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2024 Journal Article The generation of stable microvessels in ischemia is mediated by endothelial cell derived TRAILCartland, 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, eadn8760. doi: 10.1126/sciadv.adn8760 |
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2024 Journal Article The activity of early-life gene regulatory elements is hijacked in aging through pervasive AP-1-linked chromatin openingPatrick, 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 |
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2024 Journal Article Integration mapping of cardiac fibroblast single-cell transcriptomes elucidates cellular principles of fibrosis in diverse pathologiesPatrick, 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 |
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2024 Journal Article Novel mouse model for selective tagging, purification, and manipulation of cardiac myofibroblastsJanbandhu, 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 |
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2023 Journal Article Extracellular matrix protein-1 as a mediator of inflammation-induced fibrosis after myocardial infarctionHardy, 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 |
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2023 Journal Article Fibulin-3 is necessary to prevent cardiac rupture following myocardial infarctionMurtha, 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 |
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2023 Journal Article Quantitative trait and transcriptome analysis of genetic complexity underpinning cardiac interatrial septation in mice using an advanced intercross lineMoradi 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 |
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2023 Journal Article Macrophage ACE2 is necessary for SARS-CoV-2 replication and subsequent cytokine responses that restrict continued virion releaseLabzin, 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 |
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2022 Journal Article Cardiac fibroblast heterogeneity and dynamics through the lens of single-cell dual 'omicsHarvey, 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 |
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2022 Journal Article Hif-1a suppresses ROS-induced proliferation of cardiac fibroblasts following myocardial infarctionJanbandhu, 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 |
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2021 Journal Article Single cell sequencing reveals endothelial plasticity with transient mesenchymal activation after myocardial infarctionTombor, 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 |
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2020 Journal Article Sierra: discovery of differential transcript usage from polyA-captured single-cell RNA-seq dataPatrick, 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 |
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2019 Journal Article Transcriptional heterogeneity of fibroblasts is a hallmark of the aging heartVidal, 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 |
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2019 Journal Article Single cell analysis of the developing mouse kidney provides deeper insight into marker gene expression and ligand-receptor crosstalkCombes, 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 |
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2019 Journal Article Single-cell expression profiling reveals dynamic flux of cardiac stromal,vascular and immune cells in health and injuryFarbehi, 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 |
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2017 Journal Article Nkx2.5 marks angioblasts that contribute to hemogenic endothelium of the endocardium and dorsal aortaZamir, 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 |
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2017 Journal Article PhosphoPICK-SNP: quantifying the effect of amino acid variants on protein phosphorylationPatrick, 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 |
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2016 Journal Article Prediction of kinase-specific phosphorylation sites through an integrative model of protein context and sequencePatrick, 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 |
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2014 Journal Article PhosphoPICK: modelling cellular context to map kinase-substrate phosphorylation eventsPatrick, 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 |
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2014 Journal Article Predicting the dynamics of protein abundanceMehdi, 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 |
