Wang Lab Research¶
We have several focuses within the lab, but the major thrusts are highlighted below.
Community Scale Data Mining¶
Mass spectrometery has transformed into an incredibly high throughput appoach to analyze molecules. Its been so successful that we now have hundreds of thousands of samples, measuring billions of molecules publicly available. Howevever, the vast majority of the molecules detected in experiments, we simply don't know what compound they are and comprise this huge amount of molecular dark matter. We are interested in developing tools that mine this data for new mass spectrometry, chemistry, and biological insights. We uniquely have developed the computational tools that can flexibly and expediently search and mine 10s of terabytes of mass spectrometry data.
Publications
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
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
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
Computational Mass Spectrometry for Compound Discovery¶
Even in single experiments, repository scale data notwithstanding, thousands of molecules are detected routinely. However, we can only annotate to known compounds a very small percentage of this data -- ranging from 1-20% depending upon the sample matrix. The Wang Bioinformatics lab develops computational tools to help tackle this problem in several different ways. One of the key methods is the concept of molecular networking groups related compounds even if we cannot identify them. This approach transforms thousands of individual compounds into dozens of related families, reducing the chemical complexity of a dataset and enabling the ability to prioritize and propogate annotations from known to new molecules.
Publications
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 2015, PMID: 27504778
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
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
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
Crowd Sourcing Mass Spectrometry Knowledge¶
Spectral libraries, collections of tandem mass spectra of known structures, are a key unit of knowledge in mass spectrometry. However in metabolomics and natural products discovery, this knowledge is usually silo'd away in single laboratories and is not shared. We've built out the capabilities for the community to centralize this knowledge and make it reusable. A key innovation is changing the set of incentives such that there is more value for indivudual labs to contribute their knowledge to a common resource rather than keeping knowledge silo'd. We accomplish this by coupling any deposition of this knowledge with tools that amplify the utility for each deposition when labs reanalyze their data. This has successfully grown the set of public tandem mass spectra from a few thousand to over 500K in the last since 2014.
Publications
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 2015, PMID: 27504778
Interactive Mass Spectrometry Data Visualization/Sharing¶
As a lab, we are very interested in democratizing data analysis and enhancing research transparency. A key to these concerns is lowering the barrier of entry to visualize results and raw data, with seemless links that demonstrate how raw data supports scientific conclusions. Especially in mass spectrometry, visualizing mass spectrometry data is not straightforward, with an ecosystem full of proprietary vendor software and desktop applications. However, the Wang lab has developed online tools that make data visualization as simple as you'd expect in the modern web experience. Specifically, we have developed tools and infrastructure that enables data exploration in the web browser across all public data with a single click. Imagine how transformative Google Docs is for collaborative and shareable document creation. That is the ambition of the tools we create.
Publications
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 2022, PMID: 34862502. Read it for free here.