Fungal Epigenomics and Development

Poinsignon, Thibault, Mélina Gallopin, Pierre Grognet, Fabienne Malagnac, Gaëlle Lelandais, and Pierre Poulain. 2023. “3D Models of Fungal Chromosomes to Enhance Visual Integration of Omics Data.” NAR Genomics and Bioinformatics 5 (4): lqad104. https://doi.org/10.1093/nargab/lqad104.

Lignieres, Laurent, Nicolas Sénécaut, Tien Dang, Laura Bellutti, Marion Hamon, Samuel Terrier, Véronique Legros, et al. 2023. “Extending the Range of SLIM-Labeling Applications: From Human Cell Lines in Culture to Caenorhabditis Elegans Whole-Organism Labeling.” Journal of Proteome Research, February. https://doi.org/10.1021/acs.jproteome.2c00699.

Lelandais, Gaëlle, Damien Remy, Fabienne Malagnac, and Pierre Grognet. 2022. “New Insights into Genome Annotation in Podospora Anserina through Re-Exploiting Multiple RNA-Seq Data.” BMC Genomics 23 (1): 859. https://doi.org/10.1186/s12864-022-09085-4.

Lassagne, Alexandre, Sylvain Brun, Fabienne Malagnac, Henri Adreit, Joëlle Milazzo, Elisabeth Fournier, and Didier Tharreau. 2022. “Male Fertility in Pyricularia Oryzae: Microconidia Are Spermatia.” Environmental Microbiology n/a (n/a). https://doi.org/10.1111/1462-2920.16226.

Eugénie, Nicolas, Yvan Zivanovic, Gaelle Lelandais, Geneviève Coste, Claire Bouthier de la Tour, Esma Bentchikou, Pascale Servant, and Fabrice Confalonieri. 2021. “Characterization of the Radiation Desiccation Response Regulon of the Radioresistant Bacterium Deinococcus Radiodurans by Integrative Genomic Analyses.” Cells 10 (10): 2536. https://doi.org/10.3390/cells10102536.

Carlier, F., M. Li, L. Maroc, R. Debuchy, C. Souaid, D. Noordermeer, P. Grognet, and F. Malagnac. 2021. “Loss of EZH2-like or SU(VAR)3-9-like Proteins Causes Simultaneous Perturbations in H3K27 and H3K9 Tri-Methylation and Associated Developmental Defects in the Fungus Podospora Anserina.” Epigenetics & Chromatin 14 (1): 22. https://doi.org/10.1186/s13072-021-00395-7.

Sénécaut, Nicolas, Gelio Alves, Hendrik Weisser, Laurent Lignières, Samuel Terrier, Lilian Yang-Crosson, Pierre Poulain, Gaëlle Lelandais, Yi-Kuo Yu, and Jean-Michel Camadro. 2021. “Novel Insights into Quantitative Proteomics from an Innovative Bottom-Up Simple Light Isotope Metabolic (BSLIM) Labeling Data Processing Strategy.” Journal of Proteome Research, February. https://doi.org/10.1021/acs.jproteome.0c00478.

Hartmann, Fanny E., S. Lorena Ament-Velásquez, Aaron A. Vogan, Valérie Gautier, Stephanie Le Prieur, Myriam Berramdane, Alodie Snirc, et al. 2021. “Size Variation of the Non-Recombining Region on the Mating-Type Chromosomes in the Fungal Podospora Anserina Species Complex.” Molecular Biology and Evolution, February. https://doi.org/10.1093/molbev/msab040.

Ament-Velásquez, S. Lorena, Hanna Johannesson, Tatiana Giraud, Robert Debuchy, Sven J. Saupe, Alfons J. M. Debets, Eric Bastiaans, et al. 2020. “The Taxonomy of the Model Filamentous Fungus Podospora Anserina.” MycoKeys 75 (November):51–69. https://doi.org/10.3897/mycokeys.75.55968.

Hartmann, Fanny E., Marine Duhamel, Fantin Carpentier, Michael E. Hood, Marie Foulongne‐Oriol, Philippe Silar, Fabienne Malagnac, Pierre Grognet, and Tatiana Giraud. 2020. “Recombination Suppression and Evolutionary Strata around Mating-Type Loci in Fungi: Documenting Patterns and Understanding Evolutionary and Mechanistic Causes.” New Phytologist 229 (5): 2470–91. https://doi.org/https://doi.org/10.1111/nph.17039.

Hadjadj, Djihad, Thomas Denecker, Eva Guérin, Su-Jung Kim, Fabien Fauchereau, Giuseppe Baldacci, Chrystelle Maric, and Jean-Charles Cadoret. 2020. “Efficient, Quick and Easy-to-Use DNA Replication Timing Analysis with START-R Suite.” NAR Genomics and Bioinformatics 2 (2). https://doi.org/10.1093/nargab/lqaa045.

Denecker, Thomas, Youfang Zhou Li, Cécile Fairhead, Karine Budin, Jean-Michel Camadro, Monique Bolotin-Fukuhara, Adela Angoulvant, and Gaëlle Lelandais. 2020. “Functional Networks of Co-Expressed Genes to Explore Iron Homeostasis Processes in the Pathogenic Yeast Candida Glabrata.” NAR Genomics and Bioinformatics 2 (2): lqaa027. https://doi.org/10.1093/nargab/lqaa027.

Sellem, Carole H., Adeline Humbert, and Annie Sainsard-Chanet. 2019. “Mutations in the Phosphatase Domain of the 6-Phosphofructo-2-Kinase/Fructose 2,6-Bisphosphatase Result in the Transcriptional Activation of the Alternative Oxidase and Gluconeogenic Pathways in Podospora Anserina.” Fungal Genetics and Biology 130 (September):1–10. https://doi.org/10.1016/j.fgb.2019.04.005.

Grognet, Pierre, Hélène Timpano, Florian Carlier, Jinane Aït-Benkhali, Véronique Berteaux-Lecellier, Robert Debuchy, Frédérique Bidard, and Fabienne Malagnac. 2019. “A RID-like Putative Cytosine Methyltransferase Homologue Controls Sexual Development in the Fungus Podospora Anserina.” PLoS Genetics 15 (8): e1008086. https://doi.org/10.1371/journal.pgen.1008086.

Lelandais, Gaëlle, Thomas Denecker, Camille Garcia, Nicolas Danila, Thibaut Léger, and Jean-Michel Camadro. 2019. “Label-Free Quantitative Proteomics in Candida Yeast Species: Technical and Biological Replicates to Assess Data Reproducibility.” BMC Research Notes 12 (1): 470. https://doi.org/10.1186/s13104-019-4505-8.

Silar, Philippe, Jean-Marc Dauget, Valerie Gautier, Pierre Grognet, Michelle Chablat, Sylvie Hermann-Le Denmat, Arnaud Couloux, Patrick Wincker, and Robert Debuchy. 2019. “A Gene Graveyard in the Genome of the Fungus Podospora Comata.” Molecular Genetics and Genomics 294 (1): 177–90. https://doi.org/10.1007/s00438-018-1497-3.

Denecker, Thomas, William Durand, Julien Maupetit, Charles Hébert, Jean-Michel Camadro, Pierre Poulain, and Gaëlle Lelandais. 2019. “Pixel: A Content Management Platform for Quantitative Omics Data.” PeerJ 7:e6623. https://doi.org/10.7717/peerj.6623.

Murat, Claude, Thibaut Payen, Benjamin Noel, Alan Kuo, Emmanuelle Morin, Juan Chen, Annegret Kohler, et al. 2018. “Pezizomycetes Genomes Reveal the Molecular Basis of Ectomycorrhizal Truffle Lifestyle.” Nature Ecology & Evolution 2 (12): 1956–65. https://doi.org/10.1038/s41559-018-0710-4.

Ferrari, Roselyne, Isabelle Lacaze, Pauline Le Faouder, Justine Bertrand-Michel, Camille Oger, Jean-Marie Galano, Thierry Durand, et al. 2018. “Cyclooxygenases and Lipoxygenases Are Used by the Fungus Podospora Anserina to Repel Nematodes.” Biochimica Et Biophysica Acta-General Subjects 1862 (10): 2174–82. https://doi.org/10.1016/j.bbagen.2018.07.012.

Lalucque, Hervé, Fabienne Malagnac, Kimberly Green, Valérie Gautier, Pierre Grognet, Laetitia Chan Ho Tong, Barry Scott, and Philippe Silar. 2017. “IDC2 and IDC3, Two Genes Involved in Cell Non-Autonomous Signaling of Fruiting Body Development in the Model Fungus Podospora Anserina.” Developmental Biology 421 (2): 126–38. https://doi.org/10.1016/j.ydbio.2016.12.016.

Nguyen, Tinh-Suong, Hervé Lalucque, Fabienne Malagnac, and Philippe Silar. 2017. “Chapter 5 - Prions and Prion-Like Phenomena in Epigenetic Inheritance.” In Handbook of Epigenetics (Second Edition), edited by Trygve O. Tollefsbol, 61–72. Academic Press. https://doi.org/10.1016/B978-0-12-805388-1.00005-5.

Naruzawa, Erika Sayuri, Fabienne Malagnac, and Louis Bernier. 2016. “Effect of Linoleic Acid on Reproduction and Yeast–Mycelium Dimorphism in the Dutch Elm Disease Pathogens.” Botany 94 (1): 31–39. https://doi.org/10.1139/cjb-2015-0156.

Peraza-Reyes, Leonardo, and Fabienne Malagnac. 2016. “16 Sexual Development in Fungi.” In Growth, Differentiation and Sexuality, edited by Jürgen Wendland, 407–55. Cham: Springer International Publishing. https://doi.org/10.1007/978-3-319-25844-7_16.

Goarin, Anne, Philippe Silar, and Fabienne Malagnac. 2015. “Gene Replacement in Penicillium Roqueforti.” Current Genetics 61 (2): 203–10. https://doi.org/10.1007/s00294-014-0456-8.