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

A constraint-based model of Scheffersomyces stipitis for improved ethanol production

(2012) Ting Liu et al.   Biotechnology for Biofuels

Aspergilli: Systems biology and industrial applications

(2012) Christoph Knuf et al.   Biotechnology Journal

Genome-scale metabolic reconstructions of Pichia stipitis and Pichia pastoris and in-silico evaluation of their potentials

(2012) Luis Caspeta et al.   BMC Systems Biology

Temporal analysis of xylose fermentation by Scheffersomyces stipitis using shotgun proteomics

(2012) Eric L. Huang et al.   JOURNAL OF INDUSTRIAL MICROBIOLOGY & BIOTECHNOLOGY

Cell surface display of a β-glucosidase employing the type V secretion system on ethanologenic Escherichia coli for the fermentation of cellobiose to ethanol

(2012) Iván Muñoz-Gutiérrez et al.   JOURNAL OF INDUSTRIAL MICROBIOLOGY & BIOTECHNOLOGY

Metabolic flux profiling of recombinant protein secreting Pichia pastoris growing on glucose:methanol mixtures

(2012) Joel Jordà et al.   Microbial Cell Factories

Physiological response of Pichia pastoris GS115 to methanol-induced high level production of the Hepatitis B surface antigen: catabolic adaptation, stress responses, and autophagic processes

(2012) Ana Leticia Vanz et al.   Microbial Cell Factories

Reconstruction and analysis of a genome-scale metabolic model for Scheffersomyces stipitis

(2012) Balaji Balagurunathan et al.   Microbial Cell Factories

Scheffersomyces stipitis: a comparative systems biology study with the Crabtree positive yeast Saccharomyces cerevisiae

(2012) Marta Papini et al.   Microbial Cell Factories

Systems metabolic engineering of microorganisms for natural and non-natural chemicals

(2012) Jeong Wook Lee et al.   Nature Chemical Biology

Uncovering the Genome-Wide Transcriptional Responses of the Filamentous Fungus Aspergillus niger to Lignocellulose Using RNA Sequencing

(2012) Stéphane Delmas et al.   PLoS Genetics

A proteomic analysis of the Pichia pastoris secretome in methanol-induced cultures

(2011) Chung-Jr Huang et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

RNA-Seq of the xylose-fermenting yeast Scheffersomyces stipitis cultivated in glucose or xylose

(2011) Tiezheng Yuan et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Engineering of microorganisms for the production of biofuels and perspectives based on systems metabolic engineering approaches

(2011) Yu-Sin Jang et al.   BIOTECHNOLOGY ADVANCES

Fifteen years of large scale metabolic modeling of yeast: Developments and impacts

(2011) Tobias Österlund et al.   BIOTECHNOLOGY ADVANCES

Comparative genomics of citric-acid-producing Aspergillus niger ATCC 1015 versus enzyme-producing CBS 513.88

(2011) M. R. Andersen et al.   GENOME RESEARCH

Development of quantitative metabolomics for Pichia pastoris

(2011) Marc Carnicer et al.   Metabolomics

Introduction: Next generation biofuels

(2011) Peter Fairley   NATURE

Metabolic engineering of Escherichia coli for direct production of 1,4-butanediol

(2011) Harry Yim et al.   Nature Chemical Biology

The Development of Metabolomic Sampling Procedures for Pichia pastoris, and Baseline Metabolome Data

(2011) Gregory D. Tredwell et al.   PLoS One

Genome-Scale Consequences of Cofactor Balancing in Engineered Pentose Utilization Pathways in Saccharomyces cerevisiae

(2011) Amit Ghosh et al.   PLoS One

Comparative genomics of xylose-fermenting fungi for enhanced biofuel production

(2011) Dana J. Wohlbach et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Analysis of regulation of pentose utilisation in Aspergillus niger reveals evolutionary adaptations in Eurotiales

(2011) E. Battaglia et al.   STUDIES IN MYCOLOGY

Systems metabolic engineering for chemicals and materials

(2011) Jeong Wook Lee et al.   TRENDS IN BIOTECHNOLOGY

Integrated analysis of the global transcriptional response to α-amylase over-production by Aspergillus oryzae

(2010) Wanwipa Vongsangnak et al.   BIOTECHNOLOGY AND BIOENGINEERING

Biofuel production improvement with genome-scale models: The role of cell composition

(2010) Ryan S. Senger   Biotechnology Journal

Microbial 1-butanol production: Identification of non-native production routes andin silicoengineering interventions

(2010) Sridhar Ranganathan et al.   Biotechnology Journal

Genome-scale metabolic model of methylotrophic yeastPichia pastorisand its use forin silicoanalysis of heterologous protein production

(2010) Seung Bum Sohn et al.   Biotechnology Journal

A multi-level study of recombinant Pichia pastoris in different oxygen conditions

(2010) Kristin Baumann et al.   BMC Systems Biology

Toward design-based engineering of industrial microbes

(2010) Keith EJ Tyo et al.   CURRENT OPINION IN MICROBIOLOGY

Genome-scale metabolic reconstruction and in silico analysis of methylotrophic yeast Pichia pastoris for strain improvement

(2010) Bevan KS Chung et al.   Microbial Cell Factories

Global gene expression analysis of Aspergillus nidulans reveals metabolic shift and transcription suppression under hypoxia

(2010) Shunsuke Masuo et al.   MOLECULAR GENETICS AND GENOMICS

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

(2010) Ines Thiele et al.   Nature Protocols

Yeast evolutionary genomics

(2010) Bernard Dujon   NATURE REVIEWS GENETICS

BioMet Toolbox: genome-wide analysis of metabolism

(2010) M. Cvijovic et al.   NUCLEIC ACIDS RESEARCH

Analysis of Genome-Wide Coexpression and Coevolution of Aspergillus oryzae and Aspergillus niger

(2010) Wanwipa Vongsangnak et al.   OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY

Sampling the Solution Space in Genome-Scale Metabolic Networks Reveals Transcriptional Regulation in Key Enzymes

(2010) Sergio Bordel et al.   PLoS Computational Biology

Evidence of Selection upon Genomic GC-Content in Bacteria

(2010) Falk Hildebrand et al.   PLoS Genetics

Functional Assembly of Minicellulosomes on the Saccharomyces cerevisiae Cell Surface for Cellulose Hydrolysis and Ethanol Production

(2009) S.-L. Tsai et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Constraints-based genome-scale metabolic simulation for systems metabolic engineering

(2009) Jong Myoung Park et al.   BIOTECHNOLOGY ADVANCES

Proteome analysis of Aspergillus niger: Lactate added in starch-containing medium can increase production of the mycotoxin fumonisin B2 by modifying acetyl-CoA metabolism

(2009) Louise M Sørensen et al.   BMC MICROBIOLOGY

Assessment of the pectin degrading enzyme network of Aspergillus niger by functional genomics

(2009) Elena S. Martens-Uzunova et al.   FUNGAL GENETICS AND BIOLOGY

The filamentous fungal gene expression database (FFGED)

(2009) Zhang Zhang et al.   FUNGAL GENETICS AND BIOLOGY

The Effect of Temperature on the Proteome of RecombinantPichia pastoris

(2009) Martin Dragosits et al.   JOURNAL OF PROTEOME RESEARCH

Open access to sequence: Browsing the Pichia pastoris genome

(2009) Diethard Mattanovich et al.   Microbial Cell Factories

Genome, secretome and glucose transport highlight unique features of the protein production host Pichia pastoris

(2009) Diethard Mattanovich et al.   Microbial Cell Factories

Genome sequence of the recombinant protein production host Pichia pastoris

(2009) Kristof De Schutter et al.   NATURE BIOTECHNOLOGY

Systemic analysis of the response of Aspergillus niger to ambient pH

(2009) Mikael R Andersen et al.   GENOME BIOLOGY

Improved annotation through genome-scale metabolic modeling of Aspergillus oryzae

(2008) Wanwipa Vongsangnak et al.   BMC GENOMICS

Analysis of Aspergillus nidulans metabolism at the genome-scale

(2008) Helga David et al.   BMC GENOMICS

Importance of systems biology in engineering microbes for biofuel production

(2008) Aindrila Mukhopadhyay et al.   CURRENT OPINION IN BIOTECHNOLOGY

Protein glycosylation pathways in filamentous fungi

(2008) Nandan Deshpande et al.   GLYCOBIOLOGY

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

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

A trispecies Aspergillus microarray: Comparative transcriptomics of three Aspergillus species

(2008) M. R. Andersen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Impact of systems biology on metabolic engineering ofSaccharomyces cerevisiae

(2007) Jens Nielsen et al.   FEMS YEAST RESEARCH