Abhishek Dutta, Fabien Dutreux, Marion Garin, Claudia Caradec, Anne Friedrich, Gauthier Brach, Pia Thiele, Maxime Gaudin, Bertrand Llorente, Joseph Schacherer.
Multiple independent losses of crossover interference during yeast evolutionary history.
PLOS Genetics.
DOI: 10.1371/journal.pgen.1011426 (2024).

Victor Loegler, Anne Friedrich, Joseph Schacherer.
Preprint: Overview of the Saccharomyces cerevisiae population structure through the lens of 3,034 genomes.
DOI: 10.1101/2024.09.16.613241 (2024).

Julia Muenzner, Pauline Trébulle, Federica Agostini, Henrik Zauber, Christoph B. Messner, Martin Steger, Christiane Kilian, Kate Lau, Natalie Barthel, Andrea Lehmann, Kathrin Textoris-Taube, Elodie Caudal, Anna-Sophia Egger, Fatma Amari, Matteo De Chiara, Vadim Demichev, Toni I. Gossmann, Michael Mülleder, Gianni Liti, Joseph Schacherer, Matthias Selbach, Judith Berman & Markus Ralser.
Natural proteome diversity links aneuploidy tolerance to protein turnover.
Nature.
DOI: 10.1038/s41586-024-07442-9 (2024).

Élodie Caudal, Victor Loegler, Fabien Dutreux, Nikolaos Vakirlis, Élie Teyssonnière, Claudia Caradec, Anne Friedrich, Jing Hou, Joseph Schacherer.
Pan-transcriptome reveals a large accessory genome contribution to gene expression variation in yeast.
Nature Genetics.
DOI: 10.1038/s41588-024-01769-9 (2024).

Elie Marcel Teyssonnière, Pauline Trébulle, Julia Muenzner, Victor Loegler, Daniela Ludwig, Fatma Amari, Michael Mülleder, Anne Friedrich, Jing Hou, Markus Ralser, Joseph Schacherer.
Species-wide quantitative transcriptomes and proteomes reveal distinct genetic control of gene expression variation in yeast.
PNAS.
DOI: 10.1073/pnas.2319211121 (2024).

Sylvain Legrand*, Asma Saifudeen*, Helene Bordelet, Julien Vernerey, Arnaud Guille, Amaury Bignaut, Agnes Thierry, Laurent Acquaviva, Maxime Gaudin, Aurore Sanchez, Dominic Johnson, Anne Friedrich, Joseph Schacherer, Matthew Neale, Valerie Borde, Romain Koszul, Bertrand Llorente.
Absence of chromosome axis proteins recruitment prevents meiotic recombination chromosome-wide in the budding yeast Lachancea kluyveri.
PNAS.
DOI: 10.1073/pnas.2312820121 (2024).

Andreas Tsouris*, Gauthier Brach*, Anne Friedrich, Jing Hou, Joseph Schacherer.
Diallel panel reveals a significant impact of low-frequency genetic variants on gene expression variation in yeast.
Molecular Sytems Biology.
DOI: 10.1038/s44320-024-00021-0 (2024).

Elie M. Teyssonniere, Yuichi Shichino, Anne Friedrich, Shintaro Iwasaki, Joseph Schacherer.
Translation variation across genetic backgrounds reveals a post-transcriptional buffering signature in yeast.
Nucleid Acids Research.
DOI: 10.1093/nar/gkae030 (2024).

Andreas Tsouris, Téo Fournier, Anne Friedrich, Jing Hou, Maitreya J. Dunham, Joseph Schacherer.
Species-wide survey of the expressivity and complexity spectrum of traits in yeast.
PLOS Genetics.
DOI: 10.1371/journal.pgen.1011119 (2024).

Andreas Tsouris, Gauthier Brach, Joseph Schacherer, Jing Hou.
Non-additive genetic components contribute significantly to population-wide gene expression variation.
Cell Genomics.
DOI: 10.1016/j.xgen.2023.100459 (2023).

Samuel O’Donnell, Jia-Xing Yue, Omar Abou Saada, Nicolas Agier, Claudia Caradec, Thomas Cokelaer, Matteo De Chiara, Stéphane Delmas, Fabien Dutreux, Téo Fournier, Anne Friedrich, Etienne Kornobis, Jing Li, Zepu Miao, Lorenzo Tattini, Joseph Schacherer, Gianni Liti, Gilles Fischer.
Telomere-to-telomere assemblies of 142 strains characterize the genome structural landscape in Saccharomyces cerevisiae.
Nature Genetics.
DOI: 10.1038/s41588-023-01459-y (2023).

Arthur Jallet, Anne Friedrich, Joseph Schacherer.
Impact of the acquired subgenome on the transcriptional landscape in Brettanomyces bruxellensis allopolyploids.
G3 Genes|Genomes|Genetics.
DOI: 10.1093/g3journal/jkad115 (2023).

Anne Friedrich, Jean-Sébastien Gounot, Andreas Tsouris, Claudine Bleykasten, Kelle Freel, Claudia Caradec, Joseph Schacherer.
Contrasting genomic evolution between domesticated and wild Kluyveromyces lactis yeast populations.
Genome Biology and Evolution.
DOI: 10.1093/gbe/evad004 (2023).

Fabien Dutreux*, Abhishek Dutta*, Emilien Peltier*, Sabrina Bibi-Triki, Anne Friedrich, Bertrand Llorente, Joseph Schacherer.
Lessons from the meiotic recombination landscape of the ZMM deficient budding yeast Lachancea waltii.
PLOS Genetics.
DOI: 10.1371/journal.pgen.1010592 (2023).

Grace Avecilla, Pieter Spealman, Julia Matthews, Elodie Caudal, Joseph Schacherer, David Gresham.
Copy number variants alter local and global mutational tolerance.
Genome Research.
DOI: 10.1101/gr.277625.122 (2022).

Abhishek Dutta, Fabien Dutreux, Joseph Schacherer.
Loss of Heterozygosity Spectrum Depends on Ploidy Level in Natural Yeast Populations.
Molecular Biology and Evolution.
DOI: 10.1093/molbev/msac214 (2022).

Elodie Caudal, Anne Friedrich, Arthur Jallet, Marion Garin, Jing Hou, Joseph Schacherer.
Loss-of-function mutation survey revealed that genes with background-dependent fitness are rare and functionally related in yeast.
Proceedings of the National Academy of Sciences (PNAS).
DOI: 10.1073/pnas.2204206119 (2022).

Jackson Peter, Anne Friedrich, Gianni Liti, Joseph Schacherer.
Extensive simulations assess the performance of genome-wide association mapping in various Saccharomyces cerevisiae subpopulations.
Philosophical Proceedings of the Royal Society B.
DOI: 10.1098/rstb.2020.0514 (2022).

Andreas Tsouris, Joseph Schacherer, Olena P. Ishchuk.
RNA Interference (RNAi ) as a Tool for High-Resolution Phenotypic Screening of the Pathogenic Yeast Candida glabrata.
Yeast Functional Genomics. Methods in Molecular Biology, vol 2477, Humana Press, 2022..
DOI: 10.1007/978-1-0716-2257-5_18 (2022).

Omar Abou Saada, Anne Friedrich, Joseph Schacherer.
Towards accurate, contiguous and complete alignment-based polyploid phasing algorithms.
Genomics.
DOI: 10.1016/j.ygeno.2022.110369 (2022).

Omar Abou Saada, Andreas Tsouris, Chris Large, Anne Friedrich, Maitreya J. Dunham, Joseph Schacherer.
Phased polyploid genomes provide deeper insight into the multiple origins of domesticated Saccharomyces cerevisiae beer yeasts.
Current Biology.
DOI: 10.1016/j.cub.2022.01.068 (2022).

Jules Harrouard, Chris Eberlein, Patricia Ballestra, Marguerite Dols-Lafargue, Isabelle Masneuf-Pomarede, Cécile Miot-Sertier, Joseph Schacherer, Warren Albertin.
Brettanomyces bruxellensis: Overview of the genetic and phenotypic diversity of an anthropized yeast.
Molecular Ecology.
DOI: 10.1111/mec.16439 (2022).

Matteo De Chiara, Benjamin P. Barré, Karl Persson, Agurtzane Irizar, Chiara Vischioni, Sakshi Khaiwal, Simon Stenberg, Onyetugo Chioma Amadi, Gašper Žun, Katja Doberšek, Cristian Taccioli, Joseph Schacherer, Uroš Petrovič, Jonas Warringer, Gianni Liti.
Domestication reprogrammed the budding yeast life cycle.
Nature Ecology & Evolution.
DOI: 10.1038/s41559-022-01671-9 (2022).

Chris Eberlein, Omar Abou Saada, Anne Friedrich, Warren Albertin and Joseph Schacherer.
Different trajectories of polyploidization shape the genomic landscape of the Brettanomyces bruxellensis yeast species.
Genome Research.
DOI: 10.1101/gr.275380.121 (2021).

Ioannis A. Papaioannou, Fabien Dutreux, France A. Peltier, Hiromi Maekawa, Nicolas Delhomme, Amit Bardhan, Anne Friedrich, Joseph Schacherer & Michael Knop.
Sex without crossing over in the yeast Saccharomycodes ludwigii.
Genome Biology.
DOI: 10.1186/s13059-021-02521-w (2021).

Emilien Peltier, Charlotte Vion, Omar Abou Saada, Anne Friedrich, Joseph Schacherer and Philippe Marullo.
Flor Yeasts Rewire the Central Carbon Metabolism During Wine Alcoholic Fermentation.
Frontiers in Fungal Biology.
DOI: 10.3389/ffunb.2021.733513 (2021).

Emilien Peltier, Sabrina Bibi-Triki, Fabien Dutreux, Claudia Caradec, Anne Friedrich, Bertrand Llorente, Joseph Schacherer.
Dissection of quantitative trait loci in the Lachancea waltii yeast species highlights major hotspots.
G3 Genes|Genomes|Genetics.
DOI: 10.1093/g3journal/jkab242 (2021).

Abhishek Dutta, Fabien Dutreux, Joseph Schacherer.
Loss of heterozygosity results in rapid but variable genome homogenization across yeast genetic backgrounds.
eLife.
DOI: 10.7554/eLife.70339 (2021).

Claudine Bleykasten-Grosshans, Romeo Fabrizio, Anne Friedrich, Joseph Schacherer.
Species-Wide Transposable Element Repertoires Retrace the Evolutionary History of the Saccharomyces cerevisiae Host.
Molecular Biology and Evolution.
DOI: doi.org/10.1093/molbev/msab171 (2021).

Omar Abou Saada, Andreas Tsouris, Chris Eberlein, Anne Friedrich & Joseph Schacherer .
nPhase: an accurate and contiguous phasing method for polyploids.
Genome Biology.
DOI: 10.1186/s13059-021-02342-x (2021).

Chiann-Ling C. Yeh, Andreas Tsouris, Joseph Schacherer, Maitreya J. Dunham.
Preprint: High-throughput functional analysis of natural variants in yeast. (2021).

Melania D’Angiolo, Matteo De Chiara, Jia-Xing Yue, Agurtzane Irizar, Simon Stenberg, Karl Persson, Agnès Llored, Benjamin Barré, Joseph Schacherer, Roberto Marangoni, Eric Gilson, Jonas Warringer & Gianni Liti.
A yeast living ancestor reveals the origin of genomic introgressions.
Nature.
DOI: 10.1038/s41586-020-2889-1 (2020).

Hayley R Stoneman, Russell L Wrobel, Michael Place, Michael Graham, David J Krause, Matteo De Chiara, Gianni Liti, Joseph Schacherer, Robert Landick, Audrey P Gasch, Trey K Sato, Chris Todd Hittinger.
CRISpy-Pop: A Web Tool for Designing CRISPR/Cas9-Driven Genetic Modifications in Diverse Populations .
G3 Genes|Genomes|Genetics.
DOI: 10.1534/g3.120.401498 (2020).

Christopher R. L. Large, Noah Hanson, Andreas Tsouris, Omar Abou Saada, Jirasin Koonthongkaew, Yoichi Toyokawa, Tom Schmidlin, Daniela A. Moreno-Habel, Hal McConnellogue, Richard Preiss, Hiroshi Takagi, Joseph Schacherer, Maitreya J. Dunham.
Preprint: Genomic stability and adaptation of beer brewing yeasts during serial repitching in the brewery. (2020).

Matteo De Chiara, Anne Friedrich, Benjamin Barré, Michael Breitenbach, Joseph Schacherer & Gianni Liti.
Discordant evolution of mitochondrial and nuclear yeast genomes at population level.
BMC Biology.
DOI: 10.1186/s12915-020-00786-4 (2020).

Christian Brion, Claudia Caradec, David Pflieger, Anne Friedrich, Joseph Schacherer.
Pervasive Phenotypic Impact of a Large Nonrecombining Introgressed Region in Yeast.
Molecular Biology and Evolution.
DOI: 10.1093/molbev/msaa101 (2020).

Jean-Sébastien Gounot, Cécile Neuvéglise, Kelle C Freel, Hugo Devillers, Jure Piškur, Anne Friedrich, Joseph Schacherer.
High Complexity and Degree of Genetic Variation in Brettanomyces bruxellensis Population.
Molecular Biology and Evolution.
DOI: 10.1093/gbe/evaa077 (2020).

Téo Fournier, Omar Abou Saada, Jing Hou, Jackson Peter, Elodie Caudal, Joseph Schacherer.
Extensive impact of low-frequency variants on the phenotypic landscape at population-scale.
eLife.
DOI: 10.7554/eLife.49258 (2019).

Quentin Defenouillère, Agathe Verraes, Clotilde Laussel, Anne Friedrich, Joseph Schacherer & Sébastien Léon.
The induction of HAD-like phosphatases by multiple signaling pathways confers resistance to the metabolic inhibitor 2-deoxyglucose.
Science Signaling.
DOI: 10.1126/scisignal.aav9783 (2019).

Aubin Fleiss, Samuel O'Donnell, Téo Fournier, Wenqing Lu, Nicolas Agier, Stéphane Delmas, Joseph Schacherer, Gilles Fischer.
Reshuffling yeast chromosomes with CRISPR/Cas9.
PLoS Genetetics.
DOI: 10.1371/journal.pgen.1008332 (2019).

Olena P. Ishchuk, Khadija Mohamed Ahmad, Katarina Koruza, Klara Bojanovič, Marcel Sprenger, Lydia Kasper, Sascha Brunke, Bernhard Hube, Torbjörn Säll, Thomas Hellmark, Birgitta Gullstrand, Christian Brion, Kelle Freel, Joseph Schacherer, Birgitte Regenberg, Wolfgang Knecht and Jure Piškur.
RNAi as a Tool to Study Virulence in the Pathogenic Yeast Candida glabrata.
Frontiers Microbiology.
DOI: 10.3389/fmicb.2019.01679 (2019).

Emilien Peltier, Anne Friedrich, Joseph Schacherer and Philippe Marullo.
Quantitative Trait Nucleotides Impacting the Technological Performances of Industrial Saccharomyces cerevisiae Strains.
Frontiers in Genetics.
DOI: 10.3389/fgene.2019.00683 (2019).

Cécile Fairhead, Gilles Fischer, Gianni Liti, Cécile Neuvéglise, Joseph Schacherer.
André Goffeau's imprinting on second generation yeast “genomologists”.
Yeast.
DOI: 10.1002/yea.3377 (2019).

Vandana Raghavan, Duyen T Bui, Najla Al-Sweel, Anne Friedrich, Joseph Schacherer, Charles F Aquadro, Eric Alani.
Incompatibilities in Mismatch Repair Genes MLH1-PMS1 Contribute to a Wide Range of Mutation Rates in Human Isolates of Baker’s Yeast.
Genetics.
DOI: 10.1534/genetics.118.301550 (2018).

Jackson Peter, Matteo De Chiara, Anne Friedrich, Jia-Xing Yue, David Pflieger, Anders Bergström, Anastasie Sigwalt, Benjamin Barre, Kelle Freel, Agnès Llored, Corinne Cruaud, Karine Labadie, Jean-Marc Aury, Benjamin Istace, Kevin Lebrigand, Pascal Barbry, Stefan Engelen, Arnaud Lemainque, Patrick Wincker, Gianni Liti & Joseph Schachere.
Genome evolution across 1,011 Saccharomyces cerevisiae isolates.
Nature.
DOI: 10.1038/s41586-018-0030-5 (2018).

Marta Avramova, Alice Cibrario, Emilien Peltier, Monika Coton, Emmanuel Coton, Joseph Schacherer, Giuseppe Spano, Vittorio Capozzi, Giuseppe Blaiotta, Franck Salin, Marguerite Dols-Lafargue, Paul Grbin, Chris Curtin, Warren Albertin & Isabelle Masneuf-Pomarede .
Brettanomyces bruxellensis population survey reveals a diploid-triploid complex structured according to substrate of isolation and geographical distribution.
Scientific Reports.
DOI: 10.1038/s41598-018-22580-7 (2018).

Téo Fournier, Jean-Sébastien Gounot, Kelle Freel, Corinne Cruaud, Arnaud Lemainque, Jean-Marc Aury, Patrick Wincker, Joseph Schacherer, Anne Friedrich.
High-Quality de Novo Genome Assembly of the Dekkera bruxellensis Yeast Using Nanopore MinION Sequencing.
G3 Genes|Genomes|Genetics.
DOI: 10.1534/g3.117.300128 (2017).

Téo Fournier, Joseph Schacherer.
Genetic backgrounds and hidden trait complexity in natural populations.
Current Opinion in Genetics & Development.
DOI: 10.1016/j.gde.2017.08.009 (2017).

Caiti Smukowski Heil, Joshua N. Burton, Ivan Liachko, Anne Friedrich, Noah A. Hanson, Cody L. Morris, Joseph Schacherer, Jay Shendure, James H. Thomas, Maitreya J. Dunham.
Identification of a novel interspecific hybrid yeast from a metagenomic spontaneously inoculated beer sample using Hi-C.
Yeast.
DOI: 10.1002/yea.3280 (2017).

Nerve Zhou, Samuele Bottagisi, Michael Katz, Joseph Schacherer, Anne Friedrich, Zoran Gojkovic, Krishna B. S. Swamy, Wolfgang Knecht, Concetta Compagno, Jure Piškur.
Yeast–bacteria competition induced new metabolic traits through large-scale genomic rearrangements in Lachancea kluyveri.
FEMS Yeast Research.
DOI: 10.1093/femsyr/fox060 (2017).

Shinsuke Ohnuki, Hiroki Okada, Anne Friedrich, Yoichiro Kanno, Tetsuya Goshima, Hirokazu Hasuda, Masaaki Inahashi, Naoto Okazaki, Hiroyasu Tamura, Ryo Nakamura, Dai Hirata, Hisashi Fukuda, Hitoshi Shimoi, Katsuhiko Kitamoto, Daisuke Watanabe, Joseph Schacherer, Takeshi Akao, Yoshikazu Ohya.
Phenotypic Diagnosis of Lineage and Differentiation During Sake Yeast Breeding.
G3 Genes|Genomes|Genetics.
DOI: 10.1534/g3.117.044099 (2017).

Christian Brion, Sylvain Legrand, Jackson Peter, Claudia Caradec, David Pflieger, Jing Hou, Anne Friedrich, Bertrand Llorente, Joseph Schacherer.
Variation of the meiotic recombination landscape and properties over a broad evolutionary distance in yeasts.
PLOS Genetics.
DOI: 10.1371/journal.pgen.1006917 (2017).

Duyen T Bui, Anne Friedrich, Najla Al-Sweel, Gianni Liti, Joseph Schacherer, Charles F Aquadro, Eric Alani.
Mismatch Repair Incompatibilities in Diverse Yeast Populations.
Genetics.
DOI: 10.1534/genetics.116.199513 (2017).

Benjamin Istace, Anne Friedrich, Léo d'Agata, Sébastien Faye, Emilie Payen, Odette Beluche, Claudia Caradec, Sabrina Davidas, Corinne Cruaud, Gianni Liti, Arnaud Lemainque, Stefan Engelen, Patrick Wincker, Joseph Schacherer, Jean-Marc Aury.
de novo assembly and population genomic survey of natural yeast isolates with the Oxford Nanopore MinION sequencer.
GigaScience.
DOI: 10.1093/gigascience/giw018 (2017).

Jing Hou, Joseph Schacherer.
Fitness Trade-Offs Lead to Suppressor Tolerance in Yeast.
Molecular Biology and Evolution.
DOI: 10.1093/molbev/msw225 (2016).

Anastasie Sigwalt, Claudia Caradec, Christian Brion, Jing Hou, Jacky de Montigny, Paul Jung, Gilles Fischer, Bertrand Llorente, Anne Friedrich, Joseph Schacherer.
Dissection of quantitative traits by bulk segregant mapping in a protoploid yeast species.
FEMS Yeast Research.
DOI: 10.1093/femsyr/fow056 (2016).

Jing Hou, Téo Fournier, Joseph Schacherer.
Species-wide survey reveals the various flavors of intraspecific reproductive isolation in yeast.
FEMS Yeast Research.
DOI: 10.1093/femsyr/fow048 (2016).

Joseph Schacherer, Yves Tourrette, Serge Potier, Jean-Luc Souciet, Jacky De Montigny.
Spontaneous duplications in diploid Saccharomyces cerevisiae cells.
DNA Repair.
DOI: 10.1016/j.dnarep.2007.04.006 (2007).

Yves Tourrette, Joseph Schacherer, Emilie Fritsch, Serge Potier, Jean-Luc Souciet, Jacky De Montigny.
Spontaneous deletions and reciprocal translocations in Saccharomyces cerevisiae: influence of ploidy.
Molecular Biology.
DOI: 10.1111/j.1365-2958.2007.05660.x (2007).