Comprehensive reconstruction and in silico analysis of Aspergillus niger genome-scale metabolic network model that accounts for 1210 ORFs

Integration and Validation of the Genome-Scale Metabolic Models of Pichia pastoris: A Comprehensive Update of Protein Glycosylation Pathways, Lipid and Energy Metabolism

(2016) Màrius Tomàs-Gamisans et al.   PLoS One

Comprehensive evaluation of two genome-scale metabolic network models forScheffersomyces stipitis

(2015) Andrew L. Damiani et al.   BIOTECHNOLOGY AND BIOENGINEERING

Computational methods in metabolic engineering for strain design

(2015) Matthew R Long et al.   CURRENT OPINION IN BIOTECHNOLOGY

Development of tools for quantitative intracellular metabolomics of Aspergillus niger chemostat cultures

(2015) Francisca Lameiras et al.   Metabolomics

Overview of citric acid production fromAspergillus niger

(2015) Pau Loke Show et al.   Frontiers in Life Science

Genome and transcriptome of the porcine whipworm Trichuris suis

(2014) Aaron R Jex et al.   NATURE GENETICS

Constraint-based models predict metabolic and associated cellular functions

(2014) Aarash Bordbar et al.   NATURE REVIEWS GENETICS

optGpSampler: An Improved Tool for Uniformly Sampling the Solution-Space of Genome-Scale Metabolic Networks

(2014) Wout Megchelenbrink et al.   PLoS One

Altered sterol composition renders yeast thermotolerant

(2014) L. Caspeta et al.   SCIENCE

Metabolic engineering of Corynebacterium glutamicum for L-arginine production

(2014) Seok Hyun Park et al.   Nature Communications

Systematic Evaluation of Methods for Integration of Transcriptomic Data into Constraint-Based Models of Metabolism

(2014) Daniel Machado et al.   PLoS Computational Biology

Genome-scale reconstruction and in silico analysis of Aspergillus terreus metabolism

(2013) Jie Liu et al.   Molecular BioSystems

Aspergilli: Systems biology and industrial applications

(2012) Christoph Knuf et al.   Biotechnology Journal

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

(2012) Pengcheng Pan et al.   PLoS One

Computational identification of gene over-expression targets for metabolic engineering of taxadiene production

(2011) Brett A. Boghigian et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Production of recombinant proteins by filamentous fungi

(2011) Owen P. Ward   BIOTECHNOLOGY ADVANCES

Industrial glucoamylase fed-batch benefits from oxygen limitation and high osmolarity

(2011) Lasse Pedersen et al.   BIOTECHNOLOGY AND BIOENGINEERING

Integration of in vivo and in silico metabolic fluxes for improvement of recombinant protein production

(2011) Habib Driouch et al.   METABOLIC ENGINEERING

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

(2011) Jan Schellenberger et al.   Nature Protocols

The Aspergillus Genome Database (AspGD): recent developments in comprehensive multispecies curation, comparative genomics and community resources

(2011) M. B. Arnaud et al.   NUCLEIC ACIDS RESEARCH

Shotgun Proteomics of Aspergillus niger Microsomes upon D-Xylose Induction

(2010) J. M. P. F. de Oliveira et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

The biomass objective function

(2010) Adam M Feist et al.   CURRENT OPINION IN MICROBIOLOGY

What is flux balance analysis?

(2010) Jeffrey D Orth et al.   NATURE BIOTECHNOLOGY

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

(2010) Ines Thiele et al.   Nature Protocols

Physiology ofAspergillus nigerin oxygen-limited continuous cultures: Influence of aeration, carbon source concentration and dilution rate

(2009) A. Diano et al.   BIOTECHNOLOGY AND BIOENGINEERING

13C-based metabolic flux analysis

(2009) Nicola Zamboni et al.   Nature Protocols

In-depth analysis of the Aspergillus niger glucoamylase (glaA) promoter performance using high-throughput screening and controlled bioreactor cultivation techniques

(2008) M GANZLIN et al.   JOURNAL OF BIOTECHNOLOGY

Metabolic model integration of the bibliome, genome, metabolome and reactome of Aspergillus niger

(2008) Mikael Rørdam Andersen et al.   Molecular Systems Biology

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi et al.   NATURE METHODS

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS