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Technische Universität München
Technische Universität München

Frank Johannes

Fellowship
Rudolf Mößbauer Tenure Track

Appointment
2015

Institution
Technical University of Munich

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

2023

  • Agius, Dolores Rita; Kapazoglou, Aliki; Avramidou, Evangelia; Baranek, Miroslav; Carneros, Elena; Caro, Elena; Castiglione, Stefano; Cicatelli, Angela; Radanovic, Aleksandra; Ebejer, Jean-Paul; Gackowski, Daniel; Guarino, Francesco; Gulyás, Andrea; Hidvégi, Norbert; Hoenicka, Hans; Inácio, Vera; Johannes, Frank; Karalija, Erna; Lieberman-Lazarovich, Michal; Martinelli, Federico; Maury, Stéphane; Mladenov, Velimir; Morais-Cecílio, Leonor; Pecinka, Ales; Tani, Eleni; Testillano, Pilar S.; Todorov, Dimitar; Valledor, Luis; Vassileva, Valya: Exploring the crop epigenome: a comparison of DNA methylation profiling techniques. Frontiers in Plant Science 14, 2023 mehr… BibTeX Volltext ( DOI )
  • Goeldel, Constantin; Johannes, Frank: Stochasticity in gene body methylation. Current Opinion in Plant Biology 75, 2023, 102436 mehr… BibTeX Volltext ( DOI )
  • Kakoulidou, Ioanna; Johannes, Frank: <scp>DNA</scp> methylation remodeling in <scp>F1</scp> hybrids. The Plant Journal, 2023 mehr… BibTeX Volltext ( DOI )
  • Kuhlmann, Markus; Jiang, Hua; Catoni, Marco; Johannes, Frank: Editorial: DNA methylation in plants associated with abiotic stress, volume II. Frontiers in Plant Science 14, 2023 mehr… BibTeX Volltext ( DOI )
  • T. Sellinger, F. Johannes, A. Tellier,: Improved inference of population histories by integrating genomic and epigenomic data. bioRxiv, 2023, mehr… BibTeX
  • Yao, N.; Zhang, Z.; Yu, L.; Hazarika, R.; Yu, C.; Jang, H.; Smith, L. M.; Ton, J.; Liu, L.; Stachowicz, J. J.; Reusch, T. B. H.; Schmitz, R. J.; Johannes, F.: An evolutionary epigenetic clock in plants. Science 381 (6665), 2023, 1440-1445 mehr… BibTeX Volltext ( DOI )

2022

  • Giansanti, Piero; Samaras, Patroklos; Bian, Yangyang; Meng, Chen; Coluccio, Andrea; Frejno, Martin; Jakubowsky, Hannah; Dobiasch, Sophie; Hazarika, Rashmi R.; Rechenberger, Julia; Calzada-Wack, Julia; Krumm, Johannes; Mueller, Sebastian; Lee, Chien-Yun; Wimberger, Nicole; Lautenbacher, Ludwig; Hassan, Zonera; Chang, Yun-Chien; Falcomatà, Chiara; Bayer, Florian P.; Bärthel, Stefanie; Schmidt, Tobias; Rad, Roland; Combs, Stephanie E.; The, Matthew; Johannes, Frank; Saur, Dieter; de Angelis, Martin Hrabe; Wilhelm, Mathias; Schneider, Günter; Kuster, Bernhard: Mass spectrometry-based draft of the mouse proteome. Nature Methods 19 (7), 2022, 803-811 mehr… BibTeX Volltext ( DOI )
  • Hazarika, Rashmi R.; Serra, Michele; Zhang, Zhilin; Zhang, Yinwen; Schmitz, Robert J.; Johannes, Frank: Molecular properties of epimutation hotspots. Nature Plants 8 (2), 2022, 146-156 mehr… BibTeX Volltext ( DOI )
  • Hüther, Patrick; Hagmann, Jörg; Nunn, Adam; Kakoulidou, Ioanna; Pisupati, Rahul; Langenberger, David; Weigel, Detlef; Johannes, Frank; Schultheiss, Sebastian J.; Becker, Claude: MethylScore, a pipeline for accurate and context-aware identification of differentially methylated regions from population-scale plant whole-genome bisulfite sequencing data. Quantitative Plant Biology 3, 2022 mehr… BibTeX Volltext ( DOI )
  • I. Kakoulidou, R. S. Piecyk, R. C. Meyer, M. Kuhlmann, C. Gutjahr, T. Altmann, F. Johannes: Parental pericentromeric methylation status drives methylome remodelling and heterosis in epigenetic hybrids. bioRxiv, 2022, mehr… BibTeX
  • Piecyk, Robert S.; Schlegel, Luca; Johannes, Frank: Predicting 3D chromatin interactions from DNA sequence using Deep Learning. Computational and Structural Biotechnology Journal 20, 2022, 3439-3448 mehr… BibTeX Volltext ( DOI )

2021

  • Denkena, Johanna; Johannes, Frank; Colomé-Tatché, Maria: Region-level epimutation rates in Arabidopsis thaliana. Heredity 127 (2), 2021, 190-202 mehr… BibTeX Volltext ( DOI )
  • Johannes, Frank: Epigenomics in trees: decoding the plastic lives of mangroves. New Phytologist 233 (5), 2021, 1971-1973 mehr… BibTeX Volltext ( DOI )
  • Kakoulidou, Ioanna; Avramidou, Evangelia V.; Baránek, Miroslav; Brunel-Muguet, Sophie; Farrona, Sara; Johannes, Frank; Kaiserli, Eirini; Lieberman-Lazarovich, Michal; Martinelli, Federico; Mladenov, Velimir; Testillano, Pilar S.; Vassileva, Valya; Maury, Stéphane: Epigenetics for Crop Improvement in Times of Global Change. Biology 10 (8), 2021, 766 mehr… BibTeX Volltext ( DOI )
  • Symeonidi, Aikaterini; Nicolaou, Anguelos; Johannes, Frank; Christlein, Vincent: Recursive Convolutional Neural Networks for Epigenomics. 2020 25th International Conference on Pattern Recognition (ICPR), IEEE, 2021 mehr… BibTeX Volltext ( DOI )
  • Yao, Nan; Schmitz, Robert J.; Johannes, Frank: Epimutations Define a Fast-Ticking Molecular Clock in Plants. Trends in Genetics 37 (8), 2021, 699-710 mehr… BibTeX Volltext ( DOI )
  • Zhang, Yinwen; Jang, Hosung; Xiao, Rui; Kakoulidou, Ioanna; Piecyk, Robert S.; Johannes, Frank; Schmitz, Robert J.: Heterochromatin is a quantitative trait associated with spontaneous epiallele formation. Nature Communications 12 (1), 2021 mehr… BibTeX Volltext ( DOI )

2020

  • Costa, Maria-Cecilia D.; Johannes, Frank: Epigenetics: Switching Genes On and Off. Frontiers for Young Minds 8, 2020 mehr… BibTeX Volltext ( DOI )
  • 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.; Jacobsen, Daniel; Tuskan, Gerald A.; Schmutz, Jeremy; Johannes, Frank; Schmitz, Robert J.: A genome assembly and the somatic genetic and epigenetic mutation rate in a wild long-lived perennial Populus trichocarpa. Genome Biology 21 (1), 2020 mehr… BibTeX Volltext ( DOI )
  • Mergner, Julia; Frejno, Martin; List, Markus; Papacek, Michael; Chen, Xia; Chaudhary, Ajeet; Samaras, Patroklos; Richter, Sandra; Shikata, Hiromasa; Messerer, Maxim; Lang, Daniel; Altmann, Stefan; Cyprys, Philipp; Zolg, Daniel P.; Mathieson, Toby; Bantscheff, Marcus; Hazarika, Rashmi R.; Schmidt, Tobias; Dawid, Corinna; Dunkel, Andreas; Hofmann, Thomas; Sprunck, Stefanie; Falter-Braun, Pascal; Johannes, Frank; Mayer, Klaus F. X.; Jürgens, Gerd; Wilhelm, Mathias; Baumbach, Jan; Grill, Erwin; Schneitz, Kay; Schwechheimer, Claus; Kuster, Bernhard: Mass-spectrometry-based draft of the Arabidopsis proteome. Nature 579 (7799), 2020, 409-414 mehr… BibTeX Volltext ( DOI )
  • Shahryary, Yadollah; Hazarika, Rashmi R.; Johannes, Frank: MethylStar: A fast and robust pre-processing pipeline for bulk or single-cell whole-genome bisulfite sequencing data. BMC Genomics 21 (1), 2020 mehr… BibTeX Volltext ( DOI )
  • 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 mehr… BibTeX Volltext ( DOI )

2019

  • Furci, Leonardo; Jain, Ritushree; Stassen, Joost; Berkowitz, Oliver; Whelan, James; Roquis, David; Baillet, Victoire; Colot, Vincent; Johannes, Frank; Ton, Jurriaan: Identification and characterisation of hypomethylated DNA loci controlling quantitative resistance in Arabidopsis. eLife 8, 2019 mehr… BibTeX Volltext ( DOI )
  • 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 mehr… BibTeX Volltext ( DOI )
  • Johannes, Frank: DNA methylation makes mutational history. Nature Plants 5 (8), 2019, 772-773 mehr… BibTeX Volltext ( 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 mehr… BibTeX Volltext ( 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 mehr… BibTeX Volltext ( 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 mehr… BibTeX Volltext ( 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 mehr… BibTeX

2018

  • Johannes, Frank; Schmitz, Robert J.: Spontaneous epimutations in plants. New Phytologist 221 (3), 2018, 1253-1259 mehr… BibTeX Volltext ( DOI )
  • Kooke, Rik; Morgado, Lionel; Becker, Frank; van Eekelen, Henriëtte; Hazarika, Rashmi; Zheng, Qunfeng; de Vos, Ric C.H.; Johannes, Frank; Keurentjes, Joost J.B.: Epigenetic mapping of the <i>Arabidopsis</i> metabolome reveals mediators of the epigenotype-phenotype map. Genome Research 29 (1), 2018, 96-106 mehr… BibTeX Volltext ( DOI )
  • Taudt, Aaron; Roquis, David; Vidalis, Amaryllis; Wardenaar, René; Johannes, Frank; Colomé-Tatché, Maria: METHimpute: imputation-guided construction of complete methylomes from WGBS data. BMC Genomics 19 (1), 2018 mehr… BibTeX Volltext ( DOI )

2017

  • L. Morgado, R. C. Jansen, F. Johannes: Learning sequence patterns of AGO-sRNA affinity from high-throughput sequencing libraries to improve in silico functional small RNA detection and classification in plants. bioRxiv, 2017, mehr… BibTeX
  • 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 mehr… BibTeX Volltext ( DOI )
  • Morgado, Lionel; Johannes, Frank: Computational tools for plant small RNA detection and categorization. Briefings in Bioinformatics, 2017 mehr… BibTeX Volltext ( 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 mehr… BibTeX Volltext ( DOI )

2016

  • A. Taudt, M. A. Nguyen, M. Heinig, F. Johannes, M. Colomé-Tatché: chromstaR: Tracking combinatorial chromatin state dynamics in space and time. bioRxiv, 2016, mehr… BibTeX
  • 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&amp;#58; Genes|Genomes|Genetics 6 (6), 2016, 1549-1562 mehr… BibTeX Volltext ( DOI )
  • Taudt, Aaron; Colomé-Tatché, Maria; Johannes, Frank: Genetic sources of population epigenomic variation. Nature Reviews Genetics 17 (6), 2016, 319-332 mehr… BibTeX Volltext ( DOI )
  • Vidalis, Amaryllis; Živković, Daniel; Wardenaar, René; Roquis, David; Tellier, Aurélien; Johannes, Frank: Methylome evolution in plants. Genome Biology 17 (1), 2016 mehr… BibTeX Volltext ( DOI )

2015

  • Colomé-Tatché, Maria; Johannes, Frank: Signatures of Dobzhansky–Muller Incompatibilities in the Genomes of Recombinant Inbred Lines. Genetics 202 (2), 2015, 825-841 mehr… BibTeX Volltext ( DOI )
  • 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 mehr… BibTeX Volltext ( DOI )
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