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Preprints

  • Schumacher J, Mueller P, Sulzer J, Faber F, Molitor B, Maier L. (2024) Proton-pump inhibitors increase C. difficile infection risk by altering pH rather than by affecting the gut microbiome based on a bioreactor model. bioRxiv. doi: 10.1101/2024.07.10.602898.

  • Kippnich J, Benz F, Uecker H, Baumdicker F. (2024) Effectiveness of CRISPR-Cas in Sensitizing Bacterial Populations with Plasmid-Encoded Antimicrobial Resistance. bioRxiv. doi: 10.1101/2024.07.05.602127.

  • Rosenstein R, Torres Salazar BO, Sauer C, Heilbronner S, Krismer B, Peschel A. (2024) Siderophore piracy enables the nasal commensal Staphylococcus lugdunensis to antagonize the pathogen Staphylococcus aureus. bioRxiv. doi: 10.1101/2024.02.29.582731.

  • Samir S, Doello S, Zimmer E, Haffner M, Enkerlin AM, Müller T, Dengler L, Lambidis SP, Sivabalasarma S, Albers SV, Selim KA. (2023) The second messenger c-di-AMP controls natural competence via ComFB signaling protein. bioRxiv. doi: 10.1101/2023.11.27.568819.

  • Haffner M, Mantovani O, Spät P, Maček B, Hagemann M, Forchhammer K, Selim KA. (2023) Diurnal rhythm causes metabolic crises in the cyanobacterial mutants of c-di-AMP signalling cascade. bioRxiv. doi: 10.1101/2023.11.14.567006.

  • Lubrano P, Schramm T, Lorenz E, Alvarado A, Eigenmann SC, Stadelmann A, Thavapalan S, Waffenschmidt N, Peter S, Drescher K, Link H. (2023) Purine nucleotide limitation undermines antibiotic action in clinical Escherichia coli. bioRxiv. doi: 10.1101/2023.06.22.546106.

  • Tchoupa AK, Elsherbini AMA, Xiaoqing F, Ghaneme O, Seibert L, Böcker MA, Lebtig M, Camus J, Lambidis SP, Schittek B, Kretschmer D, Lämmerhofer M, Peschel A. (2023) Lipase-mediated detoxification of host-derived antimicrobial fatty acids by Staphylococcus aureus. bioRxiv. doi: 10.1101/2023.05.15.540481.

  • Gautam A, Bhowmik D, Basu S, Lahiri A, Zeng W, Paul S. (2023) Microbiome Metabolome Integration Platform (MMIP): a web-based platform for microbiome and metabolome data integration and feature identification. bioRxiv. doi: 10.1101/2023.04.04.535534.

  • Stincone P, Pakkir Shah AK, Schmid R, Graves L, Lambidis SP, Torres R, Xia S, Minda V, Aron A, Wang M, Hughes CC, Petras D. (2023) Evaluation of Data Dependent MS/MS Acquisition Parameters for Non-targeted Metabolomics and Molecular Networking of Environmental Samples - Focus on the Q Exactive Platform. ChemRxiv. doi: 6416f0bfaad2a62ca1017b3f.

  • Leonidou N, Fritze E, Renz A, Dräger A. (2023) SBOannotator: a Python Tool for the Automated Assignment of Systems Biology Ontology Terms. Preprints 2023020317. doi: 10.20944/preprints202302.0317.v1.

  • Walsh D, Salzer A, Wolz C, Aylott J, Hardie KR. (2023) The biocide triclosan induces (p)ppGpp dependent antibiotic tolerance and alters SarA dependent biofilm structures in Staphylococcus aureus. bioRxiv. doi: 10.1101/2023.02.01.525840.

  • Adolf LA, Müller-Jochim A, Kricks L, Puls JS, Lopez D, Grein Fabian, Heilbronner S. (2023) Functional membrane  microdomains and the hydroxamate siderophore transporter ATPase FhuC govern Isd-dependent heme acquisition in Staphyloccocus aureus. bioRxiv. doi: 10.1101/2023.01.11.523574.

  • Babele PK, Srivastava A, Selim KA, Kumar A. (2022) Millet-inspired systems metabolic engineering of NUE in crops. Trends Biotechnol. doi: 10.1016/j.tibtech.2022.10.008.

  • Bork F, Greve C L, Youn C, Chen S, Wang Y, Nasri M, Focken J, Scheurer J, Engels P, Dubbelaar M, Hipp K, Schittek B, Bugl S, Löffler M W, Skokowa J, Archer N K, Weber A. (2022) naRNA is a canonical neutrophil extracellular trap (NET) component and novel inflammation-amplifying composite DAMP. bioRxiv. doi: 10.1101/2022.07.26.499571.

  • Casini I, McCubbin T, Esquivel-Elizondo S, Luque GG, Evseeva D, Fink C, Beblawy S, Youngblut ND, Aristilde L, Huson DH, Dräger A, Ley RE, Marcellin E, Angenent LT, Molitor B. (2022) An integrated systems-biology platform for power-to-gas technology. bioRxiv. doi: 10.1101/2022.12.30.522236.

  • Krauss S, Harbig TA, Rapp J, Schaefle T, Franz-Wachtel M, Reetz L, Elsherbini AMA, Macek B, Grond S, Link H, Nieselt K, Krismer B, Peschel A, Heilbronner S. (2022) Horizontal Transfer of Bacteriocin Biosynthesis Genes Requires Metabolic Adaptation To Improve Compound Podruction and Cellular Fitness. Microbiol. Spectr. doi: 10.1128/spectrum.03176-22.

  • Renz A, Hohner M, Breitenbach M, Josephs-Spaulding J, Dürrwald J, Best L, Jami R, Marinos G, Cabreiro F, Dräger A, Schindler M, Kaleta Christoph. (2022) Metabolic Modeling Elucidates Phenformin and Atpenin A4 as Broad-Spectrum Antiviral Drugs. Preprints. doi: 10.20944/preprints202210.0223.v1.

  • Hauser JN, Tchoupa AK, Zabel, Nieselt K, Ernst CM, Slavetinsky CJ, Peschel A. (2022) Prokaryotic phospholipid translocation by ubiquitous PplT domain proteins. bioRxiv. doi: 10.1101/2022.03.11.483950.

  • Farke N, Schramm T, Verhuelsdonk A, Link H. (2022) Systematic analysis of in-source modifications of primary metabolites during flow-injection time-of-flight mass spectrometry. bioRxiv. doi: 10.1101/2022.09.28.509873.

  • Jarmusch AK, Aron AT, Petras D, Phelan VV, Bittremieux W, Acharya DD, Ahmed MMA, Bauermeister A, Bertin MJ, Boudreau PD, Borges RM, Bowen BP, Brown CJ, Chagas FO, Clevenger KD, Correia MSP, Crandrall WJ, Crüsemann M, Damiani T, Fiehn O, Garg N, Gerwick WH, Gilbert JR, Globisch D, Gomes PWP, Heuckeroth S, James CA, Jarmusch SA, Kakhkhorov SA, Kang KB, Kersten RD, Kim H, Kirk RD, Kohlbacher O, Kontou EE, Liu K, Lizama-Chamu I, Luu GT, Knaan TL, Marty MT, McAvoy AC, McCall LI, Mohamed OG, Nahor O, Niedermeyer THJ, Northern TR, Overdahl KE, Pluskal T, Rainer J, Reher R, Rodriguez E, Sachsenberg TT, Sanchez LM, Schmid R, Stevens C, Tian Zhenyu, Tripathi A, Tsugawa H, Nishida K, Matsuzawa Y, van der Hooft JJJ, Vicini A, Walter A, Weber T, Xiong Q, Xu T, Zhao HN, Dorrestein PC, Wang M. (2022) A Universal Language for Finding Mass Spectrometry Data Patterns. bioRxiv. doi: 10.1101/2022.08.06.503000.

  • Selim KA, Haffner M, Albrecht R, Zhu H, Forchhammer K, Hartmann MD. (2022) Carbon signaling protein SbtB possesses redox-regulated apyrase activity to facilitate regulation of bicarbonate transporter SbtA. bioRxiv. doi: 10.1101/2022.05.18.492403.

  • Clasen S J, Bell M E W, Lee D H, Henseler Z M, Borbón A, de la Cuesta-Zuluaga J, Parys K, Zou J, Youngblut N D, Gewirtz, Belkhadir Y, Ley R E. (2022) Silent recognition of flagellins from human gut commensal bacterial by Toll-like receptor 5. bioRxiv. doi: https://doi.org/10.1101/2022.04.12.488020.

  • Fink C, Martinez-Cano G, Shuster J, Panzera A, Angenent LT, Molitor B. The targeted deletion of genes responsible for expression of the Mth60 fimbriae leads to loss of cell-cell connections in M. thermautotrophicus ΔH. https://doi.org/10.1101/2022.05.13.491833.

  • Garcia SL, Nuy JK, Mehrshad M, Hampel JJ, Sedano-Nuñez VT, Buck M, Divne A, Lindström ES, Petras D, Hawkes J, Bertilsson S. (2022) Taxonomic and functional diversity of aquatic heterotrophs is sustained by dissolved organic matter chemodiversity. bioRxiv. doi: https://doi.org/10.1101/2022.03.21.485019.

  • Leonidou N, Renz A, Mostolizadeh R, Dräger A. (2022) New Workflow Predicts Drug Targets Against SARS-CoV-2 via Metabolic Changes in Infected Cells. Preprints. doi: https://doi.org/10.20944/preprints202203.0290.v1.

  • Clasen SJ, Bell ME, Lee D, Henseler Z, Borbon A, de la Cuesta-Zuluaga J, Parys K, Zou J, Youngblut ND, Gewirtz AT, Belkhadir Y, Ley RE. (2022) Silent recognition of flagellins from human gut commensal bacteria by Toll-like receptor 5. bioRxiv. doi: https://doi.org/10.1101/2022.04.12.488020.

  • Hauser J N, Kengmo Tchoupa A, Zabel S, Nieselt K, Ernst CM, Slavetinsky CJ, Peschel A. (2022) Prokaryotic phospholipid translocation by ubiquitous PplT domain proteins. bioRxiv. doi: https://doi.org/10.1101/2022.03.11.483950.

  • Dahal S, Renz A, Dräger A, Yang L. (2021) Genome-scale modeling of Pseudomonas aeruginosa PA14 unveils its broad metabolic capabilities and role of metabolism in drug potentiation. bioRxiv. doi: https://doi.org/10.1101/2021.04.15.439930

  • Burger KE, Pfaffelhuber P, Baumdicker F. (2021) Neural Networks for self-adjusting Mutation Rate Estimation when the Recombination Rate is unknown. bioRxiv. doi: https://doi.org/10.1101/2021.09.02.457550.

  • Baumdicker F, Bisschop G, Goldstein D, Gower G, Ragsdale AP, Tsambos G, Zhu S, Eldon B, Ellerman CE, Galloway JG, Gladstein AL, Gorjanc G, Guo B, Jeffery B, Kretzschmar WW, Lohse K, Matschiner M, Nelson D, Pope NS, Quinto-Cortés CD, Rodrigues MF, Saunack K, Sellinger T, Thornton K, van Kemenade H, Wohns AW, Wong HY, Gravel S, Kern AD, Koskela J, Ralph PL, Kelleher J. (2021) Efficient ancestry and mutation simulation with msprime 1.0. bioRxiv. doi: https://doi.org/10.1101/2021.08.31.457499.

  • Reher R, Aron AT, Fajtova P, Liu C, Shalom IYB, Bittremieux W, Wang M, Matos-Hernandez ML, Alexander KL, Caro-Diaz EJ, Naman CB, Dorrestein PC, O’Donoghue AJ, Gerwick WH, Petras D. (2021) Native Metabolomics Identifies the Rivulariapeptolide Family of Protease Inhibitors. bioRxiv. doi: https://doi.org/10.1101/2021.09.03.458897.

  • Klask CM, Jäger B, Angenent LTMolitor B. (2021) Genetic evidence reveals the indispensable role of the rseC gene for autotrophy and the importance of a functional electron balance for nitrate reduction in Clostridium ljungdahliibioRxiv. doi: https://doi.org/10.1101/2021.08.03.455012.

  • Maier L, Goemans CV, Pruteanu M, Wirbel J, Kuhn M, Cacace E, Banerjee T, Anderson EE, Milanese A, Löber U, Forslund SK, Patil KR, Zeller G, Bork P, Typas A. (2020) Dissecting the collateral damage of antibiotics on gut microbes. bioRxiv. doi: https://doi.org/10.1101/2020.01.09.893560.

  • Bittner Z, Liu X, Shankar S, Tapia-Abellán A, Kalbacher H, Andreeva L, Mangan M, Düwell P, Lovotti M, Bosch K, Dickhöfer S, Marcu A, Stevanović S, Herster F, Löffler MW, Wolz OO, Schilling N, Kümmerle-Deschner J, Wagner S, Delor A, Grimbacher B, Wu H, Latz E, Weber ANR. (2020) BTK operates a phospho-tyrosine switch to regulate NLRP3 inflammasome activity. bioRxiv. doi: https://doi.org/10.1101/864702.

  • Geißert JK, Bohn E, Mostolizadeh R, Dräger A, Autenrieth IB, Beier S, Deusch O, Eichner M, Schütz MS. (2020) Model-based prediction of bacterial population dynamics ingastrointestinal infection. bioRxiv. doi: https://doi.org/10.1101/2020.08.11.244202.

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