In 1999 JB pioneered the introduction of multiple channel imaging and later on image warping into the analysis of 2-D protein gels. In 2003 he and co-workers described the application of an experiment wide spot consensus for analyzing dozens of 2-D gels to generate 100% complete expression profiles. This made it possible to apply algorithms which have been developed for DNA array analysis for knowledge extraction from 2D gel based proteome experiments. These ideas directly affect the development of Delta2D, a commercial system for the analysis of 2D gels.

This progress in image analysis had deep impact on the efficiency and reliability of large content gene expression studies of Bacillus subtilis and Staphylococcus aureus during stress and starvation which have been performed by him and his colleagues. To come to a quantitative gel based proteomics JB engaged in the improvement of analytical techniques among them quantitative cell disruption, the introduction of marker proteins of exactly known molar concentration and staining behaviour, sensitivity, specificity and linearity tests of available fluorescent dyes and improvement of imaging techniques like HDR imaging and for semi quantitative but highly sensitive studies a silver staining based algorithm generating non saturated ultra wide grey level images.

To integrate data from the major OMICS fields since 2000 JB supervised the development of Protecs – a web accessible data management system for functional genomics studies (Protecs). In this context very recently JB forced the development of a Voronoi treemap based visualization technique of gene/protein expression and gene/protein functional classification data. This made it possible to analyse and percieve gene expression changes in context with metabolic and functional gene/protein clusters in its entirety.

For making GCxGC based metabolic profiling available for high throughput metabolome analysis of volatiles JB and others adapted 2D gel image analysis algorithms for the analysis of GCxGC chromatograms.

Currently JB is interested in meta-omics analyses of environmental as well as human and microbial samples. For this purpose he and his co-workers complement treemaps with new vis-techniques such as streamgraphs and others. He is engaged in a joined project to establish so called proteomaps for the appropriate visualization of absolute protein quantitation data sets (Proteomaps). Furthermore he is setting up a public science wiki system for collection, storage and improvement of gene functional information of S. aureus genes (AureoWiki).

2011: Invitrogen CRC Grant

2010-2014: Extension of DFG Collaborative Research Initiative TransRegio34 – Z1 Project for Bioinformatics work bench development

2009: Supervision of Database Development within MIMAS Marine Microbiology BMBF Project

2006-2010: DFG Collaborative Research Initiative TransRegio34 Supervision of the Central Z1 Project for Data base development

1999
Poster Award of the Japanese Electrophoresis Society
Tokyo Proteome conference

2000
Dissertation Award
University of Greifswald

2011
EMBO Cover Title Award Finalist
Cover of EMBO Volume 30 Number 24

2011
Poster Award at the VizBi2011 Boston
Conference on Visualization in Biology

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• Schmarr, HG; Ganß, S; Fischer, U; Koschinski, S; Bernhardt, J; Ferreira, V; Lopez, R.; ,Profiling Analysis of Volatile and Non-Volatile Compounds in Wine for a Better Understanding of Wine Quality,”Flavour Science” – Proceedings from XIII Weurman Flavour Research Symposium, ISBN: 978-0-12-398549-1″,361-365,2014,Elsevier Science Publishing Co Inc

• Bonn F, Pané-Farré J, Schlüter R, Schaffer M, Fuchs S, Bernhardt J, Riedel K, Otto A, Völker U, van Dijl JM, Hecker M, Mäder U, Becher D. Global analysis of the impact of linezolid onto virulence factor production in S. aureus USA300. Int J Med Microbiol.2016 Feb 17. PMID: 26996810.
  
  
• Vanzo E, Merl-Pham J, Velikova V, Ghirardo A, Lindermayr C, Hauck SM, Bernhardt J, Riedel K, Durner J, Schnitzler JP. Modulation of protein S-nitrosylation by isoprene emission in poplar. Plant Physiol.2016 Feb 5. PMID: 26850277.
  
  
• Aurass P, Gerlach T, Becher D, Voigt B, Karste S, Bernhardt J, Riedel K, Hecker M, Flieger A. Life Stage-specific Proteomes of Legionella pneumophila Reveal a Highly Differential Abundance of Virulence-associated Dot/Icm effectors. Mol Cell Proteomics.2016 Jan;15(1):177-200. PMID: 26545400.
  
  
• Nett JE, Zarnowski R, Cabezas-Olcoz J, Brooks EG, Bernhardt J, Marchillo K, Mosher DF, Andes DR. Host contributions to construction of three device-associated Candida albicans biofilms. Infect Immun.2015 Dec;83(12):4630-8. PMID: 26371129.
  
  
• Hennig A, Bernhardt J, Nieselt K. Pan-Tetris: an interactive visualisation for Pan-genomes. BMC Bioinformatics.2015;16 Suppl 11:S3. PMID: 26328606.
  
  
• 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 Nov;15(21):3648-61. PMID: 26224020.
  
  
• 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 Oct 14;128:203-17. PMID: 26244908.
  
  
• Moche M, Schlüter R, Bernhardt J, Plate K, Riedel K, Hecker M, Becher D. Time-Resolved Analysis of Cytosolic and Surface-Associated Proteins of Staphylococcus aureus HG001 under Planktonic and Biofilm Conditions. J Proteome Res.2015 Sep 4;14(9):3804-22. PMID: 26152824.
  
  
• Kohler C,, Lourenço RF, Bernhardt J, Albrecht D, Schüler J, Hecker M, Gomes SL. A comprehensive genomic, transcriptomic and proteomic analysis of a hyperosmotic stress sensitive α-proteobacterium. BMC Microbiol.2015 Mar 26;15:71. PMID: 25879753.
  
  
• Lassek C, Burghartz M, Chaves-Moreno D, Otto A, Hentschker C, Fuchs S, Bernhardt J, Jauregui R, Neubauer R, Becher D, Pieper DH, Jahn M, Jahn D, Riedel K. A metaproteomics approach to elucidate host and pathogen protein expression during catheter-associated urinary tract infections (CAUTIs). Mol Cell Proteomics.2015 Apr;14(4):989-1008. PMID: 25673765.
  
  
• Cecil A, Ohlsen K, Menzel T, François P, Schrenzel J, Fischer A, Dörries K, Selle M, Lalk M, Hantzschmann J, Dittrich M, Liang C, Bernhardt J, Ölschläger TA, Bringmann G, Bruhn H, Unger M, Ponte-Sucre A, Lehmann L, Dandekar T. Modelling antibiotic and cytotoxic isoquinoline effects in Staphylococcus aureus, Staphylococcus epidermidis and mammalian cells. Int J Med Microbiol.2015 Jan;305(1):96-109. PMID: 25500547.
  
  
• Surmann K, Michalik S, Hildebrandt P, Gierok P, Depke M, Brinkmann L, Bernhardt J, Salazar MG, Sun Z, 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. PMID: 25136337.
  
  
• Zarnowski R, Westler WM, Lacmbouh GA, Marita JM, Bothe JR, Bernhardt J, Lounes-Hadj Sahraoui A, Fontaine J, Sanchez H, Hatfield RD, Ntambi JM, Nett JE, Mitchell AP, Andes DR. Novel entries in a fungal biofilm matrix encyclopedia. MBio.2014 Aug 5;5(4):e01333-14. PMID: 25096878.
  
  
• Liebermeister W, Noor E, Flamholz A, Davidi D, Bernhardt J, Milo R. Visual account of protein investment in cellular functions. Proc Natl Acad Sci U S A.2014 Jun 10;111(23):8488-93. PMID: 24889604.
  
  
• Maaβ S, Wachlin G, Bernhardt J, Eymann C, Fromion V, Riedel K, Becher D, Hecker M. Highly precise quantification of protein molecules per cell during stress and starvation responses in Bacillus subtilis. Mol Cell Proteomics.2014 Sep;13(9):2260-76. PMID: 24878497.
  
  
• Schröder W, Bernhardt J, Marincola G, Klein-Hitpass L, Herbig A, Krupp G, Nieselt K, Wolz C. Altering gene expression by aminocoumarins: the role of DNA supercoiling in Staphylococcus aureus. BMC Genomics.2014 Apr 16;15:291. PMID: 24734910.
  
  
• Hessling B, Bonn F, Otto A, Herbst FA, Rappen GM, Bernhardt J, Hecker M, Becher D. Global proteome analysis of vancomycin stress in Staphylococcus aureus. Int J Med Microbiol.2013 Dec;303(8):624-34. PMID: 24161710.
  
  
• Fraunholz M, Bernhardt J, Schuldes J, Daniel R, Hecker M, Sinha B. Complete Genome Sequence of Staphylococcus aureus 6850, a Highly Cytotoxic and Clinically Virulent Methicillin-Sensitive Strain with Distant Relatedness to Prototype Strains. Genome Announc.2013 Sep 26;1(5). PMID: 24072870.
  
  
• Mehlan H, Schmidt F, Weiss S, Schüler J, Fuchs S, Riedel K, Bernhardt J. Data visualization in environmental proteomics. Proteomics.2013 Oct;13(18-19):2805-21. PMID: 23913834.
  
  
• Becher D, Bernhardt J, Fuchs S, Riedel K. Metaproteomics to unravel major microbial players in leaf litter and soil environments: challenges and perspectives. Proteomics.2013 Oct;13(18-19):2895-909. PMID: 23894095.
  
  
• 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 Sep;13(17):2608-21. PMID: 23794223.
  
  
• 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. PMID: 23643866.
  
  
• 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. PMID: 23141770.
  
  
• Heinz E, Williams TA, Nakjang S, Noël CJ, Swan DC, Goldberg AV, Harris SR, Weinmaier T, Markert S, Becher D, Bernhardt J, Dagan T, Hacker C, Lucocq JM, Schweder T, Rattei T, Hall N, Hirt RP, Embley TM. The genome of the obligate intracellular parasite Trachipleistophora hominis: new insights into microsporidian genome dynamics and reductive evolution. PLoS Pathog.2012;8(10):e1002979. PMID: 23133373.
  
  
• Marincola G, Schäfer T, Behler J, Bernhardt J, Ohlsen K, Goerke C, Wolz C. RNase Y of Staphylococcus aureus and its role in the activation of virulence genes. Mol Microbiol.2012 Sep;85(5):817-32. PMID: 22780584.
  
  
• Krueger B, Friedrich T, Förster F, Bernhardt J, Gross R, Dandekar T. Different evolutionary modifications as a guide to rewire two-component systems. Bioinform Biol Insights.2012;6:97-128. PMID: 22586357.
  
  
• 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. PMID: 22556279.
  
  
• Teeling H, Fuchs BM, Becher D, Klockow C, Gardebrecht A, Bennke CM, Kassabgy M, Huang S, Mann AJ, Waldmann J, Weber M, Klindworth A, Otto A, Lange J, Bernhardt J, Reinsch C, Hecker M, Peplies J, Bockelmann FD, Callies U, Gerdts G, Wichels A, Wiltshire KH, Glöckner FO, Schweder T, Amann R. Substrate-controlled succession of marine bacterioplankton populations induced by a phytoplankton bloom. Science.2012 May 4;336(6081):608-11. PMID: 22556258.
  
  
• 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. PMID: 22517742.
  
  
• Otto A, Bernhardt J, Hecker M, Becher D. Global relative and absolute quantitation in microbial proteomics. Curr Opin Microbiol.2012 Jun;15(3):364-72. PMID: 22445110.
  
  
• Liedert C, Peltola M, Bernhardt J, Neubauer P, Salkinoja-Salonen M. Physiology of resistant Deinococcus geothermalis bacterium aerobically cultivated in low-manganese medium. J Bacteriol.2012 Mar;194(6):1552-61. PMID: 22228732.
  
  
• Miller M, Dreisbach A, Otto A, Becher D, Bernhardt J, Hecker M, Peppelenbosch MP, van Dijl JM. Mapping of interactions between human macrophages and Staphylococcus aureus reveals an involvement of MAP kinase signaling in the host defense. J Proteome Res.2011 Sep 2;10(9):4018-32. PMID: 21736355.
  
  
• 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. Staphylococcus aureus physiological growth limitations: insights from flux calculations built on proteomics and external metabolite data. Proteomics.2011 May;11(10):1915-35. PMID: 21472852.
  
  
• Cecil A, Rikanović C, Ohlsen K, Liang C, Bernhardt J, Oelschlaeger TA, Gulder T, Bringmann G, Holzgrabe U, Unger M, Dandekar T. Modeling antibiotic and cytotoxic effects of the dimeric isoquinoline IQ-143 on metabolism and its regulation in Staphylococcus aureus, Staphylococcus epidermidis and human cells. Genome Biol.2011;12(3):R24. PMID: 21418624.
  
  
• Maass S, Sievers S, Zühlke D, Kuzinski J, Sappa PK, Muntel J, Hessling B, Bernhardt J, Sietmann R, Völker U, Hecker M, Becher D. 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. PMID: 21395229.
  
  
• 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. A metabolomics and proteomics study of the adaptation of Staphylococcus aureus to glucose starvation. Mol Biosyst.2011 Apr;7(4):1241-53. PMID: 21327190.
  
  
• 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. PMID: 21266987.
  
  
• Fuchs S, Mehlan H, Kusch H, Teumer A, Zühlke D, Berth M, Wolf C, Dandekar T, Hecker M, Engelmann S, Bernhardt J. Protecs, a comprehensive and powerful storage and analysis system for OMICS data, applied for profiling the anaerobiosis response of Staphylococcus aureus COL. Proteomics.2010 Aug;10(16):2982-3000. PMID: 20662099.
  
  
• Schmarr HG, Bernhardt J, Fischer U, Stephan A, Müller P, Durner D. Two-dimensional gas chromatographic profiling as a tool for a rapid screening of the changes in volatile composition occurring due to microoxygenation of red wines. Anal Chim Acta.2010 Jul 5;672(1-2):114-23. PMID: 20579499.
  
  
• 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. PMID: 20518028.
  
  
• Hammer E, Phong TQ, Steil L, Klingel K, Salazar MG, Bernhardt J, Kandolf R, Kroemer HK, Felix SB, Völker U. Viral myocarditis induced by Coxsackievirus B3 in A.BY/SnJ mice: analysis of changes in the myocardial proteome. Proteomics.2010 May;10(9):1802-18. PMID: 20213679.
  
  
• Schmarr HG, Bernhardt J. Profiling analysis of volatile compounds from fruits using comprehensive two-dimensional gas chromatography and image processing techniques. J Chromatogr A.2010 Jan 22;1217(4):565-74. PMID: 20015502.
  
  
• 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 JM, Hecker M. A proteomic view of an important human pathogen–towards the quantification of the entire Staphylococcus aureus proteome. PLoS One.2009 Dec 4;4(12):e8176. PMID: 19997597.
  
  
• Liang C, Schmid A, López-Sánchez MJ, Moya A, Gross R, Bernhardt J, Dandekar T. JANE: efficient mapping of prokaryotic ESTs and variable length sequence reads on related template genomes. BMC Bioinformatics.2009 Nov 29;10:391. PMID: 19943962.
  
  
• Liedert C, Bernhardt J, Albrecht D, Voigt B, Hecker M, Salkinoja-Salonen M, Neubauer P. Two-dimensional proteome reference map for the radiation-resistant bacterium Deinococcus geothermalis. Proteomics.2010 Feb;10(3):555-63. PMID: 19941306.
  
  
• 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. PMID: 19743422.
  
  
• Hecker M, Antelmann H, Büttner K, Bernhardt J. Gel-based proteomics of Gram-positive bacteria: a powerful tool to address physiological questions. Proteomics.2008 Dec;8(23-24):4958-75. PMID: 19003856.
  
  
• Soini J, Falschlehner C, Liedert C, Bernhardt J, Vuoristo J, Neubauer P. Norvaline is accumulated after a down-shift of oxygen in Escherichia coli W3110. Microb Cell Fact.2008 Oct 21;7:30. PMID: 18940002.
  
  
• Eymann C, Becher D, Bernhardt J, Gronau K, Klutzny A, Hecker M. Dynamics of protein phosphorylation on Ser/Thr/Tyr in Bacillus subtilis. Proteomics.2007 Oct;7(19):3509-26. PMID: 17726680.
  
  
• Berth M, Moser FM, Kolbe M, Bernhardt J. The state of the art in the analysis of two-dimensional gel electrophoresis images. Appl Microbiol Biotechnol.2007 Oct;76(6):1223-43. PMID: 17713763.
  
  
• Wolff S, Antelmann H, Albrecht D, Becher D, Bernhardt J, Bron S, Büttner K, van Dijl JM, Eymann C, Otto A, Tam le T, Hecker M. Towards the entire proteome of the model bacterium Bacillus subtilis by gel-based and gel-free approaches. J Chromatogr B Analyt Technol Biomed Life Sci.2007 Apr 15;849(1-2):129-40. PMID: 17055787.
  
  
• Tam le T, Antelmann H, Eymann C, Albrecht D, Bernhardt J, Hecker M. Proteome signatures for stress and starvation in Bacillus subtilis as revealed by a 2-D gel image color coding approach. Proteomics.2006 Aug;6(16):4565-85. PMID: 16847875.
  
  
• Linsen L, Löcherbach J, Berth M, Becher D, Bernhardt J. Visual analysis of gel-free proteome data. IEEE Trans Vis Comput Graph.2006 Jul-Aug;12(4):497-508. PMID: 16805259.
  
  
• Höper D, Bernhardt J, Hecker M. Salt stress adaptation of Bacillus subtilis: a physiological proteomics approach. Proteomics.2006 Mar;6(5):1550-62. PMID: 16440371.
  
  
• Bernhardt J. Defining the proteome. Genome Biol.2005;6(12):360. PMID: 16356278.
  
  
• Voigt B, Schweder T, Sibbald MJ, Albrecht D, Ehrenreich A, Bernhardt J, Feesche J, Maurer KH, Gottschalk G, van Dijl JM, Hecker M. The extracellular proteome of Bacillus licheniformis grown in different media and under different nutrient starvation conditions. Proteomics.2006 Jan;6(1):268-81. PMID: 16317772.
  
  
• Koburger T, Weibezahn J, Bernhardt J, Homuth G, Hecker M. Genome-wide mRNA profiling in glucose starved Bacillus subtilis cells. Mol Genet Genomics.2005 Aug;274(1):1-12. PMID: 15809868.
  
  
• Eymann C, Dreisbach A, Albrecht D, Bernhardt J, Becher D, Gentner S, Tam le T, Büttner K, Buurman G, Scharf C, Venz S, Völker U, Hecker M. A comprehensive proteome map of growing Bacillus subtilis cells. Proteomics.2004 Oct;4(10):2849-76. PMID: 15378759.
  
  
• Luhn S, Berth M, Hecker M, Bernhardt J. Using standard positions and image fusion to create proteome maps from collections of two-dimensional gel electrophoresis images. Proteomics.2003 Jul;3(7):1117-27. PMID: 12872213.
  
  

• Bernhardt J, Weibezahn J, Scharf C, Hecker M. Bacillus subtilis during feast and famine: visualization of the overall regulation of protein synthesis during glucose starvation by proteome analysis. Genome Res.2003 Feb;13(2):224-37. PMID: 12566400.