Systematic evaluation of parameters for genome-scale metabolic models of cultured mammalian cells

Genome-scale reconstructions of the mammalian secretory pathway predict metabolic costs and limitations of protein secretion

(2020) Jahir M. Gutierrez et al.   Nature Communications

A metabolic network-based approach for developing feeding strategies for CHO cells to increase monoclonal antibody production

(2020) Hamideh Fouladiha et al.   BIOPROCESS AND BIOSYSTEMS ENGINEERING

Regulation of Metabolic Homeostasis in Cell Culture Bioprocesses

(2020) Conor M. O'Brien et al.   TRENDS IN BIOTECHNOLOGY

Integration of Time-Series Transcriptomic Data with Genome-Scale CHO Metabolic Models for mAb Engineering

(2020) Zhuangrong Huang et al.   Processes

Enzyme capacity-based genome scale modelling of CHO cells

(2020) Hock Chuan Yeo et al.   METABOLIC ENGINEERING

What CHO is made of: Variations in the biomass composition of Chinese hamster ovary cell lines

(2020) Diana Széliová et al.   METABOLIC ENGINEERING

Creation and analysis of biochemical constraint-based models using the COBRA Toolbox v.3.0

(2019) Laurent Heirendt et al.   Nature Protocols

Proteogenomic Annotation of Chinese Hamsters Reveals Extensive Novel Translation Events and Endogenous Retroviral Elements

(2019) Shangzhong Li et al.   JOURNAL OF PROTEOME RESEARCH

Increasing consensus of context-specific metabolic models by integrating data-inferred cell functions

(2019) Anne Richelle et al.   PLoS Computational Biology

Metabolic engineering of Chinese hamster ovary cells towards reduced biosynthesis and accumulation of novel growth inhibitors in fed-batch cultures

(2019) Bhanu Chandra Mulukutla et al.   METABOLIC ENGINEERING

Assessing key decisions for transcriptomic data integration in biochemical networks

(2019) Anne Richelle et al.   PLoS Computational Biology

The Escherichia coli transcriptome mostly consists of independently regulated modules

(2019) Anand V. Sastry et al.   Nature Communications

Modeling metabolism of the human gut microbiome

(2018) Stefanía Magnúsdóttir et al.   CURRENT OPINION IN BIOTECHNOLOGY

Recon3D enables a three-dimensional view of gene variation in human metabolism

(2018) Elizabeth Brunk et al.   NATURE BIOTECHNOLOGY

Measuring Cellular Biomass Composition for Computational Biology Applications

(2018) Ashley Beck et al.   Processes

Extension of the yeast metabolic model to include iron metabolism and its use to estimate global levels of iron-recruiting enzyme abundance from cofactor requirements

(2018) Duygu Dikicioglu et al.   BIOTECHNOLOGY AND BIOENGINEERING

Application of a curated genome-scale metabolic model of CHO DG44 to an industrial fed-batch process

(2018) Cyrielle Calmels et al.   METABOLIC ENGINEERING

Model-based tools for optimal experiments in bioprocess engineering

(2018) Vinzenz Abt et al.   Current Opinion in Chemical Engineering

Improving the phenotype predictions of a yeast genome‐scale metabolic model by incorporating enzymatic constraints

(2017) Benjamín J Sánchez et al.   Molecular Systems Biology

iML1515, a knowledgebase that computes Escherichia coli traits

(2017) Jonathan M Monk et al.   NATURE BIOTECHNOLOGY

Optimality and sub-optimality in a bacterial growth law

(2017) Benjamin D. Towbin et al.   Nature Communications

A systems approach reveals distinct metabolic strategies among the NCI-60 cancer cell lines

(2017) Maike K. Aurich et al.   PLoS Computational Biology

Quality by control: Towards model predictive control of mammalian cell culture bioprocesses

(2017) Wolfgang Sommeregger et al.   Biotechnology Journal

A Systematic Evaluation of Methods for Tailoring Genome-Scale Metabolic Models

(2017) Sjoerd Opdam et al.   Cell Systems

Metabolic engineering of CHO cells for the development of a robust protein production platform

(2017) Sanjeev Kumar Gupta et al.   PLoS One

Quantitative feature extraction from the Chinese hamster ovary bioprocess bibliome using a novel meta-analysis workflow

(2016) Aydin Golabgir et al.   BIOTECHNOLOGY ADVANCES

A hybrid approach identifies metabolic signatures of high-producers for chinese hamster ovary clone selection and process optimization

(2016) Oliver Popp et al.   BIOTECHNOLOGY AND BIOENGINEERING

The Protein Cost of Metabolic Fluxes: Prediction from Enzymatic Rate Laws and Cost Minimization

(2016) Elad Noor et al.   PLoS Computational Biology

Applications of Genome-Scale Metabolic Models in Biotechnology and Systems Medicine

(2016) Cheng Zhang et al.   Frontiers in Physiology

A Consensus Genome-scale Reconstruction of Chinese Hamster Ovary Cell Metabolism

(2016) Hooman Hefzi et al.   Cell Systems

The use of ‘Omics technology to rationally improve industrial mammalian cell line performance

(2015) Amanda M. Lewis et al.   BIOTECHNOLOGY AND BIOENGINEERING

Optimizing eukaryotic cell hosts for protein production through systems biotechnology and genome-scale modeling

(2015) Jahir M. Gutierrez et al.   Biotechnology Journal

Determination of the maximum operating range of hydrodynamic stress in mammalian cell culture

(2015) Benjamin Neunstoecklin et al.   JOURNAL OF BIOTECHNOLOGY

Biomass composition: the “elephant in the room” of metabolic modelling

(2015) Duygu Dikicioglu et al.   Metabolomics

Modeling cancer metabolism on a genome scale

(2015) K. Yizhak et al.   Molecular Systems Biology

Optimizing eukaryotic cell hosts for protein production through systems biotechnology and genome-scale modeling

(2015) Jahir M. Gutierrez et al.   Biotechnology Journal

HTSeq--a Python framework to work with high-throughput sequencing data

(2014) S. Anders et al.   BIOINFORMATICS

Comparison and analysis of objective functions in flux balance analysis

(2014) Carlos Eduardo García Sánchez et al.   BIOTECHNOLOGY PROGRESS

Non-stationary 13C metabolic flux analysis of Chinese hamster ovary cells in batch culture using extracellular labeling highlights metabolic reversibility and compartmentation

(2014) Averina Nicolae et al.   BMC Systems Biology

Constraint-based models predict metabolic and associated cellular functions

(2014) Aarash Bordbar et al.   NATURE REVIEWS GENETICS

UniProt: a hub for protein information

(2014)   NUCLEIC ACIDS RESEARCH

Genome-scale metabolic modelling of hepatocytes reveals serine deficiency in patients with non-alcoholic fatty liver disease

(2014) Adil Mardinoglu et al.   Nature Communications

Metabolic analysis of antibody producing CHO cells in fed-batch production

(2013) Jason Dean et al.   BIOTECHNOLOGY AND BIOENGINEERING

Genomic landscapes of Chinese hamster ovary cell lines as revealed by the Cricetulus griseus draft genome

(2013) Nathan E Lewis et al.   NATURE BIOTECHNOLOGY

Using Molecular Markers to Characterize Productivity in Chinese Hamster Ovary Cell Lines

(2013) Raihana Z. Edros et al.   PLoS One

Molecular crowding limits translation and cell growth

(2013) S. Klumpp et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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 evolution of genome-scale models of cancer metabolism

(2013) Nathan E. Lewis et al.   Frontiers in Physiology

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Reconstruction of genome-scale metabolic models for 126 human tissues using mCADRE

(2012) Yuliang Wang et al.   BMC Systems Biology

Reactive oxygen species (ROS) homeostasis and redox regulation in cellular signaling

(2012) Paul D. Ray et al.   CELLULAR SIGNALLING

Metabolic engineering of Chinese hamster ovary cells: Towards a bioengineered heparin

(2012) Jong Youn Baik et al.   METABOLIC ENGINEERING

Constraining the metabolic genotype–phenotype relationship using a phylogeny of in silico methods

(2012) Nathan E. Lewis et al.   NATURE REVIEWS MICROBIOLOGY

Network Context and Selection in the Evolution to Enzyme Specificity

(2012) H. Nam et al.   SCIENCE

Integration of expression data in genome-scale metabolic network reconstructions

(2012) Anna S. Blazier et al.   Frontiers in Physiology

Metabolite profiling of recombinant CHO cells: Designing tailored feeding regimes that enhance recombinant antibody production

(2011) Christopher A. Sellick et al.   BIOTECHNOLOGY AND BIOENGINEERING

Using the reconstructed genome-scale human metabolic network to study physiology and pathology

(2011) A. Bordbar et al.   JOURNAL OF INTERNAL MEDICINE

Metabolic flux analysis of CHO cells at growth and non-growth phases using isotopic tracers and mass spectrometry

(2011) Woo Suk Ahn et al.   METABOLIC ENGINEERING

A comprehensive genome-scale reconstruction of Escherichia coli metabolism--2011

(2011) J. D. Orth et al.   Molecular Systems Biology

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

(2011) Jan Schellenberger et al.   Nature Protocols

A detailed genome-wide reconstruction of mouse metabolism based on human Recon 1

(2010) Martin I Sigurdsson et al.   BMC Systems Biology

The biomass objective function

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

Metabolomics-driven approach for the improvement of Chinese hamster ovary cell growth: Overexpression of malate dehydrogenase II

(2010) William P.K. Chong et al.   JOURNAL OF BIOTECHNOLOGY

Omic data from evolved E. coli are consistent with computed optimal growth from genome-scale models

(2010) Nathan E Lewis et al.   Molecular Systems Biology

Large-scale in silico modeling of metabolic interactions between cell types in the human brain

(2010) Nathan E Lewis et al.   NATURE BIOTECHNOLOGY

What is flux balance analysis?

(2010) Jeffrey D Orth et al.   NATURE BIOTECHNOLOGY

Induction of mammalian cell death by simple shear and extensional flows

(2009) Timm Tanzeglock et al.   BIOTECHNOLOGY AND BIOENGINEERING

BioNumbers—the database of key numbers in molecular and cell biology

(2009) Ron Milo et al.   NUCLEIC ACIDS RESEARCH