Conference Publication: 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.
Journal Article: 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
Journal Article: 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
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
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
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
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
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
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
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
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.
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
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