Frank Johannes

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 more… BibTeX Full text ( DOI )
  • Goeldel, Constantin; Johannes, Frank: Stochasticity in gene body methylation. Current Opinion in Plant Biology 75, 2023, 102436 more… BibTeX Full text ( DOI )
  • Kakoulidou, Ioanna; Johannes, Frank: <scp>DNA</scp> methylation remodeling in <scp>F1</scp> hybrids. The Plant Journal, 2023 more… BibTeX Full text ( 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 more… BibTeX Full text ( DOI )
  • T. Sellinger, F. Johannes, A. Tellier,: Improved inference of population histories by integrating genomic and epigenomic data. bioRxiv, 2023, more… 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 more… BibTeX Full text ( 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 more… BibTeX Full text ( 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 more… BibTeX Full text ( 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 more… BibTeX Full text ( 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, more… 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 more… BibTeX Full text ( DOI )

2021

  • Denkena, Johanna; Johannes, Frank; Colomé-Tatché, Maria: Region-level epimutation rates in Arabidopsis thaliana. Heredity 127 (2), 2021, 190-202 more… BibTeX Full text ( DOI )
  • Johannes, Frank: Epigenomics in trees: decoding the plastic lives of mangroves. New Phytologist 233 (5), 2021, 1971-1973 more… BibTeX Full text ( 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 more… BibTeX Full text ( 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 more… BibTeX Full text ( 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 more… BibTeX Full text ( 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 more… BibTeX Full text ( DOI )

2020

  • Costa, Maria-Cecilia D.; Johannes, Frank: Epigenetics: Switching Genes On and Off. Frontiers for Young Minds 8, 2020 more… BibTeX Full text ( 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 more… BibTeX Full text ( 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 more… BibTeX Full text ( 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 more… BibTeX Full text ( 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 more… BibTeX Full text ( 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 more… BibTeX Full text ( 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 more… BibTeX Full text ( DOI )
  • Johannes, Frank: DNA methylation makes mutational history. Nature Plants 5 (8), 2019, 772-773 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

  • Johannes, Frank; Schmitz, Robert J.: Spontaneous epimutations in plants. New Phytologist 221 (3), 2018, 1253-1259 more… BibTeX Full text ( 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 more… BibTeX Full text ( 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 more… BibTeX Full text ( 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, more… 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 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

  • A. Taudt, M. A. Nguyen, M. Heinig, F. Johannes, M. Colomé-Tatché: chromstaR: Tracking combinatorial chromatin state dynamics in space and time. bioRxiv, 2016, more… 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 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

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