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List of works by Lars K. Nielsen

'Omics driven discoveries of gene targets for apoptosis attenuation in CHO cells

scientific article published on 31 August 2020

2,2-Diphenyl-1-picrylhydrazyl as a screening tool for recombinant monoterpene biosynthesis.

scientific article

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

scientific article published on November 2016

A Pan-Genome Guided Metabolic Network Reconstruction of Five Propionibacterium Species Reveals Extensive Metabolic Diversity

scientific article published on 23 September 2020

A TetR-Family Protein (CAETHG_0459) Activates Transcription From a New Promoter Motif Associated With Essential Genes for Autotrophic Growth in Acetogens

scientific article published on 15 November 2019

A depth-first search algorithm to compute elementary flux modes by linear programming

scientific article

A general framework for thermodynamically consistent parameterization and efficient sampling of enzymatic reactions

scientific article

A liquid chromatography-tandem mass spectrometry-based investigation of the lamellar interstitial metabolome in healthy horses and during experimental laminitis induction.

scientific article published on 04 August 2015

A multi-omics analysis of recombinant protein production in Hek293 cells

scientific article

A multi-tissue genome-scale metabolic modeling framework for the analysis of whole plant systems

scientific article published on 22 January 2015

A physiological product-release model for baculovirus infected insect cells

scientific article published on September 2005

A probabilistic framework for the exploration of enzymatic capabilities based on feasible kinetics and control analysis.

scientific article published on 22 December 2015

A squalene synthase protein degradation method for improved sesquiterpene production in Saccharomyces cerevisiae.

scientific article published on 8 December 2016

A transferable sucrose utilization approach for non-sucrose-utilizing Escherichia coli strains.

scientific article

Absolute counting of neutrophils in whole blood using flow cytometry

scientific article published on 03 July 2014

Accuracy of the endpoint assay for virus titration

scientific article published in January 1992

Adaptation of hydroxymethylbutenyl diphosphate reductase enables volatile isoprenoid production

scientific article published on 12 March 2020

Advances in analytical tools for high throughput strain engineering.

scientific article published on 12 February 2018

AlgaGEM--a genome-scale metabolic reconstruction of algae based on the Chlamydomonas reinhardtii genome

scientific article

AllR Controls the Expression of Streptomyces coelicolor Allantoin Pathway Genes

scientific article published on 17 July 2015

Allantoin catabolism influences the production of antibiotics in Streptomyces coelicolor ⬇️

scientific article

Alleviating monoterpene toxicity using a two-phase extractive fermentation for the bioproduction of jet fuel mixtures in Saccharomyces cerevisiae.

scientific article published on 28 May 2012

Altered Fatty Acid Metabolism in Long Duration Road Transport: An NMR-based Metabonomics Study in Sheep

article

Amplifying the cellular reduction potential of Streptococcus zooepidemicus

scientific article published in January 2003

An expanded heterologous <i>GAL</i> promoter collection for diauxie-inducible expression in Saccharomyces cerevisiae

scientific article published on 4 January 2018

Analysis of the phase behavior of the aqueous poly(ethylene glycol)-Ficoll system.

scientific article published in July 2003

Analytical tools for unravelling the metabolism of gas-fermenting Clostridia

scientific article published in 2022

AraGEM, a genome-scale reconstruction of the primary metabolic network in Arabidopsis

scientific article

Arginine deiminase pathway provides ATP and boosts growth of the gas-fermenting acetogen Clostridium autoethanogenum

scientific article published on 22 April 2017

Assembly of multilayer PSS/PAH membrane on coherent alginate/PLO microcapsule for long-term graft transplantation

scientific article

Attenuating apoptosis in Chinese hamster ovary cells for improved biopharmaceutical production

scientific article published on 23 January 2020

Avoiding rapid growth at high cell densities: a potentially important optimisation criterion for hybridoma cultures

scientific article published on January 1992

Awakening sleeping beauty: production of propionic acid in Escherichia coli through the sbm operon requires the activity of a methylmalonyl-CoA epimerase

scientific article published on 17 July 2017

Bioreactor for Blood Product Production

article

Blood cell manufacture: current methods and future challenges

scientific article published on 06 June 2009

C4GEM, a genome-scale metabolic model to study C4 plant metabolism

scientific article published on 25 October 2010

Cell cycle model to describe animal cell size variation and lag between cell number and biomass dynamics.

scientific article published in November 1997

Cell-free pipeline for discovery of thermotolerant xylanases and endo-1,4-β-glucanases

scientific article published on 17 July 2017

Characterization of Hematopoietic Cell Expansion, Oxygen Uptake, and Glycolysis in a Controlled, Stirred-Tank Bioreactor System

scientific article published on 01 May 1998

Chemical inhibition of acetyl coenzyme A carboxylase as a strategy to increase polyhydroxybutyrate yields in transgenic sugarcane.

scientific article published on 25 September 2013

Clinical scale ex vivo manufacture of neutrophils from hematopoietic progenitor cells

scientific article published on 01 November 2009

Concise review: next-generation cell therapies to prevent infections in neutropenic patients

scientific article published on 05 March 2014

Construction of feasible and accurate kinetic models of metabolism: A Bayesian approach.

scientific article

Control of chitin and N-acetylglucosamine utilization in Saccharopolyspora erythraea

scientific article published on 9 July 2014

Controlling heterologous gene expression in yeast cell factories on different carbon substrates and across the diauxic shift: a comparison of yeast promoter activities.

scientific article published on 26 June 2015

Coupling gene regulatory patterns to bioprocess conditions to optimize synthetic metabolic modules for improved sesquiterpene production in yeast

scientific article published on 21 February 2017

Cyclic-di-AMP synthesis by the diadenylate cyclase CdaA is modulated by the peptidoglycan biosynthesis enzyme GlmM in Lactococcus lactis

scientific article published on 20 November 2015

DNase I-hypersensitive exons colocalize with promoters and distal regulatory elements

scientific article

Decline in Helicoverpa armigera nucleopolyhedrovirus occlusion body yields with increasing infection cell density in vitro is strongly correlated with viral DNA levels

scientific article published on 21 June 2015

Decline in baculovirus-expressed recombinant protein production with increasing cell density is strongly correlated to impairment of virus replication and mRNA expression

scientific article

Deep sequencing-based transcriptome analysis of Plutella xylostella larvae parasitized by Diadegma semiclausum

scientific article

Deletion of cscR in Escherichia coli W improves growth and poly-3-hydroxybutyrate (PHB) production from sucrose in fed batch culture.

scientific article published on December 2010

Design of artificial myocardial microtissues

scientific article published in January 2004

Development of chemically defined medium for Mannheimia succiniciproducens based on its genome sequence

scientific article published in May 2008

Development of quenching and washing protocols for quantitative intracellular metabolite analysis of uninfected and baculovirus-infected insect cells

scientific article

Development of sucrose-utilizing Escherichia coli K-12 strain by cloning β-fructofuranosidases and its application for L-threonine production

scientific article published on 14 August 2010

Do genome-scale models need exact solvers or clearer standards?

scientific article published on 14 October 2015

Dual gene expression cassette vectors with antibiotic selection markers for engineering in Saccharomyces cerevisiae

scientific article

Dynamic balancing of isoprene carbon sources reflects photosynthetic and photorespiratory responses to temperature stress.

scientific article published on 15 October 2014

Dynamic regulation of gene expression using sucrose responsive promoters and RNA interference in Saccharomyces cerevisiae

scientific article published on April 2015

Effect of the peak cell density of recombinant AcMNPV-infected Hi5 cells on baculovirus yields

scientific article

Emulsion strategies in the microencapsulation of cells: pathways to thin coherent membranes.

scientific article published on October 2005

Engineered protein degradation of farnesyl pyrophosphate synthase is an effective regulatory mechanism to increase monoterpene production in Saccharomyces cerevisiae

article

Engineered quorum sensing using pheromone-mediated cell-to-cell communication in Saccharomyces cerevisiae

scientific article published on 7 January 2013

Engineering Escherichia coli for propionic acid production through the Wood-Werkman cycle

scientific article published on 16 October 2019

Engineering and adaptive evolution of Escherichia coli for D-lactate fermentation reveals GatC as a xylose transporter

scientific article published on 4 August 2012

Enhanced polyhydroxybutyrate production in transgenic sugarcane

article

Escherichia coli W shows fast, highly oxidative sucrose metabolism and low acetate formation

article

Evolution of the hyaluronic acid synthesis (has) operon in Streptococcus zooepidemicus and other pathogenic streptococci

scientific article published on 13 June 2008

Evolutionary Engineering Improves Tolerance for Replacement Jet Fuels in Saccharomyces cerevisiae

scientific article published on 6 March 2015

Extracting reaction networks from databases-opening Pandora's box.

scientific article

Factors affecting polyhydroxybutyrate accumulation in mesophyll cells of sugarcane and switchgrass

scientific article

Fast-SNP: a fast matrix pre-processing algorithm for efficient loopless flux optimization of metabolic models

scientific article

Fermentative butanol production by Clostridia

scientific article published on October 2008

Filling the void: allogeneic myeloid cells for transplantation

scientific article

Flux balance analysis of CHO cells before and after a metabolic switch from lactate production to consumption

scientific article

Formulation, construction and analysis of kinetic models of metabolism: A review of modelling frameworks.

scientific article

From reconstruction to C 4 metabolic engineering: A case study for overproduction of polyhydroxybutyrate in bioenergy grasses

article

Functional proteomic analysis of GS-NS0 murine myeloma cell lines with varying recombinant monoclonal antibody production rate

scientific article published on August 2006

Functional screening in human cardiac organoids reveals a metabolic mechanism for cardiomyocyte cell cycle arrest.

scientific article

GRASP: a computational platform for building kinetic models of cellular metabolism

scientific article published in 2022

Genetic and biochemical characterization of genes involved in hyaluronic acid synthesis in Streptococcus zooepidemicus

scientific article published on 13 January 2016

Genome scale analysis of differential mRNA expression of Helicoverpa zea insect cells infected with a H. armigera baculovirus

scientific article published on July 2013

Genome scale transcriptomics of baculovirus-insect interactions.

scientific article

Genome-scale model guided design of Propionibacterium for enhanced propionic acid production.

scientific article published on 24 November 2017

Genome-wide discovery of human splicing branchpoints

scientific article

Genomic characterization of the uncultured Bacteroidales family S24-7 inhabiting the guts of homeothermic animals

scientific article

Global dynamics of Escherichia coli phosphoproteome in central carbon metabolism under changing culture conditions

scientific article

H2 drives metabolic rearrangements in gas-fermenting Clostridium autoethanogenum

scientific article published in March 2018

HR index--a simple method for the prediction of oxygen uptake

scientific article published in October 2011

Hanging-drop multicellular spheroids as a model of tumour angiogenesis

scientific article

Hemin reconstitutes proton extrusion in an H(+)-ATPase-negative mutant of Lactococcus lactis

scientific article

High-antibody-producing Chinese hamster ovary cells up-regulate intracellular protein transport and glutathione synthesis

scientific article

Hyaluronan molecular weight is controlled by UDP-N-acetylglucosamine concentration in Streptococcus zooepidemicus

scientific article published on 18 May 2009

IL10 and IL12B polymorphisms each influence IL-12p70 secretion by dendritic cells in response to LPS

article

Identification of three gene candidates for multicellular resistance in colon carcinoma

scientific article published on September 2004

Importance of virus-medium interactions on the biological activity of wild-type Heliothine nucleopolyhedroviruses propagated via suspension insect cell cultures

scientific article published on 23 May 2006

Improved production of propionic acid using genome shuffling.

scientific article published on 27 September 2016

Improving culture performance and antibody production in CHO cell culture processes by reducing the Warburg effect.

scientific article published on 28 April 2018

Improving the robustness of a low-cost insect cell medium for baculovirus biopesticides production, via hydrolysate streamlining using a tube bioreactor-based statistical optimization routine

scientific article published on 12 March 2012

In vitro production of Helicoverpa baculovirus biopesticides--automated selection of insect cell clones for manufacturing and systems biology studies

scientific article published on 17 May 2011

In vitro production of baculoviruses: identifying host and virus genes associated with high productivity.

scientific article published on 9 September 2016

Increased biomass yield of Lactococcus lactis during energetically limited growth and respiratory conditions.

scientific article published in May 2008

Insight into hyaluronic acid molecular weight control

scientific article

Intracellular Trafficking of Baculovirus Particles: A Quantitative Study of the HearNPV/HzAM1 Cell and AcMNPV/Sf9 Cell Systems

scientific article published on 5 May 2015

Kinetic characterization of the group II Helicoverpa armigera nucleopolyhedrovirus propagated in suspension cell cultures: implications for development of a biopesticides production process

scientific article published on 19 April 2011

Kinetics of baculovirus replication and release using real-time quantitative polymerase chain reaction

scientific article published in February 2002

Knock-in/Knock-out (KIKO) vectors for rapid integration of large DNA sequences, including whole metabolic pathways, onto the Escherichia coli chromosome at well-characterised loci

scientific article published on 24 June 2013

Linking genotype and phenotype in an economically viable propionic acid biosynthesis process

scientific article published on 13 August 2018

Low carbon fuels and commodity chemicals from waste gases – systematic approach to understand energy metabolism in a model acetogen

article

Low multiplicity infection of insect cells with a recombinant baculovirus: The cell yield concept

scientific article published in March 1996

MEMOTE for standardized genome-scale metabolic model testing

scientific article published on 01 March 2020

Maintenance of ATP Homeostasis Triggers Metabolic Shifts in Gas-Fermenting Acetogens

scientific article published on 16 May 2017

Mammalian cells as biopharmaceutical production hosts in the age of omics

scientific article published on 16 December 2011

Manufactured RBC--rivers of blood, or an oasis in the desert?

scientific article published on 14 May 2011

Membrane Bioreactors Enhance Microenvironmental Conditioning and Tissue Development

article

Memote: A community-driven effort towards a standardized genome-scale metabolic model test suite

Metabolic and practical considerations on microbial electrosynthesis ⬇️

scientific article published on February 23, 2011

Metabolic engineering: from retrofitting to green field

scientific article published on 17 June 2011

Metabolic flux analysis in mammalian cell culture

scientific article published on 13 October 2009

Metabolite profiling of CHO cells with different growth characteristics.

scientific article published on 30 March 2012

Method for generation of homogeneous multicellular tumor spheroids applicable to a wide variety of cell types

scientific article published on July 2003

Method for the generation and cultivation of functional three-dimensional mammary constructs without exogenous extracellular matrix

scientific article published on 16 February 2005

Microbial hyaluronic acid production

scientific article

Minimizing Clonal Variation during Mammalian Cell Line Engineering for Improved Systems Biology Data Generation

scientific article published on 16 August 2018

Modeling hybridoma cell metabolism using a generic genome-scale metabolic model of Mus musculus

scientific article published on January 2005

Modelling the growth and protein production by insect cells following infection by a recombinant baculovirus in suspension culture

scientific article published in January 1992

Molecular Control of Sucrose Utilization in Escherichia coli W, an Efficient Sucrose-Utilizing Strain ⬇️

scientific article published on November 2, 2012

Monocyte-derived DC primed with TLR agonists secrete IL-12p70 in a CD40-dependent manner under hyperthermic conditions.

scientific article published on November 2006

Network thermodynamic curation of human and yeast genome-scale metabolic models.

scientific article published on July 2014

Non-invasive monitoring of sucrose mobilization from culm storage parenchyma by magnetic resonance spectroscopy

scientific article published on 7 March 2013

OpenFLUX: efficient modelling software for 13C-based metabolic flux analysis

scientific article published on May 2009

Osmolarity effects on observed insect cell size after baculovirus infection are avoided using growth medium for sample dilution

scientific article

Overexpression of the regulatory subunit of glutamate-cysteine ligase enhances monoclonal antibody production in CHO cells

scientific article

PATHLOGIC-S: a scalable Boolean framework for modelling cellular signalling

scientific article

Physiological and transcriptional responses of Saccharomyces cerevisiae to d-limonene show changes to the cell wall but not to the plasma membrane.

scientific article published on 29 March 2013

Plant Genome-Scale Modeling and Implementation

article

Plant genome-scale metabolic reconstruction and modelling

scientific article published on September 2012

Plant genome-scale reconstruction: from single cell to multi-tissue modelling and omics analyses

scientific article published on 11 August 2017

Production of bacteriocins byStreptococcus bovisstrains from Australian ruminants

article

Production of polyhydroxybutyrate in sugarcane

article

Production of the short peptide surfactant DAMP4 from glucose or sucrose in high cell density cultures of Escherichia coli BL21(DE3).

scientific article published on 19 August 2014

Properties of a unique mutant of Helicoverpa armigera single-nucleocapsid nucleopolyhedrovirus that exhibits a partial many polyhedra and few polyhedra phenotype on extended serial passaging in suspension cell cultures

scientific article published on September 2005

Proteome analysis of the hyaluronic acid-producing bacterium, Streptococcus zooepidemicus.

scientific article published on 28 March 2009

Publisher Correction: MEMOTE for standardized genome-scale metabolic model testing

scientific article published on 01 April 2020

Quantification of l-alanyl-l-glutamine in mammalian cell culture broth: Evaluation of different detectors

scientific article published on 20 May 2011

Quantitative analysis of intracellular sugar phosphates and sugar nucleotides in encapsulated streptococci using HPAEC-PAD.

scientific article published in January 2009

Quantitative analysis of tetrahydrofolate metabolites from clostridium autoethanogenum

scientific article published on 16 February 2018

Quantitative gene profiling of long noncoding RNAs with targeted RNA sequencing

scientific article published on 9 March 2015

Quorum-sensing linked RNA interference for dynamic metabolic pathway control in Saccharomyces cerevisiae.

scientific article published on 16 March 2015

RNA-Seq highlights high clonal variation in monoclonal antibody producing CHO cells.

scientific article published on 5 January 2018

RNAi-mediated abrogation of trehalase expression does not affect trehalase activity in sugarcane

scientific article published on 21 December 2012

Re-annotation of the Saccharopolyspora erythraea genome using a systems biology approach

scientific article

Real-time method for determining the colony-forming cell content of human hematopoietic cell cultures

article

Recon 2.2: from reconstruction to model of human metabolism ⬇️

scientific article

Reconstruction of the Saccharopolyspora erythraea genome-scale model and its use for enhancing erythromycin production

scientific article published on 31 July 2012

Reducing Recon 2 for steady-state flux analysis of HEK cell culture

article

Relationship between oxygen uptake rate and time of infection of Sf9 insect cells infected with a recombinant baculovirus

scientific article published on January 1994

Representing genetic variation with synthetic DNA standards

scientific article

Revisiting the Evolution and Taxonomy of Clostridia, a Phylogenomic Update

scientific article published on 01 July 2019

Saccharopolyspora erythraea's genome is organised in high-order transcriptional regions mediated by targeted degradation at the metabolic switch

scientific article

Shedding light: The importance of reverse transcription efficiency standards in data interpretation

scientific article published on 12 February 2019

Short-term exposure of umbilical cord blood CD34+ cells to granulocyte-macrophage colony-stimulating factor early in culture improves ex vivo expansion of neutrophils

scientific article published on 22 September 2010

SmartPeak Automates Targeted and Quantitative Metabolomics Data Processing

scientific article published on 03 December 2020

Spatio-temporal characterization of polyhydroxybutyrate accumulation in sugarcane

scientific article published on 01 January 2007

Spliced synthetic genes as internal controls in RNA sequencing experiments

scientific article published on 8 August 2016

Stable production of hyaluronic acid in Streptococcus zooepidemicus chemostats operated at high dilution rate

scientific article published in June 2005

Stoichiometric gene-to-reaction associations enhance model-driven analysis performance: Metabolic response to chronic exposure to Aldrin in prostate cancer

scientific article published on 15 August 2019

Stoichiometric modeling of Clostridium acetobutylicum fermentations with non-linear constraints

article

Surface-bound stem cell factor and the promotion of hematopoietic cell expansion.

scientific article published on 28 May 2009

Suspension culture titration: A simple method for measuring baculovirus titers

scientific article published on 3 May 2012

Synergistic investigation of natural and synthetic C1-trophic microorganisms to foster a circular carbon economy

scientific article published in 2023

Synthesis and characterization of alginate/poly-L-ornithine/alginate microcapsules for local immunosuppression.

scientific article published in September 2008

Synthetic microbe communities provide internal reference standards for metagenome sequencing and analysis

scientific article published in Nature Communications

Systems analysis of methylerythritol-phosphate pathway flux in E. coli: insights into the role of oxidative stress and the validity of lycopene as an isoprenoid reporter metabolite.

scientific article

Systems biology and metabolic modelling unveils limitations to polyhydroxybutyrate accumulation in sugarcane leaves; lessons for C4 engineering.

scientific article

Systems-level engineering and characterisation of Clostridium autoethanogenum through heterologous production of poly-3-hydroxybutyrate (PHB)

scientific article published on 11 January 2019

Targeted sequencing for gene discovery and quantification using RNA CaptureSeq

scientific article published on 3 April 2014

Technoeconomic analysis of renewable aviation fuel from microalgae,Pongamia pinnata, and sugarcane

article

Temporal dynamics of the Saccharopolyspora erythraea phosphoproteome

scientific article

Tetanus toxin production is triggered by the transition from amino acid consumption to peptides

scientific article

The ascorbic acid paradox

scientific article published on 21 August 2010

The effect of cell line, phylogenetics and medium on baculovirus budded virus yield and quality

scientific article published on 25 July 2013

The genome sequence of E. coli W (ATCC 9637): comparative genome analysis and an improved genome-scale reconstruction of E. coli

scientific article

The hematopoietic stem cell niche: what are we trying to replicate?

article published in 2008

The kinetics of baculovirus adsorption to insect cells in suspension culture

scientific article

The role of hyaluronic acid precursor concentrations in molecular weight control in Streptococcus zooepidemicus

scientific article published in February 2014

The topology of genome-scale metabolic reconstructions unravels independent modules and high network flexibility

scientific article published on 27 June 2022

The trehalose phosphotransferase system (PTS) in E. coli W can transport low levels of sucrose that are sufficient to facilitate induction of the csc sucrose catabolism operon

scientific article

The use of an acetoacetyl-CoA synthase in place of a β-ketothiolase enhances poly-3-hydroxybutyrate production in sugarcane mesophyll cells

scientific article published on 23 December 2014

Toward Synthetic Biology Strategies for Adipic Acid Production: An in Silico Tool for Combined Thermodynamics and Stoichiometric Analysis of Metabolic Networks.

scientific article

Towards industrial production of isoprenoids in Escherichia coli: lessons learned from CRISPR-Cas9 based optimization of a chromosomally integrated mevalonate pathway.

scientific article published on 26 December 2017

Towards quantitative metabolomics of mammalian cells: development of a metabolite extraction protocol

scientific article published on 21 May 2010

Transcriptome sequencing of and microarray development for a Helicoverpa zea cell line to investigate in vitro insect cell-baculovirus interactions

scientific article

Ultra-high-yield manufacture of red blood cells from hematopoietic stem cells

scientific article published on 8 September 2011

Understanding plasmid effect on hyaluronic acid molecular weight produced by Streptococcus equi subsp. zooepidemicus

scientific article published on 23 September 2009

Universal Alternative Splicing of Noncoding Exons

scientific article published on 2 January 2018

ll-ACHRB: a scalable algorithm for sampling the feasible solution space of metabolic networks

scientific article published on 11 March 2016

multiTFA: a Python package for multi-variate thermodynamics-based flux analysis

scientific article published in 2021

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