Systems biology for understanding and engineering of heterotrophic oleaginous microorganisms

Functional overexpression and characterization of lipogenesis-related genes in the oleaginous yeast Yarrowia lipolytica

(2016) Andrew M. Silverman et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Genome-scale metabolic modeling and in silico analysis of lipid accumulating yeastCandida tropicalisfor dicarboxylic acid production

(2016) Pranjul Mishra et al.   BIOTECHNOLOGY AND BIOENGINEERING

Engineering of a high lipid producing Yarrowia lipolytica strain

(2016) Jonathan Friedlander et al.   Biotechnology for Biofuels

Multi-omics analysis reveals regulators of the response to nitrogen limitation in Yarrowia lipolytica

(2016) Kyle R. Pomraning et al.   BMC GENOMICS

Genome-scale metabolic modeling of Mucor circinelloides and comparative analysis with other oleaginous species

(2016) Wanwipa Vongsangnak et al.   GENE

13 C Metabolic Flux Analysis of acetate conversion to lipids by Yarrowia lipolytica

(2016) Nian Liu et al.   METABOLIC ENGINEERING

Proteomics analysis of high lipid-producing strain Mucor circinelloides WJ11: an explanation for the mechanism of lipid accumulation at the proteomic level

(2016) Xin Tang et al.   Microbial Cell Factories

Characterization of key triacylglycerol biosynthesis processes in rhodococci

(2016) Sawsan Amara et al.   Scientific Reports

13 C-metabolic flux analysis of lipid accumulation in the oleaginous fungus Mucor circinelloides

(2015) Lina Zhao et al.   BIORESOURCE TECHNOLOGY

Transcriptomics-based strain optimization tool for designing secondary metabolite overproducing strains ofStreptomyces coelicolor

(2015) Minsuk Kim et al.   BIOTECHNOLOGY AND BIOENGINEERING

Reconstruction and analysis of a genome-scale metabolic model of the oleaginous fungus Mortierella alpina

(2015) Chao Ye et al.   BMC Systems Biology

Genome-scale metabolic model of Rhodococcus jostii RHA1 (iMT1174) to study the accumulation of storage compounds during nitrogen-limited condition

(2015) Mohammad Tajparast et al.   BMC Systems Biology

Optimization of lipid production with a genome-scale model of Yarrowia lipolytica

(2015) Martin Kavšček et al.   BMC Systems Biology

Critical assessment of genome-scale metabolic networks: the need for a unified standard

(2015) A. Ravikrishnan et al.   BRIEFINGS IN BIOINFORMATICS

Using Genome-scale Models to Predict Biological Capabilities

(2015) Edward J. O’Brien et al.   CELL

Advancing metabolic engineering through systems biology of industrial microorganisms

(2015) Zongjie Dai et al.   CURRENT OPINION IN BIOTECHNOLOGY

Engineering lipid overproduction in the oleaginous yeast Yarrowia lipolytica

(2015) Kangjian Qiao et al.   METABOLIC ENGINEERING

The oxidative pentose phosphate pathway is the primary source of NADPH for lipid overproduction from glucose in Yarrowia lipolytica

(2015) Thomas M. Wasylenko et al.   METABOLIC ENGINEERING

An evolutionary metabolic engineering approach for enhancing lipogenesis in Yarrowia lipolytica

(2015) Leqian Liu et al.   METABOLIC ENGINEERING

In SilicoConstraint-Based Strain Optimization Methods: the Quest for Optimal Cell Factories

(2015) Paulo Maia et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Label-free and redox proteomic analyses of the triacylglycerol-accumulating Rhodococcus jostii RHA1

(2015) José Sebastián Dávila Costa et al.   MICROBIOLOGY-SGM

Systems strategies for developing industrial microbial strains

(2015) Sang Yup Lee et al.   NATURE BIOTECHNOLOGY

Microbial lipid-based lignocellulosic biorefinery: feasibility and challenges

(2015) Mingjie Jin et al.   TRENDS IN BIOTECHNOLOGY

Genomics and Transcriptomics Analyses of the Oil-Accumulating Basidiomycete Yeast Trichosporon oleaginosus : Insights into Substrate Utilization and Alternative Evolutionary Trajectories of Fungal Mating Systems

(2015) Robert Kourist et al.   mBio

Role of pentose phosphate pathway in lipid accumulation of oleaginous fungus Mucor circinelloides

(2015) Lina Zhao et al.   RSC Advances

Identification of a critical determinant that enables efficient fatty acid synthesis in oleaginous fungi

(2015) Haiqin Chen et al.   Scientific Reports

Comprehensive Metabolomic, Lipidomic and Microscopic Profiling of Yarrowia lipolytica during Lipid Accumulation Identifies Targets for Increased Lipogenesis

(2015) Kyle R. Pomraning et al.   PLoS One

The role of malic enzyme as the provider of NADPH in oleaginous microorganisms: a reappraisal and unsolved problems

(2014) Colin Ratledge   BIOTECHNOLOGY LETTERS

Constraint-based models predict metabolic and associated cellular functions

(2014) Aarash Bordbar et al.   NATURE REVIEWS GENETICS

Harnessing Yarrowia lipolytica lipogenesis to create a platform for lipid and biofuel production

(2014) John Blazeck et al.   Nature Communications

Toward systems metabolic engineering ofAspergillusandPichiaspecies for the production of chemicals and biofuels

(2013) Luis Caspeta et al.   Biotechnology Journal

Regulatory properties of malic enzyme in the oleaginous yeast, Yarrowia lipolytica, and its non-involvement in lipid accumulation

(2013) Huaiyuan Zhang et al.   BIOTECHNOLOGY LETTERS

The Rhodococcus opacus TadD protein mediates triacylglycerol metabolism by regulating intracellular NAD(P)H pools

(2013) Daniel P MacEachran et al.   Microbial Cell Factories

Integrated omics study delineates the dynamics of lipid droplets in Rhodococcus opacus PD630

(2013) Y. Chen et al.   NUCLEIC ACIDS RESEARCH

Comparative Proteomics Profile of Lipid-Cumulating Oleaginous Yeast: An iTRAQ-Coupled 2-D LC-MS/MS Analysis

(2013) Jiahua Shi et al.   PLoS One

Advancing oleaginous microorganisms to produce lipid via metabolic engineering technology

(2013) Ming-Hua Liang et al.   PROGRESS IN LIPID RESEARCH

Analysis of metabolic fluxes for better understanding of mechanisms related to lipid accumulation in oleaginous yeast Trichosporon cutaneum

(2012) Zhijie Liu et al.   BIORESOURCE TECHNOLOGY

A genome-scale metabolic model of the lipid-accumulating yeast Yarrowia lipolytica

(2012) Nicolas Loira et al.   BMC Systems Biology

Expanding the chemical palate of cells by combining systems biology and metabolic engineering

(2012) Kathleen A. Curran et al.   METABOLIC ENGINEERING

Engineering the push and pull of lipid biosynthesis in oleaginous yeast Yarrowia lipolytica for biofuel production

(2012) Mitchell Tai et al.   METABOLIC ENGINEERING

Reconstruction and In Silico Analysis of Metabolic Network for an Oleaginous Yeast, Yarrowia lipolytica

(2012) Pengcheng Pan et al.   PLoS One

A multi-omic map of the lipid-producing yeast Rhodosporidium toruloides

(2012) Zhiwei Zhu et al.   Nature Communications

Identification and characterization of DGA2, an acyltransferase of the DGAT1 acyl-CoA:diacylglycerol acyltransferase family in the oleaginous yeast Yarrowia lipolytica. New insights into the storage lipid metabolism of oleaginous yeasts

(2011) Athanasios Beopoulos et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

From zero to hero—Design-based systems metabolic engineering of Corynebacterium glutamicum for l-lysine production

(2011) Judith Becker et al.   METABOLIC ENGINEERING

Transcriptomic Analyses during the Transition from Biomass Production to Lipid Accumulation in the Oleaginous Yeast Yarrowia lipolytica

(2011) Nicolas Morin et al.   PLoS One

Systems biology of microbial metabolism

(2010) Matthias Heinemann et al.   CURRENT OPINION IN MICROBIOLOGY

The proteome analysis of oleaginous yeast Lipomyces starkeyi

(2010) Hongwei Liu et al.   FEMS YEAST RESEARCH

High-cell-density batch fermentation of Rhodococcus opacus PD630 using a high glucose concentration for triacylglycerol production

(2010) Kazuhiko Kurosawa et al.   JOURNAL OF BIOTECHNOLOGY

What is flux balance analysis?

(2010) Jeffrey D Orth et al.   NATURE BIOTECHNOLOGY

Lipids from heterotrophic microbes: advances in metabolism research

(2010) Matyas Kosa et al.   TRENDS IN BIOTECHNOLOGY

An overview of second generation biofuel technologies

(2009) Ralph E.H. Sims et al.   BIORESOURCE TECHNOLOGY

Production of first and second generation biofuels: A comprehensive review

(2009) S.N. Naik et al.   RENEWABLE & SUSTAINABLE ENERGY REVIEWS

Perspectives of microbial oils for biodiesel production

(2008) Qiang Li et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Towards systems metabolic engineering of microorganisms for amino acid production

(2008) Jin Hwan Park et al.   CURRENT OPINION IN BIOTECHNOLOGY

Impact of systems biology on metabolic engineering ofSaccharomyces cerevisiae

(2007) Jens Nielsen et al.   FEMS YEAST RESEARCH