CMFI Publications

2022

  • Kim L, Lee BG, Kim M, Kim MK, Kwon DH, Kim H, Brötz-Oesterhelt H, Roh SH, Song HK. Structural insights into ClpP protease side exit pore-opening by a pH drop coupled with substrate hydrolysis. EMBO J. May 20:e109755. (2022) doi: 10.15252/embj.2021109755.

  • Krysenko S, Okoniewski N, Nentwich M, Matthews A, Bäuerle M, Zinser A, Busche T, Kulik A, Gursch S, Kemeny A, Bera A, Wohlleben W. A Second Gamma-Glutamylpolyamine Synthetase, GlnA2, Is Involved in Polyamine Catabolism in Streptomyces coelicolor. Int J Mol Sci. 23(7):3752. (2022) doi: 10.3390/ijms23073752.

  • Huang J, Han M, Yang J, Kappler A, Jiang H. Salinity Impact on Composition and Activity of Nitrate-Reducing Fe(II)-Oxidizing Microorganisms in Saline Lakes. Appl Environ Microbiol. e0013222. (2022) doi: 10.1128/aem.00132-22.

  • Rath P, Rapp J, Brilisauer K, Braun M, Kolukisaoglu Ü, Forchhammer K, Grond S. Hybrid Chemoenzymatic Synthesis of C7-Sugars for Molecular Evidence of in vivo Shikimate Pathway Inhibition. Chembiochem. May 4. (2022) doi: 10.1002/cbic.202200241.

  • Doello S, Neumann N, Forchhammer K. Regulatory phosphorylation event of Phosphoglucomutase 1 tunes its activity to regulate glycogen metabolism. FEBS J. May 4. (2022) doi: 10.1111/febs.16471.

  • Stincone P, Fonseca Veras F, Micalizzi G, Donnarumma D, Vitale Celano G, Petras D, de Angelis M, Mondello L, Brandelli A. Listeria monocytogenes exposed to antimicrobial peptides displays differential regulation of lipids and proteins associated to stress response. Cell Mol Life Sci. 79(5):263. (2022) doi: 10.1007/s00018-022-04292-4.

  • Gavriilidou A, Kautsar SA, Zaburannyi N, Krug D, Müller R, Medema MH, Ziemert N. Compendium of specialized metabolite biosynthetic diversity encoded in bacterial genomes. Nat Microbiol. 7(5). (2022) doi: https://doi.org/10.1038/s41564-022-01110-2.

  • Mendes SS, Marques J, Mesterházy E, Straetener J, Arts M, Pissarro T, Reginold J, Berscheid A, Bornikoel J, Kluj RM, Mayer C, Oesterhelt F, Friães S, Royo B, Schneider T, Brötz-Oesterhelt H, Romão CC, Saraiva LM, 2022. Synergetic Antimicrobial Activity and Mechanism of Clotrimazole-Linked CO-Releasing Molecules. ACS Bio Med Chem Au.  (2022) doi: https://doi.org/10.1021/acsbiomedchemau.2c00007.

  • Jahn K, Handtke S, Palankar R, Kohler TP, Wesche J, Wolff M, Bayer J, Wolz C, Greinacher A, Hammerschmidt S. α-hemolysin of Staphylococcus aureus impairs thrombus formation. J Thromb Haemost. (2022) doi: 10.1111/jth.15703.

  • Schultz M, Mohammad M, Nguyen MT, Hu Z, Jarneborn A, Wienken CM, Froning M, Pullerits R, Ali A, Hayen H, Götz F, Jin T. Lipoproteins Cause Bone Resorption in a Mouse Model of Staphylococcus aureus Septic Arthritis. Front Microbiol. 13:843799. (2022) doi: https://doi.org/10.3389/fmicb.2022.843799.

  • Almario J, Mahmoudi M, Kroll S, Agler M, Placzek A, Mari A, Kemen E. The Leaf Microbiome of Arabidopsis Displays Reproducible Dynamics and Patterns throughout the Growing Season. mBio. (2022) Apr 14:e0282521. doi: 10.1128/mbio.02825-21.

  • Negri T, Mantri S, Angelov A, Peter S, Muth G, Eustáquio AS, Ziemert N. A rapid and efficient strategy to identify and recover biosynthetic gene clusters from soil metagenomes. Appl Microbiol Biotechnol. (2022) doi: 10.1007/s00253-022-11917-y
  • Sbierski-Kind J, Grenkowitz S, Schlickeiser S, Sandforth A, Friedrich M, Kunkel D, Glauben R, Brachs S, Mai K, Thürmer A, Radonić A, Drechsel O, Turnbaugh PJ, Bisanz JE, Volk HD, Spranger J, von Schwartzenberg RJ. Effects of caloric restriction on the gut microbiome are linked with immune senescence. Microbiome 10(1):57. (2022) doi: 10.1186/s40168-022-01249-4.
  • Bastounis E, Radhakrishnan P, Prinz CK, Theriot JA. Mechanical Forces Govern Interactions of Host Cells with Intracellular Bacterial Pathogens. Microbiol Mol Biol Rev. Mar 14:e0009420. (2022) doi: 10.1128/mmbr.00094-20.
  • Shalev O, Karasov TL, Lundberg DS, Ashkenazy H, Pramoj Na Ayutthaya P, Weigel D. Commensal Pseudomonas strains facilitate protective response against pathogens in the host plant. Nat Ecol Evol. 2022 Feb 24. (2022) doi: 10.1038/s41559-022-01673-7.
  • Huang YM, Jakus N, Straub D, Konstantinidis KT, Blackwell N, Kappler A, Kleindienst S. 'Candidatus ferrigenium straubiae' sp. nov., 'Candidatus ferrigenium bremense' sp. nov., 'Candidatus ferrigenium altingense' sp. nov., are autotrophic Fe(II)-oxidizing bacteria of the family Gallionellaceae. Syst Appl Microbiol. 45(3):126306. (2022) doi: https://doi.org/10.1016/j.syapm.2022.126306.

  • Patzner MS, Kainz N, Lundin E, Barczok M, Smith C, Herndon E, Kinsman-Costello L, Fischer S, Straub D, Kleindienst S, Kappler A, Bryce C. Seasonal Fluctuations in Iron Cycling in Thawing Permafrost Peatlands. Environ Sci Technol. 56(7):4620-4631. (2022) doi: https://doi.org/10.1021/acs.est.1c06937.

  • Abramov SM, Straub D, Tejada J, Grimm L, Schädler F, Bulaev A, Thorwarth H, Amils R, Kappler A, Kleindienst S. Biogeochemical Niches of Fe-Cycling Communities Influencing Heavy Metal Transport along the Rio Tinto, Spain. Appl Environ Microbiol. 88(4):e0229021. (2022) doi: 10.1128/AEM.02290-21.
  • Borisova M, Balbuchta K, Lovering A, Titz A, Mayer C. NamZ1 and NamZ2 from the oral pathogen Tannerella forsythia are peptidoglycan processing exo-β-N-acetylmuramidases with distinct substrate specificity. J Bacteriol. Feb 7:jb0059721. (2022) doi: 10.1128/jb.00597-21. 
  • Kuhn Cuellar L, Friedrich A, Gabernet G, de la Garza L, Fillinger S, Seyboldt A, Koch T, Zur Oven-Krockhaus S, Wanke F, Richter S, Thaiss WM, Horger M, Malek N, Harter K, Bitzer M, Nahnsen S. A data management infrastructure for the integration of imaging and omics data in life sciences. BMC Bioinformatics. 23(1):61. (2022) doi: 10.1186/s12859-022-04584-3. 
  • Huang L, Matsuo M, Calderón C, Fan SH, Ammanath AV, Fu X, Li N, Luqman A, Ullrich M, Herrmann F, Maier M, Cheng A, Zhang F, Oesterhelt F, Lämmerhofer M, Götz F. Molecular Basis of Rhodomyrtone Resistance in Staphylococcus aureus. mBio. Feb 15:e0383321. (2022) doi: 10.1128/mbio.03833-21.
  • Wegley Kelly L, Nelson CE, Petras D, Koester I, Quinlan ZA, Arts MGI, Nothias LF, Comstock J, White BM, Hopmans EC, van Duyl FC, Carlson CA, Aluwihare LI, Dorrestein PC, Haas AF. Distinguishing the molecular diversity, nutrient content, and energetic potential of exometabolomes produced by macroalgae and reef-building corals. Proc Natl Acad Sci U S A.  Feb 1;119(5):e2110283119. (2022) doi: 10.1073/pnas.2110283119. 
  • Panchiwala H, Shah S, Planatscher H, Zakharchuk M, König M, Dräger A. The systems biology simulation core library, Bioinformatics 38(3):864–865. (2022) doi: 10.1093/bioinformatics/btab669.
  • Glöckler M, Dräger A, Mostolizadeh R. NCMW: A Python Package to Analyze Metabolic Interactions in the Nasal Microbiome. Front. Bioinform. 2:827024. (2022) doi: 10.3389/fbinf.2022.827024.
  • Geißert JK, Bohn E, Mostolizadeh R, Dräger A, Autenrieth IB, Beier S, Deusch O, Renz A, Eichner M, Schütz  MS. A Computational Model of Bacterial Population Dynamics in Gastrointestinal Yersinia enterocolitica Infections in Mice. Biology 11:297. (2022) doi: 10.3390/ biology11020297

  • Krakau S, Straub D, Gourlé H, Gabernet G, Nahnsen S. nf-core/mag: a best-practice pipeline for metagenome hybrid assembly and binning, NAR Genomics and Bioinformatics 4(1):lqac007. (2022) doi: 10.1093/nargab/lqac007.

  • Tacconelli E, Göpel S, Gladstone BP, Eisenbeis S, Hölzl F, Buhl M, Górska A, Cattaneo C, Mischnik A, Rieg S, Rohde AM, Kohlmorgen B, Falgenhauer J, Trauth J, Käding N, Kramme E, Biehl LM, Walker SV, Peter S, Gastmeier P, Chakraborty T, Vehreschild MJ, Seifert H, Rupp J, Kern WV; DZIF BLOOMY study group. Development and validation of BLOOMY prediction scores for 14-day and 6-month mortality in hospitalised adults with bloodstream infections: a multicentre, prospective, cohort study. Lancet Infect Dis. Jan 19:S1473-3099(21)00587-9. (2022) doi: 10.1016/S1473-3099(21)00587-9.

  • Slavetinsky CJ, Hauser JN, Gekeler C, Slavetinsky J, Geyer A, Kraus A, Heilingbrunner D, Wagner S, Tesar M, Krismer B, Kuhn S, Ernst CM, Peschel A. Sensitizing Staphylococcus aureus to antibacterial agents by decoding and blocking the lipid flippase MprF. eLife 11:e66376. (2022) doi: 10.7554/eLife.66376.

  • Forchhammer K, Selim KA, Huergo LF. New views on PII signaling: from nitrogen sensing to global metabolic control. Trends Microbiol. (2022) doi: 10.1016/j.tim.2021.12.014.

  • Engelbrecht A, Wolf F, Esch A, Kulik A, Kozhushkov SI, de Meijere A, Hughes CC, Kaysser L. Discovery of a Cryptic Nitro Intermediate in the Biosynthesis of the 3-(trans-2'-Aminocyclopropyl)alanine Moiety of Belactosin A. Org Lett. 24(2):736-740. (2022) doi: 10.1021/acs.orglett.1c04205.
  • Lueder U, Jørgensen BB, Maisch M, Schmidt C, Kappler A. Influence of Fe(III) source, light quality, photon flux and presence of oxygen on photoreduction of Fe(III)-organic complexes - Implications for light-influenced coastal freshwater and marine sediments. Sci Total Environ. 814:152767. (2022) doi: 10.1016/j.scitotenv.2021.152767.
  • Malik IT, Hegemann JD, Brötz-Oesterhelt H. Generation of Lasso Peptide-Based ClpP Binders. International Journal of Molecular Sciences. 23(1):465. (2022) doi: https://doi.org/10.3390/ijms23010465.

 

2021

  • Bleul L, Francois P, Wolz C. Two-Component Systems of S. aureus: Signaling and Sensing Mechanisms. Genes (Basel). Dec 23;13(1):34. (2021) doi: 10.3390/genes13010034.
  • Abramov SM, Straub D, Tejada J, Grimm L, Schädler F, Bulaev A, Thorwarth H, Amils R, Kappler A, Kleindienst S. Biogeochemical Niches of Fe-cycling Communities Influencing Heavy Metal Transport Along the Rio Tinto, Spain. Appl Environ Microbiol. Dec 15:AEM0229021. (2021)  doi: 10.1128/AEM.02290-21.
  • Baumdicker F, Bisschop G, Goldstein D, Gower G, Ragsdale AP, Tsambos G, Zhu S, Eldon B, Ellerman EC, 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 Y, Gravel S, Kern AD, Koskela J, Ralph PL, Kelleher J. Efficient ancestry and mutation simulation with msprime 1.0. Genetics. Dec 13:iyab229. (2021) doi: 10.1093/genetics/iyab229. 
  • Petras D, Phelan VV, Acharya D, Allen AE, Aron AT, Bandeira N, Bowen BP, Belle-Oudry D, Boecker S, Cummings DA Jr, Deutsch JM, Fahy E, Garg N, Gregor R, Handelsman J, Navarro-Hoyos M, Jarmusch AK, Jarmusch SA, Louie K, Maloney KN, Marty MT, Meijler MM, Mizrahi I, Neve RL, Northen TR, Molina-Santiago C, Panitchpakdi M, Pullman B, Puri AW, Schmid R, Subramaniam S, Thukral M, Vasquez-Castro F, Dorrestein PC, Wang M. GNPS Dashboard: collaborative exploration of mass spectrometry data in the web browser. Nat Methods. Dec 3. (2021) doi: 10.1038/s41592-021-01339-5.
  • Nalpas N, Hoyles L, Anselm V, Ganief T, Martinez-Gili L, Grau C, Droste-Borel I, Davidovic L, Altafaj X, Dumas ME, Macek B. An integrated workflow for enhanced taxonomic and functional coverage of the mouse fecal metaproteome. Gut Microbes. Jan-Dec (2021)  doi: 10.1080/19490976.2021.1994836.
  • Schlatterer K, Peschel A, Kretschmer D. Short-chain fatty acid and FFAR2 activation - A new option for treating infections? Front. Cell. Infect. Microbiol. 1:785833. (2021) doi: 10.3389/fcimb.2021.785833.
  • Dopffel N, Jamieson J, Bryce C, Joshi P, Mansor M, Siade A, Prommer H, Kappler A.Temperature dependence of nitrate-reducing Fe(II) oxidation by Acidovorax strain BoFeN1 - evaluating the role of enzymatic vs. abiotic Fe(II) oxidation by nitrite. FEMS Microbiol Ecol. Nov 26, Online ahead of print. (2021) doi: 10.1093/femsec/fiab155.
  • Fink C, Beblawy S, Enkerlin AM, Mühling L, Angenent LT, Molitor B. A Shuttle-Vector System Allows Heterologous Gene Expression in the Thermophilic Methanogen Methanothermobacter thermautotrophicus ΔH. mBio. Nov 23; 12 (6): e02766-21. (2021) doi: 10.1128/mBio.02766-21.
  • Chevrette MG, Gavrilidou A, Mantri S, Selem-Mojica N, Ziemert N, Barona-Gómez F. The confluence of big data and evolutionary genome mining for the discovery of natural productsNat Prod Rep. Nov 17, (2021) doi: 10.1039/d1np00013f.
  • Aron AT, Petras D, Schmid R, Gauglitz JM, Büttel I, Antelo L, Zhi H, Nuccio SP, Saak CC, Malarney KP, Thines E, Dutton RJ, Aluwihare LI, Raffatellu M, Dorrestein PC. Native mass spectrometry-based metabolomics identifies metal-binding compounds. Nat Chem. Nov 18. Online ahead of print. (2021) doi: 10.1038/s41557-021-00803-1.
  • Li S, Kappler A, Haderlein SB, Zhu YG. Powering biological nitrogen removal from the environment by geobatteries. Trends Biotechnol. Nov 12, S0167-7799 (21) 00239-0. Online ahead of print. (2021) doi: 10.1016/j.tibtech.2021.10.008.
  • Fan SH, Liberini E, Götz F. Staphylococcus aureus Genomes Harbor Only MpsAB-Like Bicarbonate Transporter but Not Carbonic Anhydrase as Dissolved Inorganic Carbon Supply System. Microbiol Spectr. Nov 3: e0097021. Online ahead of print. (2021) doi: 10.1128/Spectrum.00970-21
  • Jakus N, Blackwell N, Straub D, Kappler A, Kleindienst S. Presence of Fe (II) and nitrate shapes aquifer-originating communities leading to an autotrophic enrichment dominated by a Fe(II)-oxidizing Gallionellaceae sp. FEMS Microbiol Ecol. Nov 1: fiab145. Online ahead of print. (2021) doi: 10.1093/femsec/fiab145. 
  • Mungan MD, Blin K, Ziemert N. ARTS-DB: a database for antibiotic resistant targets. Nucleic Acids Res. Oct 28; gkab940. Online ahead of print. (2021) doi: 10.1093/nar/gkab940. 
  • Rahmdel S, Götz F. The Multitasking Surface Protein of Staphylococcus epidermidis: Accumulation-Associated Protein (Aap). mBio. Oct 26; 12:e0198921. (2021) https://doi.org/10.1128/mbio.01989-21
  • Youngblut ND, Reischer GH, Dauser S, Maisch S, Walzer C, Stalder G, Farnleitner AH, Ley RE. Vertebrate host phylogeny influences gut archaeal diversity. Nat Microbiol. Oct 26; 6(11):1443-1454. (2021) doi: 10.1038/s41564-021-00980-2.
  • Huus KE, Ley RE. Blowing Hot and Cold: Body Temperature and the Microbiome. mSystems. Oct 26; 6(5):e0070721. (2021) doi: 10.1128/mSystems.00707-21.
  • Mantri SS, Negri T, Sales-Ortells H, Angelov A, Peter S, Neidhardt H, Oelmann Y, Ziemert N. Metagenomic Sequencing of Multiple Soil Horizons and Sites in Close Vicinity Revealed Novel Secondary Metabolite Diversity. mSystems. Oct 26; 6(5):e0101821. (2021) doi: 10.1128/mSystems.01018-21.

  • Ostaszewski M, Niarakis A, Mazein A, Kuperstein I, Phair R, Orta-Resendiz A, Singh V, Aghamiri SS, Acencio ML, Glaab E, Ruepp A, Fobo G, Montrone C, Brauner B, Frishman G, Monraz Gómez LC, Somers J, Hoch M, Kumar Gupta S, Scheel J, Borlinghaus H, Czauderna T, Schreiber F, Montagud A, Ponce de Leon M, Funahashi A, Hiki Y, Hiroi N, Yamada TG, Dräger A, Renz A, Naveez M, Bocskei Z, Messina F, Börnigen D, Fergusson L, Conti M, Rameil M, Nakonecnij V, Vanhoefer J, Schmiester L, Wang M, Ackerman EE, Shoemaker JE, Zucker J, Oxford K, Teuton J, Kocakaya E, Summak GY, Hanspers K, Kutmon M, Coort S, Eijssen L, Ehrhart F, Rex DAB, Slenter D, Martens M, Pham N, Haw R, Jassal B, Matthews L, Orlic-Milacic M, Senff Ribeiro A, Rothfels K, Shamovsky V, Stephan R, Sevilla C, Varusai T, Ravel JM, Fraser R, Ortseifen V, Marchesi S, Gawron P, Smula E, Heirendt L, Satagopam V, Wu G, Riutta A, Golebiewski M, Owen S, Goble C, Hu X, Overall RW, Maier D, Bauch A, Gyori BM, Bachman JA, Vega C, Grouès V, Vazquez M, Porras P, Licata L, Iannuccelli M, Sacco F, Nesterova A, Yuryev A, de Waard A, Turei D, Luna A, Babur O, Soliman S, Valdeolivas A, Esteban-Medina M, Peña-Chilet M, Rian K, Helikar T, Puniya BL, Modos D, Treveil A, Olbei M, De Meulder B, Ballereau S, Dugourd A, Naldi A, Noël V, Calzone L, Sander C, Demir E, Korcsmaros T, Freeman TC, Augé F, Beckmann JS, Hasenauer J, Wolkenhauer O, Wilighagen EL, Pico AR, Evelo CT, Gillespie ME, Stein LD, Hermjakob H, D'Eustachio P, Saez-Rodriguez J, Dopazo J, Valencia A, Kitano H, Barillot E, Auffray C, Balling R, Schneider R. COVID-19 Disease Map Community. COVID19 Disease Map, a computational knowledge repository of virus-host interaction mechanisms. Mol Syst Biol. Oct 17, (2021) doi:https://doi.org/10.15252/msb.202110387

  • Yamada TG, Ii K, König M, Feierabend M, Dräger A, Funahashi A. SBMLWebApp: Web-Based Simulation, Steady-State Analysis, and Parameter Estimation of Systems Biology Models. Processes. Oct 15; 9, 1830. (2021) doi: https://doi.org/10.3390/pr9101830.

  • Maier L, Goemans CV, Wirbel J, Kuhn M, Eberl C, Pruteanu M, Müller P, Garcia-Santamarina S, Cacace E, Zhang B, Gekeler C, Banerjee T, Anderson EE, Milanese A, Löber U, Forslund SK, Patil KR, Zimmermann M, Stecher B, Zeller G, Bork P & Typas A. Unravelling the collateral damage of antibiotics on gut bacteria. Nature, published on 13 October 2021. DOI: 10.1038/s41586-021-03986-2.
  • Payne DD, Renz A, Dunphy LJ, Lewis T, Dräger A, Papin JA. An updated genome-scale metabolic network reconstruction of Pseudomonas aeruginosa PA14 to characterize mucin-driven shifts in bacterial metabolism. NPJ Syst Biol Appl. Oct 8;7(1):37. (2021) doi: 10.1038/s41540-021-00198-2.
  • Calvete JJ, Pla D, Els J, Carranza S, Damm M, Hempel BF, John EBO, Petras D, Heiss P, Nalbantsoy A, Göçmen B, Süssmuth RD, Calderón-Celis F, Nosti AJ, Encinar JR. Combined Molecular and Elemental Mass Spectrometry Approaches for Absolute Quantification of Proteomes: Application to the Venomics Characterization of the Two Species of Desert Black Cobras, Walterinnesia aegyptia and Walterinnesia morgani. J Proteome Res. Oct 4. (2021) doi: 10.1021/acs.jproteome.1c00608.
  • Petras D, Caraballo-Rodríguez AM, Jarmusch AK, Molina-Santiago C, Gauglitz JM, Gentry EC, Belda-Ferre P, Romero D, Tsunoda SM, Dorrestein PC, Wang M. Chemical Proportionality within Molecular Networks. Anal Chem. Sep 28;93(38):12833-12839. (2021) doi: 10.1021/acs.analchem.1c01520.
  • Wang Y, Baumdicker F, Schweiger P, Kuenzel S, Staubach F. Horizontal gene transfer-mediated bacterial strain variation affects host fitness in Drosophila. BMC Biol. Sep 27;19(1):187. (2021) doi: 10.1186/s12915-021-01124-y.
  • Pfaffelhuber P, Sester-Huss E, Baumdicker F, Naue J, Lutz-Bonengel S, Staubach F. Inference of recent admixture using genotype data. Forensic Sci Int Genet. Sep 20; 56: 102593. Online ahead of print. (2021) doi: 10.1016/j.fsigen.2021.102593.
  • Orthwein T, Huergo LF, Forchhammer K, Selim KA. Kinetic Analysis of a Protein-protein Complex to Determine its Dissociation Constant (KD) and the Effective Concentration (EC50) of an Interplaying Effector Molecule Using Bio-layer Interferometry. Bio Protoc. Sep 5;11(17):e4152. (2021) doi: 10.21769/BioProtoc.4152.
  • Kretschmer D, Breitmeyer R, Gekeler C, Lebtig M, Schlatterer K, Nega M, Stahl M, Stapels D, Rooijakkers S, Peschel A. Staphylococcus aureus Depends on Eap Proteins for Preventing Degradation of Its Phenol-Soluble Modulin Toxins by Neutrophil Serine Proteases. Front. Immunol.  12:701093. (2021) doi: 10.3389/fimmu.2021.701093.
  • Conzentino MS, Santos TPC, Selim KA, Wagner B, Alford JT, Deobald N, Paula NM, Rego FGM, Zanette DL, Aoki MN, Nardin JM, Huergo MCC, Reis RA, Huergo LF. Ultra-fast, high throughput and inexpensive detection of SARS-CoV-2 seroconversion using Ni2+ magnetic beads. Anal Biochem. 631:114360. doi: 10.1016/j.ab.2021.114360.
  • Illigmann A, Thoma Y, Pan S, Reinhardt L, Brötz-Oesterhelt H. Contribution of the Clp Protease to Bacterial Survival and Mitochondrial Homoeostasis. Microb Physiol. 31(3):260-279. (2021) doi: 10.1159/000517718
  • Kopparapu PK, Deshmukh M, Hu Z, Mohammad M, Maugeri M, Götz F, Valadi H, Jin T. Lipoproteins Are Responsible for the Pro-Inflammatory Property of Staphylococcus aureus Extracellular Vesicles. Int J Mol Sci. 22(13):7099. (2021) doi: 10.3390/ijms22137099.
  • Caraballo-Rodríguez AM, Puckett SP, Kyle KE, Petras D, da Silva R, Nothias LF, Ernst M, van der Hooft JJJ, Tripathi A, Wang M, Balunas MJ, Klassen JL, Dorrestein PC. Chemical Gradients of Plant Substrates in an Atta texana Fungus Garden. mSystems. 6(4):e0060121. (2021) doi: 10.1128/mSystems.00601-21.
  • Semanjski M, Gratani FL, Englert T, Nashier P, Beke V, Nalpas N, Germain E, George S, Wolz C, Gerdes K, Macek B. Proteome Dynamics during Antibiotic Persistence and Resuscitation. mSystems 6(4):e00549-21. (2021) doi: 10.1128/mSystems.00549-21.
  • Wang CY, Lempp M, Farke N, Donati S, Glatter T, Link H. Metabolome and proteome analyses reveal transcriptional misregulation in glycolysis of engineered E. coli. Nat Commun 12:4929. (2021). doi: https://doi.org/10.1038/s41467-021-25142-0.
  • Schlatterer K, Beck C, Schoppmeier U, Peschel A, Kretschmer D: Acetate sensing by GPR43 alarms neutrophils and protects from severe sepsis. Communications Biology 4:928. (2021) doi: https://doi.org/10.1038/s42003-021-02427-0.
  • Torres Salazar BO, Heilbronner S, Peschel A, Krismer B. Secondary Metabolites Governing Microbiome Interaction of Staphylococcal Pathogens and Commensals. Microb Physiol Jul 29:1-19. (2021) doi: https://doi.org/10.1159/000517082.
  • Singh N, Kronenberger T, Eipper A, Weichel F, Franz M, Macek B, Wagner S. Conserved salt bridges facilitate assembly of the helical core export apparatus of a Salmonella enterica type III secretion system, J Mol Biol Jul 22:167175. (2021) doi: https://doi.org/10.1016/j.jmb.2021.167175.
  • Fan SH, Matsuo M, Huang L, Tribelli PM, Götz F. The MpsAB Bicarbonate Transporter Is Superior to Carbonic Anhydrase in Biofilm-Forming Bacteria with Limited CO2 Diffusion. Microbiol Spectr. Jul 21:e0030521. (2021) doi: https://doi.org/10.1128/Spectrum.00305-21.
  • Mitousis L, Maier H, Martinovic L, Kulik A, Stockert S, Wohlleben W, Stiefel A, Musiol-Kroll EM. Engineering of Streptoalloteichus tenebrarius 2444 for Sustainable Production of Tobramycin. Molecules. Jul 18;26(14):4343. (2021) doi: https://doi.org/10.3390/molecules26144343.
  • Mingyar E, Mühling L, Kulik A, Winkler A, Wibberg D, Kalinowski J, Blin K, Weber T, Wohlleben W, Stegmann E. A Regulator Based "Semi-Targeted" Approach to Activate Silent Biosynthetic Gene Clusters. Int J Mol Sci. Jul 15;22 (14): 7567. (2021) doi: 10.3390/ijms22147567.
  • Huang YM, Straub D, Kappler A, Smith N, Blackwell N, Kleindienst S. A Novel Enrichment Culture Highlights Core Features of Microbial Networks Contributing to Autotrophic Fe(II) Oxidation Coupled to Nitrate Reduction. Microb Physiol. Jul 2:1-16. (2021) doi: https://doi.org/10.1159/000517083.
  • Luqman A, Götz F. The Ambivalent Role of Skin Microbiota and Adrenaline in Wound Healing and the Interplay between Them. Int J Mol Sci., 22(9):4996. May 8 (2021) doi:10.3390/ijms22094996
  • Rapp J, Wagner B, Brilisauer K, Forchhammer K. In vivo Inhibition of the 3-Dehydroquinate Synthase by 7-Deoxysedoheptulose Depends on Promiscuous Uptake by Sugar Transporters in Cyanobacteria. Front Microbiol. 12:692986. (2021) doi: https://doi.org/10.3389/fmicb.2021.692986.
  • Dräger A, Helikar T, Barberis M, Birtwistle M, Calzone L, Chaouiya C, Hasenauer J, Karr JR, Niarakis A, Rodríguez Martínez M, Saez-Rodriguez J, Thakar J. SysMod: the ISCB community for data-driven computational modelling and multi-scale analysis of biological systems. Bioinformatics Jun 24:btab229. (2021) doi: https://doi.org/10.1093/bioinformatics/btab229.
  • Schmid R, Petras D, Nothias LF et al. Ion identity molecular networking for mass spectrometry-based metabolomics in the GNPS environment. Nat Commun 12: 3832. (2021) doi: https://doi.org/10.1038/s41467-021-23953-9.
  • Brötz-Oesterhelt H, Vorbach A. Reprogramming of the Caseinolytic Protease by ADEP Antibiotics: Molecular Mechanism, Cellular Consequences, Therapeutic Potential. Front Mol Biosci 8: 690902. (2021) doi: https://doi.org/10.3389/fmolb.2021.690902.
  • Hottmann I, Borisova M, Schäffer C, Mayer C. Peptidoglycan Salvage Enables the Periodontal Pathogen Tannerella forsythia to Survive within the Oral Microbial Community. Microb Physiol (2021) doi: https://doi.org/10.1159/000516751.
  • Du X, Larsen J, Li M, Walter A, Slavetinsky C, Both A, Sanchez Carballo P M, Stegger M, Lehmann E, Liu Y, Liu J, Slavetinsky J, Duda K A, Krismer B, Heilbronner S, Weidenmaier C, Mayer C, Rohde H, Winstel V, Peschel A. Staphylococcus epidermidis clones express Staphylococcus aureus-type wall teichoic acid to shift from commensal to pathogen behavior. Nature Microbiology 6:757–768. (2021) doi: https://doi.org/10.1038/s41564-021-00913-z.
  • Rozbeh R, Forchhammer K. Split NanoLuc technology allows quantitation of interactions between PII protein and its receptors with unprecedented sensitivity and reveals transient interactions. Sci Rep 11:12535. (2021) doi:
  • https://doi.org/10.1038/s41598-021-91856-2.
  • Renz A, Widerspick L, Dräger A. Genome-Scale Metabolic Model of Infection with SARS-CoV-2 Mutants Confirms Guanylate Kinase as Robust Potential Antiviral Target. Genes 12:796. (2021) doi: https://doi.org/10.3390/genes12060796.
  • How Can We Effectively Combat Antibiotic Resistant Bacterial Pathogens?, interview with Andreas Peschel. Latest Thinking Video Publication. (2021) doi: https://doi.org/10.21036/LTPUB10921.
  • Bier K, Schittek B. Beneficial effects of coagulase-negative Staphylococci on Staphylococcus aureus skin colonization. Exp Dermatol. May 6:1-11. (2021) doi: https://doi.org/10.1111/exd.14381.
  • Saad H, Aziz S, Gehringer M, Kramer M, Straetener J, Berscheid A, Brötz-Oesterhelt H, Gross H. Nocathioamides, uncovered by a Tunable Metabologenomic Approach, define a Novel Class of Chimeric Lanthipeptides. Angew Chem Int Ed Engl. May 14. (2021) doi: https://doi.org/10.1002/anie.202102571.
  • Neumann N, Doello S, Forchhammer K. Recovery of Unicellular Cyanobacteria from Nitrogen Chlorosis: A Model for Resuscitation of Dormant Bacteria. Microb Physiol. Apr 20:1-10. (2021) doi: 10.1159/000515742. Online ahead of print.
  • Fišarová L, Botka T, Du X, Mašlaňová I, Bárdy P, Pantůček R, Benešík M, Roudnický P, Winstel V, Larsen J, Rosenstein R, Peschel A, Doškař J. Staphylococcus epidermidis Phages Transduce Antimicrobial Resistance Plasmids and Mobilize Chromosomal Islands. mSphere. 6: e00223-21. (2021) doi: https://doi.org/10.1128/mSphere.00223-21.
  • Reich M, Spomer L, Klindt C, Fuchs K, Stindt J, Deutschmann K, Höhne J, Liaskou E, Hov JR, Karlsen TH, Beuers U, Verheij J, Ferreira-Gonzalez S, Hirschfield G, Forbes SJ, Schramm C, Esposito I, Nierhoff D, Fickert P, Fuchs CD, Trauner M, García-Beccaria M, Gabernet G, Nahnsen S, Mallm JP, Vogel M, Schoonjans K, Lautwein T, Köhrer K, Häussinger D, Luedde T, Heikenwalder M, Keitel V. Downregulation of TGR5 (GPBAR1) in biliary epithelial cells contributes to the pathogenesis of sclerosing cholangitis. J Hepatol. Apr 16:1–42. (2021) doi: 10.1016/j.jhep.2021.03.029. Online ahead of print.
  • Walter A, Friz S, Mayer C. Chitin, Chitin Oligosaccharide, and Chitin Disaccharide Metabolism of Escherichia coli Revisited: Reassignment of the Roles of ChiA, ChbR, ChbF, and ChbG. Microb Physiol. Apr 1:1–17. ( 2021) doi: 10.1159/000515178. Online ahead of print.
  • Rapp J, Rath P, Kilian J, Brilisauer K, Grond S, Forchhammer K. A bioactive molecule made by unusual salvage of radical SAM enzyme by-product 5-deoxyadenosine blurs the boundary of primary and secondary metabolism. J Biol Chem. Mar 31:100621. (2021) doi: 10.1016/j.jbc.2021.100621. Online ahead of print.
  • Zimmermann M, Patil KR, Typas A, Maier L. Towards a mechanistic understanding of reciprocal drug-microbiome interactions. Mol Syst Biol. 17:e10116. (2021) doi: 10.15252/msb.202010116.
  • Huergo LF, Selim KA, Conzentino MS, Gerhardt ECM, Santos ARS, Wagner B, Alford JT, Deobald N, Pedrosa FO, de Souza EM, Nogueira MB, Raboni SM, Souto D, Rego FGM, Zanette DL, Aoki MN, Nardin JM, Fornazari B, Morales HMP, Borges VA, Nelde A, Walz JS, Becker M, Schneiderhan-Marra N, Rothbauer U, Reis RA, Forchhammer K. Magnetic Bead-Based Immunoassay Allows Rapid, Inexpensive, and Quantitative Detection of Human SARS-CoV-2 Antibodies. ACS Sens. Mar 26;6(3):703-708. (2021) doi: 10.1021/acssensors.0c02544.
  • Hörömpöli D, Ciglia C, Glüsenkamp KH, Haustedt LO, Falkenstein-Paul H, Bendas G, Berscheid A, Brötz-Oesterhelt H. The Antibiotic Negamycin Crosses the Bacterial Cytoplasmic Membrane by Multiple Routes. Antimicrob Agents Chemother. 65:e00986-20. (2021) doi: 10.1128/AAC.00986-20.
  • Müller M, Calvert M, Hottmann I, Kluj RM, Teufel T, Balbuchta K, Engelbrecht A, Selim KA, Xu Q, Borisova M, Titz A, Mayer C. The exo-β-N-acetylmuramidase NamZ from Bacillus subtilis is the founding member of a family of exo-lytic peptidoglycan hexosaminidases. J Biol Chem. Mar 5:100519. (2021) doi: 10.1016/j.jbc.2021.100519. Online ahead of print.
  • Silber N, Mayer C, Matos de Opitz CL, Sass P. Progression of the late-stage divisome is unaffected by the depletion of the cytoplasmic FtsZ pool. Commun Biol. 4(1):270. (2021) doi: 10.1038/s42003-021-01789-9.
  • Renz A, Widerspick L, Dräger A. First Genome-Scale Metabolic Model of Dolosigranulum pigrum Confirms Multiple Auxotrophies. Metabolites. 11(4):232. (2021) doi: 10.3390/metabo11040232.
  • Mohammad M, Na M, Hu Z, Nguyen MT, Kopparapu PK, Jarneborn A, Karlsson A, Ali A, Pullerits R, Götz F, Jin T. Staphylococcus aureus lipoproteins promote abscess formation in mice, shielding bacteria from immune killing. Commun Biol. 4(1):432. (2021) doi: 10.1038/s42003-021-01947-z.
  • Ortiz A, Vega NM, Ratzke C, Gore J. Interspecies bacterial competition regulates community assembly in the C. elegans intestine. ISME J. Feb 15. (2021) doi: 10.1038/s41396-021-00910-4. Online ahead of print.
  • Orthwein T, Scholl J, Spät P, Lucius S, Koch M, Macek B, Hagemann M, Forchhammer K. The novel PII-interactor PirC identifies phosphoglycerate mutase as key control point of carbon storage metabolism in cyanobacteria. PNAS 118(6): e2019988118. (2021) doi: https://doi.org/10.1073/pnas.2019988118
  • Selim KA, Maldener I. Cellular and Molecular Strategies in Cyanobacterial Survival-"In Memory of Prof. Dr. Wolfgang Lockau". Life (Basel). Feb 9;11(2):132. (2021) doi: https://doi.org/10.3390/life11020132.
  • Doello S, Burkhardt M, Forchhammer K. The essential role of sodium bioenergetics and ATP homeostasis in the developmental transitions of a cyanobacterium. Curr Biol. 31:1-10. (2021) doi: 10.1016/j.cub.2021.01.065. Online ahead of print.
  • Michaelis L, Treß M, Löw HC, Klees J, Klameth C, Lange A, Grießhammer A, Schäfer A, Menz S, Steimle A, Schulze-Osthoff K, Frick JS. Gut Commensal-Induced IκBζ Expression in Dendritic Cells Influences the Th17 Response.  Front Immunol. Jan 19;11:612336. (2021) doi: 10.3389/fimmu.2020.612336.
  • Saur J S, Wirtz S N, Schilling N A, Krismer B, Peschel A, Grond S. Distinct Lugdunins from a New Efficient Synthesis and BroadExploitation of Its MRSA-Antimicrobial Structure. J Med Chem (2021) doi: 10.1021/acs.jmedchem.0c02170.
  • Wex K W, Saur J S, Handel F, Ortlieb N, Mokeev V, Kulik A, Niedermeyer T H J, Mast Y, Grond S, Berscheid A, Brötz-Oesterhelt H. Bioreporters for direct mode of action-informed screening of antibiotic producer strains. CellChemBio (2021) doi: 10.1016/j.chembiol.2021.02.022.
  • Koeninger L, Osbelt L, Berscheid A, Wendler J, Berger J, Hipp K, Lesker TR, Pils MC, Malek NP, Jensen BAH, Brötz-Oesterhelt H, Strowig T, Wehkamp J. Curbing gastrointestinal infections by defensin fragment modifications without harming commensal microbiota. Commun Biol. 4(1):47. (2021) doi: 10.1038/s42003-020-01582-0.
  • Esquivel-Elizondo S, Bağcı C, Temovska M, Jeon BS, Bessarab I, Williams RBH, Huson DH, Angenent LT. The Isolate Caproiciproducens sp. 7D4C2 Produces n-Caproate at Mildly Acidic Conditions From Hexoses: Genome and rBOX Comparison With Related Strains and Chain-Elongating Bacteria. Front Microbiol. Jan 14;11:594524. (2021) doi: 10.3389/fmicb.2020.594524.

2020

  • Luqman A, Zabel S, Rahmdel S, Merz B, Gruenheit N, Harter J, Nieselt K, Götz F. 2020. The Neuromodulator-Encoding sadA Gene Is Widely Distributed in the Human Skin Microbiome. Front Microbiol. Dec 20, 11:573679, (2020) https://doi.org/10.3389/fmicb.2020.573679
  • Bernardes JP, Mishra N, Tran F, Bahmer T, Best L, Blase JI, Bordoni D, Franzenburg J, Geisen U, Josephs-Spaulding J, Köhler P, Künstner A, Rosati E, Aschenbrenner AC, Bacher P, Baran N, Boysen T, Brandt B, Bruse N, Dörr J, Dräger A, Elke G, Ellinghaus D, Fischer J, Forster M, Franke A, Franzenburg S, Frey N, Friedrichs A, Fuß J, Glück A, Hamm J, Hinrichsen F, Hoeppner MP, Imm S, Junker R, Kaiser S, Kan YH, Knoll R, Lange C, Laue G, Lier C, Lindner M, Marinos G, Markewitz R, Nattermann J, Noth R, Pickkers P, Rabe KF, Renz A, Röcken C, Rupp J, Schaffarzyk A, Scheffold A, Schulte-Schrepping J, Schunk D, Skowasch D, Ulas T, Wandinger KP, Wittig M, Zimmermann J, Busch H, Hoyer BF, Kaleta C, Heyckendorf J, Kox M, Rybniker J, Schreiber S, Schultze JL, Rosenstiel P; HCA Lung Biological Network; Deutsche COVID-19 Omics Initiative (DeCOI). Longitudinal Multi-omics Analyses Identify Responses of Megakaryocytes, Erythroid Cells, and Plasmablasts as Hallmarks of Severe COVID-19. Immunity. Dec 15, (2020) doi: 10.1016/j.immuni.2020.11.017. 
  • Mostolizadeh R, Dräger A. Computational Model Informs Effective Control Interventions against Y. enterocolitica Co-Infection. Biology (Basel). Nov 30, (2020) doi: 10.3390/biology9120431.
  • Nega M, Tribelli PM, Hipp K, Stahl M, Götz F. New insights in the coordinated amidase and glucosaminidase activity of the major autolysin (Atl) in Staphylococcus aureusCommun Biol. Nov 20, 3:695, (2020) https://doi.org/10.1038/s42003-020-01405-2
  • Luqman A, Kharisma VD, Ruiz RA, Götz F.  In Silico and in Vitro Study of Trace Amines (TA) and Dopamine (DOP) Interaction with Human Alpha 1-Adrenergic Receptor and the Bacterial Adrenergic Receptor QseC. Cell Physiol Biochem. Sep 20, 54:888-898. (2020) https://doi.org/10.33594/000000276
  • Nguyen MT, Matsuo M, Niemann S, Herrmann M, Götz F. Lipoproteins in Gram-Positive Bacteria: Abundance, Function, Fitness. Front Microbiol. Sep 18; 11:582582, (2020) https://doi.org/10.3389/fmicb.2020.582582
  • Carey MA, Dräger A, Beber ME, Papin JA, Yurkovich JT. Community standards to facilitate development and address challenges in metabolic modeling. Mol Syst Biol.  Aug, (2020) doi: 10.15252/msb.20199235.
  • Keating SM, Waltemath D, König M, Zhang F, Dräger A, Chaouiya C, Bergmann FT, Finney A, Gillespie CS, Helikar T, Hoops S, Malik-Sheriff RS, Moodie SL, Moraru II, Myers CJ, Naldi A, Olivier BG, Sahle S, Schaff JC, Smith LP, Swat MJ, Thieffry D, Watanabe L, Wilkinson DJ, Blinov ML, Begley K, Faeder JR, Gómez HF, Hamm TM, Inagaki Y, Liebermeister W, Lister AL, Lucio D, Mjolsness E, Proctor CJ, Raman K, Rodriguez N, Shaffer CA, Shapiro BE, Stelling J, Swainston N, Tanimura N, Wagner J, Meier-Schellersheim M, Sauro HM, Palsson B, Bolouri H, Kitano H, Funahashi A, Hermjakob H, Doyle JC, Hucka M; SBML Level 3 Community members. SBML Level 3: an extensible format for the exchange and reuse of biological models. Mol Syst Biol. Aug 16, (2020) doi: 10.15252/msb.20199110
  • Zhang F, Smith LP, Blinov ML, Faeder J, Hlavacek WS, Juan Tapia J, Keating SM, Rodriguez N, Dräger A, Harris LA, Finney A, Hu B, Hucka M, Meier-Schellersheim M. Systems biology markup language (SBML) level 3 package: multistate, multicomponent and multicompartment species, version 1, release 2. J Integr Bioinform. Jul 6,  (2020) doi: 10.1515/jib-2020-0015. 
  • Gardiner JH, Komazin G, Matsuo M, Cole K, Götz F, Meredith TC. Lipoprotein N-Acylation in Staphylococcus aureus Is Catalyzed by a Two-Component Acyl Transferase System. mBio. 11 (4) .(2020) https://doi.org/10.1128/mBio.01619-20
  • Belikova D, Jochim A, Power J, Holden MTG, Heilbronner S. "Gene accordions" cause genotypic and phenotypic heterogeneity in clonal populations of Staphylococcus aureus. Nat Commun. Jul 14;11(1):3526. (2020) https://doi.org/10.1038/s41467-020-17277-3
  • Ehmann D, Koeninger L, Wendler J, Malek NP, Stange EF, Wehkamp J, Jensen BAH. Fragmentation of Human Neutrophil α-Defensin 4 to Combat Multidrug Resistant Bacteria. Front. Microbiol. (2020) https://doi.org/10.3389/fmicb.2020.01147.
  • Jochim A, Adolf L, Belikova D, Schilling NA, Setyawati I, Chin D, Meyers S, Verhamme P, Heinrichs DE, Slotboom DJ, Heilbronner S. An ECF-type transporter scavenges heme to overcome iron-limitation in Staphylococcus lugdunensis. Elife 9 (2020) https://doi.org/10.7554/eLife.57322.
  • Raue S, Fan SH, Rosenstein R, Zabel S, Luqman A, Nieselt K, Götz F. The Genome of Staphylococcus epidermidis O47. Front Microbiol., Aug 25;11:2061. (2020) https://doi.org/10.3389/fmicb.2020.02061
  • Ostaszewski M, Mazein A, Gillespie ME, Kuperstein I, Niarakis A, Hermjakob H, Pico AR, Willighagen EL, Evelo CT, Hasenauer J, Schreiber F, Dräger A, Demir E, Wolkenhauer O, Furlong LI, Barillot E, Dopazo J, Orta-Resendiz A, Messina F, Valencia A, Funahashi A, Kitano H, Auffray C, Balling R, Schneider R. COVID-19 Disease Map, building a computational repository of SARS-CoV-2 virus-host interaction mechanisms. Sci Data. May 5, (2020) doi: 10.1038/s41597-020-0477-8.  
  • Luqman A, Muttaqin MZ, Yulaipi S, Ebner P, Matsuo M, Zabel S, Tribelli PM, Nieselt K, Hidayati D, Götz F. Trace amines produced by skin bacteria accelerate wound healing in mice. Commun Biol 3:277 (2020) doi: https://doi.org/10.1038/s42003-020-1000-7.
  • Silber N, Pan S, Schäkermann S, Mayer C, Brötz-Oesterhelt H, Sass P. Cell Division Protein FtsZ Is Unfolded for N-Terminal Degradation by Antibiotic-Activated ClpP. mBio 11(3):e01006-20. (2020) doi: 10.1128/mBio.01006-20.
  • Klask CM, Kliem-Kuster N, Molitor B, Angenent L. Nitrate Feed Improves Growth and Ethanol Production of Clostridium ljungdahlii With CO2 and H2, but Results in Stochastic Inhibition Events. Front. Microbiol. (2020) doi: https://doi.org/10.3389/fmicb.2020.00724.
  • Buchweitz LF, Yurkovich JT, Blessing C, Kohler V, Schwarzkopf F, King ZA, Yang L, Jóhannsson F, Sigurjónsson ÓE, Rolfsson Ó, Heinrich J, Dräger A. Visualizing metabolic network dynamics through time-series metabolomic data. BMC Bioinformatics. Apr 3, (2020) doi: 10.1186/s12859-020-3415-z.
  • Walter A, Unsleber S, Rismondo J, Jorge AM, Peschel A, Gründling A, Mayer C. Phosphoglycerol-type wall and lipoteichoic acids are enantiomeric polymers differentiated by the stereospecific glycerophosphodiesterase GlpQ. J Biol Chem. 295(12):4024-4034 (2020) doi: https://doi.org/10.1074/jbc.RA120.012566.
  • Wagner S, Diepold A. A Unified Nomenclature for Injectisome-Type Type III Secretion Systems. Curr Top Microbiol Immunol. 10.1007/82 (2020) doi: https://doi.org/10.1007/82_2020_210.
  • Lieven C, Beber ME, Olivier BG, Bergmann FT, Ataman M, Babaei P, Bartell JA, Blank LM, Chauhan S, Correia K, Diener C, Dräger A, et al. MEMOTE for standardized genome-scale metabolic model testing. Nat Biotechnol 38:272–276 (2020) doi: https://doi.org/10.1038/s41587-020-0446-y.
  • Ewels PA, Peltzer A, Fillinger S, Patel H, Alneberg J, Wilm A, Garcia MU, Di Tommaso P, Nahnsen S. The nf-core framework for community-curated bioinformatics pipelines. Nat Biotechnol 38:276–278 (2020) doi: https://doi.org/10.1038/s41587-020-0439-x.
  • Bafna JA, Sans-Serramitjana E, Acosta-Gutiérrez S, Bodrenko I, Hörömpöli D, Berscheid A, Brötz-Oesterhelt H, Winterhalter M, Ceccarelli M. Kanamycin Uptake into E. Coli Is Facilitated by OmpF and OmpC Porin Channels Located in the Outer Membrane. ACS Infect Dis. (2020) doi: https://doi.org/10.1021/acsinfecdis.0c00102.
  • Xia PF, Casini I, Schulz S, Klask CM, Angenent LT, Molitor B. Reprogramming acetogenic bacteria with CRISPR-targeted base editing via deamination. ACS Synth. Biol.
  • Malik IT, Pereira R, Vielberg MT, Mayer C, Straetener J, Thomy D, Famulla K, Castro H, Sass P, Groll M, Brötz‐Oesterhelt H. Functional Characterisation of ClpP Mutations Conferring Resistance to Acyldepsipeptide Antibiotics in Firmicutes. ChemBioChem 21 (2020) doi: https://doi.org/10.1002/cbic.201900787
  • Norsigian CJ, Pusarla N, McConn JL, Yurkovich JT, Dräger A, Palsson BO, King Z. BiGG Models 2020: multi-strain genome-scale models and expansion across the phylogenetic tree. Nucleic Acids Res. Jan 8, (2020) doi: 10.1093/nar/gkz1054.

 

2019

  • Macek B, Forchhammer K, Hardouin J, Weber-Ban E, Grangeasse C, Mijakovic I. Protein post-translational modifications in bacteria. Nat Rev Microbiol. 17(11):651-664. (2019) doi: 10.1038/s41579-019-0243-0.
  • Rougny A, Touré V, Moodie S, Balaur I, Czauderna T, Borlinghaus H, Dogrusoz U, Mazein A, Dräger A, Blinov ML, Villéger A, Haw R, Demir E, Mi H, Sorokin A, Schreiber F, Luna A. Systems Biology Graphical Notation: Process Description language Level 1 Version 2.0. J Integr Bioinform. Jun 13, (2019) doi: 10.1515/jib-2019-0022. 
  • Schilling NA, Berscheid A, Schumacher J, Saur JS, Konnerth MC, Wirtz SN, Beltrán Beleña JM, Zipperer A, Krismer B, Peschel A, Kalbacher H, Brötz-Oesterhelt H, Steinem C, Grond SC. Synthetic lugdunin analogues reveal essential structural motifs for antimicrobial action and proton translocation capability. Angew Chem Int Ed Engl. (2019) May 6 doi: https://doi.org/10.1002/anie.201901589.
  • George SE, Hrubesch J, Breuing I, Vetter N, Korn N, Hennemann K, Bleul L, Willmann M, Ebner P, Götz F, Wolz C. Oxidative stress drives the selection of quorum sensing mutants in the Staphylococcus aureus population. Proceedings of the National Academy of Sciences 116(38) (2019) doi: https://doi.org/10.1073/pnas.1902752116.

Preprints

  • 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.Taxonomic and functional diversity of aquatic heterotrophs is sustained by dissolved organic matter chemodiversity.

    bioRxiv (2022) doi: https://doi.org/10.1101/2022.03.21.485019.

  • Leonidou N, Renz A, Mostolizadeh R, Dräger A. New Workflow Predicts Drug Targets Against SARS-CoV-2 via Metabolic Changes in Infected Cells. Preprints (2022) 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. Silent recognition of flagellins from human gut commensal bacteria by Toll-like receptor 5. bioRxiv (2022). 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. Prokaryotic phospholipid translocation by ubiquitous PplT domain proteins. bioRxiv (2022) doi: https://doi.org/10.1101/2022.03.11.483950.
  • Dahal S, Renz A, Dräger A, Yang L.Genome-scale modeling of Pseudomonas aeruginosa PA14 unveils its broad metabolic capabilities and role of metabolism in drug potentiation. bioRxiv (2021) doi: https://doi.org/10.1101/2021.04.15.439930
  • Burger KE, Pfaffelhuber P, Baumdicker F. Neural Networks for self-adjusting Mutation Rate Estimation when the Recombination Rate is unknown. bioRxiv (2021) 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. Efficient ancestry and mutation simulation with msprime 1.0. bioRxiv (2021) 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. Native Metabolomics Identifies the Rivulariapeptolide Family of Protease Inhibitors. bioRxiv (2021) doi: https://doi.org/10.1101/2021.09.03.458897.
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