Global chemical effects of the microbiome include new bile-acid conjugations
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.
Published in Nature (London) (05.03.2020)
Published in Nature (London) (05.03.2020)
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Journal Article
SIRIUS 4: a rapid tool for turning tandem mass spectra into metabolite structure information
Dührkop, Kai, Fleischauer, Markus, Ludwig, Marcus, Aksenov, Alexander A., Melnik, Alexey V., Meusel, Marvin, Dorrestein, Pieter C., Rousu, Juho, Böcker, Sebastian
Published in Nature methods (01.04.2019)
Published in Nature methods (01.04.2019)
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A Cutibacterium acnes antibiotic modulates human skin microbiota composition in hair follicles
Claesen, Jan, Spagnolo, Jennifer B, Ramos, Stephany Flores, Kurita, Kenji L, Byrd, Allyson L, Aksenov, Alexander A, Melnik, Alexey V, Wong, Weng R, Wang, Shuo, Hernandez, Ryan D, Donia, Mohamed S, Dorrestein, Pieter C, Kong, Heidi H, Segre, Julia A, Linington, Roger G, Fischbach, Michael A, Lemon, Katherine P
Published in Science translational medicine (18.11.2020)
Published in Science translational medicine (18.11.2020)
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Best practices for analysing microbiomes
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.
Published in Nature reviews. Microbiology (01.07.2018)
Published in Nature reviews. Microbiology (01.07.2018)
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Journal Article
Untargeted mass spectrometry-based metabolomics approach unveils molecular changes in raw and processed foods and beverages
Gauglitz, Julia M., Aceves, Christine M., Aksenov, Alexander A., Aleti, Gajender, Almaliti, Jehad, Bouslimani, Amina, Brown, Elizabeth A., Campeau, Anaamika, Caraballo-Rodríguez, Andrés Mauricio, Chaar, Rama, da Silva, Ricardo R., Demko, Alyssa M., Di Ottavio, Francesca, Elijah, Emmanuel, Ernst, Madeleine, Ferguson, L. Paige, Holmes, Xavier, Jarmusch, Alan K., Jiang, Lingjing, Kang, Kyo Bin, Koester, Irina, Kwan, Brian, Li, Jie, Li, Yueying, Melnik, Alexey V., Molina-Santiago, Carlos, Ni, Bohan, Oom, Aaron L., Panitchpakdi, Morgan W., Petras, Daniel, Quinn, Robert, Sikora, Nicole, Spengler, Katharina, Teke, Bahar, Tripathi, Anupriya, Ul-Hasan, Sabah, van der Hooft, Justin J.J., Vargas, Fernando, Vrbanac, Alison, Vu, Anthony Q., Wang, Steven C., Weldon, Kelly, Wilson, Kayla, Wozniak, Jacob M., Yoon, Michael, Bandeira, Nuno, Dorrestein, Pieter C.
Published in Food chemistry (01.01.2020)
Published in Food chemistry (01.01.2020)
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Journal Article
ReDU: a framework to find and reanalyze public mass spectrometry data
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.
Published in Nature methods (01.09.2020)
Published in Nature methods (01.09.2020)
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Antimicrobials from human skin commensal bacteria protect against Staphylococcus aureus and are deficient in atopic dermatitis
Nakatsuji, Teruaki, Chen, Tiffany H, Narala, Saisindhu, Chun, Kimberly A, Two, Aimee M, Yun, Tong, Shafiq, Faiza, Kotol, Paul F, Bouslimani, Amina, Melnik, Alexey V, Latif, Haythem, Kim, Ji-Nu, Lockhart, Alexandre, Artis, Keli, David, Gloria, Taylor, Patricia, Streib, Joanne, Dorrestein, Pieter C, Grier, Alex, Gill, Steven R, Zengler, Karsten, Hata, Tissa R, Leung, Donald Y M, Gallo, Richard L
Published in Science translational medicine (22.02.2017)
Published in Science translational medicine (22.02.2017)
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Journal Article
3D molecular cartography using LC–MS facilitated by Optimus and 'ili software
Protsyuk, Ivan, Melnik, Alexey V, Nothias, Louis-Felix, Rappez, Luca, Phapale, Prasad, Aksenov, Alexander A, Bouslimani, Amina, Ryazanov, Sergey, Dorrestein, Pieter C, Alexandrov, Theodore
Published in Nature protocols (01.01.2018)
Published in Nature protocols (01.01.2018)
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Journal Article
Open access repository-scale propagated nearest neighbor suspect spectral library for untargeted metabolomics
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.
Published in Nature communications (20.12.2023)
Published in Nature communications (20.12.2023)
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Journal Article
The impact of skin care products on skin chemistry and microbiome dynamics
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
Published in BMC biology (12.06.2019)
Published in BMC biology (12.06.2019)
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Identification of the Bacterial Biosynthetic Gene Clusters of the Oral Microbiome Illuminates the Unexplored Social Language of Bacteria during Health and Disease
Aleti, Gajender, Baker, Jonathon L, Tang, Xiaoyu, Alvarez, Ruth, Dinis, Márcia, Tran, Nini C, Melnik, Alexey V, Zhong, Cuncong, Ernst, Madeleine, Dorrestein, Pieter C, Edlund, Anna
Published in mBio (16.04.2019)
Published in mBio (16.04.2019)
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Journal Article
Mass spectrometry searches using MASST
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.
Published in Nature biotechnology (2020)
Published in Nature biotechnology (2020)
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Journal Article
Spatial chemistry of citrus reveals molecules bactericidal to Candidatus Liberibacter asiaticus
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., Dorrestein, Pieter C., Roper, M. Caroline
Published in Scientific reports (02.09.2024)
Published in Scientific reports (02.09.2024)
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Journal Article
Microbial and Nonvolatile Chemical Diversities of Chinese Dark Teas Are Differed by Latitude and Pile Fermentation
Kong, Ya-Shuai, Ren, Hong-Yu, Liu, Rui, da Silva, Ricardo R., Aksenov, Alexander A., Melnik, Alexey V., Zhao, Ming, Le, Miao-Miao, Ren, Zhi-Wei, Xu, Feng-Qing, Yan, Xiao-Wei, Yu, Li-Jun, Zhou, Yu, Xie, Zhong-Wen, Li, Da-Xiang, Wan, Xiao-Chun, Long, Yan-Hua, Xu, Zhenjiang Zech, Ling, Tie-Jun
Published in Journal of agricultural and food chemistry (11.05.2022)
Published in Journal of agricultural and food chemistry (11.05.2022)
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Journal Article
Prioritizing Natural Product Diversity in a Collection of 146 Bacterial Strains Based on Growth and Extraction Protocols
Crüsemann, Max, O’Neill, Ellis C, Larson, Charles B, Melnik, Alexey V, Floros, Dimitrios J, da Silva, Ricardo R, Jensen, Paul R, Dorrestein, Pieter C, Moore, Bradley S
Published in Journal of natural products (Washington, D.C.) (24.03.2017)
Published in Journal of natural products (Washington, D.C.) (24.03.2017)
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Journal Article
Feature-Based Molecular Networking Analysis of the Metabolites Produced by In Vitro Solid-State Fermentation Reveals Pathways for the Bioconversion of Epigallocatechin Gallate
Xie, Hao-Fen, Kong, Ya-Shuai, Li, Ru-Ze, Nothias, Louis-Félix, Melnik, Alexey V, Zhang, Hong, Liu, Lu-Lu, An, Ting-Ting, Liu, Rui, Yang, Zi, Ke, Jia-Ping, Zhang, Peng, Bao, Guan-Hu, Xie, Zhong-Wen, Li, Da-Xiang, Wan, Xiao-Chun, Dai, Qian-Ying, Zhang, Liang, Zhao, Ming, An, Mao-Qiang, Long, Yan-Hua, Ling, Tie-Jun
Published in Journal of agricultural and food chemistry (29.07.2020)
Published in Journal of agricultural and food chemistry (29.07.2020)
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Journal Article
Coupling Targeted and Untargeted Mass Spectrometry for Metabolome-Microbiome-Wide Association Studies of Human Fecal Samples
Melnik, Alexey V, da Silva, Ricardo R, Hyde, Embriette R, Aksenov, Alexander A, Vargas, Fernando, Bouslimani, Amina, Protsyuk, Ivan, Jarmusch, Alan K, Tripathi, Anupriya, Alexandrov, Theodore, Knight, Rob, Dorrestein, Pieter C
Published in Analytical chemistry (Washington) (18.07.2017)
Published in Analytical chemistry (Washington) (18.07.2017)
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Journal Article
Lifestyle chemistries from phones for individual profiling
Bouslimani, Amina, Melnik, Alexey V., Xu, Zhenjiang, Amir, Amnon, da Silva, Ricardo R., Wang, Mingxun, Bandeira, Nuno, Alexandrov, Theodore, Knight, Rob, Dorrestein, Pieter C.
Published in Proceedings of the National Academy of Sciences - PNAS (29.11.2016)
Published in Proceedings of the National Academy of Sciences - PNAS (29.11.2016)
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Journal Article
Auto-deconvolution and molecular networking of gas chromatography–mass spectrometry data
Aksenov, Alexander A., Laponogov, Ivan, Zhang, Zheng, Doran, Sophie L. F., Belluomo, Ilaria, Veselkov, Dennis, Bittremieux, Wout, Nothias, Louis Felix, Nothias-Esposito, Mélissa, Maloney, Katherine N., Misra, Biswapriya B., Melnik, Alexey V., Smirnov, Aleksandr, Du, Xiuxia, Jones, Kenneth L., Dorrestein, Kathleen, Panitchpakdi, Morgan, Ernst, Madeleine, van der Hooft, Justin J. J., Gonzalez, Mabel, Carazzone, Chiara, Amézquita, Adolfo, Callewaert, Chris, Morton, James T., Quinn, Robert A., Bouslimani, Amina, Orio, Andrea Albarracín, Petras, Daniel, Smania, Andrea M., Couvillion, Sneha P., Burnet, Meagan C., Nicora, Carrie D., Zink, Erika, Metz, Thomas O., Artaev, Viatcheslav, Humston-Fulmer, Elizabeth, Gregor, Rachel, Meijler, Michael M., Mizrahi, Itzhak, Eyal, Stav, Anderson, Brooke, Dutton, Rachel, Lugan, Raphaël, Boulch, Pauline Le, Guitton, Yann, Prevost, Stephanie, Poirier, Audrey, Dervilly, Gaud, Le Bizec, Bruno, Fait, Aaron, Persi, Noga Sikron, Song, Chao, Gashu, Kelem, Coras, Roxana, Guma, Monica, Manasson, Julia, Scher, Jose U., Barupal, Dinesh Kumar, Alseekh, Saleh, Fernie, Alisdair R., Mirnezami, Reza, Vasiliou, Vasilis, Schmid, Robin, Borisov, Roman S., Kulikova, Larisa N., Knight, Rob, Wang, Mingxun, Hanna, George B., Dorrestein, Pieter C., Veselkov, Kirill
Published in Nature biotechnology (01.02.2021)
Published in Nature biotechnology (01.02.2021)
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Journal Article
Lugdunomycin, an Angucycline‐Derived Molecule with Unprecedented Chemical Architecture
Wu, Changsheng, van der Heul, Helga U., Melnik, Alexey V., Lübben, Jens, Dorrestein, Pieter C., Minnaard, Adriaan J., Choi, Young Hae, van Wezel, Gilles P.
Published in Angewandte Chemie International Edition (25.02.2019)
Published in Angewandte Chemie International Edition (25.02.2019)
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