Lista de obras - Ines Thiele - Dominio Público Uruguay

A community effort towards a knowledge-base and mathematical model of the human pathogen Salmonella Typhimurium LT2

artículo científico publicado en 2011

A community-driven global reconstruction of human metabolism. ⬇️

artículo científico publicado en 2013

A compendium of inborn errors of metabolism mapped onto the human metabolic network

artículo científico publicado en 2012

A detailed genome-wide reconstruction of mouse metabolism based on human Recon 1.

artículo científico publicado en 2010

A genome-scale metabolic reconstruction of Pseudomonas putida KT2440: iJN746 as a cell factory

artículo científico publicado en 2008

A protocol for generating a high-quality genome-scale metabolic reconstruction

artículo científico publicado en 2010

A systems approach reveals distinct metabolic strategies among the NCI-60 cancer cell lines

artículo científico

A systems biology approach to drug targets in Pseudomonas aeruginosa biofilm

artículo científico publicado en 2012

A systems biology approach to studying the role of microbes in human health.

artículo científico publicado en 2012

An in silico re-design of the metabolism in Thermotoga maritima for increased biohydrogen production

article

Anoxic Conditions Promote Species-Specific Mutualism between Gut Microbes In Silico

artículo científico publicado en 2015

Applying systems biology methods to the study of human physiology in extreme environments

artículo científico

BacArena: Individual-based metabolic modeling of heterogeneous microbes in complex communities

artículo científico publicado en 2017

Bringing Genomes to Life: The Use of Genome-Scale In Silico Models

CHRR: coordinate hit-and-run with rounding for uniform sampling of constraint-based models.

artículo científico publicado en 2017

Candidate metabolic network states in human mitochondria. Impact of diabetes, ischemia, and diet.

artículo científico publicado en 2004

Candidate states of Helicobacter pylori's genome-scale metabolic network upon application of "loop law" thermodynamic constraints.

artículo científico publicado en 2006

Cardinality optimization in constraint-based modelling: application to human metabolism

artículo científico publicado en 2023

Comparative Genomic Analysis of the Human Gut Microbiome Reveals a Broad Distribution of Metabolic Pathways for the Degradation of Host-Synthetized Mucin Glycans and Utilization of Mucin-Derived Monosaccharides

artículo científico publicado en 2017

Comparative evaluation of atom mapping algorithms for balanced metabolic reactions: application to Recon 3D.

artículo científico publicado en 2017

Comparative evaluation of open source software for mapping between metabolite identifiers in metabolic network reconstructions: application to Recon 2

artículo científico publicado en 2014

Computational Modeling of Human Metabolism and Its Application to Systems Biomedicine

artículo científico

Computationally efficient flux variability analysis

artículo científico publicado en 2010

Conditions for duality between fluxes and concentrations in biochemical networks

artículo científico publicado en 2016

Consensus and conflict cards for metabolic pathway databases

artículo científico publicado en 2013

Contextualization procedure and modeling of monocyte specific TLR signaling

artículo científico publicado en 2012

Creation and analysis of biochemical constraint-based models using the COBRA Toolbox v.3.0.

scientific article published on 01 March 2019

Detailing the optimality of photosynthesis in cyanobacteria through systems biology analysis

artículo científico publicado en 2012

DistributedFBA.jl: high-level, high-performance flux balance analysis in Julia.

artículo científico publicado en 2017

Do genome-scale models need exact solvers or clearer standards?

artículo científico publicado en 2015

Editorial: The Human Gutome: Nutrigenomics of Host-Microbiome Interactions

artículo científico publicado en 2016

Erratum to: Phenotypic differentiation of gastrointestinal microbes is reflected in their encoded metabolic repertoires.

artículo científico publicado en 2016

Estimation of the number of extreme pathways for metabolic networks

artículo científico publicado en 2007

Expanded metabolic reconstruction of Helicobacter pylori (iIT341 GSM/GPR): an in silico genome-scale characterization of single- and double-deletion mutants

artículo científico publicado en 2005

Finding useful biomarkers for Parkinson's disease

article

From Network Analysis to Functional Metabolic Modeling of the Human Gut Microbiota

artículo científico publicado en 2018

From metagenomic data to personalized in silico microbiotas: predicting dietary supplements for Crohn's disease

scientific article published on 01 August 2018

Functional characterization of alternate optimal solutions of Escherichia coli's transcriptional and translational machinery

artículo científico publicado en 2010

Functional metabolic map of Faecalibacterium prausnitzii, a beneficial human gut microbe

artículo científico publicado en 2014

Generation of genome-scale metabolic reconstructions for 773 members of the human gut microbiota.

artículo científico publicado en 2016

Genome-Scale Reconstruction, Modeling, and Simulation of E. coli℉s Metabolic Network

scholarly article published 2009

Genome-scale methods converge on key mitochondrial genes for the survival of human cardiomyocytes in hypoxia

artículo científico publicado en 2014

Genome-scale reconstruction of Escherichia coli's transcriptional and translational machinery: a knowledge base, its mathematical formulation, and its functional characterization

artículo científico publicado en 2009

Genomic Analysis of the Human Gut Microbiome Suggests Novel Enzymes Involved in Quinone Biosynthesis

artículo científico publicado en 2016

Global reconstruction of the human metabolic network based on genomic and bibliomic data ⬇️

artículo científico publicado en 2007

Gut microbiota functions: metabolism of nutrients and other food components

artículo científico publicado en 2017

Identification of potential pathway mediation targets in Toll-like receptor signaling

artículo científico publicado en 2009

Inferring the metabolism of human orphan metabolites from their metabolic network context affirms human gluconokinase activity

artículo científico publicado en 2013

Integrated stoichiometric, thermodynamic and kinetic modelling of steady state metabolism

artículo científico publicado en 2010

Integration of a physiologically-based pharmacokinetic model with a whole-body, organ-resolved genome-scale model for characterization of ethanol and acetaldehyde metabolism

artículo científico publicado en 2021

Intracellular metabolite profiling of platelets: Evaluation of extraction processes and chromatographic strategies

artículo científico publicado en 2012

Leigh map: A novel computational diagnostic resource for mitochondrial disease

artículo científico publicado en 2016

Mass conserved elementary kinetics is sufficient for the existence of a non-equilibrium steady state concentration

artículo científico publicado en 2012

Membrane transporters in a human genome-scale metabolic knowledgebase and their implications for disease

scientific article published on 11 March 2014

MetaboTools: A Comprehensive Toolbox for Analysis of Genome-Scale Metabolic Models

artículo científico publicado en 2016

Metabolic network analysis integrated with transcript verification for sequenced genomes.

artículo científico publicado en 2009

Metabolomics enables precision medicine: "A White Paper, Community Perspective"

artículo científico publicado en 2016

Model-based dietary optimization for late-stage, levodopa-treated, Parkinson's disease patients

artículo científico publicado en 2016

Modeling metabolism of the human gut microbiome

artículo científico publicado en 2017

Modeling the effects of commonly used drugs on human metabolism

artículo científico publicado en 2014

Monitoring metabolites consumption and secretion in cultured cells using ultra-performance liquid chromatography quadrupole-time of flight mass spectrometry (UPLC-Q-ToF-MS).

artículo científico publicado en 2011

Multiscale modeling of metabolism and macromolecular synthesis in E. coli and its application to the evolution of codon usage

artículo científico publicado en 2012

Personalized metabolic whole-body models for newborns and infants predict growth and biomarkers of inherited metabolic diseases

artículo científico publicado en 2024

Personalized whole-body models integrate metabolism, physiology, and the gut microbiome

artículo científico publicado en 2020

Phenotypic differentiation of gastrointestinal microbes is reflected in their encoded metabolic repertoires

artículo científico publicado en 2015

Predicting gastrointestinal drug effects using contextualized metabolic models

scientific article published on 26 June 2019

Predicting the impact of diet and enzymopathies on human small intestinal epithelial cells

artículo científico publicado en 2013

Prediction of intracellular metabolic states from extracellular metabolomic data

artículo científico publicado en 2014

Quantitative assignment of reaction directionality in a multicompartmental human metabolic reconstruction.

artículo científico publicado en 2012

Quantitative assignment of reaction directionality in constraint-based models of metabolism: application to Escherichia coli

artículo científico publicado en 2009

Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0

artículo científico publicado en 2011

Quantitative systems pharmacology and the personalized drug-microbiota-diet axis

artículo científico publicado en 2017

Recon3D enables a three-dimensional view of gene variation in human metabolism.

artículo científico publicado en 2018

ReconMap: an interactive visualization of human metabolism

artículo científico publicado en 2016

Reconstruction annotation jamborees: a community approach to systems biology

artículo científico publicado en 2010

Reliable and efficient solution of genome-scale models of Metabolism and macromolecular Expression

artículo científico publicado en 2017

Replication Protein A, the Main Eukaryotic Single-Stranded DNA Binding Protein, a Focal Point in Cellular DNA Metabolism

artículo científico publicado en 2024

Reply to "Challenges in modeling the human gut microbiome"

scientific article published on 01 August 2018

Robust flux balance analysis of multiscale biochemical reaction networks.

artículo científico publicado en 2013

Systematic assessment of secondary bile acid metabolism in gut microbes reveals distinct metabolic capabilities in inflammatory bowel disease

artículo científico publicado en 2019

Systematic genome assessment of B-vitamin biosynthesis suggests co-operation among gut microbes

artículo científico publicado en 2015

Systematic genomic analysis reveals the complementary aerobic and anaerobic respiration capacities of the human gut microbiota

artículo científico publicado en 2014

Systematic prediction of health-relevant human-microbial co-metabolism through a computational framework

artículo científico publicado en 2015

Systems biology of host-microbe metabolomics

artículo científico publicado en 2015

Systems-level characterization of a host-microbe metabolic symbiosis in the mammalian gut

artículo científico publicado en 2012

The Microbiome Modeling Toolbox: from microbial interactions to personalized microbial communities

The Virtual Metabolic Human database: integrating human and gut microbiome metabolism with nutrition and disease

artículo científico publicado en 2019

The human metabolic reconstruction Recon 1 directs hypotheses of novel human metabolic functions

artículo científico publicado en 2011

The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes

artículo científico publicado en 2005

Three-dimensional structural view of the central metabolic network of Thermotoga maritima

artículo científico publicado en 2009

Toward systems metabolic engineering in cyanobacteria: opportunities and bottlenecks

artículo científico publicado en 2013

Towards multidimensional genome annotation

artículo científico publicado en 2006

What is flux balance analysis?

artículo científico publicado en 2010

XomicsToModel: Multiomics data integration and generation of thermodynamically consistent metabolic models

artículo científico publicado en 2021

fastGapFill: efficient gap filling in metabolic networks

artículo científico publicado en 2014

rBioNet: A COBRA toolbox extension for reconstructing high-quality biochemical networks

artículo científico publicado en 2011

von Bertalanffy 1.0: a COBRA toolbox extension to thermodynamically constrain metabolic models

artículo científico publicado en 2010

Lista de obras de Ines Thiele

A community effort towards a knowledge-base and mathematical model of the human pathogen Salmonella Typhimurium LT2

A community-driven global reconstruction of human metabolism. ⬇️

A compendium of inborn errors of metabolism mapped onto the human metabolic network

A detailed genome-wide reconstruction of mouse metabolism based on human Recon 1.

A genome-scale metabolic reconstruction of Pseudomonas putida KT2440: iJN746 as a cell factory

A protocol for generating a high-quality genome-scale metabolic reconstruction

A systems approach reveals distinct metabolic strategies among the NCI-60 cancer cell lines

A systems biology approach to drug targets in Pseudomonas aeruginosa biofilm

A systems biology approach to studying the role of microbes in human health.

An in silico re-design of the metabolism in Thermotoga maritima for increased biohydrogen production

Anoxic Conditions Promote Species-Specific Mutualism between Gut Microbes In Silico

Applying systems biology methods to the study of human physiology in extreme environments

BacArena: Individual-based metabolic modeling of heterogeneous microbes in complex communities

Bringing Genomes to Life: The Use of Genome-Scale In Silico Models

CHRR: coordinate hit-and-run with rounding for uniform sampling of constraint-based models.

Candidate metabolic network states in human mitochondria. Impact of diabetes, ischemia, and diet.

Candidate states of Helicobacter pylori's genome-scale metabolic network upon application of "loop law" thermodynamic constraints.

Cardinality optimization in constraint-based modelling: application to human metabolism

Comparative Genomic Analysis of the Human Gut Microbiome Reveals a Broad Distribution of Metabolic Pathways for the Degradation of Host-Synthetized Mucin Glycans and Utilization of Mucin-Derived Monosaccharides

Comparative evaluation of atom mapping algorithms for balanced metabolic reactions: application to Recon 3D.

Comparative evaluation of open source software for mapping between metabolite identifiers in metabolic network reconstructions: application to Recon 2

Computational Modeling of Human Metabolism and Its Application to Systems Biomedicine

Computationally efficient flux variability analysis

Conditions for duality between fluxes and concentrations in biochemical networks

Consensus and conflict cards for metabolic pathway databases

Contextualization procedure and modeling of monocyte specific TLR signaling

Creation and analysis of biochemical constraint-based models using the COBRA Toolbox v.3.0.

Detailing the optimality of photosynthesis in cyanobacteria through systems biology analysis

DistributedFBA.jl: high-level, high-performance flux balance analysis in Julia.

Do genome-scale models need exact solvers or clearer standards?

Editorial: The Human Gutome: Nutrigenomics of Host-Microbiome Interactions

Erratum to: Phenotypic differentiation of gastrointestinal microbes is reflected in their encoded metabolic repertoires.

Estimation of the number of extreme pathways for metabolic networks

Expanded metabolic reconstruction of Helicobacter pylori (iIT341 GSM/GPR): an in silico genome-scale characterization of single- and double-deletion mutants

Finding useful biomarkers for Parkinson's disease

From Network Analysis to Functional Metabolic Modeling of the Human Gut Microbiota

From metagenomic data to personalized in silico microbiotas: predicting dietary supplements for Crohn's disease

Functional characterization of alternate optimal solutions of Escherichia coli's transcriptional and translational machinery

Functional metabolic map of Faecalibacterium prausnitzii, a beneficial human gut microbe

Generation of genome-scale metabolic reconstructions for 773 members of the human gut microbiota.

Genome-Scale Reconstruction, Modeling, and Simulation of E. coli℉s Metabolic Network

Genome-scale methods converge on key mitochondrial genes for the survival of human cardiomyocytes in hypoxia

Genome-scale reconstruction of Escherichia coli's transcriptional and translational machinery: a knowledge base, its mathematical formulation, and its functional characterization

Genomic Analysis of the Human Gut Microbiome Suggests Novel Enzymes Involved in Quinone Biosynthesis

Global reconstruction of the human metabolic network based on genomic and bibliomic data ⬇️

Gut microbiota functions: metabolism of nutrients and other food components

Identification of potential pathway mediation targets in Toll-like receptor signaling

Inferring the metabolism of human orphan metabolites from their metabolic network context affirms human gluconokinase activity

Integrated stoichiometric, thermodynamic and kinetic modelling of steady state metabolism

Integration of a physiologically-based pharmacokinetic model with a whole-body, organ-resolved genome-scale model for characterization of ethanol and acetaldehyde metabolism

Intracellular metabolite profiling of platelets: Evaluation of extraction processes and chromatographic strategies

Leigh map: A novel computational diagnostic resource for mitochondrial disease

Mass conserved elementary kinetics is sufficient for the existence of a non-equilibrium steady state concentration

Membrane transporters in a human genome-scale metabolic knowledgebase and their implications for disease

MetaboTools: A Comprehensive Toolbox for Analysis of Genome-Scale Metabolic Models

Metabolic network analysis integrated with transcript verification for sequenced genomes.

Metabolomics enables precision medicine: "A White Paper, Community Perspective"

Model-based dietary optimization for late-stage, levodopa-treated, Parkinson's disease patients

Modeling metabolism of the human gut microbiome

Modeling the effects of commonly used drugs on human metabolism

Monitoring metabolites consumption and secretion in cultured cells using ultra-performance liquid chromatography quadrupole-time of flight mass spectrometry (UPLC-Q-ToF-MS).

Multiscale modeling of metabolism and macromolecular synthesis in E. coli and its application to the evolution of codon usage

Personalized metabolic whole-body models for newborns and infants predict growth and biomarkers of inherited metabolic diseases

Personalized whole-body models integrate metabolism, physiology, and the gut microbiome

Phenotypic differentiation of gastrointestinal microbes is reflected in their encoded metabolic repertoires

Predicting gastrointestinal drug effects using contextualized metabolic models

Predicting the impact of diet and enzymopathies on human small intestinal epithelial cells

Prediction of intracellular metabolic states from extracellular metabolomic data

Quantitative assignment of reaction directionality in a multicompartmental human metabolic reconstruction.

Quantitative assignment of reaction directionality in constraint-based models of metabolism: application to Escherichia coli

Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0

Quantitative systems pharmacology and the personalized drug-microbiota-diet axis

Recon3D enables a three-dimensional view of gene variation in human metabolism.

ReconMap: an interactive visualization of human metabolism

Reconstruction annotation jamborees: a community approach to systems biology

Reliable and efficient solution of genome-scale models of Metabolism and macromolecular Expression

Replication Protein A, the Main Eukaryotic Single-Stranded DNA Binding Protein, a Focal Point in Cellular DNA Metabolism

Reply to "Challenges in modeling the human gut microbiome"

Robust flux balance analysis of multiscale biochemical reaction networks.