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Items: 41

1.

Recovery of gut microbiota of healthy adults following antibiotic exposure.

Palleja A, Mikkelsen KH, Forslund SK, Kashani A, Allin KH, Nielsen T, Hansen TH, Liang S, Feng Q, Zhang C, Pyl PT, Coelho LP, Yang H, Wang J, Typas A, Nielsen MF, Nielsen HB, Bork P, Wang J, Vilsbøll T, Hansen T, Knop FK, Arumugam M, Pedersen O.

Nat Microbiol. 2018 Nov;3(11):1255-1265. doi: 10.1038/s41564-018-0257-9. Epub 2018 Oct 22.

PMID:
30349083
2.

Thermal proteome profiling in bacteria: probing protein state in vivo.

Mateus A, Bobonis J, Kurzawa N, Stein F, Helm D, Hevler J, Typas A, Savitski MM.

Mol Syst Biol. 2018 Jul 6;14(7):e8242. doi: 10.15252/msb.20188242.

3.

Species-specific activity of antibacterial drug combinations.

Brochado AR, Telzerow A, Bobonis J, Banzhaf M, Mateus A, Selkrig J, Huth E, Bassler S, Zamarreño Beas J, Zietek M, Ng N, Foerster S, Ezraty B, Py B, Barras F, Savitski MM, Bork P, Göttig S, Typas A.

Nature. 2018 Jul;559(7713):259-263. doi: 10.1038/s41586-018-0278-9. Epub 2018 Jul 4.

PMID:
29973719
4.

Pervasive Protein Thermal Stability Variation during the Cell Cycle.

Becher I, Andrés-Pons A, Romanov N, Stein F, Schramm M, Baudin F, Helm D, Kurzawa N, Mateus A, Mackmull MT, Typas A, Müller CW, Bork P, Beck M, Savitski MM.

Cell. 2018 May 31;173(6):1495-1507.e18. doi: 10.1016/j.cell.2018.03.053. Epub 2018 Apr 26.

5.

Nutritional preferences of human gut bacteria reveal their metabolic idiosyncrasies.

Tramontano M, Andrejev S, Pruteanu M, Klünemann M, Kuhn M, Galardini M, Jouhten P, Zelezniak A, Zeller G, Bork P, Typas A, Patil KR.

Nat Microbiol. 2018 Apr;3(4):514-522. doi: 10.1038/s41564-018-0123-9. Epub 2018 Mar 19.

PMID:
29556107
6.

Extensive impact of non-antibiotic drugs on human gut bacteria.

Maier L, Pruteanu M, Kuhn M, Zeller G, Telzerow A, Anderson EE, Brochado AR, Fernandez KC, Dose H, Mori H, Patil KR, Bork P, Typas A.

Nature. 2018 Mar 29;555(7698):623-628. doi: 10.1038/nature25979. Epub 2018 Mar 19.

7.

Phenotype inference in an Escherichia coli strain panel.

Galardini M, Koumoutsi A, Herrera-Dominguez L, Cordero Varela JA, Telzerow A, Wagih O, Wartel M, Clermont O, Denamur E, Typas A, Beltrao P.

Elife. 2017 Dec 27;6. pii: e31035. doi: 10.7554/eLife.31035.

8.

Systematically investigating the impact of medication on the gut microbiome.

Maier L, Typas A.

Curr Opin Microbiol. 2017 Oct;39:128-135. doi: 10.1016/j.mib.2017.11.001. Review.

PMID:
29169088
9.

Salt-responsive gut commensal modulates TH17 axis and disease.

Wilck N, Matus MG, Kearney SM, Olesen SW, Forslund K, Bartolomaeus H, Haase S, Mähler A, Balogh A, Markó L, Vvedenskaya O, Kleiner FH, Tsvetkov D, Klug L, Costea PI, Sunagawa S, Maier L, Rakova N, Schatz V, Neubert P, Frätzer C, Krannich A, Gollasch M, Grohme DA, Côrte-Real BF, Gerlach RG, Basic M, Typas A, Wu C, Titze JM, Jantsch J, Boschmann M, Dechend R, Kleinewietfeld M, Kempa S, Bork P, Linker RA, Alm EJ, Müller DN.

Nature. 2017 Nov 30;551(7682):585-589. doi: 10.1038/nature24628. Epub 2017 Nov 15.

10.

Emerging and evolving concepts in gene essentiality.

Rancati G, Moffat J, Typas A, Pavelka N.

Nat Rev Genet. 2018 Jan;19(1):34-49. doi: 10.1038/nrg.2017.74. Epub 2017 Oct 16. Review.

PMID:
29033457
11.

Yeast Creates a Niche for Symbiotic Lactic Acid Bacteria through Nitrogen Overflow.

Ponomarova O, Gabrielli N, Sévin DC, Mülleder M, Zirngibl K, Bulyha K, Andrejev S, Kafkia E, Typas A, Sauer U, Ralser M, Patil KR.

Cell Syst. 2017 Oct 25;5(4):345-357.e6. doi: 10.1016/j.cels.2017.09.002. Epub 2017 Sep 27.

12.

Correction: A Chemical-Genomic Screen of Neglected Antibiotics Reveals Illicit Transport of Kasugamycin and Blasticidin S.

Shiver AL, Osadnik H, Kritikos G, Li B, Krogan N, Typas A, Gross CA.

PLoS Genet. 2017 Jul 21;13(7):e1006902. doi: 10.1371/journal.pgen.1006902. eCollection 2017 Jul.

13.

Host-Microbe Co-metabolism Dictates Cancer Drug Efficacy in C. elegans.

Scott TA, Quintaneiro LM, Norvaisas P, Lui PP, Wilson MP, Leung KY, Herrera-Dominguez L, Sudiwala S, Pessia A, Clayton PT, Bryson K, Velagapudi V, Mills PB, Typas A, Greene NDE, Cabreiro F.

Cell. 2017 Apr 20;169(3):442-456.e18. doi: 10.1016/j.cell.2017.03.040.

14.

A tool named Iris for versatile high-throughput phenotyping in microorganisms.

Kritikos G, Banzhaf M, Herrera-Dominguez L, Koumoutsi A, Wartel M, Zietek M, Typas A.

Nat Microbiol. 2017 Feb 17;2:17014. doi: 10.1038/nmicrobiol.2017.14.

15.

Construction and Analysis of Two Genome-Scale Deletion Libraries for Bacillus subtilis.

Koo BM, Kritikos G, Farelli JD, Todor H, Tong K, Kimsey H, Wapinski I, Galardini M, Cabal A, Peters JM, Hachmann AB, Rudner DZ, Allen KN, Typas A, Gross CA.

Cell Syst. 2017 Mar 22;4(3):291-305.e7. doi: 10.1016/j.cels.2016.12.013. Epub 2017 Feb 8.

16.

An atlas of human kinase regulation.

Ochoa D, Jonikas M, Lawrence RT, El Debs B, Selkrig J, Typas A, Villén J, Santos SD, Beltrao P.

Mol Syst Biol. 2016 Dec 1;12(12):888. doi: 10.15252/msb.20167295.

17.

A Chemical-Genomic Screen of Neglected Antibiotics Reveals Illicit Transport of Kasugamycin and Blasticidin S.

Shiver AL, Osadnik H, Kritikos G, Li B, Krogan N, Typas A, Gross CA.

PLoS Genet. 2016 Jun 29;12(6):e1006124. doi: 10.1371/journal.pgen.1006124. eCollection 2016 Jun. Erratum in: PLoS Genet. 2017 Jul 21;13(7):e1006902.

18.

Integration of multi-omics data of a genome-reduced bacterium: Prevalence of post-transcriptional regulation and its correlation with protein abundances.

Chen WH, van Noort V, Lluch-Senar M, Hennrich ML, Wodke JA, Yus E, Alibés A, Roma G, Mende DR, Pesavento C, Typas A, Gavin AC, Serrano L, Bork P.

Nucleic Acids Res. 2016 Feb 18;44(3):1192-202. doi: 10.1093/nar/gkw004. Epub 2016 Jan 14.

19.

Editorial overview: Microbial systems biology.

Brown ED, Typas A.

Curr Opin Microbiol. 2015 Oct;27:viii-ix. doi: 10.1016/j.mib.2015.09.007. Epub 2015 Oct 20. No abstract available.

PMID:
26483052
20.

Bacterial protein networks: properties and functions.

Typas A, Sourjik V.

Nat Rev Microbiol. 2015 Sep;13(9):559-72. doi: 10.1038/nrmicro3508. Epub 2015 Aug 10. Review.

PMID:
26256789
21.

Coordination of peptidoglycan synthesis and outer membrane constriction during Escherichia coli cell division.

Gray AN, Egan AJ, Van't Veer IL, Verheul J, Colavin A, Koumoutsi A, Biboy J, Altelaar AF, Damen MJ, Huang KC, Simorre JP, Breukink E, den Blaauwen T, Typas A, Gross CA, Vollmer W.

Elife. 2015 May 7;4. doi: 10.7554/eLife.07118.

22.

Detecting envelope stress by monitoring β-barrel assembly.

Cho SH, Szewczyk J, Pesavento C, Zietek M, Banzhaf M, Roszczenko P, Asmar A, Laloux G, Hov AK, Leverrier P, Van der Henst C, Vertommen D, Typas A, Collet JF.

Cell. 2014 Dec 18;159(7):1652-64. doi: 10.1016/j.cell.2014.11.045.

23.

Outer-membrane lipoprotein LpoB spans the periplasm to stimulate the peptidoglycan synthase PBP1B.

Egan AJ, Jean NL, Koumoutsi A, Bougault CM, Biboy J, Sassine J, Solovyova AS, Breukink E, Typas A, Vollmer W, Simorre JP.

Proc Natl Acad Sci U S A. 2014 Jun 3;111(22):8197-202. doi: 10.1073/pnas.1400376111. Epub 2014 May 12.

24.

Individuality and temporal stability of the human gut microbiome.

Sunagawa S, Schloissnig S, Arumugam M, Forslund K, Mitreva M, Tap J, Zhu A, Waller A, Mende DR, Kultima JR, Martin J, Kota K, Sunyaev SR, Typas A, Weinstock GM, Bork P.

Cent Asian J Glob Health. 2014 Mar 27;2(Suppl):120. doi: 10.5195/cajgh.2013.120. eCollection 2013.

25.

Dynamic protein complexes for cell growth.

Banzhaf M, Typas A.

Proc Natl Acad Sci U S A. 2014 Mar 25;111(12):4355-6. doi: 10.1073/pnas.1402016111. Epub 2014 Mar 17. No abstract available.

26.

A genome-wide screen for bacterial envelope biogenesis mutants identifies a novel factor involved in cell wall precursor metabolism.

Paradis-Bleau C, Kritikos G, Orlova K, Typas A, Bernhardt TG.

PLoS Genet. 2014 Jan;10(1):e1004056. doi: 10.1371/journal.pgen.1004056. Epub 2014 Jan 2.

27.

Fe-S cluster biosynthesis controls uptake of aminoglycosides in a ROS-less death pathway.

Ezraty B, Vergnes A, Banzhaf M, Duverger Y, Huguenot A, Brochado AR, Su SY, Espinosa L, Loiseau L, Py B, Typas A, Barras F.

Science. 2013 Jun 28;340(6140):1583-7. doi: 10.1126/science.1238328.

PMID:
23812717
28.

Country-specific antibiotic use practices impact the human gut resistome.

Forslund K, Sunagawa S, Kultima JR, Mende DR, Arumugam M, Typas A, Bork P.

Genome Res. 2013 Jul;23(7):1163-9. doi: 10.1101/gr.155465.113. Epub 2013 Apr 8.

29.

High-throughput approaches to understanding gene function and mapping network architecture in bacteria.

Brochado AR, Typas A.

Curr Opin Microbiol. 2013 Apr;16(2):199-206. doi: 10.1016/j.mib.2013.01.008. Epub 2013 Feb 9. Review.

PMID:
23403119
30.

From the regulation of peptidoglycan synthesis to bacterial growth and morphology.

Typas A, Banzhaf M, Gross CA, Vollmer W.

Nat Rev Microbiol. 2011 Dec 28;10(2):123-36. doi: 10.1038/nrmicro2677. Review.

31.

Selective ribosome profiling reveals the cotranslational chaperone action of trigger factor in vivo.

Oh E, Becker AH, Sandikci A, Huber D, Chaba R, Gloge F, Nichols RJ, Typas A, Gross CA, Kramer G, Weissman JS, Bukau B.

Cell. 2011 Dec 9;147(6):1295-308. doi: 10.1016/j.cell.2011.10.044.

32.

Escherichia coli σ⁷⁰ senses sequence and conformation of the promoter spacer region.

Singh SS, Typas A, Hengge R, Grainger DC.

Nucleic Acids Res. 2011 Jul;39(12):5109-18. doi: 10.1093/nar/gkr080. Epub 2011 Mar 11.

33.

Phenotypic landscape of a bacterial cell.

Nichols RJ, Sen S, Choo YJ, Beltrao P, Zietek M, Chaba R, Lee S, Kazmierczak KM, Lee KJ, Wong A, Shales M, Lovett S, Winkler ME, Krogan NJ, Typas A, Gross CA.

Cell. 2011 Jan 7;144(1):143-56. doi: 10.1016/j.cell.2010.11.052. Epub 2010 Dec 23.

34.

Regulation of peptidoglycan synthesis by outer-membrane proteins.

Typas A, Banzhaf M, van den Berg van Saparoea B, Verheul J, Biboy J, Nichols RJ, Zietek M, Beilharz K, Kannenberg K, von Rechenberg M, Breukink E, den Blaauwen T, Gross CA, Vollmer W.

Cell. 2010 Dec 23;143(7):1097-109. doi: 10.1016/j.cell.2010.11.038.

35.

High-throughput, quantitative analyses of genetic interactions in E. coli.

Typas A, Nichols RJ, Siegele DA, Shales M, Collins SR, Lim B, Braberg H, Yamamoto N, Takeuchi R, Wanner BL, Mori H, Weissman JS, Krogan NJ, Gross CA.

Nat Methods. 2008 Sep;5(9):781-7.

36.
37.
38.

The molecular basis of selective promoter activation by the sigmaS subunit of RNA polymerase.

Typas A, Becker G, Hengge R.

Mol Microbiol. 2007 Mar;63(5):1296-306. Review.

39.
40.

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