID: 29668671; PMCID: PMC5927460.
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    37. Bioactivity-Based Molecular Networking for the Discovery of Drug Leads in Natural Product Bioassay-Guided Fractionation. J Nat Prod. 2018 04 27; 81(4):758-767. Nothias LF, Nothias-Esposito M, da Silva R, Wang M, Protsyuk I, Zhang Z, Sarvepalli A, Leyssen P, Touboul D, Costa J, Paolini J, Alexandrov T, Litaudon M, Dorrestein PC. PMID: 29498278.
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    38. Significance estimation for large scale metabolomics annotations by spectral matching. Nat Commun. 2017 11 14; 8(1):1494. Scheubert K, Hufsky F, Petras D, Wang M, Nothias LF, Dührkop K, Bandeira N, Dorrestein PC, Böcker S. PMID: 29133785; PMCID: PMC5684233.
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    39. 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; PMCID: PMC6267898.
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    40. 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; PMCID: PMC5441867.
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    41. Discovering and linking public omics data sets using the Omics Discovery Index. Nat Biotechnol. 2017 05 09; 35(5):406-409. Perez-Riverol Y, Bai M, da Veiga Leprevost F, Squizzato S, Park YM, Haug K, Carroll AJ, Spalding D, Paschall J, Wang M, Del-Toro N, Ternent T, Zhang P, Buso N, Bandeira N, Deutsch EW, Campbell DS, Beavis RC, Salek RM, Sarkans U, Petryszak R, Keays M, Fahy E, Sud M, Subramaniam S, Barbera A, Jiménez RC, Nesvizhskii AI, Sansone SA, Steinbeck C, Lopez R, Vizcaíno JA, Ping P, Hermjakob H. PMID: 28486464; PMCID: PMC5831141.
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    42. 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; PMCID: PMC5137711.
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    43. SPLASH, a hashed identifier for mass spectra. Nat Biotechnol. 2016 11 08; 34(11):1099-1101. Wohlgemuth G, Mehta SS, Mejia RF, Neumann S, Pedrosa D, Pluskal T, Schymanski EL, Willighagen EL, Wilson M, Wishart DS, Arita M, Dorrestein PC, Bandeira N, Wang M, Schulze T, Salek RM, Steinbeck C, Nainala VC, Mistrik R, Nishioka T, Fiehn O. PMID: 27824832; PMCID: PMC5515539.
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    44. The ProteomeXchange consortium in 2017: supporting the cultural change in proteomics public data deposition. Nucleic Acids Res. 2017 01 04; 45(D1):D1100-D1106. Deutsch EW, Csordas A, Sun Z, Jarnuczak A, Perez-Riverol Y, Ternent T, Campbell DS, Bernal-Llinares M, Okuda S, Kawano S, Moritz RL, Carver JJ, Wang M, Ishihama Y, Bandeira N, Hermjakob H, Vizcaíno JA. PMID: 27924013; PMCID: PMC5210636.
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    45. Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking. Nat Biotechnol. 2016 08 09; 34(8):828-837. 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. PMID: 27504778; PMCID: PMC5321674.
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    46. SweetNET: A Bioinformatics Workflow for Glycopeptide MS/MS Spectral Analysis. J Proteome Res. 2016 08 05; 15(8):2826-40. Nasir W, Toledo AG, Noborn F, Nilsson J, Wang M, Bandeira N, Larson G. PMID: 27399812.
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    47. 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; PMCID: PMC4409930.
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    48. Molecular cartography of the human skin surface in 3D. Proc Natl Acad Sci U S A. 2015 Apr 28; 112(17):E2120-9. Bouslimani A, Porto C, Rath CM, Wang M, Guo Y, Gonzalez A, Berg-Lyon D, Ackermann G, Moeller Christensen GJ, Nakatsuji T, Zhang L, Borkowski AW, Meehan MJ, Dorrestein K, Gallo RL, Bandeira N, Knight R, Alexandrov T, Dorrestein PC. PMID: 25825778; PMCID: PMC4418856.
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    49. 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; PMCID: PMC4215869.
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    50. 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; PMCID: PMC3766387.
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