Dr Ralph Patrick
Postdoctoral Research Fellow
Institute for Molecular Bioscience
Researcher biography
Ralph Patrick is a researcher focussed on understanding the molecular drivers of ageing and age-associated diseases and developing new therapeutic approaches to help alleviate diseases of ageing. He is trained as a computational biologist, with a BSc (Hons) and PhD from the University of Queensland (UQ). After completion of his PhD in 2016, he worked as a postdoctoral scientist at the Victor Chang Cardiac Research Institute (VCCRI) in Sydney for nearly six years. At the VCCRI, a major focus of his research was mapping out how the individual cells of the heart respond to a heart attack at the gene expression level and how these compare to other forms of chronic heart disease. Following the VCCRI, he joined the Ageing and Cellular Reprogramming lab at the IMB in 2022 as a postdoctoral fellow. His work at the IMB focusses on understanding the epigenetic and transcription factor drivers of the ageing process and leveraging this knowledge to develop new strategies for restoring youthful cell states. Any potential collaborators or students interested in this research area are welcome to contact him.
Journal Articles
Cartland, Siân P., Patil, Manisha S., Kelland, Elaina, Le, Natalie, Boccanfuso, Lauren, Stanley, Christopher P., Cholan, Pradeep Manuneedhi, Dona, Malathi I., Patrick, Ralph, McGrath, Jordan, Su, Qian Peter, Alwis, Imala, Ganss, Ruth, Powell, Joseph E., Harvey, Richard P., Pinto, Alexander R., Griffith, Thomas S., Loa, Jacky, Aitken, Sarah J., Robinson, David A., Patel, Sanjay and Kavurma, Mary M. (2024). The generation of stable microvessels in ischemia is mediated by endothelial cell derived TRAIL. Science Advances, 10 (40) eadn8760, 1-17. doi: 10.1126/sciadv.adn8760
Patrick, Ralph, Naval-Sanchez, Marina, Deshpande, Nikita, Huang, Yifei, Zhang, Jingyu, Chen, Xiaoli, Yang, Ying, Tiwari, Kanupriya, Esmaeili, Mohammadhossein, Tran, Minh, Mohamed, Amin R., Wang, Binxu, Xia, Di, Ma, Jun, Bayliss, Jacqueline, Wong, Kahlia, Hun, Michael L., Sun, Xuan, Cao, Benjamin, Cottle, Denny L., Catterall, Tara, Barzilai-Tutsch, Hila, Troskie, Robin-Lee, Chen, Zhian, Wise, Andrea F., Saini, Sheetal, Soe, Ye Mon, Kumari, Snehlata, Sweet, Matthew J. ... Nefzger, Christian M. (2024). The activity of early-life gene regulatory elements is hijacked in aging through pervasive AP-1-linked chromatin opening. Cell Metabolism, 36 (8), 1858-1881.e23. doi: 10.1016/j.cmet.2024.06.006
Patrick, Ralph, Janbandhu, Vaibhao, Tallapragada, Vikram, Tan, Shannon S. M., McKinna, Emily E., Contreras, Osvaldo, Ghazanfar, Shila, Humphreys, David T., Murray, Nicholas J., Tran, Yen T. H., Hume, Robert D., Chong, James J. H. and Harvey, Richard P. (2024). Integration mapping of cardiac fibroblast single-cell transcriptomes elucidates cellular principles of fibrosis in diverse pathologies. Science Advances, 10 (25) eadk8501, eadk8501. doi: 10.1126/sciadv.adk8501
Janbandhu, Vaibhao, Tallapragada, Vikram, Li, Jinyuan Vero, Shewale, Bharti, Ghazanfar, Shila, Patrick, Ralph, Cox, Charles D. and Harvey, Richard P. (2024). Novel mouse model for selective tagging, purification, and manipulation of cardiac myofibroblasts. Circulation, 149 (24), 1931-1934. doi: 10.1161/circulationaha.123.067754
Hardy, Sean A., Liesinger, Laura, Patrick, Ralph, Poettler, Maria, Rech, Lavinia, Gindlhuber, Juergen, Mabotuwana, Nishani S., Ashour, DiyaaEldin, Stangl, Verena, Bigland, Mark, Murtha, Lucy A., Starkey, Malcolm R., Scherr, Daniel, Hansbro, Philip M., Hoefler, Gerald, Campos Ramos, Gustavo, Cochain, Clement, Harvey, Richard P., Birner-Gruenberger, Ruth, Boyle, Andrew J. and Rainer, Peter P. (2023). Extracellular matrix protein-1 as a mediator of inflammation-induced fibrosis after myocardial infarction. JACC: Basic to Translational Science, 8 (12), 1539-1554. doi: 10.1016/j.jacbts.2023.05.010
Murtha, Lucy A., Hardy, Sean A., Mabotuwana, Nishani S., Bigland, Mark J., Bailey, Taleah, Raguram, Kalyan, Liu, Saifei, Ngo, Doan T., Sverdlov, Aaron L., Tomin, Tamara, Birner-Gruenberger, Ruth, Hume, Robert D., Iismaa, Siiri E., Humphreys, David T., Patrick, Ralph, Chong, James J. H., Lee, Randall J., Harvey, Richard P., Graham, Robert M., Rainer, Peter P. and Boyle, Andrew J. (2023). Fibulin-3 is necessary to prevent cardiac rupture following myocardial infarction. Scientific Reports, 13 (1) 14995, 1-12. doi: 10.1038/s41598-023-41894-9
Moradi Marjaneh, Mahdi, Kirk, Edwin P., Patrick, Ralph, Alankerage, Dimuthu, Humphreys, David T., Del Monte-Nieto, Gonzalo, Cornejo-Paramo, Paola, Janbandhu, Vaibhao, Doan, Tram B., Dunwoodie, Sally L., Wong, Emily S., Moran, Chris, Martin, Ian C.A., Thomson, Peter C. and Harvey, Richard P. (2023). Quantitative trait and transcriptome analysis of genetic complexity underpinning cardiac interatrial septation in mice using an advanced intercross line. eLife, 12 e83606, 1-36. doi: 10.7554/elife.83606
Labzin, Larisa I., Chew, Keng Yih, Eschke, Kathrin, Wang, Xiaohui, Esposito, Tyron, Stocks, Claudia J., Rae, James, Patrick, Ralph, Mostafavi, Helen, Hill, Brittany, Yordanov, Teodor E., Holley, Caroline L., Emming, Stefan, Fritzlar, Svenja, Mordant, Francesca L., Steinfort, Daniel P., Subbarao, Kanta, Nefzger, Christian M., Lagendijk, Anne K., Gordon, Emma J., Parton, Robert G., Short, Kirsty R., Londrigan, Sarah L. and Schroder, Kate (2023). Macrophage ACE2 is necessary for SARS-CoV-2 replication and subsequent cytokine responses that restrict continued virion release. Science Signaling, 16 (782) eabq1366, eabq1366. doi: 10.1126/scisignal.abq1366
Harvey, Richard P., Patrick, Ralph, Janbandhu, Vaibhao and Contreras, Osvaldo (2022). Cardiac fibroblast heterogeneity and dynamics through the lens of single-cell dual 'omics. Cardiovascular Research, 118 (6), 1380-1382. doi: 10.1093/cvr/cvac037
Janbandhu, Vaibhao, Tallapragada, Vikram, Patrick, Ralph, Li, Yanzhen, Abeygunawardena, Dhanushi, Humphreys, David T., Martin, Ella M. M. A., Ward, Alexander O., Contreras, Osvaldo, Farbehi, Nona, Yao, Ernestene, Du, Junjie, Dunwoodie, Sally L., Bursac, Nenad and Harvey, Richard P. (2022). Hif-1a suppresses ROS-induced proliferation of cardiac fibroblasts following myocardial infarction. Cell Stem Cell, 29 (2), 281-297.e12. doi: 10.1016/j.stem.2021.10.009
Tombor, Lukas S., John, David, Glaser, Simone F., Luxan, Guillermo, Forte, Elvira, Furtado, Milena, Rosenthal, Nadia, Baumgarten, Nina, Schulz, Marcel H., Wittig, Janina, Rogg, Eva-Maria, Manavski, Yosif, Fischer, Ariane, Muhly-Reinholz, Marion, Klee, Kathrin, Looso, Mario, Selignow, Carmen, Acker, Till, Bibli, Sofia-Iris, Fleming, Ingrid, Patrick, Ralph, Harvey, Richard P., Abplanalp, Wesley T. and Dimmeler, Stefanie (2021). Single cell sequencing reveals endothelial plasticity with transient mesenchymal activation after myocardial infarction. Nature Communications, 12 (1) 681, 681. doi: 10.1038/s41467-021-20905-1
Patrick, Ralph, Humphreys, David T., Janbandhu, Vaibhao, Oshlack, Alicia, Ho, Joshua W. K., Harvey, Richard P. and Lo, Kitty K. (2020). Sierra: discovery of differential transcript usage from polyA-captured single-cell RNA-seq data. Genome Biology, 21 (1) 167. doi: 10.1186/s13059-020-02071-7
Vidal, Ramon, Wagner, Julian Uwe Gabriel, Braeuning, Caroline, Fischer, Cornelius, Patrick, Ralph, Tombor, Lukas, Muhly-Reinholz, Marion, John, David, Kliem, Magdalena, Conrad, Thomas, Guimarães-Camboa, Nuno, Harvey, Richard, Dimmeler, Stefanie and Sauer, Sascha (2019). Transcriptional heterogeneity of fibroblasts is a hallmark of the aging heart. JCI Insight, 4 (22) e131092. doi: 10.1172/jci.insight.131092
Combes, Alexander N., Phipson, Belinda, Lawlor, Kynan T., Dorison, Aude, Patrick, Ralph, Zappia, Luke, Harvey, Richard P., Oshlack, Alicia and Little, Melissa H. (2019). Single cell analysis of the developing mouse kidney provides deeper insight into marker gene expression and ligand-receptor crosstalk. Development, 146 (12) dev178673, dev178673. doi: 10.1242/dev.178673
Farbehi, Nona, Patrick, Ralph, Dorison, Aude, Xaymardan, Munira, Janbandhu, Vaibhao, Wystub-Lis, Katharina, Ho, Joshua W. K., Nordon, Robert E. and Harvey, Richard P. (2019). Single-cell expression profiling reveals dynamic flux of cardiac stromal,vascular and immune cells in health and injury. eLife, 8 e43882. doi: 10.7554/elife.43882
Zamir, Lyad, Singh, Reena, Nathan, Elisha, Patrick, Ralph, Yifa, Oren, Yahalom-Ronen, Yfat, Arrafi, Alaa A., Schultheiss, Thomas M., Suo, Shengbao, Han, Jing-Dong Jackie, Peng, Guangdun, Jing, Naihe, Wang, Yuliang, Palpant, Nathan, Tam, Patrick P. L., Harveyz, Richard P. and Tzahor, Eldad (2017). Nkx2.5 marks angioblasts that contribute to hemogenic endothelium of the endocardium and dorsal aorta. ELife, 6 e20994. doi: 10.7554/eLife.20994
Patrick, Ralph, Kobe, Bostjan, Lê Cao, Kim-Anh and Bodén, Mikael (2017). PhosphoPICK-SNP: quantifying the effect of amino acid variants on protein phosphorylation. Bioinformatics, 33 (12), 1773-1781. doi: 10.1093/bioinformatics/btx072
Patrick, Ralph, Horin, Coralie, Kobe, Bostjan, Cao, Kim-Anh Le and Bodén, Mikael (2016). Prediction of kinase-specific phosphorylation sites through an integrative model of protein context and sequence. Biochimica et Biophysica Acta, 1864 (11), 1599-1608. doi: 10.1016/j.bbapap.2016.08.001
Patrick, Ralph, Lê Cao, Kim-Anh, Kobe, Bostjan and Bodén, Mikael (2014). PhosphoPICK: modelling cellular context to map kinase-substrate phosphorylation events. Bioinformatics, 31 (3), 382-389. doi: 10.1093/bioinformatics/btu663
Mehdi, Ahmed M., Patrick, Ralph, Bailey, Timothy L. and Boden, Mikael (2014). Predicting the dynamics of protein abundance. Molecular and Cellular Proteomics, 13 (5), 1330-1340. doi: 10.1074/mcp.M113.033076
Patrick, Ralph, Cao, Kim-Anh L., Davis, Melissa, Kobe, Bostjan and Bodén, Mikael (2012). Mapping the stabilome: a novel computational method for classifying metabolic protein stability. BMC Systems Biology, 6 (1) 60, 60.1-60.15. doi: 10.1186/1752-0509-6-60
Conference Papers
Patil, Manisha, Cartland, Sian, Boccanfuso, Lauren, Kelland, Elaina, Patrick, Ralph, Cholan, Pradeep, Su, Peter, Ganss, Ruth, Powell, Joseph, Harvey, Richard, Griffith, Thomas, Patel, Sanjay and Kavurma, Mary (2023). TRAIL-TRAIL-R ligation regulates EC-pericyte crosstalk to generate stable microvessel networks in ischaemia. Annual Conference of the European-Society-for-Microcirculation, Aarhus Denmark, Apr 24-27, 2023. BASEL: KARGER.
Cartland, S., Patil, M., Boccanfuso, L., Kelland, E., Patrick, R., Cholan, P. Manuneedhi, Su, Q., Ganss, R., Powell, J., Harvey, R., Griffith, T., Patel, S. and Kavurma, M. (2023). TRAIL-TRAIL-R Ligation Regulates EC-Pericyte Crosstalk To Generate Stable Microvessel Networks In Ischemia. 91st Annual Meeting of the European-Atherosclerosis-Society (EAS), Mannheim, Germany, 21-24 May 2023. Shannon, Ireland: Elsevier.
Kabir, Md Humayun, Patrick, Ralph, Ho, Joshua W. K. and O'Connor, Michael D. (2018). Identification of active signaling pathways by integrating gene expression and protein interaction data. 29th International Conference on Genome Informatics (GIW) - Systems Biology, Yunnan, China, 3 - 5 December 2018. London, United Kingdom: BioMed Central. doi: 10.1186/s12918-018-0655-x
Thesis
Patrick, Ralph (2016). Molecular interaction motifs in a system-wide network context: Computationally charting transient kinase-substrate phosphorylation events. PhD Thesis, School of Chemistry & Molecular Biosciences, The University of Queensland. doi: 10.14264/uql.2016.290