Bioinformatics Platform Publications

Below you will find the MPUSP publications, which include bioinformatics analyses carried out by members of the institute‘s bioinformatics platform (since 2017).

Preprints

  1. Cornejo FA, Driller K, Ahmed-Begrich R, Schmidt K, Jahn M, Shanmuganathan V, Hahnke K, Kondrot F, Wulff TF, Rämisch S, Alagesan K, Charpentier E and Turgay K (2025) Targeting the translation machinery: The RNase Y specificity factor Y-complex coordinates ribosome degradation. bioRxiv. doi.org/10.1101/2025.06.27.661978
  2. Alver R, Hantke I, Cornejo FA, Gunka K, Rämisch S, Molière N, Charpentier E and Turgay K (2022) Protein arginine phosphorylation and de-phosphorylation facilitates protein homeostasis by a unique AAA+ chaperone protease system. bioRxiv. doi.org/10.1101/2022.09.15.508104
  3. Alagesan K, Ahmed-Begrich R and Charpentier E (2022) Improved N- and O-Glycopeptide Identification using High-Field Asymmetric Waveform Ion Mobility Spectrometry (FAIMS). bioRxiv. doi.org/10.1101/2022.12.12.520086

 

​​​​​​​Original Articles

  1. Krause K, Franch Arroyo S, Ugolini M, Kueck T, Sullivan TJ, Gálvez EJC, Muenzner M, Goosmann C, Brinkmann V, Frese CK, Alagesan K, Vierbuchen T, Heine H, Resch U, Sander LE and Charpentier E (2025) Streptococcus pyogenes EVs induce the alternative inflammasome via caspase-4/-5 in human monocytes. EMBO Rep. 26(19):4847-4885. doi: 10.1038/s44319-025-00558-7
  2. Ignatov D, Shanmuganathan V, Ahmed-Begrich R, Alagesan K, Hahnke K, Wang C, Krause K, Cornejo FA, Funke K, Erhardt M, Frese CK and Charpentier E (2025) RNA-binding protein YebC enhances translation of proline-rich amino acid stretches in bacteria. Nat. Commun. 16(1):6262. doi: 10.1038/s41467-025-60687-4
  3. Wulff TF, Ahmed-Begrich R, Hahnke K, Jahn M and Charpentier E (2025) Novel assembly of the SF370 strain of the important human pathogen Streptococcus pyogenes serotype M1. Microbiol. Resour. Announc. 14(1):e0119724. doi: 10.1128/mra.01197-24
  4. Jahn M, Crang N, Gynnå AH, Kabova D, Frielingsdorf S, Lenz O, Charpentier E and Hudson EP (2024) The energy metabolism of Cupriavidus necator in different trophic conditions. Appl. Environ. Microbiol. 90(10):e0074824. doi: 10.1128/aem.00748-24
  5. Wulff TF, Hahnke K, Lécrivain AL, Schmidt K, Ahmed-Begrich R, Finstermeier K and Charpentier E (2024) Dynamics of diversified A-to-I editing in Streptococcus pyogenes is governed by changes in mRNA stability. Nucleic Acids Res. 52(18):11234-11253. doi: 10.1093/nar/gkae629
  6. Lautenschläger N, Schmidt K, Schiffer C, Wulff TF, Hahnke K, Finstermeier K, Mansour M, Elsholz AKW and Charpentier E (2024) Expanding the genetic toolbox for the obligate human pathogen Streptococcus pyogenes. Front. Bioeng. Biotechnol. 12:1395659. doi: 10.3389/fbioe.2024.1395659
  7. Miao R, Jahn M, Shabestary K, Peltier G and Hudson EP (2023) CRISPR interference screens reveal growth-robustness tradeoffs in Synechocystis sp. PCC 6803 across growth conditions. Plant Cell 35(11):3937-3956. doi.org/10.1093/plcell/koad208
  8. Grätz L, Kowalski-Jahn M, Scharf MM, Kozielewicz P, Jahn M, Bous J, Lambert NA, Gloriam DE and Schulte G (2023) Pathway selectivity in Frizzleds is achieved by conserved micro-switches defining pathway-determining, active conformations. Nat. Commun. 14(1):4573. doi: 10.1038/s41467-023-40213-0
  9. Christensen S, Rämisch S and André I (2022) DnaK response to expression of protein mutants is dependent on translation rate and stability. Commun. Biol. 5(1):597. doi: 10.1038/s42003-022-03542-2
  10. Stelbrink B, Von Rintelen T, Richter K, Finstermeier K, Frahnert S, Cracraft J and Hofreiter M (2022) Insights into the geographical origin and phylogeographical patterns of Paradisaea birds-of-paradise. Zool. J. Linn. Soc. Vol. 196 (4), p.1394-1407.      doi.org/10.1093/zoolinnean/zlac010
  11. Birk MS, Ahmed-Begrich R, Tran S, Elsholz AKW, Frese CK and Charpentier E (2021) Time-resolved proteome analysis of Listeria monocytogenes during infection reveals the role of the AAA+ chaperone ClpC for host cell adaptation. mSystems 6(4):e0021521. doi: 10.1128/mSystems.00215-21
  12. Hüsing S, Halte M, van Look U, Guse A, Gálvez EJC, Charpentier E, Blair DF, Erhardt M and Renault TT (2021)Control of membrane barrier during bacterial type-III protein secretion. Nat. Commun. 12(1):3999. doi: 10.1038/s41467-021-24226-1
  13. Beerens D, Franch-Arroyo S, Sullivan TJ, Goosmann C, Brinkmann V and Charpentier E (2021) Survival strategies of Streptococcus pyogenes in response to phage infection. Viruses 13(4):612. doi: 10.3390/v13040612
  14. Gálvez EJC, Iljazovic A, Amend L, Lesker TR, Renault T, Thiemann S, Hao L, Roy U, Gronow A, Charpentier E and Strowig T (2020) Distinct polysaccharide utilization determines interspecies competition between intestinal Prevotella spp. Cell Host Microbe. 28(6):838-852.e6. doi: 10.1016/j.chom.2020.09.012
  15. Bratovič M, Fonfara I, Chylinski K, Gálvez EJC, Sullivan TJ, Boerno S, Timmermann B, Boettcher M and Charpentier E (2020) Bridge helix arginines play a critical role in Cas9 sensitivity to mismatches. Nat. Chem. Biol. 16(5):587-595. doi: 10.1038/s41589-020-0490-4
  16. Broglia L, Lécrivain AL, Renault TT, Hahnke K, Ahmed-Begrich R, Le Rhun A and Charpentier E (2020) An RNA-seq based comparative approach reveals the transcriptome-wide interplay between 3'-to-5' exoRNases and RNase Y. Nat. Commun. 11(1):1587. doi: 10.1038/s41467-020-15387-6
  17. Lécrivain AL, Le Rhun A, Renault TT, Ahmed-Begrich R, Hahnke K and Charpentier E (2018) In vivo 3’-to-5’ exoribonuclease targetomes of Streptococcus pyogenes. Proc. Natl. Acad. Sci. U. S. A. 115(46):11814-11819. doi: 10.1073/pnas.1809663115
  18. Fabiani FD, Renault TT, Peters B, Dietsche T, Gálvez EJC, Guse A, Freier K, Charpentier E, Strowig T, Franz-Wachtel M, Macek B, Wagner S, Hensel M and Erhardt M (2017) A flagellum-specific chaperone facilitates assembly of the core type III export apparatus of the bacterial flagellum. PLoS Biol. 15(8):e2002267. doi: 10.1371/journal.pbio.2002267

 

 

 

 

 

 

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