1. Mäder U, Nicolas P, Depke M, Pané-Farré J, Debarbouille M, van der Kooi-Pol MM, Guérin C, Dérozier S, Hiron A, Jarmer H, Leduc A, Michalik S, Reilman E, Schaffer M, Schmidt F, Bessières P, Noirot P, Hecker M, Msadek T, Völker U, van Dijl JM. Staphylococcus aureus Transcriptome Architecture: From Laboratory to Infection-Mimicking Conditions. PLoS Genet. 2016 Apr 1;12(4):e1005962.

    eCollection 2016, Article, PubMed, Related citations

  2. Lamberti Y, Cafiero JH, Surmann K, Valdez H, Holubova J, Večerek B, Sebo P, Schmidt F, Völker U, Rodriguez ME. Proteome analysis of Bordetella pertussis isolated from human macrophages. J Proteomics. 2016 Mar 16;136:55-67.

    Epub 2016 Feb 10. Article, PubMed, Related citations


  1. Shteynberg D, Mendoza L, Hoopmann MR, Sun Z, Schmidt F, Deutsch EW, Moritz RL. reSpect: software for identification of high and low abundance ion species in chimeric tandem mass spectra. J Am Soc Mass Spectrom. 2015 Nov;26(11):1837-47.

    Epub 2015 Sep 29.Article, PubMed, Related citations

  2. Day FR, Ruth KS, Thompson DJ, Lunetta KL, Pervjakova N, Chasman DI, et al. Large-scale genomic analyses link reproductive aging to hypothalamic signaling, breast cancer susceptibility and BRCA1-mediated DNA repair. Nat Genet. 2015 Sep 28.

    Epub ahead of print, Article, PubMed, Related citations

  3. Stentzel S, Sundaramoorthy N, Michalik S, Nordengrün M, Schulz S, Kolata J, Kloppot P, Engelmann S, Steil L, Hecker M, Schmidt F, Völker U, Roghmann MC, Bröker BM. Specific serum IgG at diagnosis of Staphylococcus aureus bloodstream invasion is correlated with disease progression. J Proteomics. 2015 Jul 5;128:1-7.

    Epub ahead of print, Article, PubMed, Related citations

  4. Shteynberg D, Mendoza L, Hoopmann MR, Schmidt F, Sun Z, Deutsch EW, Moritz RL. reSpect: Software for Identification of High and Low Abundance Ion Species in Chimeric Tandem Mass Spectra. J Am Soc Mass Spectrom. 2015.


  5. Surmann K, Simon M, Hildebrandt P, Pförtner H, Michalik S, Stentzel S, Steil L, Dhople VM, Bernhardt J, Schlüter R, Depke M, Gierok P, Lalk M, Bröker BM, Schmidt F, Völker U. A proteomic perspective of the interplay of Staphylococcus aureus and human alveolar epithelial cells during infection. J Proteomics. 2015 Aug 2. pii: S1874-3919(15)30088-9.

    Epub ahead of print, Article, PubMed, Related citations

  6. Depke M, Michalik S, Rabe A, Surmann K, Brinkmann L, Jehmlich N, Bernhardt J, Hecker M, Wollscheid B, Sun Z, Moritz RL, Völker U, Schmidt F. A peptide resource for the analysis of Staphylococcus aureus in host-pathogen interaction studies. Proteomics. 2015 Jul 30.

    Epub ahead of print, Article, PubMed, Related citations

  7. Hayes JA, Lamberti Y, Surmann K, Schmidt F, Völker U, and Rodriguez ME. Shotgun proteome analysis of Bordetella pertussis reveals a distinct influence of iron availability on the bacterial metabolism, virulence, and defense response. Proteomcis. 2015.

    Epub 2015 Mar 9, Article, PubMed, Related citations

  8. Aeberhard L, Banhart S, Fischer M, Jehmlich N, Rose L, Koch S, Laue M, Renard BY, Schmidt F and Heuer D. The proteome of the isolated Chlamydia trachomatis containing vacuole reveals a complex trafficking platform enriched for retromer components. PLoS Pathog. 2015.

    Article, PubMed, Related citations


  1. Mühlhaus J, Dinter J, Nürnberg D, Rehders M, Depke M, Golchert J, Homuth G, Yi CY, Morin S, Köhrle J, Brix K, Tschöp M, Kleinau G, Biebermann H. Analysis of Human TAAR8 and Murine Taar8b Mediated Signaling Pathways and Expression Profile. Int. J. Mol. Sci. 2014, 15(11), 20638-20655.

    Article, PubMed, Related citations

  2. Müller M, Reiß S, Schlüter R, Mäder U, Beyer A, Reiß W, Marles-Wright J, Lewis RJ, Pförtner H, Völker U, Riedel K, Hecker M, Engelmann S, Pané-Farré J. Deletion of membrane-associated Asp23 leads to upregulation of cell wall stress genes in Staphylococcus aureus. Mol Microbiol. 2014. Sep;93(6):1259-68.

    Epub 2014 Aug 19, Article, PubMed, Related citations

  3. Surmann K, Michalik S, Hildebrandt P, Gierok P, Depke M, Brinkmann L, Bernhardt J, Gesell Salazar M, Zhi S, Shteynberg D, Kusebauch U, Moritz RL, Wollscheid B, Lalk M, Völker U, Schmidt F. Comparative proteome analysis reveals conserved and specific adaptation patterns of Staphylococcus aureus after internalization by different types of human non-professional phagocytic host cells. Front Microbiol. 2014 Aug 1;5:392.

    eCollection 2014, Article, PubMed, Related citations

  4. Stentzel S, Vu Hai Chi, Weyrich AM, Jehmlich N, Schmidt F, Gesell Salazar M, Steil L, Völker U, Bröker BM. Altered immune proteome of Staphylococcus aureus under iron-restricted growth conditions. Proteomics. 2014 Aug;14(16):1857-67.

    Epub 2014 Jul 9, Article, PubMed, Related citations

  5. Jehmlich N, Golatowski C, Murr A, Salazar G , Dhople VM, Hammer E, Völker U. Comparative evaluation of peptide desalting methods for salivary proteome analysis. Clin Chim Acta. 2014 Jul 1;434:16-20.

    Epub 2014 Apr 18, Article, PubMed, Related citations

  6. Auer PL, Teumer A, Schick U, O'Shaughnessy A, Lo KS, Chami N, Carlson C, de Denus S, Dubé M-P, Haessler J, Jackson RD, Kooperberg C, Lemieux Perreault L-P, Nauck M, Peters U, Rioux JD, Schmidt F , Turcot V, Völker U, Völzke H, Greinacher A, Hsu L, Tardif J-C, Diaz GA, Reiner AP, Lettre G. Rare and low-frequency coding variants in CXCR2 and other genes are associated with hematological traits. Nat Genet. 2014 Jun;46(6):629-34.

    Epub 2014 Apr 28, Article, PubMed, Related citations

  7. Depke M, Breitbach, K, Dinh Hoang Dang K, Brinkmann L, Gesell Salazar M, Dhople VM, Bast A, Steil L, Schmidt F, Steinmetz I and Völker U. Bone marrow-derived macrophages from BALB/c and C57BL/6 mice fundamentally differ in their respiratory chain complex proteins, lysosomal enzymes and components of antioxidant stress systems. J Proteomics. 2014 Apr 1;103C:72-86.

    Epub ahead of print, Article, PubMed, Related citations

  8. Pförtner H, Burian MS, Michalik S, Depke M, Hildebrandt P, Dhople VM, Pané-Farré J, Hecker M, Schmidt F, Völker U. Activation of the alternative sigma factor SigB of Staphylococcus aureus following internalization by epithelial cells - An in vivo proteomics perspective. Int J Med Microbiol. 2014 Mar;304(2):177-87.

    Epub 2013 Dec 7, Article, PubMed, Related citations

  9. Depke M, Surmann K, Hildebrandt P, Jehmlich N, Michalik S, Stanca SE, Fritzsche W, Völker U, and Schmidt F. Labeling of the pathogenic bacterium Staphylococcus aureus with gold or ferric oxide-core nanoparticles highlights new capabilities for following host-pathogen interactions. Cytometry A. 2014 Feb;85(2):140-50.

    Epub 2013 Dec 17, Article, PubMed, Related citations


  1. Otto A, Becher D, and Schmidt F. Quantitative Proteomics in the field of Microbiology. Proteomics. 2013 Dec 23.

    Epub ahead of print, Article, PubMed, Related citations

  2. Callaway A, Kostrzewa M, Willershausen B, Schmidt F, Thiede B, Küpper H, Kneist S. Identification of Lactobacilli from Deep Carious Lesions by Means of Species-Specific PCR and MALDI-TOF Mass Spectrometry. Clin Lab. 2013;59(11-12):1373-9.

    Print 2013, Article, PubMed, Related citations

  3. Herbst FA, Taubert M, Jehmlich N, Behr T, Schmidt F, von Bergen M, Seifert J. Sulfur-34S Stable Isotope Labeling of Amino Acids for Quantification (SULAQ34) of Proteomic Changes in Pseudomonas fluorescens during Naphthalene Degradation. Mol Cell Proteomics. 2013 Aug;12(8):2060-9.

    Epub 2013 Apr 19, Article, PubMed, Related citations

  4. Mehlan H, Schmidt F, Weiss S, Schüler J, Fuchs S, Riedel K, Bernhardt J. Data visualization in environmental proteomics. Proteomics. 2013 Aug 2.

    Epub ahead of print, Article, PubMed, Related citations

  5. Jehmlich N, Dinh KH, Gesell Salazar M, Hammer E, Steil L, Dhople VM, Schurmann C, Holtfreter B, Kocher T, Völker U. Quantitative analysis of the intra- and inter-subject variability of the whole salivary proteome. J Periodontal Res. 2013 Jun;48(3):392-403.

    Epub 2012 Nov 20, Article, PubMed, Related citations

  6. Winter T, Bernhardt J, Winter J, Mäder U, Schlüter R, Weltmann KD, Hecker M, Kusch H. Common versus noble Bacillus subtilis differentially responds to air and argon gas plasma. Proteomics. 2013 Jun 21.

    Epub ahead of print, Article, PubMed, Related citations

  7. Pförtner H, Wagner J, Surmann K, Hildebrandt P, Ernst S, Bernhardt J, Schurmann C, Gutjahr M, Depke M, Jehmlich U, Dhople V, Hammer E, Steil L, Völker U, Schmidt F. A proteomics workflow for quantitative and time-resolved analysis of adaptation reactions of internalized bacteria. Methods. 2013 Jun 15;61(3):244-50.

    Epub 2013 Apr 30, Article, PubMed, Related citations

  8. Kühlhorn F, Rath M, Schmoeckel K, Cziupka K, Nguyen HH, Hildebrandt P, Hünig T, Sparwasser T, Huehn J, Pötschke C, Bröker BM. Foxp3+ regulatory T cells are required for recovery from severe sepsis. PLoS One. 2013 May 28;8(5):e65109.

    Print 2013, Article, PubMed, Related citations

  9. von Bergen M, Jehmlich N, Taubert M, Vogt C, Bastida F, Herbst FA, Schmidt F, Richnow HH, Seifert J. Insights from quantitative metaproteomics and protein-stable isotope probing into microbial ecology. ISME J. 2013 May 16.

    Epub ahead of print, Article, PubMed, Related citations

  10. Schlüter R, Lippmann R, Hammer E, Gesell Salazar M, Schauer F. Novel insights into the fungal oxidation of monoaromatic and biarylic environmental pollutants by characterization of two new ring cleavage enzymes. Appl Microbiol Biotechnol. 2013 Feb 12.

    Epub ahead of print, Article, PubMed, Related citations

  11. Golatowski C, Gesell Salazar M, Dhople VM, Hammer E, Kocher T, Jehmlich N, Völker U. Comparative evaluation of saliva collection methods for proteome analysis. Clin Chim Acta. 2013 Feb 4;419C:42-46.

    Epub ahead of print, Article, PubMed, Related citations

  12. Feng J, Michalik S, Varming AN, Andersen JH, Albrecht D, Jelsbak L, Krieger S, Ohlsen K, Hecker M, Gerth U, Ingmer H, Frees D. Trapping and proteomic identification of cellular substrates of the ClpP protease in Staphylococcus aureus. J Proteome Res. 2013 Feb 1;12(2):547-58.

    Epub 2013 Jan 8, Article, PubMed, Related citations

  13. Bernhardt J, Michalik S, Wollscheid B, Völker U, Schmidt F. Proteomics approaches for the analysis of enriched microbial subpopulations and visuali­zation of complex functional information. Curr Opin Biotechnol. 2013 Feb;24(1):112-9.

    Epub 2012 Nov 7, Article, PubMed, Related citations

  14. Räth S, Ziesemer S, Witte A, Konkel A, Müller C, Hildebrandt P, Völker U, Hildebrandt JP. S. Aureus haemolysin A-induced IL-8 and IL-6 release from human airway epithelial cells is mediated by activation of p38- and Erk-MAP kinases and additional, cell type-specific signalling mechanisms. Cell Microbiol. 2013 Jan 24.

    Epub ahead of print, Article, PubMed, Related citations


  1. Seifert J, Taubert M, Jehmlich N, Schmidt F, Völker U, Vogt C, Richnow HH, von Bergen M. Protein-based stable isotope probing (protein-SIP) in functional metaproteomics. Mass Spectrom Rev. 2012 Nov;31(6):683-97.

    Epub 2012 Mar 15, Article, PubMed

  2. Delauné A, Dubrac S, Blanchet C, Poupel O, Mäder U, Hiron A, Leduc A, Fitting C, Nicolas P, Cavaillon JM, Adib-Conquy M, Msadek T. The WalKR system controls major staphylococcal virulence genes and is involved in triggering the host inflammatory response. Infect Immun. 2012 Oct;80(10):3438-53.

    Epub 2012 Jul 23, Article, PubMed

  3. Michalik S, Bernhardt J, Otto A, Moche M, Becher D, Meyer H, Lalk M, Schurmann C, Schlüter R, Kock H, Gerth U, Hecker M. Life and death of proteins: A case study of glucose-starved Staphylococcus aureus. Mol Cell Proteomics. 2012 Sep;11(9):558-70.

    Epub 2012 May 3., Article, PubMed

  4. Bieler S, Hammer E, Gesell Salazar M, Völker U, Stangl K, Meiners S. Low dose proteasome inhibition affects alternative splicing. J Proteome Res. 2012 Aug 3;11(8):3947-54.

    Epub 2012 Jul 3, Article, PubMed

  5. Lehnik-Habrink M, Lewis RJ, Mäder U, Stülke J. RNA degradation in Bacillus subtilis: An interplay of essential endo- and exoribonucleases. Mol Microbiol. 2012 Jun;84(6):1005-17.

    Epub 2012 May 8, Article, PubMed

  6. Thiele T, Iuga C, Janetzky S, Schwertz H, Gesell Salazar M, Fürll B, Völker U, Greinacher A, Steil L. Early storage lesions in apheresis platelets are induced by the activation of the integrin αIIbβ3 and focal adhesion signaling pathways. J Proteomics. 2012 May 24.

    Article, PubMed

  7. Elsholz AK, Turgay K, Michalik S, Hessling B, Gronau K, Oertel D, Mäder U, Bernhardt J, Becher D, Hecker M, Gerth U. Global impact of protein arginine phosphorylation on the physiology of Bacillus subtilis. Proc Natl Acad Sci U S A. 2012 May 8;109(19):7451-6.

    Epub 2012 Apr 19, Article, PubMed

  8. Dyshlovoy SA, Naeth I, Venz S, Preukschas M, Sievert H, Jacobsen C, Shubina LK, Gesell Salazar M, Scharf C, Walther R, Krepstakies M, Priyadarshini P, Hauber J, Fedorov SN, Bokemeyer C, Stonik VA, Balabanov S, Honecker F. Proteomic profiling of germ cell cancer cells treated with aaptamine, a marine alkaloid with antiproliferative activity. J Proteome Res. 2012 Apr 6;11(4):2316-30.

    Epub 2012 Mar 28, Article, PubMed

  9. Nannapaneni P, Hertwig F, Depke M, Hecker M, Mäder U, Völker U, Steil L, van Hijum SA. Defining the structure of the general stress regulon of Bacillus subtilis using targeted microarray analysis and random forest classification. Microbiology. 2012 Mar;158(Pt 3):696-707.

    Epub 2011 Dec 15, Article, PubMed

  10. Buescher JM, Liebermeister W, Jules M, Uhr M, Muntel J, Botella E, Hessling B, Kleijn RJ, Le Chat L, Lecointe F, Mäder U, Nicolas P, Piersma S, Rügheimer F, Becher D, Bessieres P, Bidnenko E, Denham EL, Dervyn E, Devine KM, Doherty G, Drulhe S, Felicori L, Fogg MJ, Goelzer A, Hansen A, Harwood CR, Hecker M, Hubner S, Hultschig C, Jarmer H, Klipp E, Leduc A, Lewis P, Molina F, Noirot P, Peres S, Pigeonneau N, Pohl S, Rasmussen S, Rinn B, Schaffer M, Schnidder J, Schwikowski B, Van Dijl JM, Veiga P, Walsh S, Wilkinson AJ, Stelling J, Aymerich S, Sauer U. Global network reorganization during dynamic adaptations of Bacillus subtilis metabolism. Science. 2012 Mar 2;335(6072):1099-103.

    Article, PubMed

  11. Nicolas P, Mäder U, Dervyn E, Rochat T, Leduc A, Pigeonneau N, Bidnenko E, Marchadier E, Hoebeke M, Aymerich S, Becher D, Bisicchia P, Botella E, Delumeau O, Doherty G, Denham EL, Fogg MJ, Fromion V, Goelzer A, Hansen A, Härtig E, Harwood CR, Homuth G, Jarmer H, Jules M, Klipp E, Le Chat L, Lecointe F, Lewis P, Liebermeister W, March A, Mars RA, Nannapaneni P, Noone D, Pohl S, Rinn B, Rügheimer F, Sappa PK, Samson F, Schaffer M, Schwikowski B, Steil L, Stülke J, Wiegert T, Devine KM, Wilkinson AJ, van Dijl JM, Hecker M, Völker U, Bessières P, Noirot P. Condition-dependent transcriptome reveals high-level regulatory architecture in Bacillus subtilis. Science. 2012 Mar 2;335(6072):1103-6.

    Article, PubMed

  12. Jehmlich N, Kopinke FD, Lenhard S, Vogt C, Herbst FA, Seifert J, Lissner U, Völker U, Schmidt F, von Bergen M. Sulfur-36S stable isotope labeling of amino acids for quantification (SULAQ). Proteomics. 2012 Jan;12(1):37-42.

    Epub 2011 Dec 16, Article, PubMed

  13. Mäder U, Schmeisky AG, Flórez LA, Stülke J. SubtiWiki--a comprehensive community resource for the model organism Bacillus subtilis. Nucleic Acids Res. 2012 Jan;40(Database issue):D1278-87.

    Epub 2011 Nov 16, Article, PubMed

  14. Sternberg K, Gratz M, Koeck K, Mostertz J, Begunk R, Loebler M, Semmling B, Seidlitz A, Hildebrandt P, Homuth G, Grabow N, Tuemmler C, Weitschies W, Schmitz KP, Kroemer HK. Magnesium used in bioabsorbable stents controls smooth muscle cell proliferation and stimulates endothelial cells in vitro. J Biomed Mater Res B Appl Biomater. 2012 Jan;100(1):41-50.

    Epub 2011 Nov 24, Article, PubMed

  15. Depke M, Burian M, Schäfer T, Bröker BM, Ohlsen K, Völker U. The alternative sigma factor B modulates virulence gene expression in a murine Staphylococcus aureus infection model but does not influence kidney gene expression pattern of the host. Int J Med Microbiol. 2012 Jan;302(1):33-9.

    Epub 2011 Oct 22, Article, PubMed


  1. Chi BK, Gronau K, Mäder U, Hessling B, Becher D, Antelmann H. S-bacillithiolation protects against hypochlorite stress in Bacillus subtilis as revealed by transcriptomics and redox proteomics. Mol Cell Proteomics. 2011 Nov;10(11):M111.009506.

    Epub 2011 Jul 11, Article, PubMed

  2. Gebhard S, Steil L, Peters B, Gesell Salazar M, Hammer E, Kuttler B, Clemetson KJ, Scharf C, Peters J, Völker U, Rettig R, Greinacher A. Angiotensin II-dependent hypertension causes reversible changes in the platelet proteome. J Hypertens. 2011 Nov;29(11):2126-37.

    Article, PubMed

  3. Wecke T, Bauer T, Harth H, Mäder U, Mascher T. The rhamnolipid stress response of Bacillus subtilis. FEMS Microbiol Lett. 2011 Oct;323(2):113-23.

    Epub 2011 Aug 24, Article, PubMed

  4. Opitz E, Koch A, Klingel K, Schmidt F, Prokop S, Rahnefeld A, Sauter M, Heppner FL, Völker U, Kandolf R, Kuckelkorn U, Stangl K, Krüger E, Kloetzel PM, Voigt A. Impairment of immunoproteasome function by β5i/LMP7 subunit deficiency results in severe enterovirus myocarditis. PLoS Pathog. 2011 Sep;7(9):e1002233.

    Epub 2011 Sep 1, Article, PubMed

  5. Winter T, Winter J, Polak M, Kusch K, Mäder U, Sietmann R, Ehlbeck J, van Hijum S, Weltmann KD, Hecker M, Kusch H. Characterization of the global impact of low temperature gas plasma on vegetative microorganisms. Proteomics. 2011 Sep;11(17):3518-30.

    Epub 2011 Aug 4, Article, PubMed

  6. Lehnik-Habrink M, Schaffer M, Mäder U, Diethmaier C, Herzberg C, Stülke J. RNA processing in Bacillus subtilis: identification of targets of the essential RNase Y. Mol Microbiol. 2011 Sep;81(6):1459-73.

    Epub 2011 Aug 4, Article, PubMed

  7. Pohl S, Tu WY, Aldridge PD, Gillespie C, Hahne H, Mäder U, Read TD, Harwood CR. Combined proteomic and transcriptomic analysis of the response of Bacillus anthracis to oxidative stress. Proteomics. 2011 Aug;11(15):3036-55.

    Epub 2011 Jul 4, Article, PubMed

  8. Schmidt F, Völker U. Proteome analysis of host-pathogen interactions: Investigation of pathogen responses to the host cell environment. Proteomics. 2011 Aug;11(15):3203-11.

    Epub 2011 Jun 28, Article, PubMed

  9. Elsholz AK, Hempel K, Michalik S, Gronau K, Becher D, Hecker M, Gerth U. Activity control of the ClpC adaptor McsB in Bacillus subtilis. J Bacteriol. 2011 Aug;193(15):3887-93.

    Epub 2011 May 27, Article, PubMed

  10. Schroeter R, Voigt B, Jürgen B, Methling K, Pöther DC, Schäfer H, Albrecht D, Mostertz J, Mäder U, Evers S, Maurer KH, Lalk M, Mascher T, Hecker M, Schweder T. The peroxide stress response of Bacillus licheniformis. Proteomics. 2011 Jul;11(14):2851-66.

    Epub 2011 Jun 14, Article, PubMed

  11. Schmidt F, Dahlmann B, Hustoft HK, Koehler CJ, Strozynski M, Kloss A, Zimny-Arndt U, Jungblut PR, Thiede B. Quantitative proteome analysis of the 20S proteasome of apoptotic Jurkat T cells. Amino Acids. 2011 Jul;41(2):351-61.

    Epub 2010 Apr 3, Article, PubMed

  12. Taubert M, Jehmlich N, Vogt C, Richnow HH, Schmidt F, von Bergen M, Seifert J. Time resolved protein-based stable isotope probing (Protein-SIP) analysis allows quantification of induced proteins in substrate shift experiments. Proteomics. 2011 Jun;11(11):2265-74.

    Epub 2011 May 20, Article, PubMed

  13. Frank S, Schmidt F, Klockgether J, Davenport CF, Gesell Salazar M, Völker U, Tümmler B. Functional genomics of the initial phase of cold adaptation of Pseudomonas putida KT2440. FEMS Microbiol Lett. 2011 May;318(1):47-54.

    Epub 2011 Mar 1, Article, PubMed

  14. van der Ploeg R, Mäder U, Homuth G, Schaffer M, Denham EL, Monteferrante CG, Miethke M, Marahiel MA, Harwood CR, Winter T, Hecker M, Antelmann H, van Dijl JM. Environmental salinity determines the specificity and need for Tat-dependent secretion of the YwbN protein in Bacillus subtilis. PLoS One. 2011 Mar 30;6(3):e18140.

    Article, PubMed

  15. Mäder U, Nicolas P, Richard H, Bessières P, Aymerich S. Comprehensive identification and quantification of microbial transcriptomes by genome-wide unbiased methods. Curr Opin Biotechnol. 2011 Feb;22(1):32-41.

    Epub 2010 Nov 10, Article, PubMed

  16. Zuber P, Chauhan S, Pilaka P, Nakano MM, Gurumoorthy S, Lin AA, Barendt SM, Chi BK, Antelmann H, Mäder U. Phenotype enhancement screen of a regulatory spx mutant unveils a role for the ytpQ gene in the control of iron homeostasis. PLoS One. 2011;6(9):e25066.

    Epub 2011 Sep 20, Article, PubMed

  17. Falord M, Mäder U, Hiron A, Débarbouillé M, Msadek T. Investigation of the Staphylococcus aureus GraSR regulon reveals novel links to virulence, stress response and cell wall signal transduction pathways. PLoS One. 2011;6(7):e21323.

    Epub 2011 Jul 1, Article, PubMed


  1. Jehmlich N, Schmidt F, Taubert M, Seifert J, Bastida F, von Bergen M, Richnow HH, Vogt C. Protein-based stable isotope probing. Nat Protoc. 2010 Dec;5(12):1957-66.

    Epub 2010 Nov 18, Article, PubMed

  2. Jehmlich N, Kleinsteuber S, Vogt C, Benndorf D, Harms H, Schmidt F, Von Bergen M, Seifert J. Phylogenetic and proteomic analysis of an anaerobic toluene-degrading community. J Appl Microbiol. 2010 Dec;109(6):1937-45.

    Article, PubMed

  3. Elsholz AK, Michalik S, Zühlke D, Hecker M, Gerth U. CtsR, the Gram-positive master regulator of protein quality control, feels the heat. EMBO J. 2010 Nov 3;29(21):3621-9.

    Epub 2010 Sep 17, Article, PubMed

  4. Kneist S, Schmidt F, Callaway A, Willershausen B, Rupf S, Wicht M, Thiede B. Diversity of Lactobacillus species in deep carious lesions of primary molars. Eur Arch Paediatr Dent. 2010 Aug;11(4):181-6. Erratum in: Eur Arch Paediatr Dent. 2010 Oct;11(5):262.


  5. Jehmlich N, Hübschmann T, Gesell Salazar M, Völker U, Benndorf D, Müller S, von Bergen M, Schmidt F. Advanced tool for characterization of microbial cultures by combining cytomics and proteomics. Appl Microbiol Biotechnol. 2010 Sep;88(2):575-84.

    Epub 2010 Jul 30, Article, PubMed

  6. Wolf D, Kalamorz F, Wecke T, Juszczak A, Mäder U, Homuth G, Jordan S, Kirstein J, Hoppert M, Voigt B, Hecker M, Mascher T. In-depth profiling of the LiaR response of Bacillus subtilis. J Bacteriol. 2010 Sep;192(18):4680-93.

    Epub 2010 Jul 16, Article, PubMed

  7. Grabarczyk P, Nähse V, Delin M, Przybylski G, Depke M, Hildebrandt P, Völker U, Schmidt CA. Increased expression of BCL11B leads to chemoresistance accompanied by G1 accumulation. PLoS One. 2010 Sep 2;5(9). pii: e12532.

    Article, PubMed

  8. Schmidt F, Scharf SS, Hildebrandt P, Burian M, Bernhardt J, Dhople V, Kalinka J, Gutjahr M, Hammer E, Völker U. Time-resolved quantitative proteome profiling of host-pathogen interactions: the response of Staphylococcus aureus RN1HG to internalisation by human airway epithelial cells. Proteomics. 2010 Aug;10(15):2801-11.

    Article, PubMed

  9. Karanam NK, Grabarczyk P, Hammer E, Scharf C, Venz S, Gesell Salazar M, Barthlen W, Przybylski GK, Schmidt CA, Völker U. Proteome analysis reveals new mechanisms of Bcl11b-loss driven apoptosis. J Proteome Res. 2010 Aug 6;9(8):3799-811.

    Article, PubMed

  10. Mikolasch A, Hahn V, Manda K, Pump J, Illas N, Gördes D, Lalk M, Gesell Salazar M, Hammer E, Jülich WD, Rawer S, Thurow K, Lindequist U, Schauer F. Laccase-catalyzed cross-linking of amino acids and peptides with dihydroxylated aromatic compounds. Amino Acids. 2010 Aug;39(3):671-83.

    Epub 2010 Feb 9, Article, PubMed

  11. Fetzer I, Jehmlich N, Vogt C, Richnow HH, Seifert J, Harms H, von Bergen M, Schmidt F. Calculation of partial isotope incorporation into peptides measured by mass spectrometry. BMC Res Notes. 2010 Jun 24;3:178.

    Article, PubMed

  12. Jehmlich N, Fetzer I, Seifert J, Mattow J, Vogt C, Harms H, Thiede B, Richnow HH, von Bergen M, Schmidt F. Decimal place slope, a fast and precise method for quantifying 13C incorporation levels for detecting the metabolic activity of microbial species. Mol Cell Proteomics. 2010 Jun;9(6):1221-7.

    Epub 2010 Jan 11, Article, PubMed

  13. Leibeling S, Schmidt F, Jehmlich N, von Bergen M, Müller RH, Harms H. Declining capacity of starving Delftia acidovorans MC1 to degrade phenoxypropionate herbicides correlates with oxidative modification of the initial enzyme. Environ Sci Technol. 2010 May 15;44(10):3793-9.

    Article, PubMed

  14. Gimpel M, Heidrich N, Mäder U, Krügel H, Brantl S. A dual-function sRNA from B. subtilis: SR1 acts as a peptide encoding mRNA on the gapA operon. Mol Microbiol. 2010 May;76(4):990-1009.

    Epub 2010 Apr 1, Article, PubMed

  15. Lammers CR, Flórez LA, Schmeisky AG, Roppel SF, Mäder U, Hamoen L, Stülke J. Connecting parts with processes: SubtiWiki and SubtiPathways integrate gene and pathway annotation for Bacillus subtilis. Microbiology. 2010 Mar;156(Pt 3):849-59.

    Epub 2009 Dec 3, Article, PubMed

  16. Hauberg L, Schmidt F, Scharf C, Dörr J, Völker U, Reinhold-Hurek B. Proteomic characterization of a pilR regulatory mutant of Azoarcus sp. strain BH72 with the aid of gel-based and gel-free approaches. Proteomics. 2010 Feb;10(3):458-69.

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  17. Hahne H, Mäder U, Otto A, Bonn F, Steil L, Bremer E, Hecker M, Becher D. A comprehensive proteomics and transcriptomics analysis of Bacillus subtilis salt stress adaptation. J Bacteriol. 2010 Feb;192(3):870-82.

    Epub 2009 Nov 30, Article, PubMed

  18. Sträuber H, Hübschmann T, Jehmlich N, Schmidt F, von Bergen M, Harms H, Müller S. NBDT (3-(N-(7-nitrobenz-2-oxa-1,3-diazol-4-yl)amino)-3-toluene)--a novel fluorescent dye for studying mechanisms of toluene uptake into vital bacteria. Cytometry A. 2010 Feb;77(2):113-20.

    Article, PubMed

  19. Selesi D, Jehmlich N, von Bergen M, Schmidt F, Rattei T, Tischler P, Lueders T, Meckenstock RU. Combined genomic and proteomic approaches identify gene clusters involved in anaerobic 2-methylnaphthalene degradation in the sulfate-reducing enrichment culture N47. J Bacteriol. 2010 Jan;192(1):295-306.

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  20. Hammer E, Bien S, Gesell Salazar M, Steil L, Scharf C, Hildebrandt P, Schroeder HW, Kroemer HK, Völker U, Ritter CA. Proteomic analysis of doxorubicin-induced changes in the proteome of HepG2cells combining 2-D DIGE and LC-MS/MS approaches. Proteomics. 2010 Jan;10(1):99-114.

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  21. Otto A, Bernhardt J, Meyer H, Schaffer M, Herbst FA, Siebourg J, Mäder U, Lalk M, Hecker M, Becher D. Systems-wide temporal proteomic profiling in glucose-starved Bacillus subtilis. Nat Commun. 2010;1:137.

    Article, PubMed


  1. Michalik S, Liebeke M, Zühlke D, Lalk M, Bernhardt J, Gerth U, Hecker M. Proteolysis during long-term glucose starvation in Staphylococcus aureus COL. Proteomics. 2009 Oct;9(19):4468-77.

    Article, PubMed

  2. Depke M, Steil L, Domanska G, Völker U, Schütt C, Kiank C. Altered hepatic mRNA expression of immune response and apoptosis-associated genes after acute and chronic psychological stress in mice. Mol Immunol. 2009 Sep;46(15):3018-28.

    Epub 2009 Jul 9, Article, PubMed

  3. von Bergen M, Eidner A, Schmidt F, Murugaiyan J, Wirth H, Binder H, Maier T,  Roesler U. Identification of harmless and pathogenic algae of the genus Prototheca by MALDI-MS. Proteomics Clin Appl. 2009 Jul;3(7):774-84.

    Article, PubMed

  4. Aakvik T, Degnes KF, Dahlsrud R, Schmidt F, Dam R, Yu L, Völker U, Ellingsen TE, Valla S. A plasmid RK2-based broad-host-range cloning vector useful for transfer of metagenomic libraries to a variety of bacterial species. FEMS Microbiol Lett. 2009 Jun;296(2):149-58.

    Epub 2009 May 4, Article, PubMed

  5. Jehmlich N, Schmidt F, Taubert M, Seifert J, von Bergen M, Richnow HH, Vogt C. Comparison of methods for simultaneous identification of bacterial species and determination of metabolic activity by protein-based stable isotope probing (Protein-SIP) experiments. Rapid Commun Mass Spectrom. 2009 Jun;23(12):1871-8.

    Article, PubMed

  6. Schmidt F, Fiege T, Hustoft HK, Kneist S, Thiede B. Shotgun mass mapping of Lactobacillus species and subspecies from caries related isolates by MALDI-MS. Proteomics. 2009 Apr;9(7):1994-2003.

    Article, PubMed

  7. Wecke T, Zühlke D, Mäder U, Jordan S, Voigt B, Pelzer S, Labischinski H, Homuth G, Hecker M, Mascher T. Daptomycin versus Friulimicin B: in-depth profiling of Bacillus subtilis cell envelope stress responses. Antimicrob Agents Chemother. 2009 Apr;53(4):1619-23.

    Epub 2009 Jan 21, Article, PubMed

  8. Heine F, Stahl F, Sträuber H, Wiacek C, Benndorf D, Repenning C, Schmidt F, Scheper T, von Bergen M, Harms H, Müller S. Prediction of flocculation ability of brewing yeast inoculates by flow cytometry, proteome analysis, and mRNA profiling. Cytometry A. 2009 Feb;75(2):140-7.

    Article, PubMed

  9. Nguyen TT, Eiamphungporn W, Mäder U, Liebeke M, Lalk M, Hecker M, Helmann JD, Antelmann H. Genome-wide responses to carbonyl electrophiles in Bacillus subtilis: control of the thiol-dependent formaldehyde dehydrogenase AdhA and cysteine proteinase YraA by the MerR-family regulator YraB (AdhR). Mol Microbiol. 2009 Feb;71(4):876-94.

    Epub 2008 Dec 23, Article, PubMed

  10. Kouwen TR, van der Ploeg R, Antelmann H, Hecker M, Homuth G, Mäder U, van Dijl JM. Overflow of a hyper-produced secretory protein from the Bacillus Sec pathway into the Tat pathway for protein secretion as revealed by proteogenomics. Proteomics. 2009 Feb;9(4):1018-32.

    Article, PubMed

  11. Eichstaedt S, Gäbler K, Below S, Müller C, Kohler C, Engelmann S, Hildebrandt P, Völker U, Hecker M, Hildebrandt JP. Effects of Staphylococcus aureus-hemolysin A on calcium signalling in immortalized human airway epithelial cells. Cell Calcium. 2009 Feb;45(2):165-76.

    Epub 2008 Oct 15, Article, PubMed

  12. Schmidt F, Schmid M, Thiede B, Pleissner KP, Böhme M, Jungblut PR. Assembling proteomics data as a prerequisite for the analysis of large scale experiments. Chem Cent J. 2009 Jan 23;3:2.

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  1. Jehmlich N, Schmidt F, von Bergen M, Richnow HH, Vogt C. Protein-based stable isotope probing (Protein-SIP) reveals active species within anoxic mixed cultures. ISME J. 2008 Nov;2(11):1122-33.

    Epub 2008 Jun 19, Article, PubMed

  2. Mäder U, Zig L, Kretschmer J, Homuth G, Putzer H. mRNA processing by RNases J1 and J2 affects Bacillus subtilis gene expression on a global scale. Mol Microbiol. 2008 Oct;70(1):183-96.

    Epub 2008 Aug 18, Article, PubMed

  3. Jehmlich N, Schmidt F, Hartwich M, von Bergen M, Richnow HH, Vogt C. Incorporation of carbon and nitrogen atoms into proteins measured by protein-based stable isotope probing (Protein-SIP). Rapid Commun Mass Spectrom. 2008 Sep;22(18):2889-97.

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  4. Depke M, Fusch G, Domanska G, Geffers R, Völker U, Schuett C, Kiank C. Hypermetabolic syndrome as a consequence of repeated psychological stress in mice. Endocrinology. 2008 Jun;149(6):2714-23.

    Epub 2008 Mar 6, Article, PubMed

  5. Gerth U, Kock H, Kusters I, Michalik S, Switzer RL, Hecker M. Clp-dependent proteolysis down-regulates central metabolic pathways in glucose-starved Bacillus subtilis. J Bacteriol. 2008 Jan;190(1):321-31.

    Epub 2007 Nov 2, Article, PubMed


  1. Schmidt F, Hustoft HK, Strozynski M, Dimmler C, Rudel T, Thiede B. Quantitative proteome analysis of cisplatin-induced apoptotic Jurkat T cells by stable isotope labeling with amino acids in cell culture, SDS-PAGE, and LC-MALDI-TOF/TOF MS. Electrophoresis. 2007 Dec;28(23):4359-68.

    Article, PubMed

  2. Mattow J, Siejak F, Hagens K, Schmidt F, Koehler C, Treumann A, Schaible UE,  Kaufmann SH. An improved strategy for selective and efficient enrichment of integral plasma membrane proteins of mycobacteria. Proteomics. 2007 May;7(10):1687-701.

    Article, PubMed

  3. Nguyen VD, Wolf C, Mäder U, Lalk M, Langer P, Lindequist U, Hecker M, Antelmann H. Transcriptome and proteome analyses in response to 2-methylhydroquinone and 6-brom-2-vinyl-chroman-4-on reveal different degradation systems involved in the catabolism of aromatic compounds in Bacillus subtilis. Proteomics. 2007 May;7(9):1391-408.

    Article, PubMed

  4. Grabarczyk P, Przybylski GK, Depke M, Völker U, Bahr J, Assmus K, Bröker BM, Walther R, Schmidt CA. Inhibition of BCL11B expression leads to apoptosis of malignant but not normal mature T cells. Oncogene. 2007 May 31;26(26):3797-810.

    Epub 2006 Dec 18, Article, PubMed

  5. Duy NV, Mäder U, Tran NP, Cavin JF, Tam le T, Albrecht D, Hecker M, Antelmann H. The proteome and transcriptome analysis of Bacillus subtilis in response to salicylic acid. Proteomics. 2007 Mar;7(5):698-710.

    Article, PubMed

  6. Mikolasch A, Niedermeyer TH, Lalk M, Witt S, Seefeldt S, Hammer E, Schauer F, Gesell Salazar M, Hessel S, Jülich WD, Lindequist U. Novel cephalosporins synthesized by amination of 2,5-dihydroxybenzoic acid derivatives using fungal laccases II. Chem Pharm Bull (Tokyo). 2007 Mar;55(3):412-6.

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  7. Schmidt F, Strozynski M, Salus SS, Nilsen H, Thiede B. Rapid determination of amino acid incorporation by stable isotope labeling with amino acids in cell culture (SILAC). Rapid Commun Mass Spectrom. 2007;21(23):3919-26.

    Article, PubMed

  8. Gruber CC, Nestl BM, Gross J, Hildebrandt P, Bornscheuer UT, Faber K, Kroutil W. Emulation of racemase activity by employing a pair of stereocomplementary biocatalysts. Chemistry. 2007;13(29):8271-6.

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  9. Mäder, U., Homuth, G., Völker, U., and Hecker, M. (2007). Global regulatory systems mediating general starvation responses in Bacillus subtilis. In Global Regulatory Networks in Bacillus subtilis, Y. Fujita, ed. (Kerala, India, Transworld Research Network), pp. 205-228.



  1. Manteca A, Mäder U, Connolly BA, Sanchez J. A proteomic analysis of Streptomyces coelicolor programmed cell death. Proteomics. 2006 Nov;6(22):6008-22.

    Article, PubMed

  2. Schmidt F, Dahlmann B, Janek K, Kloss A, Wacker M, Ackermann R, Thiede B, Jungblut PR. Comprehensive quantitative proteome analysis of 20S proteasome subtypes from rat liver by isotope coded affinity tag and 2-D gel-based approaches. Proteomics. 2006 Aug;6(16):4622-32.

    Article, PubMed

  3. Mattow J, Siejak F, Hagens K, Becher D, Albrecht D, Krah A, Schmidt F, Jungblut PR, Kaufmann SH, Schaible UE. Proteins unique to intraphagosomally grown Mycobacterium tuberculosis. Proteomics. 2006 Apr;6(8):2485-94.

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  4. Schmidt F, Krah A, Schmid M, Jungblut PR, Thiede B. Distinctive mass losses of tryptic peptides generated by matrix-assisted laser desorption/ionization time-of-flight/time-of-flight. Rapid Commun Mass Spectrom. 2006;20(5):933-6.

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2005 and previous

  1. Rohlfing AK, Schill T, Müller C, Hildebrandt P, Prowald A, Hildebrandt JP. Attenuation of cell cycle regulator p27Kip1 expression in vertebrate epithelial cells mediated by extracellular signals in vivo and in vitro. J Comp Physiol B. 2005 Oct;175(7):511-22.

    Epub 2005 Oct 26, Article, PubMed

  2. Ernst FD, Homuth G, Stoof J, Mäder U, Waidner B, Kuipers EJ, Kist M, Kusters JG, Bereswill S, van Vliet AH. Iron-responsive regulation of the Helicobacter pylori iron-cofactored superoxide dismutase SodB is mediated by Fur. J Bacteriol. 2005 Jun;187(11):3687-92.

    Article, PubMed

  3. Thiede B, Höhenwarter W, Krah A, Mattow J, Schmid M, Schmidt F, Jungblut PR.  Peptide mass fingerprinting. Methods. 2005 Mar;35(3):237-47.

    Epub 2005 Jan 12; Review, Article, PubMed

  4. Ernst FD, Bereswill S, Waidner B, Stoof J, Mäder U, Kusters JG, Kuipers EJ, Kist M, van Vliet AH, Homuth G. Transcriptional profiling of Helicobacter pylori Fur- and iron-regulated gene expression. Microbiology. 2005 Feb;151(Pt 2):533-46.

    Article, PubMed

  5. Mattow J, Schmidt F, Höhenwarter W, Siejak F, Schaible UE, Kaufmann SH. Protein identification and tracking in two-dimensional electrophoretic gels by minimal protein identifiers. Proteomics. 2004 Oct;4(10):2927-41.

    Article, PubMed

  6. Nickel M, Homuth G, Böhnisch C, Mäder U, Schweder T. Cold induction of the Bacillus subtilis bkd operon is mediated by increased mRNA stability. Mol Genet Genomics. 2004 Aug;272(1):98-107.

    Epub 2004 Jul 7, Article, PubMed

  7. Pleissner KP, Eifert T, Buettner S, Schmidt F, Boehme M, Meyer TF, Kaufmann SH, Jungblut PR. Web-accessible proteome databases for microbial research. Proteomics. 2004 May;4(5):1305-13.

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  8. Mäder U, Hennig S, Hecker M, Homuth G. Transcriptional organization and posttranscriptional regulation of the Bacillus subtilis branched-chain amino acid biosynthesis genes. J Bacteriol. 2004 Apr;186(8):2240-52.

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  9. Schmidt F, Donahoe S, Hagens K, Mattow J, Schaible UE, Kaufmann SH, Aebersold R, Jungblut PR. Complementary analysis of the Mycobacterium tuberculosis proteome by two-dimensional electrophoresis and isotope-coded affinity tag technology. Mol Cell Proteomics. 2004 Jan;3(1):24-42.

    Epub 2003 Oct 13, Article, PubMed

  10. Krah A, Schmidt F, Becher D, Schmid M, Albrecht D, Rack A, Büttner K, Jungblut PR. Analysis of automatically generated peptide mass fingerprints of cellular proteins and antigens from Helicobacter pylori 26695 separated by two-dimensional electrophoresis. Mol Cell Proteomics. 2003 Dec;2(12):1271-83.

    Epub 2003 Sep 29, Article, PubMed

  11. Mattow J, Schaible UE, Schmidt F, Hagens K, Siejak F, Brestrich G, Haeselbarth G, Müller EC, Jungblut PR, Kaufmann SH. Comparative proteome analysis of culture supernatant proteins from virulent Mycobacterium tuberculosis H37Rv and attenuated M. bovis BCG Copenhagen. Electrophoresis. 2003 Oct;24(19-20):3405-20.

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  12. Schmidt F, Schmid M, Jungblut PR, Mattow J, Facius A, Pleissner KP. Iterative data analysis is the key for exhaustive analysis of peptide mass fingerprints from proteins separated by two-dimensional electrophoresis. J Am Soc Mass Spectrom. 2003 Sep;14(9):943-56.

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  13. Blencke HM, Homuth G, Ludwig H, Mäder U, Hecker M, Stülke J. Transcriptional profiling of gene expression in response to glucose in Bacillus subtilis: regulation of the central metabolic pathways. Metab Eng. 2003 Apr;5(2):133-49.

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  14. Mäder U, Antelmann H, Buder T, Dahl MK, Hecker M, Homuth G. Bacillus subtilis functional genomics: genome-wide analysis of the DegS-DegU regulon by transcriptomics and proteomics. Mol Genet Genomics. 2002 Dec;268(4):455-67.

    Epub 2002 Nov 16, Article, PubMed

  15. Kaan T, Homuth G, Mäder U, Bandow J, Schweder T. Genome-wide transcriptional profiling of the Bacillus subtilis cold-shock response. Microbiology. 2002 Nov;148(Pt 11):3441-55.

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  16. Mäder U, Homuth G, Scharf C, Büttner K, Bode R, Hecker M. Transcriptome and proteome analysis of Bacillus subtilis gene expression modulated by amino acid availability. J Bacteriol. 2002 Aug;184(15):4288-95.

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  17. Hildebrandt P, Musidlowska A, Bornscheuer UT, Altenbuchner J. Cloning, functional expression and biochemical characterization of a stereoselective alcohol dehydrogenase from Pseudomonas fluorescens DSM50106. Appl Microbiol Biotechnol. 2002 Aug;59(4-5):483-7.

    Epub 2002 Jun 26, Article, PubMed

  18. Schmidt F, Lueking A, Nordhoff E, Gobom J, Klose J, Seitz H, Egelhofer V, Eickhoff H, Lehrach H, Cahill DJ. Generation of minimal protein identifiers of proteins from two-dimensional gels and recombinant proteins. Electrophoresis. 2002 Feb;23(4):621-5.

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  19. Büttner K, Bernhardt J, Scharf C, Schmid R, Mäder U, Eymann C, Antelmann H, Völker A, Völker U, Hecker M. A comprehensive two-dimensional map of cytosolic proteins of Bacillus subtilis. Electrophoresis. 2001 Aug;22(14):2908-35.

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  20. Hildebrandt JP, Hildebrandt P. Lysophosphatidic acid depletes intracellular calcium stores different from those mediating capacitative calcium entry in C6 rat glioma cells. Glia. 1997 Jan;19(1):67-73.

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  21. Jewers RJ, Hildebrandt P, Ludlow JW, Kell B, McCance DJ. Regions of human papillomavirus type 16 E7 oncoprotein required for immortalization of human keratinocytes.J Virol. 1992 Mar;66(3):1329-35.

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  23. Schneider T, Harthus HP, Hildebrandt P, Niedrig M, Bröker M, Weigelt W, Beck A, Pauli G. Epitopes of the HIV-1-negative factor (nef) reactive with murine monoclonal antibodies and human HIV-1-positive sera. AIDS Res Hum Retroviruses. 1991 Jan;7(1):37-44.

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