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Bottom-up Metabolic Reconstruction of Arabidopsis and Its Application to Determining the Metabolic Costs of Enzyme Production

Plant physiology (Bethesda), 2014-07, Vol.165 (3), p.1380-1391

2014

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Integrating molecular markers into metabolic models improves genomic selection for Arabidopsis growth

Nature communications, 2020-05, Vol.11 (1), p.2410-2410, Article 2410

2020

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GeneReg: a constraint-based approach for design of feasible metabolic engineering strategies at the gene level

Bioinformatics, 2021-07, Vol.37 (12), p.1717-1723

2021

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Gene regulatory network inference using mixed-norms regularized multivariate model with covariance selection

PLoS computational biology, 2023-07, Vol.19 (7), p.e1010832-e1010832

2023

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Editorial: Isotopic labeling approaches for exploring plant metabolism dynamics

Frontiers in Plant Science, 2024-01, Vol.14, p.1356153-1356153

2024

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COMMIT: Consideration of metabolite leakage and community composition improves microbial community reconstructions

PLoS computational biology, 2022-03, Vol.18 (3), p.e1009906-e1009906

2022

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Systematic comparison of local approaches for isotopically nonstationary metabolic flux analysis

Frontiers in plant science, 2023-06, Vol.14, p.1178239-1178239

2023

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A structural property for reduction of biochemical networks

Scientific reports, 2021-08, Vol.11 (1), p.17415-17415, Article 17415

2021

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Maximizing multi-reaction dependencies provides more accurate and precise predictions of intracellular fluxes than the principle of parsimony

PLoS computational biology, 2023-09, Vol.19 (9), p.e1011489-e1011489

2023

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Data integration across conditions improves turnover number estimates and metabolic predictions

Nature communications, 2023-03, Vol.14 (1), p.1485-1485, Article 1485

2023

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The effective deficiency of biochemical networks

Scientific reports, 2023-09, Vol.13 (1), p.14589-14589, Article 14589

2023

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The unraveling of balanced complexes in metabolic networks

Scientific reports, 2023-04, Vol.13 (1), p.5712-5712, Article 5712

2023

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Identification of flux trade-offs in metabolic networks

Scientific reports, 2021-12, Vol.11 (1), p.23776-23776, Article 23776

2021

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Genome-Wide Association in Tomato Reveals 44 Candidate Loci for Fruit Metabolic Traits

Plant physiology (Bethesda), 2014-07, Vol.165 (3), p.1120-1132

2014

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Relationships of Leaf Net Photosynthesis, Stomatal Conductance, and Mesophyll Conductance to Primary Metabolism: A Multispecies Meta-Analysis Approach

Plant physiology (Bethesda), 2016-05, Vol.171 (1), p.265-279

2016

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Integration of relative metabolomics and transcriptomics time-course data in a metabolic model pinpoints effects of ribosome biogenesis defects on Arabidopsis thaliana metabolism

Scientific reports, 2021-02, Vol.11 (1), p.4787-4787, Article 4787

2021

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A network-based framework for shape analysis enables accurate characterization of leaf epidermal cells

Nature communications, 2021-01, Vol.12 (1), p.458-458, Article 458

2021

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Integration of transcriptomics and metabolomics data specifies the metabolic response of Chlamydomonas to rapamycin treatment

The Plant journal : for cell and molecular biology, 2015-03, Vol.81 (5), p.822-835

2015

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Reaction lumping in metabolic networks for application with thermodynamic metabolic flux analysis

Scientific reports, 2021-04, Vol.11 (1), p.8544-8544, Article 8544

2021

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Characterization of effects of genetic variants via genome-scale metabolic modelling

Cellular and molecular life sciences : CMLS, 2021-06, Vol.78 (12), p.5123-5138

2021

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Kingdom-wide comparison reveals the evolution of diurnal gene expression in Archaeplastida

Nature communications, 2019-02, Vol.10 (1), p.737-737, Article 737

2019

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Supervised learning of gene-regulatory networks based on graph distance profiles of transcriptomics data

NPJ systems biology and applications, 2020-06, Vol.6 (1), p.21-21, Article 21

2020

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Comparative Analysis of ROS Network Genes in Extremophile Eukaryotes

International journal of molecular sciences, 2020-11, Vol.21 (23), p.9131

2020

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Metabolic Fluxes in an Illuminated Arabidopsis Rosette

The Plant cell, 2013-02, Vol.25 (2), p.694-714

2013

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Identification and Mode of Inheritance of Quantitative Trait Loci for Secondary Metabolite Abundance in Tomato

The Plant cell, 2015-03, Vol.27 (3), p.485-512

2015

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Bottom-up Metabolic Reconstruction of Arabidopsis and Its Application to Determining the Metabolic Costs of Enzyme Production

Integrating molecular markers into metabolic models improves genomic selection for Arabidopsis growth

GeneReg: a constraint-based approach for design of feasible metabolic engineering strategies at the gene level

Gene regulatory network inference using mixed-norms regularized multivariate model with covariance selection

Editorial: Isotopic labeling approaches for exploring plant metabolism dynamics

COMMIT: Consideration of metabolite leakage and community composition improves microbial community reconstructions

Systematic comparison of local approaches for isotopically nonstationary metabolic flux analysis

A structural property for reduction of biochemical networks

Maximizing multi-reaction dependencies provides more accurate and precise predictions of intracellular fluxes than the principle of parsimony

Data integration across conditions improves turnover number estimates and metabolic predictions

The effective deficiency of biochemical networks

The unraveling of balanced complexes in metabolic networks

Identification of flux trade-offs in metabolic networks

Genome-Wide Association in Tomato Reveals 44 Candidate Loci for Fruit Metabolic Traits

Relationships of Leaf Net Photosynthesis, Stomatal Conductance, and Mesophyll Conductance to Primary Metabolism: A Multispecies Meta-Analysis Approach

Integration of relative metabolomics and transcriptomics time-course data in a metabolic model pinpoints effects of ribosome biogenesis defects on Arabidopsis thaliana metabolism

A network-based framework for shape analysis enables accurate characterization of leaf epidermal cells

Integration of transcriptomics and metabolomics data specifies the metabolic response of Chlamydomonas to rapamycin treatment

Reaction lumping in metabolic networks for application with thermodynamic metabolic flux analysis

Characterization of effects of genetic variants via genome-scale metabolic modelling

Kingdom-wide comparison reveals the evolution of diurnal gene expression in Archaeplastida

Supervised learning of gene-regulatory networks based on graph distance profiles of transcriptomics data

Comparative Analysis of ROS Network Genes in Extremophile Eukaryotes

Metabolic Fluxes in an Illuminated Arabidopsis Rosette

Identification and Mode of Inheritance of Quantitative Trait Loci for Secondary Metabolite Abundance in Tomato

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