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Rossius M, Hochgräfe F, Antelmann H. Thiol-Redox Proteomics to Study Reversible Protein Thiol Oxidations in Bacteria. Methods Mol Biol. 2018;1841:261-275


Barbieri G, Voigt B, Albrecht D, Hecker M, Albertini AM, Sonenshein AL, Ferrari E, Belitsky BR (2015): CodY regulates expression of the Bacillus subtilis extracellular proteases Vpr and Mpr. J. Bacteriol. 197, 1423-1432.

Dihazi GH, Mueller GA, Asif AR, Eltoweissy M, Wessels JT, Dihazi H (2015): Proteomic characterization of adrenal gland embryonic development reveals early initiation of steroid metabolism and reduction of the retinoic acid pathway. Proteome Science 2015, 13:6.

Helmholz H, Lassen S, Ruhnau C, Pröfrock D, Erbslöh HB, Prange A (2015): Investigation on the proteome response of transplanted blue mussel (Mytilus sp.) during a long term exposure experiment at differently impacted field stations in the German Bight (North Sea). Mar Environ Res. 2015 Aug 1;110:69-80. doi: 10.1016/j.marenvres.2015.07.021. [Epub ahead of print]

Kierul K, Voigt B, Albrecht D, Chen XH, Carvalhais LC, Borriss R (2015): Influence of root exudates on the extracellular proteome of the plant- growth promoting bacterium Bacillus amyloliquefaciens FZB42. Microbiology 161, 131-147.

Raeven RH, van der Maas L, Tilstra W, Uittenbogaard JP, Bindels TH, Kuipers B, van der Ark A, Pennings JL, van Riet E, Jiskoot W, Kersten GF, Metz B: Immunoproteomic Profiling of Bordetella pertussis Outer Membrane Vesicle Vaccine Reveals Broad and Balanced Humoral Immunogenicity. J Proteome Res. 2015 Jun 2. [Epub ahead of print]

Rurek M, Woyda-Ploszczycab AM, Jarmuszkiewicz W (2015): Biogenesis of mitochondria in cauliflower (Brassica oleracea var. botrytis) curds subjected to temperature stress and recovery involves regulation of the complexome, respiratory chain activity, organellar translation and ultrastructure. Biochimica et Biophysica Acta (BBA) - Bioenergetics Volume 1847, Issues 4–5, April–May 2015, Pages 399–417.


Brandt U, Waletzko C, Voigt B, Hecker M, Steinbüchel A (2014): Mercaptosuccinate metabolism in Variovorax paradoxus strain B4-a proteomic approach. Appl Microbiol Biotechnol. 98, 6039-6050.

Handtke S , Schroeter R, Jürgen B, Methling K, Schlüter R, Albrecht D, van Hijum S, Bongaerts J, Maurer KH, Lalk M, Schweder T, Hecker M, Voigt B (2014): Bacillus pumilus reveals a remarkably high resistance to hydrogen peroxide provoked oxidative stress. PLoS One 9, e85625.

Irrgang A, Weise C, Murugaiyan J, Roesler U. (2014): Identification of immunodominant proteins of microalgae Prototheca sp. using proteomic analysis. New Microbes and New Infections.

Lorenza C, Rolletschekb H, Sunderhausa S, Braun HP. (2014): Functional and differential proteomic analyses to identify platelet derived factors affecting ex vivo expansion of mesenchymal stromal cells. J. Proteomics 108, 382–426.

Raberg M, Voigt B, Hecker M, Steinbüchel A (2014): A Closer Look on the Polyhydroxybutyrate- (PHB-) Negative Phenotype of Ralstonia eutropha PHB-4. PLoS One. 9, e95907.



Behrens C, Blume C, Senkler M, Eubel H, Peterhänsel C, Braun HP. (2013): The ‘protein complex proteome’ of chloroplasts in Arabidopsis thaliana. Journal of Proteomics. 2013 July, 91(2013):73-83.

Griebel, A., Obermaier, C., Westermeier, R., Moche, M., Büttner, K. (2013): Simplification and Improvement of protein detection in two-dimensional electrophoresis gels with SERVA HPETM Lightning Red. Archives of Physiology and Biochemistry 2013, Arch Physiol Biochem. 2013 Jun 20.

Hildebrandt H, Viscomi C, Di Meo I, Zeviani M, Braun HP (2013): Proteome adaptations in Ethe1 deficient mice indicate a role in lipid catabolism and cytoskeleton organization via post-translational protein modifications. Biosci. Rep. 33, art:e00052, doi 10.1042/BSR20130051

Kiirika LM, Behrens C, Braun HP, Colditz F (2013): The mitochondrial complexome of Medicago truncatula. Frontiers in Plant Proteomics, doi: 10.3389/fpls.2013.00084

Kinzebach S, Dietz L, Klüter H, Thierse HJ, Bieback K. (2013): Functional and differential proteomic analyses to identify platelet derived factors affecting ex vivo expansion of mesenchymal stromal cells. BMC Cell Biology 2013, 14:48. doi:10.1186/1471-2121-14-48

Murugaiyan J, Rockstroh M, Wagner J, Baumann S, Schorsch K, Trump S, Lehmann I, Bergen Mv, Tomm JM. (2013): Benzo[a]pyrene affects Jurkat T cells in the activated state via the antioxidant response element dependent Nrf2 pathway leading to decreased IL-2 secretion and redirecting glutamine metabolism. Toxicol Appl Pharmacol. 2013 Jun 15;269(3):307-16. doi: 10.1016/j.taap.2013.03.032. Epub 2013 Apr 10.

Murugaiyan J, Weise C, von Bergen M, Roesler U. (2013): Two-dimensional proteome reference map of Prototheca zopfii revealed reduced metabolism and enhanced signal transduction as adaptation to an infectious life style. Proteomics, 2013 Jul 12. doi: 10.1002/pmic.201300037.

Mwangi JW, Rode C, Colditz F, Haase C, Braun HP, Winkelmann T (2013): Proteomic and histological analyses of endosperm development in Cyclamen persicum as a basis for optimization of somatic embryogenesis. Plant Science 201/202, 52-65.

Nietzel T, Dudkina NV, Haase C, Denolf P, Semchonok D, Boekema EJ, Braun HP, Sunderhaus S (2013): The native structure and composition of the Cruciferin complex in Brassica napus. J. Biol. Chem. 288, 2238–2245.

Noah AM, Niemenak N, Sunderhaus S, Haase C, Omokolo DN, Winkelmann T, Braun HP (2013): Comparative proteomic analysis of early somatic and zygotic embryogenesis in Theobroma cacao L. J. Proteomics 78, 123-133.

Schroeter R, Hoffmann T, Voigt B, Meyer H, Bleisteiner B, Muntel J, Jürgen B, Albrecht D, Becher D, Lalk M, Evers S, Bongaerts J, Maurer KH, Putzer H, Hecker M, Schweder T, Bremer E (2013): Stress responses of the industrial workhorse Bacillus licheniformis to osmotic challenges. PLOS ONE 8, e80956.

Shi H, Hayes MT, Kirana C, Miller RJ, Keating JP, Stubbs RS. (2013): Overexpression of aminoacylase 1 is associated with colorectal cancer progression. Hum Pathol. 2013 Jun;44(6):1089-97. doi: 10.1016/j.humpath.2012.09.015. Epub 2013 Jan 11.

Spelten O, Wetsch WA, Wrettos G, Kalenka A, Hinkelbein J. (2013): Response of rat lung tissue to short-term hyperoxia: a proteomic approach. Mol Cell Biochem. 2013 Aug 11. Epub 2013 Aug 11.

Triboulet S, Aude-Garcia C, Carriere M, Diemer H, Proamer F, Habert A, Chevallet M, Collin-Faure V, Strub JM, Hanau D, Van Dorsselaer A, Herlin-Boime N, Rabilloud T. (2013): Molecular responses of mouse macrophages to copper and copper oxide nanoparticles inferred from proteomic analyses. Mol Cell Proteomics. 2013 Jul 23. Epub 2013 Jul 23.

Voigt B, Schroeter R, Jürgen B, Albrecht D, Evers S, Bongaerts J, Maurer KH, Schweder T, Hecker M (2013): The response of Bacillus licheniformis to heat and ethanol stress and the role of the SigB regulon. Proteomics 13, 2140-2161.

Wiegand S, Voigt B, Albrecht A, Bongaerts J, Evers S, Hecker M, Daniel R, Liesegang H (2013): Fermentation stage-dependent adaptations of Bacillus licheniformis during enzyme production. Microbial Cell Factories 12, 120.


Boleij, A., Dutilh, B.E., Kortman, G., Roelofs, R., Laarakkers, C.M., Engelke, U.F., Tjalsma, H. (2012): Bacterial responses to a simulated colon tumor microenvironment. Mol Cell Proteomics. 2012 Oct;11(10):851-62. Epub 2012 Jun 19.

Chiarini, A., Marconi, M., Pacchiana, R., Prà, I.D., Wu, J., Armato, U. (2012). Role-Shifting PKCζ Fosters Its Own Proapoptotic Destruction by Complexing with Bcl10 at the Nuclear Envelope of Human Cervical Carcinoma Cells: A Proteomic and Biochemical Study. J Proteome Res. 2012 Aug 3;11(8):3996-4012. Epub 2012 Jul 19.

Deng, X., Hahne, T., Schröder, S., Redweik, S., Nebija, D., Schmidt, H., Janssen, O., Lachmann, B., Wätzig, H. (2012): The challenge to quantify proteins with charge trains due to isoforms or conformers. Electrophoresis. 2012 Jan;33(2):263-9. doi: 10.1002/elps.201100321. Epub 2011 Dec 14.

Gündel, U., Kalkhof, S., Zitzkat, D., von Bergen, M., Altenburger, R., Küster, E. (2012). Concentration-response concept in ecotoxicoproteomics: effects of different phenanthrene concentrations to the zebrafish (Danio rerio) embryo proteome. Ecotoxicol Environ Saf. 2012 Feb;76(2):11-22. Epub 2011 Nov 5.

Haas, S., Jahnke, H.G., Moerbt, N., von Bergen, M., Aharinejad, S., Andrukhova, O., Robitzki, A.A. (2012). DIGE proteome analysis reveals suitability of ischemic cardiac in vitro model for studying cellular response to acute ischemia and regeneration. PLoS One. 2012;7(2):e31669. Epub 2012 Feb 22.

Hanreich, A., Heyer, R., Benndorf, D., Rapp, E., Pioch, M., Reichl, U., Klocke, M. (2012). Metaproteome analysis to determine the metabolically active part of a thermophilic microbial community producing biogas from agricultural biomass. Can J Microbiol. 2012 Jul;58(7):917-22. Epub 2012 Jun 12.

Hastie, M.L., Headlam, M.J., Patel, N.B., Bukreyev, A.A., Buchholz, U.J., Dave, K.A., Norris, E.L., Wright, C.L., Spann, K.M., Collins, P.L., Gorman, J.J. (2012). The Human Respiratory Syncytial Virus Nonstructural Protein 1 Regulates Type I and Type II Interferon Pathways. Mol Cell Proteomics. 2012 May;11(5):108-27. Epub 2012 Feb 8.

Kirana C, Shi H, Laing E, Hood K, Miller R, Bethwaite P, Keating J, Jordan TW, Hayes M, Stubbs R. Cathepsin D Expression in Colorectal Cancer: From Proteomic Discovery through Validation Using Western Blotting, Immunohistochemistry, and Tissue Microarrays. Int J Proteomics. 2012;2012:245819. doi: 10.1155/2012/245819. Epub 2012 Aug 7.

Lelong C, Chevallet M, Diemer H, Luche S, Van Dorsselaer A, Rabilloud T. (2012): Improved proteomic analysis of nuclear proteins, as exemplified by the comparison of two myeloid cell lines nuclear proteomes. J Proteomics. 2012 Dec 21;77:577-602. doi: 10.1016/j.jprot.2012.09.034. Epub 2012 Oct 10.

Liedert C, Peltola M, Bernhardt J, Neubauer P, Salkinoja-Salonen M. (2012). Physiology of resistant Deinococcus geothermalis bacterium aerobically cultivated in low-manganese medium. J Bacteriol. 2012 Mar;194(6):1552-61.

Meisrimler, C.N., Lüthje, S. (2012). IPG-strips versus off-gel fractionation: advantages and limits of two-dimensional PAGE in separation of microsomal fractions of frequently used plant species and tissues. J Proteomics. 2012 May 17;75(9):2550-62. Epub 2012 Mar 3.

Millioni, R, Polati, R, Menini, M, Puricelli, L, Miuzzo, M, Tessari, P, Novelli, E, Righetti, PG, Cecconi, D. (2012): Polar electrophoresis: shape of two-dimensional maps is as important as size. PLoS One. 2012;7(1):e30911. Epub 2012 Jan 23.

Ohlmeier, S., Mazur, W., Linja-Aho, A., Louhelainen, N., Rönty, M., Toljamo, T., Bergmann, U., Kinnula VL. (2012). Sputum proteomics identifies elevated PIGR levels in smokers and mild-to-moderate COPD. J Proteome Res. 2012 Feb 3;11(2):599-608. Epub 2011 Nov 18.

Rode, C., Lindhorst, K., Braun, H.P. and Winkelmann, T. (2012). From callus to embryo - a proteomic view on the development and maturation of somatic embryos in Cyclamen persicum. Planta. 2012 May;235(5):995-1011.

Rode, C., Winkelmann, T., Braun, H.P., Colditz, F. (2012). DIGE analysis of plant tissue proteomes using a phenolic protein extraction method. Meth. Mol. Biol. 854 (2012), 335-342.

Shi H, Hayes M, Kirana C, Miller R, Keating J, Macartney-Coxson D, Stubbs R. TUFM is a potential new prognostic indicator for colorectal carcinoma. Pathology. 2012 Oct;44(6):506-12.

Stanley, D.W., Goodman, C., An, S, Song, Q. (2012): Prostaglandin A(2) influences gene expression in an established insect cell line (BCIRL-HzAM1) cells. J Insect Physiol. 2012 Mar 23.

Tomanek, L., Zuzow, M.J., Hitt, L., Serafini, L., Valenzuela, J.J. (2012): Proteomics of hyposaline stress in blue mussel congeners (genus Mytilus): implications for biogeographic range limits in response to climate change. J Exp Biol. 2012 Nov 15;215(Pt 22):3905-16. doi: 10.1242/jeb.076448. Epub 2012 Aug 16.

Ummanni, R., Barreto, F., Venz, S., Scharf, C., Barett, C., Mannsperger, H.A., Brase, J.C., Kuner, R., Schlomm, T., Sauter, G., Sültmann, H., Korf, U., Bokemeyer, C., Walther, R., Brümmendorf, T.H., Balabanov, S. (2012). Peroxiredoxins 3 and 4 are overexpressed in prostate cancer tissue and affect the proliferation of prostate cancer cells in vitro. J Proteome Res. 2012 Apr 6;11(4):2452-66. Epub 2012 Mar 28.


Bouwman, F.G., de Roos, B., Rubio-Aliaga, I., Crosley, L.K., Duthie, S.J., Mayer, C., Horgan, G., Polley, A.C., Heim, C., Coort, S.L., Evelo, C.T., Mulholland, F., Johnson, I.T., Elliott, R.M., Daniel, H., Mariman, E.C. (2011): 2D-electrophoresis and multiplex immunoassay proteomic analysis of different body fluids and cellular components reveal known and novel markers for extended fasting. BMC Med Genomics. 2011 Mar 25;4:24.

Burkhead, J.L., Ralle, M., Wilmarth, P., David, L., Lutsenko, S. (2011). Elevated copper remodels hepatic RNA processing machinery in the mouse model of Wilson's disease. J Mol Biol. 2011 Feb 11;406(1):44-58. Epub 2010 Dec 10.

Diedrich, M., Kitada, T, Nebrich, G., Koppelstaetter, A., Shen, J., Zabel, C., Klose, J., Mao, L. (2011): Brain region specific mitophagy capacity could contribute to selective neuronal vulnerability in Parkinson's disease. Proteome Sci. 2011 Sep 23;9:59.

Dihazi, H., Dihazi, G.H., Jahn, O., Meyer, S., Nolte, J., Asif, A.R., Mueller, G.A., Engel, W. (2012). Multipotent adult germline stem cells and embryonic stem cells functional proteomics revealed an important role of eukaryotic initiation factor 5A (Eif5a) in stem cell differentiation. J Proteome Res. 2011 Apr 1;10(4):1962-73. Epub 2011 Mar 16.

Dubinin, J., Braun, H.P., Schmitz, U.K. and Colditz, F. (2011). The mitochondrial proteome of the model legume Medicago truncatula. Biochem. Biophys. Acta (Proteins and Proteomics) 1814 (2011), 1658-1668.

Fields, P.A., Zuzow, M.J., Tomanek, L. (2011). Proteomic responses of blue mussel (Mytilus) congeners to temperature acclimation. J Exp Biol. 2012 Apr 1;215(Pt 7):1106-16.

Gauci, V.J., Wright, E.P., Coorssen, J.R. (2011). Quantitative proteomics: assessing the spectrum of in-gel protein detection methods. J Chem Biol. 2011 Jan;4(1):3-29. Epub 2010 Jun 19.

Giannopoulou, E.G., Lepouras, G., Manolakos, E.S. (2011). Visualizing meta-features in proteomic maps. BMC Bioinformatics. 2011 Jul 28;12:308.

Guha Thakurta, S., Subramanian, A. (2011). Evaluation of in situ albumin binding surfaces: a study of protein adsorption and platelet adhesion. J Mater Sci Mater Med. 2011 Jan;22(1):137-49. Epub 2010 Dec 1.

Junker, H., Venz, S., Zimmermann, U., Thiele, A., Scharf, C., Walther, R. (2011): Stage-related alterations in renal cell carcinoma--comprehensive quantitative analysis by 2D-DIGE and protein network analysis. PLoS One. 2011;6(7):e21867. Epub 2011 Jul 7.

Klodmann, J., Senkler, M., Rode, C. and Braun, H.P. (2011). Defining the protein complex proteome of plant mitochondria. Plant Physiology 157 (2011), 587-598.

Klose, P., Weise, C., Bondzio, A., Multhaup, G., Einspanier, R., Gruber, A.D., Klopfleisch, R. (2012). Is there a malignant progression associated with a linear change in protein expression levels from normal canine mammary gland to metastatic mammary tumors? J Proteome Res. 2011 Oct 7;10(10):4405-15. Epub 2011 Sep 27.

Kratochwill, K., Boehm, M., Herzog, R., Lichtenauer, A.M., Salzer, E., Lechner, M., Kuster, L., Bergmeister, K., Rizzi, A., Mayer, B., Aufricht, C. (2011). Alanyl-glutamine dipeptide restores the cytoprotective stress proteome of mesothelial cells exposed to peritoneal dialysis fluids. Nephrol Dial Transplant. 2012 Mar;27(3):937-46. Epub 2011 Aug 19.

Kratochwill, K., Lechner, M., Lichtenauer, A.M., Herzog, R., Lederhuber, H.C., Siehs, C., Endemann, M., Mayer, B., Rizzi, A., Aufricht, C. (2011): Interleukin-1 receptor-mediated inflammation impairs the heat shock response of human mesothelial cells. Am J Pathol. 2011 Apr;178(4):1544-55.

Krishnan, H.B., Nelson, R.L. (2011): Proteomic analysis of high protein soybean (Glycine max) accessions demonstrates the contribution of novel glycinin subunits. J Agric Food Chem. 2011 Mar 23;59(6):2432-9. Epub 2011 Feb 23.

Liang C, Liebeke M, Schwarz R, Zühlke D, Fuchs S, Menschner L, Engelmann S, Wolz C, Jaglitz S, Bernhardt J, Hecker M, Lalk M, Dandekar T. (2011). Staphylococcus aureus physiological growth limitations: insights from flux calculations built on proteomics and external metabolite data. Proteomics. 2011 May;11(10):1915-35.

Lewandowska-Gnatowska, E., Johnston, M. L., Wesner, A., Szczegielniak, j., Muszynska, G., Miernyk, J.A. (2011). Using multiplex-staining to study changes in the maize leaf phosphoproteome in response to mechanical wounding. Phytochemistry 72 (2011) 1285–1292.

Liebeke M, Dörries K, Zühlke D, Bernhardt J, Fuchs S, Pané-Farré J, Engelmann S, Völker U, Bode R, Dandekar T, Lindequist U, Hecker M, Lalk M. (2011). A metabolomics and proteomics study of the adaptation of Staphylococcus aureus to glucose starvation. Mol Biosyst. 2011 Apr;7(4):1241-53.

Lohsse, A., Ullrich, S., Katzmann, E., Borg, S., Wanner, G., Richter, M., Voigt, B., Schweder, T., Schüler, D. (2011): Functional analysis of the magnetosome island in Magnetospirillum gryphiswaldense: the mamAB operon is sufficient for magnetite biomineralization. PLoS One. 2011;6(10):e25561. Epub 2011 Oct 17.

Maass S, Sievers S, Zühlke D, Kuzinski J, Sappa PK, Muntel J, Hessling B, Bernhardt J, Sietmann R, Völker U, Hecker M, Becher D. (2011). Efficient, global-scale quantification of absolute protein amounts by integration of targeted mass spectrometry and two-dimensional gel-based proteomics. Anal Chem. 2011 Apr 1;83(7):2677-84.

Markert, S., Gardebrecht, A., Felbeck, H., Sievert, S.M., Klose, J., Becher, D., Albrecht, D., Thürmer, A., Daniel, R., Kleiner, M., Hecker, M., Schweder, T. (2011): Status quo in physiological proteomics of the uncultured Riftia pachyptila endosymbiont. Proteomics. 2011 Aug;11(15):3106-17. doi: 10.1002/pmic.201100059. Epub 2011 Jun 28.

Mehmeti, I., Jönsson, M., Fergestad, E.M., Mathiesen, G., Nes, I.F., Holo, H. (2011). Transcriptome, proteome, and metabolite analyses of a lactate dehydrogenase-negative mutant of Enterococcus faecalis V583. Appl Environ Microbiol. 2011 Apr;77(7):2406-13. Epub 2011 Feb 4.

Miettinen, J.A., Pietilä, M., Salonen, R.J., Ohlmeier, S., Ylitalo, K., Huikuri, H.V., Lehenkari, P. (2011). Tumor necrosis factor alpha promotes the expression of immunosuppressive proteins and enhances the cell growth in a human bone marrow-derived stem cell culture. Exp Cell Res. 2011 Apr 1;317(6):791-801. Epub 2010 Dec 21.

Oberbach A, Blüher M, Wirth H, Till H, Kovacs P, Kullnick Y, Schlichting N, Tomm JM, Rolle-Kampczyk U, Murugaiyan J, Binder H, Dietrich A, von Bergen M. (2011). Combined proteomic and metabolomic profiling of serum reveals association of the complement system with obesity and identifies novel markers of body fat mass changes. J Proteome Res. 2011 Oct 7;10(10):4769-88. Epub 2011 Aug 29.

Pešic, I., Dihazi, G.H., Müller, G.A., Jahn, O., Hoffmann, M., Eltoweissy, M., Koziolek, M., Dihazi, H. (2011). Short-term increase of glucose concentration in PDS results in extensive removal and high glycation level of vital proteins during continuous ambulatory peritoneal dialysis. Nephrol Dial Transplant. 2011 Aug;26(8):2674-83. Epub 2011 Feb 1.

Pešić, I., Stefanović, V., Müller, G.A., Müller, C.A., Cukuranović, R., Jahn, O., Bojanić, V., Koziolek, M., Dihazi, H. (2012). Identification and validation of six proteins as marker for endemic nephropathy. J Proteomics. 2011 Sep 6;74(10):1994-2007. Epub 2011 May 19.

Rahman, H., Qasim, M., Schultze, F.C., Oellerich, M., R. Asif, A.. (2011). Fetal calf serum heat inactivation and lipopolysaccharide contamination influence the human T lymphoblast proteome and phosphoproteome. Proteome Sci. 2011 Nov 15;9(1):71.

Rode C., Gallien S., Heintz D., Van Dorsselaer, A., Braun, H.P. and Winkelmann, T. (2011). Enolases-storage compounds in seeds? Evidence from a proteomic comparison of zygotic and somatic embryos of Cyclamen persicum Mill. Plant Mol. Biol. Volume 75 (2011), 305-319.

Rode, C., Senkler, M., Klodmann, J., Winkelmann, T. and Braun, H.P. (2011). GelMap - A novel software tool for building and presenting proteome reference maps. J. Proteomics 74 (2011), 2214-2219.

Rogasevskaia, T.P., Coorssen, J.R. (2011). A new approach to the molecular analysis of docking, priming, and regulated membrane fusion. J Chem Biol. 2011 Jul;4(3):117-36. Epub 2011 Feb 8.

Schramedei, K., Mörbt, N., Pfeifer, G., Läuter, J., Rosolowski, M., Tomm, J.M., von Bergen, M., Horn, F., Brocke-Heidrich, K. (2011). MicroRNA-21 targets tumor suppressor genes ANP32A and SMARCA4. Oncogene. 2011 Jun 30;30(26):2975-85. doi: 10.1038/onc.2011.15. Epub 2011 Feb 14.

Schräder, E., Scholz, S., Sandig, V., Hoffrogge, R., Noll, T. (2011): Analysis of the mitochondrial subproteome of the human cell line AGE1.HN - a contribution to a systems biology approach. BMC Proc. 2011 Nov 22;5 Suppl 8:P86. Epub 2011 Nov 22. doi:  10.1186/1753-6561-5-S8-P86 PMCID: PMC3284977

Serafini, L., Hann, J.B., Kültz, D., Tomanek, L. (2011). The proteomic response of sea squirts (genus Ciona) to acute heat stress: a global perspective on the thermal stability of proteins. Comp Biochem Physiol Part D Genomics Proteomics. 2011 Sep;6(3):322-34. doi: 10.1016/j.cbd.2011.07.002. Epub 2011 Jul 23.

Shi H, Hood KA, Hayes MT, Stubbs RS. (2012). Proteomic analysis of advanced colorectal cancer by laser capture microdissection and two-dimensional difference gel electrophoresis? J Proteomics. 2011 Dec 21;75(2):339-51. doi: 10.1016/j.jprot.2011.07.025. Epub 2011 Aug 6.

Tomanek, L., Zuzow, M.J., Ivanina, A.V., Beniash, E., Sokolova, I.M. (2011). Proteomic response to elevated PCO2 level in eastern oysters, Crassostrea virginica: evidence for oxidative stress. J Exp Biol. 2011 Jun 1;214(Pt 11):1836-44.

Ummanni, R., Mundt, F., Pospisil, H., Venz, C., Scharf, C., Barett, C., Fälth, M., Köllermann, J., Walther, R., Schlomm, T., Sauter, G., Bokemeyer, C., Sültmann, H., Schuppert, A., Brümmendorf, T.H., Balabanov, S. (2011). Identification of clinically relevant protein targets in prostate cancer with 2D-DIGE coupled mass spectrometry and systems biology network platform. PLoS One. 2011 Feb 11;6(2):e16833.

Vogel, H., Altincicek, B., Glöckner, G., Vilcinskas, A. (2011): A comprehensive transcriptome and immune-gene repertoire of the lepidopteran model host Galleria mellonella. BMC Genomics. 2011 Jun 11;12:308.

Wölfler, M.M., Meinhold-Heerlein, I.M., Söhngen, L., Rath, W., Knüchel, R., Neulen, J., Maass, N., Henkel, C. (2011). Two-dimensional gel electrophoresis in peritoneal fluid samples identifies differential protein regulation in patients suffering from peritoneal or ovarian endometriosis. Fertil Steril. 2011 Jun 30;95(8):2764-8. Epub 2011 Apr 16.

Yildirim V, Ozcan S, Becher D, Büttner K, Hecker M, Ozcengiz G. (2011). Characterization of proteome alterations in Phanerochaete chrysosporium in response to lead exposure. Proteome Sci. 2011 Mar 9;9:12.

Zeiser, J.J., Klodmann, J., Braun, H.P., Gerhard, R., Just, I., Pich, A. (2011). Effects of Clostridium difficile Toxin A on the proteome of colonocytes studied by differential 2D electrophoresis. J Proteomics. 2011 Dec 21;75(2):469-79. Epub 2011 Aug 26.

Zilliges, Y., Kehr, J.C., Meissner, S., Ishida, K., Mikkat, S., Hagemann, M., Kaplan, A., Börner, T., Dittmann, E. (2011). The cyanobacterial hepatotoxin microcystin binds to proteins and increases the fitness of microcystis under oxidative stress conditions. PLoS One. 2011 Mar 18;6(3):e17615.


Bandow, J. E. (2010). Comparison of protein enrichment strategies for proteome analysis of plasma. Proteomics 2010, 10, 1416–1425.

Burgula S, Medisetty R, Jammulamadaka N, Musturi S, Ilavazhagan G, Singh SS. (2010): Downregulation of PEBP1 in rat brain cortex in hypoxia. J Mol Neurosci. 2010 May;41(1):36-47. Epub 2009 Aug 25.

Campanale JP, Tomanek L, Adams NL (2010): Exposure to ultraviolet radiation causes proteomic changes in embryos of the purple sea urchin, Strongylocentrotus purpuratus. Journal of Experimental Marine Biology and Ecology 397 (2011) 106–120.

Doroshenk, K.A., Crofts, A.J., Washida, H., Satoh-Cruz, M., Crofts, N., Sugino, A., Okita, T.W., Morris, R.T., Wyrick, J.J., Fukuda, M., Kumamaru, K., Satoh, H. (2011): Characterization of the rice glup4 mutant suggests a role for the small GTPase Rab5 in the biosynthesis of carbon and nitrogen storage reserves in developing endosperm. Breeding Science Vol. 60 (2010), No. 5 556-567

Dowd, W. W., Harris, B. N., Cech, J. J., Jr., and D. Kültz (2010). Proteomic and physiological responses of leopard sharks (Triakis semifasciata) to salinity change. J. Exp. Biol. 213: 210-224.

Dowd, W.W., Renshaw, G.M.C., Cech, J.J., Jr., Kültz, D. (2010). Compensatory proteome adjustments following anoxic and hypoxic preconditioning in the brain and rectal gland of the epaulette shark (Hemiscyllium ocellatum). Physiol Genomics. 2010 Jun;42(1):93-114. Epub 2010 Apr 6.

Fedorova, M., Kuleva, N., Hoffmann, R. (2010). Identification, Quantification, and Functional Aspects of Skeletal Muscle Protein-Carbonylation in Vivo during Acute Oxidative Stress. J Proteome Res 2010, 9, 2516 -2526.

Fuchs S., Mehlan H., Kusch H., Teumer A., Zühlke D., Berth M., Wolf C., Dandekar T., Hecker M., Engelmann S., Bernhardt J. (2010). Protecs, a comprehensive and powerful storage and analysis system for OMICS data, applied for profiling the anaerobiosis response of Staphylococcus aureus COL. Proteomics 2010 (10), 2982–3000.

Georgieva, D., Ohler, M., Seifert, J., von Bergen, M., Arni, R.K., Genov, N., Betzel, C. (2010). Snake venomic of Crotalus durissus terrificus – correlation with pharmacological activities. J Proteome res. 2010 May 7;9(5):2302-16.

Hammer, E., Bien, S., Gesell Salazar, M., Steil, L., Scharf, C., Hildebrandt, P., Schroeder, H. W. S., Kroemer, H. K., Völker, U., Ritter, C. A. (2010). Proteomic analysis of doxorubicin-induced changes in the proteome of HepG2cells combining 2-D DIGE and LC-MS/MS approaches. Proteomics 2010, 10, 99–114.

Hammer E., Quoc Phong T., Steil L., Klingel K., Gesell Salazar M., Bernhardt J., Kandolf R., Kroemer H.K., Felix S.B., Völker U. (2010). Viral myocarditis induced by Coxsackievirus B3 in A.BY/SnJ mice: Analysis of changes in the myocardial proteome. Proteomics 2010 (10), 1802-18.

Karanam, N.K., Grabarczyk, P., Hammer, E., Scharf, C., Venz, S., Gesell-Salazar, M., Barthlen, W., Przybylski, G.K., Schmidt, C.A., Völker, U. (2010). Proteome analysos revials new mechanism of Bcl11b-loss driven apoptosis. J Proeteome Res. 2010 Aug 6;9(8):3799-811.

Liedert C., Bernhardt J., Albrecht D., Voigt B., Hecker M., Salkinoja-Salonen M., Neubauer P. (2010). Two-dimensional proteome reference map for the radiation-resistant bacterium Deinococcus geothermalis. Proteomics 2010 (10), 555-63.

Miettinen JA, Pietilä M, Salonen RJ, Ohlmeier S, Ylitalo K, Huikuri HV, Lehenkari P.(2010). Tumor necrosis factor alpha promotes the expression of immunosuppressive proteins and enhances the cell growth in a human bone marrow-derived stem cell culture. Exp Cell Res. 2011 Apr 1;317(6):791-801. Epub 2010 Dec 21.

Millioni, R., Miuzzo, M., Sbrignadello, S., Murphy, E., Puricelli, L., Tura, A., Bertacco, E., Rattazzi, M., Iori, E., Tessari, P.  (2010). Delta2D and Proteomweaver: Performance evaluation of two different approaches for 2-DE analysis. Electrophoresis. 2010 Apr;31(8):1311-7.

Nilo, R., Saffie, C., Lilley, K., Baeza-Yates, R., Cambiazo, V., Campos-Vargas, R., González, M., Meisel, L.A., Retamales, J., Silva, H., Orellana, A. (2010). Proteomic analysis of peach fruit mesocarp softening and chilling injury using difference gel electrophoresis (DIGE). BMC Genomics. 2010 Jan 18;11:43.

Pasztor, L., Ziebandt, A-K., Nega, M., Schlag, M., Haase, S., Franz-Wachtel, M., Madlung, J., Nordheim, A., Heinrichs, D.E., Götz, F. (2010). The staphylococcal major autolysin (ATL) in involved in secretion of cytoplasmic proteins. The Journal of Biological Chemistry, 2010, Sep. 16.

Pink, M., Verma, N., Rettenmeier, A.W., Schmitz-Spanke, S. (2010). CBB staining protocol with higher sensitivity and mass spectrometric compatibility. Electrophoresis 2010, 31, 593–598.

Rabilloud, T., Chevallet, M., Luche, S., Lelong, C., (2010): Two-dimensional gel electrophoresis in proteomics: past, present and future. J Proteomics. 2010 Oct 10;73(11):2064-77. Epub 2010 Jun 1.

Schmidl, S. R., Gronau, K., Pietack, N., Hecker, M., Becher, D., Stülke, J. (2010). The phosphoproteome of the minimal bacterium Mycoplasma pneumoniae: Analysis of the complete known Ser/ Thr kinome suggests the existence of novel kinases. Mol Cell Proteomics M900267-MCP200.

Teutschbein, J., Albrecht, D., Pötsch, M., Guthke, R., Aimanianda, V., Clavaud, C., Latgé, J.P., Brakhage, A.A., Kniemeyer, O. (2010). Proteome Profiling and Functional Classification of Intracellular Proteins from Conidia of the Human-Pathogenic Mold Aspergillus fumigatus. J Proteome Res. 2010 Jul 2;9(7):3427-42.

Tomanek L, Zuzow MJ. (2010). The proteomic response of the mussel congeners Mytilus galloprovincialis and M. trossulus to acute heat stress: implications for thermal tolerance limits and metabolic costs of thermal stress. J Exp Biol. 2010 Oct 15;213(Pt 20):3559-74.

Trimborn, M., Ghani, M., Walther, D.J., Dopatka, M., Dutrannoy, V., Busche, A., Meyer, F., Nowak, S., Nowak, .J, Zabel, C., Klose, J., Esquitino, V., Garshasbi, M., Kuss, A.W., Ropers, H.H., Mueller, S., Poehlmann, C., Gavvovidis, I., Schindler, D., Sperling, K., Neitzel, H. (2010). Establishment of a mouse model with misregulated chromosome condensation due to defective Mcph1 function. PLoS One. 2010 Feb 16;5(2):e9242.

Weist, S., Brunkau, C., Wittke, J., Eravci, M., Broedel, O., Krause, E., Stephanowitz, H., Eravci, S., Baumgartner, A. (2010). Effects of thawing, refreezing and storage conditions of tissue samples and protein extracts on 2-DE spot intensity. Proteomics 2010, 10, 1515–1521.


Amitai, S., Kolodkin-Gal, I., Hananya-Meltabashi, M., Sacher, A., Engelbert-Kulka, H. (2009). Escherichia coli MazF Leads to the Simultaneous Selective Synthesis of Both “Death Proteins” and “Survival Proteins”. PLos Genet. 2009 Mar;5(3).

Bartkowiak, K., Wieczorek, M., Buck, F., Harder, S., Moldenhauer, J., Effenberger, K.E., Pantel, K., Peter-Katalinic, J., Brandt, B.H. (2009). Two-Dimensional Differential Gel Electrophoresis of a Cell Line Derived from a Breast Cancer Micrometastasis Revealed a Stem/Progenitor Cell Protein Profile. J Proteome Res. 2009 Feb 12. 

Becher D., Hempel K., Sievers S., Zühlke D., Pané-Farré J., Otto A., Fuchs S., Albrecht D., Bernhardt J., Engelmann S., Völker U., van Dijl J.M., Hecker M. (2009). A Proteomic View of an Important Human Pathogen – Towards the Quantification of the Entire Staphylococcus aureus Proteome. PLoS ONE, 4(12), pp. e8176.

Benndorf, D., Vogt, C., Jehmlich, N., Schmidt, Y., Thomas, H., Woffendin, G., Shevchenko, A., Richnow, H.H., von Bergen, M. (2009). Improving protein extraction and separation methods for investigating the metaproteome of anaerobic benzene communities within sediments. Biodegradation. 2009 Nov; 20(6):737-50.

Bilalic, S., Veltinger, M., Ahrer, K.-H., Gruber, V., Zellner, M., Brostjan, C., Bartel, G., Cejka, D., Reichel, C., Jordam, V., Burghuber, C., Mühlbacher, F., Böhmig, G.A., Oehler, R. (2009). Identification of Non-HLA Antigens Targeted by Alloreactive Antibodies in Patients Undergoing Chronic Hemodialysis. J Proteom Res 2010 Feb 5;9(2):1041-9.

Broedel, O., Krause, E., Stephanowitz, H., Schuemann, M., Eravci, M., Weist, S., Brunkau, C., Wittke, J., Eravci, S., Baumgartner, A. (2009). In-Gel 18O labeling for improved identification of proteins from 2-DE Gel spots in comparative proteomic experiments. J Proteome Res. 2009 Jul;8(7):3771-7.

Dietz, L., Bosque, A., Pankert, P., Ohnesorge, S., Merz, P., Anel, A., Schnölzer, M., Thierse, H.J. (2009). Quantitative DY-maleimide-based proteomic 2-DE-labeling strategies using human skin proteins. Proteomics. 2009 Sep;9(18):4298-308.

Farajzadeh Deroee, A., Oweinah, J., Naraghi, M., Hosemann, W., Athari, B., Völker, U., Scharf, C. (2009). Regression of polypoid nasal mucosa after systemic corticosteroid therapy: a proteomics study. Am J Rhinol Allergy. 2009 Sep-Oct;23(5):480-5. Epub 2009 Aug 31.

Heller T, Asif AR, Petrova DT, Doncheva Y, Wieland E, Oellerich M, Shipkova M, Armstrong VW. Differential proteomic analysis of lymphocytes treated with mycophenolic acid reveals caspase 3-induced cleavage of rho GDP dissociation inhibitor 2. Ther Drug Monit. 2009 Apr;31(2):211-7.

Högy P, Zörb C, Langenkämper G, Betsche T, Fangmeier A. Atmospheric CO2 enrichment changes the wheat grain proteome. Journal of Cereal Science. 2009 (50):248-54.

Kawase T., Okuda K., Kogami H., Nakayama H., Nagata M., Nakata K., Yoshie H. (2009). Characterization of human cultured periosteal sheets expressing bone-forming potential: in vitro and in vivo animal studies. J Tissue Eng Regen Med 2009; 3: 218–229.

Kirana C, Ward T, Jordan TW, Rawson P, Royds J, Shi HJ, Stubbs R, Hood K. (2009). Compatibility of toluidine blue with laser microdissection and saturation labeling DIGE. Proteomics. 2009 Jan;9(2):485-90. doi: 10.1002/pmic.200800197.

Michalik S., Liebeke M., Zühlke D., Lalk M., Bernhardt J., Gerth U., Hecker M. (2009). Proteolysis during long-term glucose starvation in Staphylococcus aureus COL. Proteomics. 2009 9(9):4468–4477.

Mörbt, N., Mögel, I., Kalkhof, S., Feltens, R., Röder-Stolinski, C., Zheng, Z., Vogt, C., Lehmann, I., von Bergen, M.(2009). Proteome changes in human bronchoalvaeolar cells following styrene exposure indicate involvement of oxidative stress in the molecular-response mechanism. Proteomics. 2009 Aug 10;9, 4920-4933.

Nebrich, G., Herrmann, M., Hartl, D., Diedrich, M., Kreitler, T., Wierling, C., Klose, J., Giavalisco, P., Zabel, C., Mao, L. (2009). PROTEOMER: A workflow-optimized laboratory information management system for 2-D electrophoresis-centered proteomics. Proteomics. 2009 Apr;9(7):1795-808.

Schwerin, S., Zeis, B., Lamkemeyer, T., Paul, R.J., Koch, M., Madlung, J., Fladerer, C., Pirow, R. (2009). Acclimatory responses of the Daphnia pulex proteome to environmental changes. II. Chronic exposure to different temperatures (10 and 20°C) mainly affects protein metabolism. BMC Physiology. 2009, 9:8.

Stessl, M., Noe, C.R., Lachmann, B. (2009). Influence of image-analysis software on quantitation of two-dimensional gel electrophoresis data. Electrophoresis. 2009 Jan; 30(2):325-8.

Svendsen, I.E., Lindh, L. (2009). The composition of enamel salivary films is different from the ones formed on dental materials. Biofouling,25(3), pp.255-61.

Voigt B, Antelmann H, Albrecht D, Ehrenreich A, Maurer KH, Evers S, Gottschalk G, van Dijl JM, Schweder T, Hecker M. (2009). Cell physiology and protein secretion of Bacillus licheniformis compared to Bacillus subtilis. J Mol Microbiol Biotechnol. 2009;16(1-2):53-68. Epub 2008 Oct 29.

Zeis, B., Lamkemeyer, T., Paul, R.J., Nunes, F., Schwerin, S., Koch, M., Schuetz, W., Madlung, J., Fladerer, C., Pirow, R. (2009). Acclimatory responses of the Daphnia pulex proteome to environmental changes. I. Chronic exposure to hypoxia affects the oxygen transport system and carbohydrate metabolism. BMC Physiology, 2009, 9:7.

Zörb C, Betsche T, Langenkämper G. Search for diagnostic proteins to prove authenticity of organic wheat grains (Triticum aestivum L.). Journal of Agricultural and Food Chemistry. 2009 Apr 8;57(7):2932-7.

Zörb C, Steinfurth D, Seling S, Langenkämper G, Köhler P, Wieser H, Lindhauer MG, Mühling KH. Quantitative protein composition and baking quality of winter wheat as affected by late sulfur fertilization. Journal of Agricultural and Food Chemistry. 2009 May 13;57(9):3877-85.


Bandow J.E., Baker J.D., Berth M., Painter C., Sepulveda O.J., Clark K.A., Kilty I., VanBogelen R.A. (2008). Improved image analysis workflow for 2-D gels enables large-scale 2-D gel-based proteomics studies – COPD biomarker discovery study. Proteomics, 8(15), pp. 3030-41.

Brown, S. Horowitz, Yarden, O., Gollop, N., Chen, S., Zveibil, A., Belausov, E., & Freemann, S. (2008). Differential protein expression in Colletotrichum acutatum: changes associated with reactive oxygen species and nitrogen starvation implicated in pathogenicity on strawberry. Molecular Plant Pathology, 9(2), pp. 171–190.

Chevallet M, Luche S, Diemer H, Strub JM, Van Dorsselaer A, Rabilloud T. (2008): Sweet silver: a formaldehyde-free silver staining using aldoses as developing agents, with enhanced compatibility with mass spectrometry. Proteomics. 2008 Dec;8(23-24):4853-61.

Dowd, W. W., Wood, C. M., Kajimura, M., Walsh, P. J., and D. Kültz (2008). Natural feeding influences protein expression in the dogfish shark rectal gland: A proteomic analysis. Comp. Biochem. Physiol. D:Genomics & Proteomics 3:118-127

Engelmann, S., & Hecker, M. (2008). Proteomic Analysis to Investigate Regulatory Networks in Staphylococcus aureus. Bacterial Pathogenesis, pp. 25–45.

Eravci, M., Fuxius, S., Broedel, O., Weist, S., Krause, E., Stephanowitz, H., Schluter, H., Eravci, S., Baumgartner, A. (2008). The whereabouts of transmembrane proteins from rat brain synaptosomes during two-dimensional gel electrophoresis. Proteomics, 8(9), pp. 1762-70.

Fuxius, S., Eravci, M., Broedel, O., Weist, S., Mansmann, U., Eravci, S., Baumgartner, A. (2008). Technical strategies to reduce the amount of "false significant" results in quantitative proteomics. Proteomics, 8(9), 1780-4.

Gerth, U., Kock, H., Kusters, I., Michalik, S., Switzer, R. L., & Hecker, M. (2008). Clp-Dependent Proteolysis Down-Regulates Central Metabolic Pathways in Glucose-Starved Bacillus subtilis. J.Bacteriol., 190(1), pp. 321–331.

Hecker M., Antelmann H., Büttner K., Bernhardt J. (2008). Gel-based proteomics of Gram-positive bacteria: A powerful tool to address physiological questions. Proteomics, 8(9), 4958–4975.

Hirner, S., Krohne, C., Schuster, A., Hoffmann, S., Witt, S., & Erber, R., et al. (2008/6/13). MuRF1-dependent Regulation of Systemic Carbohydrate Metabolism as Revealed from Transgenic Mouse Studies. Journal of Molecular Biology, 379 (4), pp. 666–677.

Hochgrafe, F., Wolf, C., Fuchs, S., Liebeke, M., Lalk, M., Engelmann, S., & Hecker, M. (2008). Nitric oxide stress induces different responses but mediates comparable protein thiol protection in Bacillus subtilis and Staphylococcus aureus. J. Bacteriol., pp. JB.01846-07.

Joerchel, S., Raap, M., Bigl, M., Eschrich, K., & Schliebs, R. (2008). Oligomeric [beta]-amyloid(1-42) induces the expression of Alzheimer disease-relevant proteins in cholinergic SN56.B5.G4 cells as revealed by proteomic analysis. International Journal of Developmental Neuroscience, 26(3-4), pp. 301–308.

Kusch, H., Engelmann, S., Bode, R., Albrecht, D., Morschhäuser, J., & Hecker, M. (2008). A proteomic view of Candida albicans yeast cell metabolism in exponential and stationary growth phases. International Journal of Medical Microbiology, 298 (3-4), pp. 291–318.

Palminiello, S., Kida, E., Kaur, K., Walus, M., Wisniewski, K. E., & Wierzba-Bobrowicz, T. (2008). Increased levels of carbonic anhydrase II in the developing Down syndrome brain. Brain Research, 1190, pp. 193–205.

Raberg, M., Reinecke, F., Reichelt, R., Malkus, U., Konig, S., Potter, M. (2008). Ralstonia eutropha H16 changes flagellation according to nutrient supply and state of poly(3-hydroxybutyrate) accumulation. Appl. Environ. Microbiol., pp. AEM.00440-08.

Schlag S, Fuchs S, Nerz C, Gaupp R, Engelmann S, Liebeke M, Lalk M, Hecker M, Götz F. (2008). Characterization of the oxygen-responsive NreABC regulon of Staphylococcus aureus. J Bacteriol. 2008 Dec;190(23):7847-58. Epub 2008 Sep 26.

Thierse, H.-J., Helm, S., & Pankert, P. (2008). Metalloproteomics in the molecular study of cell physiology and disease. Methods Mol Biol, 425, pp. 139–147. , from doi:10.1007/978-1-60327-210-0_12.


Altincicek, B., Linder, M., Linder, D., Preissner, K. T., & Vilcinskas, A. (2007). Microbial Metalloproteinases Mediate Sensing of Invading Pathogens and Activate Innate Immune Responses in the Lepidopteran Model Host Galleria mellonella. Infect. Immun., 75(1), pp. 175–183.

Berth, M., Moser, F., Kolbe, M., & Bernhardt, J. (2007). The state of the art in the analysis of two dimensional gel electrophoresis images. Applied Microbiology and Biotechnology, 76(6), pp.1223–1243.

Brüsehaber, E., Böttcher, D., Musidlowska-Persson, A., Albrecht, D., Hecker, M., Doderer, K., & Bornscheuer, U. T. (2007). Identification of pig liver esterase variants by tandem mass spectroscopy analysis and their characterization. Appl Microbiol Biotechnol, 76 (4), pp. 853–859. , from doi:10.1007/s00253-007-1061-2.

Chavez de Paz, L.E., Bergenholtz, G., Dahlen, G., & Svensater, G. (May 2007). Response to alkaline stress by root canal bacteria in biofilms. International Endodontic Journal, 40, pp. 344–355.

Eravci, M., Fuxius, S., Broedel, O., Weist, S., Eravci, S., & Mansmann, U., et al. (2007). Improved comparative proteome analysis based on two-dimensional gel electrophoresis. Proteomics, 7(4), pp. 513–523.

Eymann, C., Becher D., Bernhardt J., Gronau K., Klutzny A., Hecker M. (2007). Dynamics of protein phosphorylation on Ser/Thr/Tyr in Bacillus subtilis. Proteomics, 7, pp. 3509–3526.

Fuchs, S., Pane-Farre, J., Kohler, C., Hecker, M., & Engelmann, S. (2007). Anaerobic Gene Expression in Staphylococcus aureus. J. Bacteriol., 189(11), pp. 4275–4289.

Galka, F., Wai, S. N., Kusch, K., Engelmann, S., Hecker, M., Schmeck, B., Hippenstiel, S., Uhlin,B. E., Steinert, M. (2007). Proteomic Characterization of the Whole Secretome of Legionella pneumophila and Functional Analysis of Outer Membrane Vesicles. Infection and Immunity, May 2008, p. 1825-1836, Vol. 76, No. 5.

Halbedel, S., Eilers, H., Jonas, B., Busse, J., Hecker, M., Engelmann, S., & Stülke, J. (2007/8/17). Transcription in Mycoplasma pneumoniae: Analysis of the Promoters of the ackA and ldh Genes. Journal of Molecular Biology, 371(3), pp. 596–607.

Hyyryläinen, H. L., Pietiäinen, M., Lundén, T., Ekman, A., Gardemeister, M., & Murtomäki-Repo, S., et al. (2007). The density of negative charge in the cell wall influences two-component signal transduction in Bacillus subtilis. Microbiology, 153 (Pt 7), pp. 2126–2136.

Kuhla, S., Rudolph, P. E., Albrecht, D., Schoenhusen, U., Zitnan, R., & Tomek, W., et al. (2007). A Milk Diet Partly Containing Soy Protein Does Not Change Growth but Regulates Jejunal Proteins in Young Goats. J. Dairy Sci., 90(9), pp. 4334–4345.

Kultz, D., Fiol, D., Valkova, N., Gomez-Jimenez, S., Chan, S. Y., & Lee, J. (2007). Functional genomics and proteomics of the cellular osmotic stress response in `non-model' organisms. J Exp Biol, 210 (9), pp.1593–1601.

Mao, L., Zabel, C., Herrmann, M., Nolden, T., Mertes, F., & Magnol, L., et al. (2007). Proteomic Shifts in Embryonic Stem Cells with Gene Dose Modifications Suggest the Presence of Balancer Proteins in Protein Regulatory Networks. PLoS ONE, 2(11), pp. e1218.

Markert, S., Arndt, C., Felbeck, H., Becher, D., Sievert, S. M., & Hügler, M., et al. (2007). Physiological proteomics of the uncultured endosymbiont of Riftia pachyptila. Science, 315 (5809), pp. 247–250.

Neubauer, H., Fehm, T., Schütz, C., Speer, R., Solomayer, E., Schrattenholz, A., Cahill, M., & Kurek, R. (2007). Proteomic Expression Profiling of Breast Cancer. Targeted Therapies in Cancer, pp. 89–120.

Ozcan, S., Yildirim, V., Kaya, L., Albrecht, D., Becher, D., Hecker, M., & Ozcengiz, G. (2007). Phanerochaete chrysosporium soluble proteome as a prelude for the analysis of heavy metal stress response. Proteomics, 7(8), pp. 1249–1260.

Schwarz, K., Fiedler, T., Fischer, R.-J., & Bahl, H. (2007/2). A Standard Operating Procedure (SOP) for the preparation of intra- and extracellular proteins of Clostridium acetobutylicum for proteome analysis. Journal of Microbiological Methods, 68(2), pp. 396–402.

Tam, L. T., Eymann, C., Antelmann, H., Albrecht, D., & Hecker, M. (2007). Global Gene Expression Profiling of Bacillus subtilis in Response to Ammonium and Tryptophan Starvation as Revealed by Transcriptome and Proteome Analysis. Journal of Molecular Microbiology and Biotechnology, 12(1-2), pp. 121–130.

Voigt, B., Le Hoi, T., Jürgen, B., Albrecht, D., Ehrenreich, A., & Veith, B., et al. (2007). The glucose and nitrogen starvation response of Bacillus licheniformis. Proteomics, 7 (3), pp. 413–423.

Wolff, S., Antelmann, H., Albrecht, D., Becher, D., Bernhardt, J., & Bron, S., et al. (2007). Towards the entire proteome of the model bacterium Bacillus subtilis by gel-based and gel-free approaches: Analytical Tools for Proteomics. Journal of Chromatography B, 849 (1-2), pp. 129–140.


Becher, B., Knöfel, A.-K., & Peters, J. (2006). Time-based analysis of silver-stained proteins in acrylamide gels. Electrophoresis, 27(10), pp. 1867–1873.

Bhojwani, M., Rudolph, E., Kanitz, W., Zuehlke, H., Schneider, F., & Tomek, W. (2006). Molecular Analysis of Maturation Processes by Protein and Phosphoprotein Profiling during In Vitro Maturation of Bovine Oocytes: A Proteomic Approach. Cloning and Stem Cells, 8 (4), p. 259.

Budde, I., Steil, L., Scharf, C., Völker, U., & Bremer, E. (2006). Adaptation of Bacillus subtilis to growth at low temperature: a combined transcriptomic and proteomic appraisal. Microbiology, 152 (Pt 3), pp. 831–853.

Batzilla CF, Rachid S, Engelmann S, Hecker M, Hacker J, Ziebuhr W. (2006): Impact of the accessory gene regulatory system (Agr) on extracellular proteins, codY expression and amino acid metabolism in Staphylococcus epidermidis. Proteomics. 2006 Jun;6(12):3602-13.

Heidrich, N., Chinali, A., Gerth, U., & Brantl, S. (2006). The small untranslated RNA SR1 from the Bacillus subtilis genome is involved in the regulation of arginine catabolism. Mol Microbiol, 62(2), pp.520–536.

Hoffrogge, R., Beyer, S., Völker, U., Uhrmacher, A. M., & Rolfs, A. (2006). 2-DE Proteomic Profiling of Neuronal Stem Cells. Neurodegenerative Diseases, 3(1-2), pp. 112–121.

Höper, D., Bernhardt, J., & Hecker, M. (2006). Salt stress adaptation of Bacillus subtilis: a physiological proteomics approach. Proteomics, 6 (5), pp. 1550–1562.

Leong, W. Fook, & Chow, V. T. K. (2006). Transcriptomic and proteomic analyses of rhabdomyosarcoma cells reveal differential cellular gene expression in response to enterovirus 71 infection. Cellular Microbiology, 8 (4), pp. 565–580.

Meyer zu Schwabedissen, Henriette Elisabeth, Grube, M., Dreisbach, A., Jedlitschky, G., Meissner, K., & Linnemann, K., et al. (2006). Epidermal growth factor (EGF) mediated activation of the MAP kinase cascade results in altered expression and function of ABCG2 (BCRP). Drug Metab Dispos, pp. dmd.105.007591.

Pamp, S. Johanna, Frees, D., Engelmann, S., Hecker, M., & Ingmer, H. (2006). Spx Is a Global Effector Impacting Stress Tolerance and Biofilm Formation in Staphylococcus aureus. J. Bacteriol., 188 (13), pp.4861–4870.

Perroud, B., Lee, J., Valkova, N., Dhirapong, A., Lin, P.-Y., Fiehn, O., Kultz, D., & Weiss, R. (2006). Pathway analysis of kidney cancer using proteomics and metabolic profiling. Molecular Cancer, 5 (1), p.64.

Sibbald, M. J., Ziebandt, A. K., Engelmann, S., Hecker, M., Jong, A. de, & Harmsen, H. J., et al. (2006). Mapping the pathways to staphylococcal pathogenesis by comparative secretomics. Microbiol Mol Biol Rev, 70(3), pp. 755–788.

Rogasch, K., Ruhmling, V., Pane-Farre, J., Hoper, D., Weinberg, C., Fuchs, S., Schmudde, M., Broker, B. M., Wolz, C., Hecker, M., Engelmann, S. (2006). Influence of the Two-Component System SaeRS on Global Gene Expression in Two Different Staphylococcus aureus Strains. J. Bacteriol. 2006 188: 7742-7758

Valkova, N., & Kültz, D. (2006). Constitutive and inducible stress proteins dominate the proteome of the murine inner medullary collecting duct-3 (mIMCD3) cell line. Biochim Biophys Acta, 1764 (6), pp.1007–1020.

Voigt, B., Schweder, T., Sibbald, M. J., Albrecht, D., Ehrenreich, A., & Bernhardt, J., et al. (2006). The extracellular proteome of Bacillus licheniformis grown in different media and under different nutrient starvation conditions. Proteomics, 6(1), pp. 268–281.

Wolff, S., Otto, A., Albrecht, D., Zeng, J. Stahl, Buttner, K., Gluckmann, M., Hecker, M., & Becher, D. (2006). Gel-free and Gel-based Proteomics in Bacillus subtilis: A Comparative Study. Mol Cell Proteomics, 5(7), pp. 1183–1192.

Zabel, C., Sagi, D., Kaindl, A. M., Steireif, N., Kläre, Y., & Mao, L., et al. (2006). Comparative proteomics in neurodegenerative and non-neurodegenerative diseases suggest nodal point proteins in regulatory networking. J Proteome Res, 5(8), pp. 1948–1958.

Zimmermann, U., Junker, H., Krämer, F., Balabanov, S., Kleist, B., Kammer, W., Nordheim, A., & Walther, R. (2006). Comparative proteomic analysis of neoplastic and non-neoplastic germ cell tissue. Biological Chemistry, 387 (4), p. 437.


Beckers, G., Strosser, J., Hildebrandt, U., Kalinowski, J., Farwick, M., Kramer, R., & Burkovski, A. (2005). Regulation of AmtR-controlled gene expression in Corynebacterium glutamicum: mechanism and characterization of the AmtR regulon. Molecular Microbiology, 58 (2), pp. 580–595.

Brötz-Oesterhelt, H., Bandow, J. E., & Labischinski, H. (2005). Bacterial proteomics and its role in antibacterial drug discovery. Mass Spectrom Rev, 24(4), pp. 549–565.

Ernst, F. D., Homuth, G., Stoof, J., Mäder, U., Waidner, B., & Kuipers, E. J., et al. (2005). Ironresponsive regulation of the Helicobacter pylori iron-cofactored superoxide dismutase SodB is mediated by Fur. J Bacteriol, 187 (11), pp. 3687–3692.

Farhoud, M. H., Wessels, H. J., Wevers, R. A., vanEngelen, B. G., vandenHeuvel, L. P., & Smeitink, J.A. (2005). Serial Isoelectric Focusing as an Effective and Economic Way to Obtain Maximal Resolution and High-Throughput in 2D-Based Comparative Proteomics of Scarce Samples: Proof-of-Principle. J. Proteome Res., 4(6), pp. 2364–2368.

Hochgrafe, F., Mostertz, J., Albrecht, D., & Hecker, M. (2005). Fluorescence thiol modification assay: oxidatively modified proteins in Bacillus subtilis. Molecular Microbiology, 58(2), pp. 409–425.

Jürgen, B., Tobisch, S., Wümpelmann, M., Gördes, D., Koch, A., & Thurow, K., et al. (2005). Global expression profiling of Bacillus subtilis cells during industrial-close fed-batch fermentations with different nitrogen sources. Biotechnol Bioeng, 92 (3), pp. 277–298.

Kohler, C., Wolff, S., Albrecht, D., Fuchs, S., Becher, D., Büttner, K., Engelmann, S., & Hecker, M. (2005/12/5). Proteome analyses of Staphylococcus aureus in growing and non-growing cells: A physiological approach. International Journal of Medical Microbiology, 295(8), pp. 547–565.

Peng, J., Raddatz, K., Labeit, S., Granzier, H., & Gotthardt, M. (2005/12/30/). Muscle atrophy in Titin Mline deficient mice. Journal of Muscle Research and Cell Motility, 26 (6), pp. 381–388.

Silberbach, M., Schäfer, M., Hüser, A. T., Kalinowski, J., Pühler, A., Krämer, R., & Burkovski, A. (2005). Adaptation of Corynebacterium glutamicum to ammonium limitation: a global analysis using transcriptome and proteome techniques. Appl Environ Microbiol, 71(5), pp. 2391–2402.

Stübs, D., Fuchs, T. M., Schneider, B., Bosserhoff, A., & Gross, R. (2005). Identification and regulation of cold-inducible factors of Bordetella bronchiseptica. Microbiology, 151 (Pt 6), pp. 1895–1909.

Valkova, N., Yunis, R., Mak, S. K., Kang, K., & Kültz, D. (2005). Nek8 mutation causes overexpression of galectin-1, sorcin, and vimentin and accumulation of the major urinary protein in renal cysts of jck mice. Mol Cell Proteomics, 4 (7), pp. 1009–1018.

Williams, T., Joseph, B., Beier, D., Goebel, W., & Kuhn, M. (2005). Response regulator DegU of Listeria monocytogenes regulates the expression of flagella-specific genes. FEMS Microbiology Letters, 252 (2), pp. 287–298.

Xie, J., Techritz, S., Haebel, S., Horn, A., Neitzel, H., Klose, J., & Schuelke, M. (2005). A twodimensional electrophoretic map of human mitochondrial proteins from immortalized lymphoblastoid cell lines: a prerequisite to study mitochondrial disorders in patients. Proteomics, 5 (11), pp. 2981–2999. ,from doi:10.1002/pmic.200401191.


Beckers, G., Bendt, A. K., Krämer, R., & Burkovski, A. (2004). Molecular identification of the urea uptake system and transcriptional analysis of urea transporter- and urease-encoding genes in Corynebacterium glutamicum. J Bacteriol, 186 (22), pp. 7645–7652.

Bendt, A. K., Beckers, G., Silberbach, M., Wittmann, A., & Burkovski, A. (2004). Utilization of creatinine as an alternative nitrogen source in Corynebacterium glutamicum. Arch Microbiol, 181 (6), pp. 443–450.

Duncan, M. K., Xie, L., David, L. L., Robinson, M. L., Taube, J. R., Cui, W., & Reneker, L. W. (2004). Ectopic Pax6 expression disturbs lens fiber cell differentiation. Invest Ophthalmol Vis Sci, 45(10), pp. 3589–3598.

Eymann, C., Dreisbach, A., Albrecht, D., Bernhardt, J., Becher, D., & Gentner, S., et al. (2004). A comprehensive proteome map of growing Bacillus subtilis cells. Proteomics, 4(10), pp. 2849–2876.

Holtmann, G., Brigulla, M., Steil, L., Schütz, A., Barnekow, K., Völker, U., & Bremer, E. (2004). RsbVindependent induction of the SigB-dependent general stress regulon of Bacillus subtilis during growth at high temperature. J Bacteriol, 186 (18), pp. 6150–6158.

Kock, H., Gerth, U., & Hecker, M. (2004). The ClpP peptidase is the major determinant of bulk protein turnover in Bacillus subtilis. J Bacteriol, 186 (17), pp. 5856–5864.

Kusch, H., Biswas, K., Schwanfelder, S., Engelmann, S., Rogers, P. D., Hecker, M., & Morschhäuser, J. (2004). A proteomic approach to understanding the development of multidrug-resistant Candida albicans strains. Mol Genet Genomics, 271(5), pp. 554–565.

Laukel, M., Rossignol, M., Borderies, G., Völker, U., & Vorholt, J. A. (2004). Comparison of the proteome of Methylobacterium extorquens AM1 grown under methylotrophic and nonmethylotrophic conditions. Proteomics, 4 (5), pp. 1247–1264.

Leichert, L. I., & Jakob, U. (2004). Protein thiol modifications visualized in vivo. PLoS Biol, 2(11), pp.e333.

Mostertz, J., Scharf, C., Hecker, M., & Homuth, G. (2004). Transcriptome and proteome analysis of Bacillus subtilis gene expression in response to superoxide and peroxide stress. Microbiology, 150 (Pt 2), pp. 497–512.

Rosen, R., Becher, D., Büttner, K., Biran, D., Hecker, M., & Ron, E. Z. (2004). Highly phosphorylated bacterial proteins. Proteomics, 4 (10), pp. 3068–30770.

Rosen, R., Sacher, A., Shechter, N., Becher, D., Büttner, K., Biran, D., Hecker, M., & Ron, E. Z. (2004). Two-dimensional reference map of Agrobacterium tumefaciens proteins. Proteomics, 4 (4), pp.1061–1073.

Tjalsma, H., Antelmann, H., Jongbloed, J. D., Braun, P. G., Darmon, E., & Dorenbos, R., et al. (2004). Proteomics of protein secretion by Bacillus subtilis: separating the "secrets" of the secretome. Microbiol Mol Biol Rev, 68 (2), pp. 207–233.

Voigt, B., Schweder, T., Becher, D., Ehrenreich, A., Gottschalk, G., Feesche, J., Maurer, K. H., & Hecker, M. (2004). A proteomic view of cell physiology of Bacillus licheniformis. Proteomics, 4(5), pp.1465–1490.

Ziebandt, A. K., Becher, D., Ohlsen, K., Hacker, J., Hecker, M., & Engelmann, S. (2004). The influence of agr and sigmaB in growth phase dependent regulation of virulence factors in Staphylococcus aureus. Proteomics, 4(10), pp. 3034–3047.


Antelmann, H., Darmon, E., Noone, D., Veening, J. W., Westers, H., & Bron, S., et al. (2003). The extracellular proteome of Bacillus subtilis under secretion stress conditions. Mol Microbiol, 49(1), pp.143–156.

Bandow, J. E., Becher, D., Büttner, K., Hochgräfe, F., Freiberg, C., Brötz, H., & Hecker, M. (2003). The role of peptide deformylase in protein biosynthesis: a proteomic study. Proteomics, 3 (3), pp. 299–306.

Bandow, J. E., Brötz, H., Leichert, L. I., Labischinski, H., & Hecker, M. (2003). Proteomic approach to understanding antibiotic action. Antimicrob Agents Chemother, 47(3), pp. 948–955.

Bendt, A. K., Burkovski, A., Schaffer, S., Bott, M., Farwick, M., & Hermann, T. (2003). Towards a phosphoproteome map of Corynebacterium glutamicum. Proteomics, 3 (8), pp. 1637–1646.

Bernhardt, J., Weibezahn, J., Scharf, C., & Hecker, M. (2003). Bacillus subtilis During Feast and Famine: Visualization of the Overall Regulation of Protein Synthesis During Glucose Starvation by Proteome Analysis. Genome Res., 13(2), pp. 224–237.

Cahill, M. A., Wozny, W., Schwall, G., Schroer, K., Hölzer, K., & Poznanovic, S., et al. (2003). Analysis of relative isotopologue abundances for quantitative profiling of complex protein mixtures labelled with the acrylamide/D3-acrylamide alkylation tag system. Rapid Commun Mass Spectrom, 17 (12), pp.1283–1290.

Kohler, C., Eiff, C. von, Peters, G., Proctor, R. A., Hecker, M., & Engelmann, S. (2003). Physiological characterization of a heme-deficient mutant of Staphylococcus aureus by a proteomic approach. JBacteriol, 185(23), pp. 6928–6937.

Leichert, L. I., Scharf, C., & Hecker, M. (2003). Global characterization of disulfide stress in Bacillus subtilis. J Bacteriol, 185 (6), pp. 1967–1975.

Luhn, S., Berth, M., Hecker, M., & Bernhardt, J. (2003). Using standard positions and image fusion to create proteome maps from collections of two-dimensional gel electrophoresis images. Proteomics, 3(7), pp. 1117–1127.

Medjahed, D., Smythers, G. W., Powell, D. A., Stephens, R. M., Lemkin, P. F., & Munroe, D. J. (2003). VIRTUAL2D: A web-accessible predictive database for proteomics analysis. Proteomics, 3 (2), pp. 129–138.

Westers, H., Dorenbos, R., van, D. M., Kabel, J., Flanagan, T., & Devine, K. M., et al. (2003). Genome engineering reveals large dispensable regions in Bacillus subtilis. Mol Biol Evol, 20 (12), pp. 2076–2090. , from doi:10.1093/molbev/msg219.


Antelmann, H., Yamamoto, H., Sekiguchi, J., & Hecker, M. (2002). Stabilization of cell wall proteins in Bacillus subtilis: a proteomic approach. Proteomics, 2 (5), pp. 591–602.

Bandow, J. E., Brötz, H., & Hecker, M. (2002). Bacillus subtilis tolerance of moderate concentrations of rifampin involves the sigma(B)-dependent general and multiple stress response. J Bacteriol, 184 (2), pp.459–467.

Eymann, C., Homuth, G., Scharf, C., & Hecker, M. (2002). Bacillus subtilis functional genomics: global characterization of the stringent response by proteome and transcriptome analysis. J Bacteriol, 184(9), pp. 2500–2520.

Jongbloed, J. D., Antelmann, H., Hecker, M., Nijland, R., Bron, S., & Airaksinen, U., et al. (2002). Selective contribution of the twin-arginine translocation pathway to protein secretion in Bacillus subtilis. J Biol Chem, 277 (46), pp. 44068–44078.

Kaan, T., Homuth, G., Mäder, U., Bandow, J., & Schweder, T. (2002). Genome-wide transcriptional profiling of the Bacillus subtilis cold-shock response. Microbiology, 148 (Pt 11), pp. 3441–3455.

Mäder, U., Antelmann, H., Buder, T., Dahl, M. K., Hecker, M., & Homuth, G. (2002). Bacillus subtilis functional genomics: genome-wide analysis of the DegS-DegU regulon by transcriptomics and proteomics. Mol Genet Genomics, 268(4), pp. 455–467.

Mäder, U., Homuth, G., Scharf, C., Büttner, K., Bode, R., & Hecker, M. (2002). Transcriptome and proteome analysis of Bacillus subtilis gene expression modulated by amino acid availability. J Bacteriol, 184 (15), pp. 4288–4295.

Rosen, R., Biran, D., Gur, E., Becher, D., Hecker, M., & Ron, E. Z. (2002). Protein aggregation in Escherichia coli: role of proteases. FEMS Microbiol Lett, 207(1), pp. 9–12.

Rosen, R., Büttner, K., Becher, D., Nakahigashi, K., Yura, T., Hecker, M., & Ron, E. Z. (2002). Heat shock proteome of Agrobacterium tumefaciens: evidence for new control systems. J Bacteriol, 184(6), pp. 1772–1778.

Rosen, R., & Ron, E. Z. (2002). Proteome analysis in the study of the bacterial heat-shock response. Mass Spectrom Rev, 21 (4), pp. 244–265.

2001 and before

Antelmann, H., Tjalsma, H., Voigt, B., Ohlmeier, S., Bron, S., van, D. M., & Hecker, M. (2001). A proteomic view on genome-based signal peptide predictions. Genome Res, 11 (9), pp. 1484–1502.

Büttner, K., Bernhardt, J., Scharf, C., Schmid, R., Mäder, U., & Eymann, C., et al. (2001). A comprehensive two-dimensional map of cytosolic proteins of Bacillus subtilis. Electrophoresis, 22 (14), pp. 2908–2935.

Ziebandt, A. K., Weber, H., Rudolph, J., Schmid, R., Höper, D., Engelmann, S., & Hecker, M. (2001). Extracellular proteins of Staphylococcus aureus and the role of SarA and sigma B. Proteomics, 1(4), pp.480–493.

Bernhardt, J., Büttner, K., Scharf, C., & Hecker, M. (1999). Dual channel imaging of two-dimensional electropherograms in Bacillus subtilis. Electrophoresis, 20 (11), pp. 2225–2240.

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