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2022 Journal Article Profiling of lung SARS-CoV-2 and influenza virus infection dissects virus-specific host responses and gene signaturesKulasinghe, Arutha, Tan, Chin Wee, dos Santos Miggiolaro, Anna Flavia Ribeiro, Monkman, James, SadeghiRad, Habib, Bhuva, Dharmesh D., da Silva Motta Junior, Jarbas, Vaz de Paula, Caroline Busatta, Nagashima, Seigo, Baena, Cristina Pellegrino, Souza-Fonseca-Guimaraes, Paulo, de Noronha, Lucia, McCulloch, Timothy, Rodrigues Rossi, Gustavo, Cooper, Caroline, Tang, Benjamin, Short, Kirsty R., Davis, Melissa J., Souza-Fonseca-Guimaraes, Fernando, Belz, Gabrielle T. and O'Byrne, Ken (2022). Profiling of lung SARS-CoV-2 and influenza virus infection dissects virus-specific host responses and gene signatures. European Respiratory Journal, 59 (6) 2101881, 1-19. doi: 10.1183/13993003.01881-2021 |
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2024 Journal Article Copper chelation redirects neutrophil function to enhance anti-GD2 antibody therapy in neuroblastomaRouaen, Jourdin R. C., Salerno, Antonietta, Shai-Hee, Tyler, Murray, Jayne E., Castrogiovanni, Giulia, McHenry, Charlotte, Jue, Toni Rose, Pham, Vu, Bell, Jessica Lilian, Poursani, Ensieh, Valli, Emanuele, Cazzoli, Riccardo, Damstra, Naomi, Nelson, Delia J., Stevens, Kofi L. P., Chee, Jonathan, Slapetova, Iveta, Kasherman, Maria, Whan, Renee, Lin, Francis, Cochran, Blake J., Tedla, Nicodemus, Veli, Feyza Colakoglu, Yuksel, Aysen, Mayoh, Chelsea, Saletta, Federica, Mercatelli, Daniele, Chtanova, Tatyana, Kulasinghe, Arutha ... Vittorio, Orazio (2024). Copper chelation redirects neutrophil function to enhance anti-GD2 antibody therapy in neuroblastoma. Nature Communications, 15 (1) 10462, 10462. doi: 10.1038/s41467-024-54689-x |
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2024 Journal Article Protocol for high-plex, whole-slide imaging of human formalin-fixed paraffin-embedded tissue using PhenoCycler-FusionDonovan, Meg L., Jhaveri, Niyati, Ma, Ning, Cheikh, Bassem Ben, DeRosa, James, Mihani, Ritu, Berrell, Naomi, Suen, Jacky Y., Monkman, James, Fraser, John F. and Kulasinghe, Arutha (2024). Protocol for high-plex, whole-slide imaging of human formalin-fixed paraffin-embedded tissue using PhenoCycler-Fusion. STAR Protocols, 5 (3) 103226, 103226. doi: 10.1016/j.xpro.2024.103226 |
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2024 Journal Article Spatial resolution of the head and neck cancer tumor microenvironment to identify tumor and stromal features associated with therapy responseBerrell, Naomi, Monkman, James, Donovan, Meg, Blick, Tony, O'Byrne, Ken, Ladwa, Rahul, Tan, Chin Wee and Kulasinghe, Arutha (2024). Spatial resolution of the head and neck cancer tumor microenvironment to identify tumor and stromal features associated with therapy response. Immunology & Cell Biology, 102 (9), 830-846. doi: 10.1111/imcb.12811 |
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2024 Journal Article Spatial dynamics of tertiary lymphoid aggregates in head and neck cancer: insights into immunotherapy responseSadeghirad, Habib, Monkman, James, Tan, Chin Wee, Liu, Ning, Yunis, Joseph, Donovan, Meg L., Moradi, Afshin, Jhaveri, Niyati, Perry, Chris, Adams, Mark N., O’Byrne, Ken, Warkiani, Majid E., Ladwa, Rahul, Hughes, Brett G.M. and Kulasinghe, Arutha (2024). Spatial dynamics of tertiary lymphoid aggregates in head and neck cancer: insights into immunotherapy response. Journal of Translational Medicine, 22 (1) 677, 677. doi: 10.1186/s12967-024-05409-y |
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2024 Journal Article A mesoporous gold sensor unveils phospho PD-L1 in extracellular vesicles as a proxy for PD-L1 expression in lung cancer tissueShanmugasundaram, Karthik B., Ahmed, Emtiaz, Miao, Xinzhe, Kulasinghe, Arutha, Fletcher, James A., Monkman, James, Mainwaring, Paul, Masud, Mostafa Kamal, Park, Hyeongyu, Hossain, Md Shahriar A., Yamauchi, Yusuke, Sina, Abu A. I., O’Byrne, Kenneth, Wuethrich, Alain and Trau, Matt (2024). A mesoporous gold sensor unveils phospho PD-L1 in extracellular vesicles as a proxy for PD-L1 expression in lung cancer tissue. ACS Sensors, 9 (6), 3009-3016. doi: 10.1021/acssensors.4c00192 |
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2024 Journal Article Mapping the spatial dynamics of the CD4+ T cell spectrum in classical Hodgkin lymphomaMenéndez, Victoria, Solórzano, José L., García-Cosío, Mónica, Cereceda, Laura, Díaz, Eva, Estévez, Mónica, Roncador, Giovanna, Vega, Zaira, Montalbán, Carlos, Kulasinghe, Arutha and García, Juan F. (2024). Mapping the spatial dynamics of the CD4+ T cell spectrum in classical Hodgkin lymphoma. Modern Pathology, 37 (9) 100551, 100551. doi: 10.1016/j.modpat.2024.100551 |
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2024 Journal Article In situ characterization of the tumor microenvironmentSadeghirad, Habib, Yaghoubi Naei, Vahid, O’Byrne, Ken, Warkiani, Majid E and Kulasinghe, Arutha (2024). In situ characterization of the tumor microenvironment. Current Opinion in Biotechnology, 86 103083. doi: 10.1016/j.copbio.2024.103083 |
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2024 Journal Article Spatial insights into immunotherapy response in non-small cell lung cancer (NSCLC) by multiplexed tissue imagingMonkman, James, Moradi, Afshin, Yunis, Joseph, Ivison, Geoff, Mayer, Aaron, Ladwa, Rahul, O’Byrne, Ken and Kulasinghe, Arutha (2024). Spatial insights into immunotherapy response in non-small cell lung cancer (NSCLC) by multiplexed tissue imaging. Journal of Translational Medicine, 22 (1) 239. doi: 10.1186/s12967-024-05035-8 |
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2024 Journal Article In situ single-cell profiling sheds light on IFI27 localisation during SARS-CoV-2 infectionTan, Chin Wee, Chen, Jinjin, Liu, Ning, Bhuva, Dharmesh D., Blick, Tony, Monkman, James, Cooper, Caroline, Kharbanda, Malvika, Feher, Kristen, Phipson, Belinda, Killingbeck, Emily E., Pan, Liuliu, Kim, Youngmi, Liang, Yan, Nam, Andy, Leon, Michael, Souza-Fonseca-Guimaraes, Paulo, Nagashima, Seigo, Camargo Martins, Ana Paula, Machado-Souza, Cleber, de Noronha, Lucia, Tang, Benjamin, Short, Kirsty, Fraser, John, Belz, Gabrielle T., Souza-Fonseca-Guimaraes, Fernando, Kulasinghe, Arutha and Davis, Melissa J. (2024). In situ single-cell profiling sheds light on IFI27 localisation during SARS-CoV-2 infection. eBioMedicine, 101 105016, 1-4. doi: 10.1016/j.ebiom.2024.105016 |
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2024 Journal Article Tissue biomarkers of immune checkpoint inhibitor therapyDavoudi, Fatemeh, Moradi, Afshin, Sadeghirad, Habib and Kulasinghe, Arutha (2024). Tissue biomarkers of immune checkpoint inhibitor therapy. Immunology and Cell Biology, 102 (3), 179-193. doi: 10.1111/imcb.12723 |
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2024 Journal Article Sounding an Alarm over Spatial Biology : Scientists from across the globe highlight spatial biology's triumphs and legal trials while issuing an urgent call for antitrust actionOrr, Miranda E., Kulasinghe, Arutha, Kolar, Grant R., Heyn, Holger, Plummer, Jasmine, Kristensen, Lasse Sommer, Kjems, Jorgen, Mills, Gordon, Garcia-Vallejo, Juan J., Nijman, I.J., West, Nicholas P. and Cox, Amanda (2024). Sounding an Alarm over Spatial Biology : Scientists from across the globe highlight spatial biology's triumphs and legal trials while issuing an urgent call for antitrust action. Genetic Engineering & Biotechnology News, 44 (3), 16-17. doi: 10.1089/gen.44.03.07 |
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2024 Journal Article Poor patient outcome correlates with active engulfment of cytokeratin positive CTCs within cancer-associated monocyte population in lung cancerWiegmans, A. P., Ivanova, E., Naei, V. Y., Monkman, J., Fletcher, J., Mullally, W., Warkiani, M. E., O’Byrne, K. and Kulasinghe, A. (2024). Poor patient outcome correlates with active engulfment of cytokeratin positive CTCs within cancer-associated monocyte population in lung cancer. Clinical and Experimental Metastasis, 41 (2), 219-228. doi: 10.1007/s10585-024-10270-w |
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2024 Journal Article Whole transcriptome profiling of placental pathobiology in SARS‐CoV‐2 pregnancies identifies placental dysfunction signaturesStylianou, Nataly, Sebina, Ismail, Matigian, Nicholas, Monkman, James, Doehler, Hadeel, Röhl, Joan, Allenby, Mark, Nam, Andy, Pan, Liuliu, Rockstroh, Anja, Sadeghirad, Habib, Chung, Kimberly, Sobanski, Thais, O'Byrne, Ken, Almeida, Ana Clara Simoes Florido, Rebutini, Patricia Zadorosnei, Machado‐Souza, Cleber, Stonoga, Emanuele Therezinha Schueda, Warkiani, Majid E, Salomon, Carlos, Short, Kirsty, McClements, Lana, de Noronha, Lucia, Huang, Ruby, Belz, Gabrielle T, Souza‐Fonseca‐Guimaraes, Fernando, Clifton, Vicki and Kulasinghe, Arutha (2024). Whole transcriptome profiling of placental pathobiology in SARS‐CoV‐2 pregnancies identifies placental dysfunction signatures. Clinical and Translational Immunology, 13 (2) e1488, e1488. doi: 10.1002/cti2.1488 |
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2024 Journal Article The in situ transcriptomic landscape of breast tumour-associated and normal adjacent endothelial cellsRavichandran, Akhilandeshwari, Monkman, James, Mehdi, Ahmed M., Blick, Tony, Snell, Cameron, Kulasinghe, Arutha and Bray, Laura J. (2024). The in situ transcriptomic landscape of breast tumour-associated and normal adjacent endothelial cells. Biochimica et Biophysica Acta (BBA) - Molecular Basis of Disease, 1870 (2) 166985. doi: 10.1016/j.bbadis.2023.166985 |
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2024 Journal Article Host transcriptomics and machine learning for secondary bacterial infections in patients with COVID-19: a prospective, observational cohort studyCarney, Meagan, Pelaia, Tiana Maria, Chew, Tracy, Teoh, Sally, Phu, Amy, Kim, Karan, Wang, Ya, Iredell, Jonathan, Zerbib, Yoann, McLean, Anthony, Schughart, Klaus, Tang, Benjamin, Shojaei, Maryam, Short, Kirsty R, PREDICT-19 consortium and Kulasinghe, Arutha (PREDICT-19 consortium member) (2024). Host transcriptomics and machine learning for secondary bacterial infections in patients with COVID-19: a prospective, observational cohort study. The Lancet Microbe, 5 (3), e272-e281. doi: 10.1016/S2666-5247(23)00363-4 |
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2024 Journal Article Inhibition of Aurora B kinase (AURKB) enhances the effectiveness of 5-fluorouracil chemotherapy against colorectal cancer cellsShah, Esha T., Molloy, Christopher, Gough, Madeline, Kryza, Thomas, Samuel, Selwin G., Tucker, Amos, Bhatia, Maneet, Ferguson, Genevieve, Heyman, Rebecca, Vora, Shivam, Monkman, James, Bolderson, Emma, Kulasinghe, Arutha, He, Yaowu, Gabrielli, Brian, Hooper, John D., Richard, Derek J., O’Byrne, Kenneth J. and Adams, Mark N. (2024). Inhibition of Aurora B kinase (AURKB) enhances the effectiveness of 5-fluorouracil chemotherapy against colorectal cancer cells. British Journal of Cancer, 130 (7), 1196-1205. doi: 10.1038/s41416-024-02584-z |
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2024 Journal Article Characterisation of circulating tumor‐associated and immune cells in patients with advanced‐stage non‐small cell lung cancerYaghoubi Naei, Vahid, Ivanova, Ekaterina, Mullally, William, O'Leary, Connor G, Ladwa, Rahul, O'Byrne, Ken, Warkiani, Majid E and Kulasinghe, Arutha (2024). Characterisation of circulating tumor‐associated and immune cells in patients with advanced‐stage non‐small cell lung cancer. Clinical & Translational Immunology, 13 (6) e1516, e1516. doi: 10.1002/cti2.1516 |
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2024 Journal Article standR: spatial transcriptomic analysis for GeoMx DSP dataLiu, Ning, Bhuva, Dharmesh D, Mohamed, Ahmed, Bokelund, Micah, Kulasinghe, Arutha, Tan, Chin Wee and Davis, Melissa J (2024). standR: spatial transcriptomic analysis for GeoMx DSP data. Nucleic Acids Research, 52 (1) e2, 1-11. doi: 10.1093/nar/gkad1026 |
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2024 Journal Article Leveraging spatial omics for the development of precision sarcoma treatmentsTu, Cui, Kulasinghe, Arutha, Barbour, Andrew and Souza-Fonseca-Guimaraes, Fernando (2024). Leveraging spatial omics for the development of precision sarcoma treatments. Trends in Pharmacological Sciences, 45 (2), 134-144. doi: 10.1016/j.tips.2023.12.006 |
