Publications


2024

Backofen R, Costa F, Theis F, et al (2017) MicroRNA as an Integral Part of Cell Communication: Regularized Target Prediction and Network Prediction.  Lecture Notes in Bioengineering: Information- and Communication Theory in Molecular Biology:85-99.

Balao F, Trucchi E, Wolfe T, et al. (2017) Adaptive sequence evolution is driven by biotic stress in a pair of orchid species (Dactylorhiza) with distinct ecological optima. Mol Ecol 26(14):3649-62.

Barbez E, Dünser K, ..., Busch W (2017) Auxin steers root cell expansion via apoplastic pH regulation in Arabidopsis thaliana. Proc Natl Acad Sci USA 114(24):4884-93.

Barbez F, Kleine-Vehn J, Barbez E (2017) Low-Cost Microprocessor-Controlled Rotating Stage for Medium-Throughput Time-Lapse Plant Phenotyping. Methods Mol Biol 1497:37-45.

Batoko H, Dagdas Y, Baluska F, et al. (2017) Understanding and exploiting autophagy signaling in plants. Essays Biochem 61(6):675-85.

Becker C (2017) Paternal effects: Like father, like son. eLife 2017;6:e25669.

Bente H and Mittelsten Scheid O (2017) Epigenetic contribution to diversification. Proc Natl Acad Sci USA 114(14):3558-60.

Bosch J, Djamei A (2017) Isolation of Ustilago bromivora Strains from Infected Spikelets through Spore Recovery and Germination. Bio Protoc 7(14):e2392.

Bowman JL, Kohchi T, Yamato KT et al. (2017) Insights into Land Plant Evolution Garnered from the Marchantia polymorpha Genome. Cell 171(2):287-304.

Carlson KD, Fernandez-Pozo N, Bombarely A et al. (2017) Natural variation in stress response gene activity in the allopolyploid Arabidopsis suecica. BMC Genomics 18(1):653.

Catoni M, Griffiths J, Becker C, et al. (2017) DNA sequence properties that predict susceptibility to epiallelic switching. EMBO J 36(5):617-28.

Czedik-Eysenberg A, Rabe F, ... Djamei A (2017) Overrepresentation Analyses of Differentially Expressed Genes in the Smut Fungus Ustilago bromivora during Saprophytic and in planta Growth. Bio Protoc 7(5):e2426.

Daccord N, Celton JM, Linsmith G, et al. (2017) High-quality de novo assembly of the apple genome and methylome dynamics of early fruit development. Nat Genet 49(7):1099-106.

Di Mambro R, De Ruvo M, Pacifici E, et al. (2017) Auxin minimum triggers the developmental switch from cell division to cell differentiation in the Arabidopsis root. Proc Natl Acad Sci USA 114(36):e7641-9.

Ditengou FA, Gomes D, Nziengui H et al. (2017) Characterization of auxin transporter PIN6 plasma membrane targeting reveals a function for PIN6 in plant bolting. New Phytol 217(4):1610-24.

Doblas VG, Smakowska-Luzan E, Fujita S, et al. (2017) Root diffusion barrier control by a vasculature-derived peptide binding to the SGN3 receptor. Science 355(6322):280-4.

Filiault DL, Seymour DK, Maruthachalam R, et al. (2017) The Generation of Doubled Haploid Lines for QTL Mapping. Methods Mol Biol. 1610:39-57.

Friesner J, Assmann SM, Bastow R et al. (2017) The Next Generation of Training for Arabidopsis Researchers: Bioinformatics and Quantitative Biology. Plant Physiol 175(4):1499-509.

Giovannetti M, Małolepszy A, ..., Busch W (2017) Large-Scale Phenotyping of Root Traits in the Model Legume Lotus japonicus. Methods Mol Biol. 1610:155-167.

Hagmann J, Becker C (2017) Assessing Distribution and Variation of Genome-Wide DNA Methylation Using Short-Read Sequencing. Methods Mol Biol. 1610:61-72.

Ikeda Y, Pélissier T, Bourguet P, et al. (2017) Arabidopsis proteins with a transposon-related domain act in gene silencing. Nat Commun. 8:15122.

Imprialou M, Kahles A, Steffen JG, et al. (2017) Genomic Rearrangements in Arabidopsis Considered as Quantitative Traits. Genetics 205(4):1425-41.

Ingouff M, Selles B, Michaud C, et al. (2017) Live-cell analysis of DNA methylation during sexual reproduction in Arabidopsis reveals context and sex-specific dynamics controlled by noncanonical RdDM. Genes Dev 31(1):72-83.

Jiang D and Berger F (2017) DNA replication-coupled histone modification maintains Polycomb gene silencing in plants. Science 357(6356):1146-9.

Kerdaffrec E, Nordborg M (2017) The maternal environment interacts with genetic variation in regulating seed dormancy in Swedish Arabidopsis thaliana. PLoS One 12(12):e0190242.

Kujirai T, Machida S, Osakabe A, et al. (2017) Influence of polynucleosome preparation methods on sedimentation velocity analysis of chromatin. J Biochem 161(4):381-8.

Lee CR, Svardal H, Farlow A, et al. (2017) On the post-glacial spread of human commensal Arabidopsis thaliana. Nat Comm 8:14458.

Lorković Z, Park C, Goiser M, et al. (2017) Compartmentalization of DNA Damage Response between Heterochromatin and Euchromatin Is Mediated by Distinct H2A Histone Variants. Curr Biol 27(8):1192-9.

Lorković ZJ, Berger F (2017) Heterochromatin and DNA damage repair: use different histone variants and relax. Nucleus 8(6)583-8.

Lozano-Duran R and Belkhadir Y. (2017) A technical framework for studying the signaling nexus of brassinosteroids and immunity. Methods Mol Biol 1564:49-61

Lutzmayer S, Enugutti B, Nodine M (2017) Novel small RNA spike-in oligonucleotides enable absolute normalization of small RNA-Seq data. Sci Reports 7:5913.

Mittelsten Scheid O (2017) Nicht-Mendelsche Genetik. Nova Acta Leopoldina NF 413: 231-250.

Motomura K, Kawashima T, Berger F et al. (2017) A pharmacological study of Arabidopsis cell fusion between the persistent synergid and endosperm. J Cell Sci 131(2):jcs204123.

Nikitaki Z, Pavlopoulou A, Holá M, et al. (2017) Bridging Plant and Human Radiation Response and DNA Repair through an In Silico Approach. Cancers (Basel) 9(6):E65.

Novikova P, Tsuchimatsu T, Simon S, et al. (2017) Genome sequencing reveals the origin of the allotetraploid Arabidopsis suecica. Mol Biol Evol 34(4):957-68.

Opalińska M, Parys K, Jańska H (2017) Identification of Physiological Substrates and Binding Partners of the Plant Mitochondrial Protease FTSH4 by the Trapping Approach. Int J Mol Sci. 18(11):E2455.

Osman K, Yang J, Roitinger E etal. (2017) Affinity proteomics reveals extensive phosphorylation of the Brassica chromosome axis protein ASY1 and a network of associated proteins at prophase I of meiosis. Plant J 93(1):17-33.

Pisupati R, Reichardt I, Seren Ü, et al. (2017) Verification of Arabidopsis stock collections using SNPmatch, a tool for genotyping high-plexed samples. Sci Data 4:170184.

Possart A, Xu T, Paik I, et al. (2017) Characterization Of Phytochrome Interacting Factors From The Moss Physcomitrella Patens Illustrates Conservation Of Phytochrome Signaling Modules In Land Plants. Plant Cell 29(2):310-30.

Rabanal FA, Mandáková T, Soto-Jiménez LM, et al. (2017) Epistatic and allelic interactions control expression of ribosomal RNA gene clusters in Arabidopsis thaliana. Genome Biol. 18(1):75.

Rabanal FA, Nizhynska V, Mandáková T, et al. (2017) Unstable Inheritance of 45S rRNA Genes in Arabidopsis. G3 7(4):1201-9.

Racolta A, Nodine MD, Davies K et al. (2017) A Common Pathway of Root Growth Control and Response to CLE Peptides Through Two Receptor Kinases in Arabidopsis. Genetics 208(2):687-704.

Rao S, Sigl V, Wimmer RA, et al. (2017) RANK rewires energy homeostasis in lung cancer cells and drives primary lung cancer. Genes Dev 31(20)2099-112.

Richards CL, Alonso C, Becker C et al. (2017) Ecological plant epigenetics: Evidence from model and non-model species, and the way forward. Ecol Lett 20(12) 1576-90.

Ristova D, Busch W (2017) Genome-Wide Association Mapping of Root Traits in the Context of Plant Hormone Research. Methods Mol Biol 1497:47-55.

Satbhai SB, Göschl C, Busch W (2017) Automated High-Throughput Root Phenotyping of Arabidopsis thaliana Under Nutrient Deficiency Conditions. Methods Mol Biol. 1610:135-153.

Satbhai SB, Setzer C, ..., Busch W (2017) Natural allelic variation of FRO2 modulates Arabidopsis root growth under iron deficiency. Nat Commun 8:15603.

Schon M and Nodine M (2017) Widespread Contamination of Arabidopsis Embryo and Endosperm Transcriptome Datasets. Plant Cell 29(4):608-17.

Seymour D and Becker C (2017) The causes and consequences of DNA methylome variation in plants. Curr Opin Plant Biol 36:56-63.

Stadlmann J, Taubenschmid J, Wenzel D et al. (2017) Comparative glycoproteomics of stem cells identifies new players in ricin toxicity. Nature 549(7673):538-542.

Stegmann M, Monaghan J, Smakowska-Luzan E, et al. (2017) The receptor kinase FER is a RALF-regulated scaffold controlling plant immune signaling. Science 355(6322):287-9.

Stoeva D, Göschl C, ..., Busch W (2017) Long-Term Confocal Imaging of Arabidopsis thaliana Roots for Simultaneous Quantification of Root Growth and Fluorescent Signals. Methods Mol Biol. 1610:169-183.

Susaki D, Maruyama D, Yelagandula R, et al. (2017) Live-Cell Imaging of F-Actin Dynamics During Fertilization in Arabidopsis thaliana. Methods Mol Biol 1668:47-54.

Svardal H, Jasinska AJ, Apetrei C et al. (2017) Ancient hybridization and strong adaptation to viruses across African vervet monkey populations. Nat Genet 49(12):1705-13.

Togninalli M,  Seren Ü,  Meng D, et al. (2017) The AraGWAS Catalog: a curated and standardized Arabidopsis thaliana GWAS catalog. Nucl Acid Res 46(D1):D1150-6.

Tsuchimatsu T, Goubet PM, Gallina S, et al. (2017) Patterns of polymorphism at the self-incompatibility locus in 1,083 Arabidopsis thaliana genomes. Mol Biol Evol 34(8):1878-89.

Vad V, Cedrim D, Busch W, et al. (2017) Generalized box-plot for root growth ensembles. BMC Bioinformatics 18(Suppl 2):65-80.

Valuchova S, Fulnecek J, Prokop Z, et al. (2017) Protection of Arabidopsis blunt-ended telomeres is mediated by a physical association with the Ku heterodimer. Plant Cell 29(6):1533-45.

Wallner ES, López-Salmerón V, Belevich I, et al. (2017) Strigolactone- and Karrikin-Independent SMXL Proteins Are Central Regulators of Phloem Formation. Curr Biol 27(8):1241-7.

Wójcik AM, Nodine MD, Gaj MD (2017) miR160 and miR166/165 Contribute to the LEC2-Mediated Auxin Response Involved in the Somatic Embryogenesis Induction in Arabidopsis. Front Plant Sci. 8:2024.

Wollmann H, Stroud H, Yelagandula R, et al. (2017) The histone H3 variant H3.3 regulates gene body DNA methylation in Arabidopsis thaliana. Genome Biol 18(1):94.

Wu D, Schandry N, Lahaye T (2017) A modular toolbox for Golden-Gate-based plasmid assembly streamlines generation of Ralstonia solanacearum species complex knockout strains and multi-cassette complementation constructs. Mol Plant Pathol 19(6):1511-22.

Yelagandula R, Osakabe A, Axelsson E, et al. (2017) Genome-Wide Profiling of Histone Modifications and Histone Variants in Arabidopsis thaliana and Marchantia polymorpha. Methods Mol Biol. 1610:93-106.

Zhang X, Liu W, Nagae TT et al. (2017) Structural basis for receptor recognition of pollen tube attraction peptides. Nat Commun 8(1):1331.

Zhou T, Dagdas YF, Zhu X, et al. (2017) The glycogen synthase kinase MoGsk1, regulated by Mps1 MAP kinase, is required for fungal development and pathogenicity in Magnaporthe oryzae. Sci Rep 7(1):945.

Zhu W, Hu B, Becker C et al. (2017) Altered chromatin compaction and histone methylation drive non-additive gene expression in an interspecific Arabidopsis hybrid. Genome Biol 18(1):157.