2024 (30)

• Aldehoff, A.S., Karkossa, I., Goerdeler, C., Krieg, L., Schor, J., Engelmann, B., Wabitsch, M., Landgraf, K., Hackermüller, J., Körner, A., Rolle-Kampczyk, U., Schubert, K., von Bergen, M. (2024):
  Unveiling the dynamics of acetylation and phosphorylation in SGBS and 3T3-L1 adipogenesis
  iScience 27 (6), art. 109711 10.1016/j.isci.2024.109711
• Braeuning, A., Balaguer, P., Bourguet, W., Carreras-Puigvert, J., Feiertag, K., Kamstra, J.H., Knapen, D., Lichtenstein, D., Marx-Stoelting, P., Rietdijk, J., Schubert, K., Spjuth, O., Stinckens, E., Thedieck, K., van den Boom, R., Vergauwen, L., von Bergen, M., Wewer, N., Zalko, D. (2024):
  Corrigendum: Development of new approach methods for the identification and characterization of endocrine metabolic disruptors—a PARC project
  Front. Toxicol. 6 , art. 1394396 10.3389/ftox.2024.1394396
• Castañeda-Monsalve, V., Fröhlich, L.-F., Haange, S.-B., Homsi, M.N., Rolle-Kampczyk, U., Fu, Q., von Bergen, M., Jehmlich, N. (2024):
  High-throughput screening of the effects of 90 xenobiotics on the simplified human gut microbiota model (SIHUMIx): A metaproteomic and metabolomic study
  Front. Microbiol. 15 , art. 1349367 10.3389/fmicb.2024.1349367
• Cole, L., Goodall, T., Jehmlich, N., Griffiths, R.I., Gleixner, G., Gubry-Rangin, C., Malik, A.A. (2024):
  Land use effects on soil microbiome composition and traits with consequences for its ecosystem carbon use efficiency
  bioRxiv 10.1101/2024.04.05.588235
• Engelmann, B. (2024):
  Summary of project PR002051
  UCSD Metabolomics Workbench 10.21228/M8H521
• Farag, M.A., Hariri, M.L.M., Ehab, A., Homsi, M.N., Zhao, C., von Bergen, M. (2024):
  Cocoa seeds and chocolate products interaction with gut microbiota; mining microbial and functional biomarkers from mechanistic studies, clinical trials and 16S rRNA amplicon sequencing
  Crit. Rev. Food Sci. Nutr. 64 (10), 3122 - 3138 10.1080/10408398.2022.2130159
• Fischer, F., Pierzchalski, A., Riesbeck, S., Aldehoff, A.S., Castañeda-Monsalve, V., Haange, S.-B., von Bergen, M., Rolle-Kampczyk, U.E., Jehmlich, N., Zenclussen, A.C., Herberth, G. (2024):
  An in vitro model system for testing chemical effects on microbiome-immune interactions - examples with BPX and PFAS mixtures
  Front. Immunol. 15 , art. 1298971 10.3389/fimmu.2024.1298971
• Funkner, K., Poehlein, A., Jehmlich, N., Egelkamp, R., Daniel, R., von Bergen, M., Rother, M. (2024):
  Proteomic and transcriptomic analysis of selenium utilization in Methanococcus maripaludis
  mSystems 9 (5), e01338-23 10.1128/msystems.01338-23
• Goerdeler, C., Engelmann, B., Aldehoff, A.S., Schaffert, A., Blüher, M., Heiker, J.T., Wabitsch, M., Schubert, K., Rolle-Kampczyk, U., von Bergen, M. (2024):
  Metabolomics in human SGBS cells as new approach method for studying adipogenic effects: Analysis of the effects of DINCH and MINCH on central carbon metabolism
  Environ. Res. 252 , art. 118847 10.1016/j.envres.2024.118847
• Haange, S.-B., Riesbeck, S., Aldehoff, A.S., Engelmann, B., Jensen Pedersen, K., Castañeda-Monsalve, V., Rolle-Kampczyk, U., von Bergen, M., Jehmlich, N. (2024):
  Chemical mixture effects on the simplified human intestinal microbiota: Assessing xenobiotics at environmentally realistic concentrations
  J. Hazard. Mater. 474 , art. 134683 10.1016/j.jhazmat.2024.134683
• Huber, C., Brack, W., Röder, S., von Bergen, M., Rolle-Kampczyk, U., Zenclussen, A.C., Krauss, M., Herberth, G. (2024):
  Pesticide residues and polyphenols in urine – A combined LC-HRMS screening to reveal intake patterns
  Environ. Int. 191 , art. 108981 10.1016/j.envint.2024.108981
• Huillet, M., Lasserre, F., Gratacap, M.-P., Engelmann, B., Bruse, J., Polizzi, A., Fougeray, T., Martin, C.M.P., Rives, C., Fougerat, A., Naylies, C., Lippi, Y., Garcia, G., Rousseau-Bacquie, E., Canlet, C., Debrauwer, L., Rolle-Kampczyk, U., von Bergen, M., Payrastre, B., Boutet-Robinet, E., Gamet-Payrastre, L., Guillou, H., Loiseau, N., Ellero-Simatos, S. (2024):
  Pharmacological activation of constitutive androstane receptor induces female-specific modulation of hepatic metabolism
  JHEP Rep. 6 (1), art. 100930 10.1016/j.jhepr.2023.100930
• Jaeger, J.W., Brandt, A., Gui, W., Yergaliyev, T., Hernández-Arriaga, A., Muthu, M.M., Edlund, K., Elashy, A., Molinaro, A., Möckel, D., Sarges, J, Halibasic, E., Trauner, M., Kahles, F., Rolle-Kampczyk, U., Hengstler, J., Schneider, C.V., Lammers, T., Marschall, H.-U., von Bergen, M., Camarinha-Silva, A., Bergheim, I., Trautwein, C., Schneider, K.M. (2024):
  Microbiota modulation by dietary beta-glucan prevents steatotic liver disease progression
  JHEP Rep. 6 (3), art. 100987 10.1016/j.jhepr.2023.100987
• Jax, M., Weßendorf, A., Lichter, J., Stief, L., Lobes, N., Egele, K., Rolle-Kampczyk, U., Engelmann, B., von Bergen, M., Bock, U., Blömeke, B. (2024):
  Response of innate immune cells and alveolar type 1 cell line to 4,4'-methylenediphenyl diisocyanate
  Naunyn-Schmiedebergs Arch. Pharmacol. 397 (Suppl. 1), S73 - P231 10.1007/s00210-024-02974-3
• Kipping, L., Jehmlich, N., Moll, J., Noll, M., Gossner, M.M., Van Den Bossche, T., Edelmann, P., Borken, W., Hofrichter, M., Kellner, H. (2024):
  Enzymatic machinery of wood-inhabiting fungi that degrade temperate tree species
  ISME J. 18 (1), wrae050 10.1093/ismejo/wrae050
• Krause, J.L., Engelmann, B., Schaepe, S.S., Rolle-Kampczyk, U., Jehmlich, N., Chang, H.-D., Slanina, U., Hoffmann, M., Lehmann, J., Zenclussen, A.C., Herberth, G., von Bergen, M., Haange, S.-B. (2024):
  DSS treatment does not affect murine colonic microbiota in absence of the host
  Gut Microbes 16 (1), art. 2297831 10.1080/19490976.2023.2297831
• Medawar, E., Beyer, F., Thieleking, R., Haange, S.-B., Rolle-Kampczyk, U., Reinicke, M., Chakaroun, R., von Bergen, M., Stumvoll, M., Villringer, A., Witte, A.V. (2024):
  Prebiotic diet changes neural correlates of food decision-making in overweight adults: a randomised controlled within-subject cross-over trial
  Gut 73 (2), 298 - 310 10.1136/gutjnl-2023-330365
• Myrmel, L.S., Fjære, E., Han, M., Jensen, B.A.H., Rolle-Kampczyk, U., Danneskiold-Samsøe, N.B., Ho, Q.T., Smette, A., von Bergen, M., Xiao, L., Kristiansen, K., Madsen, L. (2024):
  The food sources in western diets modulate obesity development, insulin sensitivity, and the plasma and cecal metabolome in mice
  Mol. Nutr. Food Res. 68 (16), art. 2400246 10.1002/mnfr.202400246
• Patt, M., Karkossa, I., Krieg, L., Massier, L., Makki, K., Tabei, S., Karlas, T., Dietrich, A., Gericke, M., Stumvoll, M., Blüher, M., von Bergen, M., Schubert, K., Kovacs, P., Chakaroun, R.M. (2024):
  FGF21 reflects a responsive adipose tissue-liver axis in both cardiometabolic burden and following metabolic surgery
  medRxiv 10.1101/2024.05.31.24307065
• Radushev, V., Karkossa, I., Berg, J., von Bergen, M., Engelmann, B., Rolle-Kampczyk, U.E., Blüher, M., Wagner, U., Schubert, K., Rossol, M. (2024):
  Dysregulated cytokine and oxidative response in hyper-glycolytic monocytes in obesity
  Front. Immunol. 15 , art. 1416543 10.3389/fimmu.2024.1416543
• Raps, S., Bahr, L., Karkossa, I., Rossol, M., von Bergen, M., Schubert, K. (2024):
  Triclosan and its alternatives, especially chlorhexidine, modulate macrophage immune response with distinct modes of action
  Sci. Total Environ. 941 , art. 169650 10.1016/j.scitotenv.2023.169650
• Raps, S., Schubert, K. (2024):
  Effects of Triclosan and its alternatives on LPS-stimulated THP-1 macrophages
  ProteomeXchange 10.6019/PXD044828
• Raulien, N., Friedrich, K., Strobel, S., Raps, S., Hecker, F., Pierer, M., Schilling, E., Lainka, E., Kallinich, T., Baumann, S., Fritz-Wallace, K., Rolle-Kampczyk, U., von Bergen, M., Aigner, A., Ewe, A., Schett, G., Cross, M., Rossol, M., Wagner, U. (2024):
  Glucose-oxygen deprivation constrains HMGCR function and Rac1 prenylation and activates the NLRP3 inflammasome in human monocytes
  Sci. Signal. 17 (845), eadd8913 10.1126/scisignal.add8913
• Schubert, K., Aldehoff, A.S. (2024):
  Acetylome dynamics during differentiation of 3T3-L1 adipocytes
  PRoteomics IDEntifications Database (PRIDE) 10.6019/PXD045776
• Schubert, K., Aldehoff, A.S. (2024):
  Phosphoproteome dynamics during differentiation of 3T3-L1 adipocytes
  PRoteomics IDEntifications Database (PRIDE) 10.6019/PXD045778
• Schubert, K., Aldehoff, A.S. (2024):
  Phosphoproteome dynamics during differentiation of SGBS adipocytes
  PRoteomics IDEntifications Database (PRIDE) 10.6019/PXD045770
• Schubert, K., Aldehoff, A.S. (2024):
  Acetylome dynamics during differentiation of SGBS adipocytes
  PRoteomics IDEntifications Database (PRIDE) 10.6019/PXD045768
• Schubert, K., Aldehoff, A.S. (2024):
  Proteome dynamics during differentiation of SGBS adipocytes
  PRoteomics IDEntifications Database (PRIDE) 10.6019/PXD045767
• Schubert, K., Aldehoff, A.S. (2024):
  Proteome dynamics during differentiation of 3T3-L1 adipocytes
  PRoteomics IDEntifications Database (PRIDE) 10.6019/PXD045772
• Viehof, A., Haange, S.-B., Streidl, T., Schubert, K., Engelmann, B., Haller, D., Rolle-Kampczyk, U., von Bergen, M., Clavel, T. (2024):
  The human intestinal bacterium Eggerthella lenta influences gut metabolomes in gnotobiotic mice
  Microbiome Research Reports 3 , art. 14 10.20517/mrr.2023.65

2023 (44)

• Aldehoff, A.S., Karkossa, I., Engelmann, B., Rolle-Kampczyk, U., von Bergen, M., Schubert, K. (2023):
  Exploring the regulatory effects of lysine acetylation and phosphorylation in adipocyte differentiation and their exposure to emerging plastic additives
  Toxicol. Lett. 384 (Suppl. 1), S133 - S133 10.1016/S0378-4274(23)00578-7
• Auer, E., Lazuka, A., Huguenin-Bizot, B., Jehmlich, N., Déjean, S., Lombard, V., Henrissat, B., O'Donohue, M., Hernandez-Raquet, G. (2023):
  Horizontal metaproteomics and CAZymes analysis of lignocellulolytic microbial consortia selectively enriched from cow rumen and termite gut
  ISME Commun. 3 (1), art. 134 10.1038/s43705-023-00339-0
• Beckers, L.-M., Altenburger, R., Brack, W., Escher, B.I., Hackermüller, J., Hassold, E., Illing, G., Krauss, M., Krüger, J., Michaelis, P., Schüttler, A., Stevens, S., Busch, W. (2023):
  A data-derived reference mixture representative of European wastewater treatment plant effluents to complement mixture assessment
  Environ. Int. 179 , art. 108155 10.1016/j.envint.2023.108155
• Bifari, F., Dolci, S., Mannino, L., Campanelli, A., Bottani, E., Karkossa, I., Setten, E., Gianoli, S., Di Chio, M., Ciarpella, F., Busetto, G., Pezzotta, A., Castagna, A., Pruonto, G., Binaschi, L., Amenta, A., Scupoli, M., Cavallini, C., Boschi, F., Doherty, A., Malpeli, G., Rossi, E., Martinelli, N., Ferretti, S., Malik, Z., Sandri, M., Pistocchi, A., Schubert, K., Endrizzi, M., Bossolasco, P., Fumagalli, G., Locati, M., Decimo, I. (2023):
  Adoptive transfer of tumor-educated macrophages promote neural tissue regeneration and motor recovery following severe spinal cord injury
  Cytotherapy 25 (6, Suppl.), E8 - E9 10.1016/S1465-3249(23)00711-9
• Braeuning, A., Balaguer, P., Bourguet, W., Carreras-Puigvert, J., Feiertag, K., Kamstra, J.H., Knapen, D., Lichtenstein, D., Marx-Stoelting, P., Rietdijk, J., Schubert, K., Spjuth, O., Stinckens, E., Thedieck, K., van den Boom, R., Vergauwen, L., von Bergen, M., Wewer, N., Zalko, D. (2023):
  Development of new approach methods for the identification and characterization of endocrine metabolic disruptors—a PARC project
  Front. Toxicol. 5 , art. 1212509 10.3389/ftox.2023.1212509
• Buchenauer, L., Haange, S.-B., Bauer, M., Rolle-Kampczyk, U.E., Wagner, M., Stucke, J., Elter, E., Fink, B., Vass, M., von Bergen, M., Schulz, A., Zenclussen, A.C., Junge, K.M., Stangl, G.I., Polte, T. (2023):
  Maternal exposure of mice to glyphosate induces depression- and anxiety-like behavior in the offspring via alterations of the gut-brain axis
  Sci. Total Environ. 905 , art. 167034 10.1016/j.scitotenv.2023.167034
• Carido, M., Völkner, M., Steinheuer, L.M., Wagner, F., Kurth, T., Dumler, N., Ulusoy, S., Wieneke, S., Norniella, A.V., Golfieri, C., Khattak, S., Schönfelder, B., Scamozzi, M., Zoschke, K., Canzler, S., Hackermüller, J., Ader, M., Karl, M.O. (2023):
  Reliability of human retina organoid generation from hiPSC-derived neuroepithelial cysts
  Front. Cell. Neurosci. 17 , art. 1166641 10.3389/fncel.2023.1166641
• Cerdó, T., Ruiz-Rodríguez, A., Acuña, I., Torres-Espínola, F.J., Menchén-Márquez, S., Gámiz, F., Gallo, M., Jehmlich, N., Haange, S.-B., von Bergen, M., Campoy, C., Suárez, A. (2023):
  Infant gut microbiota contributes to cognitive performance in mice
  Cell Host Microbe 31 (12), 1974 - 1988.e4 10.1016/j.chom.2023.11.004
• Engelberts, J.P., Robbins, S.J., Herbold, C.W., Moeller, F.U., Jehmlich, N., Laffy, P.W., Wagner, M., Webster, N.S. (2023):
  Metabolic reconstruction of the near complete microbiome of the model sponge Ianthella basta
  Environ. Microbiol. 25 (3), 646 - 660 10.1111/1462-2920.16302
• Engelmann, B. (2023):
  Untangling the dynamics of lysine acetylation and phosphorylation in adipogenesis in the established human and mouse adipocyte cell lines SGBS and 3T3L1
  UCSD Metabolomics Workbench 10.21228/M8GX42
• Farag, M.A., Baky, M.H., von Bergen, M., Hegazi, N.M. (2023):
  The use of omics in monitoring food gut microbiota interaction outcomes: a review of novel trends and technologies
  Curr. Opin. Food Sci. 52 , art. 101064 10.1016/j.cofs.2023.101064
• Farag, M.A., von Bergen, M., Shao, P., Güven, E.Ç. (2023):
  How do food and drugs interact with gut microbiota? Toward better or worse health outcomes. Editorial
  J. Adv. Res. 52 , 1 - 1 10.1016/j.jare.2023.09.006
• Gant, T.W., Auerbach, S.S., von Bergen, M., Bouhifd, M., Botham, P.A., Caiment, F., Currie, R.A., Harrill, J., Johnson, K., Li, D., Rouquie, D., van Ravenzwaay, B., Sistare, F., Tralau, T., Viant, M.R., van de Laan, J.W., Yauk, C. (2023):
  Applying genomics in regulatory toxicology: a report of the ECETOC workshop on omics threshold on non-adversity
  Arch. Toxicol. 97 (8), 2291 - 2302 10.1007/s00204-023-03522-3
• Gerhards, M., Böhme, A., Schubert, K., Kodritsch, B., Ulrich, N. (2023):
  DNA adducts as link between in vitro and in vivo carcinogenicity – A case study with benzo[a]pyrene
  Curr. Res. Toxicol. 4 , art. 100097 10.1016/j.crtox.2022.100097
• Gurbuz, B., Guldiken, N., Reuken, P., Fu, L., Remih, K., Preisinger, C., Brůha, R., Leníček, M., Petrtýl, J., Reissing, J., Aly, M., Fromme, M., Zhou, B., Karkossa, I., Schubert, K., von Bergen, M., Stallmach, A., Bruns, T., Strnad, P. (2023):
  Biomarkers of hepatocellular synthesis in patients with decompensated cirrhosis
  Hepatol. Int. 17 (3), 698 - 708 10.1007/s12072-022-10473-x
• Heinze, B.M., Küsel, K., Jehmlich, N., von Bergen, M., Taubert, M. (2023):
  Metabolic versatility enables sulfur-oxidizers to dominate primary production in groundwater
  Water Res. 244 , art. 120426 10.1016/j.watres.2023.120426
• Hoffmann, A., Meir, A.Y., Hagemann, T., Czechowski, P., Müller, L., Engelmann, B., Haange, S.-B., Rolle-Kampczyk, U., Tsaban, G., Zelicha, H., Rinott, E., Kaplan, A., Shelef, I., Stumvoll, M., Blüher, M., Liang, L., Ceglarek, U., Isermann, B., von Bergen, M., Kovacs, P., Keller, M., Shai, I. (2023):
  A polyphenol-rich green Mediterranean diet enhances epigenetic regulatory potential: the DIRECT PLUS randomized controlled trial
  Metab.-Clin. Exp. 145 , art. 155594 10.1016/j.metabol.2023.155594
• Höper, T., Karkossa, I., Dumit, V.I., von Bergen, M., Schubert, K., Haase, A. (2023):
  A comparative proteomics analysis of four contact allergens in THP-1 cells shows distinct alterations in key metabolic pathways
  Toxicol. Appl. Pharmacol. 475 , art. 116650 10.1016/j.taap.2023.116650
• Jehmlich, N. (2023):
  Microbiomes: A new open section in Microorganisms. Editorial
  Microorganisms 11 (12), art. 2889 10.3390/microorganisms11122889
• Karkossa, I., Fürst, S., Großkopf, H., von Bergen, M., Schubert, K. (2023):
  Oxidation is an underappreciated post-translational modification in the regulation of immune responses associated with changes in phosphorylation
  Front. Immunol. 14 , art. 1244431 10.3389/fimmu.2023.1244431
• Khan, N., Muge, E., Mulaa, F.J., Wamalwa, B., von Bergen, M., Jehmlich, N., Wick, L.Y. (2023):
  Mycelial nutrient transfer promotes bacterial co-metabolic organochlorine pesticide degradation in nutrient-deprived environments
  ISME J. 17 (4), 570 - 578 10.1038/s41396-023-01371-7
• Kister, B., Viehof, A., Rolle-Kampczyk, U., Schwentker, A., Treichel, N.S., Jennings, S., Wirtz, T.H., Blank, L.M., Hornef, M.W., von Bergen, M., Clavel, T., Kuepfer, L. (2023):
  A physiologically-based model of bile acid metabolism in mice
  iScience 26 (10), art. 107922 10.1016/j.isci.2023.107922
• Krüger, M., Chaudhari, N., Thamdrup, B., Overholt, W.A., Bristow, L.A., Taubert, M., Küsel, K., Jehmlich, N., von Bergen, M., Herrmann, M. (2023):
  Differential contribution of nitrifying prokaryotes to groundwater nitrification
  ISME J. 17 (10), 1601 - 1611 10.1038/s41396-023-01471-4
• Lipaeva, P., Karkossa, I., Bedulina, D., Schubert, K., Luckenbach, T. (2023):
  Cold-adapted amphipod species upon heat stress: Proteomic responses and their correlation with transcriptomic responses
  Comp. Biochem. Physiol. D-Genomics Proteomics 45 , art. 101048 10.1016/j.cbd.2022.101048
• Meir, A.Y., Keller, M., Hoffmann, A., Rinott, E., Tsaban, G., Kaplan, A., Zelicha, H., Hagemann, T., Ceglarek, U., Isermann, B., Shelef, I., Blüher, M., Stumvoll, M., Li, J., Haange, S.-B., Engelmann, B., Rolle-Kampczyk, U., von Bergen, M., Hu, F.B., Stampfer, M.J., Kovacs, P., Liang, L., Shai, I. (2023):
  The effect of polyphenols on DNA methylation-assessed biological age attenuation: the DIRECT PLUS randomized controlled trial
  BMC Med. 21 , art. 364 10.1186/s12916-023-03067-3
• Meyer Cifuentes, I.E., Degenhardt, J., Neumann-Schaal, M., Jehmlich, N., Ngugi, D.K., Öztürk, B. (2023):
  Comparative biodegradation analysis of three compostable polyesters by a marine microbial community
  Appl. Environ. Microb. 89 (12), e01060-23 10.1128/aem.01060-23
• O’Rourke, K., Engelmann, B., Altenburger, R., Rolle-Kampczyk, U., Grintzalis, K. (2023):
  Molecular responses of daphnids to chronic exposures to pharmaceuticals
  Int. J. Mol. Sci. 24 (4), art. 4100 10.3390/ijms24044100
• Panagiotidis, K., Engelmann, B., Krauss, M., Rolle-Kampczyk, U.E., Altenburger, R., Rochfort, K.D., Grintzalis, K. (2023):
  The impact of amine and carboxyl functionalised microplastics on the physiology of daphnids
  J. Hazard. Mater. 458 , art. 132023 10.1016/j.jhazmat.2023.132023
• Ramos-Nascimento, A., Grenga, L., Haange, S.-B., Himmelmann, A., Arndt, F.S., Ly, Y.-T., Miotello, G., Pible, O., Jehmlich, N., Engelmann, B., von Bergen, M., Mulder, E., Frings-Meuthen, P., Hellweg, C.E., Jordan, J., Rolle-Kampczyk, U., Armengaud, J., Moeller, R. (2023):
  Human gut microbiome and metabolite dynamics under simulated microgravity
  Gut Microbes 15 (2), art. 2259033 10.1080/19490976.2023.2259033
• Remih, K., Hufnagel, F., Durkalski-Mauldin, V., Lee, W.M., Su, C., Rule, J., Krieg, L., Karkossa, I., Schubert, K., von Bergen, M., Fontana, R., Strnad, P. (2023):
  Serum proteomics in American adults with acute liver failure
  J. Hepatol. 78 (Suppl. 1), S136 - S138 10.1016/S0168-8278(23)00638-4
• Remih, K., Hufnagel, F.-M., Durkalski-Mauldin, V., Lee, W., Su, Z., Rule, J., Krieg, L., Karkossa, I., Schubert, K., von Bergen, M., Fontana, R., Strnad, P. (2023):
  Serum proteomics in adults with Acute Liver Failure
  Z. Gastroent. 61 (08), e460 - e461 10.1055/s-0043-1771831
• Riva, A., Rasoulimehrabani, H., Cruz-Rubio, J.M., Schnorr, S.L., von Baeckmann, C., Inan, D., Nikolov, G., Herbold, C.W., Hausmann, B., Pjevac, P., Schintlmeister, A., Spittler, A., Palatinszky, M., Kadunic, A., Hieger, N., Del Favero, G., von Bergen, M., Jehmlich, N., Watzka, M., Lee, K.S., Wiesenbauer, J., Khadem, S., Viernstein, H., Stocker, R., Wagner, M., Kaiser, C., Richter, A., Kleitz, F., Berry, D. (2023):
  Identification of inulin-responsive bacteria in the gut microbiota via multi-modal activity-based sorting
  Nat. Commun. 14 , art. 8210 10.1038/s41467-023-43448-z
• Ruiz-Rodriguez, A., Acuña, I., Cerdo, T., Torres-Espinola, F.J., Menchen-Marquez, S., Gámiz, F., Gallo, M., Jehmlich, N., Haange, S.-B., von Bergen, M., Campoy, C., Suarez, A. (2023):
  Gut microbiota contributes to cognitive performance in infants
  IBRO Neurosci. Rep. 15 (Suppl. 1), S821 - S822 10.1016/j.ibneur.2023.08.1703
• Schmeisser, S., Miccoli, A., von Bergen, M., Berggren, E., Braeuning, A., Busch, W., Desaintes, C., Gourmelon, A., Grafström, R., Harrill, J., Hartung, T., Herzler, M., Kass, G.E.N., Kleinstreuer, N., Leist, M., Luijten, M., Marx-Stoelting, P., Poetz, O., van Ravenzwaay, B., Roggeband, R., Rogiers, V., Roth, A., Sanders, P., Thomas, R.S., Vinggaard, A.M., Vinken, M., van de Water, B., Luch, A., Tralau, T. (2023):
  New approach methodologies in human regulatory toxicology – Not if, but how and when!
  Environ. Int. 178 , art. 108082 10.1016/j.envint.2023.108082
• Schubert, K., Karkossa, I. (2023):
  Effects of high molecular weight phthalates on LPS-stimulated THP-1 macrophages - proteome
  PRoteomics IDEntifications Database (PRIDE) 10.6019/PXD043025
• Schubert, K., Karkossa, I. (2023):
  Effects of high molecular weight phthalates on LPS-stimulated THP-1 macrophages - phosphoproteome
  PRoteomics IDEntifications Database (PRIDE) 10.6019/PXD042912
• Schubert, K., Karkossa, I. (2023):
  Effects of high molecular weight phthalates on LPS-stimulated THP-1 macrophages - redoxome
  PRoteomics IDEntifications Database (PRIDE) 10.6019/PXD043139
• Silva, S.G., Homsi, M.N., Keller-Costa, T., Nunes da Rocha, U., Costa, R. (2023):
  Natural product biosynthetic potential reflects macroevolutionary diversification within a widely distributed bacterial taxon
  mSystems 8 (6), e00643-23 10.1128/msystems.00643-23
• Tomm, J., von Bergen, M., Simon, J.-C., Treudler, R. (2023):
  Anti-inflammatory metabolites and allergenic proteins from Green Lipped Mussel (Perna canaliculus)
  Integr. J. Vet. Biosci. 7 (1), 1 - 3 10.31038/IJVB.2023711
• Torow, N., Li, R., Hitch, T.C.A., Mingels, C., Al Bounny, S., van Best, N., Stange, E.-L., Simons, B., Maié, T., Rüttger, L., Gubbi, N.M.K.P., Abbott, D.A., Benabid, A., Gadermayr, M., Runge, S., Treichel, N., Merhof, D., Rosshart, S.P., Jehmlich, N., Hand, T.W., von Bergen, M., Heymann, F., Pabst, O., Clavel, T., Tacke, F., Lelouard, H., Gesteira Costa, I., Hornef, M.W. (2023):
  M cell maturation and cDC activation determine the onset of adaptive immune priming in the neonatal Peyer’s patch
  Immunity 56 (6), 1220 - 1238 10.1016/j.immuni.2023.04.002
• Uthoff, C., Homsi, M.N., von Bergen, M. (2023):
  Acoustic and vibration monitoring of honeybee colonies for beekeeping-relevant aspects of presence of queen bee and swarming
  Comput. Electron. Agric. 205 , art. 107589 10.1016/j.compag.2022.107589
• Wang, Z., Haange, S.-B., Haake, V., Huisinga, M., Kamp, H., Buesen, R., Schubert, K., Canzler, S., Hackermüller, J., Rolle-Kampczyk, U., von Bergen, M. (2023):
  Assessing the influence of propylthiouracil and phenytoin on the metabolomes of the thyroid, liver, and plasma in a rats
  Metabolites 13 (7), art. 847 10.3390/metabo13070847
• Wilmes, P., Trezzi, J.-P., Aho, V., Jäger, C., Schade, S., Janzen, A., Hickl, O., Kunath, B., Thomas, M., Schmit, K., Garcia, P., Sciortino, A., Martin-Gallausiaux, C., Halder, R., Huarte, O.U., Heurtaux, T., Heins-Marroquin, U., Gomez-Giro, G., Weidenbach, K., Delacour, L., Laczny, C., Novikova, P., Ramiro-Garcia, J., Singh, R., Andújar, B.T., Lebrun, L., Daujeumont, A., Habier, J., Dong, X., Gavotto, F., Heintz-Buschart, A., Schneider, J., Jehmlich, N., von Bergen, M., Schymanski, E., Schmitz, R., Schwamborn, J., Glaab, E., Linster, C., Kitami, T., Buttini, M., May, P., Trenkwalder, C., Oertel, W., Mollenhauer, B. (2023):
  Artefactual source of 2-hydroxypyridine
  Research Square 10.21203/rs.3.rs-1827631/v2
• Zhang, L., Toplak, M., Saleem-Batcha, R., Höing, L., Jakob, R., Jehmlich, N., von Bergen, M., Maier, T., Teufel, R. (2023):
  Bacterial dehydrogenases facilitate oxidative inactivation and bioremediation of chloramphenicol
  ChemBioChem 24 (2), e202200632 10.1002/cbic.202200632

2022 (50)

• Brede, M., Haange, S.-B., Riede, S., Engelmann, B., Jehmlich, N., Rolle-Kampczyk, U.E., Rohn, K., Von Soosten, D., von Bergen, M., Breves, G. (2022):
  Effects of different formulations of glyphosate on rumen microbial metabolism and microbial community composition in the Rumen Simulation Technique system
  Front. Microbiol. 13 , art. 873101 10.3389/fmicb.2022.873101
• Buchenauer, L., Junge, K.M., Haange, S.-B., Simon, J.C., von Bergen, M., Hoh, A.-L., Aust, G., Zenclussen, A.C., Stangl, G.I., Polte, T. (2022):
  Glyphosate differentially affects the allergic immune response across generations in mice
  Sci. Total Environ. 850 , art. 157973 10.1016/j.scitotenv.2022.157973
• Dey, P., Malik, A., Singh, D.K., Haange, S.-B., von Bergen, M., Jehmlich, N. (2022):
  Insight to the molecular mechanisms underpinning the mycoremediation of multiple metals by proteomic technique
  Front. Microbiol. 13 , art. 872576 10.3389/fmicb.2022.872576
• Fernandes, M.L.P., Bastida, F., Jehmlich, N., Martinović, T., Větrovský, T., Baldrian, P., Delgado-Baquerizo, M., Starke, R. (2022):
  Functional soil mycobiome across ecosystems
  J. Proteomics 252 , art. 104428 10.1016/j.jprot.2021.104428
• Fries, C.M., Haange, S.-B., Rolle-Kampczyk, U., Till, A., Lammert, M., Grasser, L., Medawar, E., Dietrich, A., Horstmann, A., von Bergen, M., Fenske, W.K. (2022):
  Metabolic profile and metabolite analyses in extreme weight responders to gastric bypass surgery
  Metabolites 12 (5), art. 417 10.3390/metabo12050417
• Geesink, P., Taubert, M., Jehmlich, N., von Bergen, M., Küsel, K. (2022):
  Bacterial necromass is rapidly metabolized by heterotrophic bacteria and supports multiple trophic levels of the groundwater microbiome
  Microbiol. Spectr. 10 (4), e00437 10.1128/spectrum.00437-22
• Grosjean, I., Roméo, B., Domdom, M.-A., Belaid, A., D’Andréa, G., Guillot, N., Gherardi, R.K., Gal, J., Milano, G., Marquette, C.H., Hung, R.J., Landi, M.T., Han, Y., Brest, P., von Bergen, M., Klionsky, D.J., Amos, C.I., Hofman, P., Mograbi, B. (2022):
  Autophagopathies: from autophagy gene polymorphisms to precision medicine for human diseases
  Autophagy 18 (11), 2519 - 2536 10.1080/15548627.2022.2039994
• Gwak, J.-H., Awala, S.I., Nguyen, N.-L., Yu, W.-J., Yang, H.-Y., von Bergen, M., Jehmlich, N., Kits, K.D., Loy, A., Dunfield, P.F., Dahl, C., Hyun, J.-H., Rhee, S.-K. (2022):
  Sulfur and methane oxidation by a single microorganism
  Proc. Natl. Acad. Sci. U.S.A. 119 (32), e2114799119 10.1073/pnas.2114799119
• Haange, S.-B., Till, A., Bergh, P.-O., Fauler, G., Gigl, M., Löfgren-Sandblom, A., Schaap, F.G., Clavel, T., Trautwein, C., Fenske, W., Kleigrewe, K., Marschall, H.-U., Olde Damink, S.W.M., Moustafa, T., von Bergen, M., Rolle-Kampczyk, U. (2022):
  Ring trial on quantitative assessment of bile acids reveals a method- and analyte-specific accuracy and reproducibility
  Metabolites 12 (7), art. 583 10.3390/metabo12070583
• Hoeger, A.-L., Jehmlich, N., Kipping, L., Griehl, C., Noll, M. (2022):
  Associated bacterial microbiome responds opportunistic once algal host Scenedesmus vacuolatus is attacked by endoparasite Amoeboaphelidium protococcarum
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• Jacoby, C., Ebenau-Jehle, C., Saum, K., Jehmlich, N., von Bergen, M., Brüls, T., Boll, M. (2022):
  Genes and enzymes involved in the biodegradation of the quaternary carbon compound pivalate in the denitrifying Thauera humireducens strain PIV-1
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• Jensen Pedersen, K. (2022):
  Supplementary material - Eggerthella lenta DSM 2243 alleviates bile acid stress response in Clostridium ramosum and Anaerostipes caccae by transformation of bile acids (Version 2) [Data set]
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• Jensen Pedersen, K., Haange, S.-B., Žížalová, K., Viehof, A., Clavel, T., Leniček, M., Engelmann, B., Wick, L.Y., Schaap, F.G., Jehmlich, N., Rolle-Kampczyk, U., von Bergen, M. (2022):
  Eggerthella lenta DSM 2243 alleviates bile acid stress response in Clostridium ramosum and Anaerostipes caccae by transformation of bile acids
  Microorganisms 10 (10), art. 2025 10.3390/microorganisms10102025
• Junge, K.M., Buchenauer, L., Strunz, S., Seiwert, B., Thürmann, L., Rolle-Kampczyk, U.E., Röder, S., Borte, M., Kiess, W., von Bergen, M., Simon, J.C., Zenclussen, A.C., Schöneberg, T., Stangl, G.I., Herberth, G., Lehmann, I., Reemtsma, T., Polte, T. (2022):
  Effects of exposure to single and multiple parabens on asthma development in an experimental mouse model and a prospective cohort study
  Sci. Total Environ. 814 , art. 152676 10.1016/j.scitotenv.2021.152676
• Kage, P., Schubert, K., Treudler, R., Simon, J.-C., von Bergen, M., Tomm, J. (2022):
  Identification of new potential allergens from green-lipped mussel (Perna canaliculus)
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• Kaplan, A., Zelicha, H., Meir, A.Y., Rinott, E., Tsaban, G., Levakov, G., Prager, O., Salti, M., Yovell, Y., Ofer, J., Huhn, S., Beyer, F., Witte, V., Villringer, A., Meiran, N., Emesh, T.B., Kovacs, P., von Bergen, M., Ceglarek, U., Blüher, M., Stumvoll, M., Hu, F.B., Stampfer, M.J., Friedman, A., Shelef, I., Avidan, G., Shai, I. (2022):
  The effect of a high-polyphenol Mediterranean diet (Green-MED) combined with physical activity on age-related brain atrophy: the Dietary Intervention Randomized Controlled Trial Polyphenols Unprocessed Study (DIRECT PLUS)
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• Kipping, L., Gossner, M.M., Koschorreck, M., Muszynski, S., Maurer, F., Weiser, W., Jehmlich, N., Noll, M. (2022):
  Emission of CO₂ and CH₄ from 13 deadwood tree species is linked to tree species identity and management intensity in forest and grassland habitats
  Glob. Biogeochem. Cycles 36 (5), e2021GB007143 10.1029/2021GB007143
• Kipping, L., Maurer, F., Gossner, M.M., Muszynski, S., Kahl, T., Kellner, H., Weiser, W.W., Jehmlich, N., Noll, M. (2022):
  Drivers of deadwood decay of 13 temperate tree species are similar between forest and grassland habitats
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• König, R., Kiebist, J., Kalmbach, J., Herzog, R., Schmidtke, K.-U., Kellner, H., Ullrich, R., Jehmlich, N., Hofrichter, M., Scheibner, K. (2022):
  Novel unspecific peroxygenase from Truncatella angustata catalyzes the synthesis of bioactive lipid mediators
  Microorganisms 10 (7), art. 1267 10.3390/microorganisms10071267
• Kraft, B., Jehmlich, N., Larsen, M., Bristow, L.A., Könneke, M., Thamdrup, B., Canfield, D.E. (2022):
  Oxygen and nitrogen production by an ammonia-oxidizing archaeon
  Science 375 (6576), 97 - 100 10.1126/science.abe6733
• Krause, J.L., Engelmann, B., Nunes da Rocha, U., Pierzchalski, A., Chang, H.D., Zenclussen, A.C., von Bergen, M., Rolle-Kampczyk, U., Herberth, G. (2022):
  MAIT cell activation is reduced by direct and microbiota-mediated exposure to bisphenols
  Environ. Int. 158 , art. 106985 10.1016/j.envint.2021.106985
• Krieg, L., Didt, K., Karkossa, I., Bernhart, S.H., Kehr, S., Subramanian, N., Lindhorst, A., Schaudinn, A., Tabei, S., Keller, M., Stumvoll, M., Dietrich, A., von Bergen, M., Stadler, P.F., Laurencikiene, J., Krüger, M., Blüher, M., Gericke, M., Schubert, K., Kovacs, P., Chakaroun, R., Massier, L. (2022):
  Multiomics reveal unique signatures of human epiploic adipose tissue related to systemic insulin resistance
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• Lai, C., Poschen, C., Steinheuer, L.M., Hackermüller, J. (2022):
  Preserving cluster features in imputing high dimensional data with extensive missing rate
  2022 IEEE International Conference on Big Data (Big Data), Osaka, Japan, 17-20 December 2022
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  Human chorionic gonadotropin promotes murine Treg cells and restricts pregnancy-harmful proinflammatory Th17 responses
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• Menanteau-Ledouble, S., Skov, J., Lukassen, M.B., Rolle-Kampczyk, U., Haange, S.-B., Dalsgaard, I., von Bergen, M., Nielsen, J.L. (2022):
  Modulation of gut microbiota, blood metabolites, and disease resistance by dietary β-glucan in rainbow trout (Oncorhynchus mykiss)
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• Münzker, J., Haase, N., Till, A., Sucher, R., Haange, S.-B., Nemetschke, L., Gnad, T., Jäger, E., Chen, J., Riede, S.J., Chakaroun, R., Massier, L., Kovacs, P., Ost, M., Rolle-Kampczyk, U., Jehmlich, N., Weinert, J., Heiker, J.T., Klöting, N., Seeger, G., Morawski, M., Keitel, V., Pfeifer, A., von Bergen, M., Heeren, J., Krügel, U., Fenske, W.K. (2022):
  Functional changes of the gastric bypass microbiota reactivate thermogenic adipose tissue and systemic glucose control via intestinal FXR-TGR5 crosstalk in diet-induced obesity
  Microbiome 10 , art. 96 10.1186/s40168-022-01264-5
• Murthy, S., Karkossa, I., Schmidt, C., Hoffmann, A., Hagemann, T., Rothe, K., Seifert, O., Anderegg, U., von Bergen, M., Schubert, K., Rossol, M. (2022):
  Danger signal extracellular calcium initiates differentiation of monocytes into SPP1/osteopontin-producing macrophages
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• Nagel, M., Moretti, R., Paschke, R., von Bergen, M., Meiler, J., Kalkhof, S. (2022):
  Integrative model of the FSH receptor reveals the structural role of the flexible hinge region
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• Puiggené, Ò., Cárdenas Espinosa, M.J., Schlosser, D., Thies, S., Jehmlich, N., Kappelmeyer, U., Schreiber, S., Wibberg, D., Kalinowski, J., Harms, H., Heipieper, H.J., Eberlein, C. (2022):
  Extracellular degradation of a polyurethane oligomer involving outer membrane vesicles and further insights on the degradation of 2,4-diaminotoluene in Pseudomonas capeferrum TDA1
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• Riesbeck, S., Petruschke, H., Rolle-Kampczyk, U., Schori, C., Ahrens, C.H., Eberlein, C., Heipieper, H.J., von Bergen, M., Jehmlich, N. (2022):
  Adaptation and resistance: How Bacteroides thetaiotaomicron copes with the bisphenol A substitute bisphenol F
  Microorganisms 10 (8), art. 1610 10.3390/microorganisms10081610
• Saborowski, R., Korez, Š., Riesbeck, S., Weidung, M., Bickmeyer, U., Gutow, L. (2022):
  Shrimp and microplastics: A case study with the Atlantic ditch shrimp Palaemon varians
  Ecotox. Environ. Safe. 234 , art. 113394 10.1016/j.ecoenv.2022.113394
• Sallam, I.E., Rolle-Kampczyk, U., Schäpe, S.S., Zaghloul, S.S., El Dine, R.S., Shao, P., von Bergen, M., Farag, M.A. (2022):
  Evaluation of antioxidant activity and biotransformation of Opuntia ficus fruit: The effect of in vitro and ex vivo gut microbiota metabolism
  Molecules 27 (21), art. 7568 10.3390/molecules27217568
• Schaffert, A., Karkossa, I., Ueberham, E., Schlichting, R., Walter, K., Arnold, J., Blüher, M., Heiker, J.T., Lehmann, J., Wabitsch, M., Escher, B.I., von Bergen, M., Schubert, K. (2022):
  Di-(2-ethylhexyl) phthalate substitutes accelerate human adipogenesis through PPARγ activation and cause oxidative stress and impaired metabolic homeostasis in mature adipocytes
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• Scholz, S., Brack, W., Escher, B.I., Hackermüller, J., Liess, M., von Bergen, M., Wick, L.Y., Zenclussen, A.C., Altenburger, R. (2022):
  The EU chemicals strategy for sustainability: an opportunity to develop new approaches for hazard and risk assessment
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• Scholz, S., Nichols, J.W., Escher, B.I., Ankley, G.T., Altenburger, R., Blackwell, B., Brack, W., Burkhard, L., Collette, T.W., Doering, J.A., Ekman, D., Fay, K., Fischer, F., Hackermüller, J., Hoffman, J.C., Lai, C., Leuthold, D., Martinovic-Weigelt, D., Reemtsma, T., Pollesch, N., Schroeder, A., Schüürmann, G., von Bergen, M. (2022):
  The eco‐exposome concept: Supporting an integrated assessment of mixtures of environmental chemicals
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• Schöne, C., Poehlein, A., Jehmlich, N., Adlung, N., Daniel, R., von Bergen, M., Scheller, S., Rother, M. (2022):
  Deconstructing Methanosarcina acetivorans into an acetogenic archaeon
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• Schroeter, S.A., Eveillard, D., Chaffron, S., Zoppi, J., Kampe, B., Lohmann, P., Jehmlich, N., von Bergen, M., Sanchez-Arcos, C., Pohnert, G., Taubert, M., Küsel, K., Gleixner, G. (2022):
  Microbial community functioning during plant litter decomposition
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• Schubert, K., Karkossa, I. (2022):
  Proteomic characterization of calcium macrophages
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• Schubert, K., Schaffert, A. (2022):
  Effects of plasticizers on human preadipocytes (SGBS) using global proteomics
  PRoteomics IDEntifications Database (PRIDE) 10.6019/PXD031041
• Schubert, K., Schaffert, A. (2022):
  Effects of plasticizers on adult human adipocytes (SGBS) using global proteomics
  PRoteomics IDEntifications Database (PRIDE) 10.6019/PXD030843
• Schubert, K., Schaffert, A. (2022):
  THP-1 cells treated with plasticizer DINCH and metabolite MINCH
  PRoteomics IDEntifications Database (PRIDE) 10.6019/PXD027744
• Starke, R., Fiore-Donno, A.M., White III, R.A., Parente Fernandes, M.L., Martinović, T., Bastida, F., Delgado-Baquerizo, M., Jehmlich, N. (2022):
  Biomarker metaproteomics for relative taxa abundances across soil organisms
  Soil Biol. Biochem. 175 , art. 108861 10.1016/j.soilbio.2022.108861
• Starke, R., Schäpe, S.S., Van Den Bossche, T., Martinovic, T., Fernandes, M.L.P., Delgado-Baquerizo, M., Bastida, F., Jehmlich, N. (2022):
  Database-independent analysis of probable post-translational modifications of soil proteins across ecosystems
  bioRxiv 10.1101/2022.02.24.481781
• Taubert, M., Overholt, W.A., Heinze, B.M., Matanfack, G.A., Houhou, R., Jehmlich, N., von Bergen, M., Rösch, P., Popp, J., Küsel, K. (2022):
  Bolstering fitness via CO₂ fixation and organic carbon uptake: mixotrophs in modern groundwater
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• Torow, N., Li, R., Hitch, T., Mingels, C., Al Bounny, S., van Best, N., Stange, E.-L., Benabid, A., Rüttger, L., Gadermayr, M., Runge, S., Treichel, N., Merhof, D., Rosshart, S., Jehmlich, N., von Bergen, M., Heymann, F., Clavel, T., Tacke, F., Lelouard, H., Costa, I. (2022):
  Neonatal Peyer's patch cDC activation as a pacemaker of postnatal immune maturation
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• Bastida, F., Jehmlich, N., Starke, R., Benndorf, D., López-Mondéjar, R., Plaza, C., Freixino, Z., Ramírez-Ortuño, C., Ruiz-Navarro, A., Díaz-López, M., Vera, A., Moreno, J.L., Eldridge, D.J., García, C., Delgado-Baquerizo, M. (2021):
  Structure and function of bacterial metaproteomes across biomes
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• Bedulina, D., Drozdova, P., Gurkov, A., von Bergen, M., Stadler, P.F., Luckenbach, T., Timofeyev, M., Kalkhof, S. (2021):
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  Differences in the sperm metabolomes of smoking and nonsmoking men
  Biol. Reprod. 105 (6), 1484 - 1493 10.1093/biolre/ioab179
• Farag, M.A., von Bergen, M., Saleh, B.M., Homsi, M.N., Abd El-Al, M.S. (2021):
  How do green and black coffee brews and bioactive interaction with gut microbiome affect its health outcomes? Mining evidence from mechanistic studies, metagenomics and clinical trials
  Trends Food Sci. Technol. 118 (Part B), 920 - 937 10.1016/j.tifs.2021.11.004
• Frissen, M., Liao, L., Schneider, K.M., Djudjaj, S., Haybaeck, J., Wree, A., Rolle-Kampczyk, U., von Bergen, M., Latz, E., Boor, P., Trautwein, C. (2021):
  Bidirectional role of NLRP3 during acute and chronic cholestatic liver injury
  Hepatology 73 (5), 1836 - 1854 10.1002/hep.31494
• Genath, A., Petruschke, H., von Bergen, M., Einspanier, R. (2021):
  Influence of formic acid treatment on the proteome of the ectoparasite Varroa destructor
  PLOS One 16 (10), e0258845 10.1371/journal.pone.0258845
• Greiner–Haas, F., von Bergen, M., Sawers, R.G., Lechner, U., Türkowsky, D. (2021):
  Changes of the proteome and acetylome during transition into the stationary phase in the organohalide-respiring Dehalococcoides mccartyi strain CBDB1
  Microorganisms 9 (2), art. 365 10.3390/microorganisms9020365
• Großkopf, H., Vogel, S., Müller, C.D., Köhling, S., Dürig, J.-N., Möller, S., Schnabelrauch, M., Rademann, J., Hempel, U., von Bergen, M., Schubert, K. (2021):
  Identification of intracellular glycosaminoglycan-interacting proteins by affinity purification mass spectrometry
  Biol. Chem. 402 (11), 1427 - 1440 10.1515/hsz-2021-0167
• Großkopf, H., Walter, K., Karkossa, I., von Bergen, M., Schubert, K. (2021):
  Non-genomic AhR-signaling modulates the immune response in endotoxin-activated macrophages after activation by the environmental stressor BaP
  Front. Immunol. 12 , art. 620270 10.3389/fimmu.2021.620270
• Höper, T., Siewert, K., Dumit, V.I., von Bergen, M., Schubert, K., Haase, A. (2021):
  The contact allergen NiSO₄ triggers a distinct molecular response in primary human dendritic cells compared to bacterial LPS
  Front. Immunol. 12 , art. 644700 10.3389/fimmu.2021.644700
• Ismail, W.S., Homsi, M.N. (2021):
  Recent advances and challenges of Arabic why question answering systems
  In: Abu Talib, M., Benhlima, L., El Maghraoui, K. (eds.)
  ArabWIC 2021: 7th Annual International Conference on Arab Women in Computing in Conjunction with the 2nd Forum of Women in Research, August 25, 2021, Sharjah, United Arab Emirates and virtually
  Association for Computing Machinery, New York, NY, p. 1 - 7, art. 13
• Junge, K.M., Buchenauer, L., Elter, E., Butter, K., Kohajda, T., Herberth, G., Röder, S., Borte, M., Kiess, W., von Bergen, M., Simon, J.C., Rolle-Kampczyk, U.E., Lehmann, I., Gminski, R., Ohlmeyer, M., Polte, T. (2021):
  Wood emissions and asthma development: Results from an experimental mouse model and a prospective cohort study
  Environ. Int. 151 , art. 106449 10.1016/j.envint.2021.106449
• Karkossa, I., Bannuscher, A., Hellack, B., Wohlleben, W., Laloy, J., Stan, M.S., Dinischiotu, A., Wiemann, M., Luch, A., Haase, A., von Bergen, M., Schubert, K. (2021):
  Omics reveal different oxidative stress levels induced by nanomaterials in vitro and in vivo
  Toxicol. Lett. 350 (Suppl.), S125 10.1016/S0378-4274(21)00541-5
• Karkossa, I., Bannuscher, A., Hellack, B., Wohlleben, W., Laloy, J., Stan, M.S., Dinischiotu, A., Wiemann, M., Luch, A., Haase, A., von Bergen, M., Schubert, K. (2021):
  Nanomaterials induce different levels of oxidative stress, depending on the used model system: Comparison of in vitro and in vivo effects
  Sci. Total Environ. 801 , art. 149538 10.1016/j.scitotenv.2021.149538
• Kasmanas, J.C., Bartholomäus, A., Borim Corrêa, F., Tal, T., Jehmlich, N., Herberth, G., von Bergen, M., Stadler, P.F., de Carvalho, A.C.P.L.F., Nunes da Rocha, U. (2021):
  HumanMetagenomeDB: a public repository of curated and standardized metadata for human metagenomes
  Nucleic Acids Res. 49 (D1), D743 - D750 10.1093/nar/gkaa1031
• Kimani, V., Ullrich, R., Büttner, E., Herzog, R., Kellner, H., Jehmlich, N., Hofrichter, M., Liers, C. (2021):
  First dye-decolorizing peroxidase from an ascomycetous fungus secreted by Xylaria grammica
  Biomolecules 11 (9), art. 1391 10.3390/biom11091391
• Kruse, S., Türkowsky, D., Birkigt, J., Matturro, B., Franke, S., Jehmlich, N., von Bergen, M., Westermann, M., Rossetti, S., Nijenhuis, I., Adrian, L., Diekert, G., Goris, T. (2021):
  Interspecies metabolite transfer and aggregate formation in a co-culture of Dehalococcoides and Sulfurospirillum dehalogenating tetrachloroethene to ethene
  ISME J. 15 (6), 1794 - 1809 10.1038/s41396-020-00887-6
• Le Duc, D., Lin, C.-C., Popkova, Y., Yang, Z., Akhil, V., Çakir, M.V., Grunewald, S., Simon, J.-C., Dietz, A., Dannenberger, D., Garten, A., Lemke, J.R., Schiller, J., Blüher, M., Nono Nankam, P.A., Rolle-Kampczyk, U., von Bergen, M., Kelso, J., Schöneberg, T. (2021):
  Reduced lipolysis in lipoma phenocopies lipid accumulation in obesity
  Int. J. Obes. 45 (3), 565 - 576 10.1038/s41366-020-00716-y
• Li, Q., Cooper, R.E., Wegner, C.-E., Taubert, M., Jehmlich, N., von Bergen, M., Küsel, K. (2021):
  Insights into autotrophic activities and carbon flow in iron-rRich pelagic aggregates (iron snow)
  Microorganisms 9 (7), art. 1368 10.3390/microorganisms9071368
• Lovera, F.A., Cardinale, Y., Buscaldi, D., Charnois, T., Homsi, M.N. (2021):
  Deep learning enhanced with graph knowledge for sentiment analysis
  X-SENTIMENT 2021: Sixth International Workshop on eXplainable SENTIment Mining and EmotioN deTection, June 07, 2021, Hersonissos, Greece
• Lovera, F.A., Cardinale, Y.C., Homsi, M.N. (2021):
  Sentiment analysis in twitter based on knowledge graph and deep learning classification
  Electronics 10 (22), art. 2739 10.3390/electronics10222739
• Medawar, E., Haange, S.-B., Rolle-Kampczyk, U., Engelmann, B., Dietrich, A., Thieleking, R., Wiegank, C., Fries, C., Horstmann, A., Villringer, A., von Bergen, M., Fenske, W., Witte, A.V. (2021):
  Gut microbiota link dietary fiber intake and short-chain fatty acid metabolism with eating behavior
  Transl. Psychiatr. 11 , art. 500 10.1038/s41398-021-01620-3
• Monikh, F.A., Chupani, L., Karkossa, I., Gardian, Z., Arenas-Logo, D., von Bergen, M., Schubert, K., Piackova, V., Zuskova, E., Jiskoot, W., Vijver, M.G., Peijnenburg, W.J.G.M. (2021):
  An environmental ecocorona influences the formation and evolution of the biological corona on the surface of single-walled carbon nanotubes
  NanoImpact 22 , art. 100315 10.1016/j.impact.2021.100315
• Müller-Deile, J., Sarau, G., Kotb, A., Daniel, C., Kalkhof, S., Christiansen, S., Schiffer, M. (2021):
  Novel diagnostic and therapeutic techniques reveal changed metabolomic profile in recurrent focal segmental glomerulosclerosis
  Nephrol. Dial. Transplant. 36 (Suppl. 1), art. 7286 10.1093/ndt/gfab104.005
• Müller-Deile, J., Sarau, G., Kotb, A.M., Jaremenko, C., Rolle-Kampczyk, U.E., Daniel, C., Kalkhof, S., Christiansen, S.H., Schiffer, M. (2021):
  Novel diagnostic and therapeutic techniques reveal changed metabolic profiles in recurrent focal segmental glomerulosclerosis
  Sci. Rep. 11 , art. 4577 10.1038/s41598-021-83883-w
• Nickel, S., Vlaic, S., Christ, M., Schubert, K., Henschler, R., Tautenhahn, F., Burger, C., Kühne, H., Erler, S., Roth, A., Wild, C., Brach, J., Hammad, S., Gittel, C., Baunack, M., Lange, U., Broschewitz, J., Stock, P., Metelmann, I., Bartels, M., Pietsch, U.-C., Krämer, S., Eichfeld, U., von Bergen, M., Dooley, S., Tautenhahn, H.-M., Christ, B. (2021):
  Mesenchymal stromal cells mitigate liver damage after extended resection in the pig by modulating thrombospondin-1/TGF-β
  npj Regen. Med. 6 , art. 84 10.1038/s41536-021-00194-4
• Petruschke, H., Schori, C., Canzler, S., Riesbeck, S., Poehlein, A., Daniel, R., Frei, D., Segessemann, T., Zimmerman, J., Marinos, G., Kaleta, C., Jehmlich, N., Ahrens, C.H., von Bergen, M. (2021):
  Discovery of novel community-relevant small proteins in a simplified human intestinal microbiome
  Microbiome 9 , art. 55 10.1186/s40168-020-00981-z
• Rughöft, S., Jehmlich, N., Gutierrez, T., Kleindienst, S. (2021):
  Comparative proteomics of Marinobacter sp. TT1 reveals corexit impacts on hydrocarbon metabolism, chemotactic motility, and biofilm formation
  Microorganisms 9 (1), art. 3 10.3390/microorganisms9010003
• Sallam, I.E., Abdelwareth, A., Attia, H., Aziz, R.K., Homsi, M.N., von Bergen, M., Farag, M.A. (2021):
  Effect of gut microbiota biotransformation on dietary tannins and human health implications
  Microorganisms 9 (5), art. 965 10.3390/microorganisms9050965
• Schaffert, A., Arnold, J., Karkossa, I., Blüher, M., von Bergen, M., Schubert, K. (2021):
  The emerging plasticizer alternative DINCH and its metabolite MINCH induce oxidative stress and enhance inflammatory responses in human THP-1 macrophages
  Cells 10 (9), art. 2367 10.3390/cells10092367
• Schaffert, A., Krieg, L., Weiner, J., Schlichting, R., Ueberham, E., Karkossa, I., Bauer, M., Landgraf, K., Junge, K.M., Wabitsch, M., Lehmann, J., Escher, B.I., Zenclussen, A.C., Körner, A., Blüher, M., Heiker, J.T., von Bergen, M., Schubert, K. (2021):
  Alternatives for the worse: Molecular insights into adverse effects of bisphenol a and substitutes during human adipocyte differentiation
  Environ. Int. 156 , art. 106730 10.1016/j.envint.2021.106730
• Schaffert, A., Krieg, L., Weinert, J., Schlichting, R., Ueberham, E., Karkossa, I., Bauer, M., Junge, K., Wabitsch, M., Lehmann, J., Escher, B.I., Zenclussen, A.C., Körner, A., Blüher, M., Heiker, J.T., von Bergen, M., Schubert, K. (2021):
  Emerging substitutes of BPA cause inflammation-like state and impaired insulin sensitivity in differentiating human adipocytes
  Toxicol. Lett. 350 (Suppl.), S130 10.1016/S0378-4274(21)00552-X
• Schubert, K., Karkossa, I., Schor, J., Engelmann, B., Steinheuer, L.M., Bruns, T., Rolle-Kampczyk, U., Hackermüller, J., von Bergen, M. (2021):
  A multi-omics analysis of mucosal-associated-invariant T cells reveals key drivers of distinct modes of activation
  Front. Immunol. 12 , art. 616967 10.3389/fimmu.2021.616967
• Shahid, N., Rolle-Kampczyk, U., Siddique, A., von Bergen, M., Liess, M. (2021):
  Pesticide-induced metabolic changes are amplified by food stress
  Sci. Total Environ. 792 , art. 148350 10.1016/j.scitotenv.2021.148350
• Shiva Nagendra, S.M., Schlink, U., Müller, A., Khare, M. (eds., 2021):
  Urban air quality monitoring, modelling and human exposure assessment
  Springer Transactions in Civil and Environmental Engineering (STICEE)
  Springer Singapore, Singapore, 440 pp. 10.1007/978-981-15-5511-4
• Shiva Nagendra, S.M., Schlink, U., Müller, A., Menon, J.S., Chithra, V.S. (2021):
  Personal exposure and health risk assessment
  In: Shiva Nagendra, S.M., Schlink, U., Müller, A., Khare, M. (eds.)
  Urban air quality monitoring, modelling and human exposure assessment
  Springer Transactions in Civil and Environmental Engineering (STICEE)
  Springer Singapore, Singapore, p. 75 - 87 10.1007/978-981-15-5511-4_6
• Smith, L., Martin, C., Lasserre, F., Engelmann, B., Klément, W., Fougerat, A., Polizzi, A., Canlet, C., Rolle-Kampczyk, U., von Bergen, M., Lippi, Y., Guillou, H., Loiseau, N., Payastre, L., Ellero-Simatos, S. (2021):
  Impact d’une exposition alimentaire chronique au glyphosate à des doses de référence sur le microbiote intestinal et le métabolisme énergétique chez la souris
  Nutr. Clin. Metab. 35 (1), 74 - 74 10.1016/j.nupar.2021.01.110
• Starke, R., Fernandes, M.L.P., Morais, D.K., Odriozola, I., Baldrian, P., Jehmlich, N. (2021):
  Explorative meta-analysis of 417 extant archaeal genomes to predict their contribution to the total microbiome functionality
  Microorganisms 9 (2), art. 381 10.3390/microorganisms9020381
• Starke, R., Schäpe, S.S., Jehmlich, N., von Bergen, M. (2021):
  Protein stable isotope probing with H₂¹⁸O differentiated cold stress response at permissive temperatures from general growth at optimal conditions in Escherichia coli K12
  Rapid Commun. Mass Spectrom. 35 (1), e8941 10.1002/rcm.8941
• Starke, R., Siles, J.A., Fernandes, M.L.P., Schallert, K., Benndorf, D., Plaza, C., Jehmlich, N., Delgado-Baquerizo, M., Bastida, F. (2021):
  The structure and function of soil archaea across biomes
  J. Proteomics 237 , art. 104147 10.1016/j.jprot.2021.104147
• Streidl, T., Karkossa, I., Segura Muñoz, R.R., Eberl, C., Zaufel, A., Plagge, J., Schmaltz, R., Schubert, K., Basic, M., Schneider, K.M., Afify, M., Trautwein, C., Tolba, R., Stecher, B., Doden, H.L., Ridlon, J.M., Ecker, J., Moustafa, T., von Bergen, M., Ramer-Tait, A.E., Clavel, T. (2021):
  The gut bacterium Extibacter muris produces secondary bile acids and influences liver physiology in gnotobiotic mice
  Gut Microbes 13 (1), 1 - 21 10.1080/19490976.2020.1854008
• Thürmann, L., Herberth, G., Seiwert, B., Schlittenbauer, L., Rolle-Kampczyk, U., Röder, S., Sack, U., Borte, M., von Bergen, M., Trump, S., Reemtsma, T., Lehmann, I. (2021):
  Prenatal paraben exposure and atopic dermatitis-related outcomes among children
  Allergy 76 (10), 3122 - 3132 10.1111/all.14890
• Tsaban, G., Meir, A.Y., Rinott, E., Zelicha, H., Kaplan, A., Shalev, A., Katz, A., Rudich, A., Tirosh, A., Shelef, I., Youngster, I., Lebovitz, S., Israeli, N., Shabat, M., Brikner, D., Pupkin, E., Stumvoll, M., Thiery, J., Ceglarek, U., Heiker, J.T., Körner, A., Landgraf, K., von Bergen, M., Blüher, M., Stampfer, M.J., Shai, I. (2021):
  The effect of green Mediterranean diet on cardiometabolic risk; a randomised controlled trial
  Heart 107 (13), 1054 - 1061 10.1136/heartjnl-2020-317802
• Van Den Bossche, T., Arntzen, M.Ø., Becher, D., Benndorf, D., Eijsink, V.G.H., Henry, C., Jagtap, P.D., Jehmlich, N., Juste, C., Kunath, B.J., Mesuere, B., Muth, T., Pope, P.B., Seifert, J., Tanca, A., Uzzau, S., Wilmes, P., Hettich, R.L., Armengaud, J. (2021):
  The Metaproteomics Initiative: a coordinated approach for propelling the functional characterization of microbiomes
  Microbiome 9 , art. 243 10.1186/s40168-021-01176-w
• Van Den Bossche, T., Kunath, B.J., Schallert, K., Schäpe, S.S., Abraham, P.E., Armengaud, J., Arntzen, M.Ø., Bassignani, A., Benndorf, D., Fuchs, S., Giannone, R.J., Griffin, T.J., Hagen, L.H., Halder, R., Henry, C., Hettich, R.L., Heyer, R., Jagtap, P., Jehmlich, N., Jensen, M., Juste, C., Kleiner, M., Langella, O., Lehmann, T., Leith, E., May, P., Mesuere, B., Miotello, G., Peters, S.L., Pible, O., Queiros, P.T., Reichl, U., Renard, B.Y., Schiebenhoefer, H., Sczyrba, A., Tanca, A., Trappe, K., Trezzi, J.-P., Uzzau, S., Verschaffelt, P., von Bergen, M., Wilmes, P., Wolf, M., Martens, L., Muth, T. (2021):
  Critical Assessment of MetaProteome Investigation (CAMPI): a multi-laboratory comparison of established workflows
  Nat. Commun. 12 , art. 7305 10.1038/s41467-021-27542-8
• Venkat, K., Hoyos, M., Haycocks, J.R.J., Cassidy, L., Engelmann, B., Rolle-Kampczyk, U., von Bergen, M., Tholey, A., Grainger, D.C., Papenfort, K. (2021):
  A dual-function RNA balances carbon uptake and central metabolism in Vibrio cholerae
  Embo J. 40 (24), e108542 10.15252/embj.2021108542
• Walter, K., Grosskopf, H., Karkossa, I., von Bergen, M., Schubert, K. (2021):
  Proteomic characterization of the cellular effects of AhR activation by microbial tryptophan catabolites in endotoxin-activated human macrophages
  Int. J. Environ. Res. Public Health 18 (19), 10336 10.3390/ijerph181910336
• Wang, Z., Karkossa, I., Großkopf, H., Canzler, S., Rolle-Kampczyk, U., Hackermüller, J., von Bergen, M., Schubert, K. (2021):
  Quantitative proteomics reveal mechanistic insights into direct and indirect drug-induced thyroid toxicity in rats
  Toxicol. Lett. 350 (Suppl.), S129 10.1016/S0378-4274(21)00550-6
• Warmt, E., Grosser, S., Blauth, E., Xie, X., Kubitschke, H., Stange, R., Sauer, F., Schnauß, J., Tomm, J.M., von Bergen, M., Käs, J.A. (2021):
  Differences in cortical contractile properties between healthy epithelial and cancerous mesenchymal breast cells
  New J. Phys. 23 (10), art. 103020 10.1088/1367-2630/ac254e
• Warrick, P.A., Lostanlen, V., Eickenberg, M., Homsi, M.N., Rodríguez, A.C., Andén, J. (2021):
  Arrhythmia classification of reduced-lead electrocardiograms by scattering-recurrent networks
  Computing in Cardiology 48 , 1 - 4 10.23919/CinC53138.2021.9662908
• Yaskolka Meir, A., Tuohy, K., von Bergen, M., Krajmalnik-Brown, R., Heinig, U., Zelicha, H., Tsaban, G., Rinott, E., Kaplan, A., Aharoni, A., Zeibich, L., Chang, D., Dirks, B., Diotallevi, C., Arapitsas, P., Vrhovsek, U., Ceglarek, U., Haange, S.-B., Rolle-Kampczyk, U., Engelmann, B., Lapidot, M., Colt, M., Sun, Q., Shai, I. (2021):
  The metabolomic-gut-clinical axis of Mankai plant-derived dietary polyphenols
  Nutrients 13 (6), art. 1866 10.3390/nu13061866

2020 (47)

• Ananbeh, H., Merlos Rodrigo, M.A., Jelinkova, P., Strmiska, V., Splichal, Z., Jehmlich, N., Michalkova, H., Stojanović, M., Voberkova, S., Adam, V., Moulick, A. (2020):
  Soil protein as a potential antimicrobial agent against methicillin-resistant Staphylococcus aureus
  Environ. Res. 188 , art. 109320 10.1016/j.envres.2020.109320
• Balogh, G., Bernhart, S.H., Stadler, P.F., Schor, J. (2020):
  A probabilistic version of Sankoff’s maximum parsimony algorithm
  J. Bioinform. Comput. Biol. 18 (1), art. 2050004 10.1142/S0219720020500043
• Bannuscher, A., Karkossa, I., Buhs, S., Nollau, P., Kettler, K., Balas, M., Dinischiotu, A., Hellack, B., Wiemann, M., Luch, A., von Bergen, M., Haase, A., Schubert, K. (2020):
  A multi-omics approach reveals mechanisms of nanomaterial toxicity and structure–activity relationships in alveolar macrophages
  Nanotoxicology 14 (2), 181 - 195 10.1080/17435390.2019.1684592
• Canzler, S., Hackermüller, J. (2020):
  multiGSEA: a GSEA-based pathway enrichment analysis for multi-omics data
  BMC Bioinformatics 21 , art. 561 10.1186/s12859-020-03910-x
• Canzler, S., Schor, J., Busch, W., Schubert, K., Rolle-Kampczyk, U.E., Seitz, H., Kamp, H., von Bergen, M., Buesen, R., Hackermüller, J. (2020):
  Prospects and challenges of multi‑omics data integration in toxicology
  Arch. Toxicol. 94 (2), 371 - 388 10.1007/s00204-020-02656-y
• Dey, P., Malik, A., Mishra, A., Singh, D.K., von Bergen, M., Jehmlich, N. (2020):
  Mechanistic insight to mycoremediation potential of a metal resistant fungal strain for removal of hazardous metals from multimetal pesticide matrix
  Environ. Pollut. 262 , art. 114255 10.1016/j.envpol.2020.114255
• Ernst, J., Gert, K., Kraus, F.B., Rolle-Kampczyk, U.E., Wabitsch, M., Dehghani, F., Schaedlich, K. (2020):
  Androstenedione changes steroidogenic activity of SGBS cells
  Endocr. Connect. 9 (7), 587 - 598 10.1530/EC-19-0549
• Farag, M.A., Abdelwareth, A., Sallam, I.E., el Shorbagi, M., Jehmlich, N., Fritz, K., Schaepe, S., Rolle-Kampczyk, U., Ehrlich, A., Wessjohann, L.A., von Bergen, M. (2020):
  Metabolomics reveals impact of seven functional foods on metabolic pathways in a gut microbiota model
  J. Adv. Res. 23 , 47 - 59 10.1016/j.jare.2020.01.001
• Friedrich, M., Wiedemann, K., Reiche, K., Puppel, S.-H., Pfeifer, G., Zipfel, I., Binder, S., Köhl, U., Müller, G.A., Engeland, K., Aigner, A., Füssel, S., Fröhner, M., Peitzsch, C., Dubrovska, A., Rade, M., Christ, S., Schreiber, S., Hackermüller, J., Lehmann, J., Toma, M.I., Muders, M.H., Sommer, U., Baretton, G.B., Wirth, M., Horn, F. (2020):
  The role of lncRNAs TAPIR-1 and -2 as diagnostic markers and potential therapeutic targets in prostate cancer
  Cancers 12 (5), art. 1122 10.3390/cancers12051122
• Fritz-Wallace, K., Engelmann, B., Krause, J.L., Schäpe, S.S., Pöppe, J., Herberth, G., Rösler, U., Jehmlich, N., von Bergen, M., Rolle-Kampczyk, U. (2020):
  Quantification of glyphosate and AMPA from microbiome reactor fluids
  Rapid Commun. Mass Spectrom. 34 (7), e8668 10.1002/rcm.8668
• Haange, S.-B., Groeger, N., Froment, J., Rausch, T., Burkhardt, W., Gonnermann, S., Braune, A., Blaut, M., von Bergen, M., Rolle-Kampczyk, U. (2020):
  Multiplexed quantitative assessment of the fate of taurine and sulfoquinovose in the intestinal microbiome
  Metabolites 10 (11), art. 430 10.3390/metabo10110430
• Haange, S.-B., Jehmlich, N., Krügel, U., Hintschich, C., Wehrmann, D., Hankir, M., Seyfried, F., Froment, J., Hübschmann, T., Müller, S., Wissenbach, D.K., Kang, K.H., Buettner, C., Panagiotou, G., Noll, M., Rolle-Kampczyk, U., Fenske, W., von Bergen, M. (2020):
  Gastric bypass surgery in a rat model alters the community structure and functional composition of the intestinal microbiota independently of weight loss
  Microbiome 8 , art. 13 10.1186/s40168-020-0788-1
• Hsu, M.-J., Karkossa, I., Schäfer, I., Christ, M., Kühne, H., Schubert, K., Rolle-Kampczyk, U.E., Kalkhof, S., Nickel, S., Seibel, P., von Bergen, M., Christ, B. (2020):
  Mitochondrial transfer by human mesenchymal stromal cells ameliorates hepatocyte lipid load in a mouse model of NASH
  Biomedicines 8 (9), art. 350 10.3390/biomedicines8090350
• Jacoby, C., Krull, J., Andexer, J., Jehmlich, N., von Bergen, M., Brüls, T., Boll, M. (2020):
  Channeling C1 metabolism toward S-adenosylmethionine-dependent conversion of estrogens to androgens in estrogen-degrading bacteria
  mBio 11 (4), e01259-20 10.1128/mBio.01259-20
• Jakobs, G., Krüger, J., Schüttler, A., Altenburger, R., Busch, W. (2020):
  Mixture toxicity analysis in zebrafish embryo a time and concentration resolved study on mixture effect predictivity
  Environ. Sci. Eur. 32 , art. 143 10.1186/s12302-020-00409-3
• Kalkhof, S., Krieg, L., Büttner, P., Wabitsch, M., Küntzel, C., Friebe, D., Landgraf, K., Hanschkow, M., Schubert, K., Kiess, W., Krohn, K., Blüher, M., von Bergen, M., Körner, A. (2020):
  In depth quantitative proteomic and transcriptomic characterization of human adipocyte differentiation using the SGBS cell line
  Proteomics 20 (15-16), art. 1900405 10.1002/pmic.201900405
• Karkossa, I., Raps, S., von Bergen, M., Schubert, K. (2020):
  Systematic review of multi-omics approaches to investigate toxicological effects in macrophages
  Int. J. Mol. Sci. 21 (24), art. 9371 10.3390/ijms21249371
• Kipping, L., Holzscheck, N., Maurer, F., Muszynski, S., Noll, M., Jehmlich, N. (2020):
  Microbial metaproteome data from decayed beech dead wood
  Data Brief 29 , art. 105285 10.1016/j.dib.2020.105285
• Krämer, S., Busch, W., Schüttler, A. (2020):
  A self-organizing map of the fathead minnow liver transcriptome to identify consistent toxicogenomic patterns across chemical fingerprints
  Environ. Toxicol. Chem. 39 (3), 526 - 537 10.1002/etc.4646
• Krause, J.L., Haange, S.-B., Schäpe, S.S., Engelmann, B., Rolle-Kampczyk, U., Fritz-Wallace, K., Wang, Z., Jehmlich, N., Türkowsky, D., Schubert, K., Pöppe, J., Bote, K., Rösler, U., Herberth, G., von Bergen, M. (2020):
  The glyphosate formulation Roundup^® LB plus influences the global metabolome of pig gut microbiota in vitro
  Sci. Total Environ. 745 , art. 140932 10.1016/j.scitotenv.2020.140932
• Krause, J.L., Schaepe, S.S., Fritz-Wallace, K., Engelmann, B., Rolle-Kampczyk, U., Kleinsteuber, S., Schattenberg, F., Liu, Z., Müller, S., Jehmlich, N., von Bergen, M., Herberth, G. (2020):
  Following the community development of SIHUMIx – a new intestinal in vitro model for bioreactor use
  Gut Microbes 11 (4), 1116 - 1129 10.1080/19490976.2019.1702431
• Krause, J.L., Schäpe, S.S., Schattenberg, F., Müller, S., Ackermann, G., Rolle-Kampczyk, U.E., Jehmlich, N., Pierzchalski, A., von Bergen, M., Herberth, G. (2020):
  The activation of mucosal-associated invariant T (MAIT) cells is affected by microbial diversity and riboflavin utilization in vitro
  Front. Microbiol. 11 , art. 755 10.3389/fmicb.2020.00755
• Kreuz, M., Otto, D.J., Fuessel, S., Blumert, C., Bertram, C., Bartsch, S., Loeffler, D., Puppel, S.-H., Rade, M., Buschmann, T., Christ, S., Erdmann, K., Friedrich, M., Froehner, M., Muders, M.H., Schreiber, S., Specht, M., Toma, M.I., Benigni, F., Freschi, M., Gandaglia, G., Briganti, A., Baretton, G.B., Loeffler, M., Hackermüller, J., Reiche, K., Wirth, M., Horn, F. (2020):
  ProstaTrend—A multivariable prognostic RNA expression score for aggressive prostate cancer
  Eur. Urol. 78 (3), 452 - 459 10.1016/j.eururo.2020.06.001
• Krieg, L., Schaffert, A., Kern, M., Landgraf, K., Wabitsch, M., Beck-Sickinger, A.G., Koerner, A., Blüher, M., von Bergen, M., Schubert, K. (2020):
  An MRM-based multiplexed quantification assay for human adipokines and apolipoproteins
  Molecules 25 (4), art. 775 10.3390/molecules25040775
• Leppert, B., Strunz, S., Seiwert, B., Schlittenbauer, L., Schlichting, R., Pfeifer, C., Röder, S., Bauer, M., Borte, M., Stangl, G.I., Schöneberg, T., Schulz, A., Karkossa, I., Rolle-Kampczyk, U.E., Thürmann, L., von Bergen, M., Escher, B.I., Junge, K.M., Reemtsma, T., Lehmann, I., Polte, T. (2020):
  Maternal paraben exposure triggers childhood overweight development
  Nat. Commun. 11 , art. 561 10.1038/s41467-019-14202-1
• Lohmann, P., Benk, S., Gleixner, G., Potthast, K., Michalzik, B., Jehmlich, N., von Bergen, M. (2020):
  Seasonal patterns of dominant microbes involved in central nutrient cycles in the subsurface
  Microorganisms 8 (11), art. 1694 10.3390/microorganisms8111694
• Lohmann, P., Schäpe, S.S., Haange, S.-B., Oliphant, K., Allen-Vercoe, E., Jehmlich, N., von Bergen, M. (2020):
  Function is what counts: how microbial community complexity affects species, proteome and pathway coverage in metaproteomics
  Expert Rev. Proteomics 17 (2), 163 - 173 10.1080/14789450.2020.1738931
• Mahdi, D.H., Wissenbach, D.K., von Bergen, M., Vissiennon, Z., Chougourou, D., Nieber, K., Ahyi, V., Vissiennon, C. (2020):
  Ethnomedicinal survey and in vitro confirmation of anti-inflammatory and antispasmodic properties of the termite strain Macrotermes bellicosus used in traditional medicine in the Republic of Benin
  J. Ethnopharmacol. 254 , art. 112705 10.1016/j.jep.2020.112705
• Massier, L., Chakaroun, R., Tabei, S., Crane, A., Didt, K.D., Fallmann, J., von Bergen, M., Haange, S.-B., Heyne, H., Stumvoll, M., Gericke, M., Dietrich, A., Blüher, M., Musat, N., Kovacs, P. (2020):
  Adipose tissue derived bacteria are associated with inflammation in obesity and type 2 diabetes
  Gut 69 (10), 1796 - 1806 10.1136/gutjnl-2019-320118
• Mendler, A., Geier, F., Haange, S.-B., Pierzchalski, A., Krause, J.L., Nijenhuis, I., Froment, J., Jehmlich, N., Berger, U., Ackermann, G., Rolle-Kampczyk, U., von Bergen, M., Herberth, G. (2020):
  Mucosal-associated invariant T-Cell (MAIT) activation is altered by chlorpyrifos- and glyphosate-treated commensal gut bacteria
  J. Immunotoxicol. 17 (1), 10 - 20 10.1080/1547691X.2019.1706672
• Mendler, A., Pierzchalski, A., Bauer, M., Röder, S., Sattler, A., Standl, M., Borte, M., von Bergen, M., Rolle-Kampczyk, U., Herberth, G. (2020):
  MAIT cell activation in adolescents is impacted by bile acid concentrations and body weight
  Clin. Exp. Immunol. 200 (2), 199 - 213 10.1111/cei.13423
• Meyer-Cifuentes, I.E., Werner, J., Jehmlich, N., Will, S.E., Neumann-Schaal, M., Öztürk, B. (2020):
  Synergistic biodegradation of aromatic-aliphatic copolyester plastic by a marine microbial consortium
  Nat. Commun. 11 , art. 5790 10.1038/s41467-020-19583-2
• Meyer-Cifuentes, I., Gruhl, S., Haange, S.-B., Lünsmann, V., Jehmlich, N., von Bergen, M., Heipieper, H.J., Müller, J.A. (2020):
  Benzylsuccinate synthase is post-transcriptionally regulated in the toluene-degrading denitrifier Magnetospirillum sp. strain 15-1
  Microorganisms 8 (5), art. 681 10.3390/microorganisms8050681
• Pereira, F.C., Wasmund, K., Cobankovic, I., Jehmlich, N., Herbold, C.W., Lee, K.S., Sziranyi, B., Vesely, C., Decker, T., Stocker, R., Warth, B., von Bergen, M., Wagner, M., Berry, D. (2020):
  Rational design of a microbial consortium of mucosal sugar utilizers reduces Clostridiodes difficile colonization
  Nat. Commun. 11 , art. 5104 10.1038/s41467-020-18928-1
• Petruschke, H., Anders, J., Stadler, P.F., Jehmlich, N., von Bergen, M. (2020):
  Enrichment and identification of small proteins in a simplified human gut microbiome
  J. Proteomics 213 , art. 103604 10.1016/j.jprot.2019.103604
• Riba, A., Hassani, K., Walker, A., van Best, N., von Zeschwitz, D., Anslinger, T., Sillner, N., Rosenhain, S., Eibach, D., Maiga-Ascofaré, O., Rolle-Kampczyk, U., Basic, M., Binz, A., Mocek, S., Sodeik, B., Bauerfeind, R., Mohs, A., Trautwein, C., Kiessling, F., May, J., Klingenspor, M., Gremse, F., Schmitt-Kopplin, P., Bleich, A., Torow, N., von Bergen, M., Hornef, M.W. (2020):
  Disturbed gut microbiota and bile homeostasis in Giardia-infected mice contributes to metabolic dysregulation and growth impairment
  Sci. Transl. Med. 12 (565), eaay7019 10.1126/scitranslmed.aay7019
• Rohwerder, T., Rohde, M.-T., Jehmlich, N., Purswani, J. (2020):
  Actinobacterial degradation of 2-hydroxyisobutyric acid proceeds via acetone and formyl-CoA by employing a thiamine-dependent lyase reaction
  Front. Microbiol. 11 , art. 691 10.3389/fmicb.2020.00691
• Rolle-Kampczyk, U., Gebauer, S., Haange, S.-B., Schubert, K., Kern, M., Moulla, Y., Dietrich, A., Schön, M.R., Klöting, N., von Bergen, M., Blüher, M. (2020):
  Accumulation of distinct persistent organic pollutants is associated with adipose tissue inflammation
  Sci. Total Environ. 748 , art. 142458 10.1016/j.scitotenv.2020.142458
• Ros, M., Blaya, J., Baldrian, P., Bastida, F., Richnow, H.H., Jehmlich, N., Pascual, J.A. (2020):
  In vitro elucidation of suppression effects of composts to soil-borne pathogen Phytophthora nicotianae on pepper plants using 16S amplicon sequencing and metaproteomics
  Renew. Agr. Food Syst. 35 (2), 206 - 214 10.1017/S1742170518000467
• Schäpe, S.S., Krause, J.L., Masanetz, R.K., Riesbeck, S., Starke, R., Rolle-Kampczyk, U., Eberlein, C., Heipieper, H.J., Herberth, G., von Bergen, M., Jehmlich, N. (2020):
  Environmentally relevant concentration of bisphenol S shows slight effects on SIHUMIx
  Microorganisms 8 (9), art. 1436 10.3390/microorganisms8091436
• Shatilina, Z., Drozdova, P., Bedulina, D., Rivarola-Duarte, L., Schreiber, S., Otto, C., Jühling, F., Aulhorn, S., Busch, W., Lubyaga, Y., Kondrateva, E., Pobezhimova, T., Jakob, L., Lucassen, M., Sartoris, F.J., Hackermüller, J., Pörtner, H.-O., Stadler, P.F., Luckenbach, T., Timofeyev, M. (2020):
  Transcriptome-level effects of the model organic pollutant phenanthrene and its solvent acetone in three amphipod species
  Comp. Biochem. Physiol. D-Genomics Proteomics 33 , art. 100630 10.1016/j.cbd.2019.100630
• Starke, R., Capek, P., Morais, D., Callister, S.J., Jehmlich, N. (2020):
  The total microbiome functions in bacteria and fungi
  J. Proteomics 213 , art. 103623 10.1016/j.jprot.2019.103623
• Starke, R., Capek, P., Morais, D., Jehmlich, N., Baldrian, P. (2020):
  Explorative meta-analysis of 377 extant fungal genomes predicted a total mycobiome functionality of 42.4 million KEGG functions
  Front. Microbiol. 11 , art. 143 10.3389/fmicb.2020.00143
• Starke, R., Oliphant, K., Jehmlich, N., Schäpe, S.S., Sachsenberg, T., Kohlbacher, O., Allen-Vercoe, E., von Bergen, M. (2020):
  Tracing incorporation of heavy water into proteins for species-specific metabolic activity in complex communities
  J. Proteomics 222 , art. 103791 10.1016/j.jprot.2020.103791
• van Best, N., Rolle-Kampczyk, U., Schaap, F.G., Basic, M., Olde Damink, S.W.M., Bleich, A., Savelkoul, P.H.M., von Bergen, M., Penders, J., Hornef, M.W. (2020):
  Bile acids drive the newborn’s gut microbiota maturation
  Nat. Commun. 11 , art. 3692 10.1038/s41467-020-17183-8
• Wang, Z., Karkossa, I., Großkopf, H., Rolle-Kampczyk, U., Hackermüller, J., von Bergen, M., Schubert, K. (2020):
  Comparison of quantitation methods in proteomics to define relevant toxicological information on AhR activation of HepG2 cells by BaP
  Toxicology 448 , art. 152652 10.1016/j.tox.2020.152652
• Warrick, P.A., Lostanlen, V., Eickenberg, M., Andén, J., Homsi, M.N. (2020):
  Arrhythmia classification of 12-lead electrocardiograms by hybrid scattering-LSTM networks
  Computing in Cardiology 47 , 1 - 4 10.23919/CinC53138.2021.9662908

2019 (44)

• Anselmann, S.E.L., Löffler, C., Stärk, H.-J., Jehmlich, N., von Bergen, M., Brüls, T., Boll, M. (2019):
  The class II benzoyl‐coenzyme A reductase complex from the sulfate‐reducing Desulfosarcina cetonica
  Environ. Microbiol. 21 (11), 4241 - 4252 10.1111/1462-2920.14784
• Bastida, F., García, C., Fierer, N., Eldridge, D.J., Bowker, M.A., Abades, S., Alfaro, F.D., Berhe, A.A., Cutler, N.A., Gallardo, A., García-Velázquez, L., Hart, S.C., Hayes, P.E., Hernández, T., Hseu, Z.-Y., Jehmlich, N., Kirchmair, M., Lambers, H., Neuhauser, S., Peña-Ramírez, V.M., Pérez, C.A., Reed, S.C., Santos, F.A.M., Siebe, C., Sullivan, B.W., Trivedi, P., Vera, A., Williams, M.A., Moreno, J.L., Delgado-Baquerizo, M. (2019):
  Global ecological predictors of the soil priming effect
  Nat. Commun. 10 , art. 3481 10.1038/s41467-019-11472-7
• Bastida, F., Jehmlich, N., Martínez-Navarro, J., Bayona, V., García, C., Moreno, J.L. (2019):
  The effects of struvite and sewage sludge on plant yield and the microbial community of a semiarid Mediterranean soil
  Geoderma 337 , 1051 - 1057 10.1016/j.geoderma.2018.10.046
• Bastida, F., López-Mondéjar, R., Baldrian, P., Andrés-Abellán, M., Jehmlich, N., Torres, I.F., García, C., López-Serrano, F.R. (2019):
  When drought meets forest management: Effects on the soil microbial community of a Holm oak forest ecosystem
  Sci. Total Environ. 662 , 276 - 286 10.1016/j.scitotenv.2019.01.233
• Bauer, M., Hackermüller, J., Schor, J., Schreiber, S., Fink, B., Pierzchalski, A., Herberth, G. (2019):
  Specific induction of the unique GPR15 expression in heterogeneous blood lymphocytes by tobacco smoking
  Biomarkers 24 (3), 217 - 224 10.1080/1354750X.2018.1539769
• Buettner, C., von Bergen, M., Jehmlich, N., Noll, M. (2019):
  Pseudomonas spp. are key players in agricultural biogas substrate degradation
  Sci. Rep. 9 , 12871 10.1038/s41598-019-49313-8
• Donath, A., Jühling, F., Al-Arab, M., Bernhart, S.H., Reinhardt, F., Stadler, P.F., Middendorf, M., Bernt, M. (2019):
  Improved annotation of protein-coding genes boundaries in metazoan mitochondrial genomes
  Nucleic Acids Res. 47 (20), 10543 - 10552 10.1093/nar/gkz833
• Drozdova, P., Bedulina, D., Madyarova, E., Rivarola-Duarte, L., Schreiber, S., Stadler, P.F., Luckenbach, T., Timofeyev, M. (2019):
  Description of strongly heat-inducible heat shock protein 70 transcripts from Baikal endemic amphipods
  Sci. Rep. 9 , art. 8907 10.1038/s41598-019-45193-0
• Drozdova, P., Rivarola-Duarte, L., Bedulina, D., Axenov-Gribanov, D., Schreiber, S., Gurkov, A., Shatilina, Z., Vereshchagina, K., Lubyaga, Y., Madyarova, E., Otto, C., Jühling, F., Busch, W., Jakob, L., Lucassen, M., Sartoris, F.J., Hackermüller, J., Hoffmann, S., Pörtner, H.-O., Luckenbach, T., Timofeyev, M., Stadler, P.F. (2019):
  Comparison between transcriptomic responses to short-term stress exposures of a common Holarctic and endemic Lake Baikal amphipods
  BMC Genomics 20 , art. 712 10.1186/s12864-019-6024-3
• Engel, K.M., Baumann, S., Rolle-Kampczyk, U., Schiller, J., von Bergen, M., Grunewald, S. (2019):
  Metabolomic profiling reveals correlations between spermiogram parameters and the metabolites present in human spermatozoa and seminal plasma
  PLOS One 14 (2), e0211679 10.1371/journal.pone.0211679
• Geiger, R.A., Junghare, M., Mergelsberg, M., Ebenau‐Jehle, C., Jesenofsky, V.J., Jehmlich, N., von Bergen, M., Schink, B., Boll, M. (2019):
  Enzymes involved in phthalate degradation in sulphate‐reducing bacteria
  Environ. Microbiol. 21 (10), 3601 - 3612 10.1111/1462-2920.14681
• Großkopf, H., Schubert, K., von Bergen, M. (2019):
  AhR-dependent non-genomic signaling in macrophages - A multi-PTM-omics and proteomics study
  Eur. J. Immunol. 49 (Suppl. 1), 137 10.1002/eji.201970300
• Haange, S.-B., Jehmlich, N., Hoffmann, M., Weber, K., Lehmann, J., von Bergen, M., Slanina, J. (2019):
  Disease development is accompanied by changes in bacterial protein abundance and functions in a refined model of dextran sulfate sodium (DSS)-induced colitis
  J. Proteome Res. 18 (4), 1774 - 1786 10.1021/acs.jproteome.8b00974
• Haange, S.-B., Jehmlich, N., Jacobi, T., von Bergen, M. (2019):
  Chancen und Risiken von Metaproteomik in der Mikrobiomforschung. Opportunities and pitfalls of metaproteomics in microbiome research
  Adipositas - Ursachen, Folgeerkrankungen, Therapie 13 (4), 205 - 213 10.1055/a-0966-9652
• Hartmann, T., Bernt, M., Middendorf, M. (2019):
  An exact algorithm for sorting by weighted preserving genome rearrangements
  IEEE-ACM Trans. Comput. Biol. Bioinform. 16 (1), 52 - 62 10.1109/TCBB.2018.2831661
• Huwiler, S.G., Löffler, C., Anselmann, S.E.L., Stärk, H.-J., von Bergen, M., Flechsler, J., Rachel, R., Boll, M. (2019):
  One-megadalton metalloenzyme complex in Geobacter metallireducens involved in benzene ring reduction beyond the biological redox window
  Proc. Natl. Acad. Sci. U.S.A. 116 (6), 2259 - 2264 10.1073/pnas.1819636116
• Kallies, R., Hölzer, M., Brizola Toscan, R., Nunes da Rocha, U., Anders, J., Marz, M., Chatzinotas, A. (2019):
  Evaluation of sequencing library preparation protocols for viral metagenomic analysis from pristine aquifer groundwaters
  Viruses 11 (6), art. 484 10.3390/v11060484
• Kallies, R., Kiesel, B., Schmidt, M., Ghanem, N., Zopfi, J., Hackermüller, J., Harms, H., Wick, L.Y., Chatzinotas, A. (2019):
  Complete genome sequence of Pseudoalteromonas virus vB_PspP-H6/1 that infects Pseudoalteromonas sp. strain H6
  Mar. Genom. 47 , art. 100667 10.1016/j.margen.2019.03.002
• Kämpf, C., Specht, M., Scholz, A., Puppel, S.-H., Doose, G., Reiche, K., Schor, J., Hackermüller, J. (2019):
  uap: reproducible and robust HTS data analysis
  BMC Bioinformatics 20 , art. 664 10.1186/s12859-019-3219-1
• Karkossa, I., Bannuscher, A., Hellack, B., Bahl, A., Buhs, S., Nollau, P., Luch, A., Schubert, K., von Bergen, M., Haase, A. (2019):
  An in-depth multi-omics analysis in RLE-6TN rat alveolar epithelial cells allows for nanomaterial categorization
  Part. Fibre Toxicol. 16 (1), art. 38 10.1186/s12989-019-0321-5
• Ke, X., Walker, A., Haange, S.-B., Lagkouvardos, I., Liu, Y., Schmitt-Kopplin, P., von Bergen, M., Jehmlich, N., He, X., Clavel, T., Cheung, P.C.K. (2019):
  Synbiotic-driven improvement of metabolic disturbances is associated with changes in the gut microbiome in diet-induced obese mice
  Mol. Metab. 22 , 96 - 109 10.1016/j.molmet.2019.01.012
• Kratochvil, I., Bannuscher, A., Hellack, B., von Bergen, M., Haase, A., Schubert, K. (2019):
  Nanomaterials affect oxidative phosphorylation and phagocytosis in alveolar macrophages
  Eur. J. Immunol. 49 (Suppl. 1), 232 10.1002/eji.201970300
• Kratochvil, I., Hofmann, T., Rother, S., Schlichting, R., Moretti, R., Scharnweber, D., Hintze, V., Escher, B.I., Meiler, J., Kalkhof, S., von Bergen, M. (2019):
  Mono(2‐ethylhexyl) phthalate (MEHP) and mono(2‐ethyl‐5‐oxohexyl) phthalate (MEOHP) but not di(2‐ethylhexyl) phthalate (DEHP) bind productively to the peroxisome proliferator‐activated receptor γ
  Rapid Commun. Mass Spectrom. 33 (S1), 75 - 85 10.1002/rcm.8258
• Küster, E., Kalkhof, S., Aulhorn, S., von Bergen, M., Gündel, U. (2019):
  Effects of five substances with different modes of action on cathepsin H, C and L activities in zebrafish embryos
  Int. J. Environ. Res. Public Health 16 (20), art. 3956 10.3390/ijerph16203956
• Li, Y., Kocot, K.M., Tassia, M.G., Cannon, J.T., Bernt, M., Halanych, K.M. (2019):
  Mitogenomics reveals a novel genetic code in Hemichordata
  Genome Biol. Evol. 11 (1), 29 - 40 10.1093/gbe/evy254
• Mandić, A.D., Woting, A., Jaenicke, T., Sander, A., Sabrowski, W., Rolle-Kampczyk, U., von Bergen, M., Blaut, M. (2019):
  Clostridium ramosum regulates enterochromaffin cell development and serotonin release
  Sci. Rep. 9 , art. 1177 10.1038/s41598-018-38018-z
• Medawar, E., Huhn, S., Villringer, A., Witte, A.-V. (2019):
  The effects of plant-based diets on the body and the brain: a systematic review
  Transl. Psychiatr. 9 (1), art. 226 10.1038/s41398-019-0552-0
• Mueller, A., Ulrich, N., Hollmann, J., Zapata Sanchez, C.E., Rolle-Kampczyk, U.E., von Bergen, M. (2019):
  Characterization of a multianalyte GC-MS/MS procedure for detecting and quantifying polycyclic aromatic hydrocarbons (PAHs) and PAH derivatives from air particulate matter for an improved risk assessment
  Environ. Pollut. 255 (Part 2), art. 112967 10.1016/j.envpol.2019.112967
• Ordiz, M.I., Semba, R.D., Moaddel, R., Rolle-Kampczyk, U., von Bergen, M., Herberth, G., Khadeer, M., Röder, S., Manary, M.J. (2019):
  Serum amino acid concentrations in infants from Malawi are associated with linear growth
  Curr. Dev. Nutr. 3 (10), nzz100 10.1093/cdn/nzz100
• Reina, R., Kellner, H., Hess, J., Jehmlich, N., García-Romera, I., Aranda, E., Hofrichter, M., Liers, C. (2019):
  Genome and secretome of Chondrostereum purpureum correspond to saprotrophic and phytopathogenic life styles
  PLOS One 14 (3), e0212769 10.1371/journal.pone.0212769
• Schäpe, S.S., Krause, J.L., Engelmann, B., Fritz-Wallace, K., Schattenberg, F., Liu, Z., Müller, S., Jehmlich, N., Rolle-Kampczyk, U., Herberth, G., von Bergen, M. (2019):
  The simplified human intestinal microbiota (SIHUMIx) shows high structural and functional resistance against changing transit times in in vitro bioreactors
  Microorganisms 7 (12), art. 641 10.3390/microorganisms7120641
• Schmidt, J.R., Geurtzen, K., von Bergen, M., Schubert, K., Knopf, F. (2019):
  Glucocorticoid treatment leads to aberrant ion and macromolecular transport in regenerating zebrafish fins
  Front. Endocrinol. 10 , art. 674 10.3389/fendo.2019.00674
• Schmidt, J.R., Vogel, S., Moeller, S., Kalkhof, S., Schubert, K., von Bergen, M., Hempel, U. (2019):
  Sulfated hyaluronic acid and dexamethasone possess a synergistic potential in the differentiation of osteoblasts from human bone marrow stromal cells
  J. Cell. Biochem. 120 (5), 8706 - 8722 10.1002/jcb.28158
• Schubert, K., Collins, L.E., Green, P., Nagase, H., Troeberg, L. (2019):
  LRP1 controls TNF release via the TIMP-3/ADAM17 axis in endotoxin-activated macrophages
  J. Immunol. 202 (4), 1501 - 1509 10.4049/jimmunol.1800834
• Schubert, K., Schor, J., Kratochvil, I., Hackermüller, J., von Bergen, M. (2019):
  Multi-omics profiling of MAIT cells reveals specific patterns of antigen-dependent and -independent activation
  Eur. J. Immunol. 49 (Suppl. 1), 141 10.1002/eji.201970300
• Schüttler, A., Altenburger, R., Ammar, M., Bader-Blukott, M., Jakobs, G., Knapp, J., Krüger, J., Reiche, K., Wu, G.-M., Busch, W. (2019):
  Map and model—moving from observation to prediction in toxicogenomics
  GigaScience 8 (6), giz057 10.1093/gigascience/giz057
• Starke, R., Jehmlich, N., Alfaro, T., Dohnalkova, A., Capek, P., Bell, S.L., Hofmockel, K.S. (2019):
  Incomplete cell disruption of resistant microbes
  Sci. Rep. 9 , art. 5618 10.1038/s41598-019-42188-9
• Starke, R., Jehmlich, N., Bastida, F. (2019):
  Using proteins to study how microbes contribute to soil ecosystem services: The current state and future perspectives of soil metaproteomics
  J. Proteomics 198 , 50 - 58 10.1016/j.jprot.2018.11.011
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  Communal metabolism by Methylococcaceae and Methylophilaceae is driving rapid aerobic methane oxidation in sediments of a shallow seep near Elba, Italy
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• Thürmann, L., Herberth, G., Rolle-Kampczyk, U., Röder, S., Borte, M., von Bergen, M., Lehmann, I., Trump, S. (2019):
  Elevated gestational IL-13 during fetal development is associated with hyperactivity and inattention in eight-year-old children
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  Expanding the use of spectral libraries in proteomics
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  Early-onset childhood atopic dermatitis is related to NLRP2 repression
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  Complete genome sequence of Pseudoalteromonas phage vB_PspS-H40/1 (formerly H40/1) that infects Pseudoalteromonas sp. strain H40 and is used as biological tracer in hydrological transport studies
  Stand. Genomic Sci. 12 , art. 20 10.1186/s40793-017-0235-5
• Kauffmann, H.-M., Kamp, H., Fuchs, R., Chorley, B.N., Deferme, L., Ebbels, T., Hackermüller, J., Perdichizzi, S., Poole, A., Sauer, U.G., Tollefsen, K.E., Tralau, T., Yauk, C., van Ravenzwaay, B. (2017):
  Framework for the quality assurance of ’omics technologies considering GLP requirements
  Regul. Toxicol. Pharmacol. 91 (Suppl. 1), S27 - S35 10.1016/j.yrtph.2017.10.007
• Kiebist, J., Schmidtke, K.-U., Zimmermann, J., Kellner, H., Jehmlich, N., Ullrich, R., Zänder, D., Hofrichter, M., Scheibner, K. (2017):
  A peroxygenase from Chaetomium globosum catalyzes the selective oxygenation of testosterone
  ChemBioChem 18 (6), 563 - 569 10.1002/cbic.201600677
• Morawe, M., Hoeke, H., Wissenbach, D.K., Lentendu, G., Wubet, T., Kröber, E., Kolb, S. (2017):
  Acidotolerant Bacteria and fungi as a sink of methanol-derived carbon in a deciduous forest soil
  Front. Microbiol. 8 , 1361 10.3389/fmicb.2017.01361
• Oberbach, A., Haange, S.-B., Schlichting, N., Heinrich, M., Lehmann, S., Till, H., Hugenholtz, F., Kullnick, Y., Smidt, H., Frank, K., Seifert, J., Jehmlich, N., von Bergen, M. (2017):
  Metabolic in vivo labeling highlights differences of metabolically active microbes from the mucosal gastrointestinal microbiome between high-fat and normal chow diet
  J. Proteome Res. 16 (4), 1593 - 1604 10.1021/acs.jproteome.6b00973
• Pinaud, L., Ferrari, M.L., Friedman, R., Jehmlich, N., von Bergen, M., Phalipon, A., Sansonetti, P.J., Campbell-Valois, F.-X. (2017):
  Identification of novel substrates of Shigella T3SA through analysis of its virulence plasmid-encoded secretome
  PLOS One 12 (10), e0186920 10.1371/journal.pone.0186920
• Potratz, S., Tarnow, P., Jungnickel, H., Baumann, S., von Bergen, M., Tralau, T., Luch, A. (2017):
  Combination of metabolomics with cellular assays reveals new biomarkers and mechanistic insights on xenoestrogenic exposures in MCF-7 cells
  Chem. Res. Toxicol. 30 (4), 883 - 892 10.1021/acs.chemrestox.6b00106
• Raulien, N., Friedrich, K., Strobel, S., Rubner, S., Baumann, S., von Bergen, M., Körner, A., Krueger, M., Rossol, M., Wagner, U. (2017):
  Fatty acid oxidation compensates for lipopolysaccharide-induced Warburg effect in glucose-deprived monocytes
  Front. Immunol. 8 , art. 609 10.3389/fimmu.2017.00609
• Rösch, C., Wissenbach, D.K., Franck, U., Wendisch, M., Schlink, U. (2017):
  Degradation of indoor limonene by outdoor ozone: A cascade of secondary organic aerosols
  Environ. Pollut. 226 , 463 - 472 10.1016/j.envpol.2017.04.030
• Sauer, U.G., Deferme, L., Gribaldo, L., Hackermüller, J., Tralau, T., van Ravenzwaay, B., Yauk, C., Poole, C., Tong, W., Gant, T.W. (2017):
  The challenge of the application of 'omics technologies in chemicals risk assessment: Background and outlook
  Regul. Toxicol. Pharmacol. 91 (Suppl. 1), S14 - S26 10.1016/j.yrtph.2017.09.020
• Schubert, K., Olde Damink, S.W.M., von Bergen, M., Schaap, F.G. (2017):
  Interactions between bile salts, gut microbiota, and hepatic innate immunity
  Immunol. Rev. 279 (1), 23 - 35 10.1111/imr.12579
• Schulze, T., Ahel, M., Ahlheim, J., Aït-Aïssa, S., Brion, F., Di Paolo, C., Froment, J., Hidasi, A.O., Hollender, J., Hollert, H., Hu, M., Kloß, A., Koprivica, S., Krauss, M., Muz, M., Oswald, P., Petre, M., Schollée, J.E., Seiler, T.-B., Shao, Y., Slobodnik, J., Sonavane, M., Suter, M.J.-F., Tollefsen, K.E., Tousova, Z., Walz, K.-H., Brack, W. (2017):
  Assessment of a novel device for onsite integrative large-volume solid phase extraction of water samples to enable a comprehensive chemical and effect-based analysis
  Sci. Total Environ. 581–582 , 350 - 358 10.1016/j.scitotenv.2016.12.140
• Schüttler, A., Reiche, K., Altenburger, R., Busch, W. (2017):
  The transcriptome of the zebrafish embryo after chemical exposure: a meta-analysis
  Toxicol. Sci. 157 (2), 291 - 304 10.1093/toxsci/kfx045
• Starke, R., Bastida, F., Abadía, J., García, C., Nicolás, E., Jehmlich, N. (2017):
  Ecological and functional adaptations to water management in a semiarid agroecosystem: a soil metaproteomics approach
  Sci. Rep. 7 , art. 10221 10.1038/s41598-017-09973-w
• Starke, R., Müller, M., Gaspar, M., Marz, M., Küsel, K., Totsche, K.U., von Bergen, M., Jehmlich, N. (2017):
  Candidate Brocadiales dominates C, N and S cycling in anoxic groundwater of a pristine limestone-fracture aquifer
  J. Proteomics 152 , 153 - 160 10.1016/j.jprot.2016.11.003
• Taubert, M., Grob, C., Howar, A.M., Burns, O.J., Pratscher, J., Jehmlich, N., von Bergen, M., Richnow, H.H., Chen, Y., Murrell, J.C. (2017):
  Methylamine as a nitrogen source for microorganisms from a coastal marine environment
  Environ. Microbiol. 19 (6), 2246 - 2257 10.1111/1462-2920.13709
• Tautenhahn, H.-M., Brückner, S., Uder, C., Erler, S., Hempel, M., von Bergen, M., Brach, J., Winkler, S., Pankow, F., Gittel, C., Baunack, M., Lange, U., Broschewitz, J., Dollinger, M., Bartels, M., Pietsch, U., Amann, K., Christ, B. (2017):
  Mesenchymal stem cells correct haemodynamic dysfunction associated with liver injury after extended resection in a pig model
  Sci. Rep. 7 , art. 2617 10.1038/s41598-017-02670-8
• Teumer, A., Qi, Q., Nethander, M., Aschard, H., Bandinelli, S., Beekman, M., Berndt, S.I., Bidlingmaier, M., Broer, L., Cappola, A., Ceda, G.P., Chanock, S., Chen, M.-H., Chen, T.C., Chen, Y.-D.I., Chung, J., Del Greco Miglianico, F., Eriksson, J., Ferrucci, L., Friedrich, N., Gnewuch, C., Goodarzi, M.O., Grarup, N., Guo, T., Hammer, E., Hayes, R.B., Hicks, A.A., Hofman, A., Houwing-Duistermaat, J.J., Hu, F., Hunter, D.J., Husemoen, L.L., Isaacs, A., Jacobs, K.B., Janssen, J.A.M.J.L., Jansson, J.-O., Jehmlich, N., Johnson, S., Juul, A., Karlsson, M., Kilpelainen, T.O., Kovacs, P., Kraft, P., Li, C., Linneberg, A., Liu, Y., Loos, R.J.F., Lorentzon, M., Lu, Y., Maggio, M., Magi, R., Meigs, J., Mellström, D., Nauck, M., Newman, A.B., Pollak, M.N., Pramstaller, P.P., Prokopenko, I., Psaty, B.M., Reincke, M., Rimm, R.B., Rotter, J.I., Saint Pierre, A., Schurmann, C., Seshadri, S., Sjögren, K., Slagboom, P.E., Strickler, H.D., Stumvoll, M., Suh, Y., Sun, Q., Zhang, C., Svensson, J., Tanaka, T., Tare, A., Tönjes, A., Uh, H.-W., van Duijn, C., van Heemst, D., Vandenput, L., Vasan, R.S., Völker, U., Willems, S.M., Ohlsson, C., Wallaschofski, H., Kaplan, R.C. (2017):
  Erratum: Genomewide meta-analysis identifies loci associated with IGF-I and IGFBP-3 levels with impact on age-related traits (vol 15, pg 811, 2016)
  Aging Cell 16 (4), 898 10.1111/acel.12612
• Tousova, Z., Oswald, P., Slobodnik, J., Blaha, L., Muz, M., Hu, M., Brack, W., Krauss, M., Di Paolo, C., Tarcai, Z., Seiler, T.-B., Hollert, H., Koprivica, S., Ahel, M., Schollée, J.E., Hollender, J., Suter, M.J.-F., Hidasi, A.O., Schirmer, K., Sonavane, M., Ait-Aissa, S., Creusot, N., Brion, F., Froment, J., Almeida, A.C., Thomas, K., Tollefsen, K.E., Tufi, S., Ouyang, X., Leonards, P., Lamoree, M., Torrens, V.O., Kolkman, A., Schriks, M., Spirhanzlova, P., Tindall, A., Schulze, T. (2017):
  European demonstration program on the effect-based and chemical identification and monitoring of organic pollutants in European surface waters
  Sci. Total Environ. 601-602 , 1849 - 1868 10.1016/j.scitotenv.2017.06.032
• Warnke, M., Jacoby, C., Jung, T., Agne, M., Mergelsberg, M., Starke, R., Jehmlich, N., von Bergen, M., Richnow, H.-H., Brüls, T., Boll, M. (2017):
  A patchwork pathway for oxygenase-independent degradation of side chain containing steroids
  Environ. Microbiol. 19 (11), 4684 - 4699 10.1111/1462-2920.13933
• Wewering, F., Jouy, F., Caliskan, S., Kalkhof, S., von Bergen, M., Luch, A., Zellmer, S. (2017):
  Hepatic co-cultures in vitro reveal suitable to detect Nrf2-mediated oxidative stress responses on the bladder carcinogen o-anisidine
  Toxicol. Vitro 40 , 153 - 160 10.1016/j.tiv.2017.01.006
• Wewering, F., Jouy, F., Wissenbach, D.K., Gebauer, S., Blüher, M., Gebhardt, R., Pirow, R., von Bergen, M., Kalkhof, S., Luch, A., Zellmer, K. (2017):
  Characterization of chemical-induced sterile inflammation in vitro: application of the model compound ketoconazole in a human hepatic co-culture system
  Arch. Toxicol. 91 (2), 799 - 810 10.1007/s00204-016-1686-y
• Winkler, S., Kalkhof, S., Brückner, S., Hempel, M., Baumann, S., von Bergen, M., Christ, B. (2017):
  Metabolic fingerprint of an immunodeficient NASH mouse model and impact after stem cell therapy
  J. Hepatol. 66 (1 (Suppl.)), S606 - S607 10.1016/S0168-8278(17)31648-3
• Winter, M., Thürmann, L., Gu, Z., Schüürmann, G., Herberth, G., Hinz, D., von Bergen, M., Harms, H., Olek, S., Röder, S., Borte, M., Eils, R., Lehmann, I., Trump, S. (2017):
  The benzene metabolite 1,4-benzoquinone reduces regulatory T-cell function: A potential mechanism for tobacco smoke–associated atopic dermatitis
  J. Allergy Clin. Immunol. 140 (2), 603 - 605 10.1016/j.jaci.2017.01.034
• Yazbeck, A.M., Tout, K.R., Stadler, P.F., Hertel, J. (2017):
  Towards a consistent, quantitative evaluation of microRNA evolution
  J. Integr. Bioinform. 14 (1) 10.1515/jib-2016-0013

2016 (60)

• Aigner, A., Buesen, R., Gant, C., Gooderham, N., Greim, H., Hackermüller, J., Hubesch, B., Laffont, M., Marczylo, E., Meister, G., Petrick, J.S., Rasoulpour, R.J., Sauer, U.G., Schmidt, K., Seitz, H., Slack, F., Sukata, T., van der Vies, S.M., Verhaert, J., Witwer, K.W., Poole, A. (2016):
  Advancing the use of noncoding RNA in regulatory toxicology: Report of an ECETOC workshop
  Regul. Toxicol. Pharmacol. 82 , 127 - 139 10.1016/j.yrtph.2016.09.018
• Aurich, S., Seitz, A.-T., Tomm, J., Simon, J.-C., Treudler, R. (2016):
  A case of anaphylaxis to patent blue in a patient with sentinel lymph node excision
  Iran. J. Allergy Asthma Immunol. 15 (6), 547 - 550
• Bastida, F., Jehmlich, N. (2016):
  It's all about functionality: How can metaproteomics help us to discuss the attributes of ecological relevance in soil?
  J. Proteomics 144 , 159 - 161 10.1016/j.jprot.2016.06.002
• Bastida, F., Jehmlich, N., Lima, K., Morris, B.E.L., Richnow, H.H., Hernández, T., von Bergen, M., García, C. (2016):
  The ecological and physiological responses of the microbial community from a semiarid soil to hydrocarbon contamination and its bioremediation using compost amendment
  J. Proteomics 135 , 162 - 169 10.1016/j.jprot.2015.07.023
• Bastida, F., Torres, I.F., Moreno, J.L., Baldrian, P., Ondoño, S., Ruiz-Navarro, A., Hernández, T., Richnow, H.H., Starke, R., García, C., Jehmlich, N. (2016):
  The active microbial diversity drives ecosystem multifunctionality and is physiologically related to carbon availability in Mediterranean semi-arid soils
  Mol. Ecol. 25 (18), 4660 - 4673 10.1111/mec.13783
• Bauer, T., Trump, S., Ishaque, N., Thürmann, L., Gu, L., Bauer, M., Bieg, M., Gu, Z., Weichenhan, D., Mallm, J.-P., Röder, S., Herberth, G., Takada, E., Mücke, O., Winter, M., Junge, K.M., Grützmann, K., Rolle-Kampczyk, U., Wang, Q., Lawerenz, C., Borte, M., Polte, T., Schlesner, M., Schanne, M., Wiemann, S., Geörg, C., Stunnenberg, H.G., Plass, C., Rippe, K., Mizuguchi, J., Herrmann, C., Eils, R., Lehmann, I. (2016):
  Environment-induced epigenetic reprogramming in genomic regulatory elements in smoking mothers and their children
  Mol. Syst. Biol. 12 (3), art. 861 10.15252/msb.20156520
• Bhattacharya, D.P., Canzler, S., Kehr, S., Hertel, J., Grosse, I., Stadler, P.F. (2016):
  Phylogenetic distribution of plant snoRNA families
  BMC Genomics 17 , art. 969 10.1186/s12864-016-3301-2
• Braasch, I., Gehrke, A.R., Smith, J.J., Kawasaki, K., Manousaki, T., Pasquier, J., Amores, A., Desvignes, T., Batzel, P., Catchen, J., Berlin, A.M., Campbell, M.S., Barrell, D., Martin, K.J., Mulley, J.F., Ravi, V., Lee, A.P., Nakamura, T., Chalopin, D., Fan, S., Wcisel, D., Cañestro, C., Sydes, J., Beaudry, F.E.G., Sun, Y., Hertel, J., Beam, M.J., Fasold, M., Ishiyama, M., Johnson, J., Kehr, S., Lara, M., Letaw, J.H., Litman, G.W., Litman, R.T., Mikami, M., Ota, T., Saha, N.R., Williams, L., Stadler, P.F., Wang, H., Taylor, J.S., Fontenot, Q., Ferrara, A., Searle, S.M.J., Aken, B., Yandell, M., Schneider, I., Yoder, J.A., Volff, J.-N., Meyer, A., Amemiya, C.T., Venkatesh, B., Holland, P.W.H., Guiguen, Y., Bobe, J., Shubin, N.H., Di Palma, F., Alföldi, J., Lindblad-Toh, K., Postlethwait, J.H. (2016):
  The spotted gar genome illuminates vertebrate evolution and facilitates human-teleost comparisons
  Nature Genet. 48 (4), 427 - 437 10.1038/ng.3526
• Canzler, S., Stadler, P.F., Hertel, J. (2016):
  U6 snRNA intron insertion occurred multiple times during fungi evolution
  RNA Biol. 13 (2), 119 - 127 10.1080/15476286.2015.1132139
• de Araujo Oliveira, J.V., Costa, F., Backofen, R., Stadler, P.F., Walter, M.E.M.T., Hertel, J. (2016):
  SnoReport 2.0: new features and a refined Support Vector Machine to improve snoRNA identification
  BMC Bioinformatics 17 (Suppl 18), art. 464 10.1186/s12859-016-1345-6
• Dey, P., Gola, D., Mishra, A., Malik, A., Kumar, P., Singh, D.K., Patel, N., von Bergen, M., Jehmlich, N. (2016):
  Comparative performance evaluation of multi-metal resistant fungal strains for simultaneous removal of multiple hazardous metals
  J. Hazard. Mater. 318 , 679 - 685 10.1016/j.jhazmat.2016.07.025
• Dietrich, S., Floegel, A., Troll, M., Kühn, T., Rathmann, W., Peters, A., Sookthai, D., von Bergen, M., Kaaks, R., Adamski, J., Prehn, C., Boeing, H., Schulze, M.B., Illig, T., Pischon, T., Knüppel, S., Wang-Sattler, R., Drogan, D. (2016):
  Random Survival Forest in practice: a method for modelling complex metabolomics data in time to event analysis
  Int. J. Epidemiol. 45 (5), 1406 - 1420 10.1093/ije/dyw145
• Dragelj, J.L., Stanković, I.M., Božinovski, D.M., Meyer, T., Veljković, D.Ž., Medaković, V.B., Knapp, E.W., Zarić, S.D. (2016):
  C–H/O interactions of aromatic CH donors within proteins: a crystallographic study
  Cryst. Growth Des. 16 (4), 1948 - 1957 10.1021/acs.cgd.5b01543
• Els-Heindl, S., Kostelnik, K.B., Klöting, N., Baumann, S., von Bergen, M., Beck-Sickinger, A.G. (2016):
  A palmitoylated ghrelin receptor ligand shows high metabolic invivo stability and bioavailability
  Neuropeptides 55 , 1 - 12 10.1016/j.npep.2015.11.031
• Fontenot, Q., Ferrara, A., Searle, S.M.J., Aken, B., Yandell, M., Schneider, I., Yoder, J.A., Volff, J.-N., Meyer, A., Amemiya, C.T., Venkatesh, B., Holland, P.W.H., Guiguen, Y., Bobe, J., Shubin, N.H., Di Palma, F., Alföldi, J., Lindblad-Toh, K., Postlethwait, J.H., Martin, K.J., Mulley, J.F., Ravi, V., Lee, A.P., Nakamura, T., Chalopin, D., Fan, S., Wcisel, D., Cañestro, C., Sydes, J., Beaudry, F.E.G., Sun, Y., Hertel, J., Beam, M.J., Fasold, M., Ishiyama, M., Johnson, J., Kehr, S., Lara, M., Letaw, J.H., Litman, G.W., Litman, R.T., Mikami, M., Ota, T., Saha, N.R., Williams, L., Stadler, P.F., Wang, H., Taylor, J.S., Braasch, I., Gehrke, A.R., Smith, J.J., Kawasaki, K., Manousaki, T., Pasquier, J., Amores, A., Desvignes, T., Batzel, P., Catchen, J., Berlin, A.M., Campbell, M.S., Barrell, D. (2016):
  Corrigendum: The spotted gar genome illuminates vertebrate evolution and facilitates human-teleost comparisons (vol 48, pg 427, 2016)
  Nature Genet. 48 (6), 700 - 700 10.1038/ng0616-700c
• Förster, Y., Schmidt, J.R., Wissenbach, D.K., Pfeiffer, S.E.M., Baumann, S., Hofbauer, L.C., von Bergen, M., Kalkhof, S., Rammelt, S. (2016):
  Microdialysis sampling from wound fluids enables quantitative assessment of cytokines, proteins, and metabolites reveals bone defect-specific molecular profiles
  PLOS One 11 (7), e0159580 10.1371/journal.pone.0159580
• Gjesing Welinder, K., Hansen, R., Toft Overgaard, M., Brohus, M., Sønderkær, M., von Bergen, M., Rolle-Kampczyk, U., Otto, W., Lindahl, T.L., Arinell, K., Evans, A.L., Swenson, J.E., Revsbech, I.G., Frøbert, O. (2016):
  Biochemical foundations of health and energy conservation in hibernating free-ranging subadult brown bear Ursus arctos
  J. Biol. Chem. 291 , 22509 - 22523 10.1074/jbc.M116.742916
• Goris, T., Schiffmann, C.L., Gadkari, J., Adrian, L., von Bergen, M., Diekert, G., Jehmlich, N. (2016):
  Proteomic data set of the organohalide-respiring Epsilonproteobacterium Sulfurospirillum multivorans adapted to tetrachloroethene and other energy substrates
  Data Brief 8 , 637 - 642 10.1016/j.dib.2016.06.022
• Haange, S.-B., Jehmlich, N. (2016):
  Proteomic interrogation of the gut microbiota: potential clinical impact
  Expert Rev. Proteomics 13 (6), 535 - 537 10.1080/14789450.2016.1190652
• Herbst, F.-A., Lünsmann, V., Kjeldal, H., Jehmlich, N., Tholey, A., von Bergen, M., Nielsen, J.L., Hettich, R.L., Seifert, J., Nielsen, P.H. (2016):
  Enhancing metaproteomics—The value of models and defined environmental microbial systems
  Proteomics 16 (5), 783 - 798 10.1002/pmic.201500305
• Hoeke, H., Roeder, S., Bertsche, T., Borte, M., von Bergen, M., Wissenbach, D.K. (2016):
  Assessment of maternal drug intake by urinary bio monitoring during pregnancy and postpartally until the third perinatal year
  Pharmacoepidemiol. Drug Saf. 25 (4), 431 - 437 10.1002/pds.3943
• Hoeke, H., Roeder, S., Mueller, A., Bertsche, T., Borte, M., Rolle-Kampczyk, U., von Bergen, M., Wissenbach, D.K. (2016):
  Biomonitoring of prenatal analgesic intake and correlation with infantile anti-aeroallergens IgE
  Allergy 71 (6), 901 - 906 10.1111/all.12897
• Hörnig, F., Kohajda, T., Röder, S., Herberth, G., von Bergen, M., Borte, M., Diez, U., Rolle-Kampczyk, U., Simon, J.-C., Denburg, J.A., Lehmann, I., Junge, K.M. (2016):
  The LINA study: higher sensitivity of infant compared to maternal eosinophil/basophil progenitors to indoor chemical exposures
  J. Environ. Public Health 2016 , art. 5293932 10.1155/2016/5293932
• Huber, K., Dänicke, S., Rehage, J., Sauerwein, H., Otto, W., Rolle-Kampczyk, U., von Bergen, M. (2016):
  Metabotypes with properly functioning mitochondria and antiinflammation predict extended productive life span in dairy cows
  Sci. Rep. 6 , art. 24642 10.1038/srep24642
• Jehmlich, N., Vogt, C., Lünsmann, V., Richnow, H.H., von Bergen, M. (2016):
  Protein-SIP in environmental studies
  Curr. Opin. Biotechnol. 41 , 26 - 33 10.1016/j.copbio.2016.04.010
• Kalkhof, S., Schildbach, S., Blumert, C., Horn, F., von Bergen, M., Labudde, D. (2016):
  PIPINO: a software package to facilitate the identification of protein-protein interactions from affinity purification mass spectrometry data
  Biomed Res. Int. 2016 , art. 2891918 10.1155/2016/2891918
• Kenéz, Á., Dänicke, S., Rolle-Kampczyk, U., von Bergen, M., Huber, K. (2016):
  A metabolomics approach to characterize phenotypes of metabolic transition from late pregnancy to early lactation in dairy cows
  Metabolomics 12 (11), art. 165 10.1007/s11306-016-1112-8
• Kjeldal, H., Zhou, N.A., Wissenbach, D.K., von Bergen, M., Gough, H.L., Nielsen, J.L. (2016):
  Genomic, proteomic, and metabolite characterization of gemfibrozil-degrading organism Bacillus sp. GeD10
  Environ. Sci. Technol. 50 (2), 744 - 755 10.1021/acs.est.5b05003
• Kublik, A., Deobald, D., Hartwig, S., Schiffmann, C.L., Andrades, A., von Bergen, M., Sawers, R.G., Adrian, L. (2016):
  Identification of a multi-protein reductive dehalogenase complex in Dehalococcoides mccartyi strain CBDB1 suggests a protein-dependent respiratory electron transport chain obviating quinone involvement
  Environ. Microbiol. 18 (9), 3044 - 3056 10.1111/1462-2920.13200
• Kühn, T., Floegel, A., Sookthai, D., Johnson, T., Rolle-Kampczyk, U., Otto, W., von Bergen, M., Boeing, H., Kaaks, R. (2016):
  Higher plasma levels of lysophosphatidylcholine 18:0 are related to a lower risk of common cancers in a prospective metabolomics study
  BMC Med. 14 , art. 13 10.1186/s12916-016-0552-3
• Kühn, T., Sookthai, D., Rolle-Kampczyk, U., Otto, W., Otto, W., von Bergen, M., Kaaks, R., Johnson, T. (2016):
  Mid- and long-term correlations of plasma metabolite concentrations measured by a targeted metabolomics approach
  Metabolomics 12 (12), art. 184 10.1007/s11306-016-1133-3
• Lünsmann, V., Kappelmeyer, U., Benndorf, R., Martínez-Lavanchy, P.M., Taubert, A., Adrian, L., Duarte, M., Pieper, D.H., von Bergen, M., Müller, J.A., Heipieper, H.J., Jehmlich, N. (2016):
  In situ protein-SIP highlights Burkholderiaceae as key players degrading toluene by para ring hydroxylation in a constructed wetland model
  Environ. Microbiol. 18 (4), 1176 - 1186 10.1111/1462-2920.13133
• Lünsmann, V., Kappelmeyer, U., Taubert, A., Nijenhuis, I., von Bergen, M., Heipieper, H.J., Müller, J.A., Jehmlich, N. (2016):
  Aerobic toluene degraders in the rhizosphere of a constructed wetland model show diurnal polyhydroxyalkanoate metabolism
  Appl. Environ. Microb. 82 (14), 4126 - 4132 10.1128/AEM.00493-16
• Mahnke, H., Ballent, M., Baumann, S., Imperiale, F., von Bergen, M., Lanusse, C., Lifschitz, A.L., Honscha, W., Halwachs, S. (2016):
  The ABCG2 efflux transporter in the mammary gland mediates veterinary drug secretion across the blood-milk barrier into milk of dairy cows
  Drug Metab. Dispos. 44 (5), 700 - 708 10.1124/dmd.115.068940
• Malik, A.A., Chowdhury, S., Schlager, V., Oliver, A., Puissant, J., Vazquez, P.G.M., Jehmlich, N., von Bergen, M., Griffiths, R.I., Gleixner, G. (2016):
  Soil fungal:bacterial ratios are linked to altered carbon cycling
  Front. Microbiol. 7 , art. 1247 10.3389/fmicb.2016.01247
• Men, Y., Han, P., Helbling, D.E., Jehmlich, N., Herbold, C., Gulde, R., Onnis-Hayden, A., Gu, A.Z., Johnson, D.R., Wagner, M., Fenner, K. (2016):
  Biotransformation of two pharmaceuticals by the ammonia-oxidizing archaeon Nitrososphaera gargensis
  Environ. Sci. Technol. 50 (9), 4682 - 4692 10.1021/acs.est.5b06016
• Mussotter, F., Tomm, J.M., El Ali, Z., Pallardy, M., Kerdine-Römer, S., Götz, M., von Bergen, M., Haase, A., Luch, A. (2016):
  Proteomics analysis of dendritic cell activation by contact allergens reveals possible biomarkers regulated by Nrf2
  Toxicol. Appl. Pharmacol. 313 , 170 - 179 10.1016/j.taap.2016.11.001
• Oberbach, A., Adams, V., Schlichting, N., Heinrich, M., Kullnick, Y., Lehmann, S., Feder, S., Correia, J.C., Mohr, F.-W., Völker, U., Jehmlich, N. (2016):
  Proteome profiles of HDL particles of patients with chronic heart failure are associated with immune response and also include bacteria proteins
  Clin. Chim. Acta 453 , 114 - 122 10.1016/j.cca.2015.12.005
• Pham, H.T., Arnhard, K., Asad, Y.J., Deng, L., Felder, T.K., St. John-Williams, L., Kaever, V., Leadley, M., Mitro, N., Muccio, S., Prehn, C., Rauh, M., Rolle-Kampczyk, U., Thompson, J.W., Uhl, O., Ulaszewska, M., Vogeser, M., Wishart, D.S., Koal, T. (2016):
  Inter-laboratory robustness of next-generation bile acid study in mice and humans: international ring trial involving 12 laboratories
  J. Appl. Lab. Med. 1 (2), 129 - 142 10.1373/jalm.2016.020537
• Rabus, R., Boll, M., Heider, J., Meckenstock, R.U., Buckel, W., Einsle, O., Ermler, U., Golding, B.T., Gunsalus, R.P., Kroneck, P.M.H., Krüger, M., Lueders, T., Martins, B.M., Musat, F., Richnow, H.H., Schink, B., Seifert, J., Szaleniec, M., Treude, T., Ullmann, G.M., Vogt, C., von Bergen, M., Wilkes, H. (2016):
  Anaerobic microbial degradation of hydrocarbons: from enzymatic reactions to the environment
  J. Mol. Microbiol. Biotechnol. 26 (1-3), 5 - 28 10.1159/000443997
• Rolle-Kampczyk, U.E., Krumsiek, J., Otto, W., Röder, S.W., Kohajda, T., Borte, M., Theis, F., Lehmann, I., von Bergen, M. (2016):
  Metabolomics reveals effects of maternal smoking on endogenous metabolites from lipid metabolism in cord blood of newborns
  Metabolomics 12 (4), art. 76 10.1007/s11306-016-0983-z
• Rother, S., Samsonov, S.A., Hofmann, T., Blaszkiewicz, J., Köhling, S., Moeller, S., Schnabelrauch, M., Rademann, J., Kalkhof, S., von Bergen, M., Pisabarro, M.T., Scharnweber, D., Hintze, V. (2016):
  Structural and functional insights into the interaction of sulfated glycosaminoglycans with tissue inhibitor of metalloproteinase-3 – A possible regulatory role on extracellular matrix homeostasis
  Acta Biomater. 45 , 143 - 154 10.1016/j.actbio.2016.08.030
• Schaarschmidt, J., Nagel, M.B.M., Huth, S., Jaeschke, H., Moretti, R., Hintze, V., von Bergen, M., Kalkhof, S., Meiler, J., Paschke, R. (2016):
  Rearrangement of the extracellular domain/extracellular loop 1 interface is critical for thyrotropin receptor activation
  J. Biol. Chem. 291 , 14095 - 14108 10.1074/jbc.M115.709659
• Schaubeck, M., Clavel, T., Calasan, J., Lagkouvardos, I., Haange, S.B., Jehmlich, N., Basic, M., Dupont, A., Hornef, M., von Bergen, M., Bleich, A., Haller, D. (2016):
  Dysbiotic gut microbiota causes transmissible Crohn's disease-like ileitis independent of failure in antimicrobial defence
  Gut 65 , 225 - 237 10.1136/gutjnl-2015-309333
• Schiffmann, C.L., Otto, W., Hansen, R., Nielsen, P.H., Adrian, L., Seifert, J., von Bergen, M., Jehmlich, N. (2016):
  Proteomic dataset of the organohalide-respiring bacterium Dehalococcoides mccartyi strain CBDB1 grown on hexachlorobenzene as electron acceptor
  Data Brief 7 , 253 - 256 10.1016/j.dib.2016.02.037
• Schmidt, J.R., Kliemt, S., Preissler, C., Moeller, S., von Bergen, M., Hempel, U., Kalkhof, S. (2016):
  Osteoblast-released matrix vesicles, regulation of activity and composition by sulfated and non-sulfated glycosaminoglycans
  Mol. Cell. Proteomics 15 , 558 - 572 10.1074/mcp.M115.049718
• Schütze, N., Trojandt, S., Kuhn, S., Tomm, J.M., von Bergen, M., Simon, J.C., Polte, T. (2016):
  Allergen-induced IL-6 regulates IL-9/IL-17A balance in CD4⁺ T cells in allergic airway inflammation
  J. Immunol. 197 (7), 2653 - 2664 10.4049/jimmunol.1501599
• Starke, R., Keller, A., Jehmlich, N., Vogt, C., Richnow, H.H., Kleinsteuber, S., von Bergen, M., Seifert, J. (2016):
  Pulsed ¹³C₂-acetate protein-SIP unveils Epsilonproteobacteria as dominant acetate utilizers in a sulfate-reducing microbial community mineralizing benzene
  Microb. Ecol. 71 (4), 901 - 911 10.1007/s00248-016-0731-y
• Starke, R., Kermer, R., Ullmann-Zeunert, L., Baldwin, I.T., Seifert, J., Bastida, F., von Bergen, M., Jehmlich, N. (2016):
  Bacteria dominate the short-term assimilation of plant-derived N in soil
  Soil Biol. Biochem. 96 , 30 - 38 10.1016/j.soilbio.2016.01.009
• Tautenhahn, H.-M., Brückner, S., Baumann, S., Winkler, S., Otto, W., von Bergen, M., Bartels, M., Christ, B. (2016):
  Attenuation of postoperative acute liver failure by mesenchymal stem cell treatment due to metabolic implications
  Ann. Surg. 263 (3), 546 - 556 10.1097/SLA.0000000000001155
• Teumer, A., Qi, Q., Nethander, M., Aschard, H., Bandinelli, S., Beekman, M., Berndt, S.I., Bidlingmaier, M., Broer, L., Cappola, A., Ceda, G.P., Chanock, S., Chen, M.-H., Chen, T.C., Chen, Y.-D.I., Chung, J., Del Greco Miglianico, F., Eriksson, J., Ferrucci, L., Friedrich, N., Gnewuch, C., Goodarzi, M.O., Grarup, N., Guo, T., Hammer, E., Hayes, R.B., Hicks, A.A., Hofman, A., Houwing-Duistermaat, J.J., Hu, F., Hunter, D.J., Husemoen, L.L., Isaacs, A., Jacobs, K.B., Janssen, J.A.M.J.L., Jansson, J.-O., Jehmlich, N., Johnson, S., Juul, A., Karlsson, M., Kilpelainen, T.O., Kovacs, P., Kraft, P., Li, C., Linneberg, A., Liu, Y., Loos, R.J.F., Lorentzon, M., Lu, Y., Maggio, M., Magi, R., Meigs, J., Mellström, D., Nauck, M., Newman, A.B., Pollak, M.N., Pramstaller, P.P., Prokopenko, I., Psaty, B.M., Reincke, M., Rimm, R.B., Rotter, J.I., Saint Pierre, A., Schurmann, C., Seshadri, S., Sjögren, K., Slagboom, P.E., Strickler, H.D., Stumvoll, M., Suh, Y., Sun, Q., Zhang, C., Svensson, J., Tanaka, T., Tare, A., Tönjes, A., Uh, H.-W., van Duijn, C., van Heemst, D., Vandenput, L., Vasan, R.S., Völker, U., Willems, S.M., Ohlsson, C., Wallaschofski, H., Kaplan, R.C. (2016):
  Genomewide meta‐analysis identifies loci associated with IGF‐I and IGFBP‐3 levels with impact on age‐related traits
  Aging Cell 15 (5), 811 - 824 10.1111/acel.12490
• Tiedt, O., Mergelsberg, M., Boll, K., Müller, M., Adrian, L., Jehmlich, N., von Bergen, M., Boll, M. (2016):
  ATP-dependent C–F bond cleavage allows the complete degradation of 4-fluoroaromatics without oxygen
  mBio 7 (4), e00990-16 10.1128/mBio.00990-16
• Trump, S., Bieg, M., Gu, Z., Thürmann, L., Bauer, T., Bauer, M., Ishaque, N., Röder, S., Gu, L., Herberth, G., Lawerenz, C., Borte, M., Schlesner, M., Plass, C., Diessl, N., Eszlinger, M., Mücke, O., Elvers, H.-D., Wissenbach, D.K., von Bergen, M., Herrmann, C., Weichenhan, D., Wright, R.J., Lehmann, I., Eils, R. (2016):
  Prenatal maternal stress and wheeze in children: novel insights into epigenetic regulation
  Sci. Rep. 6 , art. 28616 10.1038/srep28616
• Vogt, C., Lueders, T., Richnow, H.H., Krüger, M., von Bergen, M., Seifert, J. (2016):
  Stable isotope probing approaches to study anaerobic hydrocarbon degradation and degraders
  J. Mol. Microbiol. Biotechnol. 26 (1-3), 195 - 210 10.1159/000440806
• Vorreiter, F., Richter, S., Peter, M., Baumann, S., von Bergen, M., Tomm, J.M. (2016):
  Comparison and optimization of methods for the simultaneous extraction of DNA, RNA, proteins, and metabolites
  Anal. Biochem. 508 , 25 - 33 10.1016/j.ab.2016.05.011
• Warnke, M., Jung, T., Dermer, J., Hipp, K., Jehmlich, N., von Bergen, M., Ferlaino, S., Fries, A., Müller, M., Boll, M. (2016):
  25-hydroxyvitamin D₃ synthesis by enzymatic steroid side-chain hydroxylation with water
  Angew. Chem.-Int. Edit. 55 (5), 1881 - 1884 10.1002/anie.201510331
• Winkler, S., Kalkhof, S., Brückner, S., Hempel, M., Baumann, S., von Bergen, M., Christ, B. (2016):
  Identification of molecular pathways for stem cell therapy of non-alcoholic steatohepatitis in an immunodeficient mouse model
  J. Hepatol. 64 (2 (Suppl.)), S683 10.1016/S0168-8278(16)01297-6
• Wissenbach, D.K., Oliphant, K., Rolle-Kampczyk, U., Yen, S., Höke, H., Baumann, S., Haange, S.B., Verdu, E.F., Allen-Vercoe, E., von Bergen, M. (2016):
  Optimization of metabolomics of defined in vitro gut microbial ecosystems
  Int. J. Med. Microbiol. 306 (5), 280 - 289 10.1016/j.ijmm.2016.03.007
• Wissenbach, D.K., Winkler, B., Otto, W., Kohajda, T., Roeder, S., Müller, A., Hoeke, H., Matysik, S., Schlink, U., Borte, M., Herbarth, O., Lehmann, I., von Bergen, M. (2016):
  Long-term indoor VOC concentrations assessment a trend analysis of distribution, disposition, and personal exposure in cohort study samples
  Air Qual. Atmos. Health 9 (8), 941 - 950 10.1007/s11869-016-0396-1
• Wohlleben, W., Driessen, M.D., Raesch, S., Schaefer, U.F., Schulze, C., von Vacano, B., Vennemann, A., Wiemann, M., Ruge, C.A., Platsch, H., Mues, S., Ossig, R., Tomm, J.M., Schnekenburger, J., Kuhlbusch, T.A.J., Luch, A., Lehr, C.-M., Haase, A. (2016):
  Influence of agglomeration and specific lung lining lipid/protein interaction on short-term inhalation toxicity
  Nanotoxicology 10 (7), 970 - 980 10.3109/17435390.2016.1155671

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• Ahrens, V.M., Kostelnik, K.B., Rennert, R., Böhme, D., Kalkhof, S., Kosel, D., Weber, L., von Bergen, M., Beck-Sickinger, A.G. (2015):
  A cleavable cytolysin–neuropeptide Y bioconjugate enables specific drug delivery and demonstrates intracellular mode of action
  J. Control. Release 209 , 170 - 178 10.1016/j.jconrel.2015.04.037
• Bargiela, R., Herbst, F.-A., Martínez-Martínez, M., Seifert, J., Rojo, D., Cappello, S., Genovese, M., Crisafi, F., Denaro, R., Chernikova, T.N., Barbas, C., von Bergen, M., Yakimov, M.M., Ferrer, M., Golyshin, P.N. (2015):
  Metaproteomics and metabolomics analyses of chronically petroleum-polluted sites reveal the importance of general anaerobic processes uncoupled with degradation
  Proteomics 15 (20), 3508 - 3520 10.1002/pmic.201400614
• Bastida, F., García, C., von Bergen, M., Moreno, J.L., Richnow, H.H., Jehmlich, N. (2015):
  Deforestation fosters bacterial diversity and the cyanobacterial community responsible for carbon fixation processes under semiarid climate: a metaproteomics study
  Appl. Soil Ecol. 93 , 65 - 67 10.1016/j.apsoil.2015.04.006
• Beyer, A., Baumann, S., Scherz, G., Stahl, J., von Bergen, M., Friese, A., Roesler, U., Kietzmann, M., Honscha, W. (2015):
  Effects of ceftiofur treatment on the susceptibility of commensal porcine E.coli – comparison between treated and untreated animals housed in the same stable
  BMC Vet. Res. 11 , art. 265 10.1186/s12917-015-0578-3
• Brückner, S., Tautenhahn, H.-M., Baumann, S., Winkler, S., Bartels, M., von Bergen, M., Christ, B. (2015):
  Mesenchymal stem cells (MSC) prevent liver failure after huge liver resection in rat
  Transplantation 99 (7S), 267 10.1097/01.tp.0000469973.81769.3c
• Daims, H., Lebedeva, E.V., Pjevac, P., Han, P., Herbold, C., Albertsen, M., Jehmlich, N., Palatinszky, M., Vierheilig, J., Bulaev, A., Kirkegaard, R.H., von Bergen, M., Rattei, T., Bendinger, B., Nielsen, P.H., Wagner, M. (2015):
  Complete nitrification by Nitrospira bacteria
  Nature 528 (7583), 504 - 509 10.1038/nature16461
• Goris, T., Schiffmann, C.L., Gadkari, J., Schubert, T., Seifert, J., Jehmlich, N., von Bergen, M., Diekert, G. (2015):
  Proteomics of the organohalide-respiring Epsilonproteobacterium Sulfurospirillum multivorans adapted to tetrachloroethene and other energy substrates
  Sci. Rep. 5 , art. 13794 10.1038/srep13794
• Grob, C., Taubert, M., Howat, A.M., Burns, O.J., Dixon, J.L., Richnow, H.H., Jehmlich, N., von Bergen, M., Chen, Y., Murrell, J.C. (2015):
  Combining metagenomics with metaproteomics and stable isotope probing reveals metabolic pathways used by a naturally occurring marine methylotroph
  Environ. Microbiol. 17 (10), 4007 - 4018 10.1111/1462-2920.12935
• Halwachs, S., Mahnke, H., Ballent, M., Baumann, S., von Bergen, M., Viviani, P., Lanusse, C., Honscha, W., Lifschitz, A. (2015):
  ABCG2-mediated transport of anthelmintic drugs in the mammary gland of dairy cows
  J. Vet. Pharmacol. Ther. 38 (S1), 43 - 44 10.1111/jvp.12246
• Hartwig, S., Thomas, C., Krumova, N., Quitzke, V., Türkowsky, D., Jehmlich, N., Adrian, L., Sawers, R.G. (2015):
  Heterologous complementation studies in Escherichia coli with the Hyp accessory protein machinery from Chloroflexi provide insight into [NiFe]-hydrogenase large subunit recognition by the HypC protein family
  Microbiology-(UK) 161 (11), 2204 - 2219 10.1099/mic.0.000177
• Herberth, G., Offenberg, K., Rolle-Kampczyk, U., Bauer, M., Otto, W., Röder, S., Grützmann, K., Sack, E., Simon, J.-C., Borte, M., von Bergen, M., Lehmann, I. (2015):
  Endogenous metabolites and inflammasome activity in early childhood and links to respiratory diseases
  J. Allergy Clin. Immunol. 136 (2), 495 - 497 10.1016/j.jaci.2015.01.022
• Hoeke, H., Roeder, S., Bertsche, T., Lehmann, I., Borte, M., von Bergen, M., Wissenbach, D.K. (2015):
  Monitoring of drug intake during pregnancy by questionnaires and LC-MS/MS drug urine screening: evaluation of both monitoring methods
  Drug Test. Anal. 7 (8), 695 - 702 10.1002/dta.1767
• Hofmann, T., Fischer, A.W., Meiler, J., Kalkhof, S. (2015):
  Protein structure prediction guided by crosslinking restraints – A systematic evaluation of the impact of the crosslinking spacer length
  Methods 89 , 79 - 90 10.1016/j.ymeth.2015.05.014
• Hofmann, T., Samsonov, S.A., Pichert, A., Lemmnitzer, K., Schiller, J., Huster, D., Pisabarro, M.T., von Bergen, M., Kalkhof, S. (2015):
  Structural analysis of the interleukin-8/glycosaminoglycan interactions by amide hydrogen/deuterium exchange mass spectrometry
  Methods 89 , 45 - 53 10.1016/j.ymeth.2015.02.011
• Hoth, N., Gniese, C., Rakoczy, J., Weber, A., Kümmel, S., Reichel, S., Freese, C., Hache, M., Kassahun, A., Schulz, A., Fischer, H., Mühling, M., Starke, R., Kahnt, R., Vogt, C., Richnow, H.-H., Krüger, M., Schippers, A., Schlömann, M. (2015):
  CO₂BioPerm — influence of bio-geochemical CO₂-transformation processes on the long-term permeability
  In: Liebscher, A., Münch, U. (eds.)
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  Advanced Technologies in Earth Sciences
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• Jouy, F., Müller, S.A., Wagner, J., Otto, W., von Bergen, M., Tomm, J.M. (2015):
  Integration of conventional quantitative and phospho-proteomics reveals new elements in activated Jurkat T-cell receptor pathway maintenance
  Proteomics 15 (1), 25 - 33 10.1002/pmic.201400119
• Kalkhof, S., Dautel, F., Loguercio, S., Baumann, S., Trump, S., Jungnickel, H., Otto, W., Rudzok, S., Potratz, S., Luch, A., Lehmann, I., Beyer, A., von Bergen, M. (2015):
  Pathway and time-resolved benzo[a]pyrene toxicity on Hepa1c1c7 cells at toxic and subtoxic exposure
  J. Proteome Res. 14 (1), 164 - 182 10.1021/pr500957t
• Keller, A.H., Schleinitz, K.M., Starke, R., Bertilsson, S., Vogt, C., Kleinsteuber, S. (2015):
  Metagenome-based metabolic reconstruction revealsthe ecophysiological function of Epsilonproteobacteria in a hydrocarbon-contaminated sulfidic aquifer
  Front. Microbiol. 6 , art. 1396 10.3389/fmicb.2015.01396
• Kirsten, H., Al-Hasani, H., Holdt, L., Gross, A., Beutner, F., Krohn, K., Ahnert, P., Burkhardt, R., Reiche, K., Hackermüller, J., Löffler, M., Teupser, D., Thiery, J., Scholz, M. (2015):
  Dissecting the genetics of the human transcriptome identifies novel trait-related trans-eQTLs and corroborates the regulatory relevance of non-protein coding loci
  Hum. Mol. Genet. 24 (16), 4746 - 4763 10.1093/hmg/ddv194
• Klöting, N., Hesselbarth, N., Gericke, M., Kunath, A., Biemann, R., Chakaroun, R., Kosacka, J., Kovacs, P., Kern, M., Stumvoll, M., Fischer, B., Rolle-Kampczyk, U., Feltens, R., Otto, W., Wissenbach, D.K., von Bergen, M., Blüher, M. (2015):
  Di-(2-ethylhexyl)-phthalate (DEHP) causes impaired adipocyte function and alters serum metabolites
  PLOS One 10 (12), e0143190 10.1371/journal.pone.0143190
• Kostelnik, K.B., Els-Heindl, S., Klöting, N., Baumann, S., von Bergen, M., Beck-Sickinger, A.G. (2015):
  High metabolic in vivo stability and bioavailability of a palmitoylated ghrelin receptor ligand assessed by mass spectrometry
  Bioorg. Med. Chem. 23 (14), 3925 - 3932 10.1016/j.bmc.2014.12.008
• Kümmel, S., Herbst, F.-A., Bahr, A., Duarte, M., Pieper, D.H., Jehmlich, N., Seifert, J., von Bergen, M., Bombach, P., Richnow, H.H., Vogt, C. (2015):
  Anaerobic naphthalene degradation by sulfate-reducing Desulfobacteraceae from various anoxic aquifers
  FEMS Microbiol. Ecol. 91 (3), fiv006 10.1093/femsec/fiv006
• Kurteva-Yaneva, N., Zahn, M., Weichler, M.-T., Starke, R., Harms, H., Müller, R.H., Sträter, N., Rohwerder, T. (2015):
  Structural basis of the stereospecificity of bacterial B₁₂-dependent 2-hydroxyisobutyryl-CoA mutase
  J. Biol. Chem. 290 , 9727 - 9737 10.1074/jbc.M115.645689
• Linton, S.M., Cameron, M.S., Gray, M.C., Donald, J.A., Saborowski, R., von Bergen, M., Tomm, J.M., Allardyce, B.J. (2015):
  A glycosyl hydrolase family 16 gene is responsible for the endogenous production of β-1,3-glucanases within decapod crustaceans
  Gene 569 (2), 203 - 217 10.1016/j.gene.2015.05.056
• Martínez-Lavanchy, P.M., Chen, Z., Lünsmann, V., Marin-Cevada, V., Vilchez-Vargas, R., Pieper, D.H., Reiche, N., Kappelmeyer, U., Imparato, V., Junca, H., Nijenhuis, I., Müller, J.A., Kuschk, P., Heipieper, H.J. (2015):
  Microbial toluene removal in hypoxic model constructed wetlands occurs predominantly via the ring monooxygenation pathway
  Appl. Environ. Microb. 81 (18), 6241 - 6252 10.1128/AEM.01822-15
• Müller, A. (2015):
  Gesundheitsrisiko Schimmelpilze
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• Müller, S.A., Pernitzsch, S.R., Haange, S.-B., Uetz, P., von Bergen, M., Sharma, C.M., Kalkhof, S. (2015):
  Stable isotope labeling by amino acids in cell culture based proteomics reveals differences in protein abundances between spiral and coccoid forms of the gastric pathogen Helicobacter pylori
  J. Proteomics 126 , 34 - 45 10.1016/j.jprot.2015.05.011
• Nitsche, A., Rose, D., Fasold, M., Reiche, K., Stadler, P.F. (2015):
  Comparison of splice sites reveals that long noncoding RNAs are evolutionarily well conserved
  RNA 21 (5), 801 - 812 10.1261/rna.046342.114
• Pagani, M., Rockstroh, M., Schuster, M., Rossetti, G., Moro, M., Crosti, M., Tomm, J.M. (2015):
  Reference proteome of highly purified human Th1 cells reveals strong effects on metabolism and protein ubiquitination upon differentiation
  Proteomics 15 (21), 3644 - 3647 10.1002/pmic.201400139
• Palatinszky, M., Herbold, C., Jehmlich, N., Pogoda, M., Han, P., von Bergen, M., Lagkouvardos, I., Karst, S.M., Galushko, A., Koch, H., Berry, D., Daims, H., Wagner, M. (2015):
  Cyanate as an energy source for nitrifiers
  Nature 524 (7563), 105 - 108 10.1038/nature14856
• Pöritz, M., Schiffmann, C.L., Hause, G., Heinemann, U., Seifert, J., Jehmlich, N., von Bergen, M., Nijenhuis, I., Lechner, U. (2015):
  Dehalococcoides mccartyi strain DCMB5 respires a broad spectrum of chlorinated aromatic compounds
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• Remane, D., Grunwald, S., Hoeke, H., Mueller, A., Roeder, S., von Bergen, M., Wissenbach, D.K. (2015):
  Validation of a multi-analyte HPLC-DAD method for determination of uric acid, creatinine, homovanillic acid, niacinamide, hippuric acid, indole-3-acetic acid and 2-methylhippuric acid in human urine
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• Sachsenberg, T., Herbst, F.-A., Taubert, M., Kermer, R., Jehmlich, N., von Bergen, M., Seifert, J., Kohlbacher, O. (2015):
  MetaProSIP: Automated inference of stable isotope incorporation rates in proteins for functional metaproteomics
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• Schaubeck, M., Clavel, T., Lagkouvardos, M., Calasan, J., Haange, S.B., Jehmlich, N., von Bergen, M., Basic, M., Bleich, A., Haller, D. (2015):
  Transmissive Crohn's disease-like ileitis is caused by functional dysbiosis in the intestinal microbiota independent of inflammation-driven Paneth cell failure
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• Scherz, G., Beyer, A., Stahl, J., Roesler, U., Friese, A., von Bergen, M., Kietzmann, M., Honscha, W. (2015):
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  Maternal and newborn vitamin D status and its impact on food allergy development in the German LINA cohort study
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• Abburi, R., Kalkhof, S., Oehme, R., Kiontke, A., Birkemeyer, C. (2012):
  Artifacts in amine analysis from anodic oxidation of organic solvents upon electrospray ionization for mass spectrometry
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• Baumgarten, T., Sperling, S., Seifert, J., von Bergen, M., Steiniger, F., Wick, L.Y., Heipieper, H.J. (2012):
  Membrane vesicle formation as a multiple-stress response mechanism enhances Pseudomonas putida DOT-T1E cell surface hydrophobicity and biofilm formation
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• Blaschke, U., Eismann, K., Böhme, A., Paschke, A., Schüürmann, G. (2012):
  Structural alerts for the excess toxicity of acrylates, methacrylates, and propiolates derived from their short-term and long-term bacterial toxicity
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• Bönisch, U., Böhme, A., Kohajda, T., Mögel, I., Schütze, N., von Bergen, M., Simon, J.C., Lehmann, I., Polte, T. (2012):
  Volatile organic compounds enhance allergic airway inflammation in an experimental mouse model
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• Bozinovski, D., Herrmann, S., Richnow, H.-H., von Bergen, M., Seifert, J., Vogt, C. (2012):
  Functional analysis of an anaerobic m-xylene-degrading enrichment culture using protein-based stable isotope probing
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• Goettsch, C., Kliemt, S., Sinningen, K., von Bergen, M., Hofbauer, L.C., Kalkhof, S. (2012):
  Quantitative proteomics reveals novel functions of osteoclast-associated receptor in STAT signaling and cell adhesion in human endothelial cells
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• Gündel, U., Kalkhof, S., Zitzkat, D.P., 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
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• Haange, S.-B., Oberbach, A., Schlichting, N., Hugenholtz, F., Smidt, H., von Bergen, M., Till, H., Seifert, J. (2012):
  Metaproteome analysis and molecular genetics of rat intestinal microbiota reveals section and localisation resolved species distribution and enzymatic functionalities
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  DIGE proteome analysis reveals suitability of ischemic cardiac in vitro model for studying cellular response to acute ischemia and regeneration
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• Hörnig, F., Weisse, K., Röder, S., Kohajda, T., von Bergen-Tomm, M., Borte, M., Diez, U., Simon, J., Denburg, J., Lehmann, I. (2012):
  Infantile eosinophil/basophil progenitors are more sensitive to indoor chemical exposures compared to their mothers
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  Occupational IgE-mediated softwood allergy: characterization of the causative allergen
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  Non-conserved Ca²⁺/calmodulin binding sites in Munc13s differentially control synaptic short-term plasticity
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  Microbial interactions during residual oil and n-fatty acid metabolism by a methanogenic consortium
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• Müller, A. (2012):
  Schimmelpilzexposition im Innenraum und deren gesundheitlichen Auswirkungen
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• Oberbach, A., von Bergen, M., Blueher, S., Lehmann, S., Till, H. (2012):
  Combined serum proteomic and metabonomic profiling after laparoscopic sleeve gastrectomy in children and adolescents
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• Pohler, P., Lehmann, J., Veneruso, V., Tomm, J., von Bergen, M., Lambrecht, B., Kohn, B., Weingart, C., Müller, T.H., Seltsam, A. (2012):
  Evaluation of the tolerability and immunogenicity of ultraviolet C-irradiated autologous platelets in a dog model
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• Reinhold, A., Westermann, M., Seifert, J., von Bergen, M., Schubert, T., Diekert, G. (2012):
  Impact of vitamin B₁₂ on the formation of the tetrachloroethene reductive dehalogenase in Desulfitobacterium hafniense strain Y51
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• Salbach, J., Kliemt, S., Rauner, M., Rachner, T.D., Goettsch, C., Kalkhof, S., von Bergen, M., Möller, S., Schnabelrauch, M., Hintze, V., Scharnweber, D., Hofbauer, L.C. (2012):
  The effect of the degree of sulfation of glycosaminoglycans on osteoclast function and signaling pathways
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• Schmidt, A.-C., Lauckner, S., Lindner, K. (2012):
  CZE of sulfur-containing amino acids and peptides and its application to the quantitative study of heavy metal-caused thiol oxidations
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• Seifert, J., Taubert, M., Jehmlich, N., Schmidt, F., Völker, U., Vogt, C., Richnow, H.H., von Bergen, M. (2012):
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• Sultana, M., Vogler, S., Zargar, K., Schmidt, A.-C., Saltikov, C., Seifert, J., Schlömann, M. (2012):
  New clusters of arsenite oxidase and unusual bacterial groups in enrichments from arsenic-contaminated soil
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• Taubert, M., Vogt, C., Wubet, T., Kleinsteuber, S., Tarkka, M.T., Harms, H., Buscot, F., Richnow, H.-H., von Bergen, M., Seifert, J. (2012):
  Protein-SIP enables time-resolved analysis of the carbon flux in a sulfate-reducing, benzene-degrading microbial consortium
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• von Bergen, M., Reiche, K., Hösler, N., Rockstroh, M., Horn, F., Hackermüller, J., Tomm, J. (2012):
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  Immunology 137 (Suppl. S1), 364 - 364 10.1111/imm.12001
• Wagner, A., Cooper, M., Ferdi, S., Seifert, J., Adrian, L. (2012):
  Growth of Dehalococcoides mccartyi strain CBDB1 by reductive dehalogenation of brominated benzenes to benzene
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• Weisse, K., Lehmann, I., Heroux, D., Kohajda, T., Herberth, G., Röder, S., von Bergen, M., Borte, M., Denburg, J. (2012):
  The LINA cohort: indoor chemical exposure, circulating eosinophil/basophil (Eo/B) progenitors and early life skin manifestations
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• Weisse, K., Winkler, S., Stangl, G.I., Hirche, F., Herberth, G., Hinz, D., Bauer, M., Röder, S., Rolle-Kampczyk, U., von Bergen-Tomm, M., Olek, S., Sack, U., Borte, M., Richter, T., Lehmann, I. (2012):
  Maternal and newborn vitamin D status and its impact on fetal regulatory T cell development and children's atopy risk in the German LINA cohort study
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  Mining SOM expression portraits: feature selection and integrating concepts of molecular function
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• Wirth, H., von Bergen, M., Murugaiyan, J., Roesler, U., Stokowy, T., Binder, H. (2012):
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• Wuttig, D., Zastrow, S., Füssel, S., Toma, M.I., Meinhardt, M., Kalman, K., Junker, K., Sanjmyatav, J., Boll, K., Hackermüller, J., Rolle, A., Grimm, M.O., Wirth, M.P. (2012):
  CD31, EDNRB and TSPAN7 are promising prognostic markers in clear-cell renal cell carcinoma revealed by genome-wide expression analyses of primary tumors and metastases
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• Bastida, F., Jechalke, S., Bombach, P., Franchini, A.G., Seifert, J., von Bergen, M., Vogt, C., Richnow, H.H. (2011):
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• Dautel, F., Kalkhof, S., Trump, S., Lehmann, I., Beyer, A., von Bergen, M. (2011):
  Large-scale 2-D DIGE studies - guidelines to overcome pitfalls and challenges along the experimental procedure
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• Dautel, F., Kalkhof, S., Trump, S., Michaelson, J., Beyer, A., Lehmann, I., von Bergen, M. (2011):
  DIGE-based protein expression analysis of B[a]P-exposed hepatoma cells reveals a complex stress response including alterations in oxidative stress, cell cycle control, and cytoskeleton motility at toxic and subacute concentrations
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• Dietrich, A., Blüher, M., Jonas, S., Shang, E., Till, H., von Bergen, M., Oberbach, A. (2011):
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• Diez, U., Müller, A. (2011):
  Einfluss der Schimmelpilzbelastung in Wohnungen auf die Gesundheit
  Pädiatrische Allergologie in Klinik und Praxis 14 (2), 40 - 42
• Georgieva, D., Seifert, J., Öhler, M., von Bergen, M., Spencer, P., Arni, R.K., Genov, N., Betzel, C. (2011):
  Pseudechis australis venomics: adaptation for a defense against microbial pathogens and recruitment of body transferrin
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• Goodman, V., Müller, A., Gröger-Arndt, H., Schlosser, D., Jehmlich, N., Treudler, R., Lehmann, I., Simon, J.-C., von Bergen, M. (2011):
  Identification of spore specific allergen candidates from Penicillium chrysogenum
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• Hedrich, S., Lünsdorf, H., Kleeberg, G., Heide, G., Seifert, J., Schlömann, M. (2011):
  Schwertmannite formation adjacent to bacterial cells in a mine water treatment plant and in pure cultures of ‘Ferrovum myxofaciens’
  Environ. Sci. Technol. 45 (18), 7685 - 7692 10.1021/es201564g
• Hempel, K., Herbst, F.-A., Moche, M., Hecker, M., Becher, D. (2011):
  Quantitative proteomic view on secreted, cell surface-associated, and cytoplasmic proteins of the methicillin-resistant human pathogen Staphylococcus aureus under iron-limited conditions
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• Herbarth, O., Müller, A. (2011):
  Allergien durch Schimmelpilze: Ergebnisse aus epidemiologischen, umweltmedizinischen und interventionellen Studie. Allergic disorders caused by mould: results of epidemiological, environmental health and intervention studies
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• Hösler, N., Hackermüller, J., Reiche, K., Horn, F. (2011):
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• Marco-Urrea, E., Paul, S., Khodaverdi, V., Seifert, J., von Bergen, M., Kretzschmar, U., Adrian, L. (2011):
  Identification and characterization of a Re-Citrate synthase in Dehalococcoides strain CBDB1
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  Characterization of polycyclic aromatic hydrocarbon profiles by multivariate statistical analysis
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  Transcriptional signatures of regulatory and toxic responses to benzo-[a]-pyrene exposure
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• Mögel, I., Baumann, S., Böhme, A., Kohajda, T., von Bergen, M., Simon, J.-C., Lehmann, I. (2011):
  The aromatic volatile organic compounds toluene, benzene and styrene induce COX-2 and prostaglandins in human lung epithelial cells via oxidative stress and p38 MAPK activation
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  Chlorinated benzenes cause concomitantly oxidative stress and induction of apoptotic markers in lung epithelial cells (A549) at non-acute toxic concentrations
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  Combined proteomic and metabolomic profiling of serum reveals association of the complement system with obesity and identifies novel markers of body fat mass changes
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• Oberbach, A., Till, H., Dietrich, A., Shang, E., von Bergen, M. (2011):
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• Otto, W., Stadler, P.F., Prohaska, S.J. (2011):
  Phylogenetic footprinting and consistent sets of local aligments
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  Cell fractionation - an important tool for compartment proteomics
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• Rose, D., Hiller, M., Schutt, K., Hackermüller, J., Backofen, R., Stadler, P.F. (2011):
  Computational discovery of human coding and non-coding transcripts with conserved splice sites
  Bioinformatics 27 (14), 1894 - 1900 10.1093/bioinformatics/btr314
• Rudzok, S., Krejči, S., Graebsch, C., Herbarth, O., Mueller, A., Bauer, M. (2011):
  Toxicity profiles of four metals and 17 xenobiotics in the human hepatoma cell line HepG2 and the protozoa Tetrahymena pyriformis - A comparison
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• 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
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• Schramm, F., Müller, A., Hammer, H., Paschke, A., Schüürmann, G. (2011):
  Epoxide and thiirane toxicity in vitro with the ciliates Tetrahymena pyriformis: structural allerts indicating excess toxicity
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• Sultana, M., Härtig, C., Planer-Friedrich, B., Seifert, J., Schlömann, M. (2011):
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• Taubert, M., Baumann, S., von Bergen, M., Seifert, J. (2011):
  Exploring the limits of robust detection of incorporation of 13C by mass spectrometry in protein-based stable isotope probing (protein-SIP)
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• Taubert, M., Jehmlich, N., Vogt, C., Richnow, H.H., Schmidt, F., von Bergen, M., Seifert, J. (2011):
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• Tischer, C.G., Hohmann, C., Thiering, E., Herbarth, O., Müller, A., Henderson, J., Granell, R., Fantini, M.P., Luciano, L., Bergström, A., Kull, I., Link, E., von Berg, A., Kuehni, C.E., Strippoli, M.P.F., Gehring, U., Wijga, A., Eller, E., Bindslev-Jensen, C., Keil, T., Heinrich, J. (2011):
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  Elucidating MTBE degradation in a mixed consortium using a multidisciplinary approach
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• Binder, H., Wirth, H., Galle, J. (2010):
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• Feltens, R., Görner, R., Kalkhof, S., Gröger-Arndt, H., von Bergen, M. (2010):
  Discrimination of different species from the genus Drosophila by intact protein profiling using matrix-assisted laser desorption ionization mass spectrometry
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• Fetzer, I., Jehmlich, N., Vogt, C., Richnow, H.H., Seifert, J., Harms, H., von Bergen, M., Schmidt, F. (2010):
  Calculation of partial isotope incorporation into peptides measured by mass spectrometry
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• Georgieva, D., Öhler, M., Seifert, J., von Bergen, M., Arni, R.K., Genov, N., Betzel, C. (2010):
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• Georgieva, D., Redecke, L., von Bergen, M., Genov, N., Betzel, C. (2010):
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• Gündel, U., Kalkhof, S., von Bergen, M., Altenburger, R., Küster, E. (2010):
  Concentration-response concept in ecotoxicoproteomics: an optimised design for the detection of robust chemical stress associated protein markers: Effects of different concentrations of phenanthren to the proteome of Danio rerio embryos
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• Heinrich, U.-R., Selivanova, O., Schmidtmann, I., Feltens, R., Brieger, J., Mann, W.J. (2010):
  Noise exposure alters cyclooxygenase 1 (COX-1) and 5-lipoxygenase (5-LO) expression in the guinea pig cochlea
  Acta Oto-Laryngol. 130 (3), 358 - 365 10.3109/00016480903168066
• Jehmlich, N., Fetzer, I., Seifert, J., Mattow, J., Vogt, C., Harms, H., Thiede, B., Richnow, H.H., von Bergen, M., Schmidt, F. (2010):
  Decimal place slope: a fast and precise method for quantifying ¹³C incorporation levels for detecting the metabolic activity of microbial species
  Mol. Cell. Proteomics 9 (6), 1221 - 1227 10.1074/mcp.M900407-MCP200
• Jehmlich, N., Hübschmann, T., Gesell Salazar, M., Völker, U., Benndorf, D., Müller, S., von Bergen, M., Schmidt, F. (2010):
  Advanced tool for characterization of microbial cultures by combining cytomics and proteomics
  Appl. Microbiol. Biotechnol. 88 (2), 575 - 584 10.1007/s00253-010-2753-6
• Jehmlich, N., Kleinsteuber, S., Vogt, C., Benndorf, D., Harms, H., Schmidt, F., von Bergen, M., Seifert, J. (2010):
  Phylogenetic and proteomic analysis of an anaerobic toluene-degrading community
  J. Appl. Microbiol. 109 (6), 1937 - 1945 10.1111/j.1365-2672.2010.04823.x
• Jehmlich, N., Schmidt, F., Taubert, M., Seifert, J., Bastida, F., von Bergen, M., Richnow, H.-H., Vogt, C. (2010):
  Protein-based stable isotope probing
  Nat. Protoc. 5 (12), 1957 - 1966 10.1038/nprot.2010.166
• Kalkhof, S., Haehn, S., Paulsson, M., Smyth, N., Meiler, J., Sinz, A. (2010):
  Computational modeling of laminin N-terminal domains using sparse distance constraints from disulfide bonds and chemical cross-linking
  Proteins 78 (16), 3409 - 3427 10.1002/prot.22848
• Kalkhof, S., Witte, K., Ihling, C.H., Müller, M.Q., Keller, M.V., Haehn, S., Smyth, N., Paulsson, M., Sinz, A. (2010):
  A novel disulfide pattern in laminin-type epidermal growth factor-like (LE) modules of laminin β1 and γ1 chains
  Biochemistry 49 (38), 8359 - 8366 10.1021/bi101187f
• Kung, J.W., Baumann, S., von Bergen, M., Müller, M., Hagedoorn, P.-L., Hagen, W.R., Boll, M. (2010):
  Reversible biological Birch reduction at an extremely low redox potential
  J. Am. Chem. Soc. 132 (28), 9850 - 9856 10.1021/ja103448u
• Leibeling, S., Schmidt, F., Jehmlich, N., von Bergen, M., Müller, R.H., Harms, H. (2010):
  Declining capacity of starving Delftia acidovorans MC1 to degrade phenoxypropionate herbicides correlates with oxidative modification of the initial enzyme
  Environ. Sci. Technol. 44 (10), 3793 - 3799 10.1021/es903619j
• Leibeling, S., Taubert, M., Seifert, J., von Bergen, M., Harms, H., Müller, R.H. (2010):
  Adaptation of the herbicide-degrading strain Delftia acidovorans MC1 through carbonylation of RdpA as key enzyme
  J. Biotechnol. 150 (Suppl. 1), S262 - S263 10.1016/j.jbiotec.2010.09.160
• Massolo, L., Rehwagen, M., Porta, A., Ronco, A., Herbarth, O., Mueller, A. (2010):
  Indoor-outdoor distribution and risk assessment of volatile organic compounds in the atmosphere of industrial and urban areas
  Environ.Toxicol. 25 (4), 339 - 349 10.1002/tox.20504
• Müller, S.A., Kohajda, T., Findeiß, S., Stadler, P.F., Washietl, S., Kellis, M., von Bergen, M., Kalkhof, S. (2010):
  Optimization of parameters for coverage of low molecular weight proteins
  Anal. Bioanal. Chem. 398 (7-8), 2867 - 2881 10.1007/s00216-010-4093-x
• Öhler, M., Georgieva, D., Seifert, J., von Bergen, M., Arni, R.K., Genov, N., Betzel, C. (2010):
  The venomics of Bothrops alternatus is a pool of acidic proteins with predominant hemorrhagic and coagulopathic activities
  J. Proteome Res. 9 (5), 2422 - 2437 10.1021/pr901128x
• Otto, A., Bernhardt, J., Meyer, H., Schaffer, M., Herbst, F.-A., Siebourg, J., Mäder, U., Lalk, M., Hecker, M., Becher, D. (2010):
  Systems-wide temporal proteomic profiling in glucose-starved Bacillus subtilis
  Nat. Commun. 1 , art. 137 10.1038/ncomms1137
• Picotti, P., Rinner, O., Stallmach, R., Dautel, F., Farrah, T., Domon, B., Wenschuh, H., Aebersold, R. (2010):
  High-throughput generation of selected reaction-monitoring assays for proteins and proteomes
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• Saalbach, A., Klein, C., Schirmer, C., Briest, W., Anderegg, U., Simon, J.-C. (2010):
  Dermal fibroblasts promote the migration of dendritic cells
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• Schirmer, C., Klein, C., von Bergen, M., Simon, J.-C., Saalbach, A. (2010):
  Human fibroblasts support the expansion of IL-17-producing T cells via up-regulation of IL-23 production by dendritic cells
  Blood 116 (10), 1715 - 1725 10.1182/blood-2010-01-263509
• Schirmer, C., Klein, C., von Bergen, M., Simon, J.C., Saalbach, A. (2010):
  Differentiation of IL-17 secreting T cells is supported by human dermal fibroblasts via up-regulation of IL-23 production by dendritic cells
  Exp. Dermatol. 19 (2), 181 / P085 10.1111/j.1600-0625.2009.01051.x
• Selesi, D., Jehmlich, N., von Bergen, M., Schmidt, F., Rattei, T., Tischler, P., Lueders, T., Meckenstock, R.U. (2010):
  Combined genomic and proteomic approaches identify gene clusters involved in anaerobic 2-methylnaphthalene degradation in the dulfate-reducing enrichment culture N47
  J. Bacteriol. 192 (1), 295 - 306 10.1128/JB.00874-09
• Sträuber, H., Hübschmann, T., Jehmlich, N., Schmidt, F., von Bergen, M., Harms, H., Müller, S. (2010):
  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
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• Tischler, D., Kermer, R., Gröning, J.A., Kaschabek, S.R., van Berkel, W.J.H., Schlömann, M. (2010):
  StyA1 and StyA2B from Rhodococcus opacus 1CP: a multifunctional styrene monooxygenase system
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2009 (25)

• 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 20 (6), 737 - 750 10.1007/s10532-009-9261-3
• Bruegel, M., Planert, M., Baumann, S., Focke, A., Bergh, F.T., Leichtle, A., Ceglarek, U., Thiery, J., Fiedler, G.M. (2009):
  Standardized peptidome profiling of human cerebrospinal fluid by magnetic bead separation and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry
  J. Proteomics 72 (4), 608 - 615 10.1016/j.jprot.2008.11.018
• Cianni, N., Müller, A., Lespade, P., Aguilar, M., Matamoros, N., Colman, E., Martin, M., Chiapperini, V., Bussi, L., Massolo, L., Wichmann, F., Porta, A. (2009):
  Calidad del aire y salud infantil en áreas urbanas e industriales de La Plata y Ensenada, Argentina
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• Dimova, K., Kalkhof, S., Pottratz, I., Ihling, C., Rodriguez-Castaneda, F., Liepold, T., Griesinger, C., Brose, N., Sinz, A., Jahn, O. (2009):
  Structural insights into the calmodulin-Munc13 interaction obtained by cross-linking and mass spectrometry
  Biochemistry 48 (2), 5908 - 5921 10.1021/bi900300r
• Ehinger, S., Seifert, J., Kassahun, A., Schmalz, L., Hoth, N., Schlömann, M. (2009):
  Predominance of Methanolobus spp. and Methanoculleus spp. in the archaeal communities of saline gas field formation fluids
  Geomicrobiol. J. 26 (5), 326 - 338 10.1080/01490450902754441
• Fiedler, G.M., Leichtle, A.B., Kase, J., Baumann, S., Ceglarek, U., Felix, K., Conrad, T., Witzigmann, H., Weimann, A., Schütte, C., Hauss, J., Büchler, M., Thiery, J. (2009):
  Serum peptidome profiling revealed platelet factor 4 as a potential discriminating peptide associated with pancreatic cancer
  Clin. Cancer Res. 15 (11), 3812 - 3819 10.1158/1078-0432.CCR-08-2701
• Gniese, C., Kruger, M., Frerichs, J., Kassahun, A., Hoth, N., Seifert, J. (2009):
  Determination of active microorganisms in the gas reservoir Altmark and their role in CO₂ turnover
  Geochim. Cosmochim. Acta 73 (13 Suppl.), A442 10.1016/j.gca.2009.05.025
• Heine, F., Stahl, F., Sträuber, H., Wiacek, C., Benndorf, D., Repenning, C., Schmidt, F., Scheper, T., von Bergen, M., Harms, H., Müller, S. (2009):
  Prediction of flocculation ability of brewing yeast inoculates by flow cytometry, proteome analysis, and mRNA profiling
  Cytom. Part A 75A (2), 140 - 147 10.1002/cyto.a.20661
• Heinzel, E., Hedrich, S., Janneck, E., Glombitza, F., Seifert, J., Schlömann, M. (2009):
  Bacterial diversity in a mine water treatment plant
  Appl. Environ. Microb. 75 (3), 858 - 861 10.1128/AEM.01045-08
• Heinzel, E., Janneck, E., Glombitza, F., Schlömann, M., Seifert, J. (2009):
  Population dynamics of iron-oxidizing communities in pilot plants for the treatment of acid mine waters
  Environ. Sci. Technol. 43 (16), 6138 - 6144 10.1021/es900067d
• Jehmlich, N., Schmidt, F., Taubert, M., Seifert, J., von Bergen, M., Richnow, H.-H., Vogt, C. (2009):
  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. 23 (12), 1871 - 1878 10.1002/rcm.4084
• Junghanns, C., Pecyna, M.J., Böhm, D., Jehmlich, N., Martin, C., von Bergen, M., Schauer, F., Hofrichter, M., Schlosser, D. (2009):
  Biochemical and molecular genetic characterisation of a novel laccase produced by the aquatic ascomycete Phoma sp. UHH 5-1-03
  Appl. Microbiol. Biotechnol. 84 (6), 1095 - 1105 10.1007/s00253-009-2028-2
• Manolaridis, I., Mumtsidu, E., Konarev, P., Makhov, A.M., Fullerton, S.W., Sinz, A., Kalkhof, S., McGeehan, J.E., Cary, P.D., Griffith, J.D., Svergun, D., Kneale, G.G., Tucker, P.A. (2009):
  Structural and biophysical characterization of the proteins interacting with the herpes simplex virus 1 origin of replication
  J. Biol. Chem. 284 (24), 16343 - 16353 10.1074/jbc.M806134200
• Massolo, L., Müller, A., Rehwagen, M., Porta, A., Herbarth, O., Ronco, A. (2009):
  Estimación del riesgo asociado a PAHs en ambientes urbanos e industriales
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• Matysik, S., Herbarth, O., Mueller, A. (2009):
  Determination of microbial volatile organic compounds (MVOCs) by passive sampling onto charcoal sorbents
  Chemosphere 76 (1), 114 - 119 10.1016/j.chemosphere.2009.02.010
• Mörbt, N., Mögel, I., Kalkhof, S., Feltens, R., Röder-Stolinski, C., Zheng, J., Vogt, C., Lehmann, I., von Bergen, M. (2009):
  Proteome changes in human bronchoalveolar cells following styrene exposure indicate involvement of oxidative stress in the molecular-response mechanism
  Proteomics 9 (21), 4909 - 4933 10.1002/pmic/200800836
• Rehders, D., Classen, B., Redecke, L., Buschke, A., Reibe, C., Jehmlich, N., von Bergen, M., Betzel, A., Meyer, B. (2009):
  Peptide NMHRYPNQ of the Cellular Prion Protein (PrP^C) Inhibits Aggregation and Is a Potential Key for Understanding Prion-Prion Interactions
  J. Mol. Biol. 392 (1), 198 - 207 10.1016/j.jmb.2009.07.014
• Risch, M., Georgieva, D., von Bergen, M., Jehmlich, N., Genov, N., Arni, R.K., Betzel, C. (2009):
  Snake venomics of the Siamese Russell's viper (Daboia russelli siamensis) - Relation to pharmacological activities
  J. Proteomics 72 (2), 256 - 269 10.1016/j.jprot.2009.01.006
• Saalbach, A., Klein, C., Schirmer, C., Anderegg, U., Simon, J.C. (2009):
  Role of dermal fibroblasts in the regulation of dendritic cellmigration
  Exp. Dermatol. 18 (3), 291 - 291 10.1111/j.1600-0625.2008.00834.x
• Schleinitz, K.M., Schmeling, S., Jehmlich, N., von Bergen, M., Harms, H., Kleinsteuber, S., Vogt, C., Fuchs, G. (2009):
  Phenol degradation in the strictly anaerobic iron-reducing bacterium Geobacter metallireducens GS-15
  Appl. Environ. Microb. 75 (12), 3912 - 3919 10.1128/aem.01525-08
• Seifert, J., Jehmlich, N., Schmidt, F., Taubert, M., von Bergen, M., Richnow, H.-H., Vogt, C. (2009):
  Protein-stable isotope probing (Protein-SIP) for simultaneous identification of bacterial species and determination of metabolic activity
  Geochim. Cosmochim. Acta 73 (13 Suppl.), A1191 10.1016/j.gca.2009.05.015
• von Bergen, M., Eidner, A., Schmidt, F., Murugaiyan, J., Wirth, H., Binder, H., Maier, T., Roesler, U. (2009):
  Identification of harmless and pathogenic algae of the genus Prototheca by MALDI-MS
  Proteom. Clin. Appl. 3 (7), 774 - 787 10.1002/prca.200780138
• Wichmann, F.A., Müller, A., Busi, L.E., Cianni, N., Massolo, L., Schlink, U., Porta, A., Sly, P.D. (2009):
  Increased asthma and respiratory symptoms in children exposed to petrochemical pollution
  J. Allergy Clin. Immunol. 123 (3), 632 - 638 10.1016/j.jaci.2008.09.052
• Wichmann, G., Franck, U., Herbarth, O., Rehwagen, M., Dietz, A., Massolo, L., Ronco, A., Müller, A. (2009):
  Different immunomodulatory effects associated with sub-micrometer particles in ambient air from rural, urban and industrial areas
  Toxicology 257 (3), 127 - 136 10.1016/j.tox.2008.12.024
• Wischgoll, S., Taubert, M., Peters, F., Jehmlich, N., von Bergen, M., Boll, M. (2009):
  Decarboxylating and nondecarboxylating glutaryl-coenzyme A dehydrogenases in the aromatic metabolism of obligately anaerobic bacteria
  J. Bacteriol. 191 (13), 4401 - 4409 10.1128/JB.00205-09

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• Andronesi, O.C., von Bergen, M., Biernat, J., Seidel, K., Griesinger, C., Mandelkow, E., Baldus, M. (2008):
  Characterization of Alzheimer's-like paired helical filaments from the core domain of tau protein using solid-state NMR spectroscopy
  J. Am. Chem. Soc. 130 (18), 5922 - 5928 10.1021/ja7100517
• Balcke, G.U., Wegener, S., Kiesel, B., Benndorf, D., Schlömann, M., Vogt, C. (2008):
  Kinetics of chlorobenzene biodegradation under reduced oxygen levels
  Biodegradation 19 (4), 507 - 518 10.1007/s10532-007-9156-0
• Benndorf, D., Müller, A., Bock, K., Manuwald, O., Herbarth, O., von Bergen, M. (2008):
  Identification of spore allergens from the indoor mould Aspergillus versicolor
  Allergy 63 (4), 454 - 460 10.1111/j.1398-9995.2007.01603.x
• Bock, K., Benndorf, D., Müller, A., Bauer, M., von Bergen, M. (2008):
  Identification of allergens from the indoor mold Aspergillus versicolor
  Allergy 63 (Suppl. 88), 530 - 531 10.1111/j.1398-9995.2008.01760.x
• Georgieva, D., Risch, M., Kardas, A., Buck, F., von Bergen, M., Betzel, C. (2008):
  Comparative Analysis of the Venom Proteomes of Vipera ammodytes ammodytes and Vipera ammodytes meridionalis
  J. Proteome Res. 7 (3), 866 - 886 10.1021/pr070376c
• Hehemann, J.H., Redecke, L., Murugaiyan, J., von Bergen, M., Betzel, C., Saborowski, R. (2008):
  Autoproteolytic stability of a trypsin from the marine crab Cancer pagurus
  Biochem. Biophys. Res. Commun. 370 (4), 566 - 571 10.1016/j.bbrc.2008.03.128
• Jeganathan, S., von Bergen, M., Mandelkow, E. (2008):
  In search for the pathological conformation of tau protein
  Eur. J. Cell Biol. 87 (Suppl. 1), 49 10.1016/j.ejcb.2008.01.004
• Jeganathan, S., von Bergen, M., Mandelkow, E.-M., Mandelkow, E. (2008):
  The natively unfolded character of tau and its aggregation to Alzheimer-like paired helical filaments
  Biochemistry 47 (40), 10526 - 10539 10.1021/bi800783d
• Jehmlich, N., Schmidt, F., Hartwich, M., von Bergen, M., Richnow, H.H., Vogt, C. (2008):
  Incorporation of carbon and nitrogen atoms into proteins measured by protein-based stable isotope probing (Protein-SIP)
  Rapid Commun. Mass Spectrom. 22 (18), 2889 - 2897 10.1002/rcm.3684
• Jehmlich, N., Schmidt, F., von Bergen, M., Richnow, H.H., Vogt, C. (2008):
  Protein-based stable isotope probing (Protein-SIP) reveals active species within anoxic mixed cultures
  ISME J. 2 (11), 1122 - 1133 10.1038/ismej.2008.64
• Johannes, J., Bluschke, A., Jehmlich, N., von Bergen, M., Boll, M. (2008):
  Purification and characterization of active-site components of the putative p-cresol methylhydroxylase membrane complex from Geobacter metallireducens
  J. Bacteriol. 190 (19), 6493 - 6500 10.1128/jb.00790-08
• Kalkhof, S., Haehn, S., Ihling, C., Paulsson, M., Smyth, N., Sinz, A. (2008):
  Determination of disulfide bond patterns in laminin β1 chain N-terminal domains by nano-high-performance liquid chromatography/matrix-assisted laser desorption/ionization time-of-flight/time-of-flight mass spectrometry
  Rapid Commun. Mass Spectrom. 22 (12), 1933 - 1940 10.1002/rcm.3576
• Kalkhof, S., Sinz, A. (2008):
  Chances and pitfalls of chemical cross-linking with amine-reactive N-hydroxysuccinimide esters
  Anal. Bioanal. Chem. 392 (1-2), 305 - 312 10.1007/s00216-008-2231-5
• Massolo, L., Müller, A., Herbarth, O., Ronco, A.E., Porta, A. (2008):
  Contaminación atmosférica y salud infantil en áreas urbanas e industriales de La Plata, Argentina. Air pollution and children's health in urban and industrial areas of La Plata, Argentina
  Acta Bioquim. Clin. Latinoam. 42 (4), 567 - 574
• Matysik, S., Herbarth, O., Müller, A. (2008):
  Determination of volatile metabolites originating from mould growth on wall paper and synthetic media
  J. Microbiol. Methods 75 (2), 182 - 187 10.1016/j.mimet.2008.05.027
• Rehders, D., Claasen, B., Redecke, L., Reibe, C., Buschke, A., Jehmlich, N., von Bergen, M., Betzel, C., Meyer, B. (2008):
  Aggregation of the human cellular prion protein (PrPC) is quantitatively inhibited by the octapeptide NMHRVPNQ
  J. Pept. Sci. 14 (S1), 125 - 126 10.1002/psc.1090
• Röder-Stolinski, C., Fischäder, G., Oostingh, G.J., Feltens, R., Kohse, F., von Bergen, M., Mörbt, N., Eder, K., Duschl, A., Lehmann, I. (2008):
  Styrene induces an inflammatory response in human lung epithelial cells via oxidative stress and NF-κB activation
  Toxicol. Appl. Pharmacol. 231 (2), 241 - 247 10.1016/j.taap.2008.04.010
• Thiele, B., Rieder, O., Jehmlich, N., von Bergen, M., Müller, M., Boll, M. (2008):
  Aromatizing cyclohexa-1,5-diene-1-carbonyl-coenzyme A oxidase. Characterization and its role in anaerobic aromatic metabolism
  J. Biol. Chem. 283 (30), 20713 - 20721 10.1074/jbc.m802841200
• Veeranagouda, Y., Benndorf, D., Heipieper, H.J., Karegoudar, T.B. (2008):
  Purification and characterization of NAD dependent n-butanol dehydrogenase from solvent tolerant n-butanol degrading Enterobacter sp VKGH12
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• Anh, D.H., Ullrich, R., Benndorf, D., Svatos, A., Muck, A., Hofrichter, M. (2007):
  The coprophilous mushroom Coprinus radians secretes a haloperoxidase that catalyzes aromatic peroxygenation
  Appl. Environ. Microb. 73 (17), 5477 - 5485 10.1128/AEM.00026-07
• Benndorf, D., Balcke, G.U., Harms, H., von Bergen, M. (2007):
  Functional metaproteome analysis of protein extracts from contaminated soil and groundwater
  ISME J. 1 (3), 224 - 234 10.1038/ismej.2007.39
• Fischer, D., Mukrasch, M.D., von Bergen, M., Klos-Witkowska, A., Biernat, J., Griesinger, C., Mandelkow, E., Zweckstetter, M. (2007):
  Structural and microtubule binding properties of tau mutants of frontotemporal dementias
  Biochemistry 46 (10), 2574 - 2582 10.1021/bi061318s
• Fischer, W., Zadori, Z., Kullnick, Y., Gröger-Arndt, H., Franke, H., Wirkner, K., Illes, P., Mager, P.P. (2007):
  Conserved lysin and arginin residues in the extracellular loop of P2X(3) receptors are involved in agonist binding
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• Fitzpatrick, P.F., Bozinovski, D.M., Heroux, A., Shaw, P.G., Valley, M.P., Orville, A.M. (2007):
  Mechanistic and structural analyses of the roles of Arg409 and Asp402 in the reaction of the flavoprotein nitroalkane oxidase
  Biochemistry 46 (48), 13800 - 13808 10.1021/bi701557k
• Gündel, U., Benndorf, D., von Bergen, M., Altenburger, R., Küster, E. (2007):
  Vitellogenin cleavage products as indicators for toxic stress in zebra fish embryos: a proteomic approach
  Proteomics 7 (24), 4541 - 4554 10.1002/pmic.200700381
• Heine, F., Wiacek, C., Benndorf, D., Sträuber, H., Stahl, F., von Bergen, M., Harms, H., Müller, S. (2007):
  Evidence of flocculation in brewing yeast strains by flow cytometry, proteome and mRNA profiling
  Cytom. Part A 71A (9), 761 10.1002/cyto.a.20451
• Heine, F., Wiacek, C., Benndorf, D., Sträuber, H., Stahl, F., von Bergen, M., Harms, H., Müller, S. (2007):
  Evidence of flocculation in brewing yeast strains by flow cytometry, proteome and mRNA profiling
  Cytom. Part A 71A (7), 513 10.1002/cyto.a.20421
• Kellner, H., Jehmlich, N., Benndorf, D., Hoffmann, R., Rühl, M., Hoegger, P.J., Majcherczyk, A., Kües, U., von Bergen, M., Buscot, F. (2007):
  Detection, quantification and identification of fungal extracellular laccases using polyclonal antibody and mass spectrometry
  Enzyme Microb. Technol. 41 (6-7), 694 - 701 10.1016/j.enzmictec.2007.06.002
• Krejči, S., Herbarth, O., Rudzok, S., Schmücking, E., Müller, A. (2007):
  Chronic effects of metals, organophosphates and polycyclic aromatic hydrocarbons (PAH) on tetrahymena pyriformis
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• Mandelkow, E., von Bergen, M., Biernat, J., Mandelkow, E.-M. (2007):
  Structural principles of tau and the paired helical filaments of Alzheimer's disease
  Brain Pathol. 17 (1), 83 - 90 10.1111/j.1750-3639.2007.00053.x
• Martin, C., Pecyna, M., Kellner, H., Jehmlich, N., Junghanns, C., Benndorf, D., von Bergen, M., Schlosser, D. (2007):
  Purification and biochemical characterization of a laccase from the aquatic fungus Myrioconium sp. UHH 1-13-18-4 and molecular analysis of the laccase-encoding gene
  Appl. Microbiol. Biotechnol. 77 (3), 613 - 624 10.1007/s00253-007-1207-2
• Mattow, J., Siejak, F., Hagens, K., Schmidt, F., Koehler, C., Treumann, A., Schaible, U.E., Kaufmann, S.H.E. (2007):
  An improved strategy for selective and efficient enrichment of integral plasma membrane proteins of mycobacteria
  Proteomics 7 (10), 1687 - 1701 10.1002/pmic.200600928
• Milius, D., Gröger-Arndt, H., Stanchev, D., Lange-Dohna, C., Rossner, S., Sperlágh, B., Wirkner, K., Illes, P. (2007):
  Oxygen/glucose deprivation increases the integration of recombinant P2X(7) receptors into the plasma membrane of HEK293 cells
  Toxicology 238 (1), 60 - 69 10.1016/j.tox.2007.05.028
• Mukrasch, M.D., Markwick, P., von Bergen, M., Bernado, P., Griesinger, C., Mandelkow, E., Zweckstetter, M., Blackledge, M. (2007):
  Highly populated turn conformations in natively unfolded tau protein identified from residual dipolar couplings and molecular simulation
  J. Am. Chem. Soc. 129 (16), 5235 - 5243 10.1021/ja0690159
• Mukrasch, M.D., von Bergen, M., Biernat, J., Fischer, D., Griesinger, C., Mandelkow, E., Zweckstetter, M. (2007):
  The "jaws" of the tau-microtubule interaction
  J. Biol. Chem. 282 (16), 12230 - 12239 10.1074/jbc.M607159200
• Redecke, L., von Bergen, M., Clos, J., Konarev, P.V., Svergun, D.I., Fittschen, U.E., Broekaert, J.A., Bruns, O., Georgieva, D., Mandelkow, E., Genov, N., Betzel, C. (2007):
  Structural characterization of β-sheeted oligomers formed on the pathway of oxidative prion protein aggregation in vitro
  J. Struct. Biol. 157 (2), 308 - 320 10.1016/j.jsb.2006.06.013
• Rohwerder, T., Breuer, U., Benndorf, D., Lechner, U., Müller, R.H. (2007):
  The MTBE and ETBE intermediate 2-HIBA is degraded via a cobalamin-dependent mutase pathway
  In: Bastiaens, L. (ed.)
  MTBE & other fuel oxygenates : proceedings of the 3^rd European Conference, Antwerp, June 7-8, 2007
  Vito, Mol, 11 - 14
• Santos, P.M., Roma, V., Benndorf, D., von Bergen, M., Harms, H., Sá-Correia, I. (2007):
  Mechanistic insights into the global response to phenol in the phenol-biodegrading strain Pseudomonas sp. M1 revealed by quantitative proteomics
  OMICS 11 (3), 233 - 251 10.1089/omi.2007.0009
• Schäfer, F., Breuer, U., Benndorf, D., von Bergen, M., Harms, H., Müller, R.H. (2007):
  Growth of Aquincola tertiaricarbonis L108 on tert-butyl alcohol leads to the induction of a phthalate dioxygenase-related protein and its associated oxidoreductase subunit
  Eng. Life Sci. 7 (5), 512 - 519 10.1002/elsc.200700011
• Schmidt, F., Hustoft, H.K., Strozynski, M., Dimmler, C., Rudel, T., Thiede, B. (2007):
  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 28 (23), 4359 - 4368 10.1002/elps.200700119
• Schmidt, F., Strozynski, M., Salus, S.S., Nilsen, H., Thiede, B. (2007):
  Rapid determination of amino acid incorporation by stable isotope labeling with amino acids in cell culture (SILAC)
  Rapid Commun. Mass Spectrom. 21 (23), 3919 - 3926 10.1002/rcm.3290
• Schubert, T., Maskow, T., Benndorf, D., Harms, H., Breuer, U. (2007):
  Continuous synthesis and excretion of the compatible solute ectoine by a transgenic, nonhalophilic bacterium
  Appl. Environ. Microb. 73 (10), 3343 - 3347 10.1128/aem.02482-06
• Schulz, D.M., Kalkhof, S., Schmidt, A., Ihling, C., Stingl, C., Mechtler, K., Zschoernig, O., Sinz, A. (2007):
  Annexin A2/P11 interaction: New insights into annexin A2 tetramer structure by chemical crosslinking, high-resolution mass spectrometry, and computational modeling
  Proteins 69 (2), 254 - 269 10.1002/prot.21445
• Tomm, J.M., Filippowa, K., Vestweber, D. (2007):
  Multiple domain interactions between VE-cadherin and VE-PTP
  Eur. J. Cell Biol. 86 , 49 10.1016/j.ejcb.2007.02.002

2006 (14)

• Benndorf, D., Thiersch, M., Loffhagen, N., Kunath, C., Harms, H. (2006):
  Pseudomonas putida KT2440 responds specifically to chlorophenoxy herbicides and their initial metabolites
  Proteomics 6 (11), 3319 - 3329 10.1002/pmic.200500781
• Georgieva, D., Schwark, D., von Bergen, M., Redecke, L., Genov, N., Betzel, C. (2006):
  Interactions of recombinant prions with compounds of therapeutical significance
  Biochem. Biophys. Res. Commun. 344 (2), 463 - 470 10.1016/j.bbrc.2006.03.135
• Ihling, C., Schmidt, A., Kalkhof, S., Schulz, D.M., Stingl, C., Mechtler, K., Haack, M., Beck-Sickinger, A.G., Cooper, D.M.F., Sinz, A. (2006):
  Isotope-labeled cross-linkers and Fourier transform ion cyclotron resonance mass spectrometry for structural analysis of a protein/peptide complex
  J. Am. Soc. Mass Spectrom. 17 (8), 1100 - 1113 10.1016/j.jasms.2006.04.020
• Jeganathan, S., von Bergen, M., Brutlach, H., Steinhoff, H.J., Mandelkow, E. (2006):
  Global hairpin folding of tau in solution
  Biochemistry 45 (7), 2283 - 2293 10.1021/bi0521543
• Khlistunova, I., Biernat, J., Wang, Y.P., Pickhardt, M., von Bergen, M., Gazova, Z., Mandelkow, E., Mandelkow, E.-M. (2006):
  Inducible expression of tau repeat domain in cell models of tauopathy - Aggregation is toxic to cells but can be reversed by inhibitor drugs
  J. Biol. Chem. 281 (2), 1205 - 1214 10.1074/jbc.M507753200
• Mandelkow, E., Pickhardt, M., Gazova, Z., von Bergen, M., Biernat, J., Khlistunova, I., Wang, Y.P., Hascher, A., Mandelkow, E.-M. (2006):
  Inhibition of tau aggregation and disaggregation of PHFs by low MW compounds in vitro and in cells
  Neurobiol. Aging 27 (Suppl. 1), S13 10.1016/j.jalz.2006.05.1573
• Mattow, J., Siejak, F., Hagens, K., Becher, D., Albrecht, D., Krah, A., Schmidt, F., Jungblut, P.R., Kaufmann, S.H.E., Schaible, U.E. (2006):
  Proteins unique to intraphagosomally grown Mycobacterium tuberculosis
  Proteomics 6 (8), 2485 - 2494 10.1002/pmic.200500547
• Rohwerder, T., Breuer, U., Benndorf, D., Lechner, U., Müller, R.H. (2006):
  The alkyl tert-butyl ether intermediate 2-hydroxyisobutyrate is degraded via a novel cobalamin-dependent mutase pathway
  Appl. Environ. Microb. 72 (6), 4128 - 4135 10.1128/AEM.00080-06
• Schmidt, F., Dahlmann, B., Janek, K., Kloss, A., Wacker, M., Ackermann, R., Thiede, B., Jungblut, P.R. (2006):
  Comprehensive quantitative proteome analysis of 20S proteasome subtypes from rat liver by isotope coded affinity tag and 2-D gel-based approaches
  Proteomics 6 (16), 4622 - 4632 10.1002/pmic.200500920
• Schmidt, F., Krah, A., Schmid, M., Jungblut, P.R., Thiede, B. (2006):
  Distinctive mass losses of tryptic peptides generated by matrix-assisted laser desorption/ionization time-of-flight/time-of-flight
  Rapid Commun. Mass Spectrom. 20 (5), 933 - 936 10.1002/rcm.2382
• von Bergen, M., Barghorn, S., Jeganathan, S., Mandelkow, E.-M., Mandelkow, E. (2006):
  Spectroscopic approaches to the conformation of tau protein in solution and in paired helical filaments
  Neurodegener. Dis. 3 (4-5), 197 - 206 10.1159/000095257
• von Bergen, M., Barghorn, S., Müller, S.A., Pickhardt, M., Biernat, J., Mandelkow, E.-M., Davies, P., Aebi, U., Mandelkow, E. (2006):
  The core of tau-paired helical filaments studied by scanning transmission electron microscopy and limited proteolysis
  Biochemistry 45 (20), 6446 - 6457 10.1021/bi052530j
• Westendorf, A., Benndorf, D., Pribyl, T., Harms, H., Müller, R.H. (2006):
  Kinetic traits and enzyme form patterns of (R)-2-(2,4-Dichlorophenoxy)propionate/a-ketoglutarate dioxygenase (RdpA) after expression in different bacterial strains
  Eng. Life Sci. 6 (6), 552 - 559 10.1002/elsc.200620165
• Wiacek, C., Müller, S., Benndorf, D. (2006):
  A cytomic approach reveals population heterogeneity of Cupriavidus necator in response to harmful phenol concentrations
  Proteomics 6 (22), 5983 - 5994 10.1002/pmic.200600244

2005 (13)

• Ferraroni, M., Seifert, J., Travkin, V.M., Thiel, M., Kaschabek, S., Scozzafava, A., Golovleva, L., Schlömann, M., Briganti, F. (2005):
  Crystal structure of the hydroxyquinol 1,2-dioxygenase from Nocardioides simplex 3E, a key enzyme involved in polychlorinated aromatics biodegradation
  J. Biol. Chem. 280 (22), 21144 - 21154 10.1074/jbc.M500666200
• Fischer, W., Franke, H., Gröger-Arndt, H., Illes, P. (2005):
  Evidence for the existence of P2Y_1,2,4 receptor subtypes in HEK-293 cells: reactivation of P2Y₁ receptors after repetitive agonist application
  Naunyn-Schmiedebergs Arch. Pharmacol. 371 (6), 466 - 472 10.1007/s00210-005-1070-6
• Guenther, A., Franke, H., Laemmer, A., Wirkner, K., Groeger-Arndt, H., Kruegel, U., Sperlágh, B., Wagner, A., Illes, P., Schneider, D. (2005):
  Role of P2X7 receptors in cerebral ischemia models - in vitro and in vivo
  J. Neurol. Sci. 238 (Suppl. 1), S398 10.1016/S0022-510X(05)81532-1
• Kalkhof, S., Ihling, C., Mechtler, K., Sinz, A. (2005):
  Chemical cross-linking and high-performance Fourier transform ion cyclotron resonance mass spectrometry for protein interaction analysis: Application to a calmodulin/target peptide complex
  Anal. Chem. 77 (2), 495 - 503 10.1021/ac0487294
• Lorbiecke, R., Steffens, M., Tomm, J.M., Scholten, S., von Wiegen, P., Kranz, E., Wienand, U., Sauter, M. (2005):
  Phytosulphokine gene regulation during maize (Zea mays L.) reproduction
  J. Exp. Bot. 56 (417), 1805 - 1819 10.1093/jxb/eri169
• Mandelkow, E., von Bergen, M., Pickhardt, M., Gazova, Z., Khlistunova, I., Wang, Y.P., Biernat, J., Mandelkow, E.-M. (2005):
  Tau aggregation and Tau aggregation inhibitors
  J. Neurochem. 94 (Suppl. 2), 213 - 214 10.1111/j.1474-1644.2005.03326.x
• Mukrasch, M.D., Biernat, J., von Bergen, M., Griesinger, C., Mandelkow, E., Zweckstetter, M. (2005):
  Sites of tau important for aggregation populate β-structure and bind to microtubules and polyanions
  J. Biol. Chem. 280 (26), 24978 - 24986 10.1074/jbc.M501565200
• Pickhardt, M., Gazova, Z., von Bergen, M., Khlistunova, I., Wang, Y.P., Hascher, A., Mandelkow, E.-M., Biernat, J., Mandelkow, E. (2005):
  Anthraquinones inhibit tau aggregation and dissolve Alzheimer's paired helical filaments in vitro and in cells
  J. Biol. Chem. 280 (5), 3628 - 3635 10.1074/jbc.M410984200
• Schmidt, A., Kalkhof, S., Ihling, C., Cooper, D.M.F., Sinz, A. (2005):
  Mapping protein interfaces by chemical cross-linking and Fourier transform ion cyclotron resonance mass spectrometry: application to a calmodulin/adenylyl cyclase 8 peptide complex
  Eur. J. Mass Spectrom. 11 (5), 525 - 534 10.1255/ejms.748
• Sinz, A., Kalkhof, S., Ihling, C. (2005):
  Mapping protein interfaces by a trifunctional cross-linker combined with MALDI-TOF and ESI-FTICR mass spectrometry
  J. Am. Soc. Mass Spectrom. 16 (12), 1921 - 1931 10.1016/j.jasms.2005.07.020
• Thiede, B., Höhenwarter, W., Krah, A., Mattow, J., Schmid, M., Schmidt, F., Jungblut, P.R. (2005):
  Peptide mass fingerprinting
  Methods 35 (3), 237 - 247 10.1016/j.ymeth.2004.08.015
• von Bergen, M., Barghorn, S., Biernat, J., Mandelkow, E.-M., Mandelkow, E. (2005):
  Tau aggregation is driven by a transition from random coil to beta sheet structure
  Biochim. Biophys. Acta-Mol. Basis Dis. 1739 (2-3), 158 - 166 10.1016/j.bbadis.2004.09.010
• Wirkner, K., Köfalvi, A., Fischer, W., Günther, A., Franke, H., Gröger-Arndt, H., Nörenberg, W., Madarász, E., Vizi, E.S., Schneider, D., Sperlágh, B., Illes, P. (2005):
  Supersensitivity of P2X₇ receptors in cerebrocortical cell cultures after in vitro ischemia
  J. Neurochem. 95 (5), 1421 - 1437 10.1111/j.1471-4159.2005.03465.x

2004 (11)

• Benndorf, D., Davidson, I., Babel, W. (2004):
  Regulation of catabolic enzymes during long-term exposure of Delftia acidovorans MC1 to chlorophenoxy herbicides
  Microbiology-(UK) 150 (4), 1005 - 1014 10.1099/mic.0.26774-0
• Benndorf, D., Loffhagen, N., Härtig, C., Babel, W. (2004):
  Growth on phenol at chemostress levels amplifies the expression of the phenol degradation pathway in Acinetobacter calcoaceticus
  Eng. Life Sci. 4 (1), 38 - 42 10.1002/elsc.200400014
• Berger, K., Wissmann, D., Ihling, C., Kalkhof, S., Beck-Sickinger, A., Sinz, A., Paschke, R., Führer, D. (2004):
  Quantitative proteome analysis in benign thyroid nodular disease using the fluorescent ruthenium II tris(bathophenanthroline disulfonate) stain
  Mol. Cell. Endocrinol. 227 (1-2), 21 - 30 10.1016/j.mce.2004.08.001
• Mandelkow, E., von Bergen, M., Barghorn, S., Li, L., Biernat, J., Mandelkow, E.-M. (2004):
  Principles of assembly of tau protein into Alzheimer paired helical filaments
  Neurobiol. Aging 25 (Suppl. 2), S47 10.1016/S0197-4580(04)80157-X
• Mandelkow, E., von Bergen, M., Pickhardt, M., Biernat, J., Mandelkow, E.-M. (2004):
  Treatment of tauopathies: How to approach it?
  Neurobiol. Aging 25 (Suppl. 1), S17 10.1016/j.neurobiolaging.2003.12.002
• Mattow, J., Schmidt, F., Höhenwarter, W., Siejak, F., Schaible, U.E., Kaufmann, S.H.E. (2004):
  Protein identification and tracking in two-dimensional electrophoretic gels by minimal protein identifiers
  Proteomics 4 (10), 2927 - 2941 10.1002/pmic.200400908
• Meinhold-Heerlein, I., Mundhenke, C., Rosel, F., Jonat, W., Nagasaki, K., von Bergen, M., Maass, N. (2004):
  Protein profiling utilizing SELDI technology may detect ductal carcinoma in situ (DCIS) with high reliability in patient's serum
  J. Clin. Oncol. 22 (14S), 9654 10.1200/jco.2004.22.90140.9654
• Pickhardt, M., Gazova, Z., von Bergen, M., Wang, Y.P., Khlistunova, I., Hascher, A., Biernat, J., Mandelkow, E.-M. (2004):
  Search for small molecule inhibitors of tau aggregation into Alzheimer paired helical filaments
  Neurobiol. Aging 25 (Suppl. 2), S428 10.1016/S0197-4580(04)81407-6
• Pleissner, K.P., Eifert, T., Buettner, S., Schmidt, F., Boehme, M., Meyer, T.F., Kaufmann, S.H.E., Jungblut, P.R. (2004):
  Web-accessible proteome databases for microbial research
  Proteomics 4 (5), 1305 - 1313 10.1002/pmic.200300737
• Santos, P.M., Benndorf, D., Sá-Correia, I. (2004):
  Insights into Pseudomonas putida KT2440 response to phenol-induced stress by quantitative proteomics
  Proteomics 4 (9), 2640 - 2652 10.1002/pmic.200300793
• von Bergen, M., Li, L., Mandelkow, E. (2004):
  Conformation and stability of tau and Alzheimer paired helical filaments probed by tryptophan scanning mutagenesis
  Neurobiol. Aging 25 (Suppl. 2), S419 10.1016/S0197-4580(04)81375-7

2003 (1)

• Krayl, M., Benndorf, D., Loffhagen, N., Babel, W. (2003):
  Use of proteomics and physiological characteristics to elucidate ecotoxic effects of methyl tert-butyl ether in Pseudomonas putida KT2440
  Proteomics 3 (8), 1544 - 1552 10.1002/pmic.200300477

2002 (11)

• Barghorn, S., von Bergen, M., Li, L., Biernat, J., Mandelkow, E.-M., Mandelkow, E. (2002):
  Some mutations of tau protein in frontotemporal dementia (FTDP-17) promote aggregation of paired helical filaments by enhancing local beta structure
  Neurobiol. Aging 23 (Suppl. 1), S528 10.1016/S0197-4580(02)00052-0
• Benndorf, D. (2002):
  Bewältigung von Chemostress durch Detoxifizierung
  Ehrenkolloquium anlässlich des 65. Geburtstages von Prof. Dr. habil. Wolfgang Babel, Leipzig, 18.7.2002
• Benndorf, D., Babel, W. (2002):
  Assimilatory detoxification of herbicides by Delftia acidovorans MC1: Induction of two chlorocatechol 1,2-dioxygenases as response to chemostress
  Microbiology-(UK) 148 (9), 2883 - 2888 10.1099/00221287-148-9-2883
• Li, L., von Bergen, M., Biernat, J., Mandelkow, E.-M., Mandelkow, E. (2002):
  Intrinsic fluorescence of tau as a marker for PHF aggregation and PHF inhibitors
  Neurobiol. Aging 23 (Suppl. 1), S292 10.1016/S0197-4580(02)00052-0
• Li, L., von Bergen, M., Biernat, J., Mandelkow, E.-M., Mandelkow, E. (2002):
  Intrinsic fluorescence of tau as a probe of conformation and aggregation of Alzheimer paired helical filaments
  Mol. Biol. Cell 13 (Suppl. S), 325A
• Li, L., von Bergen, M., Mandelkow, E.-M., Mandelkow, E. (2002):
  Structure, stability, and aggregation of paired helical filaments from tau protein and FTDP-17 mutants probed by tryptophan scanning mutagenesis
  J. Biol. Chem. 277 (44), 41390 - 41400 10.1074/jbc.M206334200
• Loffhagen, N., Härtig, C., Benndorf, D., Babel, W. (2002):
  Effects of growth temperature and lipophilic carbon sources on the fatty acid composition and membrane lipid fluidity of Acinetobacter calcoaceticus 69V
  Acta Biotechnol. 22 (3-4), 235 - 243 10.1002/1521-3846(200207)22:3/4<235::AID-ABIO235>3.0.CO;2-I
• Mandelkow, E., von Bergen, M., Li, L., Barghorn, S., Biernat, J., Mandelkow, E.-M. (2002):
  Principles underlying the formation of Alzheimer paired helical filaments from tau protein: Hotspots of beta structure embedded in a random coil environment
  Neurobiol. Aging 23 (Suppl. 1), S551 10.1016/S0197-4580(02)00052-0
• Pickhardt, M., von Bergen, M., Li, L., Mandelkow, E.-M., Mandelkow, E. (2002):
  Searching for compounds that break Alzheimer-paired helical filaments
  Neurobiol. Aging 23 (Suppl. 1), S507 10.1016/S0197-4580(02)00052-0
• Soltmann, U., Wand, H., Müller, A., Kuschk, P., Stottmeister, U. (2002):
  Exposure to xenobiotics deeply affects the bacteriocenosis in the rhizosphere of helophytes
  Acta Biotechnol. 22 (1-2), 161 - 166 10.1002/1521-3846(200205)22:1/2<161::AID-ABIO161>3.0.CO;2-#
• Westendorf, A., Benndorf, D., Müller, R.H., Babel, W. (2002):
  The two enantiospecific dichlorprop/α-ketoglutarate-dioxygenases from Delftia acidovorans MC1 - protein and sequence data of RdpA and SdpA
  Microbiol. Res. 157 (4), 317 - 322 10.1078/0944-5013-00164

2001 (4)

• Benndorf, D., Loffhagen, N., Babel, W. (2001):
  Protein synthesis patterns in Acinetobacter calcoaceticus induced by phenol and catechol show specificities of responses to chemostress
  FEMS Microbiol. Lett. 200 (2), 247 - 252 10.1016/S0378-1097(01)00228-2
• Mandelkow, E.-M., Stamer, K., Biernat, J., Trinczek, B., von Bergen, M., Mandelkow, E. (2001):
  Tau protein and Alzheimer's disease: aggregation; phosphorylation; and role in axonal traffic and neurite outgrowth
  J. Neurochem. 77 (Suppl. 1), 1 10.1111/j.1471-4159.2001.t01-13-00002.x
• von Bergen, M., Barghorn, S., Li, L., Marx, A., Biernat, J., Mandelkow, E.-M., Mandelkow, E. (2001):
  Mutations of tau protein in frontotemporal dementia promote aggregation of paired helical filaments by enhancing local beta-structure
  J. Biol. Chem. 276 (51), 48165 - 48174 10.1074/jbc.M105196200
• von Bergen, M., Li, L., Barghorn, S., Biernat, J., Mandelkow, E.-M., Mandelkow, E. (2001):
  Mutations of tau protein in frontotemporal dementia (FTDP-17) promote aggregation of paired helical filaments by enhancing local β-structure
  Mol. Biol. Cell 12 (Suppl. S), 308A

2000 (6)

• Barghorn, S., Zheng-Fischhofer, Q., Ackmann, M., Biernat, J., von Bergen, M., Mandelkow, E.-M., Mandelkow, E. (2000):
  Structure, microtubule interactions, and paired helical filament aggregation by tau mutants of frontotemporal dementias
  Biochemistry 39 (38), 11714 - 11721 10.1021/bi000850r
• Benndorf, D. (Hrsg., 2000):
  Molekulare Mechanismen der Resistenz von Bakterien gegenüber Xenobiotika
  UFZ-Bericht 22/2000
  UFZ Leipzig-Halle GmbH, Leipzig, 95 S.
• Benndorf, D. (2000):
  Molekulare Mechanismen der Resistenz von Bakterien gegenüber Xenobiotika am Beispiel von Acinetobacter calcoaceticus 69-V
  Wissenschaftliches Kolloquium am UFZ Leipzig, Sektion Umweltmikrobiologie, Leipzig, 22.2.2000
• Friedhoff, P., von Bergen, M., Mandelkow, E.-M., Mandelkow, E. (2000):
  Structure of tau protein and assembly into paired helical filaments
  Biochim. Biophys. Acta-Mol. Basis Dis. 1502 (1), 122 - 132 10.1016/S0925-4439(00)00038-7
• von Bergen, M., Friedhoff, P., Biernat, J., Heberle, J., Mandelkow, E.-M., Mandelkow, E. (2000):
  Assembly of τ protein into Alzheimer paired helical filaments depends on a local sequence motif (³⁰⁶VQIVYK³¹¹) forming β structure
  Proc. Natl. Acad. Sci. U.S.A. 97 (10), 5129 - 5134 10.1073/pnas.97.10.5129
• von Bergen, M., Friedhoff, P., Biernat, J., Heberle, J., Mandelkow, E.-M., Mandelkow, E. (2000):
  Assembly of τ protein into Alzheimer paired helical filaments depends on a local sequence motif (³⁰⁶VQIVYK³¹¹) forming β structure
  Mol. Biol. Cell 11 (Suppl. S), 363A

1999 (1)

• Benndorf, D., Loffhagen, N., Babel, W. (1999):
  Induction of heat shock proteins in response to primary alcohols in Acinetobacter calcoaceticus
  Electrophoresis 20 (4-5), 781 - 789 10.1002/(SICI)1522-2683(19990101)20:4/5<781::AID-ELPS781>3.0.CO;2-A

1997 (1)

• Benndorf, D., Loffhagen, N., Babel, W. (1997):
  Chemicals and heat generate different protein patterns in Acinetobacter calcoaceticus
  J. Basic Microbiol. 37 (3), 167 - 174 10.1002/jobm.3620370304

1996 (2)

• Arndt, K., Krumbiegel, P., Rolle-Kampczyk, U., Herbarth, O. (1996):
  ¹⁵N investigations on effects of air pollutants on the nitrogen metabolism of Tetrahymena pyriformis as a model for environmental medicine
  Isot. Environ. Health Stud. 32 (2-3), 252 - 253 10.1080/10256019608036317
• Rolle-Kampczyk, U.E., Krumbiegel, P. (1996):
  Routine determination of ¹⁵N amounts in urine samples: Emission spectroscopy coupled with Kjeldahl digestion or with dry combustion?
  Isot. Environ. Health Stud. 32 (1), 111 - 115 10.1080/10256019608036299

1994 (1)

• Müller, A., Herbarth, O. (1994):
  Tetrahymena pyriformis - ein Zelltestsystem für die Umweltmedizin. Untersuchungen zum Schadschtoffeinfluß auf die Zellmorphologie von Tetrahymena pyriformis. Tetrahymena pyriformis - a cell test system for environmental medicine investigations into the effect of pollutants on cell size of Tetrahymena pyriformis
  Zbl. Hyg. u. Umweltmed. 196 (3), 227 - 236