Publications
Cirriculum Vitae¶
Journal Publications¶
2019¶
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
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, FP 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 JJ 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
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
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
Daniel Petras, Jeremiah J Minich, Emily Kunselman, Mingxun Wang, Margot E White, Eric E Allen, Lihini I Aluwihare, Pieter C Dorrestein. "Non-Targeted Metabolomics Enables the Prioritization and Tracking of Anthropogenic Pollutants in Coastal Seawater" Preprint in ChemRxiv
Allegra T Aron, Emily Gentry, Kerry L McPhail, Louis Felix Nothias, Mélissa Nothias-Esposito, Amina Bouslimani, Daniel Petras, Julia M Gauglitz, Nicole Sikora, Fernando Vargas, 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, H Christian Martin, Marcelino Gutiérrez, Aldo Moreno Ulloa, Javier Andres Tejeda Mora, Randy Mojica-Flores, Johant Lakey-Beitia, Victor Vásquez-Chaves, Angela I Calderón, Nicole Tayler, A Robert, Fidele Tugizimana Keyzers, Nombuso Ndlovu, Alexander A Aksenov, Alan K Jarmusch, Robin Schmid, Andrew W Truman, Nuno Bandeira, Mingxun Wang, Pieter Dorrestein. "Reproducible Molecular Networking Of Untargeted Mass Spectrometry Data Using GNPS" Preprint in ChemRxiv
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 GI 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 JJ 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 HD 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 Methods
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 JJ van der Hooft. "Molnetenhancer: enhanced molecular networks by integrating metabolome mining and annotation tools" Metabolites
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 Towards Non-Invasive Drug Monitoring via Untargeted Mass Spectrometric Analysis of Human Skin" Analytical chemistry
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
Andrea G Albarracín Orio, Daniel Petras, Romina A Tobares, Alexander Aksenov, Mingxun Wang, Florencia Juncosa, Pamela Sayago, Alejandro Moyano, Pieter C Dorrestein, Andrea M Smania, Daniel A Ducasse. "Fungal-bacterial interaction selects for quorum sensing mutants and a metabolic shift towards the production of natural antifungal compounds" Preprint in Biorxiv
Louis Felix Nothias, Daniel Petras, Robin Schmid, Kai Dührkop, Johannes Rainer, Abinesh Sarvepalli, Ivan Protsyuk, Madeleine Ernst, Hiroshi Tsugawa, Markus Fleischauer, Fabian Aicheler, Alexander Aksenov, Oliver Alka, Pierre-Marie Allard, Aiko Barsch, Xavier Cachet, Mauricio Caraballo, 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, Martin H Christian, 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 JJ 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" Preprint in Biorxiv
Fernando Vargas, Kelly C Weldon, Nicole Sikora, Mingxun Wang, Zheng Zhang, Emily C Gentry, Morgan W Panitchpakdi, Mauricio Caraballo, Pieter C Dorrestein, Alan K Jarmusch. "Protocol for Community-created Public MS/MS Reference Library Within the GNPS Infrastructure." Preprint in Biorxiv
Alan K Jarmusch, Mingxun Wang, Christine M Aceves, Rohit S Advani, Shaden Aguire, 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, Melissa Nothias-Esposito, Morgan Panitchpakdi, Daniel Petras, Robert Quinn, Nicole Sikora, Justin JJ van der Hooft, Fernando Vargas, Alison Vrbanac, Kelly Weldon, Rob Knight, Nuno Bandeira, Pieter C Dorrestein. "Repository-scale Co-and Re-analysis of Tandem Mass Spectrometry Data" Preprint in Biorxiv
Neha Garg, Alexey V Melnik, Yoshiki Vasquez-Baeza, Alexander Aksenov, Embriette R Hyde, Andrew C McAvoy, Mingxun Wang, Ricardo da Silva, Ivan Protsyuk, Jason V Wu, Amina Bouslimani, Yan Wei Lim, Tal Luzzatto-Knaan, William Comstock, Robert Andrew Quinn, Richard Wong, Greg Humphrey, Gail Ackermann, Timothy Spivey, Sharon S Brouha, Nuno Bandeira, Grace Y Lin, Forest Rohwer, Douglas Conrad, Theodore Alexandrov, Pieter C Dorrestein, Rob Knight. "The Molecular and Microbial Microenvironments in Chronically Diseased Lungs." Preprint in Biorxiv
Robert A. Quinn, Alison Vrbanac, Alexey V. Melnik, Kathryn A. Patras, Mitchell Christy, Andrew T. Nelson, Alexander Aksenov, Anupriya Tripathi, Greg Humphrey, Ricardo da Silva, Robert Bussell, Taren Thron, Mingxun Wang, Fernando Vargas, Julia M. Gauglitz, Michael J. Meehan, Orit Poulsen, Brigid S. Boland, John T. Chang, William J. Sandborn, Meerana Lim, Neha Garg, Julie Lumeng, Barbara I. Kazmierczak, Ruchi Jain, Marie Egan, Kyung E. Rhee, Gabriel G. Haddad, Dionicio Siegel, Sarkis Mazmanian, Victor Nizet, Rob Knight, Pieter C. Dorrestein. "Chemical Impacts of the Microbiome Across Scales Reveal Novel Conjugated Bile Acids." Preprint in Biorxiv
Mingxun Wang, Alan K. Jarmusch, Fernando Vargas, Alexander A. Aksenov, Julia Gauglitz, Kelly Weldon, Daniel Petras et al. MASST: A Web-based Basic Mass Spectrometry Search Tool for Molecules to Search Public Data. Preprint in Biorxiv
Valentina Z. Petukhova, Alexandria N. Young, Jian Wang, Mingxun Wang, Andras Ladanyi, Rajul Kothari, Joanna E. Burdette, and 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¶
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, and Rob Knight. "Qiita: rapid, web-enabled microbiome meta-analysis", Nature Methods
Ricardo R. da Silva, Mingxun Wang, Louis-Félix Nothias, Justin JJ van der Hooft, Andrés Mauricio Caraballo-Rodríguez, Evan Fox, Marcy J. Balunas, Jonathan L. Klassen, Norberto Peporine Lopes, and Pieter C. Dorrestein. "Propagating annotations of molecular networks using in silico fragmentation" PLoS Computational Biology
Louis-Félix Nothias, Mélissa Nothias-Esposito, Ricardo da Silva, Mingxun Wang, Ivan Protsyuk, Zheng Zhang, Abi Sarvepalli et al. "Bioactivity-based molecular networking for the discovery of drug leads in natural product bioassay-guided fractionation." Journal of natural products
Mingxun Wang, Jian Wang, Jeremy Carver, Benjamin Pullman, Seong Cha, Nuno Bandeira, Assembling the Community-Scale Discoverable Human Proteome, Cell Systems
2017¶
Kerstin Scheubert, Franziska Hufsky, Daniel Petras, Mingxun Wang, Louis-Felix Nothias, Kai Duehrkop, Nuno Bandeira, Pieter Dorrestein, Sebastian Boecker, "Significance estimation for large scale untargeted metabolomics annotations", Nature Communications
Neha Garg, Mingxun Wang, Embriette Hyde, Ricardo R. da Silva, Alexey V. Melnik, Ivan Protsyuk, Amina Bouslimani, Yan Wei Lim, William Comstock, Richard Wong, Greg Humphrey, James Gaffney, 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 volume cartography of microbiome and metabolome data onto radiological images of the human lung", Cell Host Microbe
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
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
2016¶
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, Ariana Barbera, Rafael C Jiménez, Alexey I Nesvizhskii, Susanna-Assunta Sansone, Christoph Steinbeck, Rodrigo Lopez, Juan Antonio Vizcaíno, Peipei Ping, Henning Hermjakob, "Omics Discovery Index – Discovering and Linking Public ‘Omics’ Datasets", Nature Biotechnology
Amina Bouslimania, Alexey V Melnik, Zhenjiang Xu, Amnon Amir, Ricardo R da Silva, Mingxun Wang, Nuno Bandeira, Theodore Alexandrov, Rob Knight, and Pieter C. Dorrestein, "Lifestyle chemistries from phones for individual profiling", Proceedings of the National Academy of Sciences
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
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, Daniel Torres-Mendoza, David J Gonzalez, Denise B Silva, Lucas M Marques, Daniel P Demarque, Egle Pociute, Ellis C O’Neill, Enora Briand, Eric JN 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 MC 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 Ø 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
Waqas Nasir, Alejandro Gomez Toledo, Fredrik Noborn, Jonas Nilsson, Mingxun Wang, Nuno Bandeira, Goran Larson, "SweetNET: A bioinformatics workflow for glycopeptide MS/MS spectral analysis" Journal of Proteome Research
2015¶
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
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
2014¶
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
2013¶
Mingxun Wang, Nuno Bandeira, Spectral library generating function for assessing spectrum-spectrum match significance, Journal of Proteome Research
PhD Work¶
You can find my PhD Defense here and the written thesis here.