Journal Article: LowTempGAL: a highly responsive low temperature-inducible GAL system in Saccharomyces cerevisiae
Lu, Zeyu, Shen, Qianyi, Bandari, Naga Chandra, Evans, Samuel, Mcdonnell, Liam, Liu, Lian, Jin, Wanli, Luna-Flores, Carlos Horacio, Collier, Thomas, Talbo, Gert, Mccubbin, Tim, Esquirol, Lygie, Myers, Chris, Trau, Matt, Dumsday, Geoff, Speight, Robert, Howard, Christopher B., Vickers, Claudia E. and Peng, Bingyin (2024). LowTempGAL: a highly responsive low temperature-inducible GAL system in Saccharomyces cerevisiae. Nucleic Acids Research gkae460. doi: 10.1093/nar/gkae460
Heffernan, James, Garcia Gonzalez, R. Axayactl, Mahamkali, Vishnu, McCubbin, Tim, Daygon, Dara, Liu, Lian, Palfreyman, Robin, Harris, Audrey, Koepke, Michael, Valgepea, Kaspar, Nielsen, Lars Keld and Marcellin, Esteban (2024). Adaptive laboratory evolution of Clostridium autoethanogenum to metabolize CO2 and H2 enhances growth rates in chemostat and unravels proteome and metabolome alterations. Microbial Biotechnology, 17 (4) e14452, e14452. doi: 10.1111/1751-7915.14452
Journal Article: A universal molecular control for DNA, mRNA and protein expression
Gunter, Helen M., Youlten, Scott E., Reis, Andre L. M., McCubbin, Tim, Madala, Bindu Swapna, Wong, Ted, Stevanovski, Igor, Cipponi, Arcadi, Deveson, Ira W., Santini, Nadia S., Kummerfeld, Sarah, Croucher, Peter I., Marcellin, Esteban and Mercer, Tim R. (2024). A universal molecular control for DNA, mRNA and protein expression. Nature Communications, 15 (1) 2480, 1-13. doi: 10.1038/s41467-024-46456-9
(2023–2025) Grains Research & Development Corporation
LowTempGAL: a highly responsive low temperature-inducible GAL system in Saccharomyces cerevisiae
Lu, Zeyu, Shen, Qianyi, Bandari, Naga Chandra, Evans, Samuel, Mcdonnell, Liam, Liu, Lian, Jin, Wanli, Luna-Flores, Carlos Horacio, Collier, Thomas, Talbo, Gert, Mccubbin, Tim, Esquirol, Lygie, Myers, Chris, Trau, Matt, Dumsday, Geoff, Speight, Robert, Howard, Christopher B., Vickers, Claudia E. and Peng, Bingyin (2024). LowTempGAL: a highly responsive low temperature-inducible GAL system in Saccharomyces cerevisiae. Nucleic Acids Research gkae460. doi: 10.1093/nar/gkae460
Heffernan, James, Garcia Gonzalez, R. Axayactl, Mahamkali, Vishnu, McCubbin, Tim, Daygon, Dara, Liu, Lian, Palfreyman, Robin, Harris, Audrey, Koepke, Michael, Valgepea, Kaspar, Nielsen, Lars Keld and Marcellin, Esteban (2024). Adaptive laboratory evolution of Clostridium autoethanogenum to metabolize CO2 and H2 enhances growth rates in chemostat and unravels proteome and metabolome alterations. Microbial Biotechnology, 17 (4) e14452, e14452. doi: 10.1111/1751-7915.14452
A universal molecular control for DNA, mRNA and protein expression
Gunter, Helen M., Youlten, Scott E., Reis, Andre L. M., McCubbin, Tim, Madala, Bindu Swapna, Wong, Ted, Stevanovski, Igor, Cipponi, Arcadi, Deveson, Ira W., Santini, Nadia S., Kummerfeld, Sarah, Croucher, Peter I., Marcellin, Esteban and Mercer, Tim R. (2024). A universal molecular control for DNA, mRNA and protein expression. Nature Communications, 15 (1) 2480, 1-13. doi: 10.1038/s41467-024-46456-9
Amino acid degradation pathway inhibitory by‐products trigger apoptosis in CHO cells
Martínez, Verónica S., Rodriguez, Karen, McCubbin, Timothy, Tong, Junjie, Mahler, Stephen, Shave, Evan, Baker, Kym, Munro, Trent P. and Marcellin, Esteban (2024). Amino acid degradation pathway inhibitory by‐products trigger apoptosis in CHO cells. Biotechnology Journal, 19 (2) ARTN e2300338, e2300338. doi: 10.1002/biot.202300338
Quantitative subcellular reconstruction reveals a lipid mediated inter-organelle biogenesis network
Lee, Richard G., Rudler, Danielle L., Raven, Samuel A., Peng, Liuyu, Chopin, Anaelle, Moh, Edward S. X., McCubbin, Tim, Siira, Stefan J., Fagan, Samuel V., Debono, Nicholas J., Stentenbach, Maike, Browne, Jasmin, Rackham, Filip F., Li, Ji, Simpson, Kaylene J., Marcellin, Esteban, Packer, Nicolle H., Reid, Gavin E., Padman, Benjamin S., Rackham, Oliver and Filipovska, Aleksandra (2024). Quantitative subcellular reconstruction reveals a lipid mediated inter-organelle biogenesis network. Nature Cell Biology, 26 (1), 57-71+. doi: 10.1038/s41556-023-01297-4
Quantitative subcellular reconstruction reveals a lipid mediated inter-organelle biogenesis network
Lee, Richard G., Rudler, Danielle L., Raven, Samuel A., Peng, Liuyu, Chopin, Anaëlle, Moh, Edward S. X., McCubbin, Tim, Siira, Stefan J., Fagan, Samuel V., DeBono, Nicholas J., Stentenbach, Maike, Browne, Jasmin, Rackham, Filip F., Li, Ji, Simpson, Kaylene J., Marcellin, Esteban, Packer, Nicolle H., Reid, Gavin E., Padman, Benjamin S., Rackham, Oliver and Filipovska, Aleksandra (2023). Quantitative subcellular reconstruction reveals a lipid mediated inter-organelle biogenesis network. Nature Cell Biology, 26 (1), 57-71. doi: 10.1038/s41556-023-01297-4
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
Casini, Isabella, McCubbin, Tim, Esquivel-Elizondo, Sofia, Luque, Guillermo G., Evseeva, Daria, Fink, Christian, Beblawy, Sebastian, Youngblut, Nicholas D., Aristilde, Ludmilla, Huson, Daniel H., Dräger, Andreas, Ley, Ruth E., Marcellin, Esteban, Angenent, Largus T. and Molitor, Bastian (2023). An integrated systems biology approach reveals differences in formate metabolism in the genus Methanothermobacter. iScience, 26 (10) 108016, 1-26. doi: 10.1016/j.isci.2023.108016
Multi-omic profiling reveals an RNA processing rheostat that predisposes to prostate cancer
Stentenbach, Maike, Ermer, Judith A, Rudler, Danielle L, Perks, Kara L, Raven, Samuel A, Lee, Richard G, McCubbin, Tim, Marcellin, Esteban, Siira, Stefan J, Rackham, Oliver and Filipovska, Aleksandra (2023). Multi-omic profiling reveals an RNA processing rheostat that predisposes to prostate cancer. EMBO Molecular Medicine, 15 (6) e17463, 1-22. doi: 10.15252/emmm.202317463
Hughes, Laetitia A., Rudler, Danielle L., Siira, Stefan J., McCubbin, Tim, Raven, Samuel A., Browne, Jasmin M., Ermer, Judith A., Rientjes, Jeanette, Rodger, Jennifer, Marcellin, Esteban, Rackham, Oliver and Filipovska, Aleksandra (2023). Copy number variation in tRNA isodecoder genes impairs mammalian development and balanced translation. Nature Communications, 14 (1) 2210, 1-19. doi: 10.1038/s41467-023-37843-9
Dysregulated energy metabolism impairs chondrocyte function in osteoarthritis
Wu, X., Liyanage, C., Plan, M., Stark, T., McCubbin, T., Barrero, R. A., Batra, J., Crawford, R., Xiao, Y. and Prasadam, I. (2023). Dysregulated energy metabolism impairs chondrocyte function in osteoarthritis. Osteoarthritis and Cartilage, 31 (5), 613-626. doi: 10.1016/j.joca.2022.11.004
Lee, Richard G., Balasubramaniam, Shanti, Stentenbach, Maike, Kralj, Tom, McCubbin, Tim, Padman, Benjamin, Smith, Janine, Riley, Lisa G., Priyadarshi, Archana, Peng, Liuyu, Nuske, Madison R., Webster, Richard, Peacock, Ken, Roberts, Philip, Stark, Zornitza, Lemire, Gabrielle, Ito, Yoko A., Boycott, Kym M., Geraghty, Michael T., Klinken, Jan Bert, Ferdinandusse, Sacha, Zhou, Ying, Walsh, Rebecca, Marcellin, Esteban, Thorburn, David R., Rosciolli, Tony, Fletcher, Janice, Rackham, Oliver, Vaz, Frédéric M. ... Care4Rare Canada Consortium (2022). Deleterious variants in CRLS1 lead to cardiolipin deficiency and cause an autosomal recessive multi-system mitochondrial disease. Human Molecular Genetics, 31 (21), 3597-3612. doi: 10.1093/hmg/ddac040
He, Bingqing, Cai, Chen, McCubbin, Tim, Muriel, Jorge Carrasco, Sonnenschein, Nikolaus, Hu, Shihu, Yuan, Zhiguo and Marcellin, Esteban (2022). A genome-scale metabolic model of Methanoperedens nitroreducens: assessing bioenergetics and thermodynamic feasibility. Metabolites, 12 (4) 314. doi: 10.3390/metabo12040314
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
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
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
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
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
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
Exploring the metabolism of propionibacteria using genome-scale modelling
McCubbin, Timothy John (2018). Exploring the metabolism of propionibacteria using genome-scale modelling. PhD Thesis, Aust Institute for Bioengineering & Nanotechnology, The University of Queensland. doi: 10.14264/uql.2018.233
(2023–2025) Grains Research & Development Corporation