The University of Queensland

Metabolic modeling and omics data integration: a systems biology approach to food science

de Mas, Igor Marin, de Leeuw, Marina, Ghaffari, Pouyan and Nielsen, Lars K. (2021). Metabolic modeling and omics data integration: a systems biology approach to food science. Comprehensive foodomics. (pp. 396-417) edited by Alejandro Cifuentes. Amsterdam, Netherlands: Elsevier. doi: 10.1016/B978-0-08-100596-5.22914-4

Algae genome-scale reconstruction, modelling and applications

Dal'Molin, Cristiana G. O. and Nielsen, Lars K. (2016). Algae genome-scale reconstruction, modelling and applications. The Physiology of Microalgae. (pp. 591-598) edited by Michael A. Borowitzka, John Beardall and John A. Raven. Switzerland: Springer International Publishing. doi: 10.1007/978-3-319-24945-2_22

Metabolic pathway engineering for hyaluronic acid production

Marcellin, Esteban, Chen, Wendy Y. and Nielsen, Lars K. (2016). Metabolic pathway engineering for hyaluronic acid production. Handbook of carbohydrate-modifying biocatalysts. (pp. 683-696) edited by Peter Grunwald. Singapore: Pan Stanford Publishing. doi: 10.1201/9781315185392-21

Production of industrially-relevant isoprenoid compounds in engineered microbes

Vickers, Claudia E., Behrendorff, James B. Y. H., Bongers, Mareike, Brennan, Timothy C. R., Bruschi, Michele and Nielsen, Lars K. (2015). Production of industrially-relevant isoprenoid compounds in engineered microbes. Microorganisms in biorefineries. (pp. 303-334) edited by Birgit Kamm. Berlin, Heidelberg: Springer. doi: 10.1007/978-3-662-45209-7_11

Customization of 13C-MFA Strategy According to Cell Culture System

Quek, Lake-Ee and Nielsen, Lars K. (2014). Customization of 13C-MFA Strategy According to Cell Culture System. Metabolic Flux Analysis: Methods and Protocols. (pp. 81-90) edited by Jens O. Kromer, Lars K. Nielsen and Lars M. Blank. New York, NY United States: Humana Press. doi: 10.1007/978-1-4939-1170-7_5

NExT: integration of thermodynamic constraints and metabolomics data into a metabolic network

Martínez, Veronica Sofía and Nielsen, LK (2014). NExT: integration of thermodynamic constraints and metabolomics data into a metabolic network. Metabolic Flux Analysis: Methods and Protocols. (pp. 65-78) edited by Jens O. Kromer, Lars K. Nielsen and Lars M. Blank. New York, NY United States: Humana Press. doi: 10.1007/978-1-4939-1170-7_4

Plant genome-scale modeling and implementation

Dal'Molin, Cristiana G. O., Quek, Lake-Ee, Palfreyman, Robin W. and Nielsen, Lars K. (2014). Plant genome-scale modeling and implementation. In DieuaideNoubhani, M and Alonso, AP (Ed.), Plant metabolic flux analysis: methods and protocols (pp. 317-332) New York, NY, United States: Humana Press. doi:10.1007/978-1-62703-688-7_19

Steady-State 13C Fluxomics Using OpenFLUX

Quek, Lake-Ee and Nielsen, Lars K. (2014). Steady-State 13C Fluxomics Using OpenFLUX. Metabolic Flux Analysis: Methods and Protocols. (pp. 209-224) edited by Jens O. Kromer, Lars K. Nielsen and Lars M. Blank. New York, NY United States: Humana Press. doi: 10.1007/978-1-4939-1170-7_13

Large scale ex vivo manufacture of blood cells

Timmins, Nicholas E. and Nielsen, Lars K. (2012). Large scale ex vivo manufacture of blood cells. Proceedings of the 21st Annual Meeting of the European Society for Animal Cell Technology (ESACT), Dublin, Ireland, June 7-10, 2009. (pp. 557-571) edited by Nigel Jenkins, Niall Barron and Paula Alves. Dordrecht, Netherlands: Springer.

Metabolic pathway engineering for hyaluronic acid production

Marcellin, Esteban, Chen, Wendy Y. and Nielsen, Lars K. (2012). Metabolic pathway engineering for hyaluronic acid production. Carbohydrate modifying biocatalysts. (pp. 571-584) edited by Peter Grundwald. Singapore: Pan Stanford Publishing. doi: 10.4032/9789814303484

Metabolomic analysis of CHO cultures with different growth characteristics – development of a metabolite extraction protocol for suspension adapted mammalian cells

Dietmair, Stefanie, Timmins, Nicholas E., Chrysanthopoulos, Panagiotis, Gray, Peter P., Krömer, Jens O. and Nielsen, Lars K. (2012). Metabolomic analysis of CHO cultures with different growth characteristics – development of a metabolite extraction protocol for suspension adapted mammalian cells. Proceedings of the 21st Annual Meeting of the European Society for Animal Cell Technology (ESACT), Dublin, Ireland, June 7-10, 2009. (pp. 37-41) edited by Nigel Jenkins, Niall Barron and Paula Alves. Dordrecht, Netherlands: Springer.

Baculovirus kinetics, insect cell culture

Chan, Leslie, Reid, Steven and Nielsen, Lars Keld (2010). Baculovirus kinetics, insect cell culture. Encyclopedia of industrial biotechnology: Bioprocess, bioseparation, and cell technology. (pp. 1-24) edited by Michael C. Flickinger. Hoboken, N.J. USA: John Wiley and Sons. doi: 10.1002/9780470054581.eib584

Metabolic engineering of mammalian cells

Quek L-E and Nielsen LK (2009). Metabolic engineering of mammalian cells. The Metabolic Pathway Engineering Handbook - Fundamentals. (pp. 26-1-26-22) edited by CD Smolke. Boca Raton Florida, USA: CRC Press Taylor & Francis Group.

Microbial hyaluronic acid biosynthesis

Marcellin, Esteban, Chen, Wendy and Nielsen, Lars Keld (2009). Microbial hyaluronic acid biosynthesis. Microbial Production of Biopolymers and Polymer Precursors: Applications and Perspectives. (pp. 163-180) edited by B.H.A. Rehm. Norfolk, UK: Caister Academic Press.

Generation of Multicellular Tumour Spheroids by the Hanging Drop Method

Timmins, Nicholas E. and Nielsen, Lars K. (2007). Generation of Multicellular Tumour Spheroids by the Hanging Drop Method. Tissue Engineering. (pp. 141-151) edited by John M. Walker. Totowa, N. J.: Humana Press. doi: 10.1007/978-1-59745-443-8_8

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, 3. doi: 10.1186/s12859-023-05616-2

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. doi: 10.1021/acssynbio.3c00662

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. doi: 10.1093/bioinformatics/btae140

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 (2023). Harnessing metabolic plasticity in CHO cells for enhanced perfusion cultivation. Biotechnology and Bioengineering. doi: 10.1002/bit.28613

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

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

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

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

An automated workflow for multi-omics screening of microbial model organisms

Donati, Stefano, Mattanovich, Matthias, Hjort, Pernille, Jacobsen, Simo Abdessamad Baallal, Blomquist, Sarah Dina, Mangaard, Drude, Gurdo, Nicolas, Pastor, Felix Pacheco, Maury, Jérôme, Hanke, Rene, Herrgård, Markus J., Wulff, Tune, Jakočiūnas, Tadas, Nielsen, Lars Keld and McCloskey, Douglas (2023). An automated workflow for multi-omics screening of microbial model organisms. npj Systems Biology and Applications, 9 (1) 14, 1-12. doi: 10.1038/s41540-023-00277-6

A protocol for the automatic construction of highly curated genome-scale models of human metabolism

Marin de Mas, Igor, Herand, Helena, Carrasco, Jorge, Nielsen, Lars K. and Johansson, Pär I. (2023). A protocol for the automatic construction of highly curated genome-scale models of human metabolism. Bioengineering, 10 (5) 576. doi: 10.3390/bioengineering10050576

Enhancing CHO cell productivity through a dual selection system using Aspg and Gs in glutamine free medium

Ha, Tae Kwang, Òdena, Andreu, Karottki, Karen Julie la Cour, Kim, Che Lin, Hefzi, Hooman, Lee, Gyun Min, Faustrup Kildegaard, Helene, Nielsen, Lars K., Grav, Lise Marie and Lewis, Nathan E. (2023). Enhancing CHO cell productivity through a dual selection system using Aspg and Gs in glutamine free medium. Biotechnology and Bioengineering, 120 (4), 1159-1166. doi: 10.1002/bit.28318

A multi-level systems biology analysis of Aldrin’s metabolic effects on prostate cancer cells

Bedia, Carmen, Dalmau, Nuria, Nielsen, Lars K., Tauler, Romà and Marín de Mas, Igor (2023). A multi-level systems biology analysis of Aldrin’s metabolic effects on prostate cancer cells. Proteomes, 11 (2) 11, 1-19. doi: 10.3390/proteomes11020011

Protocol for absolute quantification of proteins in Gram-negative bacteria based on QconCAT-based labeled peptides

Gurdo, Nicolás, Taylor Parkins, Shannara Kayleigh, Fricano, Martina, Wulff, Tune, Nielsen, Lars Keld and Nikel, Pablo Iván (2023). Protocol for absolute quantification of proteins in Gram-negative bacteria based on QconCAT-based labeled peptides. STAR Protocols, 4 (1) 102060, 1-2. doi: 10.1016/j.xpro.2023.102060

Endothelial cell phenotypes demonstrate different metabolic patterns and predict mortality in trauma patients

Henriksen, Hanne H., Marín de Mas, Igor, Nielsen, Lars K., Krocker, Joseph, Stensballe, Jakob, Karvelsson, Sigurður T., Secher, Niels H., Rolfsson, Óttar, Wade, Charles E. and Johansson, Pär I. (2023). Endothelial cell phenotypes demonstrate different metabolic patterns and predict mortality in trauma patients. International Journal of Molecular Sciences, 24 (3) 2257, 1-14. doi: 10.3390/ijms24032257

Biogas upgrading using Clostridium autoethanogenum for value-added products

Heffernan, James K., Lai, Chun-Yu, Gonzalez-Garcia, R. Axayacatl, Nielsen, Lars Keld, Guo, Jianhua and Marcellin, Esteban (2023). Biogas upgrading using Clostridium autoethanogenum for value-added products. Chemical Engineering Journal, 452 (Part 1) 138950, 1-7. doi: 10.1016/j.cej.2022.138950

Author Correction: Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network (Nature Communications, (2021), 12, 1, (3297), 10.1038/s41467-021-23143-7)

Grapotte, Mathys, Saraswat, Manu, Bessière, Chloé, Menichelli, Christophe, Ramilowski, Jordan A., Severin, Jessica, Hayashizaki, Yoshihide, Itoh, Masayoshi, Tagami, Michihira, Murata, Mitsuyoshi, Kojima-Ishiyama, Miki, Noma, Shohei, Noguchi, Shuhei, Kasukawa, Takeya, Hasegawa, Akira, Suzuki, Harukazu, Nishiyori-Sueki, Hiromi, Frith, Martin C., Abugessaisa, Imad, Aitken, Stuart, Aken, Bronwen L., Alam, Intikhab, Alam, Tanvir, Alasiri, Rami, Alhendi, Ahmad M. N., Alinejad-Rokny, Hamid, Alvarez, Mariano J., Andersson, Robin, Arakawa, Takahiro ... Lecellier, Charles-Henri (2022). Author Correction: Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network (Nature Communications, (2021), 12, 1, (3297), 10.1038/s41467-021-23143-7). Nature Communications, 13 (1) 1200. doi: 10.1038/s41467-022-28758-y

Elucidating dynamics and mechanism of cyclic bioreaction networks using topologically-equivalent electrical circuits

Nath, Sarang S., Nielsen, Lars K. and Villadsen, John (2022). Elucidating dynamics and mechanism of cyclic bioreaction networks using topologically-equivalent electrical circuits. Chemical Engineering Science, 262 118015, 1-11. doi: 10.1016/j.ces.2022.118015

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

Matos, Marta R. A., Saa, Pedro A, Cowie, Nicholas, Volkova, Svetlana, de Leeuw, Marina and Nielsen, Lars K. (2022). GRASP: a computational platform for building kinetic models of cellular metabolism. Bioinformatics Advances, 2 (1) vbac066, 1-3. doi: 10.1093/bioadv/vbac066

RNA-seq sample preparation kits strongly affect transcriptome profiles of a gas-fermenting bacterium

de Lima, Lorena Azevedo, Reinmets, Kristina, Nielsen, Lars Keld, Marcellin, Esteban, Harris, Audrey, Köpke, Michael and Valgepea, Kaspar (2022). RNA-seq sample preparation kits strongly affect transcriptome profiles of a gas-fermenting bacterium. Microbiology Spectrum, 10 (4), 1-7. doi: 10.1128/spectrum.02303-22

Recycling carbon for sustainable protein production using gas fermentation

Marcellin, Esteban, Angenent, Largus T., Nielsen, Lars K. and Molitor, Bastian (2022). Recycling carbon for sustainable protein production using gas fermentation. Current Opinion in Biotechnology, 76 102723, 102723. doi: 10.1016/j.copbio.2022.102723

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

Martínez, Verónica S., Saa, Pedro A., Jooste, Jason, Tiwari, Kanupriya, Quek, Lake-Ee and Nielsen, Lars K. (2022). The topology of genome-scale metabolic reconstructions unravels independent modules and high network flexibility. PLoS Computational Biology, 18 (6) e1010203, e1010203. doi: 10.1371/journal.pcbi.1010203

Engineering death resistance in CHO cells for improved perfusion culture

MacDonald, Michael A., Nöbel, Matthias, Martínez, Verónica S., Baker, Kym, Shave, Evan, Gray, Peter P., Mahler, Stephen, Munro, Trent, Nielsen, Lars K. and Marcellin, Esteban (2022). Engineering death resistance in CHO cells for improved perfusion culture. mAbs, 14 (1) e2083465, 1-13. doi: 10.1080/19420862.2022.2083465

Analytical tools for unravelling the metabolism of gas-fermenting Clostridia

Heffernan, James K., Mahamkali, Vishnu, Valgepea, Kaspar, Marcellin, Esteban and Nielsen, Lars K. (2022). Analytical tools for unravelling the metabolism of gas-fermenting Clostridia. Current Opinion in Biotechnology, 75 102700, 102700. doi: 10.1016/j.copbio.2022.102700

Irritable bowel syndrome and microbiome; Switching from conventional diagnosis and therapies to personalized interventions

Ghaffari, Pouyan, Shoaie, Saeed and Nielsen, Lars K. (2022). Irritable bowel syndrome and microbiome; Switching from conventional diagnosis and therapies to personalized interventions. Journal of Translational Medicine, 20 (1) 173, 173. doi: 10.1186/s12967-022-03365-z

Absolute proteome quantification in the gas-fermenting acetogen Clostridium autoethanogenum

Valgepea, Kaspar, Talbo, Gert, Takemori, Nobuaki, Takemori, Ayako, Ludwig, Christina, Mahamkali, Vishnuvardhan, Mueller, Alexander P., Tappel, Ryan, Köpke, Michael, Simpson, Séan Dennis, Nielsen, Lars Keld and Marcellin, Esteban (2022). Absolute proteome quantification in the gas-fermenting acetogen Clostridium autoethanogenum. mSystems, 7 (2), 1. doi: 10.1128/msystems.00026-22

Modelling apoptosis resistance in CHO cells with CRISPR‐mediated knock‐outs of Bak1, Bax, and Bok

MacDonald, Michael A., Barry, Craig, Groves, Teddy, Martínez, Verónica S., Gray, Peter P., Baker, Kym, Shave, Evan, Mahler, Stephen, Munro, Trent, Marcellin, Esteban and Nielsen, Lars K. (2022). Modelling apoptosis resistance in CHO cells with CRISPR‐mediated knock‐outs of Bak1, Bax, and Bok. Biotechnology and Bioengineering, 119 (6), 1380-1391. doi: 10.1002/bit.28062

Soft‐sensors application for automated feeding control in high‐throughput mammalian cell cultures

Martínez‐Monge, I., Martínez, C., Decker, M., Udugama, I. A., Marín de Mas, I., Gernaey, K. V. and Nielsen, L.K. (2022). Soft‐sensors application for automated feeding control in high‐throughput mammalian cell cultures. Biotechnology and Bioengineering, 119 (4), 1077-1090. doi: 10.1002/bit.28032

Multi-omic characterisation of Streptomyces hygroscopicus NRRL 30439: detailed assessment of its secondary metabolic potential

Barry, Craig P., Gillane, Rosemary, Talbo, Gert H., Plan, Manual, Palfreyman, Robin, Haber-Stuk, Andrea K., Power, John, Nielsen, Lars K. and Marcellin, Esteban (2022). Multi-omic characterisation of Streptomyces hygroscopicus NRRL 30439: detailed assessment of its secondary metabolic potential. Molecular Omics, 18 (3), 226-236. doi: 10.1039/d1mo00150g

Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network

Grapotte, Mathys, Saraswat, Manu, Bessière, Chloé, Menichelli, Christophe, Ramilowski, Jordan A., Severin, Jessica, Hayashizaki, Yoshihide, Itoh, Masayoshi, Tagami, Michihira, Murata, Mitsuyoshi, Kojima-Ishiyama, Miki, Noma, Shohei, Noguchi, Shuhei, Kasukawa, Takeya, Hasegawa, Akira, Suzuki, Harukazu, Nishiyori-Sueki, Hiromi, Frith, Martin C., Abugessaisa, Imad, Aitken, Stuart, Aken, Bronwen L., Alam, Intikhab, Alam, Tanvir, Alasiri, Rami, Alhendi, Ahmad M. N., Alinejad-Rokny, Hamid, Alvarez, Mariano J., Andersson, Robin, Arakawa, Takahiro ... Lecellier, Charles-Henri (2021). Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network. Nature Communications, 12 (1) 3297. doi: 10.1038/s41467-021-23143-7

Model-guided dynamic control of essential metabolic nodes boosts acetyl-coenzyme A–dependent bioproduction in rewired Pseudomonas putida

Kozaeva, Ekaterina, Volkova, Svetlana, Matos, Marta R.A., Mezzina, Mariela P., Wulff, Tune, Volke, Daniel C., Nielsen, Lars K. and Nikel, Pablo I. (2021). Model-guided dynamic control of essential metabolic nodes boosts acetyl-coenzyme A–dependent bioproduction in rewired Pseudomonas putida. Metabolic Engineering, 67, 373-386. doi: 10.1016/j.ymben.2021.07.014

Towards sustainable bioinoculants: a fermentation strategy for high cell density cultivation of Paraburkholderia sp. SOS3, a plant growth-promoting bacterium isolated in Queensland, Australia

Petersen, Ian, Paungfoo-Lonhienne, Chanyarat, Marcellin, Esteban, Nielsen, Lars Keld and Gonzalez, Axayacatl (2021). Towards sustainable bioinoculants: a fermentation strategy for high cell density cultivation of Paraburkholderia sp. SOS3, a plant growth-promoting bacterium isolated in Queensland, Australia. Fermentation, 7 (2) 58, 1-17. doi: 10.3390/fermentation7020058

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

Mahamkali, Vishnuvardhan, McCubbin, Tim, Beber, Moritz Emanuel, Noor, Elad, Marcellin, Esteban and Nielsen, Lars Keld (2021). multiTFA: a Python package for multi-variate thermodynamics-based flux analysis. Bioinformatics, 37 (18), 3064-3066. doi: 10.1093/bioinformatics/btab151

Network mapping of primary CD34+ cells by Ampliseq based whole transcriptome targeted resequencing identifies unexplored differentiation regulatory relationships

Schwaber, Jessica L., Korbie, Darren, Andersen, Stacey, Lin, Erica, Chrysanthopoulos, Panagiotis K., Trau, Matt and Nielsen, Lars K. (2021). Network mapping of primary CD34+ cells by Ampliseq based whole transcriptome targeted resequencing identifies unexplored differentiation regulatory relationships. PLoS ONE, 16 (2 ) e0246107, e0246107. doi: 10.1371/journal.pone.0246107

Perfusion culture of Chinese Hamster Ovary cells for bioprocessing applications

MacDonald, Michael A., Nöbel, Matthias, Roche Recinos, Dinora, Martínez, Verónica S., Schulz, Benjamin L., Howard, Christopher B., Baker, Kym, Shave, Evan, Lee, Yih Yean, Marcellin, Esteban, Mahler, Stephen, Nielsen, Lars Keld and Munro, Trent (2021). Perfusion culture of Chinese Hamster Ovary cells for bioprocessing applications. Critical Reviews in Biotechnology, 42 (7), 1-17. doi: 10.1080/07388551.2021.1998821

SmartPeak automates targeted and quantitative metabolomics data processing

Kutuzova, Svetlana, Colaianni, Pasquale, Röst, Hannes, Sachsenberg, Timo, Alka, Oliver, Kohlbacher, Oliver, Burla, Bo, Torta, Federico, Schrübbers, Lars, Kristensen, Mette, Nielsen, Lars, Herrgård, Markus J. and McCloskey, Douglas (2020). SmartPeak automates targeted and quantitative metabolomics data processing. Analytical Chemistry, 92 (24), 15968-15974. doi: 10.1021/acs.analchem.0c03421

Time-course transcriptomics reveals that amino acids catabolism plays a key role in toxinogenesis and morphology in Clostridium tetani

Orellana, Camila A., Zaragoza, Nicolas E., Licona-Cassani, Cuauhtemoc, Palfreyman, Robin W., Cowie, Nicholas, Moonen, Glenn, Moutafis, George, Power, John, Nielsen, Lars K. and Marcellin, Esteban (2020). Time-course transcriptomics reveals that amino acids catabolism plays a key role in toxinogenesis and morphology in Clostridium tetani. Journal of Industrial Microbiology and Biotechnology, 47 (12), 1059-1073. doi: 10.1007/s10295-020-02330-3

A pan-genome guided metabolic network reconstruction of five Propionibacterium species reveals extensive metabolic diversity

McCubbin, Tim, Gonzalez-Garcia, R. Axayacatl, Palfreyman, Robin W., Stowers, Chris, Nielsen, Lars K. and Marcellin, Esteban (2020). A pan-genome guided metabolic network reconstruction of five Propionibacterium species reveals extensive metabolic diversity. Genes, 11 (10) 1115, 1-26. doi: 10.3390/genes11101115

Multicopy targeted Integration for accelerated development of high-producing Chinese hamster ovary cells

Sergeeva, Daria, Lee, Gyun Min, Nielsen, Lars Keld and Grav, Lise Marie (2020). Multicopy targeted Integration for accelerated development of high-producing Chinese hamster ovary cells. ACS Synthetic Biology, 9 (9) acssynbio.0c00322, 2546-2561. doi: 10.1021/acssynbio.0c00322

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

Széliová, Diana, Ruckerbauer, David E., Galleguillos, Sarah N., Petersen, Lars B., Natter, Klaus, Hanscho, Michael, Troyer, Christina, Causon, Tim, Schoeny, Harald, Christensen, Hanne B., Lee, Dong-Yup, Lewis, Nathan E., Koellensperger, Gunda, Hann, Stephan, Nielsen, Lars K., Borth, Nicole and Zanghellini, Jürgen (2020). What CHO is made of: variations in the biomass composition of Chinese hamster ovary cell lines. Metabolic Engineering, 61, 288-300. doi: 10.1016/j.ymben.2020.06.002

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

Orellana, Camila A., Martínez, Verónica S., MacDonald, Michael A., Henry, Matthew N., Gillard, Marianne, Gray, Peter P., Nielsen, Lars K., Mahler, Stephen and Marcellin, Esteban (2020). ‘Omics driven discoveries of gene targets for apoptosis attenuation in CHO cells. Biotechnology and Bioengineering, 118 (1) bit.27548, 481-490. doi: 10.1002/bit.27548

Redox controls metabolic robustness in the gas-fermenting acetogen Clostridium autoethanogenum

Mahamkali, Vishnuvardhan, Valgepea, Kaspar, de Souza Pinto Lemgruber, Renato, Plan, Manuel, Tappel, Ryan, Köpke, Michael, Simpson, Séan Dennis, Nielsen, Lars Keld and Marcellin, Esteban (2020). Redox controls metabolic robustness in the gas-fermenting acetogen Clostridium autoethanogenum. Proceedings of the National Academy of Sciences of the United States of America, 117 (23), 13168-13175. doi: 10.1073/pnas.1919531117

Heterologous production of 6-deoxyerythronolide B in Escherichia coli through the wood werkman cycle

Gonzalez-Garcia, R. Axayacatl, Nielsen, Lars K. and Marcellin, Esteban (2020). Heterologous production of 6-deoxyerythronolide B in Escherichia coli through the wood werkman cycle. Metabolites, 10 (6) 228, 228. doi: 10.3390/metabo10060228

Correction to: Deletion of the hypothetical protein SCO2127 of Streptomyces coelicolor allowed identification of a new regulator of actinorhodin production (Applied Microbiology and Biotechnology, (2016), 100, 21, (9229-9237), 10.1007/s00253-016-7811-2)

Tierrafría, Víctor H., Licona-Cassani, Cuauhtemoc, Maldonado-Carmona, Nidia, Romero-Rodríguez, Alba, Centeno-Leija, Sara, Marcellin, Esteban, Rodríguez-Sanoja, Romina, Ruiz-Villafán, Beatriz, Nielsen, Lars K. and Sánchez, Sergio (2020). Correction to: Deletion of the hypothetical protein SCO2127 of Streptomyces coelicolor allowed identification of a new regulator of actinorhodin production (Applied Microbiology and Biotechnology, (2016), 100, 21, (9229-9237), 10.1007/s00253-016-7811-2). Applied Microbiology and Biotechnology, 104 (8), 3687-3687. doi: 10.1007/s00253-020-10499-x

Enhancing CO2-valorization using Clostridium autoethanogenum for sustainable fuel and chemicals production

Heffernan, James K., Valgepea, Kaspar, Lemgruber, Renato de Souza Pinto, Casini, Isabella, Plan, Manuel, Tappel, Ryan, Simpson, Sean D., Kopke, Michael, Nielsen, Lars K. and Marcellin, Esteban (2020). Enhancing CO2-valorization using Clostridium autoethanogenum for sustainable fuel and chemicals production. Frontiers in Bioengineering and Biotechnology, 8, 1-10. doi: 10.3389/fbioe.2020.00204

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

Lieven, Christian, Beber, Moritz E., Olivier, Brett G., Bergmann, Frank T., Ataman, Meric, Babaei, Parizad, Bartell, Jennifer A., Blank, Lars M., Chauhan, Siddharth, Correia, Kevin, Diener, Christian, Dräger, Andreas, Ebert, Birgitta E., Edirisinghe, Janaka N., Faria, José P., Feist, Adam M., Fengos, Georgios, Fleming, Ronan M. T., García-Jiménez, Beatriz, Hatzimanikatis, Vassily, van Helvoirt, Wout, Henry, Christopher S., Hermjakob, Henning, Herrgård, Markus J., Kaafarani, Ali, Kim, Hyun Uk, King, Zachary, Klamt, Steffen, Klipp, Edda ... Zhang, Cheng (2020). Publisher Correction: MEMOTE for standardized genome-scale metabolic model testing. Nature Biotechnology, 38 (4), 504-504. doi: 10.1038/s41587-020-0477-4

Adaptation of hydroxymethylbutenyl diphosphate reductase enables volatile isoprenoid production

Bongers, Mareike, Perez-Gil, Jordi, Hodson, Mark P., Schrübbers, Lars, Wulff, Tune, Sommer, Morten Oa, Nielsen, Lars K. and Vickers, Claudia E. (2020). Adaptation of hydroxymethylbutenyl diphosphate reductase enables volatile isoprenoid production. eLife, 9 e48685, e48685. doi: 10.7554/eLife.48685

MEMOTE for standardized genome-scale metabolic model testing

Lieven, Christian, Beber, Moritz E., Olivier, Brett G., Bergmann, Frank T., Ataman, Meric, Babaei, Parizad, Bartell, Jennifer A., Blank, Lars M., Chauhan, Siddharth, Correia, Kevin, Diener, Christian, Dräger, Andreas, Ebert, Birgitta E., Edirisinghe, Janaka N., Faria, José P., Feist, Adam M., Fengos, Georgios, Fleming, Ronan M. T., García-Jiménez, Beatriz, Hatzimanikatis, Vassily, van Helvoirt, Wout, Henry, Christopher S., Hermjakob, Henning, Herrgård, Markus J., Kaafarani, Ali, Kim, Hyun Uk, King, Zachary, Klamt, Steffen, Klipp, Edda ... Zhang, Cheng (2020). MEMOTE for standardized genome-scale metabolic model testing. Nature Biotechnology, 38 (3), 272-276. doi: 10.1038/s41587-020-0446-y

Attenuating apoptosis in Chinese hamster ovary cells for improved biopharmaceutical production

Henry, Matthew N., MacDonald, Michael A., Orellana, Camila A., Gray, Peter P., Gillard, Marianne, Baker, Kym, Nielsen, Lars K., Marcellin, Esteban, Mahler, Stephen and Martinez, Veronica S. (2020). Attenuating apoptosis in Chinese hamster ovary cells for improved biopharmaceutical production. Biotechnology and Bioengineering, 117 (4) bit.27269, 1187-1203. doi: 10.1002/bit.27269

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

Gonzalez‐Garcia, R. A., McCubbin, T., Turner, M. S., Nielsen, L. K. and Marcellin, E. (2020). Engineering Escherichia coli for propionic acid production through the Wood‐Werkman cycle. Biotechnology and Bioengineering, 117 (1), 167-183. doi: 10.1002/bit.27182

A TetR-family protein (CAETHG_0459) activates transcription from a new promoter motif associated with essential genes for autotrophic growth in acetogens

Lemgruber, Renato de Souza Pinto, Valgepea, Kaspar, Garcia, Ricardo Axayacatl Gonzalez, de Bakker, Christopher, Palfreyman, Robin William, Tappel, Ryan, Kopke, Michael, Simpson, Sean Dennis, Nielsen, Lars Keld and Marcellin, Esteban (2019). A TetR-family protein (CAETHG_0459) activates transcription from a new promoter motif associated with essential genes for autotrophic growth in acetogens. Frontiers in Microbiology, 10 2549, 2549. doi: 10.3389/fmicb.2019.02549

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

de Mas, Igor Marin, Torrents, Laura, Bedia, Carmen, Nielsen, Lars K., Cascante, Marta and Tauler, Roma (2019). Stoichiometric gene-to-reaction associations enhance model-driven analysis performance: metabolic response to chronic exposure to Aldrin in prostate cancer. BMC Genomics, 20 (1) 652. doi: 10.1186/s12864-019-5979-4

Revisiting the Evolution and Taxonomy of Clostridia, a Phylogenomic Update

Cruz-Morales, Pablo, Orellana, Camila A., Moutafis, George, Moonen, Glenn, Rincon, Gonzalo, Nielsen, Lars K. and Marcellin, Esteban (2019). Revisiting the Evolution and Taxonomy of Clostridia, a Phylogenomic Update. Genome Biology and Evolution, 11 (7), 2035-2044. doi: 10.1093/gbe/evz096

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

de Souza Pinto Lemgruber, Renato, Valgepea, Kaspar, Tappel, Ryan, Behrendorff, James B., Palfreyman, Robin William, Plan, Manuel, Hodson, Mark P., Simpson, Séan Dennis, Nielsen, Lars K., Köpke, Michael and Marcellin, Esteban (2019). Systems-level engineering and characterization of Clostridium autoethanogenum through heterologous production of poly-3-hydroxybutyrate (PHB). Metabolic Engineering, 53, 14-23. doi: 10.1016/j.ymben.2019.01.003

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

Schwaber, Jessica, Andersen, Stacey and Nielsen, Lars (2019). Shedding light: the importance of reverse transcription efficiency standards in data interpretation. Biomolecular Detection and Quantification, 17 100077, 100077. doi: 10.1016/j.bdq.2018.12.002

Minimizing clonal variation during mammalian cell line engineering for improved systems biology data generation

Grav, Lise Marie, Sergeeva, Daria, Lee, Jae Seong, Marín De Mas, Igor, Lewis, Nathan E., Andersen, Mikael Rørdam, Nielsen, Lars K., Lee, Gyun Min and Kildegaard, Helene Faustrup (2018). Minimizing clonal variation during mammalian cell line engineering for improved systems biology data generation. ACS Synthetic Biology, 7 (9) acssynbio.8b00140, 2148-2159. doi: 10.1021/acssynbio.8b00140

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

Luna-Flores, Carlos H., Stowers, Chris C., Cox, Brad M., Nielsen, Lars K. and Marcellin, Esteban (2018). Linking genotype and phenotype in an economically viable propionic acid biosynthesis process. Biotechnology for Biofuels, 11 (1) 224, 224. doi: 10.1186/s13068-018-1222-9

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

Hardwick, Simon A., Chen, Wendy Y., Wong, Ted, Kanakamedala, Bindu S., Deveson, Ira W., Ongley, Sarah E., Santini, Nadia S., Marcellin, Esteban, Smith, Martin A., Nielsen, Lars K., Lovelock, Catherine E., Neilan, Brett A. and Mercer, Tim R. (2018). Synthetic microbe communities provide internal reference standards for metagenome sequencing and analysis. Nature Communications, 9 (1) 3096, 3096. doi: 10.1038/s41467-018-05555-0

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

Peng, Bingyin, Nielsen, Lars K., Kampranis, Sotirios C. and Vickers, Claudia E. (2018). Engineered protein degradation of farnesyl pyrophosphate synthase is an effective regulatory mechanism to increase monoterpene production in Saccharomyces cerevisiae. Metabolic Engineering, 47, 83-93. doi: 10.1016/j.ymben.2018.02.005

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

Buchsteiner, Maria, Quek, Lake-Ee, Gray, Peter and Nielsen, Lars K. (2018). Improving culture performance and antibody production in CHO cell culture processes by reducing the Warburg effect. Biotechnology and Bioengineering, 115 (9), 2315-2327. doi: 10.1002/bit.26724

From reconstruction to C4 metabolic engineering: a case study for overproduction of polyhydroxybutyrate in bioenergy grasses

Gomes de Oliveira Dal'Molin, Cristiana, Quek, Lake-Ee, Saa, Pedro A., Palfreyman, Robin and Nielsen, Lars Keld (2018). From reconstruction to C4 metabolic engineering: a case study for overproduction of polyhydroxybutyrate in bioenergy grasses. Plant Science, 273, 50-60. doi: 10.1016/j.plantsci.2018.03.027

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

Alonso-Gutierrez, Jorge, Koma, Daisuke, Hu, Qijun, Yang, Yuchen, Chan, Leanne Jade G., Petzold, Christopher J., Adams, Paul D., Vickers, Claudia E., Nielsen, Lars K., Keasling, Jay D. and Lee, Taek Soon (2018). Towards industrial production of isoprenoids in Escherichia coli: lessons learned from CRISPR-Cas9 based optimization of a chromosomally integrated mevalonate pathway. Biotechnology and Bioengineering, 115 (4), 1000-1013. doi: 10.1002/bit.26530

H2 drives metabolic rearrangements in gas-fermenting Clostridium autoethanogenum

Valgepea, Kaspar, de Souza Pinto Lemgruber, Renato, Abdalla, Tanus, Binos, Steve, Takemori, Nobuaki, Takemori, Ayako, Tanaka, Yuki, Tappel, Ryan, Köpke, Michael, Simpson, Séan Dennis, Nielsen, Lars Keld and Marcellin, Esteban (2018). H2 drives metabolic rearrangements in gas-fermenting Clostridium autoethanogenum. Biotechnology for Biofuels, 11 (1) 55, 55. doi: 10.1186/s13068-018-1052-9

Quantitative analysis of tetrahydrofolate metabolites from clostridium autoethanogenum

Lemgruber, Renato de Souza Pinto, Valgepea, Kaspar, Hodson, Mark P., Tappel, Ryan, Simpson, Sean D., Kopke, Michael, Nielsen, Lars K. and Marcellin, Esteban (2018). Quantitative analysis of tetrahydrofolate metabolites from clostridium autoethanogenum. Metabolomics, 14 (3) 35, 35. doi: 10.1007/s11306-018-1331-2

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

Orellana, Camila A., Marcellin, Esteban, Palfreyman, Robin W., Munro, Trent P., Gray, Peter P. and Nielsen, Lars K. (2018). RNA-seq highlights high clonal variation in monoclonal antibody producing CHO cells. Biotechnology Journal, 13 (3) 1700231, e1700231. doi: 10.1002/biot.201700231

Advances in analytical tools for high throughput strain engineering

Marcellin, Esteban and Nielsen, Lars Keld (2018). Advances in analytical tools for high throughput strain engineering. Current Opinion in Biotechnology, 54, 33-40. doi: 10.1016/j.copbio.2018.01.027

Universal Alternative Splicing of Noncoding Exons

Deveson, Ira W., Brunck, Marion E., Blackburn, James, Tseng, Elizabeth, Hon, Ting, Clark, Tyson A., Clark, Michael B., Crawford, Joanna, Dinger, Marcel E., Nielsen, Lars K., Mattick, John S. and Mercer, Tim R. (2018). Universal Alternative Splicing of Noncoding Exons. Cell Systems, 6 (2), 245-255. doi: 10.1016/j.cels.2017.12.005

An Expanded Heterologous GAL Promoter Collection for Diauxie-Inducible Expression in Saccharomyces cerevisiae

Peng, Bingyin, Wood, Rebecca J., Nielsen, Lars K. and Vickers, Claudia E. (2018). An Expanded Heterologous GAL Promoter Collection for Diauxie-Inducible Expression in Saccharomyces cerevisiae. ACS Synthetic Biology, 7 (2), 748-751. doi: 10.1021/acssynbio.7b00355

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

Averesch, Nils J. H., Martínez, Verónica S., Nielsen, Lars K. and Krömer, Jens O. (2017). Toward Synthetic Biology Strategies for Adipic Acid Production: An in Silico Tool for Combined Thermodynamics and Stoichiometric Analysis of Metabolic Networks. ACS Synthetic Biology, 7 (2), 490-509. doi: 10.1021/acssynbio.7b00304

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

Navone, Laura, McCubbin, Tim, Gonzalez-Garcia, Ricardo A., Nielsen, Lars K. and Marcellin, Esteban (2017). Genome-scale model guided design of Propionibacterium for enhanced propionic acid production. Metabolic Engineering Communications, 6, 1-12. doi: 10.1016/j.meteno.2017.11.001

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

Mills, Richard J., Titmarsh, Drew M., Koenig, Xaver, Parker, Benjamin L., Ryall, James G., Quaife-Ryan, Gregory A., Voges, Holly K., Hodson, Mark P., Ferguson, Charles, Drowley, Lauren, Plowright, Alleyn T., Needham, Elise J., Wang, Qing-Dong, Gregorevic, Paul, Xin, Mei, Thomas, Walter G., Parton, Robert G., Nielsen, Lars K., Launikonis, Bradley S., James, David E., Elliott, David A., Porrello, Enzo R. and Hudson, James E. (2017). Functional screening in human cardiac organoids reveals a metabolic mechanism for cardiomyocyte cell cycle arrest. Proceedings of the National Academy of Sciences of the United States of America, 114 (40), E8372-E8381. doi: 10.1073/pnas.1707316114

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

Gagoski, Dejan, Shi, Zhenyu, Nielsen, Lars Keld, Vickers, Claudia E., Mahler, Stephen, Speight, Robert, Johnston, Wayne A. and Alexandrov, Kirill (2017). Cell-free pipeline for discovery of thermotolerant xylanases and endo-1,4-β-glucanases. Journal of Biotechnology, 259, 191-198. doi: 10.1016/j.jbiotec.2017.07.014

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

Saa, Pedro A. and Nielsen, Lars K. (2017). Formulation, construction and analysis of kinetic models of metabolism: A review of modelling frameworks. Biotechnology Advances, 35 (8), 981-1003. doi: 10.1016/j.biotechadv.2017.09.005

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

Gomes de Oliveira Dal'Molin, Cristiana and Nielsen, Lars Keld (2017). Plant genome-scale reconstruction: from single cell to multi-tissue modelling and omics analyses. Current Opinion in Biotechnology, 49, 42-48. doi: 10.1016/j.copbio.2017.07.009

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

Orellana, Camila A., Marcellin, Esteban, Gray, Peter P. and Nielsen, Lars K. (2017). Overexpression of the regulatory subunit of glutamate-cysteine ligase enhances monoclonal antibody production in CHO cells. Biotechnology and Bioengineering, 114 (8), 1825-1836. doi: 10.1002/bit.26316

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

Gonzalez-Garcia, Ricardo Axayacatl, McCubbin, Tim, Wille, Annalena, Plan, Manuel, Nielsen, Lars Keld and Marcellin, Esteban (2017). Awakening sleeping beauty: production of propionic acid in Escherichia coli through the sbm operon requires the activity of a methylmalonyl-CoA epimerase. Microbial Cell Factories, 16 (1) 121, 121. doi: 10.1186/s12934-017-0735-4

Maintenance of ATP homeostasis triggers metabolic shifts in gas-fermenting acetogens

Valgepea, Kaspar, Lemgruber, Renato de Souza Pinto, Meaghan, Kieran, Palfreyman, Robin William, Abdalla, Tanus, Heijstra, Bjom Daniel, Behrendorff, James Bruce, Tappel, Ryan, Kopke, Michael, Simpson, Sean Dennis, Nielsen, Lars Keld and Marcellin, Esteban (2017). Maintenance of ATP homeostasis triggers metabolic shifts in gas-fermenting acetogens. Cell Systems, 4 (5), 505-515.e5. doi: 10.1016/j.cels.2017.04.008

Microbial Propionic Acid Production

Gonzalez Garcia, Ricardo Axayacatl, McCubbin, Timothy, Navone, Laura, Stowers, Chris, Nielsen, Lars K. and Marcellin Saldana, Esteban Stefane (2017). Microbial Propionic Acid Production. Fermentation, 3 (2) 3020021, 1-20. doi: 10.3390/fermentation3020021

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

Valgepea, Kaspar, Loi, Kim Q., Behrendorff, James B., Lemgruber, Renato de S. P., Plan, Manuel, Hodson, Mark P., Koepke, Michael, Nielsen, Lars K. and Marcellin, Esteban (2017). Arginine deiminase pathway provides ATP and boosts growth of the gas-fermenting acetogen Clostridium autoethanogenum. Metabolic Engineering, 41, 202-211. doi: 10.1016/j.ymben.2017.04.007

Genome sequence of Propionibacterium acidipropionici ATCC 55737

Luna-Flores, Carlos H., Nielsen, Lars K. and Marcellin, Estaban (2017). Genome sequence of Propionibacterium acidipropionici ATCC 55737. Genome Announcements, 4 (3) e00248-16. doi: 10.1128/genomeA.00248-16

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

Peng, Bingyin, Plan, Manuel R., Carpenter, Alexander, Nielsen, Lars K. and Vickers, Claudia E. (2017). Coupling gene regulatory patterns to bioprocess conditions to optimize synthetic metabolic modules for improved sesquiterpene production in yeast. Biotechnology for Biofuels, 10 (1) 43, 43. doi: 10.1186/s13068-017-0728-x

Improved production of propionic acid using genome shuffling

Luna-Flores, Carlos H., Palfreyman, Robin W., Kromer, Jens O., Nielsen, Lars K. and Marcellin, Esteban (2017). Improved production of propionic acid using genome shuffling. Biotechnology Journal, 12 (2) 1600120, 1600120. doi: 10.1002/biot.201600120

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

Peng, Bingyin, Plan, Manuel R., Chrysanthopoulos, Panagiotis, Hodson, Mark P., Nielsen, Lars K. and Vickers, Claudia E. (2017). A squalene synthase protein degradation method for improved sesquiterpene production in Saccharomyces cerevisiae. Metabolic Engineering, 39, 209-219. doi: 10.1016/j.ymben.2016.12.003

The Saccharomyces cerevisiae pheromone-response is a metabolically active stationary phase for bio-production

Williams, Thomas C., Peng, Bingyin, Vickers, Claudia E. and Nielsen, Lars K. (2016). The Saccharomyces cerevisiae pheromone-response is a metabolically active stationary phase for bio-production. Metabolic Engineering Communications, 3, 142-152. doi: 10.1016/j.meteno.2016.05.001

A consensus genome-scale reconstruction of Chinese hamster ovary cell metabolism

Hefzi, Hooman, Ang, Kok Siong, Hanscho, Michael, Bordbar, Aarash, Ruckerbauer, David, Lakshmanan, Meiyappan, Orellana, Camila A., Baycin-Hizal, Deniz, Huang, Yingxiang, Ley, Daniel, Martinez, Veronica S., Kyriakopoulos, Sarantos, Jimenez, Natalia E., Zielinski, Daniel C., Quek, Lake-Ee, Wulff, Tune, Arnsdorf, Johnny, Li, Shangzhong, Lee, Jae Seong, Paglia, Giuseppe, Loira, Nicolas, Spahn, Philipp N., Pedersen, Lasse E., Gutierrez, Jahir M., King, Zachary A., Lund, Anne Mathilde, Nagarajan, Harish, Thomas, Alex, Abdel-Haleem, Alyaa M. ... Lewis, Nathan E. (2016). A consensus genome-scale reconstruction of Chinese hamster ovary cell metabolism. Cell Systems, 3 (5), 434-443.e8. doi: 10.1016/j.cels.2016.10.020

Deletion of the hypothetical protein SCO2127 of Streptomyces coelicolor allowed identification of a new regulator of actinorhodin production

Tierrafría, Víctor H. , Licona-Cassani, Cuauhtemoc, Maldonado-Carmona, Nidia, Romero-Rodríguez, Alba, Centeno-Leija, Sara, Marcellin, Esteban, Rodríguez-Sanoja, Romina, Ruiz-Villafan, Beatriz, Nielsen, Lars K. and Sánchez, Sergio (2016). Deletion of the hypothetical protein SCO2127 of Streptomyces coelicolor allowed identification of a new regulator of actinorhodin production. Applied Microbiology and Biotechnology, 100 (21), 9229-9237. doi: 10.1007/s00253-016-7811-2

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

Licona-Cassani, Cuauhtemoc, Steen, Jennifer A., Zaragoza, Nicolas E., Moonen, Glenn, Moutafis, George, Hodson, Mark P., Power, John, Nielsen, Lars K. and Marcellin, Esteban (2016). Tetanus toxin production is triggered by the transition from amino acid consumption to peptides. Anaerobe, 41, 113-124. doi: 10.1016/j.anaerobe.2016.07.006

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

Nguyen, Quan, Tran, Trinh Tb, Chan, Leslie C. L., Nielsen, Lars K. and Reid, Steven (2016). In vitro production of baculoviruses: identifying host and virus genes associated with high productivity. Applied Microbiology and Biotechnology, 100 (21), 1-15. doi: 10.1007/s00253-016-7774-3

Representing genetic variation with synthetic DNA standards

Deveson, Ira W., Chen, Wendy Y., Wong, Ted, Hardwick, Simon A., Andersen, Stacey B., Nielsen, Lars K., Mattick, John S. and Mercer, Tim R. (2016). Representing genetic variation with synthetic DNA standards. Nature Methods, 13 (9), 784-791. doi: 10.1038/nmeth.3957

Spliced synthetic genes as internal controls in RNA sequencing experiments

Hardwick, Simon A., Chen, Wendy Y., Wong, Ted, Deveson, Ira W., Blackburn, James, Andersen, Stacey B., Nielsen, Lars K., Mattick, John S. and Mercer, Tim R. (2016). Spliced synthetic genes as internal controls in RNA sequencing experiments. Nature Methods, 13 (9), 792-798. doi: 10.1038/nmeth.3958

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

Higuera, Pedro Saa and Nielsen, Lars K. (2016). Fast-SNP: a fast matrix pre-processing algorithm for efficient loopless flux optimization of metabolic models. Bioinformatics, 32 (24), 3807-3814. doi: 10.1093/bioinformatics/btw555

Metabolic reconstruction of Setaria italica: a systems biology approach for integrating tissue-specific omics and pathway analysis of bioenergy grasses

de Oliveira Dal'Molin, Cristiana Gomes, Orellana, Camila, Gebbie, Leigh, Steen, Jennifer, Hodson, Mark, Plan, Manuel, Chrysanthopoulos, Panagiotis, Macqualter, Richard, Palfreyman, Robin W. and Nielsen, Lars K. (2016). Metabolic reconstruction of Setaria italica: a systems biology approach for integrating tissue-specific omics and pathway analysis of bioenergy grasses. Frontiers in Plant Science, 7 (1138) 1138, 1-18. doi: 10.3389/fpls.2016.01138

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

Saa, Pedro A. and Nielsen, Lars K. (2016). II-ACHRB: a scalable algorithm for sampling the feasible solution space of metabolic networks. Bioinformatics, 32 (15), 2330-2337. doi: 10.1093/bioinformatics/btw132

Construction of feasible and accurate kinetic models of metabolism: a Bayesian approach

Saa, Pedro A. and Nielsen, Lars K. (2016). Construction of feasible and accurate kinetic models of metabolism: a Bayesian approach. Scientific Reports, 6 (1) 29635, 29635. doi: 10.1038/srep29635

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

Ormerod, Kate L., Wood, David L. A., Lachner, Nancy, Gellatly, Shaan L., Daly, Joshua N., Parsons, Jeremy D., Dal’Molin, Cristiana G. O., Palfreyman, Robin W., Nielsen, Lars K., Cooper, Matthew A., Morrison, Mark, Hansbro, Philip M. and Hugenholtz, Philip (2016). Genomic characterization of the uncultured Bacteroidales family S24-7 inhabiting the guts of homeothermic animals. Microbiome, 4 (1) 36, 36.1-36.17. doi: 10.1186/s40168-016-0181-2

Recon 2.2: from reconstruction to model of human metabolism

Swainston, Neil, Smallbone, Kieran, Hefzi, Hooman, Dobson, Paul D., Brewer, Judy, Hanscho, Michael, Zielinski, Daniel C., Ang, Kok Siong, Gardiner, Natalie J., Gutierrez, Jahir M., Kyriakopoulos, Sarantos, Lakshmanan, Meiyappan, Li, Shangzhong, Liu, Joanne K., Martinez, Veronica S., Orellana, Camila A., Quek, Lake-Ee, Thomas, Alex, Zanghellini, Juergen, Borth, Nicole, Lee, Dong-Yup, Nielsen, Lars K., Kell, Douglas B., Lewis, Nathan E. and Mendes, Pedro (2016). Recon 2.2: from reconstruction to model of human metabolism. Metabolomics, 12 (7) 109, 109. doi: 10.1007/s11306-016-1051-4

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

Marcellin, Esteban, Behrendorff, James B., Nagaraju, Shilpa, DeTissera, Sashini, Segovia, Simon, Palfreyman, Robin W., Daniell, James, Licona-Cassani, Cuauhtemoc, Quek, Lake-ee, Speight, Robert, Hodson, Mark P., Simpson, Sean D., Mitchell, Wayne P., Kopke, Michael and Nielsen, Lars K. (2016). Low carbon fuels and commodity chemicals from waste gases-systematic approach to understand energy metabolism in a model acetogen. Green Chemistry, 18 (10), 3020-3028. doi: 10.1039/c5gc02708j

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

Zhang, Yali, Luo, Kailai, Zhao, Qiushuang, Qi, Zhengliang, Nielsen, Lars Keld and Liu, Hao (2016). Genetic and biochemical characterization of genes involved in hyaluronic acid synthesis in Streptococcus zooepidemicus. Applied Microbiology and Biotechnology, 100 (8), 3611-3620. doi: 10.1007/s00253-016-7286-1

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

Saa, Pedro A. and Nielsen, Lars K. (2016). A probabilistic framework for the exploration of enzymatic capabilities based on feasible kinetics and control analysis. Biochimica et Biophysica Acta - General Subjects, 1860 (3), 576-587. doi: 10.1016/j.bbagen.2015.12.015

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

Zhu, Yan, Pham, Thi Huong, Nhiep, Thi Hanh Nguyen, Vu, Ngoc Minh Thu, Marcellin, Esteban, Chakrabortti, Alolika, Wang, Yuanliang, Waanders, Jennifer, Lo, Raquel, Huston, Wilhelmina M., Bansal, Nidhi, Nielsen, Lars K., Liang, Zhao-Xun and Turner, Mark S. (2016). Cyclic-di-AMP synthesis by the diadenylate cyclase CdaA is modulated by the peptidoglycan biosynthesis enzyme GlmM in Lactococcus lactis. Molecular Microbiology, 99 (6), 1015-1027. doi: 10.1111/mmi.13281

Systems biology approaches to understand natural products biosynthesis

Licona-Cassani, Cuauhtemoc, Cruz-Morales, Pablo, Manteca, Angel, Barona-Gomez, Francisco, Nielsen, Lars K. and Marcellin, Esteban (2015). Systems biology approaches to understand natural products biosynthesis. Frontiers in Bioengineering and Biotechnology, 3 199, 199.1-199.8. doi: 10.3389/fbioe.2015.00199

Dynamic metabolic flux analysis using B-splines to study the effects of temperature shift on CHO cell metabolism

Martinez, Verónica S., Buchsteiner, Maria, Gray, Peter, Nielsen, Lars K. and Quek, Lake-Ee (2015). Dynamic metabolic flux analysis using B-splines to study the effects of temperature shift on CHO cell metabolism. Metabolic Engineering Communications, 2, 46-57. doi: 10.1016/j.meteno.2015.06.001

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

Bongers, Mareike, Chrysanthopoulos, Panagiotis K., Behrendorff, James B.Y.H., Hodson, Mark P., Vickers, Claudia E. and Nielsen, Lars K. (2015). 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. Microbial Cell Factories, 14 (1) 193, 193. doi: 10.1186/s12934-015-0381-7

Filling the void: allogeneic myeloid cells for transplantation

Schwaber, Jessica L., Brunck, Marion E., Levesque, Jean-Pierre and Nielsen, Lars K. (2015). Filling the void: allogeneic myeloid cells for transplantation. Current Opinion in Hematology, 23 (1), 72-77. doi: 10.1097/MOH.0000000000000205

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

Ebrahim, Ali, Almaas, Eivind, Bauer, Eugen, Bordbar, Aarash, Burgard, Anthony P., Chang, Roger L., Draeger, Andreas, Famili, Iman, Feist, Adam M., Fleming, Ronan M. T., Fong, Stephen S., Hatzimanikatis, Vassily, Herrgard, Markus J., Holder, Allen, Hucka, Michael, Hyduke, Daniel, Jamshidi, Neema, Lee, Sang Yup, Le Novere, Nicolas, Lerman, Joshua A., Lewis, Nathan E., Ma, Ding, Mahadevan, Radhakrishnan, Maranas, Costas, Nagarajan, Harish, Navid, Ali, Nielsen, Jens, Nielsen, Lars K., Nogales, Juan ... Thiele, Ines (2015). Do genome-scale models need exact solvers or clearer standards?. Molecular Systems Biology, 11 (10) 831, 831. doi: 10.15252/msb.20156157

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

Medina-Torres, C. E., van Eps, A. W., Nielsen, L. K. and Hodson, M. P. (2015). A liquid chromatography-tandem mass spectrometry-based investigation of the lamellar interstitial metabolome in healthy horses and during experimental laminitis induction. Veterinary Journal, 206 (2), 161-169. doi: 10.1016/j.tvjl.2015.07.031

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

Lim, SooA, Marcellin, Esteban, Jacob, Shana and Nielsen, Lars K. (2015). Global dynamics of Escherichia coli phosphoproteome in central carbon metabolism under changing culture conditions. Journal of Proteomics, 126, 24-33. doi: 10.1016/j.jprot.2015.05.021

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

Peng, Bingyin, Williams, Thomas C., Henry, Matthew, Nielsen, Lars K. and Vickers, Claudia E. (2015). Controlling heterologous gene expression in yeast cell factories on different carbon substrates and across the diauxic shift: a comparison of yeast promoter activities. Microbial Cell Factories, 14 (1) 91, 1-11. doi: 10.1186/s12934-015-0278-5

Intracellular trafficking of baculovirus particles: A quantitative study of the hearNPV/HzAm1 cell and AcMNPV/sf9 cell systems

Matindoost, Leila, Nielsen, Lars K and Reid, Steve (2015). Intracellular trafficking of baculovirus particles: A quantitative study of the hearNPV/HzAm1 cell and AcMNPV/sf9 cell systems. Viruses, 7 (5), 2288-2307. doi: 10.3390/v7052288

Evolutionary engineering improves tolerance for replacement jet fuels in Saccharomyces cerevisiae

Brennan, Timothy C. R., Williams, Thomas C., Schulz, Benjamin L., Palfreyman, Robin W., Kroemer, Jens O. and Nielsen, Lars K. (2015). Evolutionary engineering improves tolerance for replacement jet fuels in Saccharomyces cerevisiae. Applied and Environmental Microbiology, 81 (10), 3316-3325. doi: 10.1128/AEM.04144-14

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

Williams, T. C., Averesch, N. J. H., Winter, G., Plan, M. R., Vickers, C. E., Nielsen, L. K. and Kromer, J. O. (2015). Quorum-sensing linked RNA interference for dynamic metabolic pathway control in Saccharomyces cerevisiae. Metabolic Engineering, 29, 124-134. doi: 10.1016/j.ymben.2015.03.008

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

Saa, Pedro and Nielsen, Lars K. (2015). A general framework for thermodynamically consistent parameterization and efficient sampling of enzymatic reactions. PLoS Computational Biology, 11 (4) e1004195, 1-25. doi: 10.1371/journal.pcbi.1004195

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

Williams, Thomas C., Espinosa, Monica I., Nielsen, Lars K. and Vickers, Claudia E. (2015). Dynamic regulation of gene expression using sucrose responsive promoters and RNA interference in Saccharomyces cerevisiae. Microbial Cell Factories, 14 (43) 43, 1-10. doi: 10.1186/s12934-015-0223-7

Quantitative gene profiling of long noncoding RNAs with targeted RNA sequencing

Clark, Michael B., Mercer, Tim R., Bussotti, Giovanni, Leonardi, Tommaso, Haynes, Katelin R., Crawford, Joanna, Brunck, Marion E., Cao, Kim-Anh Le, Thomas, Gethin P., Chen, Wendy Y., Taft, Ryan J., Nielsen, Lars K., Enright, Anton J., Mattick, John S. and Dinger, Marcel E. (2015). Quantitative gene profiling of long noncoding RNAs with targeted RNA sequencing. Nature Methods, 12 (4), 339-342. doi: 10.1038/nmeth.3321

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

Orellana, Camila A., Marcellin, Esteban, Schulz, Benjamin L., Nouwens, Amanda S., Gray, Peter P. and Nielsen, Lars K. (2015). High-antibody-producing Chinese hamster ovary cells up-regulate intracellular protein transport and glutathione synthesis. Journal of Proteome Research, 14 (2), 609-618. doi: 10.1021/pr501027c

Genome-wide discovery of human splicing branchpoints

Mercer, Tim R., Clark, Michael B., Anderson, Stacey B., Brunck, Marion E., Haerty, Wilifried, Crawford, Joanna, Taft, Ryan J., Nielsen, Lars K., Dinger, Marcel E. and Mattick, John S. (2015). Genome-wide discovery of human splicing branchpoints. Genome Research, 25 (2), 290-303. doi: 10.1101/gr.182899.114

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

de Oliveira Dal'molin, Cristiana Gomes, Quek, Lake-Ee, Saa, Pedro A. and Nielsen, Lars K. (2015). A multi-tissue genome-scale metabolic modelling framework for the analysis of whole plant systems. Frontiers in Plant Science, 6 (JAN) 4, 4.1-4.12. doi: 10.3389/fpls.2015.00004

AllR controls the expression of Streptomyces coelicolor allantoin pathway genes

Navone, Laura, Pablo Macagno, Juan, Licona-Cassani, Cuauhtemoc, Marcellin, Esteban, Nielsen, Lars K., Gramajo, Hugo and Rodriguez, Eduardo (2015). AllR controls the expression of Streptomyces coelicolor allantoin pathway genes. Applied and Environmental Microbiology, 81 (19), 6649-6659. doi: 10.1128/AEM.02098-15

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

Huynh, Hoai T., Tran, Trinh T. B., Chan, Leslie C. L., Nielsen, Lars K. and Reid, Steven (2015). Decline in Helicoverpa armigera nucleopolyhedrovirus occlusion body yields with increasing infection cell density in vitro is strongly correlated with viral DNA levels. Archives of Virology, 160 (9), 2169-2180. doi: 10.1007/s00705-015-2478-z

Editorial: On the cusp of rational CHO cell engineering

Nielsen, Lars and Borth, Nicole (2015). Editorial: On the cusp of rational CHO cell engineering. Biotechnology Journal, 10 (7), 929-930. doi: 10.1002/biot.201500375

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

McQualter, Richard B., Bellasio, Chandra, Gebbie, Leigh K., Petrasovits, Lars A., Palfreyman, Robin W., Hodson, Mark P., Plan, Manuel R., Blackman, Deborah M., Brumbley, Stevens M. and Nielsen, Lars K. (2015). Systems biology and metabolic modelling unveils limitations to polyhydroxybutyrate accumulation in sugarcane leaves; lessons for C4 engineering. Plant Biotechnology Journal, 14 (2), 1-14. doi: 10.1111/pbi.12399

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

McQualter, Richard B., Petrasovits, Lars A., Gebbie, Leigh K., Schweitzer, Dirk, Blackman, Deborah M., Chrysanthopoulos, Panagiotis, Hodson, Mark P., Plan, Manuel R., Riches, James D., Snell, Kristi D., Brumbley, Stevens M. and Nielsen, Lars K. (2014). The use of an acetoacetyl-CoA synthase in place of a β-ketothiolase enhances poly-3-hydroxybutyrate production in sugarcane mesophyll cells. Plant Biotechnology Journal, 13 (5), 700-707. doi: 10.1111/pbi.12298

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

Huynh, Hoai T., Tran, Trinh T. B., Chan, Leslie C. L., Nielsen, Lars K. and Reid, Steven (2014). Effect of the peak cell density of recombinant AcMNPV-infected Hi5 cells on baculovirus yields. Applied Microbiology and Biotechnology, 99 (4), 1687-1700. doi: 10.1007/s00253-014-6260-z

Absolute counting of neutrophils in whole blood using flow cytometry

Brunck, Marion E. G., Andersen, Stacey B., Timmins, Nicholas E., Osborne, Geoffrey W. and Nielsen, Lars K. (2014). Absolute counting of neutrophils in whole blood using flow cytometry. Cytometry Part A, 85 (12), 1057-1064. doi: 10.1002/cyto.a.22503

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

Jardine, Kolby, Chambers, Jeffrey, Alves, Eliane G., Teixeira, Andrea, Garcia, Sabrina, Holm, Jennifer, Higuchi, Niro, Manzi, Antonio, Abrell, Leif, Fuentes, Jose D., Nielsen, Lars K., Torn, Margaret S. and Vickers, Claudia E. (2014). Dynamic balancing of isoprene carbon sources reflects photosynthetic and photorespiratory responses to temperature stress. Plant Physiology, 166 (4), 2051-2064. doi: 10.1104/pp.114.247494

Metabolic profiling and flux analysis of MEL-2 human embryonic stem cells during exponential growth at physiological and atmospheric oxygen concentrations

Turner, Jennifer, Quek,Lake-Ee, Titmarsh, Drew, Kromer, Jens O., Kao, Li-Pin, Nielsen, Lars, Wolvetang, Ernst and Cooper-White, Justin (2014). Metabolic profiling and flux analysis of MEL-2 human embryonic stem cells during exponential growth at physiological and atmospheric oxygen concentrations. PLoS One, 9 (11) e112757, e112757.1-e112757.13. doi: 10.1371/journal.pone.0112757

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

Arifin, Yalun, Archer, Colin, Lim, SooA, Quek, Lake-Ee, Sugiarto, Haryadi, Marcellin, Esteban, Vickers, Claudia E., Kromer, Jens O. and Nielsen, Lars K. (2014). Escherichia coli W shows fast, highly oxidative sucrose metabolism and low acetate formation. Applied Microbiology and Biotechnology, 98 (21), 9033-9044. doi: 10.1007/s00253-014-5956-4

Specific mesothelial signature marks the heterogeneity of mesenchymal stem cells from high-grade serous ovarian cancer

Verardo, Roberto, Piazza, Silvano, Klaric, Enio, Ciani, Yari, Bussadori, Giulio, Marzinotto, Stefania, Mariuzzi, Laura, Cesselli, Daniela, Beltrami, Antonio P., Mano, Miguel, Itoh, Masayoshi, Kawaji, Hideya, Lassmann, Timo, Carninci, Piero, Hayashizaki, Yoshihide, Forrest, Alistair R. R., Beltrami, Carlo A., The Fantom Consortium, Schneider, Claudio, Beckhouse, Anthony, Wells, Christine, Vijayan, Dipti, Wolvetang, Ernst, Hitchens, Kelly, Kenna, Tony, Blumenthal, Antje, Briggs, James, Ovchinnikov, Dmitry, Fearnley, Liam ... Nielsen, Lars (2014). Specific mesothelial signature marks the heterogeneity of mesenchymal stem cells from high-grade serous ovarian cancer. Stem Cells (Durham), 32 (11), 2998-3011. doi: 10.1002/stem.1791

Factors affecting polyhydroxybutyrate accumulation in mesophyll cells of sugarcane and switchgrass

McQualter, Richard B., Somleva, Maria N., Gebbie, Leigh K., Li, Xuemei, Petrasovits, Lars A., Snell, Kristi D., Nielsen, Lars K. and Brumbley, Stevens M. (2014). Factors affecting polyhydroxybutyrate accumulation in mesophyll cells of sugarcane and switchgrass. BMC Biotechnology, 14 (1) 83, 83.1-83.11. doi: 10.1186/1472-6750-14-83

Control of chitin and N-acetylglucosamine utilization in Saccharopolyspora erythraea

Liao, Chengheng, Rigali, Sebastien, Cassani, Cuauhtemoc Licona, Marcellin, Esteban, Nielsen, Lars Keld and Ye, Bang-Ce (2014). Control of chitin and N-acetylglucosamine utilization in Saccharopolyspora erythraea. Microbiology (United Kingdom), 160 (9), 1914-1928. doi: 10.1099/mic.0.078261-0

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

Quek, Lake-Ee, Dietmair, Stefanie, Hanscho, Michael, Martinez, Veronica S., Borth, Nicole and Nielsen, Lars K. (2014). Reducing Recon 2 for steady-state flux analysis of HEK cell culture. Journal of Biotechnology, 184, 172-178. doi: 10.1016/j.jbiotec.2014.05.021

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

Bruschi, Michele, Kroemer, Jens O., Steen, Jennifer A. and Nielsen, Lars K. (2014). Production of the short peptide surfactant DAMP4 from glucose or sucrose in high cell density cultures of Escherichia coli BL21(DE3). Microbial Cell Factories, 13 (1) 99, 1-9. doi: 10.1186/s12934-014-0099-y

Insight into hyaluronic acid molecular weight control

Marcellin, Esteban, Steen, Jennifer A. and Nielsen, Lars K. (2014). Insight into hyaluronic acid molecular weight control. Applied Microbiology and Biotechnology, 98 (16), 6947-6956. doi: 10.1007/s00253-014-5853-x

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

Quek, Lake-Ee and Nielsen, Lars K (2014). A depth-first search algorithm to compute elementary flux modes by linear programming. BMC Systems Biology, 8 (1) 94. doi: 10.1186/s12918-014-0094-2

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

Martinez, Veronica S., Quek, Lake-Ee and Nielsen, Lars K. (2014). Network thermodynamic curation of human and yeast genome-scale metabolic models. Biophysical Journal, 107 (2), 493-503. doi: 10.1016/j.bpj.2014.05.029

Temporal dynamics of the Saccharopolyspora erythraea phosphoproteome

Licona-Cassani, Cuauhtemoc, Lim, SooA, Marcellin, Esteban and Nielsen, Lars K. (2014). Temporal dynamics of the Saccharopolyspora erythraea phosphoproteome. Molecular and Cellular Proteomics, 13 (5), 1219-1230. doi: 10.1074/mcp.M113.033951

RECLU: a pipeline to discover reproducible transcriptional start sites and their alternative regulation using capped analysis of gene expression (CAGE)

Ohmiya, Hiroko, Vitezic, Morana, Frith, Martin C., Itoh, Masayoshi, Carninci, Piero, Forrest, Alistair R. R., Hayashizaki, Yoshihide, Lassmann, Timo, FANTOM Consortium, Beckhouse, Anthony, Wells, Christine, Vijayan, Dipti, Mason, Elizabeth, Wolvetang, Ernst, Hitchens, Kelly, Le Cao, Kim-Anh, Nielsen, Lars, Fearnley, Liam, Kenna, Tony and Blumenthal, Antje (2014). RECLU: a pipeline to discover reproducible transcriptional start sites and their alternative regulation using capped analysis of gene expression (CAGE). BMC Genomics, 15 (1) 269. doi: 10.1186/1471-2164-15-269

Analysis of the DNA methylome and transcriptome in granulopoiesis reveals timed changes and dynamic enhancer methylation

Rönnerblad, Michelle, Andersson, Robin, Olofsson, Tor, Douagi, Iyadh, Karimi, Mohsen, Lehmann, Sören, Hoof, Ilka, de Hoon, Michiel, Itoh, Masayoshi, Nagao-Sato, Sayaka, Kawaji, Hideya, Lassmann, Timo, Carninci, Piero, Hayashizaki, Yoshihide, Forrest, Alistair R. R., Sandelin, Albin, Ekwall, Karl, Amer, Erik, Lennartsson, Andreas, for the FANTOM consortium, Wells, Christine, Wolvetang, Ernst, Blumenthal, Antje, Kenna, Tony, Hitchens, Kelly, Ovchinnikov, Dmitry, Fearnley, Liam, Le Cao, Kim-Anh, Mason, Elizabeth ... Vijayan, Dipti (2014). Analysis of the DNA methylome and transcriptome in granulopoiesis reveals timed changes and dynamic enhancer methylation. Blood, 123 (17), e79-e89. doi: 10.1182/blood-2013-02-482893

Redefinition of the human mast cell transcriptome by deep-CAGE sequencing

Motakis, Efthymios, Guhl, Sven, Ishizu, Yuri, Itoh, Masayoshi, Kawaji, Hideya, de Hoon, Michiel, Lassman, Timo, Carninci, Piero, Hayashizaki, Yoshihide, Zuberbier, Torsten, Forrest, Alistair R. R., Babina, Magda, for The FANTOM Consortium, Wells, Christine, Wolvetang, Ernst, Beckhouse, Anthony, Fearnley, Liam, Hitchens, Kelly, Kenna, Tony, Le Cao, Kim-Anh, Mason, Elizabeth, Nielsen, Lars, Vijayan, Dipti, Blumenthal, Antje, Ovchinnikov, Dmitry and Briggs, James (2014). Redefinition of the human mast cell transcriptome by deep-CAGE sequencing. Blood, 123 (17), 58-67. doi: 10.1182/blood-2013-02-483792

Transcription and enhancer profiling in human monocyte subsets

Schmidl, Christian, Renner, Kathrin, Peter, Katrin, Eder, Ruediger, Lassmann, Timo, Balwierz, Piotr J., Itoh, Masayohshi, Nagao-Sato, Sayaka, Kawaji, Hideya, Carninci, Piero, Suzuki, Harukazu, Hayashizaki, Yoshihide, Andreesen, Reinhard, Hume, David A., Hoffmann, Petra, Forrest, Alistair R. R., Kreutz, Marina P., Edinger, Matthias, Rehli, Michael, for the FANTOM consortium, Beckhouse, Anthony, Wells, Christine, Vijayan, Dipti, Mason, Elizabeth, Wolvetang, Ernst, Hitchens, Kelly, Le Cao, Kim-Anh, Nielsen, Lars, Fearnley, Liam and Kenna, Tony (2014). Transcription and enhancer profiling in human monocyte subsets. Blood, 123 (17), e90-e99. doi: 10.1182/blood-2013-02-484188

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

Brunck, Marion E. G. and Nielsen, Lars K. (2014). Concise review: next-generation cell therapies to prevent infections in neutropenic patients. Stem Cells Translational Medicine, 3 (4), 541-548. doi: 10.5966/sctm.2013-0145

Interactive visualization and analysis of large-scale sequencing datasets using ZENBU

Severin, Jessica, Lizio, Marina, Harshbarger, Jayson, Kawaji, Hideya, Daub, Carsten O., Hayashizaki, Yoshihide, Bertin, Nicolas, Forrest, Alistair R. R., FANTOM Consortium, Beckhouse, Anthony, Wells, Christine, Vijayan, Dipti, Mason, Elizabeth, Wolvetang, Ernst, Hitchens, Kelly, Le Cao, Kim-Anh, Nielsen, Lars, Fearnley, Liam and Kenna, Tony (2014). Interactive visualization and analysis of large-scale sequencing datasets using ZENBU. Nature Biotechnology, 32 (3), 217-219. doi: 10.1038/nbt.2840

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

Steen, Jennifer A., Bohlke, Nina, Vickers, Claudia E. and Nielsen, Lars K. (2014). 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. PLoS One, 9 (2) e88688, e88688.1-e88688.10. doi: 10.1371/journal.pone.0088688

A simple metric of promoter architecture robustly predicts expression breadth of human genes suggesting that most transcription factors are positive regulators

Hurst, Laurence D., Sachenkova, Oxana, Daub, Carsten, Forrest, Alistair R. R., the FANTOM consortium, Huminiecki, Lukasz, Beckhouse, Anthony, Wells, Christine, Vijayan, Dipti, Wolvetang, Ernst, Hitchens, Kelly, Kenna, Tony, Blumenthal, Antje, Briggs, James, Ovchinnikov, Dmitry, Fearnley, Liam, Le Cao, Kim-Anh, Mason, Elizabeth and Nielsen, Lars (2014). A simple metric of promoter architecture robustly predicts expression breadth of human genes suggesting that most transcription factors are positive regulators. Genome Biology, 15 (7) 413. doi: 10.1186/s13059-014-0413-3

A transient disruption of fibroblastic transcriptional regulatory network facilitates trans-differentiation

Tomaru, Yasuhiro, Hasegawa, Ryota, Suzuki, Takahiro, Sato, Taiji, Kubosaki, Atsutaka, Suzuki, Masanori, Kawaji, Hideya, Forrest, Alistair R. R., Hayashizaki, Yoshihide, FANTOM Consortium, Shin, Jay W., Suzuki, Harukazu, Beckhouse, Anthony, Wells, Christine, Vijayan, Dipti, Wolvetang, Ernst, Hitchens, Kelly, Fearnley, Liam, Kenna, Tony, Blumenthal, Antje, Briggs, James, Ovchinnikov, Dmitry, Le Cao, Kim-Anh, Mason, Elizabeth and Nielsen, Lars (2014). A transient disruption of fibroblastic transcriptional regulatory network facilitates trans-differentiation. Nucleic Acids Research, 42 (14), 8905-8913. doi: 10.1093/nar/gku567

Allantoin catabolism influences the production of antibiotics in Streptomyces coelicolor

Navone, Laura, Casati, Paula, Licona-Cassani, Cuauhtémoc, Marcellin, Esteban, Nielsen, Lars K., Rodriguez, Eduardo and Gramajo, Hugo (2014). Allantoin catabolism influences the production of antibiotics in Streptomyces coelicolor. Applied Microbiology and Biotechnology., 98 (1), 351-360. doi: 10.1007/s00253-013-5372-1

Mesencephalic dopaminergic neurons express a repertoire of olfactory receptors and respond to odorant-like molecules

Grison, Alice, Zucchelli, Silvia, Urzi, Alice, Zamparo, Ilaria, Lazarevic, Dejan, Pascarella, Giovanni, Roncaglia, Paola, Giorgetti, Alejandro, Garcia-Esparcia, Paula, Vlachouli, Christina, Simone, Roberto, Persichetti, Francesca, Forrest, Alistair R. R., Hayashizaki, Yoshihide, Carloni, Paolo, Ferrer, Isidro, Lodovichi, Claudia, Plessy, Charles, the FANTOM Consortium, Carninci, Piero, Gustincich, Stefano, Beckhouse, Anthony, Briggs, James, Hitchens, Kelly, Kenna, Tony, Ovchinnikov, Dmitry, Vijayan, Dipti, Wells, Christine, Wolvetang, Ernst ... Nielsen, Lars (2014). Mesencephalic dopaminergic neurons express a repertoire of olfactory receptors and respond to odorant-like molecules. BMC Genomics, 15 (1) 729. doi: 10.1186/1471-2164-15-729

Targeted sequencing for gene discovery and quantification using RNA CaptureSeq

Mercer, Tim R., Clark, Michael B., Crawford, Joanna, Brunck, Marion E., Gerhardt, Daniel J., Taft, Ryan J., Nielsen, Lars K., Dinger, Marcel E. and Mattick, John S. (2014). Targeted sequencing for gene discovery and quantification using RNA CaptureSeq. Nature Protocols, 9 (5), 989-1009. doi: 10.1038/nprot.2014.058

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

Matindoost, Leila, Hu, Hao, Chan, Leslie C. L., Nielsen, Lars K. and Reid, Steven (2014). The effect of cell line, phylogenetics and medium on baculovirus budded virus yield and quality. Archives of Virology, 159 (1), 91-102. doi: 10.1007/s00705-013-1789-1

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

Petrasovits, Lars A., McQualter, Richard B., Gebbie, Leigh K., Blackman, Deborah M., Nielsen, Lars K. and Brumbley, Stevens M. (2013). Chemical inhibition of acetyl coenzyme A carboxylase as a strategy to increase polyhydroxybutyrate yields in transgenic sugarcane. Plant Biotechnology Journal, 11 (9), 1146-1151. doi: 10.1111/pbi.12109

Genome scale transcriptomics of baculovirus-insect interactions

Nguyen,Quan, Nielsen, Lars K. and Reid, Steven (2013). Genome scale transcriptomics of baculovirus-insect interactions. Viruses, 5 (11), 2721-2747. doi: 10.3390/v5112721

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

Vickers C.E., Bydder S.F., Zhou Y. and Nielsen L.K. (2013). Dual gene expression cassette vectors with antibiotic selection markers for engineering in Saccharomyces cerevisiae. Microbial Cell Factories, 12 (96) 96, 96.1-96.11. doi: 10.1186/1475-2859-12-96

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

Marcellin, Esteban, Licona-Cassani, Cuauhtemoc, Mercer, Tim R., Palfreyman, Robin W. and Nielsen, Lars K. (2013). Re-annotation of the Saccharopolyspora erythraea genome using a systems biology approach. BMC Genomics, 14: Provisional (699) 699, 1-18. doi: 10.1186/1471-2164-14-699

Enhanced gametocyte formation in erythrocyte progenitor cells: A site-specific adaptation by Plasmodium falciparum

Peatey, Christopher L., Watson, Jolanta A., Trenholme, Katharine R., Brown, Christopher L., Nielson, Lars, Guenther, Marko, Timmins, Nicholas, Watson, Gregory S. and Gardiner, Donald L. (2013). Enhanced gametocyte formation in erythrocyte progenitor cells: A site-specific adaptation by Plasmodium falciparum. The Journal of Infectious Diseases, 208 (7), 1170-1174. doi: 10.1093/infdis/jit309

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

Nguyen, Quan, Chan, Leslie C. L., Nielsen, Lars K. and Reid, Steven (2013). Genome scale analysis of differential mRNA expression of Helicoverpa zea insect cells infected with a H. armigera baculovirus. Virology, 444 (1-2), 158-170. doi: 10.1016/j.virol.2013.06.004

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

Behrendorff, James B. Y. H., Vickers, Claudia E., Chrysanthopoulos, Panagiotis and Nielsen, Lars K. (2013). 2,2-Diphenyl-1-picrylhydrazyl as a screening tool for recombinant monoterpene biosynthesis. Microbial Cell Factories, 12 (76) 76, 1-11. doi: 10.1186/1475-2859-12-76

Extracting reaction networks from databases-opening Pandora's box

Fearnley, Liam, Davis, Melissa, Ragan, Mark A. and Nielsen, Lars K. (2013). Extracting reaction networks from databases-opening Pandora's box. Briefings in Bioinformatics, 15 (6), 973-983. doi: 10.1093/bib/bbt058

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

Mercer, Tim R., Edwards, Stacey L., Clark, Michael B., Neph, Shane J., Wang, Hao, Stergachis, Andrew B., John, Sam, Sandstrom, Richard, Li, Guoliang, Sandhu, Kuljeet S., Ruan, Yijun, Nielsen, Lars K., Mattick, John S. and Stamatoyannopoulos, John A. (2013). DNase I-hypersensitive exons colocalize with promoters and distal regulatory elements. Nature Genetics, 45 (8), 852-859. doi: 10.1038/ng.2677

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

Chen, Wendy Yiting, Marcellin, Esteban, Steen, Jennifer A. and Nielsen, Lars Keld (2013). The role of hyaluronic acid precursor concentrations in molecular weight control in Streptococcus zooepidemicus. Molecular Biotechnology, 56 (2), 147-156. doi: 10.1007/s12033-013-9690-4

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

Klein-Marcuschamer, Daniel, Turner, Christopher, Allen, Mark, Gray, Peter, Dietzgen, Ralf G., Gresshoff, Peter M., Hankamer, Ben, Heimann, Kirsten, Scott, Paul T., Stephens, Evan, Speight, Robert and Nielsen, Lars K. (2013). Technoeconomic analysis of renewable aviation fuel from microalgae, Pongamia pinnata, and sugarcane. Biofuels, Bioproducts and Biorefining, 7 (4), 416-428. doi: 10.1002/bbb.1404

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

Huynh, Hoai T., Tran, Trinh T. B., Chan, Leslie C. L., Nielsen, Lars K. and Reid, Steven (2013). Decline in baculovirus-expressed recombinant protein production with increasing cell density is strongly correlated to impairment of virus replication and mRNA expression. Applied Microbiology and Biotechnology, 97 (12), 5245-5257. doi: 10.1007/s00253-013-4835-8

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

Sabri, Suriana, Steen, Jennifer A., Bongers, Mareike, Nielsen, Lars K. and Vickers, Claudia E. (2013). 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. Microbial Cell Factories, 12 (1) 60, 60.1-60.14. doi: 10.1186/1475-2859-12-60

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

Brennan, Timothy C. R., Kroemer, Jens O. and Nielsen, Lars K. (2013). Physiological and transcriptional responses of saccharomyces cerevisiae to d-limonene show changes to the cell wall but not to the plasma membrane. Applied and Environmental Microbiology, 79 (12), 3590-3600. doi: 10.1128/AEM.00463-13

Plant genome-scale metabolic reconstruction and modelling

Dal'Molin, Cristiana Gomes de Oliveria and Nielsen, Lars Keld (2013). Plant genome-scale metabolic reconstruction and modelling. Current Opinion in Biotechnology, 24 (2), 271-277. doi: 10.1016/j.copbio.2012.08.007

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

Williams, Thomas C., Nielsen, Lars K. and Vickers, Claudia E. (2013). Engineered quorum-sensing using pheromone-mediated cell-to-cell communication in Saccharomyces cerevisiae. ACS Synthetic Biology, 2 (3), 136-149. doi: 10.1021/sb300110b

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

O'Neill, Brian P., Purnell, Matthew P., Kurniawan, Nyoman D., Cowin, Gary J., Galloway, Graham J., Nielsen, Lars K. and Brumbley, Stevens M. (2013). Non-invasive monitoring of sucrose mobilization from culm storage parenchyma by magnetic resonance spectroscopy. Bioscience, Biotechnology, and Biochemistry, 77 (3), 487-496. doi: 10.1271/bbb.120682

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

Martínez, Verónica S., Dietmair, Stefanie, Quek, Lake-Ee, Hodson, Mark P., Gray, Peter and Nielsen, Lars K. (2013). Flux balance analysis of CHO cells before and after a metabolic switch from lactate production to consumption. Biotechnology and Bioengineering, 110 (2), 660-666. doi: 10.1002/bit.24728

Molecular control of sucrose utilization in Escherichia coli W, an efficient sucrose-utilizing strain

Sabri, Suriana, Nielsen, Lars K. and Vickers, Claudia E. (2013). Molecular control of sucrose utilization in Escherichia coli W, an efficient sucrose-utilizing strain. Applied and Environmental Microbiology, 79 (2), 478-487. doi: 10.1128/AEM.02544-12

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

Marcellin, Esteban, Mercer, Tim R., Licona-Cassani, Cuauhtemoc, Palfreyman, Robin W., Dinger, Marcel E., Steen, Jennifer A., Mattick, John S. and Nielsen, Lars K. (2013). Saccharopolyspora erythraea's genome is organised in high-order transcriptional regions mediated by targeted degradation at the metabolic switch. BMC Genomics, 14 (1) 15, 15.1-15.9. doi: 10.1186/1471-2164-14-15

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

O'Neill, Brian P., Purnell, Matthew P., Nielsen, Lars K. and Brumbley, Stevens M. (2012). RNAi-mediated abrogation of trehalase expression does not affect trehalase activity in sugarcane. SpringerPlus, 1 (1) 74, 74:1-74:6. doi: 10.1186/2193-1801-1-74

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

Brennan, Timothy C. R., Turner, Christopher D., Kroemer, Jens O. and Nielsen, Lars K. (2012). Alleviating monoterpene toxicity using a two-phase extractive fermentation for the bioproduction of jet fuel mixtures in Saccharomyces cerevisiae. Biotechnology and Bioengineering, 109 (10), 2513-2522. doi: 10.1002/bit.24536

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

Licona-Cassani, Cuauhtemoc, Marcellin, Esteban, Quek, Lake-Ee, Jacob, Shana and Nielsen, Lars K. (2012). Reconstruction of the Saccharopolyspora erythraea genome-scale model and its use for enhancing erythromycin production. Antonie van Leeuwenhoek International Journal of General and Molecular Microbiology, 102 (3), 493-502. doi: 10.1007/s10482-012-9783-2

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

Bruschi, Michele, Boyes, Simon J., Sugiarto, Haryadi, Nielsen, Lars K. and Vickers, Claudia E. (2012). A transferable sucrose utilization approach for non-sucrose-utilizing Escherichia coli strains. Biotechnology Advances, 30 (5), 1001-1010. doi: 10.1016/j.biotechadv.2011.08.019

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

Utrilla, Jose, Licona-Cassani, Cuauhtemoc, Marcellin, Esteban, Gosset, Guillermo, Nielsen, Lars K. and Martinez, Alfredo (2012). Engineering and adaptive evolution of Escherichia coli for D-lactate fermentation reveals GatC as a xylose transporter. Metabolic Engineering, 14 (5), 469-476. doi: 10.1016/j.ymben.2012.07.007

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

Dietmair, Stefanie, Hodson, Mark P., Quek, Lake-Ee, Timmins, Nicholas E., Gray, Peter and Nielsen, Lars K. (2012). A multi-omics analysis of recombinant protein production in Hek293 cells. Plos One, 7 (8) e43394, e43394.1-e43394.15. doi: 10.1371/journal.pone.0043394

PATHLOGIC-S: A scalable boolean framework for modelling cellular signalling

Fearnley, Liam G. and Nielsen, Lars K. (2012). PATHLOGIC-S: A scalable boolean framework for modelling cellular signalling. PLoS One, 7 (8 Article. No.e41977) e41977, e41977. doi: 10.1371/journal.pone.0041977

Suspension culture titration: A simple method for measuring baculovirus titers

Matindoost, Leila, Chan, Leslie C. L., Qi, Ying Mei, Nielsen, Lars K. and Reid, Steven (2012). Suspension culture titration: A simple method for measuring baculovirus titers. Journal of Virological Methods, 183 (2), 201-209. doi: 10.1016/j.jviromet.2012.04.015

Enhanced polyhydroxybutyrate production in transgenic sugarcane

Petrasovits, Lars A., Zhao, Lihan, McQualter, Richard B., Snell, Kristi D., Somleva, Maria N., Patterson, Nii A., Nielsen, Lars K. and Brumbley, Stevens M (2012). Enhanced polyhydroxybutyrate production in transgenic sugarcane. Plant Biotechnology Journal, 10 (5), 569-578. doi: 10.1111/j.1467-7652.2012.00686.x

Metabolite profiling of CHO cells with different growth characteristics

Dietmair, Stefanie, Hodson, Mark P., Quek, Lake-Ee, Timmins, Nicholas E., Chrysanthopoulos, Panagiotis, Jacob, Shana S., Gray, Peter and Nielsen, Lars K. (2012). Metabolite profiling of CHO cells with different growth characteristics. Biotechnology and Bioengineering, 109 (6), 1404-1414. doi: 10.1002/bit.24496

Sucrose mobilisation in sugarcane stalk induced by heterotrophic axillary bud growth

O’Neill, Brian P., Purnell, Matthew P., Anderson, David J., Nielsen, Lars K. and Brumbley, Stevens M. (2012). Sucrose mobilisation in sugarcane stalk induced by heterotrophic axillary bud growth. Tropical Plant Biology, 5 (2), 173-182. doi: 10.1007/s12042-012-9097-6

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

Huynh, Hoai T., Chan, Leslie C. L., Tran, Trinh T. B., Nielsen, Lars K. and Reid, Steven (2012). 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. Biotechnology Progress, 28 (3), 788-802. doi: 10.1002/btpr.1529

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

Nguyen, Quan, Palfreyman, Robin W., Chan, Leslie C. L., Reid, Steven and Nielsen, Lars K. (2012). Transcriptome sequencing of and microarray development for a Helicoverpa zea cell line to investigate in vitro insect cell-baculovirus interactions. PLoS One, 7 (5) e36324, e36324.1-e36324.15. doi: 10.1371/journal.pone.0036324

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

Tran, Trinh T.B., Dietmair, Stefanie, Chan, Leslie C.L., Huynh, Hoai T., Nielsen, Lars K. and Reid, Steven (2012). Development of quenching and washing protocols for quantitative intracellular metabolite analysis of uninfected and baculovirus-infected insect cells. Methods, 56 (3), 396-407. doi: 10.1016/j.ymeth.2011.11.009

Bioreactor for blood product production

Doran, Michael R., Aird, Ian Alexander, Marturana, Flavia, Timmins, Nicholas, Atkinson, Kerry and Nielsen, Lars K. (2012). Bioreactor for blood product production. Cell Transplantation, 21 (6), 1235-1244. doi: 10.3727/096368911X627363

METABOLIC PATHWAY ENGINEERING FOR HYALURONIC ACID PRODUCTION

Marcellin, Esteban, Chen, Wendy Y. and Nielsen, Lars K. (2012). METABOLIC PATHWAY ENGINEERING FOR HYALURONIC ACID PRODUCTION. Carbohydrate-Modifying Biocatalysts, 571-584.

Mammalian cells as biopharmaceutical production hosts in the age of omics

Dietmair, Stefanie, Nielsen, Lars K. and Timmins, Nicholas E. (2012). Mammalian cells as biopharmaceutical production hosts in the age of omics. Biotechnology Journal, 7 (1), 75-89. doi: 10.1002/biot.201100369

AlgaGEM - A genome-scale metabolic reconstruction of Algae based on Chlamydomonas reinhardtii genome

Dal'Molin, Cristiana Gomes de Oliveira, Quek, Lake-Ee, Palfreyman, Robin W. and Nielsen, Lars K. (2011). AlgaGEM - A genome-scale metabolic reconstruction of Algae based on Chlamydomonas reinhardtii genome. BMC Genomics, 12 (S4), s5.1-s5.10. doi: 10.1186/1471-2164-12-S4-S5

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

Arifin, Yalun, Sabri, Suriana, Sugiarto, Haryadi, Krömer, Jens O., Vickers, Claudia E. and Nielsen, Lars K. (2011). Deletion of cscR in Escherichia coli W improves growth and poly-3-hydroxybutyrate (PHB) production from sucrose in fed batch culture. Journal of Biotechnology, 156 (4), 275-278. doi: 10.1016/j.jbiotec.2011.07.003

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

Timmins, N. E. and Nielsen, L. K. (2011). Manufactured RBC - Rivers of blood, or an oasis in the desert?. Biotechnology Advances, 29 (6), 661-666. doi: 10.1016/j.biotechadv.2011.05.002

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

Timmins, Nicholas E., Athanasas, Stavrosia, Gunther, Marko, Buntine, Penelope and Nielsen, Lars K. (2011). Ultra-high-yield manufacture of red blood cells from hematopoietic stem cells. Tissue Engineering Part C-Methods, 17 (11), 1131-1137. doi: 10.1089/ten.tec.2011.0207

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

Wicks, John Richard, Oldridge, Neil B., Nielsen, Lars K. and Vickers, Claudia E. (2011). HR index-a simple method for the prediction of oxygen uptake. Medicine and Science in Sports and Exercise, 43 (10), 2005-2012. doi: 10.1249/MSS.0b013e318217276e

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

Etebari, Kayvan, Palfreyman, Robin W., Schlipalius, David, Nielsen, Lars K., Glatz, Richard V. and Asgari, Sassan (2011). Deep sequencing-based transcriptome analysis of Plutella xylostella larvae parasitized by Diadegma semiclausum. BMC Genomics, 12 (1) 446, 446.1-446.18. doi: 10.1186/1471-2164-12-446

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

Kromer, Jens O., Dietmair, Stefanie, Jacob, Shana S. and Nielsen, Lars K. (2011). Quantification of L-alanyl-L-glutamine in mammalian cell culture broth: Evaluation of different detectors. Analytical Biochemistry, 416 (1), 129-131. doi: 10.1016/j.ab.2011.05.019

Synthesis of short-chain-length/medium-chain length polyhydroxyalkanoate (PHA) copolymers in peroxisomes of transgenic sugarcane plants

Anderson, David J., Gnanasambandam, Annathurai, Mills, Edwina, O'Shea, Michael G., Nielsen, Lars K. and Brumbley, Stevens M. (2011). Synthesis of short-chain-length/medium-chain length polyhydroxyalkanoate (PHA) copolymers in peroxisomes of transgenic sugarcane plants. Tropical Plant Biology, 4 (3-4), 170-184. doi: 10.1007/s12042-011-9080-7

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

Nguyen, Quan, Qi, Ying Mei, Wu, Yang, Chan, Leslie C. L., Nielsen, Lars K. and Reid, Steven (2011). In vitro production of Helicoverpa baculovirus biopesticides: Automated selection of insect cell clones for manufacturing and systems biology studies. Journal of Virological Methods, 175 (2), 197-205. doi: 10.1016/j.jviromet.2011.05.011

Engineering a mammalian super producer

Dietmair, Stefanie, Nielsen, Lars K. and Timmins, Nicholas E. (2011). Engineering a mammalian super producer. Journal of Chemical Technology and Biotechnology, 86 (7), 905-914. doi: 10.1002/jctb.2576

Metabolic and practical considerations on microbial electrosynthesis

Rabae, Korneel, Girguis, Peter and Nielsen, Lars K (2011). Metabolic and practical considerations on microbial electrosynthesis. Current Opinion in Biotechnology, 22 (3), 371-377. doi: 10.1016/j.copbio.2011.01.010

Metabolic engineering: From retrofitting to green field

Nielsen, Lars K. (2011). Metabolic engineering: From retrofitting to green field. Nature Chemical Biology, 7 (7), 408-409. doi: 10.1038/nchembio.601

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

Pedrini, Marcia R. S., Reid, Steven, Nielsen, Lars K. and Chan, Leslie C. L. (2011). Kinetic characterization of the group II helicoverpa armigera nucleopolyhedrovirus propagated in suspension cell cultures: Implications for development of a biopesticides production process. Biotechnology Progress, 27 (3), 614-624. doi: 10.1002/btpr.602

Altered fatty acid metabolism in long duration road transport: An NMR-based metabonomics study in sheep

Li, Juan, Wijffels, Gene, Yu, Yihua, Nielsen, Lars K., Niemeyer, Dominic O., Fisher, Andrew D., Ferguson, Drewe M. and Schirra, Horst Joachim (2011). Altered fatty acid metabolism in long duration road transport: An NMR-based metabonomics study in sheep. Journal of Proteome Research, 10 (3), 1073-1087. doi: 10.1021/pr100862t

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

Marturana, Flavia, Timmins, Nicholas E. and Nielsen, Lars K. (2011). Short-term exposure of umbilical cord blood CD34(+) cells to granulocyte-macrophage colony-stimulating factor early in culture improves ex vivo expansion of neutrophils. Cytotherapy, 13 (3), 366-377. doi: 10.3109/14653249.2010.518610

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

Archer, Colin T., Kim, Jihyun F., Jeong, Haeyoung, Park, Jin Hwan, Vickers, Claudia E., Lee, Sang Yup and Nielsen, Lars K. (2011). The genome sequence of E. coli W ATCC 9637: comparative genome analysis and an improved genome-scale reconstruction of E. coli. BMC Genomics, 12 (1) 9, 1-20. doi: 10.1186/1471-2164-12-9

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

Dal'Molin, Cristiana Gomes de, Quek, Lake-Ee, Palfreyman, Robin William, Brumbley, Stevens Michael and Nielsen, Lars Keld (2010). C4GEM, a genome-scale metabolic model to study C4 plant metabolism. Plant Physiology, 154 (4), 1871-1885. doi: 10.1104/pp.110.166488

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

Lee, Jeong Wook, Choi, Sol, Park, Jin Hwan, Vickers, Claudia E., Nielsen, Lars K. and Lee, Sang Yup (2010). Development of sucrose-utilizing Escherichia coli K-12 strain by cloning beta-fructofuranosidases and its application for L-threonine production. Applied Microbiology and Biotechnology, 88 (4), 905-913. doi: 10.1007/s00253-010-2825-7

The ascorbic acid paradox

Osiecki, Michael, Ghanavi, Parisa, Atkinson, Kerry, Nielsen, Lars K. and Doran, Michael R. (2010). The ascorbic acid paradox. Biochemical and Biophysical Research Communications, 400 (4), 466-470. doi: 10.1016/j.bbrc.2010.08.052

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

Dietmair, Stefanie, Timmins, Nicholas E., Gray, Peter P., Nielsen, Lars K. and Kromer, Jens O. (2010). Towards quantitative metabolomics of mammalian cells: Development of a metabolite extraction protocol. Analytical Biochemistry, 404 (2), 155-164. doi: 10.1016/j.ab.2010.04.031

Membrane bioreactors enhance microenvironmental conditioning and tissue development

Doran, Michael R., Markway, Brandon D., Clark, Angelique, Athanasas-Platsis, Stavrosia, Brooke, Gary, Atkinson, Kerry, Nielsen, Lars K. and Cooper-White, Justin J. (2010). Membrane bioreactors enhance microenvironmental conditioning and tissue development. Tissue Engineering - Part C: Methods, 16 (3), 407-415. doi: 10.1089/ten.tec.2009.0367

Metabolic flux analysis in mammalian cell culture

Quek, Lake-Ee, Dietmair, Stefanie, Kromer, Jens O. and Nielsen, Lars K. (2010). Metabolic flux analysis in mammalian cell culture. Metabolic Engineering, 12 (2), 161-171. doi: 10.1016/j.ymben.2009.09.002

Tissue transplantation by stealth — Coherent alginate microcapsules for immunoisolation

Leung, Andy, Nielsen, Lars K., Trau, Matt and Timmins, Nicholas E. (2010). Tissue transplantation by stealth — Coherent alginate microcapsules for immunoisolation. Biochemical Engineering Journal, 48 (3), 337-347. doi: 10.1016/j.bej.2009.10.007

AraGEM, a Genome-scale reconstruction of the primary metabolic network in arabidopsis

Dal'Molin, C.G.D., Quek, L.E., Palfreyman, R.W., Brumbley, S.M. and Nielsen, L.K. (2010). AraGEM, a Genome-scale reconstruction of the primary metabolic network in arabidopsis. Plant Physiology, 152 (2), 579-589. doi: 10.1104/pp.109.148817

Production of bacteriocins by Streptococcus bovis strains from Australian ruminants

Joachimsthal, E. L., Reeves, R. K. H., Hung, J., Nielsen, L. K., Ouwerkerk, D., Klieve, A. V. and Vickers, C. E. (2010). Production of bacteriocins by Streptococcus bovis strains from Australian ruminants. Journal of Applied Microbiology, 108 (2), 428-436. doi: 10.1111/j.1365-2672.2009.04432.x

Metabolic Engineering of Mammalian Cells

Quek, Lake-Ee and Nielsen, Lars Keld (2010). Metabolic Engineering of Mammalian Cells. Metabolic Pathway Engineering Handbook: Fundamentals

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

Marcellin, Esteban, Chen, Wendy Y. and Nielsen, Lars K. (2010). Understanding plasmid effect on hyaluronic acid molecular weight produced by Streptococcus equi subsp. zooepidemicus. Metabolic Engineering, 12 (1), 62-69. doi: 10.1016/j.ymben.2009.09.001

13C-fluxomics: A tool for measuring metabolic phenotypes

Krömer, Jens, Quek, Lake-Ee and Nielsen, Lars (2009). 13C-fluxomics: A tool for measuring metabolic phenotypes. Australian Biochemist, 40 (3), 17-20.

Clinical Scale Ex Vivo Manufacture of Neutrophils From Hematopoietic Progenitor Cells

Timmins, N.E., Palfreyman, E., Marturana, F., Dietmair, S., Luikenga, S., Lopez, G., Fung, Y.L., Minchinton, R. and Nielsen, L.K. (2009). Clinical Scale Ex Vivo Manufacture of Neutrophils From Hematopoietic Progenitor Cells. Biotechnology and Bioengineering, 104 (4), 832-840. doi: 10.1002/bit.22433

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

Doran, M.R., Markway, B.D., Aird, I.A., Rowlands, A.S., George, P.A., Nielsen, L.K. and Cooper-White, J.J. (2009). Surface-bound stem cell factor and the promotion of hematopoietic cell expansion. BIOMATERIALS, 30 (25), 4047-4052. doi: 10.1016/j.biomaterials.2009.04.043

Hyaluronan Molecular Weight Is Controlled by UDP-N-acetylglucosamine Concentration in Streptococcus zooepidemicus

Chen, Wendy Yiting, Marcellin, Esteban, Hung, Jacky and Nielsen, Lars Keld (2009). Hyaluronan Molecular Weight Is Controlled by UDP-N-acetylglucosamine Concentration in Streptococcus zooepidemicus. Journal of Biological Chemistry, 284 (27), 18007-18014. doi: 10.1074/jbc.M109.011999

Blood cell manufacture: current methods and future challenges

Timmins, N.E. and Nielsen, L.K. (2009). Blood cell manufacture: current methods and future challenges. Trends in Biotechnology, 27 (7), 415-422. doi: 10.1016/j.tibtech.2009.03.008

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

Quek, Lake-Ee, Wittmann, Christoph, Nielsen, Lars K. and Kromer, Jens O. (2009). OpenFLUX: Efficient modelling software for 13C-based metabolic flux analysis. Microbial Cell Factories, 8 (1) 25, 25.1-25.15. doi: 10.1186/1475-2859-8-25

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

Marcellin, Esteban, Gruber, Christian W., Archer, Colin, Craik, David J. and Nielsen, Lars K. (2009). Proteome analysis of the hyaluronic acid-producing bacterium, Streptococcus zooepidemicus. Proteome Science, 7 (13) 13, 1-13. doi: 10.1186/1477-5956-7-13

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

Leung, Andy, Trau, Matt and Nielsen, Lars Keld (2009). Assembly of multilayer PSS/PAH membrane on coherent alginate/PLO microcapsule for long-term graft transplantation. Journal of Biomedical Materials Research Part A, 88A (1), 226-237. doi: 10.1002/jbm.a.31891

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

Marcellin, Esteban, Nielsen, Lars K., Abeydeera, Peter and Kromer, Jens O. (2009). Quantitative analysis of intracellular sugar phosphates and sugar nucleotides in encapsulated streptococci using HPAEC-PAD. Biotechnology Journal, 4 (1), 58-63. doi: 10.1002/biot.200800197

An environmental life cycle assessment comparing Australian sugarcane with US corn and UK sugar beet as producers of sugars for fermentation

Renouf, M. A., Wegener, M. K. and Nielsen, L. K. (2008). An environmental life cycle assessment comparing Australian sugarcane with US corn and UK sugar beet as producers of sugars for fermentation. Biomass and Bioenergy, 32 (12), 1144-1155. doi: 10.1016/j.biombioe.2008.02.012

Evolution of Hyaluronic Acid Synthesis (has) Operon in Streptococcus zooepidemicus and other Pathogenic Streptococci

Lars M. Blank, Philip Hugenholtz and Nielsen, Lars K. (2008). Evolution of Hyaluronic Acid Synthesis (has) Operon in Streptococcus zooepidemicus and other Pathogenic Streptococci. Journal of Molecular Evolution, 67 (1), 13-22. doi: 10.1007/s00239-008-9117-1

Fermentative Butanol Production by Clostridia

Sang Up Lee, Jin Hwan Park, Seh Hee Jang, Nielsen, Lars K., Jaehyun Kim and Kwang S.Jung (2008). Fermentative Butanol Production by Clostridia. Biotechnology and Bioengineering, 101 (2), 209-228. doi: 10.1002/bit.22003

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

Song, Hyohak, Kim, Tae Yong, Choi, Bo-Kyeong, Choi, Seong Jun, Nielsen, Lars K., Chang, Ho Nam and Lee, Sang Yup (2008). Development of chemically defined medium for Mannheimia succiniciproducens based on its genome sequence. Applied Microbiology and Biotechnology., 79 (2), 263-272. doi: 10.1007/s00253-008-1425-2

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

Koebmann, Brian, Blank, Lars Mathias, Solem, Christian, Petranovic, Dina, Nielsen, Lars K. and Jensen, Peter Ruhdal (2008). Increased biomass yield of Lactococcus lactis during energetically limited growth and respiratory conditions. Biotechnology & Applied Biochemistry, 50 (Pt. 1), 25-33. doi: 10.1042/BA20070132

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

Michael Hines, Nielsen, Lars K. and Cooper-White, Justin J. (2008). The hematopoietic stem cell niche: what are we trying to replicate?. Journal of Chemical Technology and Biotechnology, 83 (4), 421-443. doi: 10.1002/jctb.1856

Lactic acid enrichment with inorganic nanofiltration and molecular sieving membranes by pervaporation

Duke, Mikel C., Lim, Agnes, Castro da Luz, Sheila and Nielsen, Lars (2008). Lactic acid enrichment with inorganic nanofiltration and molecular sieving membranes by pervaporation. Food And Bioproducts Processing, 86 (4), 290-295. doi: 10.1016/j.fbp.2008.01.005

On the reconstruction of the Mus musculus genome-scale metabolic network model

Lake-ee Quek and Nielsen, Lars K. (2008). On the reconstruction of the Mus musculus genome-scale metabolic network model. Genome Informatics, 21, 89-100. doi: 10.1142/9781848163324_0008

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

Leung, A.H.M., Lawrie, G.A., Nielsen, L.K. and Trau, M. (2008). Synthesis and characterization of alginate/poly-L-ornithine/alginate microcapsules for local immunosuppression. Journal of Microencapsulation, 25 (6), 387-398. doi: 10.1080/02652040802008857

The N-terminal presequence from F1-ATPase β-subunit of Nicotiana plumbaginifolia efficiently targets green fluorescent fusion protein to the mitochondria in diverse commercial crops

Gnanasambandam, Annathurai, Anderson, David J., Purnell, Matthew P., Nielsen, Lars K. and Brumbley, Stevens M. (2008). The N-terminal presequence from F1-ATPase β-subunit of Nicotiana plumbaginifolia efficiently targets green fluorescent fusion protein to the mitochondria in diverse commercial crops. Functional Plant Biology, 35 (2), 166-170. doi: 10.1071/FP07277

Generation of multicellular tumor spheroids by the hanging-drop method

Timmins, Nicholas E and Nielsen, Lars K (2007). Generation of multicellular tumor spheroids by the hanging-drop method. Methods in molecular medicine, 140, 141-151.

Developing the sugarcane biofactory for high-value biomaterials

Brumbley, S. M., Purnell, M. P., Petrasovits, L. A., Nielsen, L. K. and Twine, P. H. (2007). Developing the sugarcane biofactory for high-value biomaterials. International Sugar Journal, 109 (1297), 5-15.

Polyhydroxyalkanoate production in sugarcane - recognizing temporospatial complexity

Nielsen, L (2007). Polyhydroxyalkanoate production in sugarcane - recognizing temporospatial complexity. Journal of Biotechnology, 131 (2), S28-S29. doi: 10.1016/j.jbiotec.2007.07.047

Production of polyhydroxybutyrate in sugarcane

Petrasovits, L. A., Purnell, M. P., Nielsen, L. K. and Brumbley, S. M. (2007). Production of polyhydroxybutyrate in sugarcane. Plant Biotechnology Journal, 5 (1), 162-172. doi: 10.1111/j.1467-7652.2006.00229.x

Spatio-temporal characterization of polyhydroxybutyrate accumulation in sugarcane

Purnell, Matthew P., Petrasovits, Lars A., Nielsen, Lars K. and Brumbley, Stevens M. (2007). Spatio-temporal characterization of polyhydroxybutyrate accumulation in sugarcane. Plant Biotechnology Journal, 5 (1), 173-184. doi: 10.1111/j.1467-7652.2006.00230.x

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

Pedrini, Márcia R. S., Christian, Peter, Nielsen, Lars K., Reid, Steven and Chan, Leslie C. L. (2006). Importance of virus–medium interactions on the biological activity of wild-type Heliothine nucleopolyhedroviruses propagated via suspension insect cell cultures. Journal of Virological Methods, 136 (1-2), 267-272. doi: 10.1016/j.jviromet.2006.04.007

The high-carb economy

Brumbley, S.M., Twine, Peter and Nielsen, Lars (2006). The high-carb economy. Australasian Science, 27 (6), 19-22.

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

Dinnis, D. M., Stansfield, S. H., Schlatter, S., Smales, C. M., Alete, D., Birch, J. R., Racher, A. J., Marshal, C. T., Nielsen, L. K. and James, D. C. (2006). Functional proteomic analysis of GS-NS0 murine myeloma cell lines with varying recombinant monoclonal antibody production rate. Biotechnology And Bioengineering, 94 (5), 830-841. doi: 10.1002/bit.20899

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

Peng, J. C., Abu Bakar, S., Richardson, M. M., Jonsson, J. J., Frazer, I. H., Nielsen, L. K., Morahan, G. and Thomas, R. (2006). IL10 and IL12B polymorphisms each influence IL-12p70 secretion by dendritic cells in response to LPS. Immunology And Cell Biology, 84 (2), 227-232. doi: 10.1111/j.1440-1711.2006.01419.x

In vitro production of Helicoverpa armigera single-nucleocapsid nucleopolyhedrovirus

Da Silva Pedrini, M. R., Chan, L. C. L., Nielsen, L. K. and Reid, S. (2006). In vitro production of Helicoverpa armigera single-nucleocapsid nucleopolyhedrovirus. Brazilian Archives of Biology and Technology: an international journal, 49 (SPEC. ISS.), 35-41.

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

Peng, Judy C., Hyde, Claire, Pai, Saparna, O'Sullivan, Brendan J., Nielsen, Lars K. and Thomas, Ranjeny (2006). Monocyte-derived DC primed with TLR agonists secrete IL-12p70 in a CD40-dependent manner under hyperthermic conditions. Journal of Immunotherapy, 29 (6), 606-615. doi: 10.1097/01.cji.0000211308.82997.4e

Generation and maturation of dendritic cells for clinical application under serum-free conditions

Peng, Judy C., Thomas, Ranjeny and Nielsen, Lars K. (2005). Generation and maturation of dendritic cells for clinical application under serum-free conditions. Journal of Immunotherapy, 28 (6), 599-609. doi: 10.1097/01.cji.0000175491.21099.04

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

Blank, Lars M., McLaughlin, Richard L. and Nielsen, Lars K. (2005). Stable production of hyaluronic acid in Streptococcus zooppidemicus chemostats operated at high dilution rate. Biotechnology And Bioengineering, 90 (6), 685-693. doi: 10.1002/bit.20466

A physiological product-release model for baculovirus infected insect cells

Haas, Richard and Nielsen, Lars K. (2005). A physiological product-release model for baculovirus infected insect cells. Biotechnology And Bioengineering, 91 (6), 768-772. doi: 10.1002/bit.20565

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

Leung, A, Ramaswamy, Y, Munro, P, Lawrie, G, Nielsen, L and Trau, M (2005). Emulsion strategies in the microencapsulation of cells: Pathways to thin coherent membranes. Biotechnology And Bioengineering, 92 (1), 45-53. doi: 10.1002/bit.20597

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

Timmins, N. E., Harding, F. J., Smart, C. E., Brown, M. A. and Nielsen, L. K. (2005). Method for the generation and cultivation of functional three-dimensional mammary constructs without exogenous extracellular matrix. Cell And Tissue Research, 320 (1), 207-210. doi: 10.1007/s00441-004-1064-6

Microbial hyaluronic acid production

Chong, B. F., Blank, L., McLaughlin, R. L. and Nielsen, L. K. (2005). Microbial hyaluronic acid production. Applied Microbiology And Biotechnology, 66 (4), 341-351. doi: 10.1007/s00253-004-1774-4

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

Sheikh, K. M., Forster, J. and Nielsen, L. K. (2005). Modeling hybridoma cell metabolism using a generic genome-scale metabolic model of Mus musculus. Biotechnology Progress, 21 (1), 112-121. doi: 10.1021/bp0498138

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

Pedrini, Marcia R. S., Nielsen, Lars K., Reid, Steven and Chan, Leslie C. L. (2005). 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. In Vitro Cellular & Developmental Biology - Animal, 41 (8-9), 289-297. doi: 10.1290/0503019R.1

Identification of three gene candidates for multicellular resistance in colon carcinoma

Timmins, N. E., Maguire, T. L., Grimmond, S. M. and Nielsen, L. K. (2004). Identification of three gene candidates for multicellular resistance in colon carcinoma. Cytotechnology, 46 (1), 9-18. doi: 10.1007/s10616-005-1476-5

Hanging-drop multicellular spheriods as a model of tumour angiogenesis

Timmins, N. E., Dietmair, S. and Nielsen, L. K. (2004). Hanging-drop multicellular spheriods as a model of tumour angiogenesis. Angiogenesis, 7 (2), 97-103. doi: 10.1007/s10456-004-8911-7

Design of artificial myocardial microtissues

Kelm, J. M., Ehler, E., Nielsen, L. K., Schlatter, S., Perriard, J. C. and Fussenegger, M. (2004). Design of artificial myocardial microtissues. Tissue Engineering, 10 (1-2), 201-214. doi: 10.1089/107632704322791853

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

Kelm, Jens M., Timmins, Nicholas E., Brown, Catherine J., Fussenegger, Martin and Nielsen, Lars K. (2003). Method for generation of homogeneous multicellular tumor spheroids applicable to a wide variety of cell types. Biotechnology And Bioengineering, 83 (2), 173-180. doi: 10.1002/bit.10655

Aerobic cultivation of Streptococcus zooepidemicus and the role of NADH oxidase

Fong Chong, B. and Nielsen, L. K. (2003). Aerobic cultivation of Streptococcus zooepidemicus and the role of NADH oxidase. Biochemical Engineering Journal, 16 (2), 153-162. doi: 10.1016/S1369-703X(03)00031-7

Amplifying the cellular reduction potential of Streptococcus zooepidemicus

Chong, B. F. and Nielsen, L. K. (2003). Amplifying the cellular reduction potential of Streptococcus zooepidemicus. Journal of Biotechnology, 100 (1), 33-41. doi: 10.1016/S0168-1656(02)00239-0

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

Croll, T., Munro, P., Winzor, D. J., Trau, M. and Nielsen, L. K. (2003). Analysis of the phase behavior of the aqueous poly(ethylene glycol)-Ficoll system. Biotechnology Progress, 19 (4), 1269-1273. doi: 10.1021/bp025711a

Quantitative prediction of phase diagrams for polymer partitioning in aqueous two-phase systems

Croll, T., Munro, P. D., Winzor, D. J., Trau, M. and Nielsen, L. K. (2003). Quantitative prediction of phase diagrams for polymer partitioning in aqueous two-phase systems. Journal of Polymer Science Part B-polymer Physics, 41 (5), 437-443. doi: 10.1002/polb.10402

Sensitivity of Helicoverpa armigera nucleopolyhedrovirus polyhedra to sodium dodecyl sulfate

Lua, L. H. L., Nielsen, L. K. and Reid, S. (2003). Sensitivity of Helicoverpa armigera nucleopolyhedrovirus polyhedra to sodium dodecyl sulfate. Biological Control, 26 (1), 57-67. doi: 10.1016/S1049-9644(02)00116-0

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

Rosinski, Matthew, Reid, Steven and Nielsen, Lars Keld (2002). Kinetics of baculovirus replication and release using real-time quantitative polymerase chain reaction. Biotechnology And Bioengineering, 77 (4), 476-480. doi: 10.1002/bit.10126

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

Blank, L. M., Koebmann, B. J., Michelsen, O., Nielsen, L. K. and Jensen, P. R. (2001). Hemin reconstitutes proton extrusion in an H+-ATPase-negative mutant of Lactococcus lactis. Journal of Bacteriology, 183 (22), 6707-6709. doi: 10.1128/JB.183.22.6707-6709.2001

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

Rosinski, M, Reid, S and Nielsen, LK (2000). Osmolarity effects on observed insect cell size after baculovirus infection are avoided using growth medium for sample dilution. Biotechnology Progress, 16 (5), 782-785. doi: 10.1021/bp000083n

Stoichiometric modeling of Clostridium acetobutylicum fermentations with non-linear constraints

Desai, RP, Nielsen, LK and Papoutsakis, ET (1999). Stoichiometric modeling of Clostridium acetobutylicum fermentations with non-linear constraints. Journal of Biotechnology, 71 (1-3), 191-205. doi: 10.1016/S0168-1656(99)00022-X

Bioreactors for haematopoietic cell culture

Nielsen L.K. (1999). Bioreactors for haematopoietic cell culture. Annual Review of Biomedical Engineering (1), 129-152.

Bioreactors for hematopoietic cell culture

Nielsen, LK (1999). Bioreactors for hematopoietic cell culture. Annual Review Biomedical Engineering, 1 (1), 129-152. doi: 10.1146/annurev.bioeng.1.1.129

Characterization of hematopoietic cell expansion, oxygen uptake, and glycolysis in a controlled, stirred-tank bioreactor system

Collins, PC, Nielsen, LK, Patel, SD, Papoutsakis, ET and Miller, WM (1998). Characterization of hematopoietic cell expansion, oxygen uptake, and glycolysis in a controlled, stirred-tank bioreactor system. Biotechnology Progress, 14 (3), 466-472. doi: 10.1021/bp980032e

Modeling ex vivo hematopoiesis using chemical engineering metaphors

Nielsen, LK, Papoutsakis, ET and Miller, WM (1998). Modeling ex vivo hematopoiesis using chemical engineering metaphors. Chemical Engineering Science, 53 (10), 1913-1925. doi: 10.1016/S0009-2509(98)00039-6

Population balance model of in vivo neutrophil formation following bone marrow rescue therapy

Nielsen, LK, Bender, JG, Miller, WM and Papoutsakis, ET (1998). Population balance model of in vivo neutrophil formation following bone marrow rescue therapy. Cytotechnology, 28 (1-3), 157-162. doi: 10.1023/A:1008098118491

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

Collins, PC, Nielsen, LK, Wong, CK, Papoutsakis, ET and Miller, WM (1997). Real-time method for determining the colony-forming cell content of human hematopoietic cell cultures. Biotechnology and Bioengineering, 55 (4), 693-700. doi: 10.1002/(SICI)1097-0290(19970820)55:4<693::AID-BIT11>3.0.CO;2-D

Limiting dilution assay: Single or multiple dilution protocol?

Nielsen, LK (1997). Limiting dilution assay: Single or multiple dilution protocol?. British Journal of Haematology, 97 (1), 250-250.

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

Nielsen, LK, Reid, S and Greenfield, PF (1997). Cell cycle model to describe animal cell size variation and lag between cell number and biomass dynamics. Biotechnology And Bioengineering, 56 (4), 372-379. doi: 10.1002/(SICI)1097-0290(19971120)56:4<372::AID-BIT3>3.0.CO;2-L

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

Wong, KTK, Peter, CH, Greenfield, PF, Reid, S and Nielsen, LK (1996). Low multiplicity infection of insect cells with a recombinant baculovirus: The cell yield concept. Biotechnology and Bioengineering, 49 (6), 659-666. doi: 10.1002/(SICI)1097-0290(19960320)49:6<659::AID-BIT7>3.0.CO;2-N

Modelling baculovirus infection of insect cells in culture

Power, JF and Nielsen, LK (1996). Modelling baculovirus infection of insect cells in culture. Cytotechnology, 20 (1-3), 209-219. doi: 10.1007/BF00350401

The kinetics of baculovirus adsorption to insect cells in suspension culture

Power, JF, Reid, S, Greenfield, PF and Nielsen, LK (1996). The kinetics of baculovirus adsorption to insect cells in suspension culture. Cytotechnology, 21 (2), 155-163. doi: 10.1007/BF02215665

Modeling and Optimization of the Baculovirus Expression Vector System in Batch Suspension-Culture

Power, JF, Reid, S, Radford, KM, Greenfield, PF and Nielsen, LK (1994). Modeling and Optimization of the Baculovirus Expression Vector System in Batch Suspension-Culture. Biotechnology and Bioengineering, 44 (6), 710-719. doi: 10.1002/bit.260440607

Ammonia Inhibition Hybridomas Propagated in Batch, Fed-Batch, and Continuous-Culture

Newland, M, Kamal, MN, Greenfield, PF and Nielsen, LK (1994). Ammonia Inhibition Hybridomas Propagated in Batch, Fed-Batch, and Continuous-Culture. Biotechnology and Bioengineering, 43 (5), 434-438. doi: 10.1002/bit.260430512

Relationship Between Oxygen-Uptake Rate and Time of Infection of Sf9 Insect Cells Infected with a Recombinant Baculovirus

Wong, Tkk, Nielsen, LK, Greenfield, PF and Reid, S (1994). Relationship Between Oxygen-Uptake Rate and Time of Infection of Sf9 Insect Cells Infected with a Recombinant Baculovirus. Cytotechnology, 15 (1-3), 157-167. doi: 10.1007/BF00762390

Accuracy of the End-Point Assay for Virus Titration

Nielsen, LK, Smyth, GK and Greenfield, PF (1992). Accuracy of the End-Point Assay for Virus Titration. Cytotechnology, 8 (3), 231-236. doi: 10.1007/BF02522040

Avoiding Rapid Growth At High Cell Densities - a Potentially Important Optimization Criterion for Hybridoma Cultures

Nielsen, LK, Niloperbowo, W, Reid, S and Greenfield, PF (1992). Avoiding Rapid Growth At High Cell Densities - a Potentially Important Optimization Criterion for Hybridoma Cultures. Cytotechnology, 9 (1-3), 21-27. doi: 10.1007/BF02521728

Modeling the Growth and Protein-Production by Insect Cells Following Infection by a Recombinant Baculovirus in Suspension-Culture

Power, J, Greenfield, PF, Nielsen, L and Reid, S (1992). Modeling the Growth and Protein-Production by Insect Cells Following Infection by a Recombinant Baculovirus in Suspension-Culture. Cytotechnology, 9 (1-3), 149-155. doi: 10.1007/BF02521742

Hemacytometer Cell Count Distributions - Implications of Non-Poisson Behavior

Nielsen, LK, Smyth, GK and Greenfield, PF (1991). Hemacytometer Cell Count Distributions - Implications of Non-Poisson Behavior. Biotechnology Progress, 7 (6), 560-563. doi: 10.1021/bp00012a600

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

Hudson, J., Mills, R., Titmarsh, D., Koenig, X., Parker, B., Ryall, J., Quaife-Ryan, G., Voges, H., Hodson, M., Ferguson, C., Drowley, L., Plowright, A., Wang, Q., Gregorevic, P., Xin, M., Thomas, W., Parton, R., Nielsen, L., Launikonis, B., James, D., Elliott, D. and Porrello, E. (2017). Functional screening in human cardiac organoids reveals a metabolic mechanism for cardiomyocyte cell cycle arrest. Abstracts for the 65th Cardiac Society of Australia and New Zealand Annual Scientific Meeting and the International Society for Heart Research Australasian Section Annual Scientific Meeting, Perth, Australia, 10 - 13 August 2017. Chatswood, NSW, Australia: Elsevier. doi: 10.1016/j.hlc.2017.06.375

1,5-Anhydroglucitol, the most discriminatory metabolomic marker measured by Gas Chromatography-Mass Spectrometry in adolescents with Type 1 Diabetes compared to control subjects - High correlation with Glycomark assay

Conwell, Louise S., Hodson, Mark P., Chrysanthopoulos, Panagiotis K., Greer, Ristan M., Nielsen, Lars K., Cardinal, John W., Sanders, L., Gous, R. and Baskerville, Tracey (2015). 1,5-Anhydroglucitol, the most discriminatory metabolomic marker measured by Gas Chromatography-Mass Spectrometry in adolescents with Type 1 Diabetes compared to control subjects - High correlation with Glycomark assay. Children's Health Queensland Research Conference, unknown, unknown.

1,5-Anhydroglucitol, the most discriminatory metabolomic marker measured by Gas Chromatography-Mass Spectrometry in adolescents with Type 1 Diabetes compared to control subjects - high correlation with Glycomark assay

Conwell, Louise S., Hodson, Mark P., Chrysanthopoulos, Panagiotis K., Greer, Ristan M., Nielsen, Lars K., Cardinal, John W., Sanders, L., Gous, R. and Baskerville, Tracey (2015). 1,5-Anhydroglucitol, the most discriminatory metabolomic marker measured by Gas Chromatography-Mass Spectrometry in adolescents with Type 1 Diabetes compared to control subjects - high correlation with Glycomark assay. International Society of Paediatric and Adolescent Diabetes / Australasian Paediatric Endocrine Group Annual Scientific Meeting, Brisbane, QLD, Australia, October 2015.

A pan-genomic guided metabolic reconstruction and omics integration to understand Propionibacterium metabolism

McCubbins, Tim, Nielsen, Lars. K. and Marcellin, Esteban (2015). A pan-genomic guided metabolic reconstruction and omics integration to understand Propionibacterium metabolism. 4th Conference on Constraint-Based Reconstruction and Analysis (COBRA 2015), Heidelberg, Germany, 16 - 18 September 2015.

A systems biology approach for the characterization of tetanospasmin production for vaccine production in tetanus vaccines

Licona-Cassani, Cuauhtemoc, Steen, Jennifer A., Moonen, Glenn, Moutafis, George, Power, John, Nielsen, Lars Keld and Marcellin, Esteban (2015). A systems biology approach for the characterization of tetanospasmin production for vaccine production in tetanus vaccines. Clostpath 9, Freiburg, Germany, 7 - 11 September 2015.

A systems platform for the characterization and repurposing of Clostridium autoethanogenum, a model, acetogenic, gas-fermenting microbe

Marcellin, Esteban, Behrendorff, James, Brown, Steve, Dassanayake, Asela, Walker, David, DeTissera, Sashini, Segovia, Simon, Palfreyman, Robin W., Daniell, James, Reynoso, Vini R, Licona-Cassani, Cuauhtemoc, Quek, Lake-ee, Speight, Robert, Hodson, Mark P., Nielsen, Lars K., Mitchell, Wayne P., Köpke, Michael and Simpson, Sean D. (2015). A systems platform for the characterization and repurposing of Clostridium autoethanogenum, a model, acetogenic, gas-fermenting microbe. International Conference on Systems Biology , ICSB, Singapore, Singapore, 23-26 November 2015.

Multi-omics approach for comparative studies of monoclonal antibody producing CHO cells

Orellana, Camila A., Marcellin, Esteban, Munro, Trent, Gary, Peter P. and Nielsen, Lars K. (2015). Multi-omics approach for comparative studies of monoclonal antibody producing CHO cells. European Society for Animal Cell Technology (ESACT) Meeting, Barcelona, Spain, 31 May - 3 June 2015. London, United Kingdom: BioMed Central. doi: 10.1186/1753-6561-9-S9-O8

Opening pandora’s box

Marcellin, Esteban and Nielsen, Lars Keld (2015). Opening pandora’s box. Biochemical and Molecular Engineering XIX, Puerto Vallarta, Mexico, 12-16 July 2015.

Developing an integrated systems and synthetic biology platform for gas fermentation

Marcellin, Esteban, Segovia, Simon, De Tissera, Sashini, Mitchell, Wayne, Kopke, Michael and Nielsen, Lars K. (2014). Developing an integrated systems and synthetic biology platform for gas fermentation. Metabolic Engineering X, Vancouver, BC, Canada, 15-19 June 2014.

Towards a large integrated model of signal transduction and gene regulation events in mammalian cells

Fearnley, Liam G., Ragan, Mark A. and Nielsen, Lars K. (2014). Towards a large integrated model of signal transduction and gene regulation events in mammalian cells. BIOINFORMATICS 2014: 5th International Conference on Bioinformatics Models, Methods and Algorithms, Angers, Loire Valley, France, 3-6 March 2014. London, UK: SciTePress. doi: 10.5220/0004739601170122

A superior catalyst for polyhydroxybutyrate production in sugarcane

McQualter, R. B., Petrasovits, L. A., Gebbie, L. K., Hodson, M. P., Plan, M. R., Blackman D. M., Dal'Molin, C., Brumbley, S. M. and Nielsen, L. K. (2013). A superior catalyst for polyhydroxybutyrate production in sugarcane. TABBS 2013: The Australasian Bioenergy and Bioproducts Symposium, Brisbane, QLD, Australia, 25 October, 2013.

Production of a biodegradable plastic in the C4 biomass crop sugarcane

McQualter, R. B., Petrasovits, L. A., Gebbie, L. K., Hodson, M. P., Plan, M. R., Blackman, D. M., Dal'Molin, C., Brumbley, S. M. and Nielsen, L. K. (2013). Production of a biodegradable plastic in the C4 biomass crop sugarcane. AusBiotech 2013. Agriculture and Food Biotechnology Symposium, Brisbane, QLD, Australia, 1 November, 2013.

Understanding metabolic control of carbon flux through the MEP pathway: a systems and synthetic biology approach

Vickers, Claudia E., Sabri, Suriana, Bongers, Mareike and Nielsen, Lars (2013). Understanding metabolic control of carbon flux through the MEP pathway: a systems and synthetic biology approach. TERPNET 2013: 11th International Meeting on Biosynthesis, Function and Biotechnology of Isoprenoids in Terrestrial and Marine Organisms, Kolymvari, Crete, Greece, 1-5 June, 2013. Thessaloniki, Greece: Department of Pharmaceutical Science, Aristotle University of Thessaloniki.

Dynamic analysis of Saccharopolyspora erythraea life cycle in bioreactors; a systems approach

Licona Cassani, Cuauthemoc, Marcellin Saldana, Esteban Stefane and Nielsen, Lars K. (2012). Dynamic analysis of Saccharopolyspora erythraea life cycle in bioreactors; a systems approach. Actinobacteria within soil, Munster, Germany, 25-28 October 2012.

Large Scale Ex Vivo Manufacture of Blood Cells

Timmins, Nicholas E. and Nielsen, Lars K. (2012). Large Scale Ex Vivo Manufacture of Blood Cells. 21st Annual Meeting of the European-Society-for-Animal-Cell-Technology (ESACT), Dublin Ireland, Jun 07-10, 2009. DORDRECHT: SPRINGER. doi: 10.1007/978-94-007-0884-6_92

Major adjustments in metabolic flux occur to accommodate PHB production in sugarcane

McQualter, Richard, Gebbie, Leigh, Dal'Molin, Cristiana G.d., Petrasovits, Lars, Snell, K. D., Nielsen, Lars K. and Brumbley, Stevens (2012). Major adjustments in metabolic flux occur to accommodate PHB production in sugarcane. The 13th International Symposium on Biopolymers (ISBP 2012), Cairns, Australia, 7-10 October.

Metabolomic Analysis of CHO Cultures with Different Growth Characteristics - Development of a Metabolite Extraction Protocol for Suspension Adapted Mammalian Cells

Dietmair, Stefanie, Timmins, Nicholas E., Chrysanthopoulos, Panagiotis, Gray, Peter P., Kromer, Jens O. and Nielsen, Lars K. (2012). Metabolomic Analysis of CHO Cultures with Different Growth Characteristics - Development of a Metabolite Extraction Protocol for Suspension Adapted Mammalian Cells. 21st Annual Meeting of the European-Society-for-Animal-Cell-Technology (ESACT), Dublin Ireland, Jun 07-10, 2009. DORDRECHT: SPRINGER. doi: 10.1007/978-94-007-0884-6_6

Building Systems biology platforms for Actinobacteria

Marcellin Saldana, Esteban Stefane, Mercer, Timothy, Licona Cassani, Cuauthemoc and Nielsen, Lars K. (2011). Building Systems biology platforms for Actinobacteria. ISBA XVI, Puerto Vallarta, Mexico, 11-15 December 2011.

Dynamic System-level study for protein expression in Saccharopolyspora erythraea

Licona Cassani, Cuauthemoc, Marcellin Saldana, Esteban Stefane and Nielsen, Lars K. (2011). Dynamic System-level study for protein expression in Saccharopolyspora erythraea. 16th International Symposium on the Biology of Actinomycetes, Puerto Vallarta, Mexico, 11-15 December 2011.

Optimising in vitro production of baculovirus biopesticides – a transcriptomics approach to establish a platform for expression analysis and bioengineering of virus and insect cells

Nguyen, Quan, Prasath, Daniel B., Palfreyman, Robin W., Nielsen, Lars K., Chan, Leslie C. L. and Reid, Steven (2011). Optimising in vitro production of baculovirus biopesticides – a transcriptomics approach to establish a platform for expression analysis and bioengineering of virus and insect cells. Chemeca 2011: Australasian Conference on Chemical Engineering, Sydney, Australia, 18-21 September 2011. Barton, ACT, Australia: Engineers Australia.

Pha accumulation in sugarcane plastids and peroxisomes

Brumbley, S. M., Petrasovits, L. A., McQualter, R. B., Gebbie, L. K., Tilbrook, K., Patterson, N. A., Somleva, M. N., Nielsen, L. K. and Snell, K. D. (2011). Pha accumulation in sugarcane plastids and peroxisomes. 32nd Australasian Polymers Symposium, The Novotel Pacific Bay Resort, Coffs Harbour, Australia, 13-16 February.

Sucrose-to-bioproducts: Engineering a sucrose-based E. coli platform for industrial bioproduction

Vickers, Claudia E., Archer, Colin, Bruschi, Michele, Arifin, Yalun, Sabri, Suriana, Boyes, Simon and Nielsen, Lars K. (2011). Sucrose-to-bioproducts: Engineering a sucrose-based E. coli platform for industrial bioproduction. ICBE 2011: International Conference on Biomolecular Engineering, San Francisco, CA, U.S.A., 16-19 January 2011.

Systems biology for industrial microorganisms

Marcellin, E., Mercer, T. R., Licona, C. and Nielsen, L. K. (2011). Systems biology for industrial microorganisms. XIV Congreso Nacional de Biotecnología y Bioingeniería, Queretaro, Mexico, 19-24 June 2011.

HighHA: High molecular weight hyaluronic acid from bacterial fermentation

Marcellin E, Chen WY and Nielsen LK (2010). HighHA: High molecular weight hyaluronic acid from bacterial fermentation. HA2010, Kyoto , Japan, June 6-10.

Improving streptococcal production of Hyaluronic acid using a systems biotechnology approach

Marcellin, E., Chen, W. Y. and Nielsen, L. K. (2010). Improving streptococcal production of Hyaluronic acid using a systems biotechnology approach. Metabolic Engineering VIII, Jeju Isl, South Korea, June 13-18.

Increasing Production of Polyhydroxybutyrate in Sugarcane Plastids

Brumbley, Stevens M., Petrasovits, Lars A., McQualter, Richard M., Zhao, Lihan, Dal’Molin, Cristiana G. O., Snell, Kristi D. and Nielsen, Lars K. (2010). Increasing Production of Polyhydroxybutyrate in Sugarcane Plastids. Plant & Animal Genome XVIII, Town and Country Resort, San Diego, California USA, January 9-13.

Metabolic engineering of sucrose utilizing Escherichia coli for polyhydroxybutyrate production

Arifin, Y., Sugiarto, H., Sabri, S., Kromer, J. O., Vickers, C. E. and Nielsen, L. K. (2010). Metabolic engineering of sucrose utilizing Escherichia coli for polyhydroxybutyrate production. 14th International Biotechnology Symposium and Exhibition (IBS-2008), Rimini, Italy, 14-18 September 2010. AMSTERDAM: Elsevier. doi: 10.1016/j.jbiotec.2010.08.189

Of mice and men - NMR-based metabonomics between systems biology and clinical science

Schirra, Horst, Abd Rahman, S., Leong, G. M., Nielsen, L. K. and Waters, M. J. (2010). Of mice and men - NMR-based metabonomics between systems biology and clinical science. 2nd Australasian Symposium on Metabolomics, Melbourne, Australia, 30 September - 5 October 2010.

Of mice and men - NMR-metabonomics between systems biology and clinical science

Schirra, H. J., Abd Rahman, S., Leong, G. M., Nielsen, L. K. and Waters, M. J. (2010). Of mice and men - NMR-metabonomics between systems biology and clinical science. 23rd International Conference on Magnetic Resonance in Biological Systems, Cairns, Australia, 22-27 August 2010.

PHA accumulation in sugar cane

Brumbley, S. M., Petrasovits, L. A., McQualter, R. B., Patterson, N. A., Somleva, M. N., Nielsen, L. K. and Snell, K. D. (2010). PHA accumulation in sugar cane. ISBP 2010 International Symposium on Biopolymers, Stuttgart, Germany, October 3-7.

Production of the biopolymer polyhydroxybutyrate in sugarcane

Brumbley, S. M., Petrasovits, L. A., McQualter, R. B., Tillbrook, K., Patterson, N. A., Somleva, M. N., Nielsen, L. K. and Snell, K. D. (2010). Production of the biopolymer polyhydroxybutyrate in sugarcane. FAPESP Bioenergy Research Program (BIOEN) Workshop on Synthetic Biology, São Paulo, Brazil, 26-27 October.

Reconstruction of the Saccharopolyspora erythraea GEM

Licona Cassani, Cuauthemoc, Marcellin Saldana, Esteban Stefane, Quek, Lake-ee, Palfreyman, Robin William and Nielsen, Lars K. (2010). Reconstruction of the Saccharopolyspora erythraea GEM. 11th International Symposium on the Genetics of Industrial Microorganisms, Melbourne, VIC, Australia, 10-15 July 2010.

Sucrose-to-BioProducts: Metabolic engineering for PHB in sucrose-utilising E. coli

Archer, C.T., Arifin, Y., Nielsen, L.K, Sugiarto, A. and Vickers, C.E. (2010). Sucrose-to-BioProducts: Metabolic engineering for PHB in sucrose-utilising E. coli. 11th International Symposium on Genetics of Industrial Microorganisms GIM, Melbourne, Australia, 28 June – 1 July 2010.

Transferrable sucrose utilization in E. coli

Vickers, Claudia E., Bruschi, M., Boyes, S. J. and Nielsen, L.K. (2010). Transferrable sucrose utilization in E. coli. Metabolic Engineering VIII: Metabolic Engineering for Green Growth, Jeju Island, Korea, 13-17 June 2010.

Understanding the role of serine, threonine and tyrosine phosphorylation in the central carbon metabolism of E. coli

Lim, S., Marcellin, E., Jacob, S. and Nielsen, L. K. (2010). Understanding the role of serine, threonine and tyrosine phosphorylation in the central carbon metabolism of E. coli. Metabolic Engineering VIII, Jeju Isl, South Korea, 13-18 June 2010.

Developing sugarcane as a biofactory to produce plastics

Brumbley, S. M., Petrasovits, L. A., McQualter, R. B., Zhou, L., Dal'Molin, C. and Nielsen, L. K. (2009). Developing sugarcane as a biofactory to produce plastics. Tropical Crops Biotechnology Conference 2009,, Kruger, South Africa, 21-25 July 2009.

Metabolic engineering of hyaluronic acid production in streptococci

Nielsen, Lars K., Marcellin, Esteban and Chen, Wendy (2009). Metabolic engineering of hyaluronic acid production in streptococci. SIM Annual Meeting and Exhibition 2009, Toronto, Canada, 26-30 July 2009. Fairfax, VA, United States: Society for Industrial Microbiology (SIM).

Production of the biopolymer polyhydroxybutyrate in sugarcane

Brumbley, Steven M., McQualter, R. A., Nielsen, L. K, Petrasovits, L. A. and Zhou, L. (2009). Production of the biopolymer polyhydroxybutyrate in sugarcane. Plant Metabolic Engineering: Gordon Research Conference 2009, Waterville Valley, NH, U.S.A., 12-17 July 2009.

BIOT 273-Genome-scale metabolic network model of Arabidopsis

Dal'Molin, C, Quek, LE and Nielsen, LK (2008). BIOT 273-Genome-scale metabolic network model of Arabidopsis. 236th National Meeting of the American-Chemical-Society, Philadelphia, PA, USA, 17-21 August, 2008. WASHINGTON: AMER CHEMICAL SOC.

Development of a pre-glasshouse selection system for PHB-producing sugarcane and establishment of a high throughput transformation system

Petrasovits, L. A., Zhao, L., McQualter, R. B., Snell, K. D., Nielsen, L. K. and Brumbley, S. M. (2008). Development of a pre-glasshouse selection system for PHB-producing sugarcane and establishment of a high throughput transformation system. International Symposium on Biological Polyesters Conference 2008, Auckland, NZ, 23-26 November 2008.

Genome scale metabolic network model of Arabidopsis

Dal'Molin, Cristiana G., Quek, Lake-ee and Nielsen, Lars K. (2008). Genome scale metabolic network model of Arabidopsis. Health And Sustainability: Metabolic Engineering VII, Puerto Vallarta, Mexico, 14-18 September 2008.

Identification of a sucrose metabolising Escherichia coli

Arifin, Yalun, Hung, Jacky, Vickers, Claudia and Nielsen, Lars K. (2008). Identification of a sucrose metabolising Escherichia coli. Australian Society of Sugar Cane Technologists.

Immunolocalisation of PHB biosynthesis enzymes in the leaves of transgenic sugarcane plants

McQualter, R. B., Somleva, M. N., Xuemei, L., Petrasovits, L., Zhao, L., Nielsen, L. K. and Brumbley, S. M. (2008). Immunolocalisation of PHB biosynthesis enzymes in the leaves of transgenic sugarcane plants. International Symposium on Biological Polyesters Conference 2008, Auckland, NZ, 23-26 November 2008.

PHB production in sugarcane

Petrasovits, L. A., Zhao, L., McQualter, R. B., Snell, K. D., Nielsen. L. K. and Brumbley, S. M. (2008). PHB production in sugarcane. 10th International Symposium on Biological Polyesters Conference (ISBP), Auckland, New Zealand, 23 – 26 November 2008.

Production of polyhydroxyalkanoate copolymers in sugarcane

Anderson, D. J., Brumbley, W. M., Gnanasambandam, A., Nielsen, L. K., O'Shea, M. G. and Williams, E. (2008). Production of polyhydroxyalkanoate copolymers in sugarcane. International Symposium on Biological Polyesters Conference, Auckland, New Zealand, 23 – 26 November 2008.

Proteome analysis of hyaluronic acid producing bacteria for strain optimisation

Marcellin, E., Chen, W. Y. and Nielsen, L. K. (2008). Proteome analysis of hyaluronic acid producing bacteria for strain optimisation. Metabolic engineering VII, Puerto Vallarta, Mexico, 14-18 September.

Streptococcus zooepidemicus engineered to overexpress Pgi and GlmU produces high molecular weight hyaluronic acid.

Chen WY, Marcellin E, Hung J and Nielsen LK (2008). Streptococcus zooepidemicus engineered to overexpress Pgi and GlmU produces high molecular weight hyaluronic acid.. Cooperative Research Centre for Sugar Industry Innovation through Biotechnology (CRC SIIB) Symposium, Brisbane, Australia, 3-4th December.

Streptococcus zooepidemicus engineered to overexpress Pgi produces high molecular weight hyaluronic acid

Chen WY, Marcellin E, Hung J and Nielsen LK (2008). Streptococcus zooepidemicus engineered to overexpress Pgi produces high molecular weight hyaluronic acid. Metabolic engineering VII, Puerto Vallarta, Mexico, 14-18 September.

Sugarcane: An industrial crop for the production of polyhydroxyalkanoates

Brumbley, S. M., Petrasovits, L. A., Zhou, L., McQualter, R. A. and Nielsen, L. K. (2008). Sugarcane: An industrial crop for the production of polyhydroxyalkanoates. Fifth Annual World Congress on Industrial Biotechnology and Bioprocessing, Chicago, IL, U.S.A., 27-30 April 2008. National Agricultural Biotechnology Council.

Sugarcane: An industrial crop for the production of polyhydroxyalkanoates

Brumbley, S. M., Petrasovits, L. A., McQualter, R. A., Zhou, L. and Nielsen, L. K. (2008). Sugarcane: An industrial crop for the production of polyhydroxyalkanoates. ComBio 2008, Canberra, Australia, 21-25 September 2008.

Understanding molecular weight control in bacterial fermentation: a systems biotechnology approach

Marcellin E, Chen WY, Archer C and Nielsen LK (2008). Understanding molecular weight control in bacterial fermentation: a systems biotechnology approach. GIW2008, Gold Coast , QLD, Australia, 1-3 December.

Ligand-receptor interactions and membrane structure investigated by AFM and time-resolved fluorescence microscopy

Thormann, Esben, Simonsen, Adam C., Nielsen, Lars K. and Mouritsen, Ole G. (2007). Ligand-receptor interactions and membrane structure investigated by AFM and time-resolved fluorescence microscopy. doi: 10.1002/jmr.850

Genome scale model of Streptococcus zooepidemicus: understanding hyaluronic acid production

Marcellin E, Archer C and Nielsen LK (2007). Genome scale model of Streptococcus zooepidemicus: understanding hyaluronic acid production. Bioinformatics Australia, Brisbane / Brisbane Convention Centre, 23-24 October.

Genome scale model of a plant cell

Dal'Molin, Cristiana Gomes de Oliveria, Quek, Lake-Ee and Nielsen, Lars (2007). Genome scale model of a plant cell. Plant Metabolic Engineering Gordon Research Conference, Tilton School, U.S.A., 15-20 July 2007.

Metabolic engineering of sugarcane for production of industrial chemicals

Brumbley, S.M., Petrasovits, L.A., Anderson, D., Purnell, M., Su, A., Zhao, L., Abeydeera P. and Nielsen L.K. (2007). Metabolic engineering of sugarcane for production of industrial chemicals. AusBioTech Biofutures Forum, Parliament House, Canberra, Australia, 14 June, 2007.

Metabolic engineering of sugarcane for production of industrial chemicals

Brumbley, S. M., Petrasovits, L. A., Anderson, D., Purnell, M. P., Su, M. P., Su, A., Zhao, L. and Nielsen, L. K. (2007). Metabolic engineering of sugarcane for production of industrial chemicals. The Fourth Annual World Congress on Industrial Biotechnology and Bioprocessing, Florida, U.S.A., 21-24 March, 2007.

Sugarcane: A crop with the potential to function as both a biofactory producing industrial chemicals and as a large scale source of carbohydrates for future biorefineries

Brumbley, S. M., Purnell, M. P., Petrasovits, L. A., Anderson, D. A., McQualter, R. B., Chong, B. F. and Nielsen, L. K. (2007). Sugarcane: A crop with the potential to function as both a biofactory producing industrial chemicals and as a large scale source of carbohydrates for future biorefineries. 2nd EPOBIO Workshop: Products from Plants – from crops and forests to zero-waste biorefineries, Athens, Greece, 15-17 May 2007.

Efficient targeting of green fluorescent protein to sugarcane peroxisomes

Gnanasambandam, A., Anderson, D., Williams, E., Nielsen, L. and Brumbley, S. (2006). Efficient targeting of green fluorescent protein to sugarcane peroxisomes. Tropical Crops Biotechnology Conference, Cairns, Australia, 16-19 August 2006.

Efficient targeting of green fluorescent protein to sugarcane peroxisomes

Gnanasambandam, A., Anderson, D. J., Williams, E., Nielsen, L. K. and Brumbley, S. M. (2006). Efficient targeting of green fluorescent protein to sugarcane peroxisomes. 28th Conference of the Australian Society of Sugarcane Technologists, Mackay, Qld, Australia, 2-5 May, 2006.

High selectivity microporous silica membranes for lactic acid dehydration

Duke, M. C., Lim, A., Diniz da Costa, J. C. and Nielsen, L. (2006). High selectivity microporous silica membranes for lactic acid dehydration. 5th World Congress on Particle Technology, Orlando, FL, USA, 23-27 April, 2006. USA: AIChE.

LACTIC ACID PRODUCTION BY A RUMEN BACTERIUM CULTIVATED ON CHEMICALLY DEFINED MEDIUM WITH AMMONIA AS NITROGEN SOURCE

Joachimsthal, E. L., Hung, J. and Nielsen, L. K. (2006). LACTIC ACID PRODUCTION BY A RUMEN BACTERIUM CULTIVATED ON CHEMICALLY DEFINED MEDIUM WITH AMMONIA AS NITROGEN SOURCE. Australian Society of Sugar Cane Technologists.

Maximal expansion of erythroid progenitors is dependent on the cytokine cocktail

Athanasas-Platsis, S., Minchinton, R., Sparrow, R. and Nielsen, L. (2006). Maximal expansion of erythroid progenitors is dependent on the cytokine cocktail. The 2005 ISAC Samuel A. Latt conference, Gold Coast, Queensland, Australia, 6-9 November 2005. Hoboken, N.J.: Wiley-Liss. doi: 10.1002/cyto.a.20264

Production of poly-3-hydroxybutyrate in transgenic sugarcane

Brumbley, S. M., Nielsen, L. K., Petrasovits, L. A. and Purnell, M. P. (2006). Production of poly-3-hydroxybutyrate in transgenic sugarcane. Tropical Crops Biotechnology Conference, Cairns, Queensland Australia, 16-19 July, 2006.

Production of trehalose in transgenic sugarcane

Brumbley, S. M., Nielsen, L. K., O'Neill. B. A. and Purnell, M. P. (2006). Production of trehalose in transgenic sugarcane. Tropical Crops Biotechnology Conference, Cairns, Queensland Australia, 16-19 August 2006.

Spatio-Temporal characterization of polyhydroxybutyrate accumulation in sugarcane

Purnell, M. P., Petrasovits, L. A., Nielsen, L. K. and Brumbley, S. M. (2006). Spatio-Temporal characterization of polyhydroxybutyrate accumulation in sugarcane. International Society of Biological Polyesters (ISBP), Minnesota, Minneapolis, USA, 27 - 31 August 2006.

Spatio-temporal characterisation of accumulation in sugarcane

Purnell, M. P., Petrasovits, L. A., Nielsen, L. K. and Brumbley, S. M. (2006). Spatio-temporal characterisation of accumulation in sugarcane. Tropical Crop Biotechnology Conference 2006, Cairns, Qld, Australia, 16-19 August, 2006.

Sugarcane: a versatile biofactory crop capable of sustaining the accumulation of high levels of heterologous products derived from a variety of precursors

Brumbley, S. M., Purnell, M. P, Petrasovits, L. A., Fong Chong, B., O'Neill, B. P. and Nielsen, L. K. (2006). Sugarcane: a versatile biofactory crop capable of sustaining the accumulation of high levels of heterologous products derived from a variety of precursors. Tropical Crops Biotechnology Conference, Cairns, Queensland Australia, 16-19 August 2006.

Temperature and durability studies of lactic acid dehydration with inorganic membranes

Duke, M. C., Lim, A and Nielsen, L K (2006). Temperature and durability studies of lactic acid dehydration with inorganic membranes. Proceedings of the 2006 International Conference on Nonoscience and Nanotechnology, Brisbane, Queensland, Australia, 3-7 July 2006. Australia: Australian Research Council. doi: 10.1109/iconn.2006.340668

Temperature and durability studies of lactic acid dehydration with inorganic membranes

Duke, M. C., Lim, A. and Nielsen, L. (2006). Temperature and durability studies of lactic acid dehydration with inorganic membranes. International Conference on Nanoscience and Nanotechnology, Brisbane Australia, Jul 03-07, 2006. NEW YORK: IEEE.

Development of sugarcane as a biofactory for biopolymers

Brumbley, S. M., Purnell, M. P., Petrasovits, L. A., McQualter, R., Fong Chong, B., Meyer, K., Van Dyk, D. E., O'Shea, M. G., Walton, N. J., Nielsen, L. K. and Viitanen, P. V. (2005). Development of sugarcane as a biofactory for biopolymers. The Second World Congress on Industrial Biotechnology and Bioprocessing: Linking Biotechnology, Chemistry and Agriculture to Create New Value Chains, Orlando, FL, USA, 20–22 April 2005.

Effectiveness of inorganic membranes for lactic acid dehydration

Duke, M. C., Lim,, Diniz da Costa, J. C. and Nielsen, L. K. (2005). Effectiveness of inorganic membranes for lactic acid dehydration. BIONANO The Next Frontier, Brisbane, 4-7 December, 2005. Brisbane:

Effects of multiplicity of infection (MOI) and cell cycle on baculovirus infection kinetics

Haas, R, Reid, S and Nielsen, LK (2005). Effects of multiplicity of infection (MOI) and cell cycle on baculovirus infection kinetics. 18th Meeting of the European-Society-of-Animal-Cell-Technology (ESACT), Granada Spain, May 11-14, 2003. DORDRECHT: SPRINGER.

High selectivity microporous silica membranes for lactic acid dehydration

Duke, M. C., Diniz da Costa, J. C., Nielsen, L. and Lim, A. (2005). High selectivity microporous silica membranes for lactic acid dehydration. 2005 Sir Mark Oliphant Conference: BioNano: The Next Frontier, The University of Queensland, Australia, 4-7 December, 2005.

Development Of sugarcane as a biofactory for biopolymers

Brumbley, S. M., Purnell, M. P., Petrasovits, L. A., McQualter, R., Fong Chong, B., Meyer, K., Van Dyk, D. E. and Nielsen, L. K. (2004). Development Of sugarcane as a biofactory for biopolymers. International Symposium on Biological Polyesters (ISBP 2004), Beijing, China, 22-28 August 2004.

Development of sugarcane as a biofactory for biopolymers

Brumbley, Stevens M., Purnell, Matt P., Petrasovits, Lars A., O'Shea, Michael G. and Nielsen, Lars K. (2004). Development of sugarcane as a biofactory for biopolymers. Plant & Animal Genomes XII Conference, San Diego, U.S., 10-14 January 2004. San Deigo, California, U.S.: GenomeWeb.

Production of polyhydroxyalkanoates in sugarcane

Brumbley, S. M., Petrasovits, L., Purnell, M., O'Shea, M. and Nielsen, L (2003). Production of polyhydroxyalkanoates in sugarcane. 6th Asia Pacific Biochemical Engineering Conference (APBioChEC): Harnessing New Technology for Bioprocess Development, Brisbane, Australia, 30 November- 4 December 2003.

Production of polyhydroxyalkanoates in sugarcane

Brumbley, S. M., Petrasovits, L. A., Bonaventura, P. A., O'Shea, M. J., Purnell, M. P. and Nielsen, L. K. (2003). Production of polyhydroxyalkanoates in sugarcane. IVth International Workshop on Plant Biotechnology and Sustainable Development (BioVeg2003), Ciego de Avila, Cuba, 14-19 April 2003.

Production of polyhydroxyalkanoates in sugarcane

Brumbley, S. M., Petrasovits, L. A., Bonaventura, P. A., O'Shea, M. J., Purnell, M. P. and Nielsen, L. K. (2003). Production of polyhydroxyalkanoates in sugarcane. 4th ISSCT Molecular Biology Workshop, Montpelier, France, 7-14 April, 2003.

Application of biotechnology for future sugar industry diversification

Brumbley, S. M., Petrasovits, L., Purnell, M., O'Shea, M. G., Geijskes, J., Prakash Lakshmanan, Smith, G. R. and Nielsen, L. K. (2002). Application of biotechnology for future sugar industry diversification. 2002 Conference of the Australian Society of Sugar Cane Technologists, Cairns, Queensland, Australia, 29 April - 2 May, 2002. PK Editorial Services Pty Ltd.

43 Hemin reconstitutes the growth of an H+ -ATPase negative mutant of Lactococcus lactis

Blank, L., Koebmann, B. J., Nielsen, L. K. and Jensen, P. R. (2000). 43 Hemin reconstitutes the growth of an H+ -ATPase negative mutant of Lactococcus lactis. 9th International Meeting on BioThermoKinetics, Stellenbosch, South Africa, 3-7 April. South Africa: Stellenbosch University Press.

Ex vivo expansion of apheresis products: Do accessory cells support the expansion process?

Mostafa, S, Liu, J, Collins, PC, Nielsen, LK, Miller, WM and Papoutsakis, ET (1997). Ex vivo expansion of apheresis products: Do accessory cells support the expansion process?. 17th Annual Scientific Meeting and Education Day of the Society-for-Neuro-Oncology (SNO), Washington Dc, Nov 15-18, 2012. PHILADELPHIA: W B SAUNDERS CO.

Model-based analysis of the effect of TGF-beta 1 on erythropoiesis.

Nielsen, LK, Miller, WM and Papoutsakis, ET (1996). Model-based analysis of the effect of TGF-beta 1 on erythropoiesis.. PHILADELPHIA: W B SAUNDERS CO.

The use of very low multiplicities of infection with the baculovirus expression vector system

Reid, S, Greenfield, PF, Power, J, Radford, KM, Nielsen, LK, Wong, TKK and Peter, C (1995). The use of very low multiplicities of infection with the baculovirus expression vector system. ESACT/JAACT Meeting on Animal Cell Technology - Developments Towards the 21st-Century, Veldhoven Netherlands, Sep 12-16, 1994. DORDRECHT: KLUWER ACADEMIC PUBL.

Using Oxygen Uptake Rates to Time Infections in the Baculovirus Expression Vector System

Nielsen, LK, Wong, Tkk, Power, J, Reid, S and Greenfield, PF (1994). Using Oxygen Uptake Rates to Time Infections in the Baculovirus Expression Vector System. 6th International Meeting of the Japanese-Association-for-Animal-Cell-Technology; Animal Cell Technology - Basic and Applied Aspects, Nagoya Japan, Nov 09-12, 1993. DORDRECHT: KLUWER ACADEMIC PUBL.

Modeling Growth of and Antibody-Production by Hybridomas in Glutamine Limited Suspension-Cultures

Nielsen, LK, Niloperbowo, W, Reid, S and Greenfield, PF (1991). Modeling Growth of and Antibody-Production by Hybridomas in Glutamine Limited Suspension-Cultures. 10Th Meeting of the European Soc for Animal Cell Technology : Production of Biologicals From Animal Cells in Culture, Avignon France, 1990. OXFORD: BUTTERWORTH-HEINEMANN.

A unique model platform for C4 plant systems and synthetic biology

Nielsen, Lars (2015). A unique model platform for C4 plant systems and synthetic biology. Alexandria, Virginia, United States: Defense Technical Information Center.

Production of hyaluronic acid

Nielsen, Lars Keld, Chen, Wendy and Saldana Marcellin, Esteban Stefane (2010). Production of hyaluronic acid. EP 2195348 A1.

Modelling hybridoma cultures : improving the framework

Nielsen, Lars Keld (1995). Modelling hybridoma cultures : improving the framework. PhD Thesis, School of Engineering, The University of Queensland. doi: 10.14264/3417030