Publications

Featured Publications

  • Feb 2023
    Dual specificity and target gene selection by the MADS-domain protein FRUITFULL.

    van Mourik, H.+, P. Chen+, C. Smaczniak, S. Boeren, K. Kaufmann, M. Bemer, G.C. Angenent, and J.M. Muino*

    Nature Plants

    PubMed

  • May 2022
    A 3D gene expression atlas of the floral meristem based on spatial reconstruction of single nucleus RNA sequencing data.

    Neumann, M.+, X. Xu+, C. Smaczniak, J. Schumacher, W. Yan, N. Blüthgen, T. Greb, H. Jönsson, J. Traas, K. Kaufmann, and J.M. Muino*

    Nature Communications

    PubMed

  • Aug 2021
    The intervening domain is required for DNA-binding and functional identity of plant MADS transcription factors.

    Lai, X.+, R. Vega-Léon+, V. Hugouvieux+*, R. Blanc-Mathieu, F. van der Wal, J. Lucas, C.S. Silva, A. Jourdain, J.M. Muino, M.H. Nanao, R. Immink, K. Kaufmann, F. Parcy, C. Smaczniak*, and C. Zubieta*

    Nature Communications

    PubMed

  • Apr 2019
    Dynamic control of enhancer activity drives stage-specific gene expression during flower morphogenesis.

    Yan W+, D. Chen+*, J. Schumacher, D. Durantini, J. Engelhorn, M. Chen, C.C. Carles, and K. Kaufmann*

    Nature Communications

    PubMed

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

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

    Nature Communications

    Recommended by F1000

    PubMed

  • 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*

    Nature Plants

    PubMed

  • 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*

    Plant Cell

    PubMed

  • 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*

    Molecular Biology and Evolution

    PubMed

  • 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*

    Genome Biology

    PubMed

  • 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*

    Nature Communications

    Recommended by F1000

    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*

    Proceedings of the National Academy of Sciences of the United States of America

    Recommended by F1000

    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

    Science

    Recommended by F1000

    PubMed

All Publications

2024
  • Grones, C, T. Eekhout, D. Shi, M. Neumann, L.S. Berg, Y. Ke, R. Shahan, K.L. Cox, Jr, F. Gomez-Cano, H. Nelissen, J.U. Lohmann, S. Giacomello, O.C. Martin, B. Cole, J.-W. Wang, K. Kaufmann, M.T. Raissig, G. Palfalvi, T. Greb, M. Libault*, B. De Rybel*: Best practices for the execution, analysis, and data storage of plant single-cell/nucleus transcriptomics. The Plant Cell, Jan 2024; koae003. DOI: 10.1093/plcell/koae003 PubMedID: 38231860
2023
  • Atanasov, V., J. Schumacher, J.M. Muiño, C. Larasati, L. Wang, K. Kaufmann, D. Leister, T. Kleine*: Arabidopsis BBX14 is involved in high light acclimation and seedling development. The Plant Journal, Dec 2023; Online ahead of print. DOI: 10.1111/tpj.16597 PubMedID: 38128030
  • Smaczniak, C*: Immunoprecipitation-Mass Spectrometry (IP-MS) of Protein-Protein Interactions of Nuclear-Localized Plant Proteins. Book chapter in: Methods in Molecular Biology: Plant Gene Regulatory Networks, Sep 2023; 2698:163–181. DOI: 10.1007/978-1-0716-3354-0_11 PubMedID: 37682475
  • Chen, P., C. Smaczniak, J. Haffner, J.M. Muino and K. Kaufmann : Estimating DNA-Binding Specificities of Transcription Factors Using SELEX-Seq. Book chapter in: Methods in Molecular Biology: Plant Gene Regulatory Networks, Sep 2023; 2698:147–161. DOI: 10.1007/978-1-0716-3354-0_10 PubMedID: 37682474
  • Vandepoele, K. and K. Kaufmann: Characterization of Gene Regulatory Networks in Plants Using New Methods and Data Types. Book chapter in: Methods in Molecular Biology: Plant Gene Regulatory Networks, Sep 2023; 2698:1–11. DOI: 10.1007/978-1-0716-3354-0_1 PubMedID: 37682465
  • Neumann, M* and J.M. Muino: A Hands-On Guide to Generate Spatial Gene Expression Profiles by Integrating scRNA-seq and 3D-Reconstructed Microscope-Based Plant Structures. Book chapter in: Methods in Molecular Biology: Flower Development, Aug 2023; 2686:567–580. DOI: 10.1007/978-1-0716-3299-4_27 PubMedID: 37540378
  • Zhang, L., C. He, Y. Lai, Y. Wang, L. Kang, A. Liu, C. Lan, H. Su, Y. Gao, Z. Li, F. Yang, Q. Li, H. Mao, D. Chen, W. Chen, K. Kaufmann, and W. Yan*: Asymmetric gene expression and cell-type-specific regulatory networks in the root of bread wheat revealed by single-cell multiomics analysis. Genome Biology, Apr 2023; 24(1):65. DOI: 10.1186/s13059-023-02908-x PubMedID: 37016448
  • van Mourik, H.+, P. Chen+, C. Smaczniak, S. Boeren, K. Kaufmann, M. Bemer, G.C. Angenent, and J.M. Muino*: Dual specificity and target gene selection by the MADS-domain protein FRUITFULL. Nature Plants, Feb 2023; 9(3):473–485. DOI: 10.1038/s41477-023-01351-x PubMedID: 36797351
  • Richter, A.S., T. Nägele, B. Grimm, K. Kaufmann, M. Schroda, D. Leister, and T. Kleine*: Retrograde signaling in plants: A critical review focusing on the GUN pathway and beyond. Plant Communications, Jan 2023; 4(1):100511. DOI: 10.1016/j.xplc.2022.100511 PubMedID: 36575799
  • Marand, A.P.*, A.L. Eveland*, K. Kaufmann*, and N.M. Springer*: cis-Regulatory Elements in Plant Development, Adaptation and Evolution. Annual Review of Plant Biology, Jan 2023; 74:111–37. DOI: 10.1146/annurev-arplant-070122-030236 PubMedID: 36608347
2022
  • Heisler, M.G., H. Jönsson, S. Wenkel, and K. Kaufmann*: Context-specific functions of transcription factors controlling plant development: From leaves to flowers. Current Opinion in Plant Biology, Oct 2022; 69:102262. DOI: 10.1016/j.pbi.2022.102262 PubMedID: 35952407
  • Fu, L-Y.+, T. Zhu+, X. Zhou+, R. Yu+, Z. He, P. Zhang, Z. Wu, M. Chen, K. Kaufmann*, and D. Chen* : ChIP-Hub provides an integrative platform for exploring plant regulome. Nature Communications, Jun 2022; 13(1):3413. DOI: 10.1038/s41467-022-30770-1 PubMedID: 35701419
  • Neumann, M.+, X. Xu+, C. Smaczniak, J. Schumacher, W. Yan, N. Blüthgen, T. Greb, H. Jönsson, J. Traas, K. Kaufmann, and J.M. Muino*: A 3D gene expression atlas of the floral meristem based on spatial reconstruction of single nucleus RNA sequencing data. Nature Communications, May 2022; 13(1):2838. DOI: 10.1038/s41467-022-30177-y PubMedID: 35595749
2021
  • Sunaga-Franze D.Y.+, J.M. Muiño+, C. Braeuning+, X. Xu+, M. Zong, C. Smaczniak, W. Yan, C. Fischer, R. Vidal, M. Kliem, K. Kaufmann*, and S. Sauer*: Single‐nucleus RNA sequencing of plant tissues using a nanowell‐based system. The Plant Journal, Nov 2021; 108(3):859–869. DOI: 10.1111/tpj.15458 PubMedID: 34390289
  • Plant Cell Atlas Consortium, S. G. Jha, A. T. Borowsky, B. J. Cole, N. Fahlgren, A. Farmer, S. C. Huang, P. Karia, M. Libault, N. J. Provart, S. L. Rice, M. Saura-Sanchez, P. Agarwal, A. H. Ahkami, C. R. Anderton, S. P. Briggs, J. A. Brophy, P. Denolf, L. F. Di Costanzo, M. Exposito-Alonso, S. Giacomello, F. Gomez-Cano, K. Kaufmann, D. K. Ko, S. Kumar, A. V. Malkovskiy, N. Nakayama, T. Obata, M. S. Otegui, G. Palfalvi, E. H. Quezada-Rodríguez, R. Singh, R. G. Uhrig, J. Waese, K. Van Wijk, R. C. Wright, D. W. Ehrhardt, K. D. Birnbaum, and S. Y. Rhee: Science Forum: Vision, challenges and opportunities for a Plant Cell Atlas. eLife, Sep 2021; 10:e66877. DOI: 10.7554/eLife.66877 PubMedID: 34491200
  • Lai, X.+, R. Vega-Léon+, V. Hugouvieux+*, R. Blanc-Mathieu, F. van der Wal, J. Lucas, C.S. Silva, A. Jourdain, J.M. Muino, M.H. Nanao, R. Immink, K. Kaufmann, F. Parcy, C. Smaczniak*, and C. Zubieta*: The intervening domain is required for DNA-binding and functional identity of plant MADS transcription factors. Nature Communications, Aug 2021; 12(1):4760. DOI: 10.1038/s41467-021-24978-w PubMedID: 34362909
  • Xu, X., C. Smaczniak, J.M. Muino, and K. Kaufmann*: Cell identity specification in plants: lessons from flower development. Journal of Experimental Botany, May 2021; 72(12):4202-4217. DOI: 10.1093/jxb/erab110 PubMedID: 33865238
  • Kleine, T., T. Nägele, H.E. Neuhaus, C. Schmitz‐Linneweber, A.R. Fernie, P. Geigenberger, B. Grimm, K. Kaufmann, E. Klipp, J. Meurer, T. Möhlmann, T. Mühlhaus, B. Naranjo, J. Nickelsen, A. Richter, H. Ruwe, M. Schroda, S. Schwenkert, O. Trentmann, F. Willmund, R. Zoschke, and D. Leister*: Acclimation in plants – the Green Hub consortium. The Plant Journal, Apr 2021; 106(1):23-40. DOI: 10.1111/tpj.15144 PubMedID: 33368770
2020
  • Chen, L., Q.-H. Zhu, and K. Kaufmann*: Long non-coding RNAs in plants: emerging modulators of gene activity in development and stress responses. Planta, Nov 2020; 252(5):92. DOI: 10.1007/s00425-020-03480-5 PubMedID: 33099688
2019
  • 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, Sep 2019; 20(5):1865-1877. DOI: 10.1093/bib/bby057 PubMedID: 30010713
  • Lai, X.*, A. Stigliani, G. Vachon, C. Carles, C. Smaczniak, C Zubieta, K. Kaufmann, and F. Parcy*: Building transcription factor binding site models to understand gene regulation in plants. Molecular Plant, Jun 2019; 12(6):743-763. DOI: 10.1016/j.molp.2018.10.010 PubMedID: 30447332
  • Mikulski P+, M.L. Hohenstatt+, S. Farrona, C. Smaczniak, Y. Stahl, K. Kalyanikrishna, K. Kaufmann, G.C. Angenent, and D. Schubert*: The chromatin-associated protein PWO1 interacts with plant nuclear lamin-like components to regulate nuclear size. The Plant Cell, May 2019; 31(5):1141-1154. DOI: 10.1105/tpc.18.00663 PubMedID: 30914470
  • Yan W+, D. Chen+*, J. Schumacher, D. Durantini, J. Engelhorn, M. Chen, C.C. Carles, and K. Kaufmann*: Dynamic control of enhancer activity drives stage-specific gene expression during flower morphogenesis. Nature Communications, Apr 2019; 10(1):1705. DOI: 10.1038/s41467-019-09513-2 PubMedID: 30979870
2018
  • de Bruijn S.*, T. Zhao, J.M. Muiño, E.M. Schranz, G.C. Angenent, and K. Kaufmann*: PISTILLATA paralogs in Tarenaya hassleriana have diverged in interaction specificity. BMC Plant Biology, Dec 2018; 18(1):368. DOI: 10.1186/s12870-018-1574-0 PubMedID: 30577806
  • Chen, D.+*, W. Yan+, L.Y. Fu, and K. Kaufmann*: Architecture of gene regulatory networks controlling flower development in Arabidopsis thaliana. Nature Communications, Oct 2018; 9(1):4534. DOI: 10.1038/s41467-018-06772-3 PubMedID: 30382087 Recommended by F1000: 734350283
  • 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 Sep 2018; 4(9):681-689. DOI: 10.1038/s41477-018-0219-5 PubMedID: 30104650
  • 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, Jul 2018; 1(1):89. DOI: 10.1038/s42003-018-0091-x PubMedID: 30271970
  • Kaufmann, K.*, and CA. Airoldi*: Master Regulatory Transcription Factors in Plant Development: A Blooming Perspective. Book chapter in: Methods in Molecular Biology: Plant Transcription Factors, Jul 2018; 1830:3-22. DOI: 10.1007/978-1-4939-8657-6_1 PubMedID: 30043361
  • Balanzà V, I. Martínez-Fernández, S. Sato, M.F. Yanofsky, K. Kaufmann, G.C. Angenent, M. Bemer, and C. Ferrándiz*: Genetic control of meristem arrest and life span in Arabidopsis by a FRUITFULL-APETALA2 pathway. Nature Communications, Feb 2018; 9(1):565. DOI: 10.1038/s41467-018-03067-5 PubMedID: 29422669
2017
  • Pajoro A*, J.M. Muiño, G.C. Angenent, and K. Kaufmann: Profiling nucleosome occupancy by MNase-seq: experimental protocol and computational analysis. Book chapter in: Methods in Molecular Biology: Plant Chromatin Dynamics, Oct 2017; 1675:167-181. DOI: 10.1007/978-1-4939-7318-7_11 PubMedID: 29052192
  • Smaczniak, C.+, J.M. Muiño+, D. Chen, G.C. Angenent, and K. Kaufmann*: Differences in DNA-binding specificity of floral homeotic protein complexes predict organ-specific target genes. The Plant Cell, Aug 2017; 29(8):1822-1835. DOI: 10.1105/tpc.17.00145 PubMedID: 28733422
  • Chen, D.* and K. Kaufmann: Integration of Genome-Wide TF Binding and Gene Expression Data to Characterize Gene Regulatory Networks in Plant Development. Book chapter in: Methods in Molecular Biology: Plant Gene Regulatory Networks, Jun 2017; 1629:239-269. DOI: 10.1007/978-1-4939-7125-1_16 PubMedID: 28623590
  • Smaczniak, C., G.C. Angenent and K. Kaufmann*: SELEX-Seq: A Method to Determine DNA Binding Specificities of Plant Transcription Factors. Book chapter in: Methods in Molecular Biology: Plant Gene Regulatory Networks, Jun 2017; 1629:67-82. DOI: 10.1007/978-1-4939-7125-1_6 PubMedID: 28623580
  • Kaufmann, K.* and D. Chen: From Genes to Networks: Characterizing Gene-Regulatory Interactions in Plants. Book chapter in: Methods in Molecular Biology: Plant Gene Regulatory Networks, Jun 2017; 1629:1-11. DOI: 10.1007/978-1-4939-7125-1_1 PubMedID: 28623575
  • Schumacher, J., K. Kaufmann and W. Yan*: Multiplexed GuideRNA-expression to Efficiently Mutagenize Multiple Loci in Arabidopsis by CRISPR-Cas9. Bio-Protocol Mar 2017; 7(5):e2166. DOI: 10.21769/BioProtoc.2166
  • Bemer, M.*, H. van Mourik, J.M. Muiño, C Ferrándiz, K. Kaufmann, and G.C. Angenent: FRUITFULL controls SAUR10 expression and regulates Arabidopsis growth and architecture. Journal of Experimental Botany, Jun 2017; 68(13):3391-3403. DOI: 10.1093/jxb/erx184 PubMedID: 28586421
  • Ruelens, P., Z. Zhang, H. van Mourik, S. Maere, K. Kaufmann, and Geuten K.*: The origin of floral organ identity quartets. The Plant Cell, Feb 2017; 29(2):229-242. DOI: 10.1105/tpc.16.00366 PubMedID: 28100708
  • Sharma N.+, P. Ruelens+, M. D'hauw, T. Maggen, N. Dochy, S. Torfs, K. Kaufmann, A. Rohde, and K. Geuten*: An FLC homolog is a vernalization-regulated repressor in Brachypodium and is cold-regulated in wheat. Plant Physiology, Feb 2017; 173(2):1301-1315. DOI: 10.1104/pp.16.01161 PubMedID: 28034954
  • Wils, C.R. and K. Kaufmann*: Gene-regulatory networks controlling inflorescence and flower development in Arabidopsis thaliana. Biochimica et Biophysica Acta. Gene regulatory mechanisms, Jan 2017; 1860(1):95-105. DOI: 10.1016/j.bbagrm.2016.07.014 PubMedID: 27487457
2016
  • 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. Plant Methods, Apr 2016; 12(1):23. DOI: 10.1186/s13007-016-0125-7 PubMedID: 27118985
  • Yan, W., D. Chen and K. Kaufmann*: Molecular mechanisms of floral organ specification by MADS domain proteins. Current Opinion in Plant Biology, Feb 2016; 29:154-162. DOI: 10.1016/j.pbi.2015.12.004 PubMedID: 26802807
  • 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, Jan 2016; 33(1):185-200. DOI: 10.1093/molbev/msv210 PubMedID: 26429922
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 in: Methods in Molecular Biology: Plant Functional Genomics, Feb 2015; 1284:93-121. DOI: 10.1007/978-1-4939-2444-8_5 PubMedID: 25757769
2014
  • Debernardi J., M. Mecchia, L. Vercruyssen, C. Smaczniak, K. Kaufmann, D. Inze, R. Rodriguez, and J. Palatnik*: Post-transcriptional control of GRF transcription factors by microRNA miR396 and GIF co-activator affects leaf size and longevity. The Plant Journal, Aug 2014; 79(3):413-426. DOI: 10.1111/tpj.12567 PubMedID: 24888433
  • 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, Mar 2014; 15(3):R41. DOI: 10.1186/gb-2014-15-3-r41 PubMedID: 24581456
  • 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. Nucleic Acids Research, Feb 2014; 42(4):2138-2146. DOI: 10.1093/nar/gkt1172 PubMedID: 24275492
2013
  • 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. The Plant Cell, Aug 2013; 25(8):2813-2830. DOI: 10.1105/tpc.113.113480 PubMedID: 23983221
  • 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, Aug 2013; 4(1):2280. DOI: 10.1038/ncomms3280 PubMedID: 23955420 Recommended by F1000: 718077563
  • Kaufmann, K.* and W. Busch*: Plant genomics: from weed to wheat. Meeting Report. Genome Biology, Jun 2013; 14(6):308. DOI: 10.1186/gb-2013-14-6-308 PubMedID: 23805946
  • 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, Apr 2013; 3(4):1071-1079. DOI: 10.1016/j.celrep.2013.02.030 PubMedID: 23545502
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, Dec 2012; 7(12):2144-2158. DOI: 10.1038/nprot.2012.129 PubMedID: 23196971
  • 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, Sep 2012; 139(17):3081-3098. DOI: 10.1242/dev.074674 PubMedID: 22872082
  • 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, and G.C. Angenent: Characterisation of SOC1's central role in flowering by the identification of its up- and downstream regulators. Plant Physiology, Sep 2012; 160(1):433-449. DOI: 10.1104/pp.112.202614 PubMedID: 22791302
  • de Bruijn S., G.C. Angenent and K. Kaufmann*: Plant 'evo-devo' goes genomic: from candidate genes to regulatory networks. Trends in Plant Science, Aug 2012; 17(8):441-447. DOI: 10.1016/j.tplants.2012.05.002 PubMedID: 22698378
  • 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: JUNGBRUNNEN1, a reactive oxygen species-responsive NAC transcription factor, regulates longevity in Arabidopsis. The Plant Cell, Feb 2012; 24(2):482-506. DOI: 10.1105/tpc.111.090894 PubMedID: 22345491
  • 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, Jan 2012; 7(1):e28762. DOI: 10.1371/journal.pone.0028762 PubMedID: 22291882
  • 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. Proceedings of the National Academy of Sciences of the United States of America, Jan 2012; 109(5):1560-1565. DOI: 10.1073/pnas.1112871109 PubMedID: 22238427 Recommended by F1000: 13491977
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. The Plant Cell Oct 2011; 23(10):3853-3865. DOI: 10.1105/tpc.111.089771 PubMedID: 22039214
  • Muiño, J.M., G.C. Angenent and K. Kaufmann*: Visualizing and characterizing in vivo DNA-binding events and direct target genes of plant transcription factors. Book chapter in: Methods in Molecular Biology: Plant Transcription Factors, Jun 2011; 754:293-305. DOI: 10.1007/978-1-61779-154-3_17 PubMedID: 21720960
  • 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, May 2011; 7(1):11. DOI: 10.1186/1746-4811-7-11 PubMedID: 21554688
  • Kaufmann, K., C. Smaczniak, S. de Vries, G.C. Angenent, and R. Karlova*: Proteomics insights into plant signaling and development. Proteomics, Feb 2011; 11(4):744-755. DOI: 10.1002/pmic.201000418 PubMedID: 21241020
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):830-842. DOI: 10.1038/nrg2885 PubMedID: 21063441
  • 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, Jul 2010; 4(1):101. DOI: 10.1186/1752-0509-4-101 PubMedID: 20649974
  • 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, Apr 2010; 328(5974):85-89. DOI: 10.1126/science.1185244 PubMedID: 20360106 Recommended by F1000: 2972958
    Editor’s choice: P. Hines: Flower Power. Science Signaling. 2010, Apr 6; 3(116):ec106. DOI: 10.1126/scisignal.3116ec106
  • 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, Mar 2010; 5(3):457-472. DOI: 10.1038/nprot.2009.244 PubMedID: 20203663
  • Immink, R.G.H.*, K. Kaufmann*, and G.C. Angenent*: The 'ABC' of MADS domain protein behaviour and interactions. Seminars in Cell and Developmental Biology, Feb 2010; 21(1):87-93. DOI: 10.1016/j.semcdb.2009.10.004 PubMedID: 19883778
  • Kaufmann, K., M. Nagasaki and R. Jáuregui*: Modelling the molecular interactions in the flower developmental network of Arabidopsis thaliana. In Silico Biology Jan 2010; 10(1):125-143. DOI: 10.3233/ISB-2010-0414 PubMedID: 22430225
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. Apr 2009; 7(4):e1000090. DOI: 10.1371/journal.pbio.1000090 PubMedID: 19385720 Recommended by F1000: 1159888
  • 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, Jan 2009; 9(1):5. DOI: 10.1186/1471-2229-9-5 PubMedID: 19138429
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, Sep 2007; 7(1):47. DOI: 10.1186/1471-2229-7-47 PubMedID: 17868439
  • 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, Mar 2007; 24(3):670-678. DOI: 10.1093/molbev/msl197 PubMedID: 17175526
2006
  • Melzer, R., K. Kaufmann and G. Theissen: Missing links: DNA-binding and target gene specificity of floral homeotic proteins. Book chapter in: Advances in Botanical Research: Developmental Genetics of the Flower, 2006; 44:209-236. DOI: 10.1016/S0065-2296(06)44005-2
  • 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, Oct 2006; 57(13):3419-3431. DOI: 10.1093/jxb/erl144 PubMedID: 17005923
  • 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. The Plant Journal, Aug 2006; 47(4):501-518. DOI: 10.1111/j.1365-313X.2006.02800.x PubMedID: 16856983
  • Theissen, G. and K. Kaufmann: Molecular developmental genetics and the evolution of flowers. Book chapter in: The Molecular Biology and Biotechnology of Flowering, 2nd edition (CABI Publishing), May 2006, ch.6:124-149, ISBN: 9781845930424.
2002-2005
  • Kaufmann, K.: MIKC-type MADS-box genes in the development and evolution of seed plant reproductive organs. PhD Thesis, Jena University, 2005.
  • 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, Sep 2005; 274(2):103-118. DOI: 10.1007/s00438-005-0010-y PubMedID: 16080001
  • Kaufmann, K., R. Melzer, and G. Theissen*: MIKC-type MADS-domain proteins: structural modularity, protein interactions and network evolution in land plants. Gene, Mar 2005; 347(2):183-198. DOI: 10.1016/j.gene.2004.12.014 PubMedID: 15777618
  • 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, Jan 2005; 33(2):e12. DOI: 10.1093/nar/gni003 PubMedID: 15659573
  • 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, May 2002; 19(5):587-596. DOI: 10.1093/oxfordjournals.molbev.a004118 PubMedID: 11961093
  • 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, Feb 2002; 266(6):942-950. DOI: 10.1007/s00438-001-0615-8 PubMedID: 11862488
Other
  • Kaufmann, K.: Beautiful Monstrosities. German Research, 2019; 41(2):30–37. DOI: 10.1002/germ.201970209
  • Kaufmann, K.: Bildschöne Monstrositäten. Forschung, 2019; 44(1):16–21. DOI: 10.1002/fors.201970105
  • Kaufmann K.* und F. Turck: Mechanismen der transkriptionellen Regulation in der Blütenentwicklung. BIOspektrum, Apr 2011; 17:165-167. DOI: 10.1007/s12268-011-0023-5
  • Kaufmann K., C. Smaczniak and G.C. Angenent: The transcription machinery underlying flower formation. NPC Highlights, 2009; 9:5-7.
Preprints
  • Muino, J.M.*, C. Großmann, T. Kleine, and K. Kaufmann*: Natural genetic variation in GLK1-mediated photosynthetic acclimation in response to light. Preprint in: BioRxiv, Oct 2023. DOI: 10.1101/2023.10.28.564491
  • Muino, J.M., Y. Qu, H. Ruwe, S. Maschmann, W. Chen, R. Zoschke, U. Ohler*, K. Kaufmann*, and C. Schmitz-Linneweber*: MatK impacts Differential Chloroplast Translation of Ribosomal and Photosynthetic genes by limiting spliced tRNA-K(UUU) abundance. Preprint in: BioRxiv, Oct 2023. DOI: 10.1101/2023.10.25.563914
  • Hugouvieux, V.*, R. Blanc-Mathieu, M. Paul, A. Janeau, X. Xu, J. Lucas, X. Lai, A. Galien, W. Yan, M. Nanao, K. Kaufmann, F. Parcy, and C. Zubieta*: SEPALLATA-driven MADS transcription factor tetramerization is required for inner whorl floral organ development. Preprint in: BioRxiv, May 2023. DOI: 10.1101/2023.05.23.541941
  • Zhao, J., D. Shi*, K. Kaeufer, C. Song, X. Xu, L. Luzzietti,T. Bennett, K. Kaufmann, and T. Greb*: Strigolactones optimise plant water usage by modulating vessel formation. Preprint in: BioRxiv, Apr 2023. DOI: 10.1101/2023.04.05.535530
+ Contributed equally.
* Corresponding author.