New views on PII signaling: from nitrogen sensing to global metabolic control

K Forchhammer, KA Selim, LF Huergo - Trends in Microbiology, 2022 - cell.com
PII proteins are multitasking information-processing proteins occurring in bacteria, archaea,
and plastids, decoding the metabolic state of the cells and providing this information to …

A systems approach to infectious disease

M Eckhardt, JF Hultquist, RM Kaake… - Nature Reviews …, 2020 - nature.com
Ongoing social, political and ecological changes in the 21st century have placed more
people at risk of life-threatening acute and chronic infections than ever before. The …

The BioGRID interaction database: 2019 update

R Oughtred, C Stark, BJ Breitkreutz, J Rust… - Nucleic acids …, 2019 - academic.oup.com
Abstract The Biological General Repository for Interaction Datasets (BioGRID:
https://thebiogrid. org) is an open access database dedicated to the curation and archival …

Protein interaction networks revealed by proteome coevolution

Q Cong, I Anishchenko, S Ovchinnikov, D Baker - Science, 2019 - science.org
Residue-residue coevolution has been observed across a number of protein-protein
interfaces, but the extent of residue coevolution between protein families on the whole …

Thermal proteome profiling in bacteria: probing protein state in vivo

A Mateus, J Bobonis, N Kurzawa, F Stein… - Molecular systems …, 2018 - embopress.org
Increasing antibiotic resistance urges for new technologies for studying microbes and
antimicrobial mechanism of action. We adapted thermal proteome profiling (TPP) to probe …

The functional proteome landscape of Escherichia coli

A Mateus, J Hevler, J Bobonis, N Kurzawa, M Shah… - Nature, 2020 - nature.com
Recent developments in high-throughput reverse genetics, have revolutionized our ability to
map gene function and interactions,,–. The power of these approaches depends on their …

Modeling protein‐protein, protein‐peptide, and protein‐oligosaccharide complexes: CAPRI 7th edition

MF Lensink, N Nadzirin, S Velankar… - Proteins: Structure …, 2020 - Wiley Online Library
We present the seventh report on the performance of methods for predicting the atomic
resolution structures of protein complexes offered as targets to the community‐wide initiative …

Population-wide diversity and stability of serum antibody epitope repertoires against human microbiota

T Vogl, S Klompus, S Leviatan, IN Kalka… - Nature medicine, 2021 - nature.com
Serum antibodies can recognize both pathogens and commensal gut microbiota. However,
our current understanding of antibody repertoires is largely based on DNA sequencing of …

Triclosan is the predominant antibacterial compound in Ontario sewage sludge

H Barrett, J Sun, Y Gong, P Yang, C Hao… - Environmental …, 2022 - ACS Publications
Sewage treatment plants (STPs) accumulate both antibiotic and nonantibiotic antimicrobial
compounds that can select for antibiotic resistant bacteria. Herein, we aimed to identify the …

Large-scale discovery of protein interactions at residue resolution using co-evolution calculated from genomic sequences

AG Green, H Elhabashy, KP Brock… - Nature …, 2021 - nature.com
Increasing numbers of protein interactions have been identified in high-throughput
experiments, but only a small proportion have solved structures. Recently, sequence …