Zhifen Wang, Emily Giedraitis, Daniel J. Breiner, Christiane Knoop, Vanessa V. Phelan, Francoise Van Bambeke. 2024. Modeling reciprocal adaptation of Staphylococcus aureus and Pseudomonas aeruginosa co-isolates in artificial sputum media. In Revision.

 

Emily Giedraitis*, Rachel L. Neve*, Vanessa V. Phelan#. 2024. Iron content of commercial mucin contributes to compositional stability of a cystic fibrosis airway synthetic microbiota community. BioRxiv. Under Review. 

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Xianghu Wang, Michael Strobel, Allegra Aron, Vanessa V. Phelan, Deepa Acharya, Ken Clevenger, Christopher Brown, Jie Hu, Ashley Kretsch, Elizabeth Mahood, Carla Menegatti, Quanbo Xiong, Mingxun Wang. 2024. Network Topology Evaluation and Transitive Alignments for Molecular Networking. J Am Soc Mass Spectrom. Accepted.

 

Dustin G. Brown, Jonathan Manke, Michael Armstrong, John O. Marentette, James R. Roede, Nichole Reisdorph, Vanessa V. Phelan#. 2024. Impact of Overexpression of Wild-Type CFTR and Elexacaftor-Texacaftor-Ivacaftor on Oxylipin Production by Cystic Fibrosis Bronchial Epithelial Cells. SSRN. Under Review.

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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#. 2024. ModiFinder: Tandem Mass Spectral Alignment Enables Structural Modification Site Localization. J Am Soc Mass Spectrom. Accepted. 

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Rachel L. Neve*, Emily Giedraitis*, Madeline S. Akbari, Shirli Cohen, Vanessa V. Phelan#. 2024. Secondary Metabolite Profiling of Pseudomonas aeruginosa Isolates Reveals Rare Genomic Traits. mSystems. 9(5):e0033924 . 

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Justin N. Jens, Daniel J. Breiner, Rachel L. Neve, Matilda M. Fiebig, Vanessa V. Phelan#. 2023. MBRA-2: A Modified Chemostat System to Culture Biofilm. Microbiology Spectrum. 11(1):e0292822.

 

Christian Jenul, Klara Keim, Justin N. Jens, Michael J. Zeiler, Katrin Schilcher, Michael Schurr, Christian Melander, Vanessa V. Phelan#, Alexander R. Horswill#. 2023. Pyochelin Biotransformation by Staphylococcus aureus shapes bacterial competition with Pseudomonas aeruginosa in Polymicrobial Infections. Cell Rep. 42(6):112540.

 

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.

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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.

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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.

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

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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. 

 

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. 

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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. 

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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. 

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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.

 

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. 

 

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. 

 

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.

 

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.

 

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.

 

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.

 

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.

 

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.

  

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.

 

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. 

 

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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.

 

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.

 

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

 

#Denotes corresponding author. *Denotes equal contribution

 

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