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:

A, Nguyen MA, Heinig M, Johannes F,
Colomé-Tatché M.
chromstaR: Tracking combinatorial chromatin state dynamics in space and time.


Johannes F, Schmitz RJ.
Spontaneous epimutations in plants.
New Phytologist [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]


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: [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]

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]


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]

Related coverage:
[U. of Groningen: Press release]
[The Scientist magazine]

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]

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]

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]

Related coverage:
[U. of Groningen: Press release] [U. of Groningen: ScienceLinx]
[NewScientist: Featured Research, Feb. 12, 2014 (in Dutch)]
[Faculty 1000 prime]

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]

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]

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]

Related coverage:
[Science: Editor's Choice, pdf]
[Faculty 1000]

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]

Related coverage:
[The Scientist magazine: 'Hidden Jewel']
[Faculty 1000]

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]

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]

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]

Related coverage:
[Nature Reviews Genetics: Research Highlight, pdf]
[Faculty 1000]

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]

Related coverage:
[Nature Genetics: News and Views, pdf]
[Faculty 1000]

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

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

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

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]