Shahryary Dizaji Y, Hazarika RR, Johannes F. (2019). MethylStar: A fast and robust pipeline for high-throughput analysis of bulk or single-cell WGBS data. bioRxiv doi: doi.org/10.1101/2019.12.20.884536 Abstract

Shahryary Dizaji Y, Symeonidi A, Hazarika RR, Denkena J, Mubeen T, Hofmeister BT, van Gurp T, Colomé-Tatché M, Verhoeven K, Tuskan G, Schmitz RJ*, Johannes F.* (2019). AlphaBeta: Computational inference of epimutation rates and spectra from high-throughput DNA methylation data in plants. bioRxiv doi: doi.org/10.1101/862243 Abstract

Hofmeister BT, Denkena J, Colomé-Tatché M, Shahryary Dizaji Y, Hazarika RR, Grimwood J, Mamid S, Jenkins J, Grabowski PP, Sreedasyam A, Shu A, Barry K, Lail K, Adam C, Lipzen A, Sorek R, Kudrna D, Talag J, Wing R, Hall DW, Tuskan GA, Schmutz J,  Johannes F*, Schmitz RJ* (2019). The somatic genetic and epigenetic mutation rate in a wild long-lived perennial Populus trichocarpa. bioRxiv doi: doi.org/10.1101/862623 Abstract

Ricci WA, Lu Z, Ji L, Marand AP, Ethridge CL, Murphy NG, Noshay JM, Galli M, Mejía-Guerra MK, Colomé-Tatché M, Johannes F, Rowley MJ, Corces VG,  Zhai J, Scanlon MJ, Buckler ES, Gallavotti A, Springer NM, Schmitz RJ*, Zhang X* (2019). Widespread Long-range Cis-Regulatory Elements in the Maize Genome. Nature Plants doi: 10.1038/s41477-019-0547-0 Abstract

Johannes F (2019). DNA methylation makes mutational history. Nature Plants doi: 10.1038/s41477-019-0491-z. Abstract

Wendte WJ, Zhang Y, Ji L, Shi X, Hazarika RR, Shahryary Y, Johannes F, Schmitz RJ (2019). Epimutations are associated with CHROMOMETHYLASE 3-induced de novo DNA methylation. eLIFE doi: 10.7554/eLife.47891.001 Abstract

Furci L,  Jain R, Stassen J, Berkowitz O, Whelan J, Roquis D, Baillet V, Colot V, Johannes F,
Ton J (2019). Identification and characterisation of hypomethylated DNA loci controlling quantitative resistance in Arabidopsis. eLIFE doi: 10.7554/eLife.40655 Abstract

Kooke R, Morgado L, Becker F, van Eekelen H, Hazarika R, Zheng QF, de Vos RCH, Johannes F, Keurentjes JJB (2018). Epigenetic mapping of the Arabidopsis metabolome reveals mediators of the epigenotype-phenotype map. Genome Research doi: 10.1101/gr.232371.117 Abstract

Johannes F, Schmitz RJ (2018) Spontaneous epimutations in plants. New Phytologist doi.org/10.1111/nph.15434 Abstract

Taudt A, Roquis D, Vidalis A, Wardenaar R, Johannes F*, Colomé-Tatché M* (2018). METHimpute: Imputation-guided construction of complete methylomes from WGBS data. BMC Genomics 19:444 Abstract

Lauss K, Wardenaar R, van Hulten MHA, Guryev V, Keurentjes JJB, Stam M*, Johannes F* (2017).
Parental DNA methylation states are associated with heterosis in Arabidopsis epigenetic hybrids. Plant Physiology doi: doi.org/10.1104/pp.17.01054 Abstract

Morgado L* and Johannes F* (2017). Computational tools for plant small RNA detection and categorization. Briefings in Bioinformatics bbx135 Abstract

Morgado L, Preite V, Opaat C, Anava S, Ferreira de Carvalho J, Rechavi O, Johannes F, Verhoeven K (2017). Small RNAs reflect grandparental environments in apomictic dandelion. Molecular Biology and Evolution doi: 10.1093/molbev/msx150 Abstract

Morgado L*, Jansen R, Johannes F* (2017). 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 doi: doi.org/10.1101/173575

Vidali A, Živković D, Wardenaar R, Roquis D, Tellier A, Johannes F (2016). Methylome evolution in plants.
Genome Biology 17:264. Abstract

Taudt A, Colomé-Tatché M, Johannes F (2016). Genetic sources of population epigenomic variation. Nature Reviews Genetics doi:10.1038/nrg.2016.45. Abstract

Diao W, Mousset M, Vermeulen CJ, Johannes F, van de Zande L, Ritchie MG, Schmitt T, Beukeboom LW (2016). Quantitative trait locus analysis of mating behavior and male sex pheromones in Nasonia wasps.
G3: Genes | Genomes | Genetics doi: 10.1534/g3.116.029074. Abstract

Taudt A, Nguyen MA, Heinig M, Johannes F, Colomé-Tatché M (2016). chromstaR: Tracking combinatorial chromatin state dynamics in space and time. bioRxiv doi: 10.1101/038612 Abstract

Colomé-Tatché M* and Johannes F* (2015). Signatures of Dobzhansky-Muller incompatibilities in the genomes of Recombinant Inbred Lines. Genetics doi:10.1534/genetics.115.179473 Abstract

van der Graaf A, Wardenaar R, Neumann DA, Taudt A, Shaw RG, Jansen RC, Schmitz RJ, Colomé-Tatché M, Johannes F (2015). Rate, spectrum and evolutionary dynamics of spontaneous epimutations.
Proc. Natl. Acad. Sci. USA doi: 10.1073/pnas.1424254112. Abstract

Heinig M, Colomé-Tatché M, Taudt A, Rintisch C, Schafer S, Pravenec M, Hubner N, Vingron M, Johannes F (2015). histoneHMM: Differential analysis of histone modifications with broad genomic footprints. BMC Bioinformatics 16:60. Abstract

Kooke R, Johannes F, Wardenaar R, Etcheverry M, Colot V, Vreugdenhil D, Keurentjes JJB (2015). Epigenetic basis of morphological variation and phenotypic plasticity in Arabidopsis thaliana. Plant Cell doi:​10.​1105/​tpc.​114.​133025 Abstract

Rintisch C, Heinig M, Bauerfeind A, Schafer S, Mieth C, Patone G, Hummel O, Chen W, Cook S, Cuppen E, Colomé-Tatché M, Johannes F, Jansen RC, Neil H, Werner M, Pravenec M, Vingron M, Hubner N (2014). Natural variation of histone modification and its impact on gene expression in the rat genome. Genome Research doi:10.1101/gr.169029.113 Abstract

Cortijo S, Wardenaar R, Colomé-Tatché M, Gilly A, Etcheverry M, Labadie K, Caillieux E, Hospital F, Aury J-M, Wincker P, Roudier F, Jansen RC, Colot V, Johannes F (2014). Mapping the epigenetic basis of complex traits. Science doi:10.1126/science.1248127. Abstract

Cortijo S, Wardenaar R, M. Colomé-Tatché M, Johannes F*, Colot V* (2014). Genome-wide analysis of DNA methylation in Arabidopsis using MeDIP-chip. Methods in Molecular Biology 1112:125-49 doi:10.1007/978-1-62703-773-0_9 Abstract

Wardenaar R, Liu H, M. Colot V, Colomé-Tatché M, Johannes F* (2013). Evaluation of MeDIP-chip in the context of Whole Genome Bisulphite Sequencing (WGBS-seq) in Arabidopsis. Methods in Molecular Biology 1067:203-24 doi:10.1007/978-1-62703-607-8_13 Abstract

Lendvai A, Johannes F, Grimm C, Eijsink JJH, Wardenaar R, Volders HH, Klip HG, Hollema H, Jansen RC, Schuuring E, Wisman BG, van der Zee AGJ (2012). Genome-wide methylation profiling identifies hypermethylated biomarkers in high-grade cervical intraepithelial neoplasia. Epigenetics 11:1268-78 doi:10.4161/epi.22301 Abstract

Seifert M, Cortijo S, Colomé-Tatché M, Johannes F, Roudier R, Colot V (2012). MeDIP-HMM: Genome-wide identification of distinct DNA methylation states from high-density tiling arrays.
Bioinformatics doi:10.1093/bioinformatics/bts562. Abstract

Colomé-Tatché M, Cortijo S, Wardenaar R, Morgado L, Lahouze B, Sarazin A, Etcheverry M, Martin A, Feng S, Duvernois-Berthet E, Labadie K, Wincker P, Jacobsen SE, Jansen RC, Colot V, Johannes F (2012). Features of the Arabidopsis recombination landscape resulting from the combined loss of sequence variation and DNA methylation. Proc. Natl. Acad. Sci. USA doi:10.1073/pnas.1212955109. Abstract

Roux F, Colomé-Tatché M, Edelist C, Wardenaar R, Guerche P, Hospital F, Colot V, Jansen RC, Johannes F* (2011). Genome-wide epigenetic perturbation jump-starts patterns of heritable variation found in nature. Genetics 188:215–227 doi:10.1534/genetics.111.128744 Abstract

Johannes F* and Colomé-Tatché M (2011). Concerning epigenetics and inbreeding. Nature Reviews Genetics 12: 376 doi:10.1038/nrg2664-c3 Abstract

Johannes F* and Colomé-Tatché M (2011). Quantitative epigenetics through epigenomic perturbation of isogenic lines. Genetics 188:1015–1017 doi:10.1534/genetics Abstract

Concepcion D, Johannes F, Lo YH, Yao J, Fong J, Hamilton BA (2011). Modifier genes for mouse Phosphatidylinositol Transfer Protein alpha (vibrator) that bypass juvenile lethality. Genetics 187:1185–1191 doi:10.1534/genetics.110.125906 Abstract

Kooistra SM, van den Boom V, Thummer RP, Johannes F, Wardenaar R, Tesson BM, Veenhoff LM, Fusetti F, O'Neill LP, Turner B, de Haan G, Eggen BJL (2010). Undifferentiated Embryonic Cell Transcription Factor 1 Regulates ESC Chromatin Organization and Gene Expression. Stem Cells 10:1703-14 doi:10.1002/stem.497 Abstract

Johannes F*, Wardenaar R, Colomé-Tatché M, Mousson F, de Graaf P, Mokry M, Guryev V, Timmers MHTh, Cuppen E, Jansen RC (2010). Comparing genome-wide chromatin profiles using ChIP-chip or ChIP-seq. Bioinformatics 26: 1000–1006  doi:10.1093/bioinformatics/btq087 Abstract

Johannes F, Porcher E, Teixeira F, Saliba-Colombani V, Simon M, Agier N, Bulski A, Albuisson J, Heredia F, Bouchez D, Dillmann C, Guerche P, Hospital F, Colot V (2009). Assessing the impact of transgenerational epigenetic variation on complex traits. PLoS Genetics 5: e1000530 doi:10.1371/journal.pgen.1000530 Abstract

Fu J, Keurentjes JJB, Bouwmeester H, America T, Verstappen FWA, Ward JL, Beale MH, de Vos RCH, Dijkstra M, Scheltema RA, Johannes F, Koornneef M, Vreugdenhil D, Breitling R, Jansen RC (2009). System-wide molecular evidence for phenotypic buffering in Arabidopsis. Nature Genetics 41: 166-167 doi:10.1038/ng.308 Abstract

Sen S, Johannes F, Broman K (2009). Selective genotyping and phenotyping strategies in a complex trait context. Genetics 181: 1613-1626 doi:10.1534/genetics.108.094607 Abstract.

Johannes F*, Colot V, Jansen RC (2008). Epigenome dynamics: A quantitative genetic perspective.
Nature Reviews Genetics 9: 883-890 doi:10.1038/nrg2467 Abstract

Johannes F* (2007). Mapping temporally varying quantitative trait loci in time-to-failure experiments.
Genetics 175: 855-865 doi:10.1534/genetics.106.059808 Abstract

Johannes F*, Blizard DA, Lionikas A, Lang DH, Vandenbergh DJ, Stout JT, Strauss JA, McClearn GE, Vogler GP (2006). QTL influencing baseline hematocrit in the C57BL/6J and DBA/2J lineage: Age-related effects. Mammalian Genome 17: 689-699 doi:10.1007/s00335-006-0009-7 Abstract