Journal Article: Role of the substrate on Ni inhibition in biological sulfate reduction
Liu, Yun, Vaughan, James, Southam, Gordon, Serrano, Antonio, Gao, Han, Palfreyman, Robin, Marcellin, Esteban and Villa-Gomez, Denys K. (2022). Role of the substrate on Ni inhibition in biological sulfate reduction. Journal of Environmental Management, 316 115216, 115216. doi: 10.1016/j.jenvman.2022.115216
Journal Article: 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
Journal Article: Network analyses predict small RNAs that might modulate gene expression in the testis and epididymis of Bos indicus bulls
de Lima, Andressa O., Afonso, Juliana, Edson, Janette, Marcellin, Esteban, Palfreyman, Robin, Porto-Neto, Laercio R., Reverter, Antonio and Fortes, Marina R. S. (2021). Network analyses predict small RNAs that might modulate gene expression in the testis and epididymis of Bos indicus bulls. Frontiers in Genetics, 12 610116, 610116. doi: 10.3389/fgene.2021.610116
Plant Fluxomics Platform to understand the interplay of plant metabolic networks
(2012) UWA-UQ Bilateral Research Collaboration Award
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
Role of the substrate on Ni inhibition in biological sulfate reduction
Liu, Yun, Vaughan, James, Southam, Gordon, Serrano, Antonio, Gao, Han, Palfreyman, Robin, Marcellin, Esteban and Villa-Gomez, Denys K. (2022). Role of the substrate on Ni inhibition in biological sulfate reduction. Journal of Environmental Management, 316 115216, 115216. doi: 10.1016/j.jenvman.2022.115216
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
de Lima, Andressa O., Afonso, Juliana, Edson, Janette, Marcellin, Esteban, Palfreyman, Robin, Porto-Neto, Laercio R., Reverter, Antonio and Fortes, Marina R. S. (2021). Network analyses predict small RNAs that might modulate gene expression in the testis and epididymis of Bos indicus bulls. Frontiers in Genetics, 12 610116, 610116. doi: 10.3389/fgene.2021.610116
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
Palfreyman, R W, Watson, M L, Eden, C and Smith, A W (1997). Induction of biologically active interleukin-8 from lung epithelial cells by Burkholderia (Pseudomonas) cepacia products. Infection and immunity, 65 (2), 617-622. doi: 10.1128/iai.65.2.617-622.1997
Kinetic resolution of the separate GLUT1 and GLUT4 glucose transport activities in 3T3-L1 cells
Palfreyman, R W, Clark, A E, Denton, R M, Holman, G D and Kozka, I J (1992). Kinetic resolution of the separate GLUT1 and GLUT4 glucose transport activities in 3T3-L1 cells. The Biochemical Journal, 284 (1), 275-282. doi: 10.1042/bj2840275
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.
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.
Plant Fluxomics Platform to understand the interplay of plant metabolic networks
(2012) UWA-UQ Bilateral Research Collaboration Award