The University of Queensland

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. Plant metabolic flux analysis: methods and protocols. (pp. 317-332) edited by DieuaideNoubhani, M and Alonso, AP. New York, NY, United States: Humana Press. doi: 10.1007/978-1-62703-688-7_19

A snapshot of microbial diversity and function in an undisturbed sugarcane bagasse pile

Gebbie, Leigh, Dam, Tuan Tu, Ainscough, Rebecca, Palfreyman, Robin, Cao, Li, Harrison, Mark, O'Hara, Ian and Speight, Robert (2020). A snapshot of microbial diversity and function in an undisturbed sugarcane bagasse pile. BMC Biotechnology, 20 (1) 12, 12. doi: 10.1186/s12896-020-00609-y

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

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

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

Effect of plasmid design and type of integration event on recombinant protein expression in Pichia pastoris

Vogl, Thomas, Gebbie, Leigh, Palfreyman, Robin W. and Speight, Robert (2018). Effect of plasmid design and type of integration event on recombinant protein expression in Pichia pastoris. Applied and Environmental Microbiology, 84 (6) e02712-17, e02712-17. doi: 10.1128/AEM.02712-17

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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.

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.

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.