Systems biology and bioinformatics

Modern biology has a powerful arsenal of high-throughput (or “Omics”) technologies at its hands. Examples of such technologies that we exploit in our research are RNA and epigenome profiling by microarrays and next generation sequencing, proteomics and chemical biology. We collaborate with computational scientists to develop new analysis algorithms and develop tools for data visualization.

MIAME/plant - a standard for microarray experiment annotation

The MIAME/plant white paper.

Software development

Relevant publications

Baerenfaller, K., Massonnet, C., Hennig, L., Russenberger, D., Sulpice, R., Walsh, S., Stitt, M., Granier, C., Gruissem, W. (2015) A long photoperiod relaxes energy management in Arabidopsis leaf six. Current Plant Biology 2, 34-45 (PUBMED)

Shu H, Nakamura M, Siretskiy A, Borghi L, Moraes I, Wildhaber T, Gruissem W, Hennig L (2014) Arabidopsis replacement histone variant H3.3 occupies promoters of regulated genes. Genome Biolology 15: R62 (PUBMED)

Coman, D., Gruissem, W., Hennig, L. (2013) Transcript Profiling in Arabidopsis with Genome Tiling Microarrays. Methods Molecular Biology 1067:35-49. (PUBMED)

Danisman, S., van Dijk, A., Bimbo, A., van der Wal, F., Hennig, L., de Folter, S., Angenent, G., and Immink, R. (2013) Analysis of functional redundancies within the Arabidopsis TCP transcription factor family. Journal of Experimental Botany 2013 Oct 15 (PUBMED)

Baerenfaller, K., Massonnet, C., Walsh, S., Baginsky, S., Bühlmann, B., Hennig, L., Hirsch-Hoffmann, M., Howell, K., Kahlau, S., Radziejwoski, A., Russenberger, D., Rutishauser, D., Small, I., Sulpice, R., Stekhoven, D., Wuyts, N., Stitt, M., Hilson, P., Granier, C., Gruissem, W. (2012) Molecular profiling and integrated analysis of Arabidopsis leaf growth reveals adaptation to water deficit. Molecular Systems Biology 8:606 (MEDLINE)

Bassel, G.W., Gaudinier., A., Brady., S.M., Hennig, L., Rhee, S.Y., De Smet, I. (2012) Systems analysis of plant functional, transcriptional, physical interaction, and metabolic networks. Plant Cell 24, 3859-3875 (MEDLINE)

Stekhoven, D.J, Moraes, I., Sveinbjörnsson, G., Hennig, L., Maathuis, M.H., Bühlmann, P. (2012) Causal Stability Ranking. Bioinformatics 28, 2819-2823 (MEDLINE)

Müller, M., Patrignani, A., Rehrauer, H., Gruissem, W., Hennig, L. (2012) Evaluation of alternative RNA labeling protocols for transcript profiling with Arabidopsis AGRONOMICS1 tiling arrays. Plant Methods 8, 18 (MEDLINE)

Massonnet, C., Vile, D., Fabre, J., Hannah, M.A., Caldana, C., Lisec, J., Beemster, G.T., Meyer, R.C., Messerli, G., Gronlund, J.T., Perkovic, J., Wigmore, E., May, S., Bevan, M.W., Meyer, C., Rubio-Diaz, S., Weigel, D., Micol, J.L., Buchanan- Wollaston, V., Fiorani, F., Walsh, S., Rinn, B., Gruissem, W., Hilson, P., Hennig, L., Willmitzer, L., Granier, C. (2010). Probing the reproducibility of leaf growth and molecular phenotypes: a comparison of three Arabidopsis accessions cultivated in ten laboratories. Plant Physiology 152, 2142-2157

Streitner, C., Hennig, L., Korneli, C., Staiger, D. (2010) Global transcript profiling of transgenic plants constitutively overexpressing the RNA-binding protein AtGRP7. BMC Plant Biology 10, 221 (MEDLINE )

Baginsky, S., Hennig, L., Zimmermann, P., Gruissem, W. (2010) Gene expression analysis, proteomics, and network discovery. Plant Physiology 152, 402-410 (MEDLINE)

Rehrauer, H., Aquino, C., Gruissem, W., Henz, S.R., Hilson, P., Laubinger, S., Naouar, N., Patrignani, A., Rombauts, S., Shu, H., Van de, P.e.Y., Vuylsteke, M., Weigel, D., Zeller, G., Hennig, L. (2010) AGRONOMICS1: A new resource for Arabidopsis transcriptome profiling. Plant Physiology 152, 487-499 (MEDLINE) (Open Access)

Exner, V., Hirsch-Hoffmann, M., Gruissem, W., Hennig, L. (2008) PlantDB – a versatile database for managing plant research. Plant Methods 4, 1 (MEDLINE) (Open Access)

Hennig, L. (2008) Sequence analysis with WinGene/WinPep. In: The protein protocols handbook. 3rd Edition. Ed. Walker, J.M., Totowa, New Jersey: Humana Press, cop

Wille, A., Gruissem, W., Bühlmann, P., Hennig, L. (2007) EVE – External Variance Estimation increases statistical power for detecting differentially expressed genes. Plant Journal 52, 561-569 (MEDLINE)

Hennig, L. (2007) Patterns of Beauty – Omics meets Plant Development. Trends in Plant Sciences 12, 287-293 (MEDLINE)

Hennig, L., Zimmermann, P. (2006) Data warehouses – Your one-stop-shops for microarray data. In: European Training and Networking Activity. Plant Genomics and Bioinformatics Expression Micro Arrays and Beyond - a course book. Ed. J. Freitag, MPI-MPP, Potsdam-Golm

Hennig, L., and Köhler, C. (2006) Case studies for transcriptional profiling. In: Plant Systems Biology. Ed. S. Baginsky and A. Fernie; Birkhäuser, Basel (MEDLINE)

Prelic, A., Bleuler, S., Zimmermann, P., Wille, A., Bühlmann, P., Gruissem, W., Hennig, L., Thiele, L., and Zitzler, E. (2006) A Systematic Comparison and Evaluation of Biclustering Methods for Gene Expression Data. Bioinformatics 22, 1122-1129 (MEDLINE)

Zimmermann, P., Schildknecht, B., Garcia-Hernandez, M., Gruissem, W., Craigon, D., Mukherjee, G., May, S., Parkinson, H., Rhee, S., Wagner, U., Hennig, L. (2006) MIAME/Plant: adding value to plant microarray experiments. Plant Methods 2:1 (MEDLINE) (Open Access)

Hennig, L. (2005) Profiling the Arabidopsis transcriptome. In: DNA Microarrays - Advanced Methods. Ed. U. Nuber; Taylor and Francis Group, Abingdon

Vandepoele, K., Vlieghe, K., Florquin, K., Hennig, L., Beemster, G., Gruissem, W., Van de Peer, Y., Inzé, D., and De Veylder, L. (2005) Genome-wide identification of potential plant E2F target genes. Plant Physiology 139, 316-328 (MEDLINE)

Zimmermann, P., Hennig, L., and Gruissem, W. (2005) Gene function analysis and network discovery using Genevestigator. Trends in Plant Sciences 10, 407-409 (MEDLINE)

Wille, A., Zimmermann, P., Bleuler, S., Hennig, L., Prelic, A., Rohr, P., Thiele, L., Zitzler, E., Gruissem, W., and Bühlmann, P. (2004) A modified gaussian graphical modeling approach for reverse genetic engineering. Genome Biology 5, R92 (MEDLINE) (Open Access)

Zimmermann, P, Hirsch-Hoffmann, M., Hennig, L., and Gruissem, W. (2004) GENEVESTIGATOR: Arabidopsis thaliana microarray database and analysis toolbox. Plant Physioloy 136, 2621-2632 (MEDLINE)

Hennig, L., Gruissem, W., Grossniklaus, U., and Köhler, C. (2004) Transcriptional programs of reproduction. Plant Physiology 135, 1765-1775 (MEDLINE)

Hennig, L., Menges, M., Murray, J., and Gruissem, W. (2003) Arabidopsis transcript profiling on Affymetrix GeneChip arrays. Plant Molecular Biology 53, 423-442 (MEDLINE)

Menges, M., Hennig, L., Gruissem, W., and Murray, J. (2003) Genome-wide gene expression in an Arabidopsis cell suspension. Plant Molecular Biology 53, 457-465 (MEDLINE)

Menges, M., Hennig, L., Gruissem, W. and Murray, J. A. H. (2002) Cell cycle regulated gene expression in Arabidopsis. Journal of Biological Chemistry 277, 41987-49002 (MEDLINE) 

Hennig, L. (2002) Sequence analysis with WinGene/WinPep. In: The protein protocols handbook. Ed. Walker, J.M., Totowa, New Jersey : Humana Press, cop. 

Hennig, L. (1999) WinGene/WinPep: User-friendly software for the analysis of aminoacid sequences. BioTechniques 26, 1170-1172 (MEDLINE)