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Article
Growth effects of N-acylethanolamines on gut bacteria reflect altered bacterial abundances in inflammatory bowel disease
Inflammatory bowel diseases (IBD) are associated with alterations in gut microbial abundances and lumenal metabolite concentrations, but the effects of specific metabolites on the gut microbiota in health and ...
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Article
Global chemical effects of the microbiome include new bile-acid conjugations
A mosaic of cross-phylum chemical interactions occurs between all metazoans and their microbiomes. A number of molecular families that are known to be produced by the microbiome have a marked effect on the bal...
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Article
Open AccessMulti-omics of the gut microbial ecosystem in inflammatory bowel diseases
Inflammatory bowel diseases, which include Crohn’s disease and ulcerative colitis, affect several million individuals worldwide. Crohn’s disease and ulcerative colitis are complex diseases that are heterogeneo...
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Article
Open AccessChromosome and plasmid-borne PLacO3O1 promoters differ in sensitivity to critically low temperatures
Temperature shifts trigger genome-wide changes in Escherichia coli’s gene expression. We studied if chromosome integration impacts on a gene’s sensitivity to these shifts, by comparing the single-RNA production k...
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Article
Stability of the human faecal microbiome in a cohort of adult men
Characterizing the stability of the gut microbiome is important to exploit it as a therapeutic target and diagnostic biomarker. We metagenomically and metatranscriptomically sequenced the faecal microbiomes of...
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Article
Metatranscriptome of human faecal microbial communities in a cohort of adult men
The gut microbiome is intimately related to human health, but it is not yet known which functional activities are driven by specific microorganisms' ecological configurations or transcription. We report a larg...
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Article
Dynamics of metatranscription in the inflammatory bowel disease gut microbiome
Inflammatory bowel disease (IBD) is a group of chronic diseases of the digestive tract that affects millions of people worldwide. Genetic, environmental and microbial factors have been implicated in the onset ...
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Article
Erratum: Strains, functions and dynamics in the expanded Human Microbiome Project
Nature 550, 61–66 (2017); doi:10.1038/nature23889 This Article should have contained an associated Creative Commons statement in the Author Information section. This has been corrected in the online versions o...
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Article
Open AccessStrains, functions and dynamics in the expanded Human Microbiome Project
The characterization of baseline microbial and functional diversity in the human microbiome has enabled studies of microbiome-related disease, diversity, biogeography, and molecular function. The National Inst...
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Article
Open AccesssgnesR: An R package for simulating gene expression data from an underlying real gene network structure considering delay parameters
sgnesR (Stochastic Gene Network Expression Simulator in R) is an R package that provides an interface to simulate gene expression data from a given gene network using the stochastic simulation algorithm (SSA)....
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Article
Open AccessThe 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 metagenome of the human m...
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Chapter and Conference Paper
Modelling Polar Retention of Complexes in Escherichia coli
The cytoplasm of Escherichia coli is a crowded, heterogeneous environment. The spatial kinetics and heterogeneities of synthetic RNA-protein complexes have been recently studied using single-cell live imaging. A ...
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Article
Open AccessIn vivo kinetics of transcription initiation of the lar promoter in Escherichia coli. Evidence for a sequential mechanism with two rate-limiting steps
In Escherichia coli the mean and cell-to-cell diversity in RNA numbers of different genes vary widely. This is likely due to different kinetics of transcription initiation, a complex process with multiple rate-li...
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Article
Open AccessStochastic sequence-level model of coupled transcription and translation in prokaryotes
In prokaryotes, transcription and translation are dynamically coupled, as the latter starts before the former is complete. Also, from one transcript, several translation events occur in parallel. To study how ...
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Chapter
Information Propagation in the Long-Term Behavior of Gene Regulatory Networks
Gene regulatory networks (GRNs) constantly receive, process and send information. While stochastic in nature, GRNs respond differently to different inputs and similarly to identical inputs. Since cell types st...
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Article
Open AccessInformation propagation within the Genetic Network of Saccharomyces cerevisiae
A gene network's capacity to process information, so as to bind past events to future actions, depends on its structure and logic. From previous and new microarray measurements in Saccharomyces cerevisiae followi...
