Elucidating the impact of in vitro cultivation on Nicotiana tabacum metabolism through combined in silico modeling and multiomics analysis

Determination of the chemical compounds of Shuchazao tea flowers at different developmental stages and in young shoots using 1H NMR-based metabolomics

(2022) Hong Ye et al.   MONATSHEFTE FUR CHEMIE

Reconstruction of a Genome-Scale Metabolic Network for Shewanella oneidensis MR-1 and Analysis of its Metabolic Potential for Bioelectrochemical Systems

(2022) Jiahao Luo et al.   Frontiers in Bioengineering and Biotechnology

The effect of alternative membrane system, sucrose, and culture methods under photosynthetic photon flux on growth and volatile compounds of mint in vitro

(2021) Thainá de Oliveira et al.   IN VITRO CELLULAR & DEVELOPMENTAL BIOLOGY-PLANT

Impact of Various Microbial-Fermented Methods on the Chemical Profile of Dark Tea Using a Single Raw Tea Material

(2021) Jiang Shi et al.   JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY

Metabolism and Regulatory Functions of O-Acetylserine, S-Adenosylmethionine, Homocysteine, and Serine in Plant Development and Environmental Responses

(2021) Mutsumi Watanabe et al.   Frontiers in Plant Science

Silent constraints: the hidden challenges faced in plant metabolic engineering

(2021) Joseph H Lynch et al.   CURRENT OPINION IN BIOTECHNOLOGY

Flux balance analysis of metabolism during growth by osmotic cell expansion and its application to tomato fruits

(2020) Sanu Shameer et al.   PLANT JOURNAL

Next-generation metabolic engineering approaches towards development of plant cell suspension cultures as specialized metabolite producing biofactories

(2020) Sagar S. Arya et al.   BIOTECHNOLOGY ADVANCES

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

(2019) Laurent Heirendt et al.   Nature Protocols

Effect of Major Tea Insect Attack on The Formation of Quality-Related Non-Volatile Specialized Metabolites in Tea (Camellia sinensis) Leaves

(2019) Yinyin Liao et al.   JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY

Metabolomics of Thrips Resistance in Pepper (Capsicum spp.) Reveals Monomer and Dimer Acyclic Diterpene Glycosides as Potential Chemical Defenses

(2019) Mirka Macel et al.   JOURNAL OF CHEMICAL ECOLOGY

Chloroplastic metabolic engineering coupled with isoprenoid pool enhancement for committed taxanes biosynthesis in Nicotiana benthamiana

(2019) Jianhua Li et al.   Nature Communications

Colour bio-factories: Towards scale-up production of anthocyanins in plant cell cultures

(2018) Ingo Appelhagen et al.   METABOLIC ENGINEERING

Agronomic and chemical performance of field-grown tobacco engineered for triterpene and methylated triterpene metabolism

(2018) Zuodong Jiang et al.   PLANT BIOTECHNOLOGY JOURNAL

Integration of large-scale data for extraction of integrated Arabidopsis root cell-type specific models

(2018) Michael Scheunemann et al.   Scientific Reports

A genome-scale metabolic model of potato late blight suggests a photosynthesis suppression mechanism

(2018) Kelly Botero et al.   BMC GENOMICS

Mixotrophic in vitro cultivations: the way to go astray in plant physiology

(2018) Hana Ševčíková et al.   PHYSIOLOGIA PLANTARUM

Resolving the central metabolism of Arabidopsis guard cells

(2017) Semidán Robaina-Estévez et al.   Scientific Reports

Reconstruction of Oryza sativa indica Genome Scale Metabolic Model and Its Responses to Varying RuBisCO Activity, Light Intensity, and Enzymatic Cost Conditions

(2017) Ankita Chatterjee et al.   Frontiers in Plant Science

A genome-scale metabolic network reconstruction of tomato (Solanum lycopersicumL.) and its application to photorespiratory metabolism

(2016) Huili Yuan et al.   PLANT JOURNAL

Multiscale Metabolic Modeling of C4 Plants: Connecting Nonlinear Genome-Scale Models to Leaf-Scale Metabolism in Developing Maize Leaves

(2016) Eli Bogart et al.   PLoS One

Understanding the shoot apical meristem regulation: A study of the phytohormones, auxin and cytokinin, in rice

(2015) P. Azizi et al.   MECHANISMS OF DEVELOPMENT

StringTie enables improved reconstruction of a transcriptome from RNA-seq reads

(2015) Mihaela Pertea et al.   NATURE BIOTECHNOLOGY

HISAT: a fast spliced aligner with low memory requirements

(2015) Daehwan Kim et al.   NATURE METHODS

Unraveling the light-specific metabolic and regulatory signatures of rice through combined in silico modeling and multi-omics analysis

(2015) Meiyappan Lakshmanan et al.   PLANT PHYSIOLOGY

Six enzymes from mayapple that complete the biosynthetic pathway to the etoposide aglycone

(2015) Warren Lau et al.   SCIENCE

Revisiting the chlorophyll biosynthesis pathway using genome scale metabolic model of Oryza sativa japonica

(2015) Ankita Chatterjee et al.   Scientific Reports

Improved evidence-based genome-scale metabolic models for maize leaf, embryo, and endosperm

(2015) Samuel M. D. Seaver et al.   Frontiers in Plant Science

Applications of genome-scale metabolic network model in metabolic engineering

(2014) Byoungjin Kim et al.   JOURNAL OF INDUSTRIAL MICROBIOLOGY & BIOTECHNOLOGY

Modelling central metabolic fluxes by constraint-based optimization reveals metabolic reprogramming of developingSolanum lycopersicum(tomato) fruit

(2014) Sophie Colombié et al.   PLANT JOURNAL

Assessing the Metabolic Impact of Nitrogen Availability Using a Compartmentalized Maize Leaf Genome-Scale Model

(2014) M. Simons et al.   PLANT PHYSIOLOGY

The tobacco genome sequence and its comparison with those of tomato and potato

(2014) Nicolas Sierro et al.   Nature Communications

Variability of Metabolite Levels Is Linked to Differential Metabolic Pathways in Arabidopsis's Responses to Abiotic Stresses

(2014) Nadine Töpfer et al.   PLoS Computational Biology

Photosynthetic capacity, growth and water relations in ‘Golden’ papaya cultivated in vitro with modifications in light quality, sucrose concentration and ventilation

(2014) Omar Schmildt et al.   Theoretical and Experimental Plant Physiology

Genetic engineering of the chloroplast: novel tools and new applications

(2013) Ralph Bock   CURRENT OPINION IN BIOTECHNOLOGY

Integration of Genome-Scale Modeling and Transcript Profiling Reveals Metabolic Pathways Underlying Light and Temperature Acclimation in Arabidopsis

(2013) N. Topfer et al.   PLANT CELL

A method for accounting for maintenance costs in flux balance analysis improves the prediction of plant cell metabolic phenotypes under stress conditions

(2013) C. Y. Maurice Cheung et al.   PLANT JOURNAL

Elucidating Rice Cell Metabolism under Flooding and Drought Stresses Using Flux-Based Modeling and Analysis

(2013) M. Lakshmanan et al.   PLANT PHYSIOLOGY

Responses to Light Intensity in a Genome-Scale Model of Rice Metabolism

(2013) M. G. Poolman et al.   PLANT PHYSIOLOGY

An in silico platform for the design of heterologous pathways in nonnative metabolite production

(2012) Sunisa Chatsurachai et al.   BMC BIOINFORMATICS

Review: role of carbon sources for in vitro plant growth and development

(2012) Mehwish Yaseen et al.   MOLECULAR BIOLOGY REPORTS

Generation of the potent anti-malarial drug artemisinin in tobacco

(2011) Moran Farhi et al.   NATURE BIOTECHNOLOGY

GLYCOALKALOID METABOLISM1 Is Required for Steroidal Alkaloid Glycosylation and Prevention of Phytotoxicity in Tomato

(2011) M. Itkin et al.   PLANT CELL

Metabolic profiling of photoautotrophic and photomixotrophic potato plantlets (Solanum tuberosum) provides new insights into acclimatization

(2011) Ashraf Badr et al.   PLANT CELL TISSUE AND ORGAN CULTURE

What is flux balance analysis?

(2010) Jeffrey D Orth et al.   NATURE BIOTECHNOLOGY

Development and application of photoautotrophic micropropagation plant system

(2010) Yulan Xiao et al.   PLANT CELL TISSUE AND ORGAN CULTURE

Not just a circle: flux modes in the plant TCA cycle

(2010) Lee J. Sweetlove et al.   TRENDS IN PLANT SCIENCE

Natural ventilation effectively reduces hyperhydricity in shoot cultures of Aloe polyphylla Schönland ex Pillans

(2009) Mariyana Ivanova et al.   PLANT GROWTH REGULATION

Interpreting Expression Data with Metabolic Flux Models: Predicting Mycobacterium tuberculosis Mycolic Acid Production

(2009) Caroline Colijn et al.   PLoS Computational Biology

Rice germination and seedling growth in the absence of oxygen

(2008) Leonardo Magneschi et al.   ANNALS OF BOTANY

Effects of agar concentration and vessel closure on the organogenesis and hyperhydricity of adventitious carnation shoots

(2008) E. Casanova et al.   BIOLOGIA PLANTARUM

Elevated CO2increases photosynthesis, biomass and productivity, and modifies gene expression in sugarcane

(2008) AMANDA PEREIRA DE SOUZA et al.   PLANT CELL AND ENVIRONMENT