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2020

  • Selim KA, Haffner M. Heavy Metal Stress Alters the Response of the Unicellular Cyanobacterium Synechococcus elongatus PCC 7942 to Nitrogen Starvation. Life (Basel). 7;10(11): 275. (2020) doi: 10.3390/life10110275.
  • 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) doi: 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) doi: 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) doi: 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) doi: 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 aureusNat Commun. Jul 14;11(1):3526. (2020) doi: 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) doi: 10.3389/fmicb.2020.01147.
  • van Dalen R, Peschel A, van Sorge NM. Wall Teichoic Acid in Staphylococcus aureus Host Interaction. Trends Microbiol. (2020) doi: 10.1016/j.tim.2020.05.017.
  • 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 lugdunensisElife 9 (2020) doi: 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) doi: 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: 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 BAngenent 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: 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: 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: 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: 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: 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, CeccarelliM. Kanamycin Uptake into E. Coli Is Facilitated by OmpF and OmpC Porin Channels Located in the Outer Membrane. ACS Infect Dis. (2020) doi: 10.1021/acsinfecdis.0c00102.
  • Xia PF, Casini I, Schulz S, Klask CM, Angenent LTMolitor B. Reprogramming acetogenic bacteria with CRISPR-targeted base editing viadeamination. ACS Synth. Biol. (2020) doi: 10.1021/acssynbio.0c00226.
  • 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: 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.
  • Renz A, Widerspick L, Dräger A. FBA reveals guanylate kinase as a potential target for antiviral therapies against SARS-CoV-2. Zenodo (2020) doi: 10.1093/bioinformatics/btaa813.

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