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

Pichia pastoris regulates its gene-specific response to different carbon sources at the transcriptional, rather than the translational, level

(2015) Roland Prielhofer et al.   BMC GENOMICS

13C metabolic flux analysis at a genome-scale

(2015) Saratram Gopalakrishnan et al.   METABOLIC ENGINEERING

Toward metabolic engineering in the context of system biology and synthetic biology: advances and prospects

(2014) Yanfeng Liu et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Genetically engineered Pichia pastoris yeast for conversion of glucose to xylitol by a single-fermentation process

(2014) Hairong Cheng et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Isolation and characterization of the plasma membrane from the yeast Pichia pastoris

(2014) Karlheinz Grillitsch et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES

iOD907, the first genome-scale metabolic model for the milk yeastKluyveromyces lactis

(2014) Oscar Dias et al.   Biotechnology Journal

Recent advances in the reconstruction of metabolic models and integration of omics data

(2014) Rajib Saha et al.   CURRENT OPINION IN BIOTECHNOLOGY

Model based engineering of Pichia pastoris central metabolism enhances recombinant protein production

(2014) Justyna Nocon et al.   METABOLIC ENGINEERING

Carbon source dependent promoters in yeasts

(2014) Katrin Weinhandl et al.   Microbial Cell Factories

Optimizing genome-scale network reconstructions

(2014) Jonathan Monk et al.   NATURE BIOTECHNOLOGY

BioModels: ten-year anniversary

(2014) Vijayalakshmi Chelliah et al.   NUCLEIC ACIDS RESEARCH

Improving functional annotation for industrial microbes: a case study with Pichia pastoris

(2014) Duygu Dikicioglu et al.   TRENDS IN BIOTECHNOLOGY

Comparative Genome-Scale Reconstruction of Gapless Metabolic Networks for Present and Ancestral Species

(2014) Esa Pitkänen et al.   PLoS Computational Biology

Komagataella kurtzmanii sp. nov., a new sibling species of Komagataella (Pichia) pastoris based on multigene sequence analysis

(2013) Gennadi I. Naumov et al.   ANTONIE VAN LEEUWENHOEK INTERNATIONAL JOURNAL OF GENERAL AND MOLECULAR MICROBIOLOGY

Metabolic reconstruction and flux analysis of industrial Pichia yeasts

(2013) Bevan Kai-Sheng Chung et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Sphingolipid homeostasis in the web of metabolic routes

(2013) Auxiliadora Aguilera-Romero et al.   BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR AND CELL BIOLOGY OF LIPIDS

The lipidome and proteome of microsomes from the methylotrophic yeast Pichia pastoris

(2013) Lisa Klug et al.   BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR AND CELL BIOLOGY OF LIPIDS

Assimilating genome-scale metabolic reconstructions with modelBorgifier

(2013) John T. Sauls et al.   BIOINFORMATICS

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

(2013) Luis Caspeta et al.   Biotechnology Journal

InPichia pastoris, growth rate regulates protein synthesis and secretion, mating and stress response

(2013) Corinna Rebnegger et al.   Biotechnology Journal

Path2Models: large-scale generation of computational models from biochemical pathway maps

(2013) Finja Büchel et al.   BMC Systems Biology

Mapping condition-dependent regulation of metabolism in yeast through genome-scale modeling

(2013) Tobias Österlund et al.   BMC Systems Biology

Advances in metabolic pathway and strain engineering paving the way for sustainable production of chemical building blocks

(2013) Yun Chen et al.   CURRENT OPINION IN BIOTECHNOLOGY

Pichia pastoris: protein production host and model organism for biomedical research

(2013) Brigitte Gasser et al.   Future Microbiology

Mitochondrial energetic metabolism-some general principles

(2013) Jean-Pierre Mazat et al.   IUBMB LIFE

Quantitative metabolomics analysis of amino acid metabolism in recombinant Pichia pastoris under different oxygen availability conditions

(2013) Marc Carnicer et al.   Microbial Cell Factories

Defects in mitochondrial fatty acid synthesis result in failure of multiple aspects of mitochondrial biogenesis inSaccharomyces cerevisiae

(2013) V. A. Samuli Kursu et al.   MOLECULAR MICROBIOLOGY

Metabolic flux analysis of recombinant Pichia pastoris growing on different glycerol/methanol mixtures by iterative fitting of NMR-derived 13C-labelling data from proteinogenic amino acids

(2013) Joel Jordà et al.   New Biotechnology

Data, information, knowledge and principle: back to metabolism in KEGG

(2013) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

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

PMT1 gene plays a major role in O-mannosylation of insulin precursor in Pichia pastoris

(2013) Nagaraj Govindappa et al.   PROTEIN EXPRESSION AND PURIFICATION

Version 6 of the consensus yeast metabolic network refines biochemical coverage and improves model performance

(2013) Benjamin D. Heavner et al.   Database-The Journal of Biological Databases and Curation

The RAVEN Toolbox and Its Use for Generating a Genome-scale Metabolic Model for Penicillium chrysogenum

(2013) Rasmus Agren et al.   PLoS Computational Biology

Peroxisomal acyl-CoA synthetases

(2012) Paul A. Watkins et al.   BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR BASIS OF DISEASE

Unconventional microbial systems for the cost-efficient production of high-quality protein therapeutics

(2012) José Luis Corchero et al.   BIOTECHNOLOGY ADVANCES

Yeast 5 – an expanded reconstruction of the Saccharomyces cerevisiae metabolic network

(2012) Benjamin D Heavner et al.   BMC Systems Biology

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

Reconciliation of metabolites and biochemical reactions for metabolic networks

(2012) T. Bernard et al.   BRIEFINGS IN BIOINFORMATICS

Peroxisomal Fatty Acid Uptake Mechanism inSaccharomyces cerevisiae

(2012) Carlo W. T. van Roermund et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Metabolic engineering of the non-conventional yeast Pichia ciferrii for production of rare sphingoid bases

(2012) Daniel Börgel et al.   METABOLIC ENGINEERING

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

(2012) Balaji Balagurunathan et al.   Microbial Cell Factories

BRENDA in 2013: integrated reactions, kinetic data, enzyme function data, improved disease classification: new options and contents in BRENDA

(2012) Ida Schomburg et al.   NUCLEIC ACIDS RESEARCH

Comparison of the H+/ATP ratios of the H+-ATP synthases from yeast and from chloroplast

(2012) J. Petersen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Stoichiometry of proton translocation by respiratory complex I and its mechanistic implications

(2012) M. Wikstrom et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Production of yeast chitin–glucan complex from biodiesel industry byproduct

(2012) Christophe Roca et al.   PROCESS BIOCHEMISTRY

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

(2011) Tobias Österlund et al.   BIOTECHNOLOGY ADVANCES

Recent advances in reconstruction and applications of genome-scale metabolic models

(2011) Tae Yong Kim et al.   CURRENT OPINION IN BIOTECHNOLOGY

Characterisation of the gene cluster for l-rhamnose catabolism in the yeast Scheffersomyces (Pichia) stipitis

(2011) Outi M. Koivistoinen et al.   GENE

Two Pathways of Sphingolipid Biosynthesis Are Separated in the YeastPichia pastoris

(2011) Philipp Ternes et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

High-quality genome sequence of Pichia pastoris CBS7435

(2011) Andreas Küberl et al.   JOURNAL OF BIOTECHNOLOGY

Distinct roles of two ceramide synthases, CaLag1p and CaLac1p, in the morphogenesis of Candida albicans

(2011) Seon Ah Cheon et al.   MOLECULAR MICROBIOLOGY

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

(2011) Jan Schellenberger et al.   Nature Protocols

The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases

(2011) R. Caspi et al.   NUCLEIC ACIDS RESEARCH

Bioprocess engineering aspects of heterologous protein production in Pichia pastoris: A review

(2010) Gabriel Potvin et al.   BIOCHEMICAL ENGINEERING JOURNAL

Quantitative physiology of Pichia pastoris during glucose-limited high-cell density fed-batch cultivation for recombinant protein production

(2010) Jan Heyland et al.   BIOTECHNOLOGY AND BIOENGINEERING

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

(2010) Seung Bum Sohn et al.   Biotechnology Journal

BiGG: a Biochemical Genetic and Genomic knowledgebase of large scale metabolic reconstructions

(2010) Jan Schellenberger et al.   BMC BIOINFORMATICS

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

(2010) Kristin Baumann et al.   BMC Systems Biology

Further developments towards a genome-scale metabolic model of yeast

(2010) Paul D Dobson et al.   BMC Systems Biology

Identification and characterisation of novel Pichia pastoris promoters for heterologous protein production

(2010) Gerhard Stadlmayr et al.   JOURNAL OF BIOTECHNOLOGY

The Subunit Composition of Mitochondrial NADH:Ubiquinone Oxidoreductase (Complex I) FromPichia pastoris

(2010) Hannah R. Bridges et al.   MOLECULAR & CELLULAR PROTEOMICS

High-throughput generation, optimization and analysis of genome-scale metabolic models

(2010) Christopher S Henry et al.   NATURE BIOTECHNOLOGY

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

(2010) Ines Thiele et al.   Nature Protocols

The respiratory complexes I from the mitochondria of twoPichiaspecies

(2009) Hannah R. Bridges et al.   BIOCHEMICAL JOURNAL

Protein O-mannosylation: Conserved from bacteria to humans

(2009) M. Lommel et al.   GLYCOBIOLOGY

Biotechnological strains of Komagataella (Pichia) pastoris are Komagataella phaffii as determined from multigene sequence analysis

(2009) Cletus Paul Kurtzman   JOURNAL OF INDUSTRIAL MICROBIOLOGY & BIOTECHNOLOGY

Metabolic flux analysis and pharmaceutical production

(2009) Brett A. Boghigian et al.   METABOLIC ENGINEERING

Macromolecular and elemental composition analysis and extracellular metabolite balances of Pichia pastoris growing at different oxygen levels

(2009) Marc Carnicer 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

Sugar metabolism, redox balance and oxidative stress response in the respiratory yeast Kluyveromyces lactis

(2009) M Isabel González-Siso et al.   Microbial Cell Factories

Applications of genome-scale metabolic reconstructions

(2009) Matthew A Oberhardt et al.   Molecular Systems Biology

Genome sequence of the recombinant protein production host Pichia pastoris

(2009) Kristof De Schutter et al.   NATURE BIOTECHNOLOGY

Emerging methods for the production of homogeneous human glycoproteins

(2009) Jamie R Rich et al.   Nature Chemical Biology

A tandem mass spectrometric approach to the identification of O-glycosylated glargine glycoforms in active pharmaceutical ingredient expressed inPichia pastoris

(2009) Vivekanandan Kannan et al.   RAPID COMMUNICATIONS IN MASS SPECTROMETRY

Annotation Error in Public Databases: Misannotation of Molecular Function in Enzyme Superfamilies

(2009) Alexandra M. Schnoes et al.   PLoS Computational Biology

Use of In Vivo 13C Nuclear Magnetic Resonance Spectroscopy To Elucidate L-Arabinose Metabolism in Yeasts

(2008) C. Fonseca et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Significance of theKlLAC1gene in glucosylceramide production byKluyveromyces lactis

(2008) Naoya Takakuwa et al.   FEMS YEAST RESEARCH

Eukaryotic and Bacterial Gene Clusters Related to an Alternative Pathway of Nonphosphorylated L-Rhamnose Metabolism

(2008) Seiya Watanabe et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Mitochondrial Fatty Acid Synthesis Type II: More than Just Fatty Acids

(2008) J. Kalervo Hiltunen et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Thematic Review Series: Sphingolipids.New insights into sphingolipid metabolism and function in budding yeast

(2008) Robert C. Dickson   JOURNAL OF LIPID RESEARCH

A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology

(2008) Markus J Herrgård et al.   NATURE BIOTECHNOLOGY