The healthy human microbiome
Humans are virtually identical in their genetic makeup, yet the small differences in our DNA
give rise to tremendous phenotypic diversity across the human population. By contrast, the …
give rise to tremendous phenotypic diversity across the human population. By contrast, the …
Using genome-scale models to predict biological capabilities
Constraint-based reconstruction and analysis (COBRA) methods at the genome scale have
been under development since the first whole-genome sequences appeared in the mid …
been under development since the first whole-genome sequences appeared in the mid …
Deep learning-guided discovery of an antibiotic targeting Acinetobacter baumannii
Acinetobacter baumannii is a nosocomial Gram-negative pathogen that often displays
multidrug resistance. Discovering new antibiotics against A. baumannii has proven …
multidrug resistance. Discovering new antibiotics against A. baumannii has proven …
[HTML][HTML] A deep learning approach to antibiotic discovery
Due to the rapid emergence of antibiotic-resistant bacteria, there is a growing need to
discover new antibiotics. To address this challenge, we trained a deep neural network …
discover new antibiotics. To address this challenge, we trained a deep neural network …
BioTransformer: a comprehensive computational tool for small molecule metabolism prediction and metabolite identification
Y Djoumbou-Feunang, J Fiamoncini… - Journal of …, 2019 - Springer
Background A number of computational tools for metabolism prediction have been
developed over the last 20 years to predict the structures of small molecules undergoing …
developed over the last 20 years to predict the structures of small molecules undergoing …
Mutant phenotypes for thousands of bacterial genes of unknown function
MN Price, KM Wetmore, RJ Waters, M Callaghan… - Nature, 2018 - nature.com
One-third of all protein-coding genes from bacterial genomes cannot be annotated with a
function. Here, to investigate the functions of these genes, we present genome-wide mutant …
function. Here, to investigate the functions of these genes, we present genome-wide mutant …
COFACTOR: improved protein function prediction by combining structure, sequence and protein–protein interaction information
The COFACTOR web server is a unified platform for structure-based multiple-level protein
function predictions. By structurally threading low-resolution structural models through the …
function predictions. By structurally threading low-resolution structural models through the …
A map of protein-metabolite interactions reveals principles of chemical communication
Metabolite-protein interactions control a variety of cellular processes, thereby playing a
major role in maintaining cellular homeostasis. Metabolites comprise the largest fraction of …
major role in maintaining cellular homeostasis. Metabolites comprise the largest fraction of …
The EcoCyc database: reflecting new knowledge about Escherichia coli K-12
IM Keseler, A Mackie, A Santos-Zavaleta… - Nucleic acids …, 2017 - academic.oup.com
EcoCyc (EcoCyc. org) is a freely accessible, comprehensive database that collects and
summarizes experimental data for Escherichia coli K-12, the best-studied bacterial model …
summarizes experimental data for Escherichia coli K-12, the best-studied bacterial model …
Spatiotemporal microbial evolution on antibiotic landscapes
A key aspect of bacterial survival is the ability to evolve while migrating across spatially
varying environmental challenges. Laboratory experiments, however, often study evolution …
varying environmental challenges. Laboratory experiments, however, often study evolution …