Dr Ralph Patrick
Postdoctoral Research Fellow
Institute for Molecular Bioscience
Journal Articles
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 Paper
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