Hauptinhalt

Publications

Full publication list, including preprints can be found at Google Scholar

2024

27. Tim Berger, Judith alenfelder, Sophie Steinmüller, DominikHeimann, Namrata Gohain, Daniel Petras, Mingxun Wang Robert Berger, Evi Kostenis, and Raphael Reher^# A MassQL-Integrated Molecular Networking Approach for the Discovery and Substructure Annotation of Bioactive Cyclic Peptides. J. Nat. Prod. (2024)

2023

26. Paolo Stincone, Amira Naimi*, Anthony J. Saviola, Raphael Reher^#, Daniel Petras^# Decoding the Molecular Interplay in the Central Dogma: An Overview of Mass Spectrometry-based Methods to Investigate Protein-Metabolite Interactions. Proteomics (2023) (* Co-first author, # Co-Corresponding author)

25.Mullowney, M.W., Duncan, K.R., Elsayed, S.S. et al. Artificial intelligence for natural product drug discovery. Nat Rev Drug Discov (2023). https://doi.org/10.1038/s41573-023-00774-7 (free access link: https://t1p.de/uz1kf)

24. Kim, H.W., Zhang, C., Reher, R. et al. DeepSAT: Learning Molecular Structures from Nuclear Magnetic Resonance Data. J Cheminform 15, 71 (2023). https://doi.org/10.1186/s13321-023-00738-4

23. Janssen et al (2023) CyanoMetDB 2.0 (Comprehensive database of secondary metabolites from cyanobacteria) DOI: https://zenodo.org/ record/7922070

2022

22. Tiago F Leão, Mingxun Wang, Ricardo da Silva, Alexey Gurevich, Anelize Bauermeister, Paulo Wender P Gomes, Asker Brejnrod, Evgenia Glukhov, Allegra T Aron, Joris J R Louwen, Hyun Woo Kim, Raphael Reher, Marli F Fiore, Justin J J van der Hooft, Lena Gerwick, William H Gerwick, Nuno Bandeira, Pieter C Dorrestein (2022) NPOmix: A machine learning classifier to connect mass spectrometry fragmentation data to biosynthetic gene clusters. PNAS Nexus, 1, 5, pgac257, https://doi.org/10.1093/pnasnexus/pgac257

21. 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, Kyo Bin Kang, Roland D Kersten, Hyunwoo Kim, Riley D. Kirk, Oliver 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, Justin 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 Spectrometry Data Patterns. bioRxiv 2022.08.06.503000; DOI: https://doi.org/10.1101/2022.08.06.503000

20. Raphael Reher, Allegra T. Aron, Pavla Fajtová, Paolo Stincone, Berenike Wagner, Alicia I. Pérez-Lorente, Chenxi Liu, Ido Y. Ben Shalom, Wout Bittremieux, Mingxun Wang, Kyowon Jeong, Marie L. Matos-Hernandez, Kelsey L. Alexander, Eduardo J. Caro-Diaz, C. Benjamin Naman, J. H. William Scanlan, Phil M. M. Hochban, Wibke E. Diederich, Carlos Molina-Santiago, Diego Romero, Khaled A. Selim, Peter Sass, Heike Brötz-Oesterhelt, Chambers C. Hughes, Pieter C. Dorrestein, Anthony J. O’Donoghue,
William H. Gerwick, Daniel Petras (2022) Native Metabolomics Identifies the Rivulariapeptolide Family of Protease Inhibitors. Nature Communications, 13, 4619, DOI: https://doi.org/10.1038/s41467-022-32016-6

19. Arnaud Taton, Sebastian Rohrer, Brienna Diaz, Raphael Reher, Andres Mauricio Caraballo Rodriguez, Marsha L Pierce, Pieter C Dorrestein, Lena Gerwick, William H Gerwick, James W Golden (2022) Heterologous Expression in Anabaena of the Columbamide Pathway from the Cyanobacterium Moorena bouillonii and Production of New Analogs. ACS Chemical Biology, 17, 7, 1910-1923, DOI: https://doi.org/10.1021/acschembio.2c00347

2021

18. Hyun Woo Kim, Mingxun Wang, Christopher A Leber, Louis-Félix Nothias, Raphael Reher, Kyo Bin Kang, Justin JJ Van Der Hooft, Pieter C Dorrestein, William H Gerwick, Garrison W Cottrell (2021) NPClassifier: a deep neural network-based structural classification tool for natural products. Journal of Natural Products, 84, 11, 2795-2807, DOI: https://doi.org/10.1021/acs.jnatprod.1c00399

17. Wiebke Hanke, Julian Patt, Judith Alenfelder, Jan H Voss, Mitja M Zdouc, Stefan Kehraus, Jung Bong Kim, Goran V Grujičić, Vigneshwaran Namasivayam, Raphael Reher, Christa E Müller, Evi Kostenis, Max Crüsemann, Gabriele M König (2021) Feature-Based Molecular Networking for the Targeted Identification of Gq-Inhibiting FR900359 Derivatives. Journal of Natural Products, 84, 7, 1941-1953, DOI: https://doi.org/10.1021/acs.jnatprod.1c00194

16. Michelle A Schorn, Stefan Verhoeven, Lars Ridder, Florian Huber, Deepa D Acharya, Alexander A Aksenov, Gajender Aleti, Jamshid Amiri Moghaddam, Allegra T Aron, Saefuddin Aziz, Anelize Bauermeister, Katherine D Bauman, Martin Baunach, Christine Beemelmanns, J Michael Beman, María Victoria Berlanga-Clavero, Alex A Blacutt, Helge B Bode, Anne Boullie, Asker Brejnrod, Tim S Bugni, Alexandra Calteau, Liu Cao, Víctor J Carrión, Raquel Castelo-Branco, Shaurya Chanana, Alexander B Chase, Marc G Chevrette, Leticia V Costa-Lotufo, Jason M Crawford, Cameron R Currie, Bart Cuypers, Tam Dang, Tristan de Rond, Alyssa M Demko, Elke Dittmann, Chao Du, Christopher Drozd, Jean-Claude Dujardin, Rachel J Dutton, Anna Edlund, David P Fewer, Neha Garg, Julia M Gauglitz, Emily C Gentry, Lena Gerwick, Evgenia Glukhov, Harald Gross, Muriel Gugger, Dulce G Guillén Matus, Eric JN Helfrich, Benjamin-Florian Hempel, Jae-Seoun Hur, Marianna Iorio, Paul R Jensen, Kyo Bin Kang, Leonard Kaysser, Neil L Kelleher, Chung Sub Kim, Ki Hyun Kim, Irina Koester, Gabriele M König, Tiago Leao, Seoung Rak Lee, Yi-Yuan Lee, Xuanji Li, Jessica C Little, Katherine N Maloney, Daniel Männle, Christian Martin H, Andrew C McAvoy, Willam W Metcalf, Hosein Mohimani, Carlos Molina-Santiago, Bradley S Moore, Michael W Mullowney, Mitchell Muskat, Louis-Félix Nothias, Ellis C O’Neill, Elizabeth I Parkinson, Daniel Petras, Jörn Piel, Emily C Pierce, Karine Pires, Raphael Reher, Diego Romero, M Caroline Roper, Michael Rust, Hamada Saad, Carmen Saenz, Laura M Sanchez, Søren Johannes Sørensen, Margherita Sosio, Roderich D Süssmuth, Douglas Sweeney, Kapil Tahlan, Regan J Thomson, Nicholas J Tobias, Amaro E Trindade-Silva, Gilles P van Wezel, Mingxun Wang, Kelly C Weldon, Fan Zhang, Nadine Ziemert, Katherine R Duncan, Max Crüsemann, Simon Rogers, Pieter C Dorrestein, Marnix H Medema, Justin JJ van der Hooft (2021) A community resource for paired genomic and metabolomic data mining. Nature Chemical Biology, 17, 363-368, DOI: https://doi.org/10.1038/s41589-020-00724-z

15. Kai Dührkop, Louis-Félix Nothias, Markus Fleischauer, Raphael Reher, Marcus Ludwig, Martin A Hoffmann, Daniel Petras, William H Gerwick, Juho Rousu, Pieter C Dorrestein, Sebastian Böcker (2021) Systematic classification of unknown metabolites using high-resolution fragmentation mass spectra. Nature Biotechnology, 39, 462-471, DOI: https://doi.org/10.1038/s41587-020-0740-8

14. Tiago Leão, Mingxun Wang, Nathan Moss, Ricardo da Silva, Jon Sanders, Sergey Nurk, Alexey Gurevich, Gregory Humphrey, Raphael Reher, Qiyun Zhu, Pedro Belda-Ferre, Evgenia Glukhov, Syrena Whitner, Kelsey L Alexander, Robert Rex, Pavel Pevzner, Pieter C Dorrestein, Rob Knight, Nuno Bandeira, William H Gerwick, Lena Gerwick (2021) A Multi-Omics Characterization of the Natural Product Potential of Tropical Filamentous Marine Cyanobacteria. Marine Drugs, 19, 1, 20, DOI: https://doi.org/10.3390/md19010020

2020

13. Arnaud Taton, Andrew Ecker, Brienna Diaz, Nathan A Moss, Brooke Anderson, Raphael Reher, Tiago F Leão, Ryan Simkovsky, Pieter C Dorrestein, Lena Gerwick, William H Gerwick, James W Golden (2020) Heterologous Expression of Cryptomaldamide in a Cyanobacterial Host. ACS Synthetic Biology, 9, 12, 3364-3376, DOI: https://doi.org/10.1021/acssynbio.0c00431

12. Markus Kuschak,Vigneshwaran Namasivayam,Muhammad Rafehi,Jan H. Voss,Jaspal Garg,Jonathan G. Schlegel,Aliaa Abdelrahman,Stefan Kehraus,Raphael Reher,Jim Küppers,Katharina Sylvester,Sonja Hinz,Michaela Matthey,Daniela Wenzel,Bernd K. Fleischmann,Alexander Pfeifer,Asuka Inoue,Michael Gütschow,Gabriele M. König,Christa E. Müller (2020) Cell-permeable high-affinity tracers for Gq proteins provide structural insights, reveal distinct binding kinetics and identify small molecule inhibitors. Journal of the British Pharmacological Society, 177, 1898-1916, DOI: https://doi.org/10.1111/bph.14960

11. Raphael Reher*, Hyun Woo Kim*, Chen Zhang*, Huanru Henry Mao, Mingxun Wang, Louis-Félix Nothias, Andres Mauricio Caraballo-Rodriguez, Evgenia Glukhov, Bahar Teke, Tiago Leao, Kelsey L Alexander, Brendan M Duggan, Ezra L Van Everbroeck, Pieter C Dorrestein, Garrison W Cottrell, William H Gerwick(2020) A convolutional neural network-based approach for the rapid annotation of molecularly diverse natural products. Journal of the American Chemical Society, 142, 9, 4114-4120, DOI: https://doi.org/10.1021/jacs.9b13786 (* equal contribution)

2019

10. Paul D Boudreau, Bailey W Miller, Laura-Isobel McCall, Jehad Almaliti, Raphael Reher, Ken Hirata, Thu Le, Jair L Siqueira-Neto, Vivian Hook, William H Gerwick (2019) Design of Gallinamide A Analogs as Potent Inhibitors of the Cysteine Proteases Human Cathepsin L and Trypanosoma cruzi Cruzain. Journal of Medicinal Chemistry, 62, 20, 9026–9044, DOI: https://doi.org/10.1021/acs.jmedchem.9b00294

9. Daniel Tietze, Desireé Kaufmann, Alesia A. Tietze, Andreas Voll, Raphael Reher, Gabriele König, Felix Hausch (2019) Structural and Dynamical Basis of G Protein Inhibition by YM-254890 and FR900359: An Inhibitor in Action. Journal of Chemical Information and Modeling, 59, 10, 4361–4373, DOI: https://doi.org/10.1021/acs.jcim.9b00433

8. Davide Malfacini, Julian Patt, Suvi Annala, Kasper Harpsøe, Funda Eryilmaz, Raphael Reher, Max Cruesemann, Wiebke Hanke, Hang Zhang, Daniel Tietze, David E Gloriam, Hans Bräuner-Osborne, Kristian Strømgaard, Gabriele M Koenig, Asuka Inoue, Jesus Gomeza, Evi Kostenis (2019) Rational design of a heterotrimeric G protein α subunit with artificial inhibitor sensitivity. Journal of Biological Chemistry, 294, 15, 747-5758, DOI: https://doi.org/10.1074/jbc.RA118.007250

7. Suvi Annala, Xiaodong Feng, Naveen Shridhar, Funda Eryilmaz, Julian Patt, JuHee Yang, Eva M Pfeil, Rodolfo Daniel Cervantes-Villagrana, Asuka Inoue, Felix Häberlein, Tanja Slodczyk, Raphael Reher, Stefan Kehraus, Stefania Monteleone, Ramona Schrage, Nina Heycke, Ulrike Rick, Sandra Engel, Alexander Pfeifer, Peter Kolb, Gabriele König, Moritz Bünemann, Thomas Tüting, José Vázquez-Prado, J Silvio Gutkind, Evelyn Gaffal, Evi Kostenis (2019) Direct targeting of Gαq and Gα11 oncoproteins in cancer cells. Science Signaling, 12, 573, DOI: 10.1126/scisignal.aau5948

2018

6. Raphael Reher*, Toni Kühl*, Suvi Annala, Tobias Benkel, Desireé Kaufmann, Britta Nubbemeyer, Justin Patrick Odhiambo, Pascal Heimer, Charlotte Anneke Bäuml, Stefan Kehraus, Max Crüsemann, Evi Kostenis, Daniel Tietze, Gabriele M König, Diana Imhof (2018) Deciphering Specificity Determinants for FR900359‐Derived Gqalpha Inhibitors Based on Computational and Structure–Activity Studies. ChemMedChem, 13,1634 –1643, DOI: https://doi.org/10.1002/cmdc.201800304 (* equal contribution)

5. Raphael Reher, Markus Kuschak, Nina Heycke, Suvi Annala, Stefan Kehraus, Hao-Fu Dai, Christa E Müller, Evi Kostenis, Gabriele M König, Max Crüsemann (2018) Applying molecular networking for the detection of natural sources and analogues of the selective Gq protein inhibitor FR900359. Journal of Natural Products, 81, 7, 1628–1635, DOI: https://doi.org/10.1021/acs.jnatprod.8b00222

4. Manuel Grundmann, Nicole Merten, Davide Malfacini, Asuka Inoue, Philip Preis, Katharina Simon, Nelly Rüttiger, Nicole Ziegler, Tobias Benkel, Nina Katharina Schmitt, Satoru Ishida, Ines Müller, Raphael Reher, Kouki Kawakami, Ayumi Inoue, Ulrike Rick, Toni Kühl, Diana Imhof, Junken Aoki, Gabriele M König, Carsten Hoffmann, Jesus Gomeza, Jürgen Wess, Evi Kostenis (2018) Lack of beta-arrestin signaling in the absence of active G proteins. Nature communications, 9, 341, DOI:10.1038/s41467-017-02661-3

3. Max Crüsemann*, Raphael Reher*, Isabella Schamari, Alexander O Brachmann, Tsubasa Ohbayashi, Markus Kuschak, Davide Malfacini, Alexander Seidinger, Marta Pinto‐Carbó, René Richarz, Tatjana Reuter, Stefan Kehraus, Asis Hallab, Misty Attwood, Helgi B Schiöth, Peter Mergaert, Yoshitomo Kikuchi, Till F Schäberle, Evi Kostenis, Daniela Wenzel, Christa E Müller, Jörn Piel, Aurélien Carlier, Leo Eberl, Gabriele M König (2018) Heterologous Expression, Biosynthetic Studies, and Ecological Function of the Selective Gq-Signaling Inhibitor FR900359. Angewandte Chemie International Edition, 57, 836 –840, DOI:https://doi.org/10.1002/anie.201707996 (* equal contribution)

2016

2. R Reher, I Schamari, S Kehraus, S Annala, M Kuschak, T Schäberle, M Crüsemann, Aurélien Carlier, L Eberl, CE Müller, E Kostenis, GM König (2016) The endophyte Candidatus Burkholderia crenata of the TCM plant Ardisia crenata produces the selective Gq-inhibitor FR900359. Planta Medica 2016; 82(S 01): S1-S381, DOI: 10.1055/s-0036-1596736

1. Aurelien Carlier, Linda Fehr, Marta Pinto‐Carbó, Till Schäberle, Raphael Reher, Steven Dessein, Gabriele König, Leo Eberl (2016) The genome analysis of Candidatus Burkholderia crenata reveals that secondary metabolism may be a key function of the Ardisia crenata leaf nodule symbiosis. Environmental microbiology 18 (8), 2507-2522, DOI: https://doi.org/10.1111/1462-2920.13184