The University of Queensland

The activity of early-life gene regulatory elements is hijacked in aging through pervasive AP-1-linked chromatin opening

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. doi: 10.1016/j.cmet.2024.06.006

Integration mapping of cardiac fibroblast single-cell transcriptomes elucidates cellular principles of fibrosis in diverse pathologies

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

Novel Mouse Model for Selective Tagging, Purification, and Manipulation of Cardiac Myofibroblasts

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

Extracellular matrix protein-1 as a mediator of inflammation-induced fibrosis after myocardial infarction

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

Fibulin-3 is necessary to prevent cardiac rupture following myocardial infarction

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

Quantitative trait and transcriptome analysis of genetic complexity underpinning cardiac interatrial septation in mice using an advanced intercross line

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

Macrophage ACE2 is necessary for SARS-CoV-2 replication and subsequent cytokine responses that restrict continued virion release

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

Cardiac fibroblast heterogeneity and dynamics through the lens of single-cell dual 'omics

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

Hif-1a suppresses ROS-induced proliferation of cardiac fibroblasts following myocardial infarction

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

Single cell sequencing reveals endothelial plasticity with transient mesenchymal activation after myocardial infarction

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

Sierra: discovery of differential transcript usage from polyA-captured single-cell RNA-seq data

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

Transcriptional heterogeneity of fibroblasts is a hallmark of the aging heart

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

Single cell analysis of the developing mouse kidney provides deeper insight into marker gene expression and ligand-receptor crosstalk

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

Single-cell expression profiling reveals dynamic flux of cardiac stromal,vascular and immune cells in health and injury

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

Nkx2.5 marks angioblasts that contribute to hemogenic endothelium of the endocardium and dorsal aorta

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

PhosphoPICK-SNP: quantifying the effect of amino acid variants on protein phosphorylation

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

Prediction of kinase-specific phosphorylation sites through an integrative model of protein context and sequence

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

PhosphoPICK: modelling cellular context to map kinase-substrate phosphorylation events

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

Predicting the dynamics of protein abundance

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

Mapping the stabilome: a novel computational method for classifying metabolic protein stability

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

TRAIL-TRAIL-R ligation regulates EC-pericyte crosstalk to generate stable microvessel networks in ischaemia

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.

Identification of active signaling pathways by integrating gene expression and protein interaction data

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

Molecular interaction motifs in a system-wide network context: Computationally charting transient kinase-substrate phosphorylation events

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