Publications

See full publication list at Google Scholar or Pubmed.

Highlighted Publications

1. Xianghu Wang, Michael Strobel, Allegra T Aron, Vanessa V Phelan, Deepa D Acharya, Christopher J Brown, Ken Clevenger, Jie Hu, Ashley Kretsch, Elizabeth H Mahood, Carla Menegatti, Quanbo Xiong, Mingxun Wang "Network Topology Evaluation and Transitive Alignments for Molecular Networking." Journal of the American Society for Mass Spectrometry 2024, PMID: 39133821

2. Mohammad Reza Zare Shahneh, Michael Strobel, Giovanni Andrea Vitale, Christian Geibel, Yasin El Abiead, Neha Garg, Berenike Wagner, Karl Forchhammer, Allegra Aron, Vanessa V Phelan, Daniel Petras, Mingxun Wang "ModiFinder: Tandem Mass Spectral Alignment Enables Structural Modification Site Localization." Journal of the American Society for Mass Spectrometry 2024, PMID: 38830143

3. Daniel Petras, Vanessa V Phelan, Deepa Acharya, Andrew E Allen, Allegra T Aron, Nuno Bandeira, Benjamin P Bowen, Deirdre Belle-Oudry, Simon Boecker, Dale A Cummings, Jessica M Deutsch, Eoin Fahy, Neha Garg, Rachel Gregor, Jo Handelsman, Mirtha Navarro-Hoyos, Alan K Jarmusch, Scott A Jarmusch, Katherine Louie, Katherine N Maloney, Michael T Marty, Michael M Meijler, Itzhak Mizrahi, Rachel L Neve, Trent R Northen, Carlos Molina-Santiago, Morgan Panitchpakdi, Benjamin Pullman, Aaron W Puri, Robin Schmid, Shankar Subramaniam, Monica Thukral, Felipe Vasquez-Castro, Pieter C Dorrestein, Mingxun Wang "GNPS Dashboard: collaborative exploration of mass spectrometry data in the web browser." Nature methods 2021, PMID: 34862502

4. Tiago F Leao, Chase M Clark, Anelize Bauermeister, Emmanuel O Elijah, Emily C Gentry, Makhai Husband, Michelli F Oliveira, Nuno Bandeira, Mingxun Wang, Pieter C Dorrestein "Quick-start infrastructure for untargeted metabolomics analysis in GNPS." Nature metabolism 2021, PMID: 34244695

5. Daniel Petras, Andrés Mauricio Caraballo-Rodríguez, Alan K Jarmusch, Carlos Molina-Santiago, Julia M Gauglitz, Emily C Gentry, Pedro Belda-Ferre, Diego Romero, Shirley M Tsunoda, Pieter C Dorrestein, Mingxun Wang "Chemical Proportionality within Molecular Networks." Analytical chemistry 2021, PMID: 34533933

6. Louis-Félix Nothias, Daniel Petras, Robin Schmid, Kai Dührkop, Johannes Rainer, Abinesh Sarvepalli, Ivan Protsyuk, Madeleine Ernst, Hiroshi Tsugawa, Markus Fleischauer, Fabian Aicheler, Alexander A Aksenov, Oliver Alka, Pierre-Marie Allard, Aiko Barsch, Xavier Cachet, Andres Mauricio Caraballo-Rodriguez, Ricardo R Da Silva, Tam Dang, Neha Garg, Julia M Gauglitz, Alexey Gurevich, Giorgis Isaac, Alan K Jarmusch, Zdeněk Kameník, Kyo Bin Kang, Nikolas Kessler, Irina Koester, Ansgar Korf, Audrey Le Gouellec, Marcus Ludwig, Christian Martin H, Laura-Isobel McCall, Jonathan McSayles, Sven W Meyer, Hosein Mohimani, Mustafa Morsy, Oriane Moyne, Steffen Neumann, Heiko Neuweger, Ngoc Hung Nguyen, Melissa Nothias-Esposito, Julien Paolini, Vanessa V Phelan, Tomáš Pluskal, Robert A Quinn, Simon Rogers, Bindesh Shrestha, Anupriya Tripathi, Justin J J van der Hooft, Fernando Vargas, Kelly C Weldon, Michael Witting, Heejung Yang, Zheng Zhang, Florian Zubeil, Oliver Kohlbacher, Sebastian Böcker, Theodore Alexandrov, Nuno Bandeira, Mingxun Wang, Pieter C Dorrestein "Feature-based molecular networking in the GNPS analysis environment." Nature methods 2020, PMID: 32839597

7. Alan K Jarmusch, Mingxun Wang, Christine M Aceves, Rohit S Advani, Shaden Aguirre, Alexander A Aksenov, Gajender Aleti, Allegra T Aron, Anelize Bauermeister, Sanjana Bolleddu, Amina Bouslimani, Andres Mauricio Caraballo Rodriguez, Rama Chaar, Roxana Coras, Emmanuel O Elijah, Madeleine Ernst, Julia M Gauglitz, Emily C Gentry, Makhai Husband, Scott A Jarmusch, Kenneth L Jones, Zdenek Kamenik, Audrey Le Gouellec, Aileen Lu, Laura-Isobel McCall, Kerry L McPhail, Michael J Meehan, Alexey V Melnik, Riya C Menezes, Yessica Alejandra Montoya Giraldo, Ngoc Hung Nguyen, Louis Felix Nothias, Mélissa Nothias-Esposito, Morgan Panitchpakdi, Daniel Petras, Robert A Quinn, Nicole Sikora, Justin J J van der Hooft, Fernando Vargas, Alison Vrbanac, Kelly C Weldon, Rob Knight, Nuno Bandeira, Pieter C Dorrestein "ReDU: a framework to find and reanalyze public mass spectrometry data." Nature methods 2020, PMID: 32807955

8. Allegra T Aron, Emily C Gentry, Kerry L McPhail, Louis-Félix Nothias, Mélissa Nothias-Esposito, Amina Bouslimani, Daniel Petras, Julia M Gauglitz, Nicole Sikora, Fernando Vargas, Justin J J van der Hooft, Madeleine Ernst, Kyo Bin Kang, Christine M Aceves, Andrés Mauricio Caraballo-Rodríguez, Irina Koester, Kelly C Weldon, Samuel Bertrand, Catherine Roullier, Kunyang Sun, Richard M Tehan, Cristopher A Boya P, Martin H Christian, Marcelino Gutiérrez, Aldo Moreno Ulloa, Javier Andres Tejeda Mora, Randy Mojica-Flores, Johant Lakey-Beitia, Victor Vásquez-Chaves, Yilue Zhang, Angela I Calderón, Nicole Tayler, Robert A Keyzers, Fidele Tugizimana, Nombuso Ndlovu, Alexander A Aksenov, Alan K Jarmusch, Robin Schmid, Andrew W Truman, Nuno Bandeira, Mingxun Wang, Pieter C Dorrestein "Reproducible molecular networking of untargeted mass spectrometry data using GNPS." Nature protocols 2020, PMID: 32405051

9. Mingxun Wang, Alan K Jarmusch, Fernando Vargas, Alexander A Aksenov, Julia M Gauglitz, Kelly Weldon, Daniel Petras, Ricardo da Silva, Robert Quinn, Alexey V Melnik, Justin J J van der Hooft, Andrés Mauricio Caraballo-Rodríguez, Louis Felix Nothias, Christine M Aceves, Morgan Panitchpakdi, Elizabeth Brown, Francesca Di Ottavio, Nicole Sikora, Emmanuel O Elijah, Lara Labarta-Bajo, Emily C Gentry, Shabnam Shalapour, Kathleen E Kyle, Sara P Puckett, Jeramie D Watrous, Carolina S Carpenter, Amina Bouslimani, Madeleine Ernst, Austin D Swafford, Elina I Zúñiga, Marcy J Balunas, Jonathan L Klassen, Rohit Loomba, Rob Knight, Nuno Bandeira, Pieter C Dorrestein "Mass spectrometry searches using MASST." Nature biotechnology 2020, PMID: 31894142

10. Mingxun Wang, Jian Wang, Jeremy Carver, Benjamin S Pullman, Seong Won Cha, Nuno Bandeira "Assembling the Community-Scale Discoverable Human Proteome." Cell systems 2018, PMID: 30172843

11. Mingxun Wang, Jeremy J Carver, Vanessa V Phelan, Laura M Sanchez, Neha Garg, Yao Peng, Don Duy Nguyen, Jeramie Watrous, Clifford A Kapono, Tal Luzzatto-Knaan, Carla Porto, Amina Bouslimani, Alexey V Melnik, Michael J Meehan, Wei-Ting Liu, Max Crüsemann, Paul D Boudreau, Eduardo Esquenazi, Mario Sandoval-Calderón, Roland D Kersten, Laura A Pace, Robert A Quinn, Katherine R Duncan, Cheng-Chih Hsu, Dimitrios J Floros, Ronnie G Gavilan, Karin Kleigrewe, Trent Northen, Rachel J Dutton, Delphine Parrot, Erin E Carlson, Bertrand Aigle, Charlotte F Michelsen, Lars Jelsbak, Christian Sohlenkamp, Pavel Pevzner, Anna Edlund, Jeffrey McLean, Jörn Piel, Brian T Murphy, Lena Gerwick, Chih-Chuang Liaw, Yu-Liang Yang, Hans-Ulrich Humpf, Maria Maansson, Robert A Keyzers, Amy C Sims, Andrew R Johnson, Ashley M Sidebottom, Brian E Sedio, Andreas Klitgaard, Charles B Larson, Cristopher A Boya P, Daniel Torres-Mendoza, David J Gonzalez, Denise B Silva, Lucas M Marques, Daniel P Demarque, Egle Pociute, Ellis C O'Neill, Enora Briand, Eric J N Helfrich, Eve A Granatosky, Evgenia Glukhov, Florian Ryffel, Hailey Houson, Hosein Mohimani, Jenan J Kharbush, Yi Zeng, Julia A Vorholt, Kenji L Kurita, Pep Charusanti, Kerry L McPhail, Kristian Fog Nielsen, Lisa Vuong, Maryam Elfeki, Matthew F Traxler, Niclas Engene, Nobuhiro Koyama, Oliver B Vining, Ralph Baric, Ricardo R Silva, Samantha J Mascuch, Sophie Tomasi, Stefan Jenkins, Venkat Macherla, Thomas Hoffman, Vinayak Agarwal, Philip G Williams, Jingqui Dai, Ram Neupane, Joshua Gurr, Andrés M C Rodríguez, Anne Lamsa, Chen Zhang, Kathleen Dorrestein, Brendan M Duggan, Jehad Almaliti, Pierre-Marie Allard, Prasad Phapale, Louis-Felix Nothias, Theodore Alexandrov, Marc Litaudon, Jean-Luc Wolfender, Jennifer E Kyle, Thomas O Metz, Tyler Peryea, Dac-Trung Nguyen, Danielle VanLeer, Paul Shinn, Ajit Jadhav, Rolf Müller, Katrina M Waters, Wenyuan Shi, Xueting Liu, Lixin Zhang, Rob Knight, Paul R Jensen, Bernhard O Palsson, Kit Pogliano, Roger G Linington, Marcelino Gutiérrez, Norberto P Lopes, William H Gerwick, Bradley S Moore, Pieter C Dorrestein, Nuno Bandeira "Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking." Nature biotechnology 2016, PMID: 27504778

12. Mingxun Wang, Nuno Bandeira "Spectral library generating function for assessing spectrum-spectrum match significance." Journal of proteome research 2013, PMID: 23808827

All Publications

1. Xianghu Wang, Michael Strobel, Allegra T Aron, Vanessa V Phelan, Deepa D Acharya, Christopher J Brown, Ken Clevenger, Jie Hu, Ashley Kretsch, Elizabeth H Mahood, Carla Menegatti, Quanbo Xiong, Mingxun Wang "Network Topology Evaluation and Transitive Alignments for Molecular Networking." Journal of the American Society for Mass Spectrometry 2024, PMID: 39133821

2. Niek F de Jonge, Helge Hecht, Michael Strobel, Mingxun Wang, Justin J J van der Hooft, Florian Huber "Reproducible MS/MS library cleaning pipeline in matchms." Journal of cheminformatics 2024, PMID: 39075613

3. Mohammad Reza Zare Shahneh, Michael Strobel, Giovanni Andrea Vitale, Christian Geibel, Yasin El Abiead, Neha Garg, Berenike Wagner, Karl Forchhammer, Allegra Aron, Vanessa V Phelan, Daniel Petras, Mingxun Wang "ModiFinder: Tandem Mass Spectral Alignment Enables Structural Modification Site Localization." Journal of the American Society for Mass Spectrometry 2024, PMID: 38830143

4. Tim Berger, Judith Alenfelder, Sophie Steinmüller, Dominik Heimann, Namrata Gohain, Daniel Petras, Mingxun Wang, Robert Berger, Evi Kostenis, Raphael Reher "A MassQL-Integrated Molecular Networking Approach for the Discovery and Substructure Annotation of Bioactive Cyclic Peptides." Journal of natural products 2024, PMID: 38385767

5. Ipsita Mohanty, Helena Mannochio-Russo, Joshua V Schweer, Yasin El Abiead, Wout Bittremieux, Shipei Xing, Robin Schmid, Simone Zuffa, Felipe Vasquez, Valentina B Muti, Jasmine Zemlin, Omar E Tovar-Herrera, Sarah Moraïs, Dhimant Desai, Shantu Amin, Imhoi Koo, Christoph W Turck, Itzhak Mizrahi, Penny M Kris-Etherton, Kristina S Petersen, Jennifer A Fleming, Tao Huan, Andrew D Patterson, Dionicio Siegel, Lee R Hagey, Mingxun Wang, Allegra T Aron, Pieter C Dorrestein "The underappreciated diversity of bile acid modifications." Cell 2024, PMID: 38471500

6. Simone Zuffa, Robin Schmid, Anelize Bauermeister, Paulo Wender P Gomes, Andres M Caraballo-Rodriguez, Yasin El Abiead, Allegra T Aron, Emily C Gentry, Jasmine Zemlin, Michael J Meehan, Nicole E Avalon, Robert H Cichewicz, Ekaterina Buzun, Marvic Carrillo Terrazas, Chia-Yun Hsu, Renee Oles, Adriana Vasquez Ayala, Jiaqi Zhao, Hiutung Chu, Mirte C M Kuijpers, Sara L Jackrel, Fidele Tugizimana, Lerato Pertunia Nephali, Ian A Dubery, Ntakadzeni Edwin Madala, Eduarda Antunes Moreira, Leticia Veras Costa-Lotufo, Norberto Peporine Lopes, Paula Rezende-Teixeira, Paula C Jimenez, Bipin Rimal, Andrew D Patterson, Matthew F Traxler, Rita de Cassia Pessotti, Daniel Alvarado-Villalobos, Giselle Tamayo-Castillo, Priscila Chaverri, Efrain Escudero-Leyva, Luis-Manuel Quiros-Guerrero, Alexandre Jean Bory, Juliette Joubert, Adriano Rutz, Jean-Luc Wolfender, Pierre-Marie Allard, Andreas Sichert, Sammy Pontrelli, Benjamin S Pullman, Nuno Bandeira, William H Gerwick, Katia Gindro, Josep Massana-Codina, Berenike C Wagner, Karl Forchhammer, Daniel Petras, Nicole Aiosa, Neha Garg, Manuel Liebeke, Patric Bourceau, Kyo Bin Kang, Henna Gadhavi, Luiz Pedro Sorio de Carvalho, Mariana Silva Dos Santos, Alicia Isabel Pérez-Lorente, Carlos Molina-Santiago, Diego Romero, Raimo Franke, Mark Brönstrup, Arturo Vera Ponce de León, Phillip Byron Pope, Sabina Leanti La Rosa, Giorgia La Barbera, Henrik M Roager, Martin Frederik Laursen, Fabian Hammerle, Bianka Siewert, Ursula Peintner, Cuauhtemoc Licona-Cassani, Lorena Rodriguez-Orduña, Evelyn Rampler, Felina Hildebrand, Gunda Koellensperger, Harald Schoeny, Katharina Hohenwallner, Lisa Panzenboeck, Rachel Gregor, Ellis Charles O'Neill, Eve Tallulah Roxborough, Jane Odoi, Nicole J Bale, Su Ding, Jaap S Sinninghe Damsté, Xue Li Guan, Jerry J Cui, Kou-San Ju, Denise Brentan Silva, Fernanda Motta Ribeiro Silva, Gilvan Ferreira da Silva, Hector H F Koolen, Carlismari Grundmann, Jason A Clement, Hosein Mohimani, Kirk Broders, Kerry L McPhail, Sidnee E Ober-Singleton, Christopher M Rath, Daniel McDonald, Rob Knight, Mingxun Wang, Pieter C Dorrestein "microbeMASST: a taxonomically informed mass spectrometry search tool for microbial metabolomics data." Nature microbiology 2024, PMID: 38316926

7. Paolo Stincone, Abzer K Pakkir Shah, Robin Schmid, Lana G Graves, Stilianos P Lambidis, Ralph R Torres, Shu-Ning Xia, Vidit Minda, Allegra T Aron, Mingxun Wang, Chambers C Hughes, Daniel Petras "Evaluation of Data-Dependent MS/MS Acquisition Parameters for Non-Targeted Metabolomics and Molecular Networking of Environmental Samples: Focus on the Q Exactive Platform." Analytical chemistry 2023, PMID: 37578818

8. Thomas V Harwood, Daniel G C Treen, Mingxun Wang, Wibe de Jong, Trent R Northen, Benjamin P Bowen "BLINK enables ultrafast tandem mass spectrometry cosine similarity scoring." Scientific reports 2023, PMID: 37596301

9. Hyun Woo Kim, Chen Zhang, Raphael Reher, Mingxun Wang, Kelsey L Alexander, Louis-Félix Nothias, Yoo Kyong Han, Hyeji Shin, Ki Yong Lee, Kyu Hyeong Lee, Myeong Ji Kim, Pieter C Dorrestein, William H Gerwick, Garrison W Cottrell "DeepSAT: Learning Molecular Structures from Nuclear Magnetic Resonance Data." Journal of cheminformatics 2023, PMID: 37550756

10. Simone Zuffa, Robin Schmid, Anelize Bauermeister, Paulo Wender P Gomes, Andres M Caraballo-Rodriguez, Yasin El Abiead, Allegra T Aron, Emily C Gentry, Jasmine Zemlin, Michael J Meehan, Nicole E Avalon, Robert H Cichewicz, Ekaterina Buzun, Marvic Carrillo Terrazas, Chia-Yun Hsu, Renee Oles, Adriana Vasquez Ayala, Jiaqi Zhao, Hiutung Chu, Mirte C M Kuijpers, Sara L Jackrel, Fidele Tugizimana, Lerato Pertunia Nephali, Ian A Dubery, Ntakadzeni Edwin Madala, Eduarda Antunes Moreira, Leticia Veras Costa-Lotufo, Norberto Peporine Lopes, Paula Rezende-Teixeira, Paula C Jimenez, Bipin Rimal, Andrew D Patterson, Matthew F Traxler, Rita de Cassia Pessotti, Daniel Alvarado-Villalobos, Giselle Tamayo-Castillo, Priscila Chaverri, Efrain Escudero-Leyva, Luis-Manuel Quiros-Guerrero, Alexandre Jean Bory, Juliette Joubert, Adriano Rutz, Jean-Luc Wolfender, Pierre-Marie Allard, Andreas Sichert, Sammy Pontrelli, Benjamin S Pullman, Nuno Bandeira, William H Gerwick, Katia Gindro, Josep Massana-Codina, Berenike C Wagner, Karl Forchhammer, Daniel Petras, Nicole Aiosa, Neha Garg, Manuel Liebeke, Patric Bourceau, Kyo Bin Kang, Henna Gadhavi, Luiz Pedro Sorio de Carvalho, Mariana Silva Dos Santos, Alicia Isabel Pérez-Lorente, Carlos Molina-Santiago, Diego Romero, Raimo Franke, Mark Brönstrup, Arturo Vera Ponce de León, Phillip Byron Pope, Sabina Leanti La Rosa, Giorgia La Barbera, Henrik M Roager, Martin Frederik Laursen, Fabian Hammerle, Bianka Siewert, Ursula Peintner, Cuauhtemoc Licona-Cassani, Lorena Rodriguez-Orduña, Evelyn Rampler, Felina Hildebrand, Gunda Koellensperger, Harald Schoeny, Katharina Hohenwallner, Lisa Panzenboeck, Rachel Gregor, Ellis Charles O'Neill, Eve Tallulah Roxborough, Jane Odoi, Nicole J Bale, Su Ding, Jaap S Sinninghe Damsté, Xueli Li Guan, Jerry J Cui, Kou-San Ju, Denise Brentan Silva, Fernanda Motta Ribeiro Silva, Gilvan Ferreira da Silva, Hector H F Koolen, Carlismari Grundmann, Jason A Clement, Hosein Mohimani, Kirk Broders, Kerry L McPhail, Sidnee E Ober-Singleton, Christopher M Rath, Daniel McDonald, Rob Knight, Mingxun Wang, Pieter C Dorrestein "A Taxonomically-informed Mass Spectrometry Search Tool for Microbial Metabolomics Data." Research square 2023, PMID: 37577622

11. Ian Oesterle, Manuel Pristner, Sabrina Berger, Mingxun Wang, Vinicius Verri Hernandes, Annette Rompel, Benedikt Warth "Exposomic Biomonitoring of Polyphenols by Non-Targeted Analysis and Suspect Screening." Analytical chemistry 2023, PMID: 37409760

12. Robin Schmid, Steffen Heuckeroth, Ansgar Korf, Aleksandr Smirnov, Owen Myers, Thomas S Dyrlund, Roman Bushuiev, Kevin J Murray, Nils Hoffmann, Miaoshan Lu, Abinesh Sarvepalli, Zheng Zhang, Markus Fleischauer, Kai Dührkop, Mark Wesner, Shawn J Hoogstra, Edward Rudt, Olena Mokshyna, Corinna Brungs, Kirill Ponomarov, Lana Mutabdžija, Tito Damiani, Chris J Pudney, Mark Earll, Patrick O Helmer, Timothy R Fallon, Tobias Schulze, Albert Rivas-Ubach, Aivett Bilbao, Henning Richter, Louis-Félix Nothias, Mingxun Wang, Matej Orešič, Jing-Ke Weng, Sebastian Böcker, Astrid Jeibmann, Heiko Hayen, Uwe Karst, Pieter C Dorrestein, Daniel Petras, Xiuxia Du, Tomáš Pluskal "Integrative analysis of multimodal mass spectrometry data in MZmine 3." Nature biotechnology 2023, PMID: 36859716

13. Wout Bittremieux, Lev Levitsky, Matteo Pilz, Timo Sachsenberg, Florian Huber, Mingxun Wang, Pieter C Dorrestein "Unified and Standardized Mass Spectrometry Data Processing in Python Using spectrum_utils." Journal of proteome research 2023, PMID: 36688502

14. Julia M Gauglitz, Kiana A West, Wout Bittremieux, Candace L Williams, Kelly C Weldon, Morgan Panitchpakdi, Francesca Di Ottavio, Christine M Aceves, Elizabeth Brown, Nicole C Sikora, Alan K Jarmusch, Cameron Martino, Anupriya Tripathi, Michael J Meehan, Kathleen Dorrestein, Justin P Shaffer, Roxana Coras, Fernando Vargas, Lindsay DeRight Goldasich, Tara Schwartz, MacKenzie Bryant, Gregory Humphrey, Abigail J Johnson, Katharina Spengler, Pedro Belda-Ferre, Edgar Diaz, Daniel McDonald, Qiyun Zhu, Emmanuel O Elijah, Mingxun Wang, Clarisse Marotz, Kate E Sprecher, Daniela Vargas-Robles, Dana Withrow, Gail Ackermann, Lourdes Herrera, Barry J Bradford, Lucas Maciel Mauriz Marques, Juliano Geraldo Amaral, Rodrigo Moreira Silva, Flavio Protasio Veras, Thiago Mattar Cunha, Rene Donizeti Ribeiro Oliveira, Paulo Louzada-Junior, Robert H Mills, Paulina K Piotrowski, Stephanie L Servetas, Sandra M Da Silva, Christina M Jones, Nancy J Lin, Katrice A Lippa, Scott A Jackson, Rima Kaddurah Daouk, Douglas Galasko, Parambir S Dulai, Tatyana I Kalashnikova, Curt Wittenberg, Robert Terkeltaub, Megan M Doty, Jae H Kim, Kyung E Rhee, Julia Beauchamp-Walters, Kenneth P Wright, Maria Gloria Dominguez-Bello, Mark Manary, Michelli F Oliveira, Brigid S Boland, Norberto Peporine Lopes, Monica Guma, Austin D Swafford, Rachel J Dutton, Rob Knight, Pieter C Dorrestein "Enhancing untargeted metabolomics using metadata-based source annotation." Nature biotechnology 2022, PMID: 35798960

15. Wout Bittremieux, Mingxun Wang, Pieter C Dorrestein "The critical role that spectral libraries play in capturing the metabolomics community knowledge." Metabolomics : Official journal of the Metabolomic Society 2022, PMID: 36409434

16. Tiago F Leão, Mingxun Wang, Ricardo da Silva, Alexey Gurevich, Anelize Bauermeister, Paulo Wender P Gomes, Asker Brejnrod, Evgenia Glukhov, Allegra T Aron, Joris J R Louwen, Hyun Woo Kim, Raphael Reher, Marli F Fiore, Justin J J van der Hooft, Lena Gerwick, William H Gerwick, Nuno Bandeira, Pieter C Dorrestein "NPOmix: A machine learning classifier to connect mass spectrometry fragmentation data to biosynthetic gene clusters." PNAS nexus 2022, PMID: 36712343

17. Yasin El Abiead, Christoph Bueschl, Lisa Panzenboeck, Mingxun Wang, Maria Doppler, Bernhard Seidl, Jürgen Zanghellini, Pieter C Dorrestein, Gunda Koellensperger "Heterogeneous multimeric metabolite ion species observed in LC-MS based metabolomics data sets." Analytica chimica acta 2022, PMID: 36156231

18. Wout Bittremieux, Robin Schmid, Florian Huber, Justin J J van der Hooft, Mingxun Wang, Pieter C Dorrestein "Comparison of Cosine, Modified Cosine, and Neutral Loss Based Spectrum Alignment For Discovery of Structurally Related Molecules." Journal of the American Society for Mass Spectrometry 2022, PMID: 35960544

19. Gordon T Luu, Michael A Freitas, Itzel Lizama-Chamu, Catherine S McCaughey, Laura M Sanchez, Mingxun Wang "TIMSCONVERT: a workflow to convert trapped ion mobility data to open data formats." Bioinformatics (Oxford, England) 2022, PMID: 35758608

20. Raphael Reher, Allegra T Aron, Pavla Fajtová, Paolo Stincone, Berenike Wagner, Alicia I Pérez-Lorente, Chenxi Liu, Ido Y Ben Shalom, Wout Bittremieux, Mingxun Wang, Kyowon Jeong, Marie L Matos-Hernandez, Kelsey L Alexander, Eduardo J Caro-Diaz, C Benjamin Naman, J H William Scanlan, Phil M M Hochban, Wibke E Diederich, Carlos Molina-Santiago, Diego Romero, Khaled A Selim, Peter Sass, Heike Brötz-Oesterhelt, Chambers C Hughes, Pieter C Dorrestein, Anthony J O'Donoghue, William H Gerwick, Daniel Petras "Native metabolomics identifies the rivulariapeptolide family of protease inhibitors." Nature communications 2022, PMID: 35941113

21. Daniel G C Treen, Mingxun Wang, Shipei Xing, Katherine B Louie, Tao Huan, Pieter C Dorrestein, Trent R Northen, Benjamin P Bowen "SIMILE enables alignment of tandem mass spectra with statistical significance." Nature communications 2022, PMID: 35523965

22. Kiana A West, Robin Schmid, Julia M Gauglitz, Mingxun Wang, Pieter C Dorrestein "foodMASST a mass spectrometry search tool for foods and beverages." NPJ science of food 2022, PMID: 35444218

23. Daniel Petras, Vanessa V Phelan, Deepa Acharya, Andrew E Allen, Allegra T Aron, Nuno Bandeira, Benjamin P Bowen, Deirdre Belle-Oudry, Simon Boecker, Dale A Cummings, Jessica M Deutsch, Eoin Fahy, Neha Garg, Rachel Gregor, Jo Handelsman, Mirtha Navarro-Hoyos, Alan K Jarmusch, Scott A Jarmusch, Katherine Louie, Katherine N Maloney, Michael T Marty, Michael M Meijler, Itzhak Mizrahi, Rachel L Neve, Trent R Northen, Carlos Molina-Santiago, Morgan Panitchpakdi, Benjamin Pullman, Aaron W Puri, Robin Schmid, Shankar Subramaniam, Monica Thukral, Felipe Vasquez-Castro, Pieter C Dorrestein, Mingxun Wang "GNPS Dashboard: collaborative exploration of mass spectrometry data in the web browser." Nature methods 2021, PMID: 34862502

24. Jun Sang Yu, Louis-Félix Nothias, Mingxun Wang, Dong Hyun Kim, Pieter C Dorrestein, Kyo Bin Kang, Hye Hyun Yoo "Tandem Mass Spectrometry Molecular Networking as a Powerful and Efficient Tool for Drug Metabolism Studies." Analytical chemistry 2022, PMID: 34985284

25. Hyun Woo Kim, Mingxun Wang, Christopher A Leber, Louis-Félix Nothias, Raphael Reher, Kyo Bin Kang, Justin J J van der Hooft, Pieter C Dorrestein, William H Gerwick, Garrison W Cottrell "NPClassifier: A Deep Neural Network-Based Structural Classification Tool for Natural Products." Journal of natural products 2021, PMID: 34662515

26. Daniel Petras, Andrés Mauricio Caraballo-Rodríguez, Alan K Jarmusch, Carlos Molina-Santiago, Julia M Gauglitz, Emily C Gentry, Pedro Belda-Ferre, Diego Romero, Shirley M Tsunoda, Pieter C Dorrestein, Mingxun Wang "Chemical Proportionality within Molecular Networks." Analytical chemistry 2021, PMID: 34533933

27. Andrés Mauricio Caraballo-Rodríguez, Sara P Puckett, Kathleen E Kyle, Daniel Petras, Ricardo da Silva, Louis-Félix Nothias, Madeleine Ernst, Justin J J van der Hooft, Anupriya Tripathi, Mingxun Wang, Marcy J Balunas, Jonathan L Klassen, Pieter C Dorrestein "Chemical Gradients of Plant Substrates in an Fungus Garden." mSystems 2021, PMID: 34342533

28. Tiago F Leao, Chase M Clark, Anelize Bauermeister, Emmanuel O Elijah, Emily C Gentry, Makhai Husband, Michelli F Oliveira, Nuno Bandeira, Mingxun Wang, Pieter C Dorrestein "Quick-start infrastructure for untargeted metabolomics analysis in GNPS." Nature metabolism 2021, PMID: 34244695

29. Robin Schmid, Daniel Petras, Louis-Félix Nothias, Mingxun Wang, Allegra T Aron, Annika Jagels, Hiroshi Tsugawa, Johannes Rainer, Mar Garcia-Aloy, Kai Dührkop, Ansgar Korf, Tomáš Pluskal, Zdeněk Kameník, Alan K Jarmusch, Andrés Mauricio Caraballo-Rodríguez, Kelly C Weldon, Melissa Nothias-Esposito, Alexander A Aksenov, Anelize Bauermeister, Andrea Albarracin Orio, Carlismari O Grundmann, Fernando Vargas, Irina Koester, Julia M Gauglitz, Emily C Gentry, Yannick Hövelmann, Svetlana A Kalinina, Matthew A Pendergraft, Morgan Panitchpakdi, Richard Tehan, Audrey Le Gouellec, Gajender Aleti, Helena Mannochio Russo, Birgit Arndt, Florian Hübner, Heiko Hayen, Hui Zhi, Manuela Raffatellu, Kimberly A Prather, Lihini I Aluwihare, Sebastian Böcker, Kerry L McPhail, Hans-Ulrich Humpf, Uwe Karst, Pieter C Dorrestein "Ion identity molecular networking for mass spectrometry-based metabolomics in the GNPS environment." Nature communications 2021, PMID: 34158495

30. Daniel Petras, Jeremiah J Minich, Lucia B Cancelada, Ralph R Torres, Emily Kunselman, Mingxun Wang, Margot E White, Eric E Allen, Kimberly A Prather, Lihini I Aluwihare, Pieter C Dorrestein "Non-targeted tandem mass spectrometry enables the visualization of organic matter chemotype shifts in coastal seawater." Chemosphere 2021, PMID: 33460888

31. Michelle A Schorn, Stefan Verhoeven, Lars Ridder, Florian Huber, Deepa D Acharya, Alexander A Aksenov, Gajender Aleti, Jamshid Amiri Moghaddam, Allegra T Aron, Saefuddin Aziz, Anelize Bauermeister, Katherine D Bauman, Martin Baunach, Christine Beemelmanns, J Michael Beman, María Victoria Berlanga-Clavero, Alex A Blacutt, Helge B Bode, Anne Boullie, Asker Brejnrod, Tim S Bugni, Alexandra Calteau, Liu Cao, Víctor J Carrión, Raquel Castelo-Branco, Shaurya Chanana, Alexander B Chase, Marc G Chevrette, Leticia V Costa-Lotufo, Jason M Crawford, Cameron R Currie, Bart Cuypers, Tam Dang, Tristan de Rond, Alyssa M Demko, Elke Dittmann, Chao Du, Christopher Drozd, Jean-Claude Dujardin, Rachel J Dutton, Anna Edlund, David P Fewer, Neha Garg, Julia M Gauglitz, Emily C Gentry, Lena Gerwick, Evgenia Glukhov, Harald Gross, Muriel Gugger, Dulce G Guillén Matus, Eric J N Helfrich, Benjamin-Florian Hempel, Jae-Seoun Hur, Marianna Iorio, Paul R Jensen, Kyo Bin Kang, Leonard Kaysser, Neil L Kelleher, Chung Sub Kim, Ki Hyun Kim, Irina Koester, Gabriele M König, Tiago Leao, Seoung Rak Lee, Yi-Yuan Lee, Xuanji Li, Jessica C Little, Katherine N Maloney, Daniel Männle, Christian Martin H, Andrew C McAvoy, Willam W Metcalf, Hosein Mohimani, Carlos Molina-Santiago, Bradley S Moore, Michael W Mullowney, Mitchell Muskat, Louis-Félix Nothias, Ellis C O'Neill, Elizabeth I Parkinson, Daniel Petras, Jörn Piel, Emily C Pierce, Karine Pires, Raphael Reher, Diego Romero, M Caroline Roper, Michael Rust, Hamada Saad, Carmen Saenz, Laura M Sanchez, Søren Johannes Sørensen, Margherita Sosio, Roderich D Süssmuth, Douglas Sweeney, Kapil Tahlan, Regan J Thomson, Nicholas J Tobias, Amaro E Trindade-Silva, Gilles P van Wezel, Mingxun Wang, Kelly C Weldon, Fan Zhang, Nadine Ziemert, Katherine R Duncan, Max Crüsemann, Simon Rogers, Pieter C Dorrestein, Marnix H Medema, Justin J J van der Hooft "A community resource for paired genomic and metabolomic data mining." Nature chemical biology 2021, PMID: 33589842

32. Anupriya Tripathi, Yoshiki Vázquez-Baeza, Julia M Gauglitz, Mingxun Wang, Kai Dührkop, Mélissa Nothias-Esposito, Deepa D Acharya, Madeleine Ernst, Justin J J van der Hooft, Qiyun Zhu, Daniel McDonald, Asker D Brejnrod, Antonio Gonzalez, Jo Handelsman, Markus Fleischauer, Marcus Ludwig, Sebastian Böcker, Louis-Félix Nothias, Rob Knight, Pieter C Dorrestein "Chemically informed analyses of metabolomics mass spectrometry data with Qemistree." Nature chemical biology 2020, PMID: 33199911

33. Alexander A Aksenov, Ivan Laponogov, Zheng Zhang, Sophie L F Doran, Ilaria Belluomo, Dennis Veselkov, Wout Bittremieux, Louis Felix Nothias, Mélissa Nothias-Esposito, Katherine N Maloney, Biswapriya B Misra, Alexey V Melnik, Aleksandr Smirnov, Xiuxia Du, Kenneth L Jones, Kathleen Dorrestein, Morgan Panitchpakdi, Madeleine Ernst, Justin J J van der Hooft, Mabel Gonzalez, Chiara Carazzone, Adolfo Amézquita, Chris Callewaert, James T Morton, Robert A Quinn, Amina Bouslimani, Andrea Albarracín Orio, Daniel Petras, Andrea M Smania, Sneha P Couvillion, Meagan C Burnet, Carrie D Nicora, Erika Zink, Thomas O Metz, Viatcheslav Artaev, Elizabeth Humston-Fulmer, Rachel Gregor, Michael M Meijler, Itzhak Mizrahi, Stav Eyal, Brooke Anderson, Rachel Dutton, Raphaël Lugan, Pauline Le Boulch, Yann Guitton, Stephanie Prevost, Audrey Poirier, Gaud Dervilly, Bruno Le Bizec, Aaron Fait, Noga Sikron Persi, Chao Song, Kelem Gashu, Roxana Coras, Monica Guma, Julia Manasson, Jose U Scher, Dinesh Kumar Barupal, Saleh Alseekh, Alisdair R Fernie, Reza Mirnezami, Vasilis Vasiliou, Robin Schmid, Roman S Borisov, Larisa N Kulikova, Rob Knight, Mingxun Wang, George B Hanna, Pieter C Dorrestein, Kirill Veselkov "Auto-deconvolution and molecular networking of gas chromatography-mass spectrometry data." Nature biotechnology 2020, PMID: 33169034

34. Tiago Leão, Mingxun Wang, Nathan Moss, Ricardo da Silva, Jon Sanders, Sergey Nurk, Alexey Gurevich, Gregory Humphrey, Raphael Reher, Qiyun Zhu, Pedro Belda-Ferre, Evgenia Glukhov, Syrena Whitner, Kelsey L Alexander, Robert Rex, Pavel Pevzner, Pieter C Dorrestein, Rob Knight, Nuno Bandeira, William H Gerwick, Lena Gerwick "A Multi-Omics Characterization of the Natural Product Potential of Tropical Filamentous Marine Cyanobacteria." Marine drugs 2021, PMID: 33418911

35. James T Morton, Daniel McDonald, Alexander A Aksenov, Louis Felix Nothias, James R Foulds, Robert A Quinn, Michelle H Badri, Tami L Swenson, Marc W Van Goethem, Trent R Northen, Yoshiki Vazquez-Baeza, Mingxun Wang, Nicholas A Bokulich, Aaron Watters, Se Jin Song, Richard Bonneau, Pieter C Dorrestein, Rob Knight "Reply to: Examining microbe-metabolite correlations by linear methods." Nature methods 2021, PMID: 33398188

36. Andrea G Albarracín Orio, Daniel Petras, Romina A Tobares, Alexander A Aksenov, Mingxun Wang, Florencia Juncosa, Pamela Sayago, Alejandro J Moyano, Pieter C Dorrestein, Andrea M Smania "Fungal-bacterial interaction selects for quorum sensing mutants with increased production of natural antifungal compounds." Communications biology 2020, PMID: 33184402

37. Louis-Félix Nothias, Daniel Petras, Robin Schmid, Kai Dührkop, Johannes Rainer, Abinesh Sarvepalli, Ivan Protsyuk, Madeleine Ernst, Hiroshi Tsugawa, Markus Fleischauer, Fabian Aicheler, Alexander A Aksenov, Oliver Alka, Pierre-Marie Allard, Aiko Barsch, Xavier Cachet, Andres Mauricio Caraballo-Rodriguez, Ricardo R Da Silva, Tam Dang, Neha Garg, Julia M Gauglitz, Alexey Gurevich, Giorgis Isaac, Alan K Jarmusch, Zdeněk Kameník, Kyo Bin Kang, Nikolas Kessler, Irina Koester, Ansgar Korf, Audrey Le Gouellec, Marcus Ludwig, Christian Martin H, Laura-Isobel McCall, Jonathan McSayles, Sven W Meyer, Hosein Mohimani, Mustafa Morsy, Oriane Moyne, Steffen Neumann, Heiko Neuweger, Ngoc Hung Nguyen, Melissa Nothias-Esposito, Julien Paolini, Vanessa V Phelan, Tomáš Pluskal, Robert A Quinn, Simon Rogers, Bindesh Shrestha, Anupriya Tripathi, Justin J J van der Hooft, Fernando Vargas, Kelly C Weldon, Michael Witting, Heejung Yang, Zheng Zhang, Florian Zubeil, Oliver Kohlbacher, Sebastian Böcker, Theodore Alexandrov, Nuno Bandeira, Mingxun Wang, Pieter C Dorrestein "Feature-based molecular networking in the GNPS analysis environment." Nature methods 2020, PMID: 32839597

38. Alan K Jarmusch, Mingxun Wang, Christine M Aceves, Rohit S Advani, Shaden Aguirre, Alexander A Aksenov, Gajender Aleti, Allegra T Aron, Anelize Bauermeister, Sanjana Bolleddu, Amina Bouslimani, Andres Mauricio Caraballo Rodriguez, Rama Chaar, Roxana Coras, Emmanuel O Elijah, Madeleine Ernst, Julia M Gauglitz, Emily C Gentry, Makhai Husband, Scott A Jarmusch, Kenneth L Jones, Zdenek Kamenik, Audrey Le Gouellec, Aileen Lu, Laura-Isobel McCall, Kerry L McPhail, Michael J Meehan, Alexey V Melnik, Riya C Menezes, Yessica Alejandra Montoya Giraldo, Ngoc Hung Nguyen, Louis Felix Nothias, Mélissa Nothias-Esposito, Morgan Panitchpakdi, Daniel Petras, Robert A Quinn, Nicole Sikora, Justin J J van der Hooft, Fernando Vargas, Alison Vrbanac, Kelly C Weldon, Rob Knight, Nuno Bandeira, Pieter C Dorrestein "ReDU: a framework to find and reanalyze public mass spectrometry data." Nature methods 2020, PMID: 32807955

39. Allegra T Aron, Emily C Gentry, Kerry L McPhail, Louis-Félix Nothias, Mélissa Nothias-Esposito, Amina Bouslimani, Daniel Petras, Julia M Gauglitz, Nicole Sikora, Fernando Vargas, Justin J J van der Hooft, Madeleine Ernst, Kyo Bin Kang, Christine M Aceves, Andrés Mauricio Caraballo-Rodríguez, Irina Koester, Kelly C Weldon, Samuel Bertrand, Catherine Roullier, Kunyang Sun, Richard M Tehan, Cristopher A Boya P, Martin H Christian, Marcelino Gutiérrez, Aldo Moreno Ulloa, Javier Andres Tejeda Mora, Randy Mojica-Flores, Johant Lakey-Beitia, Victor Vásquez-Chaves, Yilue Zhang, Angela I Calderón, Nicole Tayler, Robert A Keyzers, Fidele Tugizimana, Nombuso Ndlovu, Alexander A Aksenov, Alan K Jarmusch, Robin Schmid, Andrew W Truman, Nuno Bandeira, Mingxun Wang, Pieter C Dorrestein "Reproducible molecular networking of untargeted mass spectrometry data using GNPS." Nature protocols 2020, PMID: 32405051

40. Fernando Vargas, Kelly C Weldon, Nicole Sikora, Mingxun Wang, Zheng Zhang, Emily C Gentry, Morgan W Panitchpakdi, Andrés Mauricio Caraballo-Rodríguez, Pieter C Dorrestein, Alan K Jarmusch "Protocol for community-created public MS/MS reference spectra within the Global Natural Products Social Molecular Networking infrastructure." Rapid communications in mass spectrometry : RCM 2020, PMID: 31930757

41. Raphael Reher, Hyun Woo Kim, Chen Zhang, Huanru Henry Mao, Mingxun Wang, Louis-Félix Nothias, Andres Mauricio Caraballo-Rodriguez, Evgenia Glukhov, Bahar Teke, Tiago Leao, Kelsey L Alexander, Brendan M Duggan, Ezra L Van Everbroeck, Pieter C Dorrestein, Garrison W Cottrell, William H Gerwick "A Convolutional Neural Network-Based Approach for the Rapid Annotation of Molecularly Diverse Natural Products." Journal of the American Chemical Society 2020, PMID: 32045230

42. Robert A Quinn, Alexey V Melnik, Alison Vrbanac, Ting Fu, Kathryn A Patras, Mitchell P Christy, Zsolt Bodai, Pedro Belda-Ferre, Anupriya Tripathi, Lawton K Chung, Michael Downes, Ryan D Welch, Melissa Quinn, Greg Humphrey, Morgan Panitchpakdi, Kelly C Weldon, Alexander Aksenov, Ricardo da Silva, Julian Avila-Pacheco, Clary Clish, Sena Bae, Himel Mallick, Eric A Franzosa, Jason Lloyd-Price, Robert Bussell, Taren Thron, Andrew T Nelson, Mingxun Wang, Eric Leszczynski, Fernando Vargas, Julia M Gauglitz, Michael J Meehan, Emily Gentry, Timothy D Arthur, Alexis C Komor, Orit Poulsen, Brigid S Boland, John T Chang, William J Sandborn, Meerana Lim, Neha Garg, Julie C Lumeng, Ramnik J Xavier, Barbara I Kazmierczak, Ruchi Jain, Marie Egan, Kyung E Rhee, David Ferguson, Manuela Raffatellu, Hera Vlamakis, Gabriel G Haddad, Dionicio Siegel, Curtis Huttenhower, Sarkis K Mazmanian, Ronald M Evans, Victor Nizet, Rob Knight, Pieter C Dorrestein "Global chemical effects of the microbiome include new bile-acid conjugations." Nature 2020, PMID: 32103176

43. Melissa M Galey, Alexandria N Young, Valentina Z Petukhova, Mingxun Wang, Jian Wang, Amrita Salvi, Angela Russo, Joanna E Burdette, Laura M Sanchez "Detection of Ovarian Cancer Using Samples Sourced from the Vaginal Microenvironment." Journal of proteome research 2019, PMID: 31738564

44. Mingxun Wang, Alan K Jarmusch, Fernando Vargas, Alexander A Aksenov, Julia M Gauglitz, Kelly Weldon, Daniel Petras, Ricardo da Silva, Robert Quinn, Alexey V Melnik, Justin J J van der Hooft, Andrés Mauricio Caraballo-Rodríguez, Louis Felix Nothias, Christine M Aceves, Morgan Panitchpakdi, Elizabeth Brown, Francesca Di Ottavio, Nicole Sikora, Emmanuel O Elijah, Lara Labarta-Bajo, Emily C Gentry, Shabnam Shalapour, Kathleen E Kyle, Sara P Puckett, Jeramie D Watrous, Carolina S Carpenter, Amina Bouslimani, Madeleine Ernst, Austin D Swafford, Elina I Zúñiga, Marcy J Balunas, Jonathan L Klassen, Rohit Loomba, Rob Knight, Nuno Bandeira, Pieter C Dorrestein "Mass spectrometry searches using MASST." Nature biotechnology 2020, PMID: 31894142

45. James T Morton, Alexander A Aksenov, Louis Felix Nothias, James R Foulds, Robert A Quinn, Michelle H Badri, Tami L Swenson, Marc W Van Goethem, Trent R Northen, Yoshiki Vazquez-Baeza, Mingxun Wang, Nicholas A Bokulich, Aaron Watters, Se Jin Song, Richard Bonneau, Pieter C Dorrestein, Rob Knight "Learning representations of microbe-metabolite interactions." Nature methods 2019, PMID: 31686038

46. Jeffrey A van Santen, Grégoire Jacob, Amrit Leen Singh, Victor Aniebok, Marcy J Balunas, Derek Bunsko, Fausto Carnevale Neto, Laia Castaño-Espriu, Chen Chang, Trevor N Clark, Jessica L Cleary Little, David A Delgadillo, Pieter C Dorrestein, Katherine R Duncan, Joseph M Egan, Melissa M Galey, F P Jake Haeckl, Alex Hua, Alison H Hughes, Dasha Iskakova, Aswad Khadilkar, Jung-Ho Lee, Sanghoon Lee, Nicole LeGrow, Dennis Y Liu, Jocelyn M Macho, Catherine S McCaughey, Marnix H Medema, Ram P Neupane, Timothy J O'Donnell, Jasmine S Paula, Laura M Sanchez, Anam F Shaikh, Sylvia Soldatou, Barbara R Terlouw, Tuan Anh Tran, Mercia Valentine, Justin J J van der Hooft, Duy A Vo, Mingxun Wang, Darryl Wilson, Katherine E Zink, Roger G Linington "The Natural Products Atlas: An Open Access Knowledge Base for Microbial Natural Products Discovery." ACS central science 2019, PMID: 31807684

47. Alexey V Melnik, Yoshiki Vázquez-Baeza, Alexander A Aksenov, Embriette Hyde, Andrew C McAvoy, Mingxun Wang, Ricardo R da Silva, Ivan Protsyuk, Jason V Wu, Amina Bouslimani, Yan Wei Lim, Tal Luzzatto-Knaan, William Comstock, Robert A Quinn, Richard Wong, Greg Humphrey, Gail Ackermann, Timothy Spivey, Sharon S Brouha, Nuno Bandeira, Grace Y Lin, Forest Rohwer, Douglas J Conrad, Theodore Alexandrov, Rob Knight, Pieter C Dorrestein, Neha Garg "Molecular and Microbial Microenvironments in Chronically Diseased Lungs Associated with Cystic Fibrosis." mSystems 2019, PMID: 31551401

48. Evan Bolyen, Jai Ram Rideout, Matthew R Dillon, Nicholas A Bokulich, Christian C Abnet, Gabriel A Al-Ghalith, Harriet Alexander, Eric J Alm, Manimozhiyan Arumugam, Francesco Asnicar, Yang Bai, Jordan E Bisanz, Kyle Bittinger, Asker Brejnrod, Colin J Brislawn, C Titus Brown, Benjamin J Callahan, Andrés Mauricio Caraballo-Rodríguez, John Chase, Emily K Cope, Ricardo Da Silva, Christian Diener, Pieter C Dorrestein, Gavin M Douglas, Daniel M Durall, Claire Duvallet, Christian F Edwardson, Madeleine Ernst, Mehrbod Estaki, Jennifer Fouquier, Julia M Gauglitz, Sean M Gibbons, Deanna L Gibson, Antonio Gonzalez, Kestrel Gorlick, Jiarong Guo, Benjamin Hillmann, Susan Holmes, Hannes Holste, Curtis Huttenhower, Gavin A Huttley, Stefan Janssen, Alan K Jarmusch, Lingjing Jiang, Benjamin D Kaehler, Kyo Bin Kang, Christopher R Keefe, Paul Keim, Scott T Kelley, Dan Knights, Irina Koester, Tomasz Kosciolek, Jorden Kreps, Morgan G I Langille, Joslynn Lee, Ruth Ley, Yong-Xin Liu, Erikka Loftfield, Catherine Lozupone, Massoud Maher, Clarisse Marotz, Bryan D Martin, Daniel McDonald, Lauren J McIver, Alexey V Melnik, Jessica L Metcalf, Sydney C Morgan, Jamie T Morton, Ahmad Turan Naimey, Jose A Navas-Molina, Louis Felix Nothias, Stephanie B Orchanian, Talima Pearson, Samuel L Peoples, Daniel Petras, Mary Lai Preuss, Elmar Pruesse, Lasse Buur Rasmussen, Adam Rivers, Michael S Robeson, Patrick Rosenthal, Nicola Segata, Michael Shaffer, Arron Shiffer, Rashmi Sinha, Se Jin Song, John R Spear, Austin D Swafford, Luke R Thompson, Pedro J Torres, Pauline Trinh, Anupriya Tripathi, Peter J Turnbaugh, Sabah Ul-Hasan, Justin J J van der Hooft, Fernando Vargas, Yoshiki Vázquez-Baeza, Emily Vogtmann, Max von Hippel, William Walters, Yunhu Wan, Mingxun Wang, Jonathan Warren, Kyle C Weber, Charles H D Williamson, Amy D Willis, Zhenjiang Zech Xu, Jesse R Zaneveld, Yilong Zhang, Qiyun Zhu, Rob Knight, J Gregory Caporaso "Author Correction: Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2." Nature biotechnology 2019, PMID: 31399723

49. Evan Bolyen, Jai Ram Rideout, Matthew R Dillon, Nicholas A Bokulich, Christian C Abnet, Gabriel A Al-Ghalith, Harriet Alexander, Eric J Alm, Manimozhiyan Arumugam, Francesco Asnicar, Yang Bai, Jordan E Bisanz, Kyle Bittinger, Asker Brejnrod, Colin J Brislawn, C Titus Brown, Benjamin J Callahan, Andrés Mauricio Caraballo-Rodríguez, John Chase, Emily K Cope, Ricardo Da Silva, Christian Diener, Pieter C Dorrestein, Gavin M Douglas, Daniel M Durall, Claire Duvallet, Christian F Edwardson, Madeleine Ernst, Mehrbod Estaki, Jennifer Fouquier, Julia M Gauglitz, Sean M Gibbons, Deanna L Gibson, Antonio Gonzalez, Kestrel Gorlick, Jiarong Guo, Benjamin Hillmann, Susan Holmes, Hannes Holste, Curtis Huttenhower, Gavin A Huttley, Stefan Janssen, Alan K Jarmusch, Lingjing Jiang, Benjamin D Kaehler, Kyo Bin Kang, Christopher R Keefe, Paul Keim, Scott T Kelley, Dan Knights, Irina Koester, Tomasz Kosciolek, Jorden Kreps, Morgan G I Langille, Joslynn Lee, Ruth Ley, Yong-Xin Liu, Erikka Loftfield, Catherine Lozupone, Massoud Maher, Clarisse Marotz, Bryan D Martin, Daniel McDonald, Lauren J McIver, Alexey V Melnik, Jessica L Metcalf, Sydney C Morgan, Jamie T Morton, Ahmad Turan Naimey, Jose A Navas-Molina, Louis Felix Nothias, Stephanie B Orchanian, Talima Pearson, Samuel L Peoples, Daniel Petras, Mary Lai Preuss, Elmar Pruesse, Lasse Buur Rasmussen, Adam Rivers, Michael S Robeson, Patrick Rosenthal, Nicola Segata, Michael Shaffer, Arron Shiffer, Rashmi Sinha, Se Jin Song, John R Spear, Austin D Swafford, Luke R Thompson, Pedro J Torres, Pauline Trinh, Anupriya Tripathi, Peter J Turnbaugh, Sabah Ul-Hasan, Justin J J van der Hooft, Fernando Vargas, Yoshiki Vázquez-Baeza, Emily Vogtmann, Max von Hippel, William Walters, Yunhu Wan, Mingxun Wang, Jonathan Warren, Kyle C Weber, Charles H D Williamson, Amy D Willis, Zhenjiang Zech Xu, Jesse R Zaneveld, Yilong Zhang, Qiyun Zhu, Rob Knight, J Gregory Caporaso "Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2." Nature biotechnology 2019, PMID: 31341288

50. Madeleine Ernst, Kyo Bin Kang, Andrés Mauricio Caraballo-Rodríguez, Louis-Felix Nothias, Joe Wandy, Christopher Chen, Mingxun Wang, Simon Rogers, Marnix H Medema, Pieter C Dorrestein, Justin J J van der Hooft "MolNetEnhancer: Enhanced Molecular Networks by Integrating Metabolome Mining and Annotation Tools." Metabolites 2019, PMID: 31315242

51. Alan K Jarmusch, Emmanuel O Elijah, Fernando Vargas, Amina Bouslimani, Ricardo R da Silva, Madeleine Ernst, Mingxun Wang, Krizia K Del Rosario, Pieter C Dorrestein, Shirley M Tsunoda "Initial Development toward Non-Invasive Drug Monitoring via Untargeted Mass Spectrometric Analysis of Human Skin." Analytical chemistry 2019, PMID: 31074958

52. Valentina Z Petukhova, Alexandria N Young, Jian Wang, Mingxun Wang, Andras Ladanyi, Rajul Kothari, Joanna E Burdette, Laura M Sanchez "Whole Cell MALDI Fingerprinting Is a Robust Tool for Differential Profiling of Two-Component Mammalian Cell Mixtures." Journal of the American Society for Mass Spectrometry 2018, PMID: 30353292

53. Mingxun Wang, Jian Wang, Jeremy Carver, Benjamin S Pullman, Seong Won Cha, Nuno Bandeira "Assembling the Community-Scale Discoverable Human Proteome." Cell systems 2018, PMID: 30172843

54. Antonio Gonzalez, Jose A Navas-Molina, Tomasz Kosciolek, Daniel McDonald, Yoshiki Vázquez-Baeza, Gail Ackermann, Jeff DeReus, Stefan Janssen, Austin D Swafford, Stephanie B Orchanian, Jon G Sanders, Joshua Shorenstein, Hannes Holste, Semar Petrus, Adam Robbins-Pianka, Colin J Brislawn, Mingxun Wang, Jai Ram Rideout, Evan Bolyen, Matthew Dillon, J Gregory Caporaso, Pieter C Dorrestein, Rob Knight "Qiita: rapid, web-enabled microbiome meta-analysis." Nature methods 2018, PMID: 30275573

55. Louis-Félix Nothias, Mélissa Nothias-Esposito, Ricardo da Silva, Mingxun Wang, Ivan Protsyuk, Zheng Zhang, Abi Sarvepalli, Pieter Leyssen, David Touboul, Jean Costa, Julien Paolini, Theodore Alexandrov, Marc Litaudon, Pieter C Dorrestein "Bioactivity-Based Molecular Networking for the Discovery of Drug Leads in Natural Product Bioassay-Guided Fractionation." Journal of natural products 2018, PMID: 29498278

56. Ricardo R da Silva, Mingxun Wang, Louis-Félix Nothias, Justin J J van der Hooft, Andrés Mauricio Caraballo-Rodríguez, Evan Fox, Marcy J Balunas, Jonathan L Klassen, Norberto Peporine Lopes, Pieter C Dorrestein "Propagating annotations of molecular networks using in silico fragmentation." PLoS computational biology 2018, PMID: 29668671

57. Kerstin Scheubert, Franziska Hufsky, Daniel Petras, Mingxun Wang, Louis-Félix Nothias, Kai Dührkop, Nuno Bandeira, Pieter C Dorrestein, Sebastian Böcker "Significance estimation for large scale metabolomics annotations by spectral matching." Nature communications 2017, PMID: 29133785

58. Neha Garg, Mingxun Wang, Embriette Hyde, Ricardo R da Silva, Alexey V Melnik, Ivan Protsyuk, Amina Bouslimani, Yan Wei Lim, Richard Wong, Greg Humphrey, Gail Ackermann, Timothy Spivey, Sharon S Brouha, Nuno Bandeira, Grace Y Lin, Forest Rohwer, Douglas J Conrad, Theodore Alexandrov, Rob Knight, Pieter C Dorrestein "Three-Dimensional Microbiome and Metabolome Cartography of a Diseased Human Lung." Cell host & microbe 2017, PMID: 29056429

59. Tal Luzzatto-Knaan, Neha Garg, Mingxun Wang, Evgenia Glukhov, Yao Peng, Gail Ackermann, Amnon Amir, Brendan M Duggan, Sergey Ryazanov, Lena Gerwick, Rob Knight, Theodore Alexandrov, Nuno Bandeira, William H Gerwick, Pieter C Dorrestein "Digitizing mass spectrometry data to explore the chemical diversity and distribution of marine cyanobacteria and algae." eLife 2017, PMID: 28492366

60. Yasset Perez-Riverol, Mingze Bai, Felipe da Veiga Leprevost, Silvano Squizzato, Young Mi Park, Kenneth Haug, Adam J Carroll, Dylan Spalding, Justin Paschall, Mingxun Wang, Noemi Del-Toro, Tobias Ternent, Peng Zhang, Nicola Buso, Nuno Bandeira, Eric W Deutsch, David S Campbell, Ronald C Beavis, Reza M Salek, Ugis Sarkans, Robert Petryszak, Maria Keays, Eoin Fahy, Manish Sud, Shankar Subramaniam, Ariana Barbera, Rafael C Jiménez, Alexey I Nesvizhskii, Susanna-Assunta Sansone, Christoph Steinbeck, Rodrigo Lopez, Juan A Vizcaíno, Peipei Ping, Henning Hermjakob "Discovering and linking public omics data sets using the Omics Discovery Index." Nature biotechnology 2017, PMID: 28486464

61. Eric W Deutsch, Attila Csordas, Zhi Sun, Andrew Jarnuczak, Yasset Perez-Riverol, Tobias Ternent, David S Campbell, Manuel Bernal-Llinares, Shujiro Okuda, Shin Kawano, Robert L Moritz, Jeremy J Carver, Mingxun Wang, Yasushi Ishihama, Nuno Bandeira, Henning Hermjakob, Juan Antonio Vizcaíno "The ProteomeXchange consortium in 2017: supporting the cultural change in proteomics public data deposition." Nucleic acids research 2016, PMID: 27924013

62. Amina Bouslimani, Alexey V Melnik, Zhenjiang Xu, Amnon Amir, Ricardo R da Silva, Mingxun Wang, Nuno Bandeira, Theodore Alexandrov, Rob Knight, Pieter C Dorrestein "Lifestyle chemistries from phones for individual profiling." Proceedings of the National Academy of Sciences of the United States of America 2016, PMID: 27849584

63. Gert Wohlgemuth, Sajjan S Mehta, Ramon F Mejia, Steffen Neumann, Diego Pedrosa, Tomáš Pluskal, Emma L Schymanski, Egon L Willighagen, Michael Wilson, David S Wishart, Masanori Arita, Pieter C Dorrestein, Nuno Bandeira, Mingxun Wang, Tobias Schulze, Reza M Salek, Christoph Steinbeck, Venkata Chandrasekhar Nainala, Robert Mistrik, Takaaki Nishioka, Oliver Fiehn "SPLASH, a hashed identifier for mass spectra." Nature biotechnology 2016, PMID: 27824832

64. Mingxun Wang, Jeremy J Carver, Vanessa V Phelan, Laura M Sanchez, Neha Garg, Yao Peng, Don Duy Nguyen, Jeramie Watrous, Clifford A Kapono, Tal Luzzatto-Knaan, Carla Porto, Amina Bouslimani, Alexey V Melnik, Michael J Meehan, Wei-Ting Liu, Max Crüsemann, Paul D Boudreau, Eduardo Esquenazi, Mario Sandoval-Calderón, Roland D Kersten, Laura A Pace, Robert A Quinn, Katherine R Duncan, Cheng-Chih Hsu, Dimitrios J Floros, Ronnie G Gavilan, Karin Kleigrewe, Trent Northen, Rachel J Dutton, Delphine Parrot, Erin E Carlson, Bertrand Aigle, Charlotte F Michelsen, Lars Jelsbak, Christian Sohlenkamp, Pavel Pevzner, Anna Edlund, Jeffrey McLean, Jörn Piel, Brian T Murphy, Lena Gerwick, Chih-Chuang Liaw, Yu-Liang Yang, Hans-Ulrich Humpf, Maria Maansson, Robert A Keyzers, Amy C Sims, Andrew R Johnson, Ashley M Sidebottom, Brian E Sedio, Andreas Klitgaard, Charles B Larson, Cristopher A Boya P, Daniel Torres-Mendoza, David J Gonzalez, Denise B Silva, Lucas M Marques, Daniel P Demarque, Egle Pociute, Ellis C O'Neill, Enora Briand, Eric J N Helfrich, Eve A Granatosky, Evgenia Glukhov, Florian Ryffel, Hailey Houson, Hosein Mohimani, Jenan J Kharbush, Yi Zeng, Julia A Vorholt, Kenji L Kurita, Pep Charusanti, Kerry L McPhail, Kristian Fog Nielsen, Lisa Vuong, Maryam Elfeki, Matthew F Traxler, Niclas Engene, Nobuhiro Koyama, Oliver B Vining, Ralph Baric, Ricardo R Silva, Samantha J Mascuch, Sophie Tomasi, Stefan Jenkins, Venkat Macherla, Thomas Hoffman, Vinayak Agarwal, Philip G Williams, Jingqui Dai, Ram Neupane, Joshua Gurr, Andrés M C Rodríguez, Anne Lamsa, Chen Zhang, Kathleen Dorrestein, Brendan M Duggan, Jehad Almaliti, Pierre-Marie Allard, Prasad Phapale, Louis-Felix Nothias, Theodore Alexandrov, Marc Litaudon, Jean-Luc Wolfender, Jennifer E Kyle, Thomas O Metz, Tyler Peryea, Dac-Trung Nguyen, Danielle VanLeer, Paul Shinn, Ajit Jadhav, Rolf Müller, Katrina M Waters, Wenyuan Shi, Xueting Liu, Lixin Zhang, Rob Knight, Paul R Jensen, Bernhard O Palsson, Kit Pogliano, Roger G Linington, Marcelino Gutiérrez, Norberto P Lopes, William H Gerwick, Bradley S Moore, Pieter C Dorrestein, Nuno Bandeira "Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking." Nature biotechnology 2016, PMID: 27504778

65. Waqas Nasir, Alejandro Gomez Toledo, Fredrik Noborn, Jonas Nilsson, Mingxun Wang, Nuno Bandeira, Göran Larson "SweetNET: A Bioinformatics Workflow for Glycopeptide MS/MS Spectral Analysis." Journal of proteome research 2016, PMID: 27399812

66. Amina Bouslimani, Carla Porto, Christopher M Rath, Mingxun Wang, Yurong Guo, Antonio Gonzalez, Donna Berg-Lyon, Gail Ackermann, Gitte Julie Moeller Christensen, Teruaki Nakatsuji, Lingjuan Zhang, Andrew W Borkowski, Michael J Meehan, Kathleen Dorrestein, Richard L Gallo, Nuno Bandeira, Rob Knight, Theodore Alexandrov, Pieter C Dorrestein "Molecular cartography of the human skin surface in 3D." Proceedings of the National Academy of Sciences of the United States of America 2015, PMID: 25825778

67. Katherine R Duncan, Max Crüsemann, Anna Lechner, Anindita Sarkar, Jie Li, Nadine Ziemert, Mingxun Wang, Nuno Bandeira, Bradley S Moore, Pieter C Dorrestein, Paul R Jensen "Molecular networking and pattern-based genome mining improves discovery of biosynthetic gene clusters and their products from Salinispora species." Chemistry & biology 2015, PMID: 25865308

68. Hosein Mohimani, Roland D Kersten, Wei-Ting Liu, Mingxun Wang, Samuel O Purvine, Si Wu, Heather M Brewer, Ljiljana Pasa-Tolic, Nuno Bandeira, Bradley S Moore, Pavel A Pevzner, Pieter C Dorrestein "Automated genome mining of ribosomal peptide natural products." ACS chemical biology 2014, PMID: 24802639

69. Mingxun Wang, Nuno Bandeira "Spectral library generating function for assessing spectrum-spectrum match significance." Journal of proteome research 2013, PMID: 23808827

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