selected publications
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academic article
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article
- 2FAST2Q: A general-purpose sequence search and counting program for FASTQ files
- A Chemical-Genomic Screen of Neglected Antibiotics Reveals Illicit Transport of Kasugamycin and Blasticidin S.
- A Dual-Mechanism Antibiotic Kills Gram-Negative Bacteria and Avoids Drug Resistance.
- A genome-wide screen for bacterial envelope biogenesis mutants identifies a novel factor involved in cell wall precursor metabolism.
- A new antibiotic selectively kills Gram-negative pathogens.
- A resource of variant effect predictions of single nucleotide variants in model organisms
- A tool named Iris for versatile high-throughput phenotyping in microorganisms.
- An atlas of human kinase regulation.
- Bacterial protein networks: properties and functions.
- Bacterial retrons encode tripartite toxin/antitoxin systems
- Bioaccumulation of therapeutic drugs by human gut bacteria
- Bioactivity assessment of natural compounds using machine learning models based on drug target similarity
- Bioactivity assessment of natural compounds using machine learning models trained on target similarity between drugs
- Chemical genetics in drug discovery.
- Construction and Analysis of Two Genome-Scale Deletion Libraries for Bacillus subtilis.
- Coordination of peptidoglycan synthesis and outer membrane constriction during Escherichia coli cell division.
- Country-specific antibiotic use practices impact the human gut resistome.
- Detecting envelope stress by monitoring β-barrel assembly.
- Differential ability of sigma(s) and sigma70 of Escherichia coli to utilize promoters containing half or full UP-element sites.
- Early midcell localization of Escherichia coli PBP4 supports the function of peptidoglycan amidases
- Editorial overview
- Editorial overview: Microbial systems biology.
- Emerging and evolving concepts in gene essentiality.
- Escherichia coli limits Salmonella Typhimurium infections after diet shifts and fat-mediated microbiota perturbation in mice
- Escherichia coli σ⁷⁰ senses sequence and conformation of the promoter spacer region.
- Extensive impact of non-antibiotic drugs on human gut bacteria.
- Fe-S cluster biosynthesis controls uptake of aminoglycosides in a ROS-less death pathway.
- From the regulation of peptidoglycan synthesis to bacterial growth and morphology.
- Global mapping of Salmonella enterica-host protein-protein interactions during infection.
- High-throughput approaches to understanding gene function and mapping network architecture in bacteria.
- High-throughput functional characterization of protein phosphorylation sites in yeast
- High-throughput, quantitative analyses of genetic interactions in E. coli.
- Host-Microbe Co-metabolism Dictates Cancer Drug Efficacy in C. elegans.
- Impact of phosphorylation on thermal stability of proteins
- Integration of multi-omics data of a genome-reduced bacterium: Prevalence of post-transcriptional regulation and its correlation with protein abundances.
- Midcell localization of PBP4 of Escherichia coli modulates the timing of divisome assembly
- Outer membrane lipoprotein NlpI scaffolds peptidoglycan hydrolases within multi-enzyme complexes in Escherichia coli.
- Outer-membrane lipoprotein LpoB spans the periplasm to stimulate the peptidoglycan synthase PBP1B.
- Pervasive Protein Thermal Stability Variation during the Cell Cycle.
- Phage proteins block and trigger retron toxin/antitoxin systems
- Phenotype prediction in an Escherichia coli strain panel
- Phenotypic landscape of a bacterial cell.
- Proton Motive Force Disruptors Block Bacterial Competence and Horizontal Gene Transfer.
- Regulation of peptidoglycan synthesis by outer-membrane proteins.
- Role of the spacer between the -35 and -10 regions in sigmas promoter selectivity in Escherichia coli.
- SARS-CoV-2 infection remodels the host protein thermal stability landscape.
- Salt-responsive gut commensal modulates TH17 axis and disease.
- Selective ribosome profiling reveals the cotranslational chaperone action of trigger factor in vivo.
- Spatiotemporal proteomics uncovers cathepsin-dependent macrophage cell death during Salmonella infection.
- Species-specific activity of antibacterial drug combinations.
- Stationary phase reorganisation of the Escherichia coli transcription machinery by Crl protein, a fine-tuner of sigmas activity and levels.
- Systematic Localization of Escherichia coli Membrane Proteins.
- Systematic localization of Gram-negative bacterial membrane proteins
- Systematically investigating the impact of medication on the gut microbiome.
- The -35 sequence location and the Fis-sigma factor interface determine sigmas selectivity of the proP (P2) promoter in Escherichia coli.
- The first wide-scale drug repurposing screen using the Prestwick Chemical Library (1200 bioactive molecules) against Neisseria gonorrhoeae identifies high in vitro activity of auranofin and many additional drugs.
- The functional proteome landscape of Escherichia coli
- The impact of the genetic background on gene deletion phenotypes in Saccharomyces cerevisiae
- The molecular basis of selective promoter activation by the sigmaS subunit of RNA polymerase.
- Thermal proteome profiling for interrogating protein interactions
- Thermal proteome profiling in bacteria: probing protein state in vivo
- Towards a mechanistic understanding of reciprocal drug–microbiome interactions
- Transcriptional and Post-Transcriptional Polar Effects in Bacterial Gene Deletion Libraries.
- Unravelling the collateral damage of antibiotics on gut bacteria
- Yeast Creates a Niche for Symbiotic Lactic Acid Bacteria through Nitrogen Overflow.