Selected publications

 

Haghikia, A., Joerg, S., Duscha, A., Berg, J., Manzel, A., Waschbisch, A., Hammer, A., Lee, D.H., May, C., Wilck, N., Balogh, A., Ostermann, A.I., Schebb, N.H., Akkad, D.A., Grohme, D.A., Kleinewietfeld, M., Kempa, S., Thoene, J., Demir, S., Mueller, D.N., Gold, R., Linker, R.A. Dietary fatty acids directly impact central nervous system autoimmunity via the small intestine. Immunity 43(4): 817-829, 2015.

 

Mackowiak, S.D., Zauber, H., Bielow, C., Thiel, D., Kutz, K., Calviello, L., Mastrobuoni, G., Rajewsky, N., Kempa, S., Selbach, M., Obermayer, B. Extensive identification and analysis of conserved small ORFs in animals. Genome Biol 16: 179, 2015.

 

Hartmann, L., Pedrotti, L., Weiste, C., Fekete, A., Schierstaedt, J., Goettler, J., Kempa, S., Krischke, M., Dietrich, K., Mueller, M.J., Vicente-Carbajosa, J., Hanson, J., Droege-Laser, W. Crosstalk between two bZIP signaling pathways orchestrates salt-induced metabolic reprogramming in arabidopsis roots. Plant Cell 27(8): 2244-2260, 2015.

 

Murakawa, Y., Hinz, M., Mothes, J., Schuetz, A., Uhl, M., Wyler, E., Yasuda, T., Mastrobuoni, G., Friedel, C.C., Doelken, L., Kempa, S., Schmidt-Supprian, M., Bluethgen, N., Backofen, R., Heinemann, U., Wolf, J., Scheidereit, C., Landthaler, M. RC3H1 post-transcriptionally regulates A20 mRNA and modulates the activity of the IKK/NF-{kappa}B pathway. Nat Commun 6: 7367, 2015.

 

Moussaieff, A., Rouleau, M., Kitsberg, D., Cohen, M., Levy, G., Barasch, D., Nemirovski, A., Shen-Orr, S., Laevsky, I., Amit, M., Bomze, D., Elena-Herrmann, B., Scherf, T., Nissim-Rafinia, M., Kempa, S., Itskovitz-Eldor, J., Meshorer, E., Aberdam, D., Nahmias, Y. Glycolysis-mediated changes in acetyl-CoA and histone acetylation control the early differentiation of embryonic stem cells. Cell Metab 21(3): 392-402, 2015.

 

Kuich, P.H.J.L., Hoffmann, N., Kempa, S. Maui-VIA: a user-friendly software for visual identification, alignment, correction, and quantification of gas chromatography-mass spectrometry data. Front Bioeng Biotechnol 2: 84, 2015.

 

Pietzke, M., Zasada, C., Mudrich, S., Kempa, S. Decoding the dynamics of cellular metabolism and the action of 3-bromopyruvate and 2-deoxyglucose using pulsed stable isotope-resolved metabolomics. Cancer Metab 2: 9, 2014.

 

Pietzke, M., Kempa, S. Pulsed stable isotope-resolved metabolomic studies of cancer cells. Methods Enzymol 543: 179-198, 2014.

 

Gregersen, L.H., Schueler, M., Munschauer, M., Mastrobuoni, G., Chen, W., Kempa, S., Dieterich, C., Landthaler, M. MOV10 is a 5' to 3' RNA helicase contributing to UPF1 mRNA target degradation by translocation along 3' UTRs. Mol Cell 54(4): 573-585, 2014.

 

Doerr, J.R., Yu, Y., Milanovic, M., Beuster, G., Zasada, C., Daebritz, J.H.M., Lisec, J., Lenze, D., Gerhardt, A., Schleicher, K., Kratzat, S., Purfuerst, B., Walenta, S., Mueller-Klieser, W., Graeler, M., Hummel, M., Keller, U., Buck, A.K., Doerken, B., Willmitzer, L., Reimann, M., Kempa, S., Lee, S., Schmitt, C.A. Synthetic lethal metabolic targeting of cellular senescence in cancer therapy. Nature 501(7467): 421-425, 2013.

 

Rohwer, N., Zasada, C., Kempa, S., Cramer, T. The growing complexity of HIF-1{alpha}'s role in tumorigenesis: DNA repair and beyond. Oncogene 32(31): 3569-3576, 2013.

 

Graf, R., Munschauer, M., Mastrobuoni, G., Mayr, F., Heinemann, U., Kempa, S., Rajewsky, N., Landthaler, M. Identification of LIN28B-bound mRNAs reveals features of target recognition and regulation. RNA Biol 10(7): 1146-1159, 2013.

 

Carlo, A.S., Gustafsen, C., Mastrobuoni, G., Nielsen, M.S., Burgert, T., Hartl, D., Rohe, M., Nykjaer, A., Herz, J., Heeren, J., Kempa, S., Petersen, C.M., Willnow, T.E. The pro-neurotrophin receptor sortilin is a major neuronal apolipoprotein E receptor for catabolism of amyloid-beta peptide in the brain. J Neurosci 33(1): 358-370, 2013.

 

Mastrobuoni, G., Qiao, H., Iovinella, I., Sagona, S., Niccolini, A., Boscaro, F., Caputo, B., Orejuela, M.R., Della Torre, A., Kempa, S., Felicioli, A., Pelosi, P., Moneti, G., Dani, F.R. A proteomic investigation of soluble olfactory proteins in Anopheles gambiae. PLoS ONE 8(11): e75162, 2013.

 

Dal Santo, S., Stampfl, H., Krasensky, J., Kempa, S., Gibon, Y., Petutschnig, E., Rozhon, W., Heuck, A., Clausen, T., Jonak, C. Stress-induced GSK3 regulates the redox stress response by phosphorylating glucose-6-phosphate dehydrogenase in Arabidopsis. Plant Cell 24(8): 3380-3392, 2012.

 

Mastrobuoni, G., Irgang, S., Pietzke, M., Wenzel, M., Assmus, H.E., Schulze, W.X., Kempa, S. Proteome dynamics and early salt stress response of the photosynthetic organism Chlamydomonas reinhardtii. BMC Genomics 13(1): 215, 2012.

 

Onal, P., Gruen, D., Adamidi, C., Rybak, A., Solana, J., Mastrobuoni, G., Wang, Y., Rahn, H.P., Chen, W., Kempa, S., Ziebold, U., Rajewsky, N. Gene expression of pluripotency determinants is conserved between mammalian and planarian stem cells. EMBO J 31(12): 2755-2769, 2012.

 

Liu, L., Ulbrich, J., Mueller, J., Wuestefeld, T., Aeberhard, L., Kress, T.R., Muthalagu, N., Rycak, L., Rudalska, R., Moll, R., Kempa, S*., Zender, L., Eilers, M., Murphy, D.J. Deregulated MYC expression induces dependence upon AMPK-related kinase 5. Nature 483(7391): 608-612, 2012.

         (* corr. metabolomics and proteomics)

 

Jungkamp, A.C., Stoeckius, M., Mecenas, D., Gruen, D., Mastrobuoni, G., Kempa, S., Rajewsky, N. In vivo and transcriptome-wide identification of RNA binding protein target sites. Mol Cell 44(5): 828-840, 2011.

 

Beato, V.M., Navarro-Gochicoa, M.T., Rexach, J., Herrera-Rodriguez, M.B., Camacho-Cristobal, J.J., Kempa, S., Weckwerth, W., Gonzalez-Fontes, A. Expression of root glutamate dehydrogenase genes in tobacco plants subjected to boron deprivation. Plant Physiol Biochem 49(11): 1350-1354, 2011.

 

Adamidi, C., Wang, Y., Gruen, D., Mastrobuoni, G., You, X., Tolle, D., Dodt, M., Mackowiak, S.D., Gogol-Doering, A., Oenal, P., Rybak, A., Ross, E., Alvarado, A.S., Kempa, S*., Dieterich, C., Rajewsky, N., Chen, W. De novo assembly and validation of planaria transcriptome by massive parallel sequencing and shotgun proteomics. Genome Res 21(7): 1193-1200, 2011. (*co-corr)

 

Wienkoop, S., Weiss, J., May, P., Kempa, S*., Irgang, S., Recuenco-Munoz, L., Pietzke, M., Schwemmer, T., Rupprecht, J., Egelhofer, V., Weckwerth, W. Targeted proteomics for Chlamydomonas reinhardtii combined with rapid subcellular protein fractionation, metabolomics and metabolic flux analyses. Mol Biosyst 6(6): 1018-1031, 2010. (* co-first)

 

Larrainzar, E., Wienkoop, S., Scherling, C., Kempa, S., Ladrera, R., Arrese-Igor, C., Weckwerth, W., Gonzalez, E.M. Carbon metabolism and bacteroid functioning are involved in the regulation of nitrogen fixation in Medicago truncatula under drought and recovery. Mol Plant Microbe Interact 22(12): 1565-1576, 2009.

 

Kempa, S., Hummel, J., Schwemmer, T., Pietzke, M., Strehmel, N., Wienkoop, S., Kopka, J., Weckwerth, W. An automated GCxGC-TOF-MS protocol for batch-wise extraction and alignment of mass isotopomer matrixes from differential 13C-labelling experiments: a case study for photoautotrophic-mixotrophic grown Chlamydomonas reinhardtii cells. J Basic Microbiol 49(1): 82-91, 2009.

 

Christian, N., May, P., Kempa, S., Handorf, T., Ebenhoeh, O. An integrative approach towards completing genome-scale metabolic networks. Mol Biosyst 5(12): 1889-1903, 2009.

 

May, P., Christian, J.O., Kempa, S., Walther, D. ChlamyCyc: an integrative systems biology database and web-portal for Chlamydomonas reinhardtii. BMC Genomics 10: 209, 2009.

 

May, P., Wienkoop, S., Kempa, S*., Usadel, B., Christian, N., Rupprecht, J., Weiss, J., Recuenco-Munoz, L., Ebenhoeh, O., Weckwerth, W., Walther, D.J. Metabolomics- and proteomics-assisted genome annotation and analysis of the draft metabolic network of Chlamydomonas reinhardtii. Genetics 179(1): 157-166, 2008. (* co-first)

 

Kempa, S., Krasensky, J., Dal Santo, S., Kopka, J., Jonak, C. A central role of abscisic acid in stress-regulated carbohydrate metabolism. PLoS ONE 3(12): e3935, 2008.

 

Kempa, S., Rozhon, W., Samaj, J., Erban, A., Baluska, F., Becker, T., Haselmayer, J., Schleiff, E., Kopka, J., Hirt, H., Jonak, C. A plastid-localized glycogen synthase kinase 3 modulates stress tolerance and carbohydrate metabolism. Plant J 49(6): 1076-1090, 2007.

 

Nikiforova, V.J., Bielecka, M., Gakiere, B., Krueger, S., Rinder, J., Kempa, S., Morcuende, R., Scheible, W.R., Hesse, H., Hoefgen, R. Effect of sulfur availability on the integrity of amino acid biosynthesis in plants. Amino Acids 30(2): 173-183, 2006.

 

Nikiforova, V.J., Gakiere, B., Kempa, S., Adamik, M., Willmitzer, L., Hesse, H., Hoefgen, R. Towards dissecting nutrient metabolism in plants: a systems biology case study on sulphur metabolism. J Exp Bot 55(404): 1861-1870, 2004.

 

Hornemann, T., Kempa, S., Himmel, M., Hayess, K., Fuerst, D.O., Wallimann, T. Muscle-type creatine kinase interacts with central domains of the M-band proteins myomesin and M-protein. J Mol Biol 332(4): 877-887, 2003.

 

Nikiforova, V., Freitag, J., Kempa, S., Adamik, M., Hesse, H., Hoefgen, R. Transcriptome analysis of sulfur depletion in Arabidopsis thaliana: interlacing of biosynthetic pathways provides response specificity. Plant J 33(4): 633-650, 2003.

 

Nikiforova, V., Kempa, S., Zeh, M., Maimann, S., Kreft, O., Casazza, A.P., Riedel, K., Tauberger, E., Hoefgen, R., Hesse, H. Engineering of cysteine and methionine biosynthesis in potato. Amino Acids 22(3): 259-278, 2002.

 

van der Ven, P.F., Wiesner, S., Salmikangas, P., Auerbach, D., Himmel, M., Kempa, S., Hayess, K., Pacholsky, D., Taivainen, A., Schroeder, R., Carpen, O., Fuerst, D.O. Indications for a novel muscular dystrophy pathway. gamma-filamin, the muscle-specific filamin isoform, interacts with myotilin. J Cell Biol 151(2): 235-248, 2000.

 

 

 

 

Book chapters         

 

Pietzke M, Kempa S. Pulsed stable isotope-resolved metabolomic studies of cancer cells. Methods Enzymol. 2014;543:179-98. doi: 10.1016/B978-0-12-801329-8.00009-X. PubMed PMID: 24924133.

 

Ebenhöh O and Kempa S. Genome-Scale Metabolic Network Inference (2013) In: Dubitzky W, Wolkenhauer O, Cho K-H, Yokota H (Eds.): Encyclopedia of Systems Biology. Springer Science+Business Media, LLC (2013)

 

Juncker B and Kempa S. Non-stationary metabolic flux analysis. (2013) In: Dubitzky W, Wolkenhauer O, Cho K-H, Yokota H (Eds.): Encyclopedia of Systems Biology. Springer Science+Business Media, LLC (2013)

 

Wolf J and Kempa S. Metabolic and signaling networks (2013) In: Dubitzky W, Wolkenhauer O, Cho K-H, Yokota H (Eds.): Encyclopedia of Systems Biology. Springer Science+Business Media, LLC (2013)

 

Kempa S, Ebenhöh O, Walter D and Weckwerth W. (2010) Metabolic engineering, Molecular biology and Biotechnology 5th edition; RSC, Cambrigde

 

Nikiforova, V; Bielecka, M; Gakiere, B; Krueger, S; Rinder, J; Kempa, S; Hesse, H; Hoefgen, R; Liszewska, F; Sirko. A (2005) Sulfur omics, Sulfur transport and assimilation in plants in the post genomic era (Backhuys Publishers) 137

 

Nikiforova V, Daub C, Freitag J, Kempa S, Riedel K, Hesse H and Höfgen R. (2003) Cluster Analysis of Gene Responses to Sulfur Depletion in Arabidopsis thaliana. In Sulfur Transport and Assimilation in Plants (Backhuys Publishers) 299-01

 

Höfgen R, Nikiforova V, Freitag J, Kempa S, Riedel K and Hesse H. (2003) Transcript Profiling of Sulfur depletion in Arabidopsis thaliana. In Sulfur Transport and Assimilation in Plants (Backhuys Publishers) 229-30