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References

This list is not meant to be complete.

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2014

Bernhardt J, Schmidt F. (2014). Staphylococcus aureus protein universe. VizBi (Visualization in Biology) 2014 Conference at the EMBL Institute in Heidelberg, Germany.

Huja S, Oren Y, Biran D, Meyer S, Dobrindt U, Bernhard J, Becher D, Hecker M, Sorek R, Ron EZ. Fur is the master regulator of the extraintestinal pathogenic Escherichia coli response to serum. MBio. 2014 Aug 12;5(4). pii: e01460-14.

Liebermeister W., Noor E., Flamholz A., Davidi D., Bernhardt J., Milo R. (2014). Visual account of protein investment in cellular functions. Proc Natl Acad Sci U S A. 2014 Jun 10;111(23):8488-93.

Liebermeister W, Noor E, Davidi D, Flamholz A, Milo R, Riedel K, Mehlan H, Schüler J, Bernhardt J (2014). Lab Mouse Proteomaps. VizBi (Visualization in Biology) 2014 Conference at the EMBL Institute in Heidelberg, Germany.

Maaβ S., Wachlin G., Bernhardt J., Eymann C., Fromion V., Riedel K., Becher D., Hecker M. (2014). 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. 

Schröder W., Bernhardt J., Marincola G., Klein-Hitpass L., Herbig A., Krupp G., Nieselt K., Wolz C. (2014). Altering gene expression by aminocoumarins: the role of DNA supercoiling in Staphylococcus aureus. BMC Genomics 2014, 15:291.

Schüler J, Bernhardt J, Spillner A, Riedel K (2014). MetabolicPathTreemap. Awarded as Best Poster at VizBi (Visualization in Biology) 2014 Conference at the EMBL Institute in Heidelberg, Germany.

Surmann K., Michalik S., Hildebrandt P., Gierok P., Depke M., Brinkmann L., Bernhardt J., Salazar MG., Sun Z., Shteynberg D., Kusebauch U., Moritz R.L., Wollscheid B., Lalk M., Völker U., Schmidt F. (2014). 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.

Zarnowski R., Westler W.M., Lacmbouh G.A., Marita J.M., Bothe J.R., Bernhardt J., Lounes-Hadj Sahraoui A., Fontaine J., Sanchez H., Hatfield R.D., Ntambi J.M., Nett J.E., Mitchell A.P., Andes D.R. (2014). Novel entries in a fungal biofilm matrix encyclopedia. MBio. 2014 Aug 5;5(4):e01333-14.

2013

Bernhardt J, Michalik S, Wollscheid B, Völker U, Schmidt F (2013). Proteomics approaches for the analysis of enriched microbial subpopulations and visualization of complex functional information. Curr Opin Microbiol. 2013 Feb;24(1):112-119. doi: 10.1016/j.copbio.2012.10.009. Epub 2013 Nov 7.

Depke M1, Surmann K, Hildebrandt P, Jehmlich N, Michalik S, Stanca SE, Fritzsche W, Völker U, Schmidt F (2013). Labeling of the pathogenic bacterium Staphylococcus aureus with gold or ferric oxide-core nanoparticles highlights new capabilities for investigation of host-pathogen interactions. Cytometry A. 2014 Feb;85(2):140-50. doi: 10.1002/cyto.a.22425. Epub 2013 Dec 17.

Fraunholz M., Bernhardt J., Schuldes J., Daniel R., Hecker M., Sinha B. (2013). 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). pii: e00775-13.

Hessling B., Bonn F., Otto A., Herbst F.A., Rappen G.M., Bernhardt J., Hecker M., Becher D. (2013). Global proteome analysis of vancomycin stress in Staphylococcus aureus. Int J Med Microbiol. 2013 Dec;303(8):624-34.

Mehlan H, Hecker M, Riedel K, Bernhardt J (2013). Streamgraphs for Biodata. VizBi (Visualization in Biology) 2013 Conference at the BROAD Institute in Boston, MA, USA.

Mehlan H., Schmidt F., Weiss S., Schüler J., Fuchs S., Riedel K., Bernhardt J. (2013). Data visualization in environmental proteomics. Proteomics. 2013 Oct;13(18-19):2805-21.

Mehlan H, Hecker M, Riedel K, Bernhardt J (2013). Wood grain. VizBi (Visualization in Biology) 2013 Conference at the BROAD Institute in Boston, MA, USA.

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. (2013). A proteomics workflow for quantitative and time-resolved analysis of adaptation reactions of internalized bacteria. Methods. 2013 Jun 15;61(3):244-50.

Winter T, Bernhardt J, Winter J, Mäder U, Schlüter R, Weltmann KD, Hecker M, Kusch H (2013). Common versus noble Bacillus subtilis differentially responds to air and argon gas plasma. Proteomics. 2013 Sep;13(17):2608-21. doi: 10.1002/pmic.201200343. Epub 2013 Aug 7.

2012

Bernhardt J, Michalik S, Wollscheid B, Völker U, Schmidt F. (2012). Proteomics approaches for the analysis of enriched microbial subpopulations and visualization of complex functional information. Curr Opin Biotechnol. 2013 Feb;24(1):112-9.

Elsholz AK, Turgay K, Michalik S, Hessling B, Gronau K, Oertel D, Mäder U, Bernhardt J, Becher D, Hecker M, Gerth U. (2012). 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.

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. (2012). The Genome of the Obligate Intracellular Parasite Trachipleistophora hominis: New Insights into Microsporidian Genome Dynamics and Reductive Evolution. PLoS Pathog. 2012 Oct;8(10):e1002979. doi: 10.1371/journal.ppat.1002979. Epub 2012 Oct 25.

Marincola G, Schäfer T, Behler J, Bernhardt J, Ohlsen K, Goerke C, Wolz C. (2012). RNase Y of Staphylococcus aureus and its role in the activation of virulence genes. Mol Microbiol. 2012 Sep;85(5):817-32. doi: 10.1111/j.1365-2958.2012.08144.x. Epub 2012 Jul 11.

Michalik S, Bernhardt J, Otto A, Moche M, Becher D, Meyer H, Lalk M, Schurmann C, Schlüter R, Kock H, Gerth U, Hecker M. (2012). 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.

Otto A, Bernhardt J, Hecker M, Becher D. (2012). Global relative and absolute quantitation in microbial proteomics. Curr Opin Microbiol. 2012 Jun;15(3):364-72. Epub 2012 Mar 21.

2011

Bernhardt J, (2011). Starvation. VizBi (Visualization in Biology) 2011 Conference at the BROAD Institute in Boston, MA, USA.

Bernhardt J, Mehlan H, Schüler J, Hecker, M (2011). OntologyMaps. Awarded as Best Poster at VizBi (Visualization in Biology) 2011 Conference at the BROAD Institute in Boston, MA, USA.

Miller M, Dreisbach A, Otto A, Becher D, Bernhardt J, Hecker M, Peppelenbosch MP, van Dijl JM. (2011). 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.

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

2010

Otto A, Bernhardt J, Herbst FA, Siebourg J, Mäder U, Hecker M, Becher D (2010). System-wide temporal profiling of proteins in glucose starved Bacillus subtilis. Nat. Commun. 1:137.

Schmidt F, Scharf SS, Hildebrandt P, Burian M, Bernhardt J, Dhople V, Kalinka J, Gutjahr M, Hammer E, Völker U (2010). Time resolved quantitative proteome profiling of host-pathogen interactions: The Staphylococcus aureus RN1HG response to human S9 cells after internalization. Proteomics. 2010 Aug;10(15):2801-11.

2009

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.

Bernhardt J, Funke S, Hecker M, Siebourg J (2009). Visualizing gene expression data via Voronoi treemaps. Voronoi Diagrams in Science and Engineering, 2009. ISVD '09. 6th International Symposium on. 0: 233-241. ISBN: 978-0-7695-3781-8.

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