Publications
1. Jeremy K. Chan, William D. Gwynne, Brandon Y. Lieng, Andrew T. Quaile, Chitra Venugopal, Sheila K. Singh, J. Rafael Montenegro-Burke, STAR Protocols, 2023, 4, Protocol for mapping the metabolome and lipidome of medulloblastoma cells using liquid chromatography-mass spectrometry.
2. Brandon Y. Lieng, Andrew T. Quaile, Xavier Domingo-Almenara, Hannes L. Röst, J. Rafael Montenegro-Burke, Analytical Chemistry, 2023, Computational Expansion of High-Resolution-MSn Spectral Libraries.
3. Willliam D. Gwynne, Yujin Suk, Stefan Custers, Nicholas Mikolajewicz, Jeremy K. Chan, Zsolt Zador, Shawn C. Chafe, Cui Zhai, Laura Escudero, Cunjie Zhang, Olga Zaslaver, Chirayu Chokshi, Muhammad Vaseem Shaikh, David Bakhshinyan, Ian Burns, Iqra Chaudhry, Omri Nachmani, Daniel Mobilio, William T. Maich, Patricia Mero, Kevin R. Brown, Andrew T. Quaile, Chitra Venugopal, Jason Moffat, J. Rafael Montenegro-Burke, Sheila K. Singh, Cancer Cell, 2022, 40, 1488-1502, Cancer-selective metabolic vulnerabilities in MYC-amplified medulloblastoma.
4. Sanna N. Masud, Megha Chandrashekhar, Michael Aregger, Guihong Tan, Xiaoyu Zhang, Patricia Mero, David A. Pirman, Olga Zaslaver, Gromoslaw A. Smolen, Zhen-Yuan Lin, Cassandra J. Wong, Charles Boone, Anne-Claude Gingras, J. Rafael Montenegro-Burke, Jason Moffat, Nature Chemical Biology, 2022, 18, 1370–1379, Chemical genomics with pyrvinium identifies C1orf115 as a regulator of drug efflux.
5. Emily Puumala, Olga Zaslaver, Amy Chen, Dustin Duncan, Meea Fogal, Rebecca S. Shapiro, Mohammad T. Mazhab-Jafari, Luke Whitesell, J. Rafael Montenegro-Burke, Nicole Robbins, Leah E. Cowen, mBio, 2022, 13, e02730-22, The tri-substituted isoxazole MMV688766 exerts broad-spectrum activity against drug-resistant fungal pathogens through inhibition of lipid homeostasis.
6. Carlos Guijas, Andrew To, J. Rafael Montenegro-Burke, Xavier Domingo-Almenara, Zaida Alipio-Gloria, Bernard P. Kok, Enrique Saez, Nicole H. Alvarez, Kristen A. Johnson, Gary Siuzdak, Metabolites, 2022, 12, 749, Drug-Initiated Activity Metabolomics Identifies Myristoylglycine as a Potent Endogenous Metabolite for Human Brown Fat Differentiation.
7. J. Rafael Montenegro-Burke, Bernard P. C. Kok, Carlos Guijas, Xavier Domingo-Almenara, Clara Moon, Seiya Kitamura, Enrique Saez, Gary Siuzdak, Dennis W. Wolan, Science Signaling, 2021, 14, eabf6584, Metabolomics activity screening of T cell-induced colitis reveals anti-inflammatory metabolites.
8. Erica L. W. Majumder, Elizabeth M. Billings, H. Paul Benton, Richard L. Martin, Amelia Palermo, Carlos Guijas, Markus M. Rinschen, Xavier Domingo-Almenara, J. Rafael Montenegro-Burke, Bradley A. Tagtow, Robert S. Plumb, Gary Siuzdak, Nature Protocols, 2021, 16, pages1376–1418, Cognitive Analysis of Metabolomics Data for Systems Biology.
9. Carlos Guijas, J. Rafael Montenegro-Burke, Rigo Cintron-Colon, Xavier Domingo-Almenara, Manuel Sanchez-Alavez, Carlos A. Aguirre, Kokila Shankar, Erica L. W. Majumder, Elizabeth Billings, Bruno Conti, Gary Siuzdak, Science Signaling, 2020, 13, eabb2490, Metabolic adaptation to calorie restriction.
10. Xavier Domingo-Almenara, Carlos Guijas, Elizabeth Billings, J. Rafael Montenegro-Burke, Winnie Uritboonthai, Aries E. Aisporna, Emily Chen, H. Paul Benton, Gary Siuzdak, Nature Communications, 2019, 10, 5811, The METLIN small molecule dataset for machine learning-based retention time prediction.
11. Markus M. Rinschen, Oleg Palygin, Carlos Guijas, Amelia Palermo, Nicolas Palacio-Escat, Xavier Domingo-Almenara, J. Rafael Montenegro-Burke, Julio Saez-Rodriguez, Alexander Staruschenko, Gary Siuzdak, Science Signaling, 2019, 12, eaax9760, Metabolic rewiring of the hypertensive kidney.
12. Andrea Galmozzi, Bernard P. Kok, Arthur S. Kim, J. Rafael Montenegro-Burke, Jae Y. Lee, Roberto Spreafico, Sarah Mosure, Verena Albert, Rigo Cintron-Colon, Cristina Godio, William R. Webb, Bruno Conti, Laura A. Solt, Douglas Kojetin, Christopher G. Parker, John J. Peluso, James K. Pru, Gary Siuzdak, Benjamin F. Cravatt, Enrique Saez, Nature, 2019, 576, 138-142, PGRMC2 is an Intracellular Heme Chaperone Critical for Adipocyte Function.
13. Rigo Cintron-Colon, Christopher W. Johnson, J. Rafael Montenegro-Burke, Carlos Guijas, Lila Faulhaber, Manuel Sanchez-Alavez, Carlos A. Aguirre, Kokila Shankar, Mona Singh, Andrea Galmozzi, Gary Siuzdak, Enrique Saez, Bruno Conti, Current Biology, 2019, 29, 1-9, Activation of Kappa Opioid Receptor Regulates the Hypothermic Response to Calorie Restriction and Limits Body Weight Loss.
14. J. Rafael Montenegro-Burke, Christopher J. Woldstad, Mingliang Fang, Aditya N. Bade, JoEllyn McMillan, Benson Edagwa, Michael D. Boska, Howard E. Gendelman, Gary Siuzdak, Molecular Neurobiology, 2019, 56, 2896-2907, Nanoformulated Antiretroviral Therapy Attenuates Brain Metabolic Oxidative Stress.
15. Xavier Domingo-Almenara, J. Rafael Montenegro-Burke, Carlos Guijas, Erica L. W. Majumder, H. Paul Benton, Gary Siuzdak, Analytical Chemistry, 2019, 91, 3246–3253, Autonomous METLIN-guided in-source fragment detection increases annotation confidence in untargeted metabolomics.
16. Carlos Guijas, J. Rafael Montenegro-Burke, Benjamin Warth, Mary E. Spilker, Gary Siuzdak, Metabolomics activity screening for identifying metabolites that modulate phenotype, Nature Biotechnology, 2018, 36, 316-320.
17. Xavier Domingo-Almenara, J. Rafael Montenegro-Burke, Julijana Ivanisevic, Aurelien Thomas, Jonathan Sidibé, Tony Teav, Carlos Guijas, Aries E. Aisporna, Duane Rinehart, Linh Hoang, Anders Nordström, María Gómez-Romero, Luke Whiley, Matthew R. Lewis, Jeremy K. Nicholson, H. Paul Benton, Gary Siuzdak, Nature Methods, 2018, 15, 681–684, XCMS-MRM and METLIN-MRM: a cloud library and public resource for targeted analysis of small molecules.
18. Carlos Guijas, J. Rafael Montenegro-Burke, Xavier Domingo-Almenara, Amelia Palermo, Benedikt Warth, Gerrit Hermann, Gunda Koellensperger, Tao Huan, Winnie Uritboonthai, Aries E. Aisporna, Dennis W. Wolan, Mary E. Spilker, H. Paul Benton, Gary Siuzdak, Analytical Chemistry, 2018, 90, 3156-3164, METLIN: A Technology Platform for Identifying Knowns and Unknowns.
19. Xavier Domingo-Almenara, J. Rafael Montenegro-Burke, Paul H. Benton, Gary Siuzdak, Annotation: A Computational Solution for Streamlining Metabolomics Analysis, Analytical Chemistry, 90, 480-489 (2018).
20. Brittney A. Beyer, Mingliang Fang, Benjamin Sadrian, J. Rafael Montenegro-Burke, Warren C. Plaisted, Bernard P. C. Kok, Enrique Saez, Toru Kondo, Gary Siuzdak, Luke L. Lairson, Nature Chemical Biology, 2018, 14, 22–28, Metabolomics-based discovery of a metabolite that enhances oligodendrocyte maturation.
21. Benedikt Warth, Scott Spangler, Mingliang Fang, Caroline H. Johnson, Erica M. Forsberg, Ana Granados, Richard L. Martin, Xavier Domingo-Almenara, Tao Huan, Duane Rinehart, J. Rafael Montenegro-Burke, Brian Hilmers, Aries Aisporna, Linh T. Hoang, Winnie Uritboonthai, H. Paul Benton, Susan D. Richardson, Antony J. Williams, Gary Siuzdak, Analytical Chemistry, 2017, 89, 11505-11513. Exposome-Scale Investigations Guided by Global Metabolomics, Pathway Analysis, and Cognitive Computing.
22. J. Rafael Montenegro-Burke, Aries E. Aisporna, H. Paul Benton, Duane Rinehart, Mingliang Fang, Tao Huan, Benedikt Warth, Erica Forsberg, Brian T. Abe, Julijana Ivanisevic, Dennis W. Wolan, Luc Teyton, Luke Lairson, Gary Siuzdak, Analytical Chemistry, 2017, 89, 1254-1259, Data Streaming for Metabolomics: Accelerating Data Processing and Analysis from Days to Minutes.
23. J. Rafael Montenegro-Burke, Thiery Phommavongsay, Aries E. Aisporna, Tao Huan, Duane Rinehart, Erica Forsberg, Farris L. Poole, Michael P. Thorgersen, Michael W. W. Adams, Gregory Krantz, Matthew W. Fields, Trent R. Northen, Paul D. Robbins, Laura J. Niedernhofer, Luke Lairson, H. Paul Benton, Gary Siuzdak, Analytical Chemistry, 2016, 88, 9753-9758, Smartphone Analytics: Mobilizing the Lab into the Cloud for Omic-Scale Analyses.
24. Benjamin R. Spears, Michael A. Marin, J. Rafael Montenegro-Burke, Brian C. Evans, John McLean, Eva Harth, Macromolecules, 2016, 49, 2022-2027, Aqueous Epoxide Ring Opening Polymerization (AEROP): Green Synthesis of Poly(glycidol) with Ultra-low Branching.
25. J. Rafael Montenegro-Burke, Jessica A. Sutton, Lisa M. Rogers, Ginger L. Milne, John A. McLean, David M. Aronoff, Prostaglandins & Other Lipid Mediators, 2016, 127, 1-8, Lipid Profiling of Polarized Human Monocyte-derived Macrophages.
26. J. Rafael Montenegro-Burke, Jackson M. Bennet, John A. McLean, David M. Hercules, Analytical and Bioanalytical Chemistry, 2016, 408, 677-681, Novel behavior of the chromatographic separation of linear and cyclic polymers.
27. Connor R. Lamberson, Libin Xu, Hubert Muchalski, J. Rafael Montenegro-Burke, Vadim V. Shmanai, Andrei V. Bekish, John A. McLean, Catherine F. Clarke, Mikhail S. Shchepinov, Ned A. Porter, Journal of the American Chemical Society, 2014, 136, 838-841, Unusual Kinetic Isotope Effects of Deuterium Reinforced Polyunsaturated Fatty Acids in Tocopherol-Mediated Free Radical Chain Oxidations.
28. Gerit Pototschnig, Christian Morales De Csáky, J. Rafael Montenegro-Burke, Georg Schitter, Arnold E. Stütz, Chris A. Tarling, Stephen G. Withers, Tanja M. Wrodnigg, Bioorganic & Medicinal Chemistry Letters, 2010, 20, 4077-4079, Synthesis and biological evaluation of novel biotin–iminoalditol conjugates.
Book Chapter
29. J. Rafael Montenegro-Burke, Carlos Guijas, Gary Siuzdak, In Computational Methods and Data Analysis for Metabolomics, Shuzhao Li (Ed.), Springer Nature: 2020, in the book series Methods in Molecular Biology. “METLIN: A Metabolite Mass Spectral Database”