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Global chemical effects of the microbiome include new bile-acid conjugations
Author / Creator:Quinn, Robert A. ; Melnik, Alexey V. ; Vrbanac, Alison ; Fu, Ting ; Patras, Kathryn A. ; Christy, Mitchell P. ; Bodai, Zsolt ; Belda-Ferre, Pedro ; Tripathi, Anupriya ; Chung, Lawton K. ; Downes, Michael ; Welch, Ryan D. ; Quinn, Melissa ; Humphrey, Greg ; Panitchpakdi, Morgan ; Weldon, Kelly C. ; Aksenov, Alexander ; da Silva, Ricardo ; Avila-Pacheco, Julian ; Clish, Clary ; Bae, Sena ; Mallick, Himel ; Franzosa, Eric A. ; Lloyd-Price, Jason ; Bussell, Robert ; Thron, Taren ; Nelson, Andrew T. ; Wang, Mingxun ; Leszczynski, Eric ; Vargas, Fernando ; Gauglitz, Julia M. ; Meehan, Michael J. ; Gentry, Emily ; Arthur, Timothy D. ; Komor, Alexis C. ; Poulsen, Orit ; Boland, Brigid S. ; Chang, John T. ; Sandborn, William J. ; Lim, Meerana ; Garg, Neha ; Lumeng, Julie C. ; Xavier, Ramnik J. ; Kazmierczak, Barbara I. ; Jain, Ruchi ; Egan, Marie ; Rhee, Kyung E. ; Ferguson, David ; Raffatellu, Manuela ; Vlamakis, Hera ; Haddad, Gabriel G. ; Siegel, Dionicio ; Huttenhower, Curtis ; Mazmanian, Sarkis K. ; Evans, Ronald M. ; Nizet, Victor ; Knight, Rob ; Dorrestein, Pieter C.
Publisher:London: Nature Publishing Group UK
Journal title:Nature (London), 2020-03, Vol.579 (7797), p.123-129
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The impact of skin care products on skin chemistry and microbiome dynamics
Author / Creator:Bouslimani, Amina ; da Silva, Ricardo ; Kosciolek, Tomasz ; Janssen, Stefan ; Callewaert, Chris ; Amir, Amnon ; Dorrestein, Kathleen ; Melnik, Alexey V ; Zaramela, Livia S ; Kim, Ji-Nu ; Humphrey, Gregory ; Schwartz, Tara ; Sanders, Karenina ; Brennan, Caitriona ; Luzzatto-Knaan, Tal ; Ackermann, Gail ; McDonald, Daniel ; Zengler, Karsten ; Knight, Rob ; Dorrestein, Pieter C
Publisher:England: BioMed Central Ltd
Journal title:BMC biology, 2019-06, Vol.17 (1), p.47-20, Article 47
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3D molecular cartography using LC–MS facilitated by Optimus and 'ili software
Author / Creator:Protsyuk, Ivan ; Melnik, Alexey V ; Nothias, Louis-Felix ; Rappez, Luca ; Phapale, Prasad ; Aksenov, Alexander A ; Bouslimani, Amina ; Ryazanov, Sergey ; Dorrestein, Pieter C ; Alexandrov, Theodore
Publisher:London: Nature Publishing Group UK
Journal title:Nature protocols, 2018-01, Vol.13 (1), p.134-154
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Spatial chemistry of citrus reveals molecules bactericidal to Candidatus Liberibacter asiaticus
Author / Creator:A. Aksenov, Alexander ; Blacutt, Alex ; Ginnan, Nichole ; Rolshausen, Philippe E. ; V. Melnik, Alexey ; Lotfi, Ali ; C. Gentry, Emily ; Ramasamy, Manikandan ; Zuniga, Cristal ; Zengler, Karsten ; Mandadi, Kranthi K. ; McCollum, Greg ; Dorrestein, Pieter C. ; Roper, M. Caroline
Publisher:London: Nature Publishing Group UK
Journal title:Scientific reports, 2024-09, Vol.14 (1), p.20306-13, Article 20306
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Lifestyle chemistries from phones for individual profiling
Author / Creator:Bouslimani, Amina ; Melnik, Alexey V. ; Xu, Zhenjiang ; Amir, Amnon ; da Silva, Ricardo R. ; Wang, Mingxun ; Bandeira, Nuno ; Alexandrov, Theodore ; Knight, Rob ; Dorrestein, Pieter C.
Publisher:United States: National Academy of Sciences
Journal title:Proceedings of the National Academy of Sciences - PNAS, 2016-11, Vol.113 (48), p.E7645-E7654
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Open access repository-scale propagated nearest neighbor suspect spectral library for untargeted metabolomics
Author / Creator:Bittremieux, Wout ; Avalon, Nicole E. ; Thomas, Sydney P. ; Kakhkhorov, Sarvar A. ; Aksenov, Alexander A. ; Gomes, Paulo Wender P. ; Aceves, Christine M. ; Caraballo-Rodríguez, Andrés Mauricio ; Gauglitz, Julia M. ; Gerwick, William H. ; Huan, Tao ; Jarmusch, Alan K. ; Kaddurah-Daouk, Rima F. ; Kang, Kyo Bin ; Kim, Hyun Woo ; Kondić, Todor ; Mannochio-Russo, Helena ; Meehan, Michael J. ; Melnik, Alexey V. ; Nothias, Louis-Felix ; O’Donovan, Claire ; Panitchpakdi, Morgan ; Petras, Daniel ; Schmid, Robin ; Schymanski, Emma L. ; van der Hooft, Justin J. J. ; Weldon, Kelly C. ; Yang, Heejung ; Xing, Shipei ; Zemlin, Jasmine ; Wang, Mingxun ; Dorrestein, Pieter C.
Publisher:London: Nature Publishing Group UK
Journal title:Nature communications, 2023-12, Vol.14 (1), p.8488-8488, Article 8488
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Author Correction: Spatial chemistry of citrus reveals molecules bactericidal to Candidatus Liberibacter asiaticus
Author / Creator:Aksenov, Alexander A. ; Blacutt, Alex ; Ginnan, Nichole ; Rolshausen, Philippe E. ; Melnik, Alexey V. ; Ali, Lotfi ; Gentry, Emily C. ; Ramasamy, Manikandan ; Zuniga, Cristal ; Zengler, Karsten ; Mandadi, Kranthi K. ; Dorrestein, Pieter C. ; Roper, M. Caroline ; McCollum, Greg
Publisher:London: Nature Publishing Group UK
Journal title:Scientific reports, 2025-02, Vol.15 (1), p.7215-1
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Intermittent Hypoxia and Hypercapnia, a Hallmark of Obstructive Sleep Apnea, Alters the Gut Microbiome and Metabolome
Author / Creator:Tripathi, Anupriya ; Melnik, Alexey V ; Xue, Jin ; Poulsen, Orit ; Meehan, Michael J ; Humphrey, Gregory ; Jiang, Lingjing ; Ackermann, Gail ; McDonald, Daniel ; Zhou, Dan ; Knight, Rob ; Dorrestein, Pieter C ; Haddad, Gabriel G
Publisher:United States: American Society for Microbiology
Journal title:mSystems, 2018-05, Vol.3 (3)
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Blackcurrant Anthocyanins Attenuate Estrogen -Deficiency-Induced Bone Loss through Modulating Microbial-Derived Short-Chain Carboxylic Acids and Phytoestrogen Metabolites in Peri- and Early Postmenopa...
Author / Creator:Nosal, Briana M ; Thornton, Staci N ; Melnik, Alexey V ; Lotfi, Ali ; Mofrad, Manije Darooghegi ; Aksenov, Alexander ; Lee, Elaine Choung-Hee ; Chun, Ock K
Publisher:Switzerland: MDPI AG
Journal title:Metabolites, 2024-10, Vol.14 (10), p.541
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The Molecular Effect of Wearing Silver-Threaded Clothing on the Human Skin
Author / Creator:Melnik, Alexey V ; Callewaert, Chris ; Dorrestein, Kathleen ; Broadhead, Rosie ; Minich, Jeremiah J ; Ernst, Madeleine ; Humphrey, Greg ; Ackermann, Gail ; Gathercole, Rob ; Aksenov, Alexander A ; Knight, Rob ; Dorrestein, Pieter C
Publisher:United States: American Society for Microbiology
Journal title:mSystems, 2023-02, Vol.8 (1), p.e0092222-e0092222
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SIRIUS 4: a rapid tool for turning tandem mass spectra into metabolite structure information
Author / Creator:Dührkop, Kai ; Fleischauer, Markus ; Ludwig, Marcus ; Aksenov, Alexander A. ; Melnik, Alexey V. ; Meusel, Marvin ; Dorrestein, Pieter C. ; Rousu, Juho ; Böcker, Sebastian
Publisher:New York: Nature Publishing Group US
Journal title:Nature methods, 2019-04, Vol.16 (4), p.299-302
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Intermittent Hypoxia and Hypercapnia Reproducibly Change the Gut Microbiome and Metabolome across Rodent Model Systems
Author / Creator:Tripathi, Anupriya ; Xu, Zhenjiang Zech ; Xue, Jin ; Poulsen, Orit ; Gonzalez, Antonio ; Humphrey, Gregory ; Meehan, Michael J ; Melnik, Alexey V ; Ackermann, Gail ; Zhou, Dan ; Malhotra, Atul ; Haddad, Gabriel G ; Dorrestein, Pieter C ; Knight, Rob
Publisher:United States: American Society for Microbiology
Journal title:mSystems, 2019-03, Vol.4 (2)
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Best practices for analysing microbiomes
Author / Creator:Knight, Rob ; Vrbanac, Alison ; Taylor, Bryn C. ; Aksenov, Alexander ; Callewaert, Chris ; Debelius, Justine ; Gonzalez, Antonio ; Kosciolek, Tomasz ; McCall, Laura-Isobel ; McDonald, Daniel ; Melnik, Alexey V. ; Morton, James T. ; Navas, Jose ; Quinn, Robert A. ; Sanders, Jon G. ; Swafford, Austin D. ; Thompson, Luke R. ; Tripathi, Anupriya ; Xu, Zhenjiang Z. ; Zaneveld, Jesse R. ; Zhu, Qiyun ; Caporaso, J. Gregory ; Dorrestein, Pieter C.
Publisher:London: Nature Publishing Group UK
Journal title:Nature reviews. Microbiology, 2018-07, Vol.16 (7), p.410-422
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From Sample to Multi-Omics Conclusions in under 48 Hours
Author / Creator:Quinn, Robert A ; Navas-Molina, Jose A ; Hyde, Embriette R ; Song, Se Jin ; Vázquez-Baeza, Yoshiki ; Humphrey, Greg ; Gaffney, James ; Minich, Jeremiah J ; Melnik, Alexey V ; Herschend, Jakob ; DeReus, Jeff ; Durant, Austin ; Dutton, Rachel J ; Khosroheidari, Mahdieh ; Green, Clifford ; da Silva, Ricardo ; Dorrestein, Pieter C ; Knight, Rob
Publisher:United States: American Society for Microbiology
Journal title:mSystems, 2016-03, Vol.1 (2)
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Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking
Author / Creator:Wang, Mingxun ; Carver, Jeremy J ; Garg, Neha ; Peng, Yao ; Nguyen, Don Duy ; Watrous, Jeramie ; Kapono, Clifford A ; Luzzatto-Knaan, Tal ; Bouslimani, Amina ; Melnik, Alexey V ; Meehan, Michael J ; Liu, Wei-Ting ; Crüsemann, Max ; Boudreau, Paul D ; Esquenazi, Eduardo ; Sandoval-Calderón, Mario ; Kersten, Roland D ; Quinn, Robert A ; Hsu, Cheng-Chih ; Floros, Dimitrios J ; Gavilan, Ronnie G ; Kleigrewe, Karin ; Northen, Trent ; Parrot, Delphine ; Carlson, Erin E ; Aigle, Bertrand ; Jelsbak, Lars ; Pevzner, Pavel ; Edlund, Anna ; McLean, Jeffrey ; Piel, Jörn ; Gerwick, Lena ; Liaw, Chih-Chuang ; Yang, Yu-Liang ; Humpf, Hans-Ulrich ; Maansson, Maria ; Keyzers, Robert A ; Sims, Amy C ; Johnson, Andrew R ; Sidebottom, Ashley M ; Klitgaard, Andreas ; Larson, Charles B ; Boya P, Cristopher A ; Torres-Mendoza, Daniel ; Gonzalez, David J ; Silva, Denise B ; Marques, Lucas M ; Demarque, Daniel P ; Pociute, Egle ; O'Neill, Ellis C ; Briand, Enora ; Helfrich, Eric J N ; Ryffel, Florian ; Houson, Hailey ; Mohimani, Hosein ; Zeng, Yi ; Vorholt, Julia A ; Kurita, Kenji L ; Charusanti, Pep ; McPhail, Kerry L ; Vuong, Lisa ; Elfeki, Maryam ; Traxler, Matthew F ; Engene, Niclas ; Koyama, Nobuhiro ; Vining, Oliver B ; Baric, Ralph ; Tomasi, Sophie ; Jenkins, Stefan ; Hoffman, Thomas ; Williams, Philip G ; Dai, Jingqui ; Neupane, Ram ; Rodríguez, Andrés M C ; Lamsa, Anne ; Zhang, Chen ; Duggan, Brendan M ; Almaliti, Jehad ; Allard, Pierre-Marie ; Nothias, Louis-Felix ; Alexandrov, Theodore ; Litaudon, Marc ; Wolfender, Jean-Luc ; Kyle, Jennifer E ; Metz, Thomas O ; Peryea, Tyler ; VanLeer, Danielle ; Shinn, Paul ; Jadhav, Ajit ; Müller, Rolf ; Waters, Katrina M ; Shi, Wenyuan ; Liu, Xueting ; Zhang, Lixin ; Knight, Rob ; Jensen, Paul R ; Pogliano, Kit ; Linington, Roger G ; Moore, Bradley S ; Dorrestein, Pieter C
Publisher:New York: Nature Publishing Group US
Journal title:Nature biotechnology, 2016-08, Vol.34 (8), p.828-837
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Mass spectrometry searches using MASST
Author / Creator:Wang, Mingxun ; Jarmusch, Alan K. ; Vargas, Fernando ; Aksenov, Alexander A. ; Gauglitz, Julia M. ; Weldon, Kelly ; Petras, Daniel ; da Silva, Ricardo ; Quinn, Robert ; Melnik, Alexey V. ; van der Hooft, Justin J. J. ; Caraballo-Rodríguez, Andrés Mauricio ; Nothias, Louis Felix ; Aceves, Christine M. ; Panitchpakdi, Morgan ; Brown, Elizabeth ; Di Ottavio, Francesca ; Sikora, Nicole ; Elijah, Emmanuel O. ; Labarta-Bajo, Lara ; Gentry, Emily C. ; Shalapour, Shabnam ; Kyle, Kathleen E. ; Puckett, Sara P. ; Watrous, Jeramie D. ; Carpenter, Carolina S. ; Bouslimani, Amina ; Ernst, Madeleine ; Swafford, Austin D. ; Zúñiga, Elina I. ; Balunas, Marcy J. ; Klassen, Jonathan L. ; Loomba, Rohit ; Knight, Rob ; Bandeira, Nuno ; Dorrestein, Pieter C.
Publisher:New York: Nature Publishing Group US
Journal title:Nature biotechnology, 2020-01, Vol.38 (1), p.23-26
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ReDU: a framework to find and reanalyze public mass spectrometry data
Author / Creator:Jarmusch, Alan K. ; Wang, Mingxun ; Aceves, Christine M. ; Advani, Rohit S. ; Aguirre, Shaden ; Aksenov, Alexander A. ; Aleti, Gajender ; Aron, Allegra T. ; Bauermeister, Anelize ; Bolleddu, Sanjana ; Bouslimani, Amina ; Caraballo Rodriguez, Andres Mauricio ; Chaar, Rama ; Coras, Roxana ; Elijah, Emmanuel O. ; Ernst, Madeleine ; Gauglitz, Julia M. ; Gentry, Emily C. ; Husband, Makhai ; Jarmusch, Scott A. ; Jones, Kenneth L. ; Kamenik, Zdenek ; Le Gouellec, Audrey ; Lu, Aileen ; McCall, Laura-Isobel ; McPhail, Kerry L. ; Meehan, Michael J. ; Melnik, Alexey V. ; Menezes, Riya C. ; Montoya Giraldo, Yessica Alejandra ; Nguyen, Ngoc Hung ; Nothias, Louis Felix ; Nothias-Esposito, Mélissa ; Panitchpakdi, Morgan ; Petras, Daniel ; Quinn, Robert A. ; Sikora, Nicole ; van der Hooft, Justin J. J. ; Vargas, Fernando ; Vrbanac, Alison ; Weldon, Kelly C. ; Knight, Rob ; Bandeira, Nuno ; Dorrestein, Pieter C.
Publisher:New York: Nature Publishing Group US
Journal title:Nature methods, 2020-09, Vol.17 (9), p.901-904
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Functional genomics and metabolomics advance the ethnobotany of the Samoan traditional medicine “matalafi”
Author / Creator:Molimau-Samasoni, Seeseei ; Woolner, Victoria Helen ; Foliga, Su’emalo Talie ; Robichon, Katharina ; Patel, Vimal ; Andreassend, Sarah K. ; Sheridan, Jeffrey P. ; Kawa, Tama Te ; Gresham, David ; Miller, Darach ; Sinclair, Daniel J. ; La Flamme, Anne C. ; Melnik, Alexey V. ; Aron, Allegra ; Dorrestein, Pieter C. ; Atkinson, Paul H. ; Keyzers, Robert A. ; Munkacsi, Andrew B.
Publisher:United States: National Academy of Sciences
Journal title:Proceedings of the National Academy of Sciences - PNAS, 2021-11, Vol.118 (45), p.1-11
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Creating a 3D microbial and chemical snapshot of a human habitat
Author / Creator:Kapono, Clifford A. ; Morton, James T. ; Bouslimani, Amina ; Melnik, Alexey V. ; Orlinsky, Kayla ; Knaan, Tal Luzzatto ; Garg, Neha ; Vázquez-Baeza, Yoshiki ; Protsyuk, Ivan ; Janssen, Stefan ; Zhu, Qiyun ; Alexandrov, Theodore ; Smarr, Larry ; Knight, Rob ; Dorrestein, Pieter C.
Publisher:London: Nature Publishing Group UK
Journal title:Scientific reports, 2018-02, Vol.8 (1), p.3669-12, Article 3669
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Indexing the Pseudomonas specialized metabolome enabled the discovery of poaeamide B and the bananamides
Author / Creator:Nguyen, Don D. ; Melnik, Alexey V. ; Koyama, Nobuhiro ; Lu, Xiaowen ; Schorn, Michelle ; Fang, Jinshu ; Aguinaldo, Kristen ; Lincecum, Tommie L. ; Ghequire, Maarten G. K. ; Carrion, Victor J. ; Cheng, Tina L. ; Duggan, Brendan M. ; Malone, Jacob G. ; Mauchline, Tim H. ; Sanchez, Laura M. ; Kilpatrick, A. Marm ; Raaijmakers, Jos M. ; De Mot, René ; Moore, Bradley S. ; Medema, Marnix H. ; Dorrestein, Pieter C.
Publisher:London: Nature Publishing Group UK
Journal title:Nature microbiology, 2016-10, Vol.2 (1), p.16197-16197, Article 16197
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Global chemical effects of the microbiome include new bile-acid conjugations

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The impact of skin care products on skin chemistry and microbiome dynamics

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3D molecular cartography using LC–MS facilitated by Optimus and 'ili software

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Spatial chemistry of citrus reveals molecules bactericidal to Candidatus Liberibacter asiaticus

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Lifestyle chemistries from phones for individual profiling

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Open access repository-scale propagated nearest neighbor suspect spectral library for untargeted metabolomics

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Author Correction: Spatial chemistry of citrus reveals molecules bactericidal to Candidatus Liberibacter asiaticus

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Intermittent Hypoxia and Hypercapnia, a Hallmark of Obstructive Sleep Apnea, Alters the Gut Microbiome and Metabolome

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Blackcurrant Anthocyanins Attenuate Estrogen -Deficiency-Induced Bone Loss through Modulating Microbial-Derived Short-Chain Carboxylic Acids and Phytoestrogen Metabolites in Peri- and Early Postmenopa...

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The Molecular Effect of Wearing Silver-Threaded Clothing on the Human Skin

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SIRIUS 4: a rapid tool for turning tandem mass spectra into metabolite structure information

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Intermittent Hypoxia and Hypercapnia Reproducibly Change the Gut Microbiome and Metabolome across Rodent Model Systems

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Best practices for analysing microbiomes

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From Sample to Multi-Omics Conclusions in under 48 Hours

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Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking

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Mass spectrometry searches using MASST

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ReDU: a framework to find and reanalyze public mass spectrometry data

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Functional genomics and metabolomics advance the ethnobotany of the Samoan traditional medicine “matalafi”

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Creating a 3D microbial and chemical snapshot of a human habitat

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Indexing the Pseudomonas specialized metabolome enabled the discovery of poaeamide B and the bananamides

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