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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.
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PubMed Mentions:
25 Fields:
Translation:
AnimalsCells
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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.
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PubMed Mentions:
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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.
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PubMed Mentions:
36 Fields:
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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.
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PubMed Mentions:
1134 Fields:
Translation:
Humans
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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.
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PubMed Mentions:
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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.
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PubMed Mentions:
1 Fields:
Translation:
Humans
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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.
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PubMed Mentions:
1 Fields:
Translation:
HumansAnimalsCells
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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.
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PubMed Mentions:
97 Fields:
Translation:
Humans
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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.
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PubMed Mentions:
21 Fields:
Translation:
Humans
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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.
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PubMed Mentions:
36 Fields:
Translation:
AnimalsCells
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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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PubMed Mentions:
33 Fields:
Translation:
Animals
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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.
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PubMed Mentions:
23 Fields:
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Three-Dimensional Microbiome and Metabolome Cartography of a Diseased Human Lung. . 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.
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PubMed Mentions:
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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.
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PubMed Mentions:
9 Fields:
Translation:
Cells
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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.
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PubMed Mentions:
51 Fields:
Translation:
Humans
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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.
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PubMed Mentions:
13 Fields:
Translation:
Humans
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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.
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PubMed Mentions:
17 Fields:
Translation:
Humans
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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.
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PubMed Mentions:
277 Fields:
Translation:
Humans
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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.
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PubMed Mentions:
528 Fields:
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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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PubMed Mentions:
18 Fields:
Translation:
Cells
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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.
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PubMed Mentions:
53 Fields:
Translation:
Cells
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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.
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PubMed Mentions:
98 Fields:
Translation:
Humans
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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:
53 Fields:
Translation:
Cells
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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:
3 Fields:
Translation:
HumansCells