Publications


Preprint
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.*
AlphaBeta: Computational inference of epimutation rates and spectra from high-throughput DNA methylation data in plants

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*
The somatic genetic and epigenetic mutation rate in a wild long-lived perennial Populus trichocarpa


2019
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*.
Widespread Long-range Cis-Regulatory Elements in the Maize Genome
Nature Plants  doi: 10.1038/s41477-019-0547-0 [pdf]

Johannes F.
DNA methylation makes mutational history.
Nature Plants doi: 10.1038/s41477-019-0491-z [pdf]

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

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


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

Johannes F, Schmitz RJ.
Spontaneous epimutations in plants.
New Phytologist
https://doi.org/10.1111/nph.15434 [pdf]

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


2017

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

Morgado L* and Johannes F*.
Computational tools for plant small RNA detection and categorization.
Briefings in Bioinformatics bbx135 [pdf]

Morgado L, Preite V, Opaat C, Anava SFerreira de Carvalho J, Rechavi O, Johannes F, Verhoeven K.
Small RNAs reflect grandparental environments in apomictic dandelion.
Molecular Biology and Evolution
doi: 10.1093/molbev/msx150 [pdf] [SI]

Morgado L*, Jansen R, Johannes F*.
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: https://doi.org/10.1101/173575


2016
Vidali A, Živković D, Wardenaar R, Roquis D, Tellier A*, Johannes F.*
Methylome evolution in plants.
Genome Biology [pdf] [SI]

Taudt A, Colomé-Tatché M, Johannes F*.
Genetic sources of population epigenomic variation.
Nature Reviews Genetics doi:10.1038/nrg.2016.45 [pdf][SI]

Diao W, Mousset M, Vermeulen CJ, Johannes F, van de Zande L, Ritchie MG, Schmitt T, Beukeboom LW.
Quantitative trait locus analysis of mating behavior and male sex pheromones in Nasonia wasps.
G3: Genes | Genomes | Genetics [pdf]

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


2015

Colomé-Tatché M* and Johannes F*.
Signatures of Dobzhansky-Muller incompatibilities in the genomes of Recombinant Inbred Lines.
Genetics doi:10.1534/genetics.115.179473 [pdf][SI]

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

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

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



2014
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.
Natural variation of histone modification and its impact on gene expression in the rat genome.
Genome Research doi:10.1101/gr.169029.113. [pdf]

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*
Mapping the epigenetic basis of complex traits.
Science doi:10.1126/science.1248127. [pdf]

Cortijo S, Wardenaar R, M. Colomé-Tatché M, Johannes F*, Colot V*.
Genome-wide analysis of DNA methylation in Arabidopsis using MeDIP-chip.
Methods in Molecular Biology 1112:125-49. [pdf] [Data1] [Data2] [Data3] [Rcode]



2013
Wardenaar R, Liu H, M. Colot V, Colomé-Tatché M, Johannes F*.
Evaluation of MeDIP-chip in the context of Whole Genome Bisulphite Sequencing (WGBS-seq) in Arabidopsis.
Methods in Molecular Biology 1067:203-24. [pdf]



2012
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.
Genome-wide methylation profiling identifies hypermethylated biomarkers in high-grade cervical intraepithelial neoplasia.
Epigenetics 11:1268-78. [pdf]

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

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*.
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. [pdf]



2011
Roux F, Colomé-Tatché M, Edelist C, Wardenaar R, Guerche P, Hospital F, Colot V, Jansen RC, Johannes F*.
Genome-wide epigenetic perturbation jump-starts patterns of heritable variation found in nature.
Genetics 188:215–227. [pdf]

Johannes F* and Colomé-Tatché M.
Concerning epigenetics and inbreeding.
Nature Reviews Genetics 12: 376. [pdf]

Johannes F* and Colomé-Tatché M.
Quantitative epigenetics through epigenomic perturbation of isogenic lines.
Genetics 188:1015–1017. [pdf]

Concepcion D, Johannes F, Lo YH, Yao J, Fong J, Hamilton BA.
Modifier genes for mouse Phosphatidylinositol Transfer Protein alpha (vibrator) that bypass juvenile lethality.
Genetics 187:1185–1191. [pdf]



2010
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.
Undifferentiated Embryonic Cell Transcription Factor 1 Regulates ESC Chromatin Organization and Gene Expression.
Stem Cells 10:1703-14. [pdf]

Johannes F*, Wardenaar R, Colomé-Tatché M, Mousson F, de Graaf P, Mokry M, Guryev V, Timmers MHTh, Cuppen E, Jansen RC.
Comparing genome-wide chromatin profiles using ChIP-chip or ChIP-seq.
Bioinformatics 26: 1000–1006. [pdf]



2009
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.
Assessing the impact of transgenerational epigenetic variation on complex traits.
PLoS Genetics 5: e1000530. [pdf]

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.
System-wide molecular evidence for phenotypic buffering in Arabidopsis.
Nature Genetics 41: 166-167. [pdf]

Sen S, Johannes F, Broman K.
Selective genotyping and phenotyping strategies in a complex trait context.
Genetics 181: 1613-1626. [pdf]



2008
Johannes F*, Colot V, Jansen RC.
Epigenome dynamics: A quantitative genetic perspective.
Nature Reviews Genetics 9: 883-890. [pdf]



2007
Johannes F*.
Mapping temporally varying quantitative trait loci in time-to-failure experiments.
Genetics 175: 855-865. [pdf]



2006
Johannes F*, Blizard DA, Lionikas A, Lang DH, Vandenbergh DJ, Stout JT, Strauss JA, McClearn GE, Vogler GP.
QTL influencing baseline hematocrit in the C57BL/6J and DBA/2J lineage: Age-related effects.
Mammalian Genome 17: 689-699. [pdf]