Genome-resolved metagenomics: a game changer for microbiome medicine
N Kim, J Ma, W Kim, J Kim, P Belenky… - Experimental & Molecular …, 2024 - nature.com
Recent substantial evidence implicating commensal bacteria in human diseases has given
rise to a new domain in biomedical research: microbiome medicine. This emerging field …
rise to a new domain in biomedical research: microbiome medicine. This emerging field …
Methyl-based methanogenesis: an ecological and genomic review
Methyl-based methanogenesis is one of three broad categories of archaeal anaerobic
methanogenesis, including both the methyl dismutation (methylotrophic) pathway and the …
methanogenesis, including both the methyl dismutation (methylotrophic) pathway and the …
eQuilibrator 3.0: a database solution for thermodynamic constant estimation
ME Beber, MG Gollub, D Mozaffari… - Nucleic acids …, 2022 - academic.oup.com
Abstract eQuilibrator (equilibrator. weizmann. ac. il) is a database of biochemical equilibrium
constants and Gibbs free energies, originally designed as a web-based interface. While the …
constants and Gibbs free energies, originally designed as a web-based interface. While the …
The 2022 Nucleic Acids Research database issue and the online molecular biology database collection
DJ Rigden, XM Fernández - Nucleic acids research, 2022 - academic.oup.com
Abstract The 2022 Nucleic Acids Research Database Issue contains 185 papers, including
87 papers reporting on new databases and 85 updates from resources previously published …
87 papers reporting on new databases and 85 updates from resources previously published …
Genome-scale models in human metabologenomics
Metabologenomics integrates metabolomics with other omics data types to comprehensively
study the genetic and environmental factors that influence metabolism. These multi-omics …
study the genetic and environmental factors that influence metabolism. These multi-omics …
Teasing out missing reactions in genome-scale metabolic networks through hypergraph learning
Abstract GEnome-scale Metabolic models (GEMs) are powerful tools to predict cellular
metabolism and physiological states in living organisms. However, due to our imperfect …
metabolism and physiological states in living organisms. However, due to our imperfect …
Genome-scale metabolic modeling enables in-depth understanding of big data
Genome-scale metabolic models (GEMs) enable the mathematical simulation of the
metabolism of archaea, bacteria, and eukaryotic organisms. GEMs quantitatively define a …
metabolism of archaea, bacteria, and eukaryotic organisms. GEMs quantitatively define a …
Emerging tools and best practices for studying gut microbial community metabolism
The human gut microbiome vastly extends the set of metabolic reactions catalysed by our
own cells, with far-reaching consequences for host health and disease. However, our …
own cells, with far-reaching consequences for host health and disease. However, our …
Gapseq: informed prediction of bacterial metabolic pathways and reconstruction of accurate metabolic models
Genome-scale metabolic models of microorganisms are powerful frameworks to predict
phenotypes from an organism's genotype. While manual reconstructions are laborious …
phenotypes from an organism's genotype. While manual reconstructions are laborious …
Identification of a deep-branching thermophilic clade sheds light on early bacterial evolution
It has been proposed that early bacteria, or even the last universal common ancestor of all
cells, were thermophilic. However, research on the origin and evolution of thermophily is …
cells, were thermophilic. However, research on the origin and evolution of thermophily is …