Publications
Complete AFMB collection in HAL: here
2025
The FUNG-GROWTH database: linking fungal phenotype to genome
Ronald de Vries, Ad Wiebenga, Guillermo Aguilar Osorio, Maria Victoria Aguilar Pontes, Evy Battaglia, Tiziano Benocci, Isabelle Benoit Gelber, Ourdia Bouzid, Sara Casado Lopez, Nancy Coconi Linares, Alfons Debets, Jan de Jong, Elodie Drula, Daniel Falkoski, Jan Grijpstra, Birgit Gruben, Sylvia Klaubauf, Claire Khosravi, Joanna Kowalczyk, Roland Kun, April Liwanag, Ronnie Lubbers, Eline Majoor, Sakinie Misiedjan, Astrid Müller, Şebnem Ozturkoglu Budak, Aleksandrina Patyshakuliyeva, Diogo Robl, Blanca Trejo-Aguilar, Joost van den Brink, Yoni Visser, Alexandra Vivas-Duarte, Aniek Vugts, Miaomiao Zhou, Mao Peng, Pedro Coutinho, Bernard Henrissat, Vincent Robert
Microbiology Resource Announcements 14:e0037825 (2025)10.1128/mra.00378-25
The Pathophysiological Functions of Heparanases: From Evolution, Structural and Tissue‐Specific Perspectives
Elham Vahdatahar, Clément Daviaud, Hugo Main, Rachel Havret, Claire Debarnot, Laure Favot-Laforge, Jean‐François Jégou, Ingrid Fruitier-Arnaudin, Antoine Dufour, Romain Vivès, Franck Morel, Yves Bourne, Kévin Baranger
FASEB Journal 39 (2025)10.1096/fj.202501859R
Pangeneric analyses reveal the divergent genome evolution and ecologies between morels and truffles in the Morchellaceae
Gregory Bonito, Shingo Miyauchi, Richard Hayes, Hao Tan, Alan Kuo, Aaron Robinson, Xinxin Wang, Jud van Wyk, Annegret Kohler, Laure Fauchery, Elodie Drula, Gian Maria Niccolò Benucci, Emmanuelle Morin, Martin Ryberg, Faheema Kalsoom Khan, Melissa Cravero, Reid Longley, Kerrie Barry, Alicia Clum, Kecia Duffy, Anna Lipzen, Kurt Labutti, Robert Riley, Vasanth Singan, Andrei Steindorff, Jie Wang, Tom Bruns, Sundy Maurice, Philippe Clowez, Saskia Bindschedler, Pilar Junier, Patrick Chain, Igor Grigoriev, Francis Martin
Current Biology 35:4135-4150.e6 (2025)10.1016/j.cub.2025.07.037
Wood decay under anoxia by the brown-rot fungus Fomitopsis pinicola
Robert Röllig, Annie Lebreton, Lucia Grenga, Rosalie Cresswell, Signe Lett, Theodora Tryfona, David Navarro, Julien Lambert, Sacha Grisel, Isabelle Gimbert, Helle Jakobe Martens, Guylaine Miotello, Xiaolan Yu, Elodie Drula, Marie-Noelle Rosso, Lionel Tarrago, Bernard Henrissat, Katja Johansen, Ray Dupree, Jean Armengaud, Paul Dupree, Jean-Guy Berrin
Nature Communications 16:7352 (2025)10.1038/s41467-025-62567-3
Snow- and ice-ecosystem cleaning capability of the pucciniomycotinous yeast Phenoliferia psychrophenolica
Jade Ezzedine, Pierre Guenzi-Tiberi, Gaëlle Villain, Riccardo Aiese Cigliano, Yacine Diagne, Enzo Franceschi, Elodie Drula, Jérôme Forêt, Jean-Gabriel Valay, Lenka Procházková, Daniel Remias, Nicolas Terrapon, Alberto Amato, Eric Maréchal
Communications Biology 8:1084 (2025)10.1038/s42003-025-08506-w
Division of the large and multifunctional glycoside hydrolase family 2: high functional specificity and biochemical assays in the uncharacterized subfamilies
Annie Lebreton, Marie-Line Garron, Marlene Vuillemin, Bo Pilgaard, Bastian Hornung, Elodie Drula, Vincent Lombard, William Helbert, Bernard Henrissat, Nicolas Terrapon
Biotechnology for Biofuels and Bioproducts 18:68 (2025)10.1186/s13068-025-02669-8
A Comparison of the Biotechnological Potential of Marine and Terrestrial Species of Two Orders of Sordariomycete Fungi
Raquel Ledo Doval, Astrid Müller, Daren Brown, Derek Johnson, C Alisha Quandt, Kerrie Barry, Alicia Clum, Hope Hundley, Kurt Labutti, Anna Lipzen, Stephen Mondo, Robin Ohm, Jasmyn Pangilinan, Robert Riley, Andrei Steindorff, Mei Wang, Elodie Drula, Bernard Henrissat, Kathryn Bushley, Joseph Spatafora, Mao Peng, Igor Grigoriev, Ronald de Vries, C. Alisha Quandt
Marine Biotechnology 27:103 (2025)10.1007/s10126-025-10484-3
Whole genome sequence, CAZyme repertoire and sugar metabolic model of the phytopathogenic fungus Kretzschmaria zonata GFP 132
Mariana Regina Almas Do Carmo, Alessia Manassero, Rafaela Zandonade Ventorim, Mao Peng, Tulio Morgan, Kurt Labutti, Anna Lipzen, Steven Ahrendt, Igor Grigoriev, Vivian Ng, Maxin Koriabine, Diane Bauer, Elodie Drula, Bernard Henrissat, Rafael Ferreira Alfenas, Ronald de Vries, Gabriela Piccolo Maitan-Alfenas
Molecular Genetics and Genomics 300:47 (2025)10.1007/s00438-025-02253-7
Dividing the α-amylase family GH57 of starch hydrolases and related enzymes into subfamilies using evolutionary, clustering and functional criteria
Adam Poláček, Vincent Lombard, Pedro Coutinho, Nicolas Terrapon, Štefan Janeček
International Journal of Biological Macromolecules 309:142823 (2025)10.1016/j.ijbiomac.2025.142823
The Holdup Multiplex, an assay for high-throughput measurement of protein-ligand affinity constants using a mass-spectrometry readout
François Delalande, So̷ren Østergaard, Gergő Gógl, Alexandra Cousido-Siah, Alastair G Mcewen, Yushi Men, Farida Salimova, Aurélien Rohrbacher, Camille Kostmann, Yves Nominé, Renaud Vincentelli, Pascal Eberling, Christine Carapito, Gilles Travé, Elodie Monsellier
Journal of the American Chemical Society 147:10886-10902 (2025)10.1101/2022.12.08.519103
A conserved motif in Henipavirus P/V/W proteins drives the fibrillation of the W protein from Hendra virus
Frank Gondelaud, Christophe Bignon, Denis Ptchelkine, Frédéric Carrière, Sonia Longhi
Protein Science 34 (2025)10.1002/pro.70085
Derivatives of MOPS : promising scaffolds for SARS coronaviruses Macro domain‐targeted inhibition
Oney Ortega Granda, Karine Alvarez, Benjamin Morin, Bruno Canard, François Ferron, Nadia Rabah
FEBS Journal (2025)10.1111/febs.70039
Report from the 30th Meeting on Toxinology, "Unlocking the Deep Secrets of Toxins", Organized by the French Society of Toxinology on 2-3 December 2024
Pascale Marchot, Ziad Faljoun, Évelyne Benoit, Sylvie Diochot
Toxins 17:1-31 (2025)10.3390/toxins17020000
A metagenomic ‘dark matter’ enzyme catalyses oxidative cellulose conversion
Clelton Santos, Mariana Morais, Fernanda Mandelli, Evandro Lima, Renan Miyamoto, Paula Higasi, Evandro Araujo, Douglas Paixão, Joaquim Junior, Maria Motta, Rodrigo Streit, Luana Morão, Claudio Silva, Lucia Wolf, Cesar Terrasan, Nathalia Bulka, Jose Diogo, Felipe Fuzita, Felippe Colombari, Camila Santos, Priscila Rodrigues, Daiane Silva, Sacha Grisel, Juliana Bernardes, Nicolas Terrapon, Vincent Lombard, Antonio Filho, Bernard Henrissat, Bastien Bissaro, Jean-Guy Berrin, Gabriela Persinoti, Mario Murakami
Nature (2025)10.1038/s41586-024-08553-z
Bacterial polysaccharide lyase family 33: Specificity from an evolutionarily conserved binding tunnel
Mélanie Loiodice, Elodie Drula, Zak Mciver, Svetlana Antonyuk, Arnaud Baslé, Marcelo Lima, Edwin A Yates, Dominic P Byrne, Jamie Coughlan, Andrew Leech, Shahram Mesdaghi, Daniel Rigden, Sophie Drouillard, William Helbert, Bernard Henrissat, Nicolas Terrapon, Gareth Wright, Marie Couturier, Alan Cartmell
Proceedings of the National Academy of Sciences of the United States of America 122:e2421623122 (2025)10.1073/pnas.2421623122
Functional Carbohydrate-Active Enzymes Acquired by Horizontal Gene Transfer from Plants in the Whitefly Bemisia tabaci
Dominique Colinet, Mireille Haon, Elodie Drula, Mathilde Boyer, Sacha Grisel, Carole Belliardo, Georgios D Koutsovoulos, Jean-Guy Berrin, Etienne G J Danchin
Genome Biology and Evolution 17:evaf012 (2025)10.1093/gbe/evaf012
Comparative genomics of Aspergillus nidulans and section Nidulantes
Sebastian Theobald, Tammi Vesth, Jane L Nybo, Jens C Frisvad, Inge Kjærbølling, Stephen Mondo, Kurt Labutti, Sajeet Haridas, Robert Riley, Alan A Kuo, Asaf A Salamov, Jasmyn Pangilinan, Anna Lipzen, Maxim Koriabine, Mi Yan, Kerrie Barry, Alicia Clum, Ellen K Lyhne, Elodie Drula, Ad Wiebenga, Astrid Müller, Ronnie J M Lubbers, Roland S Kun, Ana Carolina dos Santos Gomes, Miia R Mäkelä, Bernard Henrissat, Blake A Simmons, Jon K Magnuson, Jakob B Hoof, Uffe H Mortensen, Paul S Dyer, Michelle Momany, Thomas O Larsen, Igor V Grigoriev, Scott E Baker, Ronald P de Vries, Mikael R Andersen
Current Research in Microbial Sciences 8:100342 (2025)10.1016/j.crmicr.2025.100342
Section-level genome sequencing and comparative genomics of Aspergillus sections Cavernicolus and Usti
J.L. Nybo, T.C. Vesth, S. Theobald, J.C. Frisvad, T.O. Larsen, I. Kjaerboelling, K. Rothschild-Mancinelli, E.K. Lyhne, K. Barry, A. Clum, Y. Yoshinaga, L. Ledsgaard, C. Daum, A. Lipzen, A. Kuo, R. Riley, S. Mondo, K. Labutti, S. Haridas, J. Pangalinan, A.A. Salamov, B.A. Simmons, J.K. Magnuson, J. Chen, E. Drula, B. Henrissat, A. Wiebenga, R.J.M. Lubbers, A. Müller, A.C. dos Santos Gomes, M.R. Mäkelä, J.E. Stajich, I.V. Grigoriev, U.H. Mortensen, R.P. de Vries, S.E. Baker, Mikael R Andersen
Studies in Mycology 111:101-114 (2025)10.3114/sim.2025.111.03
Nucleotide analogues and mpox: Repurposing the repurposable
Ashleigh Shannon, Bruno Canard
Antiviral Research 234:106057 (2025)10.1016/j.antiviral.2024.106057
C -Branched Iminosugars as Selective Pharmacological Chaperones of Lysosomal α-Glucosidase for the Treatment of Pompe Disease
Anaïs Vieira da Cruz, Valentine Perraudin, Nadia Minopoli, Roberta Iacono, Véronique Roig-Zamboni, Andrea Bossio, Salia Tangara, Martine Fayolle, Alice Kanazawa, Christian Philouze, Antonietta Tarallo, Jurriaan Heming, Marta Artola, Jean-Bernard Behr, Herman Overkleeft, Marco Moracci, Gerlind Sulzenbacher, Giancarlo Parenti, Sandrine Py
Journal of Medicinal Chemistry 68:19269-19286 (2025)10.1021/acs.jmedchem.5c01349
Unraveling the molecular grammar and the structural transitions underlying the fibrillation of a viral fibrillogenic domain
Frank Gondelaud, Julien Leval, Lisha Arora, Anuja Walimbe, Christophe Bignon, Denis Ptchelkine, Stefania Brocca, Samrat Mukhopadyay, Sonia Longhi
Protein Science 34:e70068 (2025)10.1002/pro.70068
CAZac: an activity descriptor for carbohydrate-active enzymes
Vincent Lombard, Bernard Henrissat, Marie-Line Garron
Nucleic Acids Research 53:D625-D633 (2025)10.1093/nar/gkae1045
A coronavirus assembly inhibitor that targets the viral membrane protein
Manon Laporte, Dirk Jochmans, Dorothée Bardiot, Lowiese Desmarets, Oliver Debski-Antoniak, Giulia Mizzon, Rana Abdelnabi, Pieter Leyssen, Winston Chiu, Zhikuan Zhang, Norimichi Nomura, Sandro Boland, Umeharu Ohto, Yannick Stahl, Jurgen Wuyts, Steven de Jonghe, Annelies Stevaert, Martijn van Hemert, Brenda Bontes, Patrick Wanningen, G. Groenewold, Aneta Zegar, Katarzyna Owczarek, Sanjata Joshi, Mohamed Koukni, Philippe Arzel, Hugo Klaassen, Jean-Christophe Vanherck, Ilse Vandecaetsbeek, Niels Cremers, Kim Donckers, Thibault Francken, Tina van Buyten, Jasper Rymenants, Joost Schepers, Krzysztof Pyrc, Rolf Hilgenfeld, Jean Dubuisson, Berend-Jan Bosch, Frank van Kuppeveld, Cecilia Eydoux, Etienne Decroly, Bruno Canard, Lieve Naesens, Birgit Weynand, Eric Snijder, Sandrine Belouzard, Toshiyuki Shimizu, Ralf Bartenschlager, Daniel Hurdiss, Arnaud Marchand, Patrick Chaltin, Johan Neyts
Nature 640:514-523 (2025)10.1038/s41586-025-08773-x
