Dysregulation of secondary bile acid metabolism precedes islet autoimmunity and type 1 diabetes
The gut microbiota is crucial in the regulation of bile acid (BA) metabolism. However, not
much is known about the regulation of BAs during progression to type 1 diabetes (T1D) …
much is known about the regulation of BAs during progression to type 1 diabetes (T1D) …
Multimodal immune cell phenotyping in GI biopsies reveals microbiome-related T cell modulations in human GvHD
Acute graft-versus-host disease (aGvHD) is a significant complication after allogeneic
hematopoietic stem cell transplantation (aHSCT), but major factors determining disease …
hematopoietic stem cell transplantation (aHSCT), but major factors determining disease …
Systematic evaluation of genome-wide metabolic landscapes in lactic acid bacteria reveals diet-and strain-specific probiotic idiosyncrasies
L Koduru, M Lakshmanan, YQ Lee, PL Ho, PY Lim… - Cell Reports, 2022 - cell.com
Lactic acid bacteria (LAB) are well known to elicit health benefits in humans, but their
functional metabolic landscapes remain unexplored. Here, we analyze differences in …
functional metabolic landscapes remain unexplored. Here, we analyze differences in …
Metatranscriptomics-guided genome-scale metabolic modeling of microbial communities
Multi-omics data integration via mechanistic models of metabolism is a scalable and flexible
framework for exploring biological hypotheses in microbial systems. However, although …
framework for exploring biological hypotheses in microbial systems. However, although …
Panera: An innovative framework for surmounting uncertainty in microbial community modeling using pan-genera metabolic models
Utilization of 16S rRNA data in constraint-based modeling to characterize microbial
communities confronts a major hurdle of lack of species-level resolution, impeding the …
communities confronts a major hurdle of lack of species-level resolution, impeding the …
Causal inference on microbiome-metabolome relations in observational host-microbiome data via in silico in vivo association pattern analyses
Understanding the effects of the microbiome on the host's metabolism is core to enlightening
the role of the microbiome in health and disease. Herein, we develop the paradigm of in …
the role of the microbiome in health and disease. Herein, we develop the paradigm of in …
Geometric algorithms for sampling the flux space of metabolic networks
Systems Biology is a fundamental field and paradigm that introduces a new era in Biology.
The crux of its functionality and usefulness relies on metabolic networks that model the …
The crux of its functionality and usefulness relies on metabolic networks that model the …
Community metabolic modeling of host-microbiota interactions through multi-objective optimization
The human gut microbiota comprises various microorganisms engaged in intricate
interactions among themselves and with the host, affecting its health. While advancements …
interactions among themselves and with the host, affecting its health. While advancements …
[PDF][PDF] Discussion and Perspectives
A Einstein - From Nose to Lung: Using Systems …, 2022 - tobias-lib.ub.uni-tuebingen.de
In this thesis, I demonstrated (I) how the quality and predictive value of existing GEMs can be
assessed,(II) how models of high quality can be curated, and (III) how these models can be …
assessed,(II) how models of high quality can be curated, and (III) how these models can be …
Modelling Gene-Protein-Reaction Associations on an FPGA
M Coggins - bioRxiv, 2019 - biorxiv.org
Genome-Scale metabolic models have proven to be incredibly useful. Allowing researchers
to model cellular functionality based upon gene expression. However as the number of …
to model cellular functionality based upon gene expression. However as the number of …