Frank Johannes

Fellowship
Rudolf Mößbauer Tenure Track

Institution
Technische Universität München

Department
TUM School of Life Sciences Weihenstephan

Focus Group
Population Epigenetics and Epigenomics

Short CV

Prof. Frank Johannes (b. 1976) obtained his PhD in the interdisciplinary program BioBehavioral Health at the Pennsylvania State University (USA), studying statistical genetics at the, then, Centre for Developmental and Health Genetics. He spent the last year of his PhD as a Marie Curie Fellow at the French Institute for Agricultural Research (INRA) in Versailles where he was involved in one of the first population epigenetic studies in plants.
He continued this work first as a post-doc at the French National Centre for Scientific Research (CNRS) in Paris and later as a post-doc in the bioinformatics unit of the University of Groningen in the Netherlands. He stayed in Groningen as an Assistant Professor before moving to the TUM-IAS as a Rudolf Mößbauer Tenure Track Assistant Professor.

Selected Awards

2015 Wallenberg Academy Fellowship

Research Interests

Prof. Johannes conducts research in the area of population epigenetics and epigenomics. His group combines bioinformatic and statistical genetic approaches with high-throughput molecular data to characterize patterns of epigenetic variation in populations of plants.
The goal is to understand how this variation arises, how stable it is across generations and to which extent it determines agriculturally and evolutionarily relevant plant traits.
The ultimate applied goal is to be able to exploit engineered or naturally occurring epimutations for the improvement of commercial crops.

Selected Publications

  • Cortijo, S.; Wardenaar, R.; Colome-Tatche, M.; Gilly, A.; Etcheverry, M.; Labadie, K.; Caillieux, E.; Hospital, F.; Aury, J.-M.; Wincker, P.; Roudier, F.; Jansen, R. C.; Colot, V.; Johannes, F.: Mapping the Epigenetic Basis of Complex Traits. Science 343 (6175), 2014, 1145-1148 
  • Cortijo, S.; Wardenaar, R.; Colome-Tatche, M.; Gilly, A.; Etcheverry, M.; Labadie, K.; Caillieux, E.; Hospital, F.; Aury, J.-M.; Wincker, P.; Roudier, F.; Jansen, R. C.; Colot, V.; Johannes, F.: Mapping the Epigenetic Basis of Complex Traits. Science 343 (6175), 2014, 1145-1148
  • Johannes, F.; Colome-Tatche, M.: Quantitative Epigenetics Through Epigenomic Perturbation of Isogenic Lines. Genetics 188 (1), 2011, 215-227 
  • Johannes, Frank; Porcher, Emmanuelle; Teixeira, Felipe K.; Saliba-Colombani, Vera; Simon, Matthieu; Agier, Nicolas; Bulski, Agnès; Albuisson, Juliette; Heredia, Fabiana; Audigier, Pascal; Bouchez, David; Dillmann, Christine; Guerche, Philippe; Hospital, Frédéric; Colot, Vincent: Assessing the Impact of Transgenerational Epigenetic Variation on Complex Traits. PLoS Genetics 5 (6), 2009, e1000530

Publications as TUM-IAS-Fellow

2020

  • Shahryary, Yadollah; Symeonidi, Aikaterini; Hazarika, Rashmi R.; Denkena, Johanna; Mubeen, Talha; Hofmeister, Brigitte; van Gurp, Thomas; Colomé-Tatché, Maria; Verhoeven, Koen; Tuskan, Gerald; Schmitz, Robert J; Johannes, Frank: AlphaBeta: Computational inference of epimutation rates and spectra from high-throughput DNA methylation data in plants. bioRxiv, 2020 more… BibTeX Full text ( DOI )

2019

  • Hofmeister, Brigitte T.; Denkena, Johanna; Colomé-Tatché, Maria; Shahryary, Yadollah; Hazarika, Rashmi; Grimwood, Jane; Mamidi, Sujan; Jenkins, Jerry; Grabowski, Paul P.; Sreedasyam, Avinash; Shu, Shengqiang; Barry, Kerrie; Lail, Kathleen; Adam, Catherine; Lipzen, Anna; Sorek, Rotem; Kudrna, Dave; Talag, Jayson; Wing, Rod; Hall, David W.; Tuskan, Gerald A.; Schmutz, Jeremy; Johannes, Frank; Schmitz, Robert J.: The somatic genetic and epigenetic mutation rate in a wild long-lived perennial Populus trichocarpa. bioRxiv, 2019 more… BibTeX Full text ( DOI )
  • Lu, Zefu; Marand, Alexandre P.; Ricci, William A.; Ethridge, Christina L.; Zhang, Xiaoyu; Schmitz, Robert J.: The prevalence, evolution and chromatin signatures of plant regulatory elements. Nature Plants 5 (12), 2019, 1250-1259 more… BibTeX Full text ( DOI )
  • Ricci, William A.; Lu, Zefu; Ji, Lexiang; Marand, Alexandre P.; Ethridge, Christina L.; Murphy, Nathalie G.; Noshay, Jaclyn M.; Galli, Mary; Mejía-Guerra, María Katherine; Colomé-Tatché, Maria; Johannes, Frank; Rowley, M. Jordan; Corces, Victor G.; Zhai, Jixian; Scanlon, Michael J.; Buckler, Edward S.; Gallavotti, Andrea; Springer, Nathan M.; Schmitz, Robert J.; Zhang, Xiaoyu: Widespread long-range cis-regulatory elements in the maize genome. Nature Plants 5 (12), 2019, 1237-1249 more… BibTeX Full text ( DOI )
  • Wendte, Jered M; Zhang, Yinwen; Ji, Lexiang; Shi, Xiuling; Hazarika, Rashmi R; Shahryary, Yadollah; Johannes, Frank; Schmitz, Robert J: Epimutations are associated with CHROMOMETHYLASE 3-induced de novo DNA methylation. eLife 8, 2019 more… BibTeX Full text ( DOI )
  • Yadollah Shahryary, Aikaterini Symeonidi, Rashmi R. Hazarika, Johanna Denkena, Talha Mubeen, Brigitte Hofmeister, Thomas van Gurp, Maria Colomé-Tatché, Koen Verhoeven, Gerald Tuskan, Robert J Schmitz, Frank Johannes: AlphaBeta: Computational inference of epimutation rates and spectra from high-throughput DNA methylation data in plants. doi.org/10.1101/862243, 2019 more… BibTeX

2018

2017

  • Lauss, Kathrin; Wardenaar, René; Oka, Rurika; van Hulten, Marieke H. A.; Guryev, Victor; Keurentjes, Joost J. B.; Stam, Maike; Johannes, Frank: Parental DNA Methylation States Are Associated with Heterosis in Epigenetic Hybrids. Plant Physiology 176 (2), 2017, 1627-1645 more… BibTeX Full text ( DOI )
  • Morgado, Lionel; Johannes, Frank: Computational tools for plant small RNA detection and categorization. Briefings in Bioinformatics, 2017 more… BibTeX Full text ( DOI )
  • Morgado, Lionel; Preite, Veronica; Oplaat, Carla; Anava, Sarit; Ferreira de Carvalho, Julie; Rechavi, Oded; Johannes, Frank; Verhoeven, Koen J.F.: Small RNAs Reflect Grandparental Environments in Apomictic Dandelion. Molecular Biology and Evolution 34 (8), 2017, 2035-2040 more… BibTeX Full text ( DOI )

2016

  • Diao, Wenwen; Mousset, Mathilde; Horsburgh, Gavin J.; Vermeulen, Cornelis J.; Johannes, Frank; van de Zande, Louis; Ritchie, Michael G.; Schmitt, Thomas; Beukeboom, Leo W.: Quantitative Trait Locus Analysis of Mating Behavior and Male Sex Pheromones in Nasonia Wasps. G3: Genes|Genomes|Genetics 6 (6), 2016, 1549-1562 more… BibTeX Full text ( DOI )
  • Taudt, Aaron; Colomé-Tatché, Maria; Johannes, Frank: Genetic sources of population epigenomic variation. Nature Reviews Genetics 17 (6), 2016, 319-332 more… BibTeX Full text ( DOI )
  • Vidalis, Amaryllis; Živković, Daniel; Wardenaar, René; Roquis, David; Tellier, Aurélien; Johannes, Frank: Methylome evolution in plants. Genome Biology 17 (1), 2016 more… BibTeX Full text ( DOI )

2015

  • van der Graaf, Adriaan; Wardenaar, René; Neumann, Drexel A.; Taudt, Aaron; Shaw, Ruth G.; Jansen, Ritsert C.; Schmitz, Robert J.; Colomé-Tatché, Maria; Johannes, Frank: Rate, spectrum, and evolutionary dynamics of spontaneous epimutations. Proceedings of the National Academy of Sciences 112 (21), 2015, 6676-6681 more… BibTeX Full text ( DOI )