IMPRS Alumni

2024

Journal Article

Castellani, M.; Zhang, M.; Thangavel, G.; Mata Sucre, Y.; Lux, T.; Campoy, J. A.; Marek, M.; Huettel, B.; Sun, H.-Q.; Mayer, K. F. X. et al.; Schneeberger, K.; Marques, A.: Meiotic recombination dynamics in plants with repeat-based holocentromeres shed light on the primary drivers of crossover patterning. Nature Plants (2024)

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Del Toro-De León, G.; van Boven, J.; Santos-González, J.; Jiao, W.-B.; Peng, H.; Schneeberger, K.; Köhler, C.: Epigenetic and transcriptional consequences in the endosperm of chemically induced transposon mobilization in Arabidopsis. Nucleic Acids Research 53 (15), pp. 8833 - 8848 (2024)

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Goel, M.; Campoy, J. A.; Krause, K.; Baus, L. C.; Sahu, A.; Sun, H.-Q.; Walkemeier, B.; Marek, M.; Beaudry, R.; Ruiz, D., D. et al.; Huettel, B.; Schneeberger, K.: The vast majority of somatic mutations in plants are layer-specific. Genome Biology: Biology for the Post-Genomic Era 25 (1), 194 (2024)

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Lian, Q.; Huettel, B.; Walkemeier, B.; Mayjonade, B.; Lopez-Roques, C.; Gil, L.; Roux, F.; Schneeberger, K.; Mercier, R.: A pan-genome of 69 Arabidopsis thaliana accessions reveals a conserved genome structure throughout the global species range. Nature Genetics 56, pp. 982 - 991 (2024)

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Journal Article

Sun, H.-Q.; Abeli, P.; Campoy, J. A.; Ruetjes, T.; Krause, K.; Jiao, W.-B.; Beaudry, R.; Schneeberger, K.: The identification and analysis of meristematic mutations within the apple tree that developed the RubyMac sport mutation. BMC Plant Biology 24 (1), 912 (2024)

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2023

Journal Article

Campos Martin, R.; Schmickler, S.; Goel, M.; Schneeberger, K.; Tresch, A.: Reliable genotyping of recombinant genomes using a robust hidden Markov model. Plant Physiology 192 (2), pp. 821 - 836 (2023)

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2022

Journal Article

Acevedo Garcia, J.; Walden, K.; Leissing, F.; Baumgarten, K.; Drwiega, K.; Kwaaitaal, M.; Reinstadler, A.; Freh, M.; Dong, X.; James, G. V. et al.; Baus, L. C.; Mascher, M.; Stein, N.; Schneeberger, K.; Brocke-Ahmadinejad, N.; Kollmar, M.; Schulze-Lefert, P.; Panstruga, R.: Barley Ror1 encodes a class XI myosin required for mlo-based broad-spectrum resistance to the fungal powdery mildew pathogen. The Plant Journal (2022)

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Journal Article

Goel, M.; Schneeberger, K.: plotsr: visualizing structural similarities and rearrangements between multiple genomes. Bioinformatics 38 (10), pp. 2922 - 2926 (2022)

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Lian, Q.; Solier, V.; Walkemeier, B.; Durand, S.; Huettel, B.; Schneeberger, K.; Mercier, R.: The megabase-scale crossover landscape is largely independent of sequence divergence. Nature Communications 13 (1), 3828 (2022)

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Oruganti, V.; Toegelova, H.; Pecinka, A.; Madlung, A.; Schneeberger, K.: Rapid large-scale genomic introgression in Arabidopsis suecica via an autoallohexaploid bridge. Genetics (2022)

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Sun, H.-Q.; Jiao, W.-B.; Campoy, J. A.; Krause, K.; Goel, M.; Folz-Donahue, K.; Kukat, C.; Huettel, B.; Schneeberger, K.: Chromosome-scale and haplotype-resolved genome assembly of a tetraploid potato cultivar. Nature Genetics 54 (3), pp. 342 - 348 (2022)

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Journal Article

Vinegra de la Torre, N.; Vayssières, A.; Obeng-Hinneh, E.; Neumann, U.; Zhou, Y.; Lazaro, A.; Roggen, A.; Sun, H.; Stolze, S. C.; Nakagami, H. et al.; Schneeberger, K.; Timmers, T.; Albani, M.: FLOWERING REPRESSOR AAA(+) ATPase 1 is a novel regulator of perennial flowering in Arabis alpina. New Phytologist 236, pp. 729 - 744 (2022)

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2021

Journal Article

Jiao, W.-B.; Patel, V.; Klasen, J. R.; Liu, F.; Pecinkova, P.; Ferrand, M.; Gy, I.; Camilleri, C.; Effgen, S.; Koornneef, M. et al.; Pecinka, A.; Loudet, O.; Schneeberger, K.: The Evolutionary Dynamics of Genetic Incompatibilities Introduced by Duplicated Genes in Arabidopsis thaliana. Molecular Biology and Evolution 38 (4), pp. 1225 - 1240 (2021)

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Journal Article

Kawaharada, Y.; Sandal, N.; Gupta, V.; Jin, H.; Kawaharada, M.; Taniuchi, M.; Ruman, H.; Nadzieja, M.; Andersen, K.r. R.; Schneeberger, K. et al.; Stougaard, J.; Andersen, S. U.: Natural variation identifies a Pxy gene controlling vascular organisation and formation of nodules and lateral roots in Lotus japonicus. New Phytologist (2021)

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Madrid-Herrero, E.; Severing, E.; De Ansorena, E.; Kiefer, C.; Brand, L.; Martinez-Gallegos, R.; Woetzel, S.; Kemi, U.; Jiao, W.-B.; Schneeberger, K. et al.; Coupland, G.: Transposition and duplication of MADS-domain transcription factor genes in annual and perennial Arabis species modulates flowering. Proceedings of the National Academy of Sciences of the United States of America 118 (39), e2109204118 (2021)

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Mapar, M.; Chopra, D.; Stephan, L.; Schrader, A.; Sun, H.-Q.; Schneeberger, K.; Albani, M.; Coupland, G.; Huelskamp, M.: Genetic and Molecular Analysis of Root Hair Development in Arabis alpina. Frontiers in Plant Science 12, 767772 (2021)

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Journal Article

Naish, M.; Alonge, M.; Wlodzimierz, P.; Tock, A. J.; Abramson, B. W.; Schmuecker, A.; Mandakova, T.; Jamge, B.; Lambing, C.; Kuo, P. et al.; Yelina, N.; Hartwick, N.; Colt, K.; Smith, L.M.; Ton, J.; Kakutani, T.; Martienssen, R. A.; Schneeberger, K.; Lysak, M. A.; Berger, F.; Bousios, A.; Michael, T. P.; Schatz, M. C.; Henderson, I. R.: The genetic and epigenetic landscape of the Arabidopsis centromeres. SCIENCE 374 (6569), eabi7489, pp. 840 - + (2021)

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Provart, N. J.; Brady, S. M.; Parry, G.; Schmitz, R. J.; Queitsch, C.; Bonetta, D.; Waese, J.; Schneeberger, K.; Loraine, A.E.: Anno genominis XX: 20 years of Arabidopsis genomics. The Plant Cell 33 (4), pp. 832 - 845 (2021)

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Schrinner, S.; Goel, M.; Wulfert, M.; Spohr, P.; Schneeberger, K.; Klau, G. W.: Using the longest run subsequence problem within homology-based scaffolding. Algorithms for Molecular Biology 16 (1), 11 (2021)

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Journal Article

Zhao, C.; Tang, Y.; Wang, J.; Zeng, Y.; Sun, H.-Q.; Zheng, Z.; Su, R.; Schneeberger, K.; Parker, J. E.; Cui, H.: A mis-regulated cyclic nucleotide-gated channel mediates cytosolic calcium elevation and activates immunity in Arabidopsis. New Phytologist 230 (3), pp. 1078 - 1094 (2021)

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2020

Journal Article

Campoy, J. A.; Sun, H.-Q.; Goel, M.; Jiao, W.-B.; Folz-Donahue, K.; Wang, N.; Rubio, M.; Liu, C.; Kukat, C.; Ruiz, D. et al.; Huettel, B.; Schneeberger, K.: Gamete binning: chromosome-level and haplotype-resolved genome assembly enabled by high-throughput single-cell sequencing of gamete genomes. Genome Biology and Evolution 21 (1), 306 (2020)

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de Leone, M. J.; Esteban Hernando, C.; Romanowski, A.; Careno, D.l. A.; Faigon Soverna, A.; Sun, H.-Q.; Bologna, N. G.; Vazquez, M.; Schneeberger, K.; Yanovsky, M. J.: Bacterial Infection Disrupts Clock Gene Expression to Attenuate Immune Responses. Current Biology 30 (9), pp. 1740 - 1747.e6 (2020)

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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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Journal Article

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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Journal Article

Shah, N.; Wakabayashi, T.; Kawamura, Y.; Skoybjerg, C. K.; Wang, M.-Z.; Mustamin, Y.; Isomura, Y.; Gupta, V.; Jin, H.; Mun, T. et al.; Sandal, N.; Azuma, F.; Fukai, E.; Seren, U.; Kusakabe, S.; Kikuchi, Y.; Nitanda, S.; Kumaki, T.; Hashiguchi, M.; Tanaka, H.; Hayashi, A.; Sonderkaer, M.; Nielsen, K.L.; Schneeberger, K.; Vilhjalmsson, B.; Akashi, R.; Stougaard, J.; Sato, S.; Schierup, M. H.; Andersen, S.U.: Extreme genetic signatures of local adaptation during Lotus japonicus colonization of Japan. Nature Communications 11 (1), 253 (2020)

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2019

Journal Article

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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Journal Article

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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Journal Article

Goel, M.; Sun, H.-Q.; Jiao, W.-B.; Schneeberger, K.: SyRI: finding genomic rearrangements and local sequence differences from whole-genome assemblies. Genome Biology: Biology for the Post-Genomic Era 20 (1), 277 (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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Journal Article

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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Journal Article

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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2018

Journal Article

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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Journal Article

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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Journal Article

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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2017

Journal Article

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.; 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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2016

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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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2015

Journal Article

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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Publications of K. Schneeberger

Journal Article (80)