Projects

• CloVR (Fricke, F.W.), (current) mehr

Publications

Regalado, J., Lundberg, D.S., Deusch, O., Kersten, S., Karasov, T., Poersch, K., Shirsekar, G., Weigel, D., 2020. Combining whole-genome shotgun sequencing and rRNA gene amplicon analyses to improve detection of microbe–microbe interaction networks in plant leaves. The ISME Journal 1–15. doi.org/10.1038/s41396-020-0665-8

 Wehrmann, M., Toussaint, M., Pfannstiel, J., Billard, P., Klebensberger, J., 2020. The Cellular Response to Lanthanum Is Substrate Specific and Reveals a Novel Route for Glycerol Metabolism in Pseudomonas putida KT2440. mBio 11. /doi.org/10.1128/mBio.00516-20

Tajik, N., Frech, M., Schulz, O., Schälter, F., Lucas, S., Azizov, V., Dürholz, K., Steffen, F., Omata, Y., Rings, A., Bertog, M., Rizzo, A., Iljazovic, A., Basic, M., Kleyer, A., Culemann, S., Krönke, G., Luo, Y., Überla, K., Gaipl, U.S., Frey, B., Strowig, T., Sarter, K., Bischoff, S.C., Wirtz, S., Cañete, J.D., Ciccia, F., Schett, G., Zaiss, M.M., 2020. Targeting zonulin and intestinal epithelial barrier function to prevent onset of arthritis. Nat Commun 11, 1–14. doi.org/10.1038/s41467-020-15831-7

Seifert, Jana; Muth, Thilo (2019): Editorial for Special Issue. Metaproteomics. In: Proteomes 7 (1). DOI: 10.3390/proteomes7010009.

Williams, Wesley; Kunorozva, Lovemore; Klaiber, Iris; Henkel, Marius; Pfannstiel, Jens; Günther, Johannes et al. (2019): Correction to. Novel metagenome-derived ornithine lipids identified by functional screening for biosurfactants. In: Applied microbiology and biotechnology. DOI: 10.1007/s00253-019-09860-6.

Williams, Wesley; Kunorozva, Lovemore; Klaiber, Iris; Henkel, Marius; Pfannstiel, Jens; van Zyl, Leonardo J. et al. (2019): Novel metagenome-derived ornithine lipids identified by functional screening for biosurfactants. In: Applied microbiology and biotechnology 103 (11), S. 4429–4441. DOI: 10.1007/s00253-019-09768-1.

Anaya, Katya; Sus, Nadine; Gadelha, Carlos; Frank, Jan (2018): Development and validation of a rapid reversed-phase liquid chromatography method for CnAMP1 peptide quantification in human intestinal cell lines. In: Amino acids. DOI: 10.1007/s00726-018-2675-7.

Langille, Morgan G. I.; Ravel, Jacques; Fricke, W. Florian (2018): "Available upon request". Not good enough for microbiome data! In: Microbiome 6 (1), S. 8. DOI: 10.1186/s40168-017-0394-z.

Jenkins BJ, Seyssel K, Chiu S, Pan PH, Lin SY, Stanley E, et al. (2017): Odd Chain Fatty Acids; New Insights of the Relationship between the Gut Microbiota, Dietary Intake, Biosynthesis and Glucose Intolerance. Scientific Reports 2017. doi:10.1038/srep44845 

Camarinha-Silva A., Fricke, F.W (2018) Molecular Microbiome Analysis The Gut Microbiome in Health and Disease

Fricke, F.W., Bromberg JS. Checks and balances-microbiota shifts in immunosuppressed mice. Transplantation. 2017;101:26–7. doi:10.1097/TP.0000000000001493.

Tobalina L, Bargiela R, Pey J, Herbst FA, Lores I, Rojo D, et al. Context-specific metabolic network reconstruction of a naphthalene-degrading bacterial community guided by metaproteomic data. Bioinformatics 2015;31:1771–9. doi:10.1093/bioinformatics/btv036. [Co-Author: Jana Seifert]

Sachsenberg T, Herbst F, Taubert M, Kermer R, Jehmlich N, Bergen M von, et al. MetaProSIP: automated inference of stable isotope incorporation rates in proteins for functional metaproteomics. J Proteome Res 2015;14:619–27. doi:10.1021/pr500245w. [Co-Author: Jana Seifert]

White JR, Maddox C, White O, Angiuoli SV, Fricke FW. CloVR-ITS: Automated internal transcribed spacer amplicon sequence analysis pipeline for the characterization of fungal microbiota. Microbiome 2013;1. doi:10.1186/2049-2618-1-6.

Angiuoli SV, Matalka M, Gussman A, Galens K, Vangala M, Riley DR, et al. CloVR: a virtual machine for automated and portable sequence analysis from the desktop using cloud computing. BMC Bioinformatics 2011;12:356. doi:10.1186/1471-2105-12-356. [Co-Author: Florian W. Fricke]

Angiuoli SV, White JR, Matalka M, White O, Fricke FW. Resources and costs for microbial sequence analysis evaluated using virtual machines and cloud computing. PLoS ONE 2011;6:e26624. doi:10.1371/journal.pone.0026624.