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Frank Johannes, Ph.D. - Publications

Affiliations: 
2007 Pennsylvania State University, State College, PA, United States 
Area:
Genetic epidemiology of complex traits
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46 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2023 Goeldel C, Johannes F. Stochasticity in gene body methylation. Current Opinion in Plant Biology. 75: 102436. PMID 37597469 DOI: 10.1016/j.pbi.2023.102436  0.316
2023 Agius DR, Kapazoglou A, Avramidou E, Baranek M, Carneros E, Caro E, Castiglione S, Cicatelli A, Radanovic A, Ebejer JP, Gackowski D, Guarino F, Gulyás A, Hidvégi N, Hoenicka H, ... ... Johannes F, et al. Exploring the crop epigenome: a comparison of DNA methylation profiling techniques. Frontiers in Plant Science. 14: 1181039. PMID 37389288 DOI: 10.3389/fpls.2023.1181039  0.361
2022 Hüther P, Hagmann J, Nunn A, Kakoulidou I, Pisupati R, Langenberger D, Weigel D, Johannes F, Schultheiss SJ, Becker C. 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: e19. PMID 37077980 DOI: 10.1017/qpb.2022.14  0.344
2022 Hazarika RR, Serra M, Zhang Z, Zhang Y, Schmitz RJ, Johannes F. Molecular properties of epimutation hotspots. Nature Plants. PMID 35087209 DOI: 10.1038/s41477-021-01086-7  0.334
2021 Zhang Y, Jang H, Xiao R, Kakoulidou I, Piecyk RS, Johannes F, Schmitz RJ. Heterochromatin is a quantitative trait associated with spontaneous epiallele formation. Nature Communications. 12: 6958. PMID 34845222 DOI: 10.1038/s41467-021-27320-6  0.4
2021 Kakoulidou I, Avramidou EV, Baránek M, Brunel-Muguet S, Farrona S, Johannes F, Kaiserli E, Lieberman-Lazarovich M, Martinelli F, Mladenov V, Testillano PS, Vassileva V, Maury S. Epigenetics for Crop Improvement in Times of Global Change. Biology. 10. PMID 34439998 DOI: 10.3390/biology10080766  0.323
2021 Yao N, Schmitz RJ, Johannes F. Epimutations define a fast-ticking molecular clock in plants. Trends in Genetics : Tig. PMID 34016450 DOI: 10.1016/j.tig.2021.04.010  0.304
2021 Denkena J, Johannes F, Colomé-Tatché M. Region-level epimutation rates in Arabidopsis thaliana. Heredity. PMID 33966050 DOI: 10.1038/s41437-021-00441-w  0.373
2020 Shahryary Y, Symeonidi A, Hazarika RR, Denkena J, Mubeen T, Hofmeister B, van Gurp T, Colomé-Tatché M, Verhoeven KJF, Tuskan G, Schmitz RJ, Johannes F. AlphaBeta: computational inference of epimutation rates and spectra from high-throughput DNA methylation data in plants. Genome Biology. 21: 260. PMID 33023650 DOI: 10.1186/s13059-020-02161-6  0.328
2020 Shahryary Y, Hazarika RR, Johannes F. MethylStar: A fast and robust pre-processing pipeline for bulk or single-cell whole-genome bisulfite sequencing data. Bmc Genomics. 21: 479. PMID 32660416 DOI: 10.1186/S12864-020-06886-3  0.379
2020 Mergner J, Frejno M, List M, Papacek M, Chen X, Chaudhary A, Samaras P, Richter S, Shikata H, Messerer M, Lang D, Altmann S, Cyprys P, Zolg DP, Mathieson T, ... ... Johannes F, et al. Mass-spectrometry-based draft of the Arabidopsis proteome. Nature. 579: 409-414. PMID 32188942 DOI: 10.1038/S41586-020-2094-2  0.322
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, et al. Widespread long-range cis-regulatory elements in the maize genome. Nature Plants. PMID 31740773 DOI: 10.1038/S41477-019-0547-0  0.394
2019 Johannes F. DNA methylation makes mutational history. Nature Plants. 5: 772-773. PMID 31358963 DOI: 10.1038/S41477-019-0491-Z  0.377
2019 Wendte JM, 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. 8. PMID 31356150 DOI: 10.7554/Elife.47891  0.413
2019 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. 8. PMID 30608232 DOI: 10.7554/Elife.40655  0.449
2019 Wendte JM, Zhang Y, Ji L, Shi X, Hazarika RR, Shahryary Y, Johannes F, Schmitz RJ. Author response: Epimutations are associated with CHROMOMETHYLASE 3-induced de novo DNA methylation Elife. DOI: 10.7554/Elife.47891.037  0.353
2018 Kooke R, Morgado L, Becker FFM, van Eekelen H, Hazarika R, Zhang QF, de Vos RCH, Johannes F, Keurentjes JJB. Epigenetic mapping of the Arabidopsis metabolome reveals mediators of the epigenotype-phenotype map. Genome Research. PMID 30504416 DOI: 10.1101/Gr.232371.117  0.384
2018 Johannes F, Schmitz RJ. Spontaneous epimutations in plants. The New Phytologist. PMID 30216456 DOI: 10.1111/Nph.15434  0.433
2018 Taudt A, Roquis D, Vidalis A, Wardenaar R, Johannes F, Colome-Tatché-Tatché M. METHimpute: imputation-guided construction of complete methylomes from WGBS data. Bmc Genomics. 19: 444. PMID 29879918 DOI: 10.1186/S12864-018-4641-X  0.367
2018 Furci L, Jain R, Stassen J, Berkowitz O, Whelan J, Roquis D, Baillet V, Colot V, Johannes F, Ton J. Author response: Identification and characterisation of hypomethylated DNA loci controlling quantitative resistance in Arabidopsis Elife. DOI: 10.7554/Elife.40655.035  0.328
2017 Lauss K, Wardenaar R, Oka R, van Hulten MHA, Guryev V, Keurentjes JJB, Stam M, Johannes F. Parental DNA methylation states are associated with heterosis in epigenetic hybrids. Plant Physiology. PMID 29196538 DOI: 10.1104/Pp.17.01054  0.43
2017 Morgado L, Johannes F. Computational tools for plant small RNA detection and categorization. Briefings in Bioinformatics. PMID 29059285 DOI: 10.1093/Bib/Bbx136  0.317
2016 Vidalis A, Živković D, Wardenaar R, Roquis D, Tellier A, Johannes F. Methylome evolution in plants. Genome Biology. 17: 264. PMID 27998290 DOI: 10.1186/S13059-016-1127-5  0.428
2016 Taudt A, Colomé-Tatché M, Johannes F. Genetic sources of population epigenomic variation. Nature Reviews. Genetics. PMID 27156976 DOI: 10.1038/Nrg.2016.45  0.401
2015 Colomé-Tatché M, Johannes F. Signatures of Dobzhansky-Muller Incompatibilities in the Genomes of Recombinant Inbred Lines. Genetics. PMID 26680662 DOI: 10.1534/Genetics.115.179473  0.393
2015 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. Proceedings of the National Academy of Sciences of the United States of America. 112: 6676-81. PMID 25964364 DOI: 10.1073/Pnas.1424254112  0.434
2015 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. PMID 25884684 DOI: 10.1186/S12859-015-0491-6  0.345
2015 Kooke R, Johannes F, Wardenaar R, Becker F, Etcheverry M, Colot V, Vreugdenhil D, Keurentjes JJ. Epigenetic basis of morphological variation and phenotypic plasticity in Arabidopsis thaliana. The Plant Cell. 27: 337-48. PMID 25670769 DOI: 10.1105/Tpc.114.133025  0.478
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, et al. Natural variation of histone modification and its impact on gene expression in the rat genome. Genome Research. 24: 942-53. PMID 24793478 DOI: 10.1101/Gr.169029.113  0.433
2014 Cortijo S, Wardenaar R, Colomé-Tatché M, Gilly A, Etcheverry M, Labadie K, Caillieux E, Hospital F, Aury JM, Wincker P, Roudier F, Jansen RC, Colot V, Johannes F. Mapping the epigenetic basis of complex traits. Science (New York, N.Y.). 343: 1145-8. PMID 24505129 DOI: 10.1126/Science.1248127  0.478
2014 Cortijo S, Wardenaar R, Colomé-Tatché M, Johannes F, Colot V. Genome-wide analysis of DNA methylation in Arabidopsis using MeDIP-chip. Methods in Molecular Biology (Clifton, N.J.). 1112: 125-49. PMID 24478012 DOI: 10.1007/978-1-62703-773-0_9  0.456
2013 Wardenaar R, Liu H, Colot V, Colomé-Tatché M, Johannes F. Evaluation of MeDIP-chip in the context of whole-genome bisulfite sequencing (WGBS-seq) in Arabidopsis. Methods in Molecular Biology (Clifton, N.J.). 1067: 203-24. PMID 23975794 DOI: 10.1007/978-1-62703-607-8_13  0.436
2012 Lendvai Á, Johannes F, Grimm C, Eijsink JJ, Wardenaar R, Volders HH, Klip HG, Hollema H, Jansen RC, Schuuring E, Wisman GB, van der Zee AG. Genome-wide methylation profiling identifies hypermethylated biomarkers in high-grade cervical intraepithelial neoplasia. Epigenetics : Official Journal of the Dna Methylation Society. 7: 1268-78. PMID 23018867 DOI: 10.4161/Epi.22301  0.367
2012 Seifert M, Cortijo S, Colomé-Tatché M, Johannes F, Roudier F, Colot V. MeDIP-HMM: genome-wide identification of distinct DNA methylation states from high-density tiling arrays. Bioinformatics (Oxford, England). 28: 2930-9. PMID 22989518 DOI: 10.1093/bioinformatics/bts562  0.329
2012 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, et al. Features of the Arabidopsis recombination landscape resulting from the combined loss of sequence variation and DNA methylation. Proceedings of the National Academy of Sciences of the United States of America. 109: 16240-5. PMID 22988127 DOI: 10.1073/Pnas.1212955109  0.453
2012 Lendvai A, Johannes F, Grimm C, Eijsink JJ, Wardenaar R, Volders HH, Klip HG, Hollema H, Jansen RC, Schuuring E, Zee AGvd, Wisman GBA. Abstract 5011: Genome-wide methylation profiling identifies hypermethylated biomarkers in high-grade cervical intraepithelial neoplasia Cancer Research. 72: 5011-5011. DOI: 10.1158/1538-7445.Am2012-5011  0.34
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: 1015-7. PMID 21596900 DOI: 10.1534/Genetics.111.128744  0.468
2011 Johannes F, Colomé-Tatché M. Concerning epigenetics and inbreeding. Nature Reviews. Genetics. 12: 376. PMID 21423241 DOI: 10.1038/Nrg2664-C3  0.352
2011 Johannes F, Colomé-Tatché M. Quantitative epigenetics through epigenomic perturbation of isogenic lines. Genetics. 188: 215-27. PMID 21385727 DOI: 10.1534/Genetics.111.127118  0.456
2011 Concepcion D, Johannes F, Lo YH, Yao J, Fong J, Hamilton BA. Modifier genes for mouse phosphatidylinositol transfer protein α (vibrator) that bypass juvenile lethality. Genetics. 187: 1185-91. PMID 21321132 DOI: 10.1534/Genetics.110.125906  0.311
2010 Johannes F, Wardenaar R, Colomé-Tatché M, Mousson F, de Graaf P, Mokry M, Guryev V, Timmers HT, Cuppen E, Jansen RC. Comparing genome-wide chromatin profiles using ChIP-chip or ChIP-seq. Bioinformatics (Oxford, England). 26: 1000-6. PMID 20208068 DOI: 10.1093/Bioinformatics/Btq087  0.338
2009 Johannes F, Porcher E, Teixeira FK, Saliba-Colombani V, Simon M, Agier N, Bulski A, Albuisson J, Heredia F, Audigier P, Bouchez D, Dillmann C, Guerche P, Hospital F, Colot V. Assessing the impact of transgenerational epigenetic variation on complex traits. Plos Genetics. 5: e1000530. PMID 19557164 DOI: 10.1371/Journal.Pgen.1000530  0.485
2009 Fu J, Keurentjes JJ, Bouwmeester H, America T, Verstappen FW, Ward JL, Beale MH, de Vos RC, 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: 166-7. PMID 19169256 DOI: 10.1038/Ng.308  0.323
2009 Sen S, Johannes F, Broman KW. Selective genotyping and phenotyping strategies in a complex trait context. Genetics. 181: 1613-26. PMID 19153260 DOI: 10.1534/Genetics.108.094607  0.331
2008 Johannes F, Colot V, Jansen RC. Epigenome dynamics: a quantitative genetics perspective. Nature Reviews. Genetics. 9: 883-90. PMID 18927581 DOI: 10.1038/Nrg2467  0.42
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 : Official Journal of the International Mammalian Genome Society. 17: 689-99. PMID 16783647 DOI: 10.1007/S00335-006-0009-7  0.516
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