PUBLICATIONS

Justin N. Jens, Daniel J. Breiner, Rachel L. Neve, Matilda M. Fiebig, Vanessa V. Phelan#. 2022. Modification of the MiniBioreactor Array (MBRA) design to create MBRA-2. Microbiology Spectrum. Under review. 

 

Christian Jenul, Klara Keim, Justin N. Jens, Michael J. Zeiler, Katrin Schilcher, Michael Schurr, Christian Melander, Vanessa V. Phelan#, Alexander R. Horswill. 2022. Pyochelin biotransformation shapes bacterial competitionbioRxiv.

 

Alan K. Jarmusch, Allegra T. Aron, Daniel Petras,  Vanessa V. Phelan,  Wout Bittremieux, Deepa D. Acharya, Mohammed M. A. Ahmed, Anelize Bauermeister, Matthew J. Bertin, Paul D. Boudreau, Ricardo M. Borges, Benjamin P. Bowen, Christopher J. Brown, Fernanda O. Chagas, Kenneth D. Clevenger, Mario S. P. Correia, William J. Crandall, Max Crüsemann, Tito Damiani, Oliver Fiehn, Neha Garg, William H Gerwick, Jeffrey R. Gilbert, Daniel Globisch, Paulo Wender P. Gomes, Steffen Heuckeroth, C. Andrew James, Scott A. Jarmusch, Sarvar A. Kakhkhorov,  VKyo Bin Kang, Roland D. Kersten, Hyunwoo Kim, Riley D. Kirk,  View ORCID ProfileOliver Kohlbacher, Eftychia E. Kontou, Ken Liu, Itzel Lizama-Chamu, Gordon T. Luu, Tal Luzzatto Knaan,  Michael T. Marty, Andrew C. McAvoy, Laura-Isobel McCall, Osama G. Mohamed, Omri Nahor, Timo H.J. Niedermeyer, Trent R. Northen, Kirsten E. Overdahl, Tomáš Pluskal, Johannes Rainer, Raphael Reher, Elys Rodriguez, Timo T. Sachsenberg, Laura M. Sanchez, Robin Schmid, Cole Stevens, Zhenyu Tian, Ashootosh Tripathi, Hiroshi Tsugawa, Kozo Nishida, Yuki Matsuzawa,  VJustin J.J. van der Hooft, Andrea Vicini, Axel Walter,  Tilmann Weber, Quanbo Xiong, Tao Xu, Haoqi Nina Zhao, Pieter C. Dorrestein,  Mingxun Wang. 2022. A universal language for finding mass spectormetry data patterns. bioRxiv.

 

Justin N. Jens, Daniel J. Breiner, Vanessa V. Phelan#. 2022. Spray-based application of matrix to agar-based microbial samples for reproducible sample adherence in MALDI MSI. J Am Soc Mass Spectrom. 33(4):731-734.

 

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 Jr., 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. 2022. GNPS Dashboard: collaborative exploration of mass spectrometry data in the web browser. Nat Methods. 19(2):134-136.

George A. O'Toole, Aurélie Crabbé, Rolf Kümmerli, John J. LiPuma, Jennifer M. Bomberger, Jane C. Davies, Dominique Limoli, Vanessa V. Phelan, James B. Bliska, William H. DePas, Lars E. Dietrich, Thomas H. Hampton, Ryan Hunter, Cezar M. Khursigara, Alexa Price-Whelan, Alix Ashare, Robert A. Cramer, Joanna B. Goldberg, Freya Harrison, Deborah A. Hogan, Michael A. Henson, Dean R. Madden, Jared R. Mayers, Carey Nadell, Dianne Newman, Alice Prince, Damian W. Rivett, Joseph D. Schwartzman, Daniel Schultz, Donald C. Sheppard, Alan R. Smyth, Melanie A. Spero, Bruce A. Stanton, Paul E. Turner, Chris van der Gast, Fiona J. Whelan, Rachel Whitaker, Katrine Whiteson. 2021. Model systems to study the chronic, polymicrobial infections in Cystic Fibrosis: current approaches and exploring future directions. mBio. 12(5):e0176321.

Rachel L Neve, Brent D Carillo, Vanessa V. Phelan#. 2021. Impact of Artificial Sputum Medium formulation on Pseudomonas aeruginosa secondary metabolite production. J. Bacteriol. 203(21):e0025021

 

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. 2020. Feature-based molecular networking in the GNPS analysis environment. Nat Methods. 17(9):905-908. 32839597​

 

Courtney E. Price, Dustin G. Brown, Dominique H. Limoli, Vanessa V. Phelan, George A. O'Toole. 2020. Exogenous Alginate Protects Staphylococcus aureus from Killing by Pseudomonas aeruginosa. J Bacteriol. 202(8):e00559-19. PMID: 31792010

Vanessa V. Phelan. 2020. Feature-Based Molecular Networking for Metabolite Annotation. Methods Mol Biol. 2104:227-243. PMID: 31953821

Jon G. Sanders, Sergey Nurk, Rodolfo A. Salido, Jeremiah Minich, Zhenjiang Z. Xu, Qiyun Zhu, Cameron Martino, Marcus Fedarko, Timothy D. Arthur, Feng Chen, Brigid S. Boland, Greg C. Humphrey, Caitriona Brennan, Karenina Sanders, James Gaffney, Kristen Jepsen, Mahdieh Khosroheidari, Cliff Green, Marlon Liyanage, Jason W. Dang, Vanessa V. Phelan, Robert A. Quinn, Anton Bankevich, John T. Chang, Tariq M. Rana, Douglas J. Conrad, William J. Sandborn, Larry Smarr, Pieter C. Dorrestein, Pavel A. Pevzner, Rob Knight. 2019. Optimizing sequencing protocols for leaderboard metagenomics by combining long and short reads. Genome Biol. 20(1):226. PMID: 31672156

 

Michael Shaffer, Abigail J. S. Armstrong, Vanessa V. Phelan, Nichole Reisdorph, Catherine A. Lozupone. 2017. Microbiome and Metabolome Data Integration Provides Insight Into Health and Disease. Transl Res. 189: 51-64. PMID: 28764956

Neha Garg*, Tal Luzzatto-Knaan, Alexey V. Melnik, Andrés Mauricio Caraballo-Rodríguez, Dimitrios J. Floros, Daniel Petras, Rachel Gregor, Pieter C. Dorrestein#, Vanessa V. Phelan*#. 2017. Natural Products as Mediators of Disease. Nat Prod Rep. 34(2): 194-219. PMID: 27874907

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 Ø. Palsson, Kit Pogliano, Roger G. Linington, Marcelino Gutiérrez, Norberto P. Lopes, William H. Gerwick, Bradley S. Moore, Pieter C. Dorrestein, Nuno Bandeira. 2016. Sharing and Community Curation of Mass Spectrometry Data with Global Natural Products Social Molecular Networking. Nat Biotechnol. 34(8): 828-837. PMID: 27504778

Robert A. Quinn, Vanessa V. Phelan, Katrine L. Whiteson, Neha Garg, Barbara A. Bailey, Yan Wei Lim, Douglas J. Conrad, Pieter C. Dorrestein, Forest L. Rohwer. 2016.   Microbial, Host and Xenobiotic Diversity in the Cystic Fibrosis Sputum Metabolome. The ISME Journal. 10(6):1483-1498. PMID: 26623545

 

Vanessa V. Phelan#, Jinshu Fang, Pieter C. Dorrestein. 2015. Mass Spectrometry Analysis of Pseudomonas aeruginosa Treated With Azithromycin. J. Am. Soc. Mass. Spec. 26(6): 873-877. PMID: 25801585

 

Vanessa V. Phelan, Wilna J. Moree, Julieta Aguilar, Dale S. Cornett, Alexandra Koumoutsi, Suzanne M. Noble, Kit Pogliano, Carlos A. Guerrero, Pieter C. Dorrestein. 2014. The Impact of a Transposon Insertion in phzF2 on the Specialized Metabolite Production and Interkingdom Interactions of Pseudomonas aeruginosa. J. Bacteriol. 196(9): 1683-1693. PMID: 24532776

 

Don D. Nguyen, Cheng-Hsuan Wu, Wilna J. Moree, Anne Lamsa, Marnix H. Medema, Xiling Zhao, Ronnie G. Gavilan, Marystella Aparicio, Librada Atencio, Chanaye Jackson, Javier Ballesteros, Joel Sanchez, Jeramie D. Watrous, Vanessa V. Phelan, Corine van de Wiel, Roland D. Kersten, Samina Mehnaz, René De Mot, Elizabeth A. Shank, Pep Charusanti, Harish Nagarajan, Brendan M. Duggan, Bradley S. Moore, Nuno Bandeira,  Bernhard Ø. Palsson, Kit Pogliano, Marcelino Gutiérrez, Pieter C. Dorrestein. 2013. MS/MS Networking Guided Discovery of Molecule and Gene Cluster Families. PNAS. 110(28): E2611-2620. PMID:23798442

 

Jeramie Watrous*, Vanessa V. Phelan*, Cheng-Chih Hsu*, Wilna Moree, Brendan M. Duggan, Theodore Alexandrov, Pieter C. Dorrestein. 2013. Microbial Metabolic Exchange in 3D. The ISME Journal. 7(4): 770-780. PMID: 23283018

 

Wilna J. Moree, Vanessa V. Phelan, Cheng-Hsuan Wu, Nuno Bandeira, Dale S. Cornett, Brendan M. Duggan, Pieter C. Dorrestein. 2012. Interkingdom metabolic transformations caputured by microbial imaging mass spectrometry. Proc Natl Acad Sci USA, 109(34): 13811-13816. PMID: 22869730

 

Jane Y. Yang, Vanessa V. Phelan, Ryan Simkovsky, Jeramie D. Watrous, Rachel M. Trial, Tinya C. Fleming, Roland Wenter, Bradley S. Moore, Susan S. Golden, Kit Pogliano, Pieter C. Dorrestein. 2012. Primer on agar-based microbial imaging mass spectrometry. J. Bacteriol. 192(22): 6023-6028. PMID: 22821974

 

Vanessa V. Phelan*, Wei-Ting Liu*, Kit Pogliano, Pieter C. Dorrestein. 2012. Microbial metabolic exchange-the chemotype-to-phenotype link. Nat Chem Biol. 8(1): 26-35. PMID: 22173357

 

Timothy D. Panosian, David P. Nannemann, Guy Watkins, Vanessa V. Phelan, W. Hayes McDonald, Brian E. Wadzinski, Brian O. Bachmann, T.M. Iverson. 2011. The Bacillus cereus phosphopentomutase is an alkaline phosphatase family member that exhibits an altered entry point in the catalytic cycle.  J. Biol. Chem.  286(10): 8043-8054. PMID: 21193409

  

Melissa D. Carter, Vanessa V. Phelan, R.D. Sandlin, Brian O. Bachmann, David W. Wright. 2010. Lipophilic Mediated Assays for beta-Hematin Inhibitors. Combinatorial Chemistry & High Through-put Screening. 13(3): 285-292. PMID: 20230372

 

Vanessa V. Phelan, Yu Du, John A. McLean, Brian O. Bachmann. 2009. Adenylation Enzyme Characterization Using gamma-18O4-ATP Pyrophosphate Exchange. Chemistry & Biology, 16(5):473-478. PMID: 19477411

 

Yunfeng Hu, Vanessa V. Phelan, Chris M. Farnet, Emmanuel Zazopoulos, Brian O. Bachmann. 2008. Reassembly of Anthramycin Biosynthetic Gene Cluster Using Recombinogenic Cassettes. ChemBioChem, 9(10): 1603-1608. PMID: 18512205

 

Yunfeng Hu, Vanessa Phelan, Ioanna Ntai, Chris M. Farnet, Emmanuel Zazopoulos, Brian O. Bachmann. 2007. Benzodiazepine biosynthesis in Streptomyces refuineus. Chemistry & Biology, 14(6):691-701. PMID: 17584616

 

Ioanna Ntai, Vanessa V. Phelan, Brian O. Bachmann. 2006. Phosphonopeptide K-26 Intermediates in Astrosporangium Hypotensionis. Chemical Communications, (43):4518-4520. PMID: 17283804

 

#Denotes corresponding author. *Denotes equal contribution

 

For the most up-to-date list of publications, please see: google scholar or Pubmed