Wagih O, Galardini M, Busby BP, Memon D, Typas A, Beltrao P. (2018)

A resource of variant effect predictions of single nucleotide variants in model organisms.

Mol. Syst. Biol. 14(12):e8430. doi: 10.15252/msb.20188430
Europe PMC | doi

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 HB, Nielsen MF, Wang J, Bork P, Hansen T, Vilsbøll T, Arumugam M, Knop FK, Pedersen O. (2018)

Recovery of gut microbiota of healthy adults following antibiotic exposure.

Nat Microbiol 3(11) doi: 10.1038/s41564-018-0257-9
Europe PMC | doi

Mateus A, Bobonis J, Kurzawa N, Stein F, Helm D, Hevler J, Typas A, Savitski MM. (2018)

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

Mol. Syst. Biol. 14(7) doi: 10.15252/msb.20188242
Europe PMC | doi

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, Bork P, Savitski MM, Göttig S, Typas A. (2018)

Species-specific activity of antibacterial drug combinations.

Nature 559(7713):259-263. doi: 10.1038/s41586-018-0278-9
Europe PMC | doi

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. (2018)

Pervasive Protein Thermal Stability Variation during the Cell Cycle.

Cell 173(6) doi: 10.1016/j.cell.2018.03.053
Europe PMC | doi

Tramontano M, Andrejev S, Pruteanu M, Klünemann M, Kuhn M, Galardini M, Jouhten P, Zelezniak A, Zeller G, Bork P, Typas A, Patil KR. (2018)

Nutritional preferences of human gut bacteria reveal their metabolic idiosyncrasies.

Nat Microbiol 3(4) doi: 10.1038/s41564-018-0123-9
Europe PMC | doi

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. (2018)

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

Nature 555(7698) doi: 10.1038/nature25979
Europe PMC | doi

Rancati G, Moffat J, Typas A, Pavelka N. (2018)

Emerging and evolving concepts in gene essentiality.

Nat Rev Genet 19(1) doi: 10.1038/nrg.2017.74
Europe PMC | doi

Galardini M, Koumoutsi A, Herrera-Dominguez L, Cordero Varela JA, Telzerow A, Wagih O, Wartel M, Clermont O, Denamur E, Typas A, Beltrao P. (2017)

Phenotype inference in an Escherichia coli strain panel.

Elife 6 doi: 10.7554/eLife.31035
Europe PMC | doi

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. (2017)

Salt-responsive gut commensal modulates TH17 axis and disease.

Nature 551(7682):585-589. doi: 10.1038/nature24628
Europe PMC | doi

Ponomarova O, Gabrielli N, Sévin DC, Mülleder M, Zirngibl K, Bulyha K, Andrejev S, Kafkia E, Typas A, Sauer U, Ralser M, Patil KR. (2017)

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

Cell Syst S2405-4712(17):30390-30393. doi: 10.1016/j.cels.2017.09.002
Europe PMC | doi

Maier L, Typas A. (2017)

Systematically investigating the impact of medication on the gut microbiome.

Curr. Opin. Microbiol. 39:128-135. doi: 10.1016/j.mib.2017.11.001
Europe PMC | doi

Nikolay F, Pesavento M, Kritikos G, Typas N. (2017)

Learning directed acyclic graphs from large-scale genomics data.

EURASIP J Bioinform Syst Biol 2017(1) doi: 10.1186/s13637-017-0063-3
Europe PMC | doi

Cacace E, Kritikos G, Typas A. (2017)

Chemical genetics in drug discovery.

Curr Opin Syst Biol 4:35-42. doi: 10.1016/j.coisb.2017.05.020
doi

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. (2017)

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

Cell 169(3):442-456.e18. doi: 10.1016/j.cell.2017.03.040
Europe PMC | doi

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.. (2017)

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

Cell Syst 4(16) doi: 10.1016/j.cels.2016.12.013
Europe PMC | doi

Kritikos G, Banzhaf M, Herrera-Dominguez L, Koumoutsi A, Wartel M, Zietek M, Typas A.. (2017)

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

Nat Microbiol 2(2) doi: 10.1038/nmicrobiol.2017.14
Europe PMC | doi

Ochoa D, Jonikas M, Lawrence RT, El Debs B, Selkrig J, Typas A, Villén J, Santos SD, Beltrao P. (2016)

An atlas of human kinase regulation.

Mol. Syst. Biol. 12(12):888. doi: 10.15252/msb.20167295
Europe PMC | doi

Shiver AL, Osadnik H, Kritikos G, Li B, Krogan N, Typas A, Gross CA. (2016)

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

PLoS Genet. 12(6):e1006124. doi: 10.1371/journal.pgen.1006124
Europe PMC | doi

Chen WH, van Noort V, Lluch-Senar M, Hennrich ML, H Wodke JA, Yus E, Alibés A, Roma G, Mende DR, Pesavento C, Typas A, Gavin AC, Serrano L, Bork P. (2016)

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

Nucleic Acids Res. 44(3) doi: 10.1093/nar/gkw004
Europe PMC | doi

Brown ED, Typas A. (2015)

Editorial overview: Microbial systems biology.

Curr Opin Microbiol 27 doi: 10.1016/j.mib.2015.09.007
Europe PMC | doi

Typas A, Sourjik V. (2015)

Bacterial protein networks: properties and functions.

Nat. Rev. Microbiol. 13(9):559-572. doi: 10.1038/nrmicro3508
Europe PMC | doi

Gray AN, Egan AJ, Van't Veer IL, Verheul J, Colavin A, Koumoutsi A, Biboy J, Altelaar MA, Damen MJ, Huang KC, Simorre JP, Breukink E, den Blaauwen T, Typas A, Gross CA, Vollmer W. (2015)

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

Elife 4 doi: 10.7554/elife.07118
Europe PMC | doi

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. (2014)

Detecting Envelope Stress by Monitoring β-Barrel Assembly.

Cell 159(7):1652-1664. doi: 10.1016/j.cell.2014.11.045
Europe PMC | doi

Egan AJ, Jean NL, Koumoutsi A, Bougault CM, Biboy J, Sassine J, Solovyova AS, Breukink E, Typas A, Vollmer W, Simorre JP. (2014)

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

Proc. Natl. Acad. Sci. U.S.A. 111(22):8197-8202. doi: 10.1073/pnas.1400376111
Europe PMC | doi

Banzhaf M, Typas A. (2014)

Dynamic protein complexes for cell growth

Proc. Natl. Acad. Sci. U.S.A. 111(12):4355-4356. doi: 10.1073/pnas.1402016111
Europe PMC | doi

Paradis-Bleau C, Kritikos G, Orlova K, Typas A, Bernhardt TG. (2014)

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

PLoS Genet. 10(1):e1004056. doi: 10.1371/journal.pgen.1004056
Europe PMC | doi

Forslund K, Sunagawa S, Kultima JR, Mende DR, Arumugam M, Typas A, Bork P. (2013)

Country-specific antibiotic use practices impact the human gut resistome

Genome Res. 23(7):1163-1169. doi: 10.1101/gr.155465.113
Europe PMC | doi

Ezraty B, Vergnes A, Banzhaf M, Duverger Y, Huguenot A, Brochado AR, Su SY, Espinosa L, Loiseau L, Py B, Typas A, Barras F. (2013)

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

Science 340(6140):1583-1587. doi: 10.1126/science.1238328
Europe PMC | doi

Brochado AR, Typas A. (2013)

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

Curr. Opin. Microbiol. 16(2):199-206. doi: 10.1016/j.mib.2013.01.008
Europe PMC | doi

Typas A, Banzhaf M, Gross CA, Vollmer W. (2012)

From the regulation of peptidoglycan synthesis to bacterial growth and morphology

Nat. Rev. Microbiol. 10(2):123-136. doi: 10.1038/nrmicro2677
Europe PMC | doi

Oh E, Becker AH, Sandikci A, Huber D, Chaba R, Gloge F, Nichols RJ, Typas A, Gross CA, Kramer G, Weissman JS, Bukau B. (2011)

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

Cell 147(6):1295-1308. doi: 10.1016/j.cell.2011.10.044
Europe PMC | doi

Singh SS, Typas A, Hengge R, Grainger DC. (2011)

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

Nucleic Acids Res. 39(12):5109-5118. doi: 10.1093/nar/gkr080
Europe PMC | doi

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. (2011)

Phenotypic landscape of a bacterial cell

Cell 144(1):143-156. doi: 10.1016/j.cell.2010.11.052
Europe PMC | doi

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. (2010)

Regulation of peptidoglycan synthesis by outer-membrane proteins

Cell 143(7):1097-1109. doi: 10.1016/j.cell.2010.11.038
Europe PMC | doi

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. (2008)

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

Nat. Methods 5(9):781-787. doi: 10.1038/nmeth.1240
Europe PMC | doi

Typas A, Barembruch C, Possling A, Hengge R. (2007)

Stationary phase reorganisation of the Escherichia coli transcription machinery by Crl protein, a fine-tuner of sigmas activity and levels

EMBO J. 26(6):1569-1578. doi: 10.1038/sj.emboj.7601629
Europe PMC | doi

Typas A, Becker G, Hengge R. (2007)

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

Mol. Microbiol. 63(5):1296-1306. doi: 10.1111/j.1365-2958.2007.05601.x
Europe PMC | doi

Typas A, Stella S, Johnson RC, Hengge R. (2007)

The -35 sequence location and the Fis-sigma factor interface determine sigmas selectivity of the proP (P2) promoter in Escherichia coli

Mol. Microbiol. 63(3):780-796. doi: 10.1111/j.1365-2958.2006.05560.x
Europe PMC | doi

Klauck E, Typas A, Hengge R. (2007)

The sigmaS subunit of RNA polymerase as a signal integrator and network master regulator in the general stress response in Escherichia coli

Sci Prog 90(Pt 2-3):103-127.
Europe PMC

Typas A, Hengge R. (2006)

Role of the spacer between the -35 and -10 regions in sigmas promoter selectivity in Escherichia coli

Mol. Microbiol. 59(3):1037-1051. doi: 10.1111/j.1365-2958.2005.04998.x
Europe PMC | doi

Typas A, Hengge R. (2005)

Differential ability of sigma(s) and sigma70 of Escherichia coli to utilize promoters containing half or full UP-element sites

Mol. Microbiol. 55(1):250-260. doi: 10.1111/j.1365-2958.2004.04382.x
Europe PMC | doi