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Article
Open AccessProtein interaction networks in the vasculature prioritize genes and pathways underlying coronary artery disease
Population-based association studies have identified many genetic risk loci for coronary artery disease (CAD), but it is often unclear how genes within these loci are linked to CAD. Here, we perform interactio...
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Article
Open AccessA small bacteriophage protein determines the hierarchy over co-residential jumbo phage in Bacillus thuringiensis serovar israelensis
Bacillus thuringiensis serovar israelensis is the most widely used biopesticide against insects, including vectors of animal and human diseases. Among several extrachromosomal elements, this endospore-forming ent...
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Article
Open AccessGenoppi is an open-source software for robust and standardized integration of proteomic and genetic data
Combining genetic and cell-type-specific proteomic datasets can generate biological insights and therapeutic hypotheses, but a technical and statistical framework for such analyses is lacking. Here, we present...
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Article
Open AccessSystematic auditing is essential to debiasing machine learning in biology
Biases in data used to train machine learning (ML) models can inflate their prediction performance and confound our understanding of how and what they learn. Although biases are common in biological data, syst...
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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
Author Correction: Gut microbiome structure and metabolic activity in inflammatory bowel disease
In the Supplementary Tables 2, 4 and 6 originally published with this Article, the authors mistakenly included sample identifiers in the form of UMCGs rather than UMCG IBDs in the validation cohort; this has n...
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Article
Gut microbiome structure and metabolic activity in inflammatory bowel disease
The inflammatory bowel diseases (IBDs), which include Crohn’s disease (CD) and ulcerative colitis (UC), are multifactorial chronic conditions of the gastrointestinal tract. While IBD has been associated with d...
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Article
Open AccessA novel Ruminococcus gnavus clade enriched in inflammatory bowel disease patients
Inflammatory bowel disease (IBD) is characterized by chronic inflammation of the gastrointestinal tract that is associated with changes in the gut microbiome. Here, we sought to identify strain-specific functi...
