Publications

Publications

2018

Sun H, Ding J, Piednoël M, Schneeberger K.: findGSE: estimating genome size variation within human and Arabidopsis using k-mer frequencies. Bioinformatics. 2018 Feb 15;34(4):550-557. doi: 10.1093/bioinformatics/btx637.

Ibañez C, Delker C, Martinez C, Bürstenbinder K, Janitza P, Lippmann R, Ludwig W, Sun H, James GV, Klecker M, Grossjohann A, Schneeberger K, Prat S, Quint M.: Brassinosteroids Dominate Hormonal Regulation of Plant Thermomorphogenesis via BZR1. Curr Biol. 2018 Jan 22;28(2):303-310.e3. doi: 10.1016/j.cub.2017.11.077. Epub 2018 Jan 11.

2017

Jiao, W.-B., Accinelli, G.G., Hartwig, B., Kiefer, C., Baker, D., Severing, E., Willing, E.-M., Piednoel, M., Woetzel, S., Madrid-Herrero, E.M., Huettel, B., Hümann, U., Reinhard, R., Koch, M.A., Swan, D., Clavijo, B., Coupland, G. and 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): 778-786, doi: 10.1101/gr.213652.116 (2017)

Jiao, W.-B., Schneeberger, K.  The impact of third generation genomic technologies on plant genome assembly, Current Opinion in Plant Biology 36: 64-70 doi: 10.1016/j.pbi.2017.02.002 (2017)

Plötner B, Nurmi M, Fischer A, Watanabe M, Schneeberger K, Holm S, Vaid N, Schöttler MA, Walther D, Hoefgen R, Weigel D, Laitinen RAE.: Chlorosis caused by two recessively interacting genes reveals a role of RNA helicase in hybrid breakdown in Arabidopsis thaliana. Plant Journal 91 (2):251-262. doi: 10.1111/tpj.13560 (2017)

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

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)

2016

Willing, E, Piofczyk, T, Albert, A, Winkler, J. B., Schneeberger, K, Pecinka, A,: UVR2 ensures transgenerational genome stability under simulated natural UV-B in Arabidopsis thaliana. Nature Communications, doi 10.1038/ncomms13522 (2016) 

Klasen, J.R.; Barbez, E., Meier, L., Meinshausen, N., Bühlmann, P., Koornneef, M., Busch, W., Schmeeberger, K.: A multi-marker association method for genome-wide association studies without the need for population structure correction. In: Nature Communications 7, 13299 (2016), doi:10.1038/ncomms13299.

Zapata, L., Ding, J., Willing, E.-M., Hartwig, B., Bezdan, D., Jiao, W-B., Patel, V., James, C. V., Koornneef, M., Ossowski, S. and K. Schneeberger (2016) Chromosome-level assembly of Arabidopsis thaliana Ler reveals the extent of translocation and inversion polymorphisms. PNAS 2016 113 (28) E4052-E4060; published ahead of print June 27, 2016, doi:10.1073/pnas.160753211

Cartolano, M., Huettel, B., Hartwig, B., Reinhardt, R., & Schneeberger, K. (2016). cDNA Library Enrichment of Full Length Transcripts for SMRT Long Read Sequencing. PloS one, 11(6), e0157779-e0157779. doi:10.1371/journal.pone.0157779.

Schneeberger, K. (2016). Plant genic methylation: Conserved for 400 million years. Nature Plants, 2(2): 16003. doi:10.1038/NPLANTS.2016.3.

Stuttmann, J., Peine, N., Garcia, A. V., Wagner, C., Choudhury, S. R., Wang, Y., James, G. V., Griebel, T., Alcázar, R., Tsuda, K., Schneeberger, K., & Parker, J. E. (2016). Arabidopsis thaliana DM2h (R8) within the Landsberg RPP1-like Resistance Locus Underlies Three Different Cases of EDS1-Conditioned Autoimmunity. PLoS Genetics, 12(4): e1005990. doi:10.1371/journal.pgen.1005990.

Zhou, Y., Hartwig, B., James, G. V., Schneeberger, K., & Turck, F. (2016). Complementary Activities of TELOMERE REPEAT BINDING Proteins and Polycomb Group Complexes in Transcriptional Regulation of Target Genes. Plant Cell, 28(1), 87-101. doi:10.1105/tpc.15.00787.

2015

Andrés, F. L., Romera Branchat, M., Martinez-Gallegos, R., Patel, V., Schneeberger, K., Jang, S., Altmuller, J., Nurnberg, P., & Coupland, G. (2015). 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), 2187-99. doi:10.1104/pp.15.00960.

Gutjahr, C., Gobbato, E., Choi, J., Riemann, M., Johnston, M. G., Summers, W., Carbonnel, S., Mansfield, C., Yang, S.-Y., Nadal, M., Acosta, I., Takano, M., Jiao, W.-B., Schneeberger, K., Kelly, K. A., & Paszkowski, U. (2015). Rice perception of symbiotic arbuscular mycorrhizal fungi requires the karrikin receptor complex. Science 350(6267), 1521-1524. doi:10.1126/science.aac9715.

Hagmann, J., Becker, C., Mueller, J., Stegle, O., Meyer, R. C., Wang, G., Schneeberger, K., Fitz, J., Altmann, T., Bergelson, J., Borgwardt, K., & Weigel, D. (2015). Century-scale Methylome Stability in a Recently Diverged Arabidopsis thaliana Lineage. PLOS GENETICS, 11(1): e1004920. doi:10.1371/journal.pgen.1004920.

Liang, S., Hartwig, B., Perera, P., Mora-Garcia, S., de Leau, E., Thornton, H., Lima de Alves, F., Rapsilber, J., Yang, S., James, G. V., Schneeberger, K., Finnegan, E. J., Turck, F., & Goodrich, J. (2015). 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. doi:10.1371/journal.pgen.1005660.

Lu, X., Dittgen, J., Pislewska-Bednarek, M., Molina, A., Schneider, B., Svatos, A., Doubsky, J., Schneeberger, K., Weigel, D., Bednarek, P., & Schulze-Lefert, P. (2015). Mutant allele-specific uncoupling of PEN3 functions reveals engagement of the ABC transporter in distinct tryptophan metabolic pathways. Plant Physiology 168, 814-827, doi:10.1104/pp.15.00182.

Mateos, J. L., Madrigal, P., Tsuda, K., Rawat, V., Richter, R., Romera Branchat, M., Fomara, F., Schneeberger, K., Krajewski, P., & Coupland, G. (2015). Combinatorial activities of SHORT VEGETATIVE PHASE and FLOWERING LOCUS C define distinct modes of flowering regulation in Arabidopsis. Genome Biology, 16:31. doi:10.1186/s13059-015-0597-1.

Rowan, B. A., Patel, V., Weigel, D., & Schneeberger, K. (2015). Rapid and Inexpensive Whole-Genome Genotyping-by-Sequencing for Crossover Localization and Fine-Scale Genetic Mapping. G3-GENES GENOMES GENETICS, 5(3), 385-398. doi:10.1534/g3.114.016501

Sun, H.-Q., & Schneeberger, K. (2015). SHOREmap v3.0: fast and accurate identification of causal mutations from forward genetic screens. Methods in molecular biology (Clifton, N.J.), 1284, 381-95. doi:10.1007/978-1-4939-2444-8_19.

Willing, E.-M., Rawat, V., Mandakova, T., Maumus, F., James, G. V., Nordstroem, K., Becker, C., Warthmann, N., Chica, C., Szarzynska, B., 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. (2015). Genome expansion of Arabis alpina linked with retrotransposition and reduced symmetric DNA methylation. Nature Plants, 1(2):14023, pp. 1-7. doi:10.1038/NPLANTS.2014.23.

2014

Bolger, A., Scossa, F., Bolger, M. E., Lanz, C., Maumus, F., Tohge, T., Quesneville, H., Alseekh, S., Sorensen, I., Lichtenstein, G., 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. (2014). The genome of the stress-tolerant wild tomato species Solanum pennellii. Nature Reviews Genetics, 46(9), 1034-1038. doi:10.1038/ng.3046.

Delker, C., Sonntag, L., James, G. V., Janitza, P., Ibanez, C., Ziermann, H., Peterson, T., Denk, K., Mull, S., Ziegler, J., Davis, S. J., Schneeberger, K., & Quint, M. (2014). The DET1-COP1-HY5 Pathway Constitutes a Multipurpose Signaling Module Regulating Plant Photomorphogenesis and Thermomorphogenesis. Cell Reports, 9(6), 1983-1989. doi:10.1016/j.celrep.2014.11.043.

Dettmer, J., Ursache, R., Campilho, A., Miyashima, S., Belevich, I., O'Regan, S., Mullendore, D. L., Yadav, S. R., Lanz, C., Beverina, L., Papagni, A., Schneeberger, K., Weigel, D., Stierhof, Y.-D., Moritz, T., Knoblauch, M., Jokitalo, E., & Helariutta, Y. (2014). CHOLINE TRANSPORTER-LIKE1 is required for sieve plate development to mediate long-distance cell-to-cell communication. Nature Communications, 5: 4276. doi:10.1038/ncomms5276.

Juraniec, M., Lequeux, H., Hermans, C., Willems, G., Nordborg, M., Schneeberger, K., Salis, P., Vromant, M., Lutts, S. and Verbruggen, N.: Towards the discovery of novel genetic component involved in stress resistance in Arabidopsis thaliana. New Phytologist 201, 810-824, doi: 10.1111/nph.12554 (2014).

Kalhorzadeh, P., Hu, Z., Cools, T., Amiard, S., Willing, E.-M., De Winne, N., Gevaert, K., De Jaeger, G., Schneeberger, K., White, C. I., & De Veylder, L. (2014). Arabidopsis thaliana RNase H2 Deficiency Counteracts the Needs for the WEE1 Checkpoint Kinase but Triggers Genome Instability. The Plant Cell, 26(9), 3680-3692. doi:10.1105/tpc.114.128108.

Pankin, A., Campoli, C., Dong, X., Kilian, B., Sharma, R., Himmelbach, A., Saini, R., Davis, S. J., Stein, N., Schneeberger, K., & von Korff, M. (2014). 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), 383-396, doi:10.1534/genetics.114.165613.

Rishmawi, L., Sun, H., Schneeberger, K., Huelskamp, M., & Schrader, A. (2014). 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), 1280-1287. doi:10.1104/pp.114.244046.

Schneeberger, K. (2014). Using next-generation sequencing to isolate mutant genes from forward genetic screens. Nature Reviews Genetics, 15(10), 662-676. doi:10.1038/nrg3745.

Zee, P. C., Mendes-Soares, H., Yu, Y.-T.-N., Kraemer, S. A., Keller, H., Ossowski, S., Schneeberger, K., & Velicer, G. J. (2014). A SHIFT FROM MAGNITUDE TO SIGN EPISTASIS DURING ADAPTIVE EVOLUTION OF A BACTERIAL SOCIAL TRAIT. Evolution, 68(9), 2701-2708. doi:10.1111/evo.12467.

2013

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

James GV, Patel V, Nordström KJ, Klasen JR, Salomé PA, Weigel D, Schneeberger K. User guide for mapping-by-sequencing in Arabidopsis. Genome Biol. 14(6):R61 (2013).

Keurentjes, J. J. B., & Schneeberger, K. (2013). The genomic landscape of meiotic crossovers and gene conversions in Arabidopsis thaliana. ELIFE, 2: e01426. doi:10.7554/eLife.01426.

Koenig D, Jiménez-Gómez JM, Kimura S, Fulop D, Chitwood DH, Headland LR, Kumar R, Covington MF, Devisetty UK, Tat AV, Tohge T, Bolger A, Schneeberger K, Ossowski S, Lanz C, Xiong G, Taylor-Teeples M, Brady SM, Pauly M, Weigel D, Usadel B, Fernie AR, Peng J, Sinha NR, Maloof JN. Comparative transcriptomics reveals patterns of selection in domesticated and wild tomato. Proc Natl Acad Sci U S A. 2013 Jul 9;110(28):E2655-62. doi: 10.1073/pnas.1309606110.

Kopischke, M., Westphal, L., Schneeberger,  K., Clark, R., Ossowski, S., Wewer, V., Fuchs, R., Landtag, J., Hause, G., Dörmann, P., Lipka, V., Weigel, D., Schulze-Lefert, P., Scheel, D. and Rosahl, S. 2013. Impaired sterol ester synthesis alters the response of Arabidopsis thaliana to Phytophthora infestans. The Plant Journal, 73, 456–468, DOI: 10.1111/tpj.12046.

Logemann, E., Birkenbihl, R. P., Rawat, V., Schneeberger, K., Schmelzer, E. and Somssich, I. E. 2013. Functional dissection of the PROPEP2 and PROPEP3 promoters reveals the importance of WRKY factors in mediating microbe-associated molecular pattern-induced expression. New Phytologist 133, 1165-1177, doi:10.1111/nph.12233.

Nordström; K. J. V., Albani, M. C.; Velikkakam James, G.; Gutjahr, C.; Hartwig, B.; Turck, F.; Paszkowski, U.; Coupland, G. and K. Schneeberger. 2013. Mutation identification by direct comparison of whole-genome sequencing data from mutant and wild-type individuals using k-mers. Nature Biotechnology 31, 325-330, doi: 10.1038/nbt.2515.

Speth C, Willing EM, Rausch S, Schneeberger K, Laubinger S. RACK1 scaffold proteins influence miRNA abundance in Arabidopsis. Plant J. 2013 Nov;76(3):433-45. doi: 10.1111/tpj.12308. Epub 2013 Oct 5.

Wijnker E, Velikkakam James G, Ding J, Becker F, Klasen JR, Rawat V, Rowan BA, de Jong DF, de Snoo CB, Zapata L, Huettel B, de Jong H, Ossowski S, Weigel D, Koornneef M, Keurentjes JJ, Schneeberger K.: The genomic landscape of meiotic crossovers and gene conversions in Arabidopsis thaliana. ELIFE. 2013 Dec 17;2:e01426. doi: 10.7554/eLife.01426.

2012

 

Galvao, V. C., Nordstroem, K., Lanz, C., Sulz, P., Mathieu, J., Pose, D., Schmid, M., Weigel, D., & Schneeberger, K. 2012. Synteny-based mapping-by-sequencing enabled by targeted enrichment. The Plant Journal, 71, 517-526. doi:10.1111/j.1365-313X.2012.04993.x.

Hartwig B, Velikkakam James G, Konrad K, Schneeberger K, Turck F. 2012. Fast isogenic mapping-by-sequencing of EMS-induced mutant bulks. In: Plant Physiology 160:591-600.

Rutter, M. T., Roles, A., Conner, J. K., Shaw, R. G., Shaw, F. H., Schneeberger, K., Ossowski, S., Weigel, D., & Fenster, C. B. 2012. Fitness of Arabidopsis thaliana mutation accumulation lines whose spontaneous mutations are known. Evolution 66, 2335-2339.

Todesco, M., Balasubramanian, S., Cao, J., Ott, F., Sureshkumar, S., Schneeberger, K., Meyer, R. C., Altmann, T., & Weigel, D. 2012. Natural Variation in Biogenesis Efficiency of Individual Arabidopsis thaliana MicroRNAs. Current Biology 22, 166-170. doi:10.1016/j.cub.2011.11.060.

 

2011


Cao, J., Schneeberger, K., Ossowski, S., Guenther, T., Bender, S., Fitz, J., Koenig, D., Lanz, C., Stegle, O., Lippert, C., Wang, X., Ott, F., Mueller, J., Alonso-Blanco, C., Borgwardt, K., Schmid, K., & Weigel, D. 2011. Whole-genome sequencing of multiple Arabidopsis thaliana populations. Nature Genetics 43, 956-U60.

Guo YL, Fitz J, Schneeberger K, Ossowski S, Cao J, Weigel D. Genome-wide comparison of nucleotide-binding site-leucine-rich repeat-encoding genes in Arabidopsis. 2011. Plant Physiol. 157(2):757-69.

Hu TT, Pattyn P, Bakker EG, Cao J, Cheng JF, Clark RM, Fahlgren N, Fawcett JA, Grimwood J, Gundlach H, Haberer G, Hollister JD, Ossowski S, Ottilar RP, Salamov AA, Schneeberger K, Spannagl M, Wang X, Yang L, Nasrallah ME, Bergelson J, Carrington JC, Gaut BS, Schmutz J, Mayer KF, Van de Peer Y, Grigoriev IV, Nordborg M, Weigel D, Guo YL. 2011. The Arabidopsis lyrata genome sequence and the basis of rapid genome size change.Nat Genet. 43(5):476-81.

Klein, J. D., Ossowski, S., Schneeberger, K., Weigel, D., & Huson, D. H. LOCAS - A Low Coverage Assembly Tool for Resequencing Projects. 2011. PLOS ONE, 6(8). doi:10.1371/journal.pone.0023455.

Schneeberger K, Ossowski S, Ott F, Klein JD, Wang X, Lanz C, Smith LM, Cao J, Fitz J, Warthmann N, Henz SR, Huson DH, Weigel D. 2011. Reference-guided assembly of four diverse Arabidopsis thaliana genomes. Proc Natl Acad Sci U S A. 108(25):10249-54. doi: 10.1073/pnas.1107739108.

Schneeberger K, Weigel D. Fast-forward genetics enabled by new sequencing technologies. 2011. Trends Plant Sci. 16(5):282-8. Doi 10.1016/j.tplants.2011.02.006.

 

2010


Piazza P., Bailey C.D., Cartolano M., Krieger J., Cao J., Ossowski S., Schneeberger K., He F., de Meaux J., Hall N., Macleod N., Filatov D., Hay A., Tsiantis M. 2010. Arabidopsis thaliana Leaf Form Evolved via Loss of KNOX Expression in Leaves in Association with a Selective Sweep. Curr Biol. 20(24):2223-8.

Laitinen R.A., Schneeberger K., Jelly N.S., Ossowski S., Weigel D. Identification of a spontaneous frame shift mutation in a nonreference Arabidopsis accession using whole genome sequencing. Plant Physiol. 153:652-4.

Ossowski, S.*, Schneeberger, K.*, Lucas-Lledo, J.*, Warthmann, N., Clark, R., Shaw, R., Weigel, D., and Lynch, M. 2010. The Rate and Molecular Spectrum of Spontaneous Mutations in Arabidopsis thaliana. Science. 327(5961):92-4.

Werner S., Wollmann H., Schneeberger K., and Weigel D. 2010. Structure determinants for accurate processing of miR172a in Arabidopsis thaliana. Curr Biol. 20(1):42-8.


2009


Mirouze M., Reinders J., Bucher E., Nishimura T., Schneeberger K., Ossowski S., Cao J., Weigel D., Paszkowski J., and Mathieu O. 2009. Selective epigenetic control of retrotransposition in Arabidopsis. Nature 461: 427-430.

Sureshkumar S., Todesco M., Schneeberger K., Harilal R., Balasubramanian S., and Weigel, D. 2009. A genetic defect caused by a triplet repeat expansion in Arabidopsis thaliana. Science 323: 1060-1063.

Schneeberger K.*, Ossowski S.*, Lanz C., Juul, T., Petersen A.H., Nielsen K.L., Jorgensen J.E., Weigel D., and Andersen, S.U. 2009. SHOREmap: simultaneous mapping and mutation identification by deep sequencing. Nat Methods 6: 550-551.

Schneeberger K.*, Hagmann J.*, Ossowski S.*, Warthmann N., Gesing S., Kohlbacher O., and Weigel D. 2009. Simultaneous alignment of short reads against multiple genomes. Genome Biol 10: R98.

Out A.A., van Minderhout I.J., Goeman, J.J., Ariyurek, Y., Ossowski S., Schneeberger K., Weigel, D., van Galen M., Taschner P.E., Tops C.M., Breuning M.H., van Ommen G.J., den Dunnen J.T., Devilee P. and Hes F.J. 2009. Deep sequencing to reveal new variants in pooled DNA samples. Hum Mutat 30: 1703-1712.


2008


De Bona F., Ossowski S., Schneeberger K., and Ratsch G. 2008. Optimal spliced alignments of short sequence reads. Bioinformatics 24: i174-180.

Felippes F.F.*, Schneeberger K.*, Dezulian T., Huson D.H., and Weigel D. 2008. Evolution of Arabidopsis thaliana microRNAs from random sequences. Rna 14: 2455-2459.

Ossowski S.*, Schneeberger K.*, Clark R.M.*, Lanz C., Warthmann N., and Weigel D. 2008. Sequencing of natural strains of Arabidopsis thaliana with short reads. Genome Res 18: 2024-2033.

Zeller G., Clark R.M.*, Schneeberger K.*, Bohlen A., Weigel D., and Ratsch, G. 2008. Detecting polymorphic regions in Arabidopsis thaliana with resequencing microarrays. Genome Res 18: 918-929.


2005-2007


Malde K., Schneeberger K., Coward E., and Jonassen I. 2006. RBR: library-less repeat detection for ESTs. Bioinformatics 22: 2232-2236.

Schneeberger K., Malde K., Coward E., and Jonassen I. 2005. Masking repeats while clustering ESTs. Nucleic Acids Res 33: 2176-2180.

 
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