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Recon3D: A Resource Enabling A Three-Dimensional View of Gene Variation in Human Metabolism
TLDR
Recon3D is presented, a computational resource that includes three-dimensional metabolite and protein structure data and enables integrated analyses of metabolic functions in humans and is used to functionally characterize mutations associated with disease, and identify metabolic response signatures that are caused by exposure to certain drugs.
Recon3D enables a three-dimensional view of gene variation in human metabolism
TLDR
Recon3D is presented, a computational resource that includes three-dimensional metabolite and protein structure data and enables integrated analyses of metabolic functions in humans, and is used to functionally characterize mutations associated with disease, and identify metabolic response signatures that are caused by exposure to certain drugs.
iML1515, a knowledgebase that computes Escherichia coli traits
TLDR
The iML1515 knowledgebase is linked to 1,515 protein structures to provide an integrated modeling framework bridging systems and structural biology and is applied to build metabolic models of E. coli human gut microbiome strains from metagenomic sequencing data.
Antigen receptor repertoire profiling from RNA-seq data
TLDR
The final version of iML1515 will provide researchers with the best possible tools for their experiments and is expected to be in use by the end of 2017.
Mixed Quantum Mechanical/Molecular Mechanical Molecular Dynamics Simulations of Biological Systems in Ground and Electronically Excited States.
TLDR
By using feature selection algorithms to identify the most appropriate subset of relevant variables that describe a certain phenomenon, the high-dimensionality of QM/MM data can be reduced and used for further analysis with causal inference algorithms to establish unique cause-effect relationships.
Model-driven discovery of underground metabolic functions in Escherichia coli
TLDR
This study demonstrates how a targeted model-driven approach to discovery can systematically fill knowledge gaps, characterize underground metabolism, and elucidate regulatory mechanisms of adaptation in response to gene KO perturbations.
NAD metabolic dependency in cancer is shaped by gene amplification and enhancer remodelling
TLDR
A central role for tissue context is identified in determining the choice of NAD biosynthetic pathway, explain the failure of NAMPT inhibitors, and pave the way for more effective treatments.
Evolution of gene knockout strains of E. coli reveal regulatory architectures governed by metabolism
TLDR
The results indicate that metabolite levels, through metabolite-transcription factor interactions, have a dominant role in determining the function of a multi-scale regulatory architecture that has been molded by evolution.
Characterizing posttranslational modifications in prokaryotic metabolism using a multiscale workflow
TLDR
This workflow incorporates complementary approaches across scientific disciplines; provides molecular insight into how PTMs influence cellular fitness during nutrient shifts; and demonstrates how mechanistic details of PTMs can be explored at different biological scales.
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