(Q33945314)

30 July 2017

title

Automated refinement and inference of analytical models for metabolic networks (English)

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30 July 2017

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7

Hod Lipson

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30 July 2017

Michael D Schmidt

1

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30 July 2017

Ravishankar R Vallabhajosyula

2

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30 July 2017

Jerry W Jenkins

3

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30 July 2017

Jonathan E Hood

4

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30 July 2017

Abhishek S Soni

5

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30 July 2017

John P Wikswo

6

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30 July 2017

publication date

10 August 2011

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30 July 2017

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30 July 2017

volume

8

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30 July 2017

issue

5

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30 July 2017

page(s)

055011

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How do control-based approaches enter into biology?

30 July 2017

cites work

1 reference

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Towards monitoring real-time cellular response using an integrated microfluidics-matrix assisted laser desorption ionisation/nanoelectrospray ionisation-ion mobility-mass spectrometry platform

5 July 2018

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A quantitative model of glucose signaling in yeast reveals an incoherent feed forward loop leading to a specific, transient pulse of transcription

5 July 2018

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A model of yeast cell-cycle regulation based on multisite phosphorylation

5 July 2018

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The simplicity of completion time distributions for common complex biochemical processes

5 July 2018

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The automation of science.

5 July 2018

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Distilling free-form natural laws from experimental data

5 July 2018

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Recent developments in parameter estimation and structure identification of biochemical and genomic systems

5 July 2018

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Canalization of gene expression and domain shifts in the Drosophila blastoderm by dynamical attractors

5 July 2018

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System estimation from metabolic time-series data

5 July 2018

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Memory switches in chemical reaction space

5 July 2018

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Reconstructing signal transduction pathways: challenges and opportunities.

5 July 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4109817

Reconstruction of metabolic networks from high-throughput metabolite profiling data: in silico analysis of red blood cell metabolism

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4109817

Automated reverse engineering of nonlinear dynamical systems

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4109817

Genome-wide transcriptional plasticity underlies cellular adaptation to novel challenge

5 July 2018

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How to infer gene networks from expression profiles

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4109817

Integration of metabolome data with metabolic networks reveals reporter reactions

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4109817

When transcriptome meets metabolome: fast cellular responses of yeast to sudden relief of glucose limitation.

5 July 2018

1 reference

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Dynamic analysis of optimality in myocardial energy metabolism under normal and ischemic conditions

5 July 2018

1 reference

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ARACNE: An Algorithm for the Reconstruction of Gene Regulatory Networks in a Mammalian Cellular Context

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4109817

The next wave in metabolome analysis

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4109817

Uncovering transcriptional regulation of metabolism by using metabolic network topology

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4109817

Mathematical and computational techniques to deduce complex biochemical reaction mechanisms

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4109817

Metabolomics and systems biology: making sense of the soup

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4109817

Integrative analysis of cell cycle control in budding yeast

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4109817

Functional genomic hypothesis generation and experimentation by a robot scientist

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4109817

New Approaches to the Deduction of Complex Reaction Mechanisms

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4109817

Parameter estimation in biochemical pathways: a comparison of global optimization methods

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4109817

Inferring genetic networks and identifying compound mode of action via expression profiling

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4109817

Sniffers, buzzers, toggles and blinkers: dynamics of regulatory and signaling pathways in the cell

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4109817

Computational approaches to cellular rhythms

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4109817

Description and analysis of metabolic connectivity and dynamics in the human red blood cell

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4109817

Determination of causal connectivities of species in reaction networks

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4109817

Synchronizing genetic relaxation oscillators by intercell signaling

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4109817

Control analysis for autonomously oscillating biochemical networks

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4109817

Reverse engineering of metabolic pathways from observed data using genetic programming.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4109817

Effect of cellular interaction on glycolytic oscillations in yeast: a theoretical investigation

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4109817

Non-linear optimization of biochemical pathways: applications to metabolic engineering and parameter estimation

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4109817

Metabolic control analysis: a survey of its theoretical and experimental development

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4109817

Metabolic regulation and mathematical models

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4109817

Determination of critical network interactions: an augmented Boolean pseudo-dynamics approach

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4109817

Complexity reduction of biochemical rate expressions

29 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4109817

A genome-scale computational study of the interplay between transcriptional regulation and metabolism

29 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4109817

Theodor Bücher Lecture. Metabolomics, modelling and machine learning in systems biology - towards an understanding of the languages of cells. Delivered on 3 July 2005 at the 30th FEBS Congress and the 9th IUBMB conference in Budapest.

29 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4109817

Closed-loop, multiobjective optimization of analytical instrumentation: gas chromatography/time-of-flight mass spectrometry of the metabolomes of human serum and of yeast fermentations.

29 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4109817

The evolution of molecular biology into systems biology.

29 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4109817

Temperature dependency and temperature compensation in a model of yeast glycolytic oscillations.

29 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4109817

Invariant manifold methods for metabolic model reduction.

29 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4109817

On the analysis of the inverse problem of metabolic pathways using artificial neural networks.

29 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4109817

Model assessment and refinement using strategies from biochemical systems theory: application to metabolism in human red blood cells.

29 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4109817

Sustained oscillations in free-energy state and hexose phosphates in yeast

29 October 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/21832805

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1088/1478-3975/8/5/055011

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30 July 2017

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30 July 2017

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