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Journal Article (58)

Journal Article

Flood, P.; Theeuwen, T. P. J. M.; Schneeberger, K.; Keizer, P.; Kruijer, W.; Severing, E.; Kouklas, E.; Hageman, J. A.; Wijfjes, R.; Calvo-Baltanas, V. et al.; Becker, F. F. M.; Schnabel, S. K.; Willems, L. A. J.; Ligterink, W.; van Arkel, J.; Mumm, R.; Gualberto, J. M.; Savage, L.; Kramer, D. M.; Keurentjes, J. J. B.; van Eeuwijk, F.; Koornneef, M.; Harbinson, J.; Aarts, M. G. M.; Wijnker, E.: Reciprocal cybrids reveal how organellar genomes affect plant phenotypes. Nature Plants 6, pp. 13 - 21 (2020)

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Jiao, W.-B.; Schneeberger, K.: Chromosome-level assemblies of multiple Arabidopsis genomes reveal hotspots of rearrangements with altered evolutionary dynamics. Nature Communications 11 (1), 989 (2020)

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Sang, Q.; Pajoro, A.; Sun, H.-Q.; Song, B.; Yang, X.; Stolze, S. C.; Andrés Lalaguna, F.; Schneeberger, K.; Nakagami, H.; Coupland, G.: Mutagenesis of a Quintuple Mutant Impaired in Environmental Responses Reveals Roles for CHROMATIN REMODELING4 in the Arabidopsis Floral Transition. The Plant Cell (2020)

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Chopra, D.; Mapar, M.; Stephan, L.; Albani, M.; Deneer, A.; Coupland, G.; Willing, E.-M.; Schellmann, S.; Schneeberger, K.; Fleck, C. et al.; Schrader, A.; Huelskamp, M.: Genetic and molecular analysis of trichome development in Arabis alpina. Proceedings of the National Academy of Sciences of the United States of America 116 (24), pp. 12078 - 12083 (2019)

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Dittberner, H.; Becker, C.; Jiao, W.-B.; Schneeberger, K.; Hölzel, N.; Tellier, A.; de Meaux, J.: Strengths and potential pitfalls of hay transfer for ecological restoration revealed by RAD-seq analysis in floodplain Arabis species. Molecular Ecology 28 (17), pp. 3887 - 3901 (2019)

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Kiefer, C.; Willing, E.-M.; Jiao, W.-B.; Sun, H.-Q.; Piednoel, M.; Huemann, U.; Hartwig, B.; Huemann, U.; Koch, M. A.; Schneeberger, K.: Interspecies association mapping links reduced CG to TG substitution rates to the loss of gene-body methylation. Nature Plants 5 (8), pp. 846 - 855 (2019)

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Mohrholz, A.; Sun, H.-Q.; Gloeckner, N.; Hummel, S.; Kolukisaoglu, U.; Schneeberger, K.; Harter, K.: The Striking Flower-in-Flower Phenotype of Arabidopsis thaliana Nossen (No-0) is Caused by a Novel LEAFY Allele. PLANTS-BASEL 8 (12), 599 (2019)

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Rossmann, S.; Richter, R.; Sun, H.; Schneeberger, K.; Töpfer, R.; Zyprian, E.; Theres, K.: Mutations in the miR396 binding site of the growth-regulating factor gene VvGRF4 modulate inflorescence architecture in grapevine. The Plant Journal (2019)

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Sun, H.-Q.; Rowan, B. A.; Flood, P. J.; Brandt, R.; Fuss, J.; Hancock, A. M.; Michelmore, R. W.; Huettel, B.; Schneeberger, K.: Linked-read sequencing of gametes allows efficient genome-wide analysis of meiotic recombination. Nature Communications 10, 4310 (2019)

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Amorim, M. d. F.; Willing, E.-M.; Szabo, E. X.; Francisco-Mangilet, A. G.; Droste-Borel, I.; Macek, B.; Schneeberger, K.; Laubinger, S.: The U1 snRNP Subunit LUC7 Modulates Plant Development and Stress Responses via Regulation of Alternative Splicing. The Plant Cell 30 (11), pp. 2838 - 2854 (2018)

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Flood, P. J.; Theeuwen, T. P. J. M.; Schneeberger, K.; Keizer, P.; Kruijer, W.; Severing, E.; Kouklas, E.; Hageman, J. A.; Becker, F. F. M.; Schnabel, S. K. et al.; Willems, L.; Ligterink, W.; van Arkel, J.; Mumm, R.; Gualberto, J. M.; Savage, L.; Kramer, D. M.; Kreurentjes, J. J. B.; van Eeuwijk, F.; Koornneef, M.; Harbinson, J.; Aarts, M. G. M.; Wijnker, E.: Reciprocal cybrids reveal how organellar genomes affect plant phenotypes. bioRxiv, 477687 (2018)

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Ibanez, C.; Delker, C.; Martinez, C.; Buerstenbinder, K.; Janitza, P.; Lippmann, R.; Ludwig, W.; Sun, H.-Q.; James, G. V.; Klecker, M. et al.; Grossjohann, A.; Schneeberger, K.; Prat, S.; Quint, M.: Brassinosteroids Dominate Hormonal Regulation of Plant Thermomorphogenesis via BZR1. Current Biology 28 (2), pp. 303 - 310.e3 (2018)

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Sun, H.-Q.; Ding, J.; Piednoel, M.; Schneeberger, K.: findGSE: estimating genome size variation within human and Arabidopsis using k-mer frequencies. Bioinformatics 34 (4), pp. 550 - 557 (2018)

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Sun, H.-Q.; Rowan, B. A.; Flood, P. J.; Brandt, R.; Fuss, J.; Hancock, A. M.; Michelmore, R. W.; Huettel, B.; Schneeberger, K.: Linked-read sequencing of gametes allows efficient genome-wide analysis of meiotic recombination. bioRxiv, 484022 (2018)

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Jiao, W.-B.; Garcia Accinelli, G.; Hartwig, B.; Kiefer, C.; Baker, D.; Severing, E.; Willing, E.-M.; Piednoel, M.; Woetzel, S.; Madrid-Herrero, E. et al.; Huettel, B.; Huemann, U.; Reinhardt, R.; Koch, M. A.; Swan, D.; Clavijo, B.; Coupland, G.; Schneeberger, K.: Improving and correcting the contiguity of long-read genome assemblies of three plant species using optical mapping and chromosome conformation capture data. Genome Research 27 (5), pp. 778 - 786 (2017)

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Jiao, W.-B.; Schneeberger, K.: The impact of third generation genomic technologies on plant genome assembly. Current Opinion in Plant Biology 36, pp. 64 - 70 (2017)

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Schneeberger, K.; Henderson, I.: Editorial overview: Genome studies and molecular genetics. Current Opinion in Plant Biology 36, pp. IV - V (2017)

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Zhou, Y.; Tergemina, E.; Tergemina, E.; Cui, H.; Foerderer, A.; Hartwig, B.; James, G. V.; Schneeberger, K.; Turck, F.: Ctf4-related protein recruits LHP1-PRC2 to maintain H3K27me3 levels in dividing cells in Arabidopsis thaliana. Proceedings of the National Academy of Sciences of the United States of America 114 (18), pp. 4833 - 4838 (2017)

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Bewick, A.; Ji, L.; Niederhuth, C.; Willing, E.-M.; Hofmeister, B. T.; Shi, X.; Wang, L.; Lu, Z.; Rohr, N.; Hartwig, B. et al.; Kiefer, C.; Deal, R. B.; Schmutz, J.; Grimwood, J.; Stroud, H.; Jacobsen, S. E.; Schneeberger, K.; Zhang, X.; Schmitz, R. J.: On the origin and evolutionary consequences of gene body DNA methylation. Proceedings of the National Academy of Sciences of the United States of America 113 (32), pp. 9111 - 9116 (2016)

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Cartolano, M.; Huettel, B.; Hartwig, B.; Reinhardt, R.; Schneeberger, K.: cDNA Library Enrichment of Full Length Transcripts for SMRT Long Read Sequencing. PLoS One 11 (6), e0157779 (2016)

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Fransz, P.; Linc, G.; Lee, C.-R.; Aflitos, S. A.; Lasky, J. R.; Toomajian, C.; Ali, H.; Peters, J.; van Dam, P.; Ji, X. et al.; Kuzak, M.; Gerats, T.; Schubert, I.; Schneeberger, K.; Colot, V.; Martienssen, R.; Koornneef, M.; Nordborg, M.; Juenger, T. E.; de Jong, H.; Schranz, M. E.: Molecular, genetic and evolutionary analysis of a paracentric inversion in Arabidopsis thaliana. The Plant Journal 88 (2), pp. 159 - 178 (2016)

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Klasen, J. R.; Barbez, E.; Meier, L.; Meinshausen, N.; Buehlmann, P.; Koornneef, M.; Busch, W.; Schneeberger, K.: A multi-marker association method for genome-wide association studies without the need for population structure correction. Nature Communications 7, 13299 (2016)

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Schneeberger, K.: Plant genic methylation: Conserved for 400 million years. Nature Plants 2 (2), 16003 (2016)

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Stuttmann, J.; Peine, N.; Garcia, A. V.; Wagner, C.; Choudhury, S. R.; Wang, Y.; James, G. V.; Griebel, T.; Alcázar, R.; Tsuda, K. et al.; Schneeberger, K.; Parker, J. E.: Arabidopsis thaliana DM2h (R8) within the Landsberg RPP1-like Resistance Locus Underlies Three Different Cases of EDS1-Conditioned Autoimmunity. PLoS Genetics 12 (4), e1005990 (2016)

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Willing, E.-M.; Piofczyk, T. P.; Albert, A.; Winkler, J. B.; Schneeberger, K.; Pecinka, A.: UVR2 ensures transgenerational genome stability under simulated natural UV-B in Arabidopsis thaliana. Nature Communications 7, 13522 (2016)

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Zapata, L.; Ding, J.; Willing, E.-M.; Hartwig, B.; Bezdan, D.; Jiao, W.-B.; Patel, V.; James, G. V.; Koornneef, M.; Ossowski, S. et al.; Schneeberger, K.: Chromosome-level assembly of Arabidopsis thaliana Ler reveals the extent of translocation and inversion polymorphisms. Proceedings of the National Academy of Sciences of the United States of America 113 (28), pp. E4052 - E4060 (2016)

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Zhou, Y.; Hartwig, B.; James, G. V.; Schneeberger, K.; Turck, F.: Complementary Activities of TELOMERE REPEAT BINDING Proteins and Polycomb Group Complexes in Transcriptional Regulation of Target Genes. Plant Cell 28 (1), pp. 87 - 101 (2016)

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Andrés, F. L.; Romera Branchat, M.; Martinez-Gallegos, R.; Patel, V.; Schneeberger, K.; Jang, S.; Altmuller, J.; Nurnberg, P.; Coupland, G.: Floral Induction in Arabidopsis by FLOWERING LOCUS T Requires Direct Repression of BLADE-ON-PETIOLE Genes by the Homeodomain Protein PENNYWISE. Plant physiology 169 (3), pp. 2187 - 99 (2015)

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Gutjahr, C.; Gobbato, E.; Choi, J.; Riemann, M.; Johnston, M. G.; Summers, W.; Carbonnel, S.; Mansfield, C.; Yang, S.-Y.; Nadal, M. et al.; Acosta, I.; Takano, M.; Jiao, W.-B.; Schneeberger, K.; Kelly, K. A.; Paszkowski, U.: Rice perception of symbiotic arbuscular mycorrhizal fungi requires the karrikin receptor complex. Science Magazine 350 (6267), pp. 1521 - 1524 (2015)

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Hagmann, J.; Becker, C.; Mueller, J.; Stegle, O.; Meyer, R. C.; Wang, G.; Schneeberger, K.; Fitz, J.; Altmann, T.; Bergelson, J. et al.; Borgwardt, K.; Weigel, D.: Century-scale Methylome Stability in a Recently Diverged Arabidopsis thaliana Lineage. PLOS GENETICS 11 (1), e1004920 (2015)

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Liang, S.C.; Hartwig, B.; Perera, P.; Mora-Garcia, S.; de Leau, E.; Thornton, H.; Lima de Alves, F.; Rapsilber, J.; Yang, S.; James, G. V. et al.; Schneeberger, K.; Finnegan, E. J.; Turck, F.; Goodrich, J.: Kicking against the PRCs - A Domesticated Transposase Antagonises Silencing Mediated by Polycomb Group Proteins and Is an Accessory Component of Polycomb Repressive Complex 2. PLoS Genetics 11 (12), e1005660 (2015)

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Lu, X.; Dittgen, J.; Pislewska-Bednarek, M.; Molina, A.; Schneider, B.; Svatos, A.; Doubsky, J.; Schneeberger, K.; Weigel, D.; Bednarek, P. et al.; Schulze-Lefert, P.: Mutant allele-specific uncoupling of PEN3 functions reveals engagement of the ABC transporter in distinct tryptophan metabolic pathways. Plant Physiology 168, pp. 814 - 827 (2015)

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Mateos, J. L.; Madrigal, P.; Tsuda, K.; Rawat, V.; Rawat, V.; Richter, R.; Romera Branchat, M.; Fornara, F.; Schneeberger, K.; Krajewski, P. et al.; Coupland, G.: Combinatorial activities of SHORT VEGETATIVE PHASE and FLOWERING LOCUS C define distinct modes of flowering regulation in Arabidopsis. Genome Biology 16, 31 (2015)

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Rowan, B. A.; Patel, V.; Weigel, D.; Schneeberger, K.: Rapid and Inexpensive Whole-Genome Genotyping-by-Sequencing for Crossover Localization and Fine-Scale Genetic Mapping. G3-GENES GENOMES GENETICS 5 (3), pp. 385 - 398 (2015)

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Sun, H.-Q.; Schneeberger, K.: SHOREmap v3.0: fast and accurate identification of causal mutations from forward genetic screens. Methods in molecular biology (Clifton, N.J.) 1284, pp. 381 - 95 (2015)

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Willing, E.-M.; Rawat, V.; Mandakova, T.; Maumus, F.; James, G. V.; Nordstroem, K.; Becker, C.; Warthmann, N.; Chica, C.; Szarzynska, B. et al.; Zytnicki, M.; Albani, M.; Kiefer, C.; Bergonzi, S.; Castaings, L.; Mateos, J. L.; Berns, M. C.; Bujdoso, N.; Piofczyk, T. P.; de Lorenzo, L.; Barrero-Sicilia, C.; Mateos, I.; Piednoel, M.; Hagmann, J.; Chen-Min-Tao, R.; Iglesias-Fernandez, R.; Schuster, S. C.; Alonso-Blanco, C.; Roudier, F.; Carbonero, P.; Paz-Ares, J.; Davis, S. J.; Pecinka, A.; Quesneville, H.; Colot, V.; Lysak, M. A.; Weigel, D.; Coupland, G.; Schneeberger, K.: Genome expansion of Arabis alpina linked with retrotransposition and reduced symmetric DNA methylation. Nature Plants 1 (2), UNSP 14023, pp. 1 - 7 (2015)

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Bolger, A.; Scossa, F.; Bolger, M. E.; Lanz, C.; Maumus, F.; Tohge, T.; Quesneville, H.; Alseekh, S.; Sorensen, I.; Lichtenstein, G. et al.; Fich, E. A.; Conte, M.; Keller, H.; Schneeberger, K.; Schwacke, R.; Ofner, I.; Vrebalov, J.; Xu, Y.; Osorio, S.; Aflitos, S. A.; Schijlen, E.; Jimenez-Gomez, J. M.; Ryngajllo, M.; Kimura, S.; Kumar, R.; Koenig, D.; Headland, L. R.; Maloof, J. N.; Sinha, N.; van Ham, R. C. H. J.; Lankhorst, R. K.; Mao, L.; Vogel, A.; Arsova, B.; Panstruga, R.; Fei, Z.; Rose, J. K. C.; Zamir, D.; Carrari, F. F.; Giovannoni, J. J.; Weigel, D.; Usadel, B.; Fernie, A. R.: The genome of the stress-tolerant wild tomato species Solanum pennellii. Nature Reviews Genetics 46 (9), pp. 1034 - 1038 (2014)

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Delker, C.; Sonntag, L.; James, G. V.; Janitza, P.; Ibanez, C.; Ziermann, H.; Peterson, T.; Denk, K.; Mull, S.; Ziegler, J. et al.; Davis, S. J.; Schneeberger, K.; Quint, M.: The DET1-COP1-HY5 Pathway Constitutes a Multipurpose Signaling Module Regulating Plant Photomorphogenesis and Thermomorphogenesis. CELL REPORTS 9 (6), pp. 1983 - 1989 (2014)

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Dettmer, J.; Ursache, R.; Campilho, A.; Miyashima, S.; Belevich, I.; O'Regan, S.; Mullendore, D. L.; Yadav, S. R.; Lanz, C.; Beverina, L. et al.; Papagni, A.; Schneeberger, K.; Weigel, D.; Stierhof, Y.-D.; Moritz, T.; Knoblauch, M.; Jokitalo, E.; Helariutta, Y.: CHOLINE TRANSPORTER-LIKE1 is required for sieve plate development to mediate long-distance cell-to-cell communication. Nature Communications 5, 4276 (2014)

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Juraniec, M.; Lequeux, H.; Hermans, C.; Willems, G.; Nordborg, M.; Schneeberger, K.; Salis, P.; Vromant, M.; Lutts, S.; Verbruggen, N.: Towards the discovery of novel genetic component involved in stress resistance in Arabidopsis thaliana. New Phytologist 201 (3), pp. 810 - 824 (2014)

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Kalhorzadeh, P.; Hu, Z.; Cools, T.; Amiard, S.; Willing, E.-M.; De Winne, N.; Gevaert, K.; De Jaeger, G.; Schneeberger, K.; White, C. I. et al.; De Veylder, L.: Arabidopsis thaliana RNase H2 Deficiency Counteracts the Needs for the WEE1 Checkpoint Kinase but Triggers Genome Instability. The Plant Cell 26 (9), pp. 3680 - 3692 (2014)

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Pankin, A.; Campoli, C.; Dong, X.; Kilian, B.; Sharma, R.; Himmelbach, A.; Saini, R.; Davis, S. J.; Stein, N.; Schneeberger, K. et al.; von Korff, M.: Mapping-by-Sequencing Identifies HvPHYTOCHROME C as a Candidate Gene for the early maturity 5 Locus Modulating the Circadian Clock and Photoperiodic Flowering in Barley. Genetics 198 (1), pp. 383 - 396 (2014)

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Rishmawi, L.; Sun, H.; Schneeberger, K.; Huelskamp, M.; Schrader, A.: Rapid Identification of a Natural Knockout Allele of ARMADILLO REPEAT-CONTAINING KINESIN1 That Causes Root Hair Branching by Mapping-By-Sequencing. Plant Physiology 166 (3), pp. 1280 - 1287 (2014)

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Schneeberger, K.: Using next-generation sequencing to isolate mutant genes from forward genetic screens. Nature Reviews Genetics 15 (10), pp. 662 - 676 (2014)

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Zee, P. C.; Mendes-Soares, H.; Yu, Y.-T. N.; Kraemer, S. A.; Keller, H.; Ossowski, S.; Schneeberger, K.; Velicer, G. J.: A SHIFT FROM MAGNITUDE TO SIGN EPISTASIS DURING ADAPTIVE EVOLUTION OF A BACTERIAL SOCIAL TRAIT. EVOLUTION 68 (9), pp. 2701 - 2708 (2014)

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Bergonzi, S.; Albani, M.; Ver Loren van Themaat, E.; Nordstroem, K.; Wang, R.; Schneeberger, K.; Moerland, P. D.; Coupland, G.: Mechanisms of Age-Dependent Response to Winter Temperature in Perennial Flowering of Arabis alpina. Science 340 (6136), pp. 1094 - 1097 (2013)

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James, G. V.; Patel, V.; Nordstroem, K.; Klasen, J. R.; Salome, P. A.; Weigel, D.; Schneeberger, K.: User guide for mapping-by-sequencing in Arabidopsis. GENOME BIOLOGY 14 (6), R61 (2013)

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Koenig, D.; Jimenez-Gomez, J. M.; Kimura, S.; Fulop, D.; Chitwood, D. H.; Headland, L. R.; Kumar, R.; Covington, M. F.; Devisetty, U. K.; Tat, A. V. et al.; Tohge, T.; Bolger, A.; Schneeberger, K.; Ossowski, S.; Lanz, C.; Xiong, G.; Taylor-Teeples, M.; Brady, S. M.; Pauly, M.; Weigel, D.; Usadel, B.; Fernie, A. R.; Peng, J.; Sinha, N. R.; Maloof, J. N.: Comparative transcriptomics reveals patterns of selection in domesticated and wild tomato. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERLICA 110 (28), pp. E2655 - E2662 (2013)

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Kopischke, M.; Westphal, L.; Schneeberger, K.; Clark, R.; Ossowski, S.; Wewer, V.; Fuchs, R.; Landtag, J.; Hause, G.; Doermann, P. et al.; Lipka, V.; Weigel, D.; Schulze-Lefert, P.; Scheel, D.; Rosahl, S.: Impaired sterol ester synthesis alters the response of Arabidopsis thaliana to Phytophthora infestans. The Plant Journal 73 (3), pp. 456 - 468 (2013)

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Logemann, E.; Birkenbihl, R.; Rawat, V.; Schneeberger, K.; Schmelzer, E.; Somssich, I. E.: Functional dissection of the PROPEP2 and PROPEP3 promoters reveals the importance of WRKY factors in mediating microbe-associated molecular pattern-induced expression. New Phytologist 198 (4), pp. 1165 - 1177 (2013)