
Overview
Background
Professor Lars Nielsen is leading the development of experimental and computational tools to analyse and design complex biological systems. His expertise in metabolic modelling and flux analysis is available nowhere else in Australia – and in few labs across the world. Professor Nielsen’s studies of biological systems as diverse as bacteria, baker's yeast, sugarcane, insects and mammals has attracted industrial partnerships with companies including Dow, Metabolix, Amyris, LanzaTech, Boeing, Virgin Australia and GE. These metabolic engineering partnerships have focussed on developing new ways of producing aviation fuel, various materials and bioactives (antibiotics, biopesticides, monoclonal antibodies). Professor Nielsen is also applying system analysis and design approaches to tissue engineering including novel strategies for generating microtissues for drug screening and using stem cells to produce red and white blood cells for transfusion.
International links
Professor Nielsen collaborates with some of the world’s pre-eminent metabolic engineers. A joint project with Prof Sang Yup Lee (KAIST, Korea) enabled several extended mutual visits to explore use of sugar for higher value products. A separate project focused on producing synthetic aviation fuel based on isoprenoids involves Professor Nielsen collaborating with global synthetic biotechnology company Amyris and leading isoprenoid metabolic engineer Professor Jay Keasling, from UC Berkeley. Professor Nielsen has secured $8million since 2006 from industry through research grants with US, European, Japanese, Korean, New Zealand and Australian companies.
Availability
- Professor Lars Nielsen is:
- Available for supervision
- Media expert
Fields of research
Qualifications
- Masters (Coursework), Technical University of Denmark
- Doctor of Philosophy, The University of Queensland
Research impacts
Research
Systems and synthetic biology. Professor Nielsen is dedicated to both the advancement of bioengineering science and its application to specific problems. Using thermodynamic principles, novel approaches are developed for handling complex, transient dynamics in developing tissue as well as rational design of complex pathways. These novel approaches are used in the design of bioprocesses as diverse as the production of blood cells for transfusion and the production of industrial biopolymers.
Memberships, patents and funding
Professor Nielsen has been granted four patents – two in stem cells and another two in metabolic engineering. He is on the Scientific Advisory Board of InSphero (2009–), a Swiss company commercialising microtissue technology originating in the Nielsen laboratory. He is an editorial board member of ACS Synthetic Biology, Metabolic Engineering, Biotechnology Journal, Biotechnology and Bioengineering and Bioprocess and Biosystems Engineering. Professor Nielsen formed and chaired the 2005 CRC SIIB Industrial Biotechnology Panel to develop an industrial biotechnology strategy for the Australian sugar industry. He successfully lobbied for the inclusion of Industrial Biotechnology in the Queensland Biotechnology Strategic Plan 2005-2015. Since then he has served as expert advisor to government, research bodies, domestic and major international companies such as Dow Chemical, DuPont and GS Caltex. In the past decade, he has been part of successful research grant applications totalling $56 million, with $31.2 million for his own systems and synthetic biology group at AIBN.
Awards and plenaries
Professor Nielsen has received the UQ Foundation Research Excellence Award; and the Australian Institute of Political Science Queensland Young Tall Poppy Award. He was invited to speak at the 2010 Science at the Shine Dome Symposium on Genomics & Mathematics, Canberra; and the Australian Academy of Technical Sciences & Engineering’s National Symposium on Future-Proofing Australia.
Works
Search Professor Lars Nielsen’s works on UQ eSpace
2025
Conference Publication
CO(2)-Metabolism: Quantifying Mixed Carbon Oxide And Hydrogen Gas Fermentation By Clostridium Autoethanogenum.
Heffernan, James K., Gonzalez Garcia, R. Axayactl, McCubbin, Timothy, Kopke, Michael, Valgepea, Kaspar, Nielsen, Lars and Marcellin, Esteban (2025). CO(2)-Metabolism: Quantifying Mixed Carbon Oxide And Hydrogen Gas Fermentation By Clostridium Autoethanogenum.. The Carbon Recycling Network Conference 5, Cheshire, United Kingdom, 9-12 March 2025.
2025
Journal Article
Multiplex genome editing eliminates lactate production without impacting growth rate in mammalian cells
Hefzi, Hooman, Martínez-Monge, Iván, Marin de Mas, Igor, Cowie, Nicholas Luke, Toledo, Alejandro Gomez, Noh, Soo Min, Karottki, Karen Julie la Cour, Decker, Marianne, Arnsdorf, Johnny, Camacho-Zaragoza, Jose Manuel, Kol, Stefan, Schoffelen, Sanne, Pristovšek, Nuša, Hansen, Anders Holmgaard, Miguez, Antonio A., Bjørn, Sara Petersen, Brøndum, Karen Kathrine, Javidi, Elham Maria, Jensen, Kristian Lund, Stangl, Laura, Kreidl, Emanuel, Kallehauge, Thomas Beuchert, Ley, Daniel, Ménard, Patrice, Petersen, Helle Munck, Sukhova, Zulfiya, Bauer, Anton, Casanova, Emilio, Barron, Niall ... Lewis, Nathan E. (2025). Multiplex genome editing eliminates lactate production without impacting growth rate in mammalian cells. Nature Metabolism, 7 (1) P119, 1-16. doi: 10.1038/s42255-024-01193-7
2024
Journal Article
Unlocking DOE potential by selecting the most appropriate design for rAAV optimization
Tzimou, Konstantina, Catalán-Tatjer, David, Nielsen, Lars K. and Lavado-García, Jesús (2024). Unlocking DOE potential by selecting the most appropriate design for rAAV optimization. Molecular Therapy - Methods and Clinical Development, 32 (4) 101329, 1-16. doi: 10.1016/j.omtm.2024.101329
2024
Journal Article
Title: Systematic insights into cell density-dependent transcriptional responses upon medium replacements
Pérez-Rubio, Pol, Romero, Elianet Lorenzo, Cervera, Laura, Gòdia, Francesc, Nielsen, Lars Keld and Lavado-García, Jesús (2024). Title: Systematic insights into cell density-dependent transcriptional responses upon medium replacements. Biomedicine and Pharmacotherapy, 181 117640, 117640. doi: 10.1016/j.biopha.2024.117640
2024
Journal Article
Unsupervised Learning Bioreactor Regimes
Laborda, Víctor Puig I., Puiman, Lars, Groves, Teddy, Haringa, Cees and Nielsen, Lars Keld (2024). Unsupervised Learning Bioreactor Regimes. Computers & Chemical Engineering, 194 108891, 1-17. doi: 10.1016/j.compchemeng.2024.108891
2024
Journal Article
Single‐Batch Expression of an Experimental Recombinant Snakebite Antivenom Based on an Oligoclonal Mixture of Human Monoclonal Antibodies
Adams, Anna C., Grav, Lise M., Ahmadi, Shirin, Holst Dahl, Camilla, Ljungars, Anne, Laustsen, Andreas H. and Nielsen, Lars K. (2024). Single‐Batch Expression of an Experimental Recombinant Snakebite Antivenom Based on an Oligoclonal Mixture of Human Monoclonal Antibodies. Biotechnology Journal, 19 (10) e202400348, e202400348. doi: 10.1002/biot.202400348
2024
Journal Article
Unravelling the essential elements for recombinant adeno-associated virus (rAAV) production in animal cell-based platforms
Catalán-Tatjer, David, Tzimou, Konstantina, Nielsen, Lars K. and Lavado-García, Jesús (2024). Unravelling the essential elements for recombinant adeno-associated virus (rAAV) production in animal cell-based platforms. Biotechnology Advances, 73 108370. doi: 10.1016/j.biotechadv.2024.108370
2024
Journal Article
Pangenome reconstruction of Lactobacillaceae metabolism predicts species-specific metabolic traits
Ardalani, O., Phaneuf, P. V., Mohite, O. S., Nielsen, L. K. and Palsson, B. O. (2024). Pangenome reconstruction of Lactobacillaceae metabolism predicts species-specific metabolic traits. mSystems, 9 (7). doi: 10.1128/msystems.00156-24
2024
Journal Article
Integrating genome-scale metabolic models with patient plasma metabolome to study endothelial metabolism in situ
Silva-Lance, Fernando, Montejano-Montelongo, Isabel, Bautista, Eric, Nielsen, Lars K., Johansson, Pär I. and Marin de Mas, Igor (2024). Integrating genome-scale metabolic models with patient plasma metabolome to study endothelial metabolism in situ. International Journal of Molecular Sciences, 25 (10) 5406, 1-22. doi: 10.3390/ijms25105406
2024
Journal Article
Bayesian regression facilitates quantitative modeling of cell metabolism
Groves, Teddy, Cowie, Nicholas Luke and Nielsen, Lars Keld (2024). Bayesian regression facilitates quantitative modeling of cell metabolism. ACS Synthetic Biology, 13 (4), 1205-1214. doi: 10.1021/acssynbio.3c00662
2024
Journal Article
Harnessing metabolic plasticity in CHO cells for enhanced perfusion cultivation
Nöbel, Matthias, Barry, Craig, MacDonald, Michael A., Baker, Kym, Shave, Evan, Mahler, Stephen, Munro, Trent, Martínez, Verónica S., Nielsen, Lars K. and Marcellin, Esteban (2024). Harnessing metabolic plasticity in CHO cells for enhanced perfusion cultivation. Biotechnology and Bioengineering, 121 (4), 1371-1383. doi: 10.1002/bit.28613
2024
Journal Article
Adaptive laboratory evolution of Clostridium autoethanogenum to metabolize CO2 and H2 enhances growth rates in chemostat and unravels proteome and metabolome alterations
Heffernan, James, Garcia Gonzalez, R. Axayactl, Mahamkali, Vishnu, McCubbin, Tim, Daygon, Dara, Liu, Lian, Palfreyman, Robin, Harris, Audrey, Koepke, Michael, Valgepea, Kaspar, Nielsen, Lars Keld and Marcellin, Esteban (2024). Adaptive laboratory evolution of Clostridium autoethanogenum to metabolize CO2 and H2 enhances growth rates in chemostat and unravels proteome and metabolome alterations. Microbial Biotechnology, 17 (4) e14452, e14452. doi: 10.1111/1751-7915.14452
2024
Journal Article
Shu: Visualization of high dimensional biological pathways
Carrasco Muriel, Jorge, Cowie, Nicholas, Taylor Parkins, Shannara, Mansouvar, Marjan, Groves, Teddy and Nielsen, Lars Keld (2024). Shu: Visualization of high dimensional biological pathways. Bioinformatics, 40 (3) btae140, 1-4. doi: 10.1093/bioinformatics/btae140
2024
Conference Publication
CO(2)-metabolism: quantifying mixed carbon oxide and hydrogen gas fermentation by Clostridium autoethanogenum
Heffernan, James K., Gonzalez-Garcia, R. Axayactl, McCubbin, Timothy, Köpke, Michael, Valgepea, Kaspar, Nielsen, Lars K. and Marcellin, Esteban (2024). CO(2)-metabolism: quantifying mixed carbon oxide and hydrogen gas fermentation by Clostridium autoethanogenum. Gas fermentation conference 2024, Gladstone, QLD Australia, 21-25 February 2024.
2024
Journal Article
LooplessFluxSampler: an efficient toolbox for sampling the loopless flux solution space of metabolic models
Saa, Pedro A., Zapararte, Sebastian, Drovandi, Christopher C. and Nielsen, Lars K. (2024). LooplessFluxSampler: an efficient toolbox for sampling the loopless flux solution space of metabolic models. BMC Bioinformatics, 25 (1) 3, 1-8. doi: 10.1186/s12859-023-05616-2
2023
Journal Article
CRISPR-Cas12a-integrated transgenes in genomic safe harbors retain high expression in human hematopoietic iPSC-derived lineages and primary cells
Vlassis, Arsenios, Jensen, Tanja L., Mohr, Marina, Jedrzejczyk, Dominika J., Meng, Xiangyou, Kovacs, Gergo, Morera-Gómez, Martí, Barghetti, Andrea, Muyo Abad, Sergi, Baumgartner, Roland F., Natarajan, Kedar N., Nielsen, Lars K., Warnecke, Tanya and Gill, Ryan T. (2023). CRISPR-Cas12a-integrated transgenes in genomic safe harbors retain high expression in human hematopoietic iPSC-derived lineages and primary cells. iScience, 26 (12) 108287, 1-30. doi: 10.1016/j.isci.2023.108287
2023
Journal Article
Comparative constraint‐based modelling of fruit development across species highlights nitrogen metabolism in the growth‐defence trade‐off
Colombié, Sophie, Prigent, Sylvain, Cassan, Cédric, Hilbert‐Masson, Ghislaine, Renaud, Christel, Dell'Aversana, Emilia, Carillo, Petronia, Moing, Annick, Beaumont, Chloé, Beauvoit, Bertrand, McCubbin, Tim, Nielsen, Lars Keld and Gibon, Yves (2023). Comparative constraint‐based modelling of fruit development across species highlights nitrogen metabolism in the growth‐defence trade‐off. The Plant Journal, 116 (3), 786-803. doi: 10.1111/tpj.16409
2023
Journal Article
Synergistic investigation of natural and synthetic C1-trophic microorganisms to foster a circular carbon economy
Orsi, Enrico, Nikel, Pablo Ivan, Nielsen, Lars Keld and Donati, Stefano (2023). Synergistic investigation of natural and synthetic C1-trophic microorganisms to foster a circular carbon economy. Nature Communications, 14 (1) 6673, 1-9. doi: 10.1038/s41467-023-42166-w
2023
Journal Article
Omics data for sampling thermodynamically feasible kinetic models
de Leeuw, Marina, Matos, Marta R.A. and Nielsen, Lars Keld (2023). Omics data for sampling thermodynamically feasible kinetic models. Metabolic Engineering, 78, 41-47. doi: 10.1016/j.ymben.2023.05.002
2023
Conference Publication
Quantifying Co-Metabolism of CO/CO2 By Clostridium autoethanogenum in Chemostats
Heffernan, James, Gonzalez-Garcia, R. Axayacatl, McCubbin, Timothy, Köpke, Michael, Valgepea, Kaspar, Nielsen, Lars and Marcellin, Esteban (2023). Quantifying Co-Metabolism of CO/CO2 By Clostridium autoethanogenum in Chemostats. Metabolic Engineering 15, Singapore, 11-15 June 2023.
Funding
Current funding
Past funding
Supervision
Availability
- Professor Lars Nielsen is:
- Available for supervision
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Supervision history
Current supervision
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Doctor Philosophy
C1 Global Metabolic Atlas
Principal Advisor
-
Doctor Philosophy
Biorecycyling carbon using acetogens
Associate Advisor
Other advisors: Professor Gary Schenk, Dr Axa Gonzalez, Dr James Heffernan, Professor Esteban Marcellin
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Doctor Philosophy
Biorecycyling carbon using acetogens
Associate Advisor
Other advisors: Professor Gary Schenk, Dr Axa Gonzalez, Dr James Heffernan, Professor Esteban Marcellin
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Doctor Philosophy
Biological CO2 and H2 utilization for sustainable animal feed production
Associate Advisor
Other advisors: Dr James Heffernan, Professor Esteban Marcellin
-
Doctor Philosophy
Pathway engineering and systems biology for optimised isobutanol production in gas-fermenting acetogens: From strain isolation to metabolic limitations identification
Associate Advisor
Other advisors: Professor Gary Schenk, Dr Axa Gonzalez, Dr James Heffernan, Professor Esteban Marcellin
Completed supervision
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2021
Doctor Philosophy
Investigating High Dimensional Alternative Splicing During Haematopoiesis.
Principal Advisor
-
2017
Doctor Philosophy
A Bayesian framework for sampling the feasible kinetic behavior of metabolic reaction networks
Principal Advisor
-
2016
Doctor Philosophy
Unraveling metabolic flux control of the methylerythritol phosphate (MEP) pathway: a systems biology study
Principal Advisor
-
2016
Doctor Philosophy
Order from Noise: Modelling the Stochasticity of Lineage Commitment
Principal Advisor
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2016
Doctor Philosophy
Understanding CHO cells biology for enhanced biopharmaceutical production: a comparative transcriptomic and proteomic approach
Principal Advisor
Other advisors: Professor Esteban Marcellin, Professor Peter Gray
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2015
Doctor Philosophy
RNA CaptureSeq: Targeted Sequencing for Comprehensive Transcriptome Studies
Principal Advisor
Other advisors: Professor Timothy Mercer
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2015
Doctor Philosophy
Quantitative bacterial phosphoproteomics
Principal Advisor
Other advisors: Professor Esteban Marcellin
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2015
Doctor Philosophy
Systems Level Signalling Analysis A Case Study of Growth Hormone Receptor Signalling
Principal Advisor
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2014
Doctor Philosophy
Understanding and overcoming monoterpene toxicity in Saccharomyces cerevisia for the production of sustainable jet fuels
Principal Advisor
Other advisors: Professor Peter Gray
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2014
Doctor Philosophy
Global metabolic effect of manipulating pyruvate dehydrogenase complex activity in mammalian cells
Principal Advisor
Other advisors: Professor Peter Gray
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2014
Doctor Philosophy
Efficient production of a model designed peptide from sucrose in Escherichia coli
Principal Advisor
-
2014
Doctor Philosophy
Simulating Information Flow in Cellular Scale Models of Signal Transduction
Principal Advisor
-
2014
Doctor Philosophy
Characterisation of the Saccharopolyspora erythraea metabolic switch: a systems approach
Principal Advisor
Other advisors: Professor Esteban Marcellin
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2014
Doctor Philosophy
Using network thermodynamics and metabolomics for the study of dynamic mammalian cell metabolism
Principal Advisor
Other advisors: Professor Peter Gray
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2013
Doctor Philosophy
Understanding phenotypic asymmetry in Escherichia coli: Development and characterization of multi-omics datasets to explain diversity amongst strains of E. coli
Principal Advisor
-
2012
Doctor Philosophy
Characterisation of mammalian cells during protein production - a systems biology approach
Principal Advisor
Other advisors: Professor Peter Gray
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2011
Doctor Philosophy
Carbon Mobilisation and Utilisation in the Sugarcane Biofactory
Principal Advisor
-
-
2010
Doctor Philosophy
Understanding molecular weight control of hyaluronic acid production in Streptococcus zooepidemicus: towards a systems approach
Principal Advisor
-
2010
Doctor Philosophy
System level assessment of mammalian cell metabolim for production of recombinant protein
Principal Advisor
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2009
Doctor Philosophy
Directed differentiation of mouse embryonic stem cells to haematopoietic lineages using EPL induction
Principal Advisor
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2008
Doctor Philosophy
Self Assembled Nano-coats for Protection of Foreign Tissue Transplants
Principal Advisor
Other advisors: Professor Matt Trau
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2006
Doctor Philosophy
HYALURONIC ACID PRODUCTION IN CONTINUOUS CULTURES OF STREPTOCOCCUS ZOOEPIDEMICUS
Principal Advisor
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2005
Doctor Philosophy
OPTIMIZATION OF DENDRITIC CELLS FOR CANCER IMMUNOTHERAPY
Principal Advisor
Other advisors: Professor Ranjeny Thomas
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2005
Doctor Philosophy
PRODUCTION OF POLY-HYDROXYALKANOATES IN SUGARCANE
Principal Advisor
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2005
Doctor Philosophy
METABOLIC FLUX ANALYSIS OF EUKARYOTIC CELLS: A STUDY OF THEORETICAL AND EXPERIMENTAL FRAMEWORKS
Principal Advisor
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2004
Doctor Philosophy
QUANTITATIVE ELUCIDATION OF THE PHENOMENOLOGICAL SELECTIVE ADVANTAGE OF THE FEW POLYHEDRA MUTANT STRAIN OF Helicoverpa armigera NUCLEOPOLYHEDROVIRUS UNDER in-vitro CONDITIONS
Principal Advisor
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2004
Doctor Philosophy
EXTENDING THE THIRD DIMENSION: NOVEL METHODS AND APPLICATIONS FOR 3D MULTICELLULAR SPHEROIDS
Principal Advisor
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2002
Doctor Philosophy
METABOLIC ENGINEERING OF HYALURONIC ACID PRODUCTION
Principal Advisor
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2002
Doctor Philosophy
HYALURONIC ACID OVERPRODUCTION BY METABOLIC PATHWAY MANIPULATION
Principal Advisor
-
2023
Doctor Philosophy
Modelling and characterising life and death of mammalian suspension cultures
Associate Advisor
Other advisors: Dr Veronica Martinez Salazar, Dr Gert Talbo, Professor Esteban Marcellin
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2023
Doctor Philosophy
Sustainable fuel and chemical production via Gas Fermentation: exploring CO2 metabolism by Clostridium autoethanogenum
Associate Advisor
Other advisors: Dr Axa Gonzalez, Professor Esteban Marcellin
-
2021
Doctor Philosophy
Insight into acetogens metabolism through the use of thermodynamic metabolic flux analysis
Associate Advisor
Other advisors: Professor Esteban Marcellin
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2020
Doctor Philosophy
Understanding toxin production in Clostridium tetani: a systems approach
Associate Advisor
Other advisors: Professor Esteban Marcellin
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2019
Doctor Philosophy
From waste to chemicals: On the metabolism of Clostridium autoethanogenum and PHB production from gas fermentation
Associate Advisor
Other advisors: Professor Esteban Marcellin
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2018
Doctor Philosophy
Exploring the metabolism of propionibacteria using genome-scale modelling
Associate Advisor
Other advisors: Professor Esteban Marcellin
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2018
Doctor Philosophy
Modulating gene expression in yeast to optimize metabolic networks for sesquiterpene and monoterpene production
Associate Advisor
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2018
Doctor Philosophy
Bioeroding sponges in a time of change: insights into the physiology and cell biology of a photosymbiotic coral-eroding sponge
Associate Advisor
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2018
Doctor Philosophy
Metabolic Engineering of propionibacteria's Wood Werkman cycle in Escherichia coli and Saccharomyces cerevisiae
Associate Advisor
Other advisors: Professor Mark Turner, Professor Esteban Marcellin
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2017
Doctor Philosophy
Understanding high propionic acid production in Propionibacterium
Associate Advisor
Other advisors: Professor Esteban Marcellin
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2015
Doctor Philosophy
Novel Cell Engineering of the Unfolded Protein Response to Achieve Efficient Therapeutic Protein Production Cell Line
Associate Advisor
Other advisors: Professor Peter Gray
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2015
Doctor Philosophy
Separating Growth and Production Phases Using Synthetic Quorum Sensing in Saccharomyces cerevisiae
Associate Advisor
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2013
Doctor Philosophy
Metabolic engineering for bio-production of industrial isoprenoids from sucrose using Escherichia coli
Associate Advisor
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2010
Doctor Philosophy
A microfluidic platform for screening immobilised biomolecule mixtures
Associate Advisor
Other advisors: Professor Justin Cooper-White
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2008
Doctor Philosophy
Angular Momentum in Optical Tweezers
Associate Advisor
Other advisors: Professor Halina Rubinsztein-Dunlop, Dr Timo Nieminen
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2003
Doctor Philosophy
STABILITY STUDIES OF WILD TYPE BACULOVIRUSES PRODUCED VIA FERMENTATION - HELIOTHIS AS A MODEL SYSTEM
Associate Advisor
Media
Enquiries
Contact Professor Lars Nielsen directly for media enquiries about:
- Engineering - biological
- Metabolic engineering
- Synthetic biology
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