Genome wide analysis of protein production load in Trichoderma reesei

The Genomes of Three Uneven Siblings: Footprints of the Lifestyles of Three Trichoderma Species

(2016) Monika Schmoll et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

The impact of a single-nucleotide mutation of bgl2 on cellulase induction in a Trichoderma reesei mutant

(2015) Yosuke Shida et al.   Biotechnology for Biofuels

Engineering the supply chain for protein production/secretion in yeasts and mammalian cells

(2015) Tobias Klein et al.   JOURNAL OF INDUSTRIAL MICROBIOLOGY & BIOTECHNOLOGY

Genome-scale modeling for metabolic engineering

(2015) Evangelos Simeonidis et al.   JOURNAL OF INDUSTRIAL MICROBIOLOGY & BIOTECHNOLOGY

Ensembl Genomes 2016: more genomes, more complexity

(2015) Paul Julian Kersey et al.   NUCLEIC ACIDS RESEARCH

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

(2015) Ron Caspi et al.   NUCLEIC ACIDS RESEARCH

Detecting time periods of differential gene expression using Gaussian processes: an application to endothelial cells exposed to radiotherapy dose fraction

(2014) Markus Heinonen et al.   BIOINFORMATICS

Kinetic transcriptome analysis reveals an essentially intact induction system in a cellulase hyper-producer Trichoderma reesei strain

(2014) Dante Poggi-Parodi et al.   Biotechnology for Biofuels

Comparative metabolism of cellulose, sophorose and glucose in Trichoderma reesei using high-throughput genomic and proteomic analyses

(2014) Lilian dos Santos Castro et al.   Biotechnology for Biofuels

Screening of candidate regulators for cellulase and hemicellulase production in Trichoderma reesei and identification of a factor essential for cellulase production

(2014) Mari Häkkinen et al.   Biotechnology for Biofuels

Skewer: a fast and accurate adapter trimmer for next-generation sequencing paired-end reads

(2014) Hongshan Jiang et al.   BMC BIOINFORMATICS

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

(2014) Justyna Nocon et al.   METABOLIC ENGINEERING

Deciphering the Cis-Regulatory Elements for XYR1 and CRE1 Regulators in Trichoderma reesei

(2014) Rafael Silva-Rocha et al.   PLoS One

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

(2014) Daniel Machado et al.   PLoS Computational Biology

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

(2014) Esa Pitkänen et al.   PLoS Computational Biology

Transcript abundance on its own cannot be used to infer fluxes in central metabolism

(2014) Jörg Schwender et al.   Frontiers in Plant Science

Genome-wide transcriptional response of Trichoderma reesei to lignocellulose using RNA sequencing and comparison with Aspergillus niger

(2013) Laure Ries et al.   BMC GENOMICS

sybil – Efficient constraint-based modelling in R

(2013) Gabriel Gelius-Dietrich et al.   BMC Systems Biology

Regulation of Cellulase and Hemicellulase Gene Expression in Fungi

(2013) Antonella Amore et al.   CURRENT GENOMICS

Two Major Facilitator Superfamily Sugar Transporters fromTrichoderma reeseiand Their Roles in Induction of Cellulase Biosynthesis

(2013) Weixin Zhang et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Protein abundance in multiplexed samples (PAMUS) for quantitation of Trichoderma reesei secretome

(2013) Sunil S. Adav et al.   Journal of Proteomics

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

(2013) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

Systems Analysis of Lactose Metabolism in Trichoderma reesei Identifies a Lactose Permease That Is Essential for Cellulase Induction

(2013) Christa Ivanova et al.   PLoS One

Functioning of a metabolic flux sensor in Escherichia coli

(2013) K. Kochanowski et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Quantitative Analysis of Glycerol Accumulation, Glycolysis and Growth under Hyper Osmotic Stress

(2013) Elzbieta Petelenz-Kurdziel et al.   PLoS Computational Biology

Software for Computing and Annotating Genomic Ranges

(2013) Michael Lawrence et al.   PLoS Computational Biology

Imbalance of heterologous protein folding and disulfide bond formation rates yields runaway oxidative stress

(2012) Keith EJ Tyo et al.   BMC 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

Estimation of recombinant protein production in Pichia pastoris based on a constraint-based model

(2012) Marta Tortajada et al.   JOURNAL OF PROCESS CONTROL

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

(2012) Joel Jordà et al.   Microbial Cell Factories

A new stoichiometric miniaturization strategy for screening of industrial microbial strains: application to cellulase hyper-producing Trichoderma reesei strains

(2012) Etienne Jourdier et al.   Microbial Cell Factories

Re-annotation of the CAZy genes of Trichoderma reesei and transcription in the presence of lignocellulosic substrates

(2012) Mari Häkkinen et al.   Microbial Cell Factories

The putative protein methyltransferase LAE1 controls cellulase gene expression in Trichoderma reesei

(2012) Bernhard Seiboth et al.   MOLECULAR MICROBIOLOGY

Conserved and essential transcription factors for cellulase gene expression in ascomycete fungi

(2012) S. T. Coradetti et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Correlation of gene expression and protein production rate - a system wide study

(2011) Mikko Arvas et al.   BMC GENOMICS

Regulation and control of metabolic fluxes in microbes

(2011) Luca Gerosa et al.   CURRENT OPINION IN BIOTECHNOLOGY

A flux-sensing mechanism could regulate the switch between respiration and fermentation

(2011) Daphne H. E. W. Huberts et al.   FEMS YEAST RESEARCH

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

(2011) Habib Driouch et al.   METABOLIC ENGINEERING

The cargo and the transport system: secreted proteins and protein secretion in Trichoderma reesei (Hypocrea jecorina)

(2011) M. Saloheimo et al.   MICROBIOLOGY-SGM

Cellotriose and Cellotetraose as Inducers of the Genes Encoding Cellobiohydrolases in the Basidiomycete Phanerochaete chrysosporium

(2010) H. Suzuki et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Transformation System forHypocrea jecorina(Trichoderma reesei) That Favors Homologous Integration and Employs Reusable Bidirectionally Selectable Markers

(2010) Matthias G. Steiger et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Systematic discovery of regulatory motifs in Fusarium graminearum by comparing four Fusarium genomes

(2010) Lokesh Kumar et al.   BMC GENOMICS

What is flux balance analysis?

(2010) Jeffrey D Orth et al.   NATURE BIOTECHNOLOGY

The Sequence Read Archive

(2010) R. Leinonen et al.   NUCLEIC ACIDS RESEARCH

Novel Coprinopsis cinerea Polyesterase That Hydrolyzes Cutin and Suberin

(2009) H. Kontkanen et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

R/BHC: fast Bayesian hierarchical clustering for microarray data

(2009) Richard S Savage et al.   BMC BIOINFORMATICS

Perspectives and new directions for the production of bioethanol using consolidated bioprocessing of lignocellulose

(2009) Qi Xu et al.   CURRENT OPINION IN BIOTECHNOLOGY

Identification of specific binding sites for XYR1, a transcriptional activator of cellulolytic and xylanolytic genes in Trichoderma reesei

(2009) Takanori Furukawa et al.   FUNGAL GENETICS AND BIOLOGY

Metabolic characteristics and importance of the universal methionine salvage pathway recycling methionine from 5′-methylthioadenosine

(2009) Eva Albers   IUBMB LIFE

Comparative secretome analyses of two Trichoderma reesei RUT-C30 and CL847 hypersecretory strains

(2008) Isabelle Herpoël-Gimbert et al.   Biotechnology for Biofuels

Sulphur metabolism and cellulase gene expression are connected processes in the filamentous fungus Hypocrea jecorina (anamorph Trichoderma reesei)

(2008) Gabriela Gremel et al.   BMC MICROBIOLOGY

Genome sequencing and analysis of the biomass-degrading fungus Trichoderma reesei (syn. Hypocrea jecorina)

(2008) Diego Martinez et al.   NATURE BIOTECHNOLOGY

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