Publications

Featured Publications

  • Oct 2018
    Architecture of gene regulatory networks controlling flower development in Arabidopsis thaliana.

    Chen, D. *, W. Yan, L.Y. Fu and K. Kaufmann*

    Recommended by F1000

  • Aug 2018
    Dynamic and spatial restriction of Polycomb activity by plant histone demethylases.

    Yan, W.*, D. Chen, C. Smaczniak, J. Engelhorn, H. Liu, W. Yang, A. Graf, C.C. Carles, D.X. Zhou and K. Kaufmann*

  • Jul 2017
    Differences in DNA-binding specificity of floral homeotic protein complexes predict organ-specific target genes.

    Smaczniak, C., J.M. Muiño, D. Chen, G.C. Angenent and K. Kaufmann*

  • Jan 2016
    Evolution of DNA-binding sites of a floral master regulatory transcription factor.

    Muiño, J.M., S. de Bruijn, A. Pajoro, K. Geuten, M. Vingron, G.C. Angenent and K. Kaufmann*

  • Mar 2014
    Dynamics of chromatin accessibility and gene regulation by MADS-domain transcription factors in flower development.

    Pajoro A., P. Madrigal, J.M. Muiño, J.T. Matus, J.Jin, M.A. Mecchia, J.M. Debernardi, J.F. Palatnik, S. Balazadeh, M. Arif, D.S. Ó’Maoiléidigh, F. Wellmer, P. Krajewski J.L. Riechmann, G.C. Angenent and K. Kaufmann*

  • Aug 2013
    FLOWERING LOCUS C in monocots and the tandem origin of angiosperm-specific MADS-box gene subfamilies.

    Ruelens P., R. de Maagd, S. Proost, G. Theissen, K. Geuten and K. Kaufmann*

    Recommended by F1000

    Read more at PubMed

  • Jan 2012
    Characterization of MADS-domain transcription factor complexes in Arabidopsis flower development.

    Smaczniak C., R.G. Immink, J.M. Muiño, R. Blanvillain, M. Busscher, J. Busscher-Lange, Q.D. Dinh, S. Liu, A.H. Westphal, S. Boeren, F. Parcy, L. Xu, C.C. Carles, G.C. Angenent and K. Kaufmann*

    Recommended by F1000

    Read more at PubMed

  • Apr 2010
    Orchestration of Floral Initiation by APETALA1.

    Kaufmann, K.+, F. Wellmer+, J.M. Muino, T. Ferrier, S.E. Wuest, V. Kumar, A. Serrano-Mislata, F. Madueno, P. Krajewski, E.M. Meyerowitz, G.C. Angenent, and J.L. Riechmann

    Recommended by F1000

    Read more at PubMed

All Publications


2019
  • Yan W, D. Chen*, J. Schumacher, D. Durantini, J. Engelhorn, M. Chen, C.C. Carles, K. Kaufmann*: Dynamic control of enhancer activity drives stage-specific gene expression during flower morphogenesis. Nature Communications doi: 10.1038/s41467-019-09513-2.
  • Mikulski P, M.L. Hohenstatt, S. Farrona, C. Smaczniak, Y. Stahl, K. Kalyanikrishna, K. Kaufmann, G.C. Angenent, D. Schubert*: The chromatin-associated protein PWO1 interacts with plant nuclear lamin-like components to regulate nuclear size. The Plant Cell doi: 10.1105/tpc.18.00663.
2018
  • Bruijn S. de*, T. Zhao, J.M. Muiño, E.M. Schranz, G.C. Angenent, K. Kaufmann*: PISTILLATA paralogs in Tarenaya hassleriana have diverged in interaction specificity. BMC Plant Biology doi: 10.1186/s12870-018-1574-0.
  • Chen, D.*, W. Yan, L.Y. Fu and K. Kaufmann*: Architecture of gene regulatory networks controlling flower development in Arabidopsis thaliana. Nature Communications doi: 10.1038/s41467-018-06772-3. ** Recommended by F1000
  • Lai, X.*, A. Stigliani, G. Vachon, C. Carles, C. Smaczniak, C Zubieta, K. Kaufmann, F. Parcy*: Building transcription factor binding site models to understand gene regulation in plants. Molecular Plant doi: 10.1016/j.molp.2018.10.010.
  • Yan, W.*, D. Chen, C. Smaczniak, J. Engelhorn, H. Liu, W. Yang, A. Graf, C.C. Carles, D.X. Zhou and K. Kaufmann*: Dynamic and spatial restriction of Polycomb activity by plant histone demethylases. Nature Plants doi: 10.1038/s41477-018-0219-5.
  • Liu, Y., L.Y. Fu, K. Kaufmann, D. Chen* and M. Chen*: A practical guide for DNase-seq data analysis: from data management to common applications. Briefings in Bioinformatics doi: 10.1093/bib/bby057
  • Chen, D.*, L.Y. Fu, D. Hu, C. Klukas, M. Chen* and K. Kaufmann*: The HTPmod Shiny application enables modeling and visualization of large-scale biological data. Communications Biology 1(1):89. doi: 10.1038/s42003-018-0091-x
  • Kaufmann, K. and CA. Airoldi: Master Regulatory Transcription Factors in Plant Development: A Blooming Perspective. Book Chapter. Methods in Molecular Biology: Plant Transcription Factors. 1830:3-22. doi: 10.1007/978-1-4939-8657-6_1.
  • Balanzà V, I. Martínez-Fernández, S. Sato, M.F. Yanofsky, K. Kaufmann, G.C. Angenent, M. Bemer, C. Ferrándiz: Genetic control of meristem arrest and life span in Arabidopsis by a FRUITFULL-APETALA2 pathway. Nature communications 8;9(1):565. doi: 10.1038/s41467-018-03067-5.
  • Pajoro A, J.M. Muiño, G.C. Angenent, K. Kaufmann: Profiling nucleosome occupancy by MNase-seq: experimental protocol and computational analysis. Book Chapter. Methods in Molecular Biology: Plant Chromatin Dynamics. 1675:167-181. doi: 10.1007/978-1-4939-7318-7_11.
2017
  • Smaczniak, C., J.M. Muiño, D. Chen, G.C. Angenent, K. Kaufmann: Differences in DNA-binding specificity of floral homeotic protein complexes predict organ-specific target genes. The Plant Cell.29(8):1822-1835. doi: 10.1105/tpc.17.00145.
  • Chen, D., K. Kaufmann: Integration of Genome-Wide TF Binding and Gene Expression Data to Characterize Gene Regulatory Networks in Plant Development. Book Chapter. Methods in Molecular Biology: Plant Gene Regulatory Networks. 1629:239-269. doi: 10.1007/978-1-4939-7125-1_16.
  • Smaczniak, C., G.C. Angenent, K. Kaufmann: SELEX-Seq: A Method to Determine DNA Binding Specificities of Plant Transcription Factors. Book Chapter. Methods in Molecular Biology: Plant Gene Regulatory Networks. 629:67-82. doi: 10.1007/978-1-4939-7125-1_6.
  • Kaufmann, K., D. Chen: From Genes to Networks: Characterizing Gene-Regulatory Interactions in Plants. Book Chapter. Methods in Molecular Biology: Plant Gene Regulatory Networks. 1629:1-11. doi: 10.1007/978-1-4939-7125-1_1.
  • Schumacher, J., K. Kaufmann and W. Yan: Multiplexed GuideRNA-expression to Efficiently Mutagenize Multiple Loci in Arabidopsis by CRISPR-Cas9. Bio-protocol. 7(5): e2166. DOI: 10.21769/BioProtoc.2166.
  • Bemer, M., H. van Mourik, J.M. Muiño, C Ferrándiz, K. Kaufmann, G.C. Angenent: FRUITFULL controls SAUR10 expression and regulates Arabidopsis growth and architecture. J Exp Bot. doi: 10.1093/jxb/erx184.
  • Ruelens, P., Z. Zhang, H. van Mourik, S. Maere, K. Kaufmann, Geuten K.: The origin of floral organ identity quartets. The Plant Cell. 29(2):229-242.
2016
  • Sharma N., Ruelens P., D'hauw M., Maggen T., Dochy N., Torfs S., K. Kaufmann, Rohde A., Geuten K., Geuten K.: An FLC homolog is a vernalization-regulated repressor in Brachypodium and is cold-regulated in wheat. Plant Physiology.
  • Wils, C.R., and K. Kaufmann: Gene-regulatory networks controlling inflorescence and flower development in Arabidopsis thaliana. Biochim Biophys Acta. 2016 Jul 31. pii: S1874-9399(16)30164-X.
  • Yan, W., D. Chen and K. Kaufmann: Efficient multiplex mutagenesis by RNA-guided Cas9 and its use in the characterization of regulatory elements in the AGAMOUS gene. In press at Plant Methods.
  • Yan, W., D. Chen, and K. Kaufmann: Molecular mechanisms of floral organ specification by MADS domain proteins. Current Opinion in Plant Biology, pp. 154-162.
  • Muiño, J.M., S. de Bruijn, A. Pajoro, K. Geuten, M. Vingron, G.C. Angenent and K. Kaufmann: Evolution of DNA-binding sites of a floral master regulatory transcription factor. Molecular Biology and Evolution.33(1):185-200.
2015
  • van Mourik H., J.M. Muiño, A. Pajoro, G.C. Angenent, and K. Kaufmann: Characterization of in-vivo DNA-binding events of plant transcription factors by ChIP-seq: experimental protocol and computational analysis. Book Chapter. Methods in Molecular Biology: Plant Functional Genomics. 1284:93-121
2014
  • Debernardi J., M. Mecchia, L. Vercruyssen, C. Smaczniak, K. Kaufmann, D. Inze, R. Rodriguez, J. Palatnik: Post-transcriptional control of GRF transcription factors by microRNA miR396 and GIF co-activator affects leaf size and longevity. Plant Journal Aug;79(3):413-26.
  • Pajoro A., P. Madrigal, J.M. Muiño, J.T. Matus, J.Jin, M.A. Mecchia, J.M. Debernardi, J.F. Palatnik, S. Balazadeh, M. Arif, D.S. Ó’Maoiléidigh, F. Wellmer, P. Krajewski J.L. Riechmann, G.C. Angenent and K. Kaufmann: Dynamics of chromatin accessibility and gene regulation by MADS-domain transcription factors in flower development. Genome Biology 15:R41.
2013
  • Muiño, J.M., C. Smaczniak, G.C. Angenent, K. Kaufmann and A.D.J van Dijk:  Structural determinants of DNA recognition by plant MADS-domain transcription factors. Nucl. Acids Res. 2013. gkt1172 first published online November 25
  • Cheng S., E. van den Bergh, P. Zeng, X. Zhong, J. Xu, X. Liu, J. Hofberger, S. de Bruijn, A. Bhide, C. Kuelahoglu, C. Bian, J. Chen, G. Fan, K. Kaufmann, J.C. Hall, A. Becker, A. Bräutigam, A.P.M. Weber, C. Shi, Z. Zheng, L. Li, M. Lu, Y. Tao, J. Wang, H. Zou, Z. Quan , J.M. Hibberd, G. Zhang, Z-G Zhu, X. Xu and M.E. Schranz: The genome of Tarenaya hassleriana provides insights into reproductive trait and genome evolution of crucifers. Plant Cell.  2013. 25(8):2813-2830.
  • Ruelens P., R. de Maagd, S. Proost, G. Theissen, K. Geuten and K. Kaufmann*: FLOWERING LOCUS C in monocots and the tandem origin of angiosperm-specific MADS-box gene subfamilies. Nature Communications. 2013. 4:2280
  • ** Recommended by F1000
  • Kaufmann, K. and W. Busch: From Weed to Wheat. Meeting Report. Genome Biology. 2013. 14(6):308.
  • N.S. Outchkourov, J.M. Muiño, K. Kaufmann, W.F.J. van IJcken, M.J. Groot Koerkamp, D. van Leenen, P. de Graaf, F.C.P. Holstege, F.G. Grosveld, and H.T.M. Timmers: Balancing of Histone H3K4 Methylation States by the Kdm5c/SMCX Histone Demethylase Modulates Promoter and Enhancer Function. Cell Reports. 2013. 3(4). 1071–1079
2012
  • Smaczniak C, N. Li, S. Boeren, T. America, W. van Dongen, S.S. Goerdayal , S. de Vries, G.C. Angenent and K. Kaufmann*: Proteomics-based identification of low-abundant signaling and regulatory protein complexes in native plant tissues. Nature Protocols. 2012 Dec;7(12):2144-2158.
  • Smaczniak C, R.G. Immink, G.C. Angenent and K. Kaufmann*: Developmental and evolutionary diversity of plant MADS-domain factors: insights from recent studies. Development. 2012 Sep;139(17):3081-98. *
  • de Bruijn S., G.C. Angenent, K. Kaufmann*: Plant 'evo-devo' goes genomic: from candidate genes to regulatory networks. Trends Plant Sci. 2012 Aug;17(8):441-7.
  • Immink R.G., D. Pose, S. Ferrario, F. Ott, K. Kaufmann, F. Leal Valentim, S. De Folter, F. van der Wal, A.D. van Dijk, M. Schmid, G.C. Angenent: Characterisation of SOC1's central role in flowering by the identification of its up- and downstream regulators. Plant Physiol. 2012 Sep;160(1):433-49.
  • Smaczniak C., R.G. Immink, J.M. Muiño, R. Blanvillain, M. Busscher, J. Busscher-Lange, Q.D. Dinh, S. Liu, A.H. Westphal, S. Boeren, F. Parcy, L. Xu, C.C. Carles, G.C. Angenent and K. Kaufmann*: Characterization of MADS-domain transcription factor complexes in Arabidopsis flower development. Proc Natl Acad Sci U S A. 2012 Jan 31;109(5):1560-5. ** Recommended by F1000
  • Wu A., A. Allu Devi, P. Garapati, H. Siddiqui, H. Dortay, M.-I. Zanor, M.A. Asensi-Fabado, S. Munné-Bosch, C. Antonio, T. Tohge, A.R. Fernie, K. Kaufmann, G.-P. Xue, B. Mueller-Roeber and S. Balazadeh: Control of Juvenility by JUNBGRUNNEN 1, a ROS-responsive NAC Transcription Factor, in Arabidopsis thaliana. Plant Cell. 2012 Feb;24(2):482-506.
  • van Mourik, S., K. Kaufmann., A.D.J. van Dijk, G.C. Angenent, R. Merks and J. Molenaar: Simulation of organ patterning on the floral meristem using a polar auxin transport model. PloS One. 2012;7(1):e28762.
2011
  • Liu, W., W. Kohlen, A. Lillo, R. Op den Camp, S. Ivanov, M. Hartog, E. Limpens, M. Jamil, C. Smaczniak, K. Kaufmann, W.-C. Yang, G.J.E.J. Hooiveld, T. Charnikhova, H.J. Bouwmeester, T. Bisseling and R. Geurts: Strigolactone biosynthesis requires the symbiotic GRAS-type transcription factors NSP1 and NSP2. Plant Cell. 2011 Oct;23(10):3853-65.
  • Muiño, M., G.C. Angenent and K. Kaufmann*: Visualizing and characterizing in vivo DNA-binding events and direct target genes of plant transcription factors. Published as book chapter in "Methods in Molecular Biology" (Humana Press). 2011;754:293-305
  • Muiño. J.M., K. Kaufmann, R.C.H.J. van Ham, G.C. Angenent, and P. Krajewski, ChIP-seq Analysis in R (CSAR): An R package for the statistical detection of protein-bound genomic regions. Plant Methods, 2011. 7.11.
  • Kaufmann, K., C. Smaczniak, S. de Vries, G.C. Angenent, and R. Karlova, Proteomics insights into plant signaling and development. Proteomics, 2011. 11(4): li. 744-55.
2010
  • Kaufmann, K.*, A. Pajoro, and G.C. Angenent, Regulation of transcription in plants: mechanisms controlling developmental switches. Nature Reviews Genetics, Dec 2010. 11(12): li. 830-842.
  • Kaufmann, K.+, F. Wellmer+, J.M. Muino, T. Ferrier, S.E. Wuest, V. Kumar, A. Serrano-Mislata, F. Madueno, P. Krajewski, E.M. Meyerowitz, G.C. Angenent, and J.L. Riechmann, Orchestration of Floral Initiation by APETALA1. Science, 2010. 328(5974): li. 85-89. + Contributed equally.
  • ** Editor’s choice, Science Signaling Vol. 3, Issue 116, li. ec106. Pamela Hines: Flower Power. ** Recommended by F1000.
  • van Mourik, S., A.D. van Dijk, M. de Gee, R.G. Immink, K. Kaufmann, G.C. Angenent, R.C. van Ham, and J. Molenaar, Continuous-time modeling of cell fate determination in Arabidopsis flowers. BMC Systems Biology, 2010. 4: li. 101.
  • Kaufmann, K., M. Nagasaki and R. Jáuregui: Modelling the molecular interactions in the flower developmental network of Arabidopsis thaliana. In Silico Biol. 2010. 10, 0008.
  • Kaufmann, K.*, J.M. Muino, M. Osteras, L. Farinelli, P. Krajewski, and G.C. Angenent, Chromatin immunoprecipitation (ChIP) of plant transcription factors followed by sequencing (ChIP-SEQ) or hybridization to whole genome arrays (ChIP-CHIP). Nature Protocols, 2010. 5(3): li. 457-72.
2009
  • Kaufmann, K., J.M. Muino, R. Jauregui, C.A. Airoldi, C. Smaczniak, P. Krajewski, and G.C. Angenent, Target Genes of the MADS Transcription Factor SEPALLATA3: Integration of Developmental and Hormonal Pathways in the Arabidopsis Flower. Plos Biology, 2009. 7(4): li. 854-875. ** Recommended by F1000.
  • Immink, R.G.H., K. Kaufmann, and G.C. Angenent, The 'ABC' of MADS domain protein behaviour and interactions. Seminars in Cell & Developmental Biology, 2010. 21(1): li. 87-93.
  • Urbanus, S.L., S. de Folter, A.V. Shchennikova, K. Kaufmann, R.G.H. Immink, and G.C. Angenent, In planta localisation patterns of MADS domain proteins during floral development in Arabidopsis thaliana. BMC Plant Biology, 2009. 9:5.
2007
  • de Folter, S., S.L. Urbanus, L.G. van Zuijlen, K. Kaufmann, and G.C. Angenent, Tagging of MADS domain proteins for chromatin immunoprecipitation. BMC Plant Biology, 2007. 7:47.
  • Theissen, G. and K. Kaufmann: Molecular developmental genetics and the evolution of flowers. published as a book chapter in "Molecular Biology and Biotechnology of Flowering", 2nd edition (CABI Publishing), Chapter 6, li. 124.
  • Veron, A.S., K. Kaufmann, and E. Bornberg-Bauer: Evidence of interaction network evolution by whole-genome duplications: a case study in MADS-box proteins. Molecular Biology and Evolution, 2007. 24(3).
2002-2006
  • Ciannamea, S., K. Kaufmann, M. Frau, I.A. Tonaco, K. Petersen, K.K. Nielsen, G.C. Angenent, and R.G. Immink, Protein interactions of MADS box transcription factors involved in flowering in Lolium perenne. Journal of Experimental Botany, 2006. 57(13): li. 3419-31.
  • Melzer, R., K. Kaufmann, and G. Theissen, Missing links: DNA-binding and target gene specificity of floral homeotic proteins. Advances in Botanical Research: Incorporating Advances in Plant Pathology, Vol 44, 2006. 44: li. 209-236.
  • Geuten, K., A. Becker+, K. Kaufmann+, P. Caris, S. Janssens, T. Viaene, G. Theissen, and E. Smets, Petaloidy and petal identity MADS-box genes in the balsaminoid genera Impatiens and Marcgravia. Plant Journal, 2006. 47(4): li. 501-518. + Contributed equally.
  • Kaufmann, K.: MIKC-type MADS-box genes in the development and evolution of seed plant reproductive organs. PhD Thesis, Jena University 2005.
  • Nam, J., K. Kaufmann, G. Theissen, and M. Nei, A simple method for predicting the functional differentiation of duplicate genes and its application to MIKC-type MADS-box genes. Nucleic Acids Research, 2005. 33(2):e12.
  • Kaufmann, K., N. Anfang, H. Saedler, and G. Theissen, Mutant analysis, protein-protein interactions and subcellular localization of the Arabidopsis B-sister (ABS) protein. Molecular Genetics and Genomics, 2005. 274(2): li. 103-118.
  • Kaufmann, K., R. Melzer, and G. Theissen, MIKC-type MADS-domain proteins: structural modularity, protein interactions and network evolution in land plants. Gene, 2005. 347(2): li. 183-198.
  • Winter, K.U., C. Weiser, K. Kaufmann, A. Bohne, C. Kirchner, A. Kanno, H. Saedler, and G. Theissen, Evolution of class B floral homeotic proteins: Obligate heterodimerization originated from homodimerization. Molecular Biology and Evolution, 2002. 19(5): li. 587-596.
  • Becker, A., K. Kaufmann, A. Freialdenhoven, C. Vincent, M.A. Li, H. Saedler, and G. Theissen, A novel MADS-box gene subfamily with a sister-group relationship to class B floral homeotic genes. Molecular Genetics and Genomics, 2002. 266(6): li. 942-950.
  • Andere
  • Kerstin Kaufmann, Cezary Smaczniak and Gerco C Angenent: The transcription machinery underlying flower formation. NPC Highlights 9, 2009.
  • Kerstin Kaufmann und Franziska Turck: Mechanismen der transkriptionellen Regulation in der Blütenentwicklung. BIOspektrum 02/2011.