2021

Höll D. Das Gespenst der Pandemie. Politik und Poetik der Cholera in der Literatur des 19. Jahrhunderts. Stuttgart, Frommann-Holzboog, 2021. ISBN:9783772834714.
Höll D. Mikrobiom und Ethik. Ärzteblatt Baden-Württemberg 76(6): 320-323. (2021) doi: 352312651_Mikrobiom_und_Ethik.
Höll D. Zu Einer Ethik Der Ästhetik in Pandemischen Zeiten. Zeitschrift Für Praktische Philosophie 8(1). (2021) doi: 10.22613/zfpp/8.1.8.
Höll D. Microgothic: Microbial Aesthetics of Haunted Nature. Haunted Nature. (2021) doi: 10.1007/978-3-030-81869-2_2.
Selim KA, Haffner M, Burkhardt M, Mantovani O, Neumann N, Albrecht R, Seifert R, Krüger L, Stülke J, Hartmann MD, Hagemann M, Forchhammer K. Diurnal metabolic control in cyanobacteria requires perception of second messenger signaling molecule c-di-AMP by the carbon control protein SbtB. Sci. Adv. 7(50): eabk0568. (2021) doi: 10.1126/sciadv.abk0568.
Bleul L, Francois P, Wolz C. Two-Component Systems of S. aureus: Signaling and Sensing Mechanisms. Genes (Basel). 13(1): 34. (2021) doi: 10.3390/genes13010034.
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Dräger A, Waltemath D. Overview: Standards for Modeling in Systems Medicine. Systems Medicine 3: 345–353. (2021) doi: 10.1016/B978-0-12-816077-0.00001-7.
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 220(3). (2021) doi: 10.1093/genetics/iyab229.
Renz A, Mostolizadeh R, Dräger A. Clinical Applications of Metabolic Models in SBML Format. Systems Medicine. 3: 362–371. (2021) doi: 10.1016/B978-0-12-801238-3.11524-7.
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. 19: 134–136. (2021) doi: 10.1038/s41592-021-01339-5.
Touré V, Dräger A, Luna A, Dogrusoz U, Rougny A. The Systems Biology Graphical Notation: Current Status and Applications in Systems Medicine. Systems Medicine 3: 372–381. (2021) doi: 10.1016/B978-0-12-801238-3.11515-6.
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. 13(1): e1994836. (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. 97(12). (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. 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 products. Nat. Prod. Rep. 38: 2024–2040. (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. 14: 100–109. (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. 40(4): 377–380. (2021) doi: 10.1016/j.tibtech.2021.10.008.
Brüls T, Baumdicker F, Smidt H. Editorial: Synthetic Microbial Ecology. Front Microbiol. 12: eCollection. (2021) doi: 10.3389/fmicb.2021.757848.
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. 9(3): 00970-21. (2021) doi: 10.1128/Spectrum.00970-21.
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Mungan MD, Blin K, Ziemert N. ARTS-DB: a database for antibiotic resistant targets. Nucleic Acids Res. 50(D1): D736–D740. (2021) doi: 10.1093/nar/gkab940.
Rahmdel S, Götz F. The Multitasking Surface Protein of Staphylococcus epidermidis: Accumulation-Associated Protein (Aap). mBio. 12:e0198921. (2021) doi: 10.1128/mbio.01989-21.
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Huus KE, Ley RE. Blowing Hot and Cold: Body Temperature and the Microbiome. mSystems. 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. 6(5):e0101821. (2021) doi: 10.1128/mSystems.01018-21.
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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. 9: 1830. (2021) doi: 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 599: 120–124. (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. 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. 20(11): 5064–5078. (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. 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. 19(1): 187. (2021) doi: 10.1186/s12915-021-01124-y.
Panchiwala H, Shah S, Planatscher H, Zakharchuk M, König M, Dräger A. The Systems Biology Simulation Core Library. Bioinformatics. 38(3): 864–865. (2021) doi: 10.1093/bioinformatics/btab669.
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. 56: 102593. (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 (K_D) and the Effective Concentration (EC₅₀) of an Interplaying Effector Molecule Using Bio-layer Interferometry. Bio Protoc. 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.
Heilbronner S. Staphylococcus lugdunensis. Trends Microbiol. 29(12): 1143–1145. (2021) doi: 10.1016/j.tim.2021.07.008.
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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.
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Torres Salazar BO, Heilbronner S, Peschel A, Krismer B. Secondary Metabolites Governing Microbiome Interaction of Staphylococcal Pathogens and Commensals. Microb Physiol 31(3): 198–216 . (2021) doi: 10.1159/000517082.
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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. 9(1): e0030521. (2021) doi: 10.1128/Spectrum.00305-21.
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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. 22(14): 7567. (2021) doi: 10.3390/ijms22147567.
Kengmo Tchoupa A, Eijkelkamp BA, Peschel A. Bacterial adaptation strategies to host-derived fatty acids, Trends Microbiol. 30(3): 241–253. (2021) doi: 10.1016/j.tim.2021.06.002.
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. 31(3): 280–295. (2021) doi: 10.1159/000517083.
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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. (2021) doi: 10.3390/ijms22094996.
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Renz A, Dräger A. Curating and comparing 114 strain-specific genome-scale metabolic models of Staphylococcus aureus. npj Syst Biol Appl 7:30. (2021) doi: 10.1038/s41540-021-00188-4.
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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 31(2): 123–134. (2021) doi: 10.1159/000516751.
Rapp J, Forchhammer K: 5-Deoxyadenosine Metabolism: More than “Waste Disposal”. Microb Physiol 31(3): 248–259. (2021) doi: 10.1159/000516105.
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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: 10.1038/s41598-021-91856-2.
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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: 10.3390/genes12060796.
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