Systematics, Biodiversity and Evolution of Plants

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Research articles

1. Iwasaki, M., Kajiwaram, T., Yasui, Y., Yoshitake, Y., Miyazaki, M., Kawamura, S., Suetsugu, N., Nishihama, R., Yamaoka, S., Wanke, D., Hashimoto, K., Kuchitsu, K., Montgomery S. A., Singh, S., Tanizawa, Y., Yagura, M. Mochizuki, T., Sakamoto, M., Nakamura, Y., Liu, C., Berger, F., Yamato K. T., Bowman, J. L., Kohchi, T. (2021). Identification of the sex-determining factor in the liverwort Marchantia polymorpha reveals unique evolution of sex chromosomes in a haploid system.
Current Biology 31: 1-11.

2. Tessi, T. M., Brumm, S., Winklbauer, E., Schumacher, B., Pettinari, G., Lescano, I., González, C. A., Wanke, D., Maurino, V .G., Harter, K., Desimone, M. (2021). Arabidopsis AZG2 transports cytokinins in vivo and regulates lateral root emergence.
New Phytol. 229(2):979-993.

3. Theune, M.L., Bloss, U., Brand, L.H., Ladwig, F., *Wanke, D. (2019).
Phylogenetic Analyses and GAGA-Motif Binding Studies of BBR/BPC Proteins Lend to Clues in GAGA-Motif Recognition and a Regulatory Role in Brassinosteroid Signaling.
Front Plant Sci. 16;10:466

4. Shanks, C.M., Hecker, A., Cheng, C.Y., Brand, L., Collani, S., Schmid, M., Schaller, G.E., Wanke, D., Harter, K., Kieber, J.J. (2018).
Role of BASIC PENTACYSTEINE transcription factors in a subset of cytokinin signaling responses.
The Plant Journal 95(3):458-473. doi: 10.1111/tpj.13962

5. Theune M.L., Humel S., Jaspert N., Lafos M., *Wanke, D. (2017).
Dimerization of the BASIC PENTACYSTEINE domain in plant GAGA-factors is mediated by disulfide bonds and required for DNA-binding.
J. of Advances in Plant Biol. 1 (1): 27

6. Fischer S.M , Böser A., Hirsch J.P., *Wanke, D. (2016).
Quantitative Analysis of Protein-DNA Interaction by qDPI-ELISA.
Methods Mol Biol. 1482:49-66

7. Hecker, A., Brand, L.H., Peter, S., Simoncello, N., Kilian, J., Gaudin, V., *Wanke, D. (2015)
Plant Physiology 168(3):1013-1024

8. Soyk, S., Šimková, K., Zürcher, E., Luginbühl, L., Brand, L.H., Vaughan, C.K., Wanke, D., Zeeman, S.C. (2014).
The Enzyme-Like Domain of Arabidopsis Nuclear Beta-Amylases is Critical During DNA Sequence Recognition and Transcriptional Activation.
The Plant Cell 26(4):1746-1763

9. Brand, L.H., Fischer, N.M., Harter, K., Kohlbacher, O., *Wanke, D. (2013).
Elucidating the evolutionary conserved DNA-binding specificities of WRKY transcription factors by molecular dynamics and in vitro binding assays
Nucleic Acids Research 41(21): 9764-9778

10. Brand, L.H., Henneges, C., Schüssler, A., Kolukisaoglu, H.Ü., Koch, G., Wallmeroth N, Hecker A, Thurow, K., Zell, A., Harter, K., *Wanke, D. (2013).
Sscreening for protein-DNA interactions by automatable DPI-ELISA
PLoS One 8(10): e75177.

11. Eichner, J., Topf, F., Dräger, A., Wrzodek, C., Wanke, D., Zell, A. (2013).
TFpredict and SABINE: Sequence-Based Prediction of Structural and Functional Characteristics of Transcription Factors.
PLoS One 8(12): e82238.

12. Hahn, A., Kilian, J., Mohrholz, A., Ladwig, F., Peschke, F., Dautel, R., Harter, K., Berendzen, K.W., *Wanke, D. (2013).
The Plant Core Environmental Stress Response Genes are systemically coordinated during abiotic stresses
Intern. Journal of Molecular Sciences 14(4):7617-7641

13. Berendzen, K.W., Weiste, C., Wanke, D., Kilian, J., Harter, K., Dröge-Laser, W. (2012).
Bioinformatic cis-element analyses performed in Arabidopsis and Rice disclose bZIP- and MYB-related binding sites as potential AuxRE-coupling elements in auxin-mediated transcription
BMC Plant Biology 12(1):125

14. Wenke, K., Wanke, D., Kilian, J., Berendzen, K.W., Harter, K., Piechulla, B. (2012).
Volatiles of two growth-inhibiting rhizobacteria commonly engage AtWRKY18 function.
The Plant Journal 70(3):445-459

15. Tanz, S., Kilian, J., Johnsson, C., Apel, K., Small, I., Harter, K., Wanke, D., Pogson, B., Albrecht, V. (2012). SCO2 is involved in the regulation of chlorophyll biosynthesis and the formation of thylakoids by interacting with the LHCB1 chlorophyll a/b binding proteins
The Plant Journal 69(5): 743-754

16. Kilian, J., Peschke, F., Berendzen, K.W., Harter, K., *Wanke, D. (2012). Prerequisites, performance and profits of transcriptional profiling the abiotic stress response
Biochim. Biophys. Acta 1819(2):166-175

17. *Wanke, D. (2011)The ABA-mediated switch between submersed and emersed life-styles in aquatic macrophytes
Journal of Plant Research 201: 467-475

18. *Wanke, D., Hohenstatt, M.L., Dynowski, M., Bloss, U., Hecker, A., Elgass, K., Hummel, S., Hahn, A., Caesar, K., Schleifenbaum, F., Harter, K., Berendzen, K.W. (2011). Alanine Zipper-Like Coiled-Coil Domains Are Necessary for Homotypic Dimerization of Plant GAGA-Factors in the Nucleus and Nucleolus.
PLoS One. 6(2):e16070. shared first authors/equally contributing authors

19. Mangelsen, E., Kilian, J., Harter, K., Jansson, C., Wanke, D., Sundberg, E. (2011). Global gene expression analysis of high-temperature stress in developing barley (Hordeum vulgare) caryopses: Early stress response mechanisms and effects on storage compound biosynthesis
Mol Plant. 4(1):97-115.

20. Schröder, A., Eichner, J., Supper, J., Eichner, J, Wanke, D., Henneges, C., Zell, A. (2010). Predicting DNA-binding specificities of eukaryotic transcription factors.
PLoS One. 2010 Nov 30;5(11):e13876

21. Brand, L.H., Kirchler, T., Hummel, S., Chaban, C., *Wanke, D. (2010). DPI-ELISA: a fast and versatile method to specify the binding of plant transcription factors to DNA in vitro
Plant Methods 6(1):25

22. Elgass, K., Caesar, K., Wanke, D., Meixner, A., Harter, K., Schleifenbaum, F. (2010). Application of FLIM-FIDSAM for the In Vivo Analysis of Hormone Competence of Different Cell Types.
Anal. Bioanal. Chem. 398(5):1919-1925.

23. Wanke, D., Kolukisaoglu, H.Ü. (2010). An update on the ABCC/MRP transporter family in plants - many genes, many proteins, but how many functions?
Plant Biol. 12(s1):15-25.

24. Mangelsen, E., Wanke, D., Kilian, J., Sundberg, E., Harter, K., Jansson, C. (2010). Significance of light, sugar, and amino acid supply for diurnal gene regulation in developing barley caryopses.
Plant Physiol. 153(1):14-33 shared first authors/equally contributing authors

25. Wrzodek, C., Schröder, A., Dräger, A., Wanke, D., Berendzen, K.W., Kronfeld, M., Harter, K., Zell, A. (2010). ModuleMaster: A new tool to decipher transcriptional regulatory networks.
Biosystems 99(1):79-81.

26. *Wanke, D., Harter, K. (2009). Analysis of plant regulatory DNA sequences by the yeast one-hybrid assay.
In: Methods in Molecular Biology: Plant Signal Transduction (Humana Press) 479:291-309.

27. Berendzen, K.W., Harter, K., *Wanke, D. (2009). Analysis of plant regulatory DNA sequences by transient protoplast assays and computer aided sequence evaluation.
In: Methods in Molecular Biology: Plant Signal Transduction (Humana Press) 479:311-335.

28. Ciolkowski, I., Wanke, D., Birkenbiehl, R., Somssich, I.E. (2008). Studies on DNA-binding selectivity of WRKY transcription factors lend structural clues into WRKY-domain function.
Plant Mol Biol. 68, 81-92.

29. Mangelsen, E., Kilian, J., Berendzen, K.W., Kolukisaoglu, Ü., Harter, K., Jansson, C., *Wanke, D. (2008). Phylogenetic and comparative gene expression analysis of barley (Hordeum vulgare) WRKY transcription factor family reveals putatively retained functions between monocots and dicots.
BMC Genomics 9, e194.

30. Hahn, A., Zimmermann, R., Wanke, D., Harter, K., Edelmann H.G. (2008). The root cap determines ethylene-dependent growth and development in maize roots.
Mol. Plant 1, 359-367.

31. Supper, J., Strauch, M., Wanke, D., Harter, K., Zell. A. (2007). EDISA: A novel approach to extract gene modules from 3D gene-condition-time expression data.
BMC Bioinformatics 8, e334.

32. Strauch, M., Supper, J., Spieth, C., Wanke, D., Kilian, J., Harter, K., Zell, A. (2007). A two-step clustering for 3-D gene expression data reveals the main features of the Arabidopsis stress response.
J. Integrative Bioinformatics 4, e54.

33. Kilian, J., Whitehead, D., Horak, J., Wanke, D., Weinl, S., Batistic, O., D´Angelo, C., Bornberg-Bauer, E., Kudla, J., Harter, K. (2007). The AtGenExpress global stress expression data set: Protocols, evaluation and exemplary data analysis of UV-B light, drought and cold stress responses.
The Plant Journal 50, 347-363.

34. Berendzen, K.W., Stüber, K., Harter, K., *Wanke, D. (2006). Cis-motifs upstream of the transcription and translation initiation sites are effectively revealed by their positional disequilibrium in eukaryote genomes using frequency distribution curves.
BMC Bioinformatics 7, 522-541.

35. Santi, L., Wang, Y., Stile, M.R., Berendzen, K.W., Wanke, D., Roig, C., Pozzi, C., Muller, K., Muller, J., Rohde, W., Salamini, F. (2003). The GA/TC octodinucleotide repeat binding factor BBR participates in the transcriptional regulation of the homeobox gene Bkn3.
The Plant Journal 34, 813-826.

36. Kolukisaoglu, H.U., Bovet, L., Klein, M., Eggmann, T., Geisler, M., Wanke, D., Martinoia, E., Schulz B. (2002): Family business: the multidrug-resistance related protein (MRP) ABC transporter genes in Arabidopsis thaliana.
Planta. 216(1):107-119.

eBooks / books

37. Berendzen, K.W. (ed.), Kilian, J., Wanke, D. (co-eds.).(2013)
Bentham eBook, DOI: 10.2174/9781608054923113010009

38. Wenke, K., Weise, T., Warnke, R., Valverde, C., Wanke, D., Kai, M., Piechulla, B. (2012b). Bacterial volatiles mediating information between bacteria and plants.
In “Biocommunication in Plants”, Witzany, G. & Baluska, F. (eds.). Springer, Heidelberg, doi: 10.1007/978-3-642-23524-5

39. *Wanke, D., Berendzen, K.W., Kilian, J., Harter, K. (2009). Insights into Arabidopsis abiotic stress response from the AtGenExpress expression profile dataset.
In “Plant Stress Biology: Genomics Goes Systems Biology”, WILEY-VCH.


40. Brand, H. L., Satbhai, S.B., Kolukisaoglu, H. Ü., *Wanke, D. (2013)
Limits and prospects of methods for the analysis of DNA-protein interaction.
In "The Analysis of Regulatory DNA: Current Developments, Knowledge and Applications Uncovering Gene Regulation”: 124-148.
Berendzen (ed.), Kilian, Wanke (co-eds.).
Bentham eBook, DOI: 10.2174/9781608054923113010009

41. *Wanke, D., Luise H. Brand, Nina M. Fischer, Florian Peschke, Joachim Kilian, *Berendzen, K.W.(2013) Implications of DNA-nanostructures by Hoogsteen-dinucleotides on transcription factor binding. QP-PQ: Quantum Probability and White Noise Analysis - Vol. 30: 351 -362 in "Quantum Bio-Informatics V: From Quantum Information to Bio-Informatics". World Scientific (2013; ISBN: 978-981-4460-01-9)
*shared corresponding authorship

42. Schröder, A., Wrzodek, C., Wollnik, J., Dräger, A., Wanke, D., Berendzen, K.W., Zell, A. (2011). Inferring transcriptional regulators for sets of co-expressed genes by multi-objective evolutionary optimization
Proceedings of 2011 IEEE Congress on Evolutionary Computation

43. Feldmeier, K., Kilian, J., Harter, K., *Wanke, D., *Berendzen, K.W.
Quantile-Quantile Plots: An approach for the inter-species comparison of promoter architecture in eukaryotes. QP-PQ: Quantum Probability and White Noise Analysis - Vol. 28: 373 - 386 in "Quantum Bio-Informatics III: From Quantum Information to Bio-Informatics". World Scientific (2011; ISBN: 978-981-4304-05-4)
*shared corresponding authorship

44. *Wanke, D., Hahn, A., Kilian, J., Harter, K., *Berendzen, K.W. (2010). Regulatory Networks: Inferring functional relationships through Co-expression. QP-PQ: Quantum Probability and White Noise Analysis - Vol. 26: 405 - 424 in "Quantum Bio-Informatics III: From Quantum Information to Bio-Informatics". World Scientific (2010; ISBN: 978-981-4304-05-4)
*shared corresponding authorship

45. *Wanke, D., Kilian, J., Bloss, U., Mangelsen, E., Supper, J., Harter, K., Berendzen, K.W (2009). Integrating biological perspectives: A quantum leap for microarray expression analysis. QP-PQ: Quantum Probability and White Noise Analysis - Vol. 24: 327 - 344 in "Quantum Bio-Informatics II: From Quantum Information to Bio-Informatics". World Scientific (2009; ISBN: 10 981-4273-74-0)

46. Wanke, D., Kilian, J. (2009). A basic introduction to gene expression studies using microarray expression data analysis. QP-PQ: Quantum Probability and White Noise Analysis - Vol. 24: 314 - 326 "Quantum Bio-Informatics II: From Quantum Information to Bio-Informatics". World Scientific (2009; ISBN: 10 981-4273-74-0)

47. Supper, J., aufm Kampe, C., Wanke, D., Berendzen, K.W., Harter, K., Bonneau, R., Zell, A. (2008). Modeling gene regulation and spatial organization of sequence based motifs.
8th IEEE international conference on BioInformatics and BioEngineering (BIBE 2008).

48. *Wanke, D., Kilian, J., Supper, J., Berendzen, K.W., Zell, A., Harter, K. (2008). The analysis of gene expression and cis-regulatory elements in large microarray expression data sets. QP-PQ: Quantum Probability and White Noise Analysis - Vol. 21: 294 - 314 in "Quantum Bio-Informatics: From Quantum Information to Bio-Informatics". World Scientific (2008; ISSN: 1793-5121)

49. *Wanke, D. (2002): Aponogeton distachyos - Eine Bereicherung für Gartenteich und Essenstisch.
D. Aqu. u. Terr. Z. (DATZ) 55 (8): 22 – 25.

50. *Wanke, D. (2001): Die „geflügelte Schwertpflanze“.
D. Aqu. u. Terr. Z. (DATZ) 54 (6): 62 - 63; 54 (7):34 – 35.

51. *Wanke, D. (1999a): Ansichten zum „Formenkreis“ um Echinodorus cylindricus Rataj (1975) und Echinodorus glaucus Rataj (1975).
Aqua Planta 24 (3): 105 – 111.

52. *Wanke, D. (1999b): Vorkommen von Ludwigia adscendens (L.) Hara subsp. diffusa (Forssk.) Raven (1962) im Nationalpark Richtersveld, Südafrika.
Aqua Planta 24 (1): 9 – 16.

53. Schwitzer, C., Gantner, S., *Wanke, D. (1998-99): Drei südbrasilianische Echinodorus-„Arten“ vom Aussterben bedroht.
D. Aqu. u. Terr. Z. (DATZ) 51 (12): 800 – 805; 52 (1): 54 - 57

54. Roth, F., Seifert, M., *Wanke, D., Wanke, S. (1997): Ottelia alismoides (L.) Persoon (1805) in Norditalien.
Aqua Planta 22 (4): 138 - 143

55. *Wanke, D. (1996): Der südamerikanische Froschbiß.
D. Aqu. u. Terr. Z. (DATZ) 49 (7): 459 - 463

56. Roth, F., Seifert, M., Wanke, D., Wanke, S. (1995): Der Laubfrosch in der norditalienischen Po-Ebene.
Das Aquarium 317 (11): 45 - 46

57. Roth, F., Seifert, M., *Wanke, D., Wanke, S. (1995): Ein Brachsenkraut aus Oberitalien, Isoetes malinverniana Cesati & de Notaris.
D. Aqu. u. Terr. Z. (DATZ) 48 (8): 526 - 529

58. *Wanke, D., Wanke, S. (1994): Brasilien – der Echinodorus-Arten wegen.
D. Aqu. u. Terr. Z. (DATZ) 47 (9): 594 – 598); (10): 660 – 663

Book reviews

59. *Wanke, D. (2015):”Foreword”. in Asano et al. “Quantum Adaptivity in Biology: From Genetics to Cognition”. Springer, ISBN 978-94-017-9818-1

60. *Wanke, D. (2005):”Aquarienpflanzen“. by Claus-Peter Gering, Franck-Kosmos Verlag;
D. Aqu. u. Terr. Z. (DATZ) 58 (3): 66

61. *Wanke, D. (2002): "Echinodorus - Die beliebtesten Aquarienpflanzen" by C. Kasselmann, Dähne-Verlag;
D. Aqu. u. Terr. Z. (DATZ) 55 (7): 58

62. *Wanke, D. (2001): "Pflanzenaquarien gestalten" by C. Kasselmann, Franck-Kosmos Verlag;
D. Aqu. u. Terr. Z. (DATZ) 54 (12): 56 – 57