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138 results on '"Oliver, Amanda J"'

1. Gene-level alignment of single-cell trajectories

Author

Sumanaweera, Dinithi, Suo, Chenqu, Cujba, Ana-Maria, Muraro, Daniele, Dann, Emma, Polanski, Krzysztof, Steemers, Alexander S., Lee, Woochan, Oliver, Amanda J., Park, Jong-Eun, Meyer, Kerstin B., Dumitrascu, Bianca, and Teichmann, Sarah A.

Published
2025
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3. An organotypic atlas of human vascular cells

Author

Barnett, Sam N., Cujba, Ana-Maria, Yang, Lu, Maceiras, Ana Raquel, Li, Shuang, Kedlian, Veronika R., Pett, J. Patrick, Polanski, Krzysztof, Miranda, Antonio M. A., Xu, Chuan, Cranley, James, Kanemaru, Kazumasa, Lee, Michael, Mach, Lukas, Perera, Shani, Tudor, Catherine, Joseph, Philomeena D., Pritchard, Sophie, Toscano-Rivalta, Rebecca, Tuong, Zewen K., Bolt, Liam, Petryszak, Robert, Prete, Martin, Cakir, Batuhan, Huseynov, Alik, Sarropoulos, Ioannis, Chowdhury, Rasheda A., Elmentaite, Rasa, Madissoon, Elo, Oliver, Amanda J., Campos, Lia, Brazovskaja, Agnieska, Gomes, Tomás, Treutlein, Barbara, Kim, Chang N., Nowakowski, Tomasz J., Meyer, Kerstin B., Randi, Anna M., Noseda, Michela, and Teichmann, Sarah A.

Published
2024
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4. Single-cell integration reveals metaplasia in inflammatory gut diseases

Author

Oliver, Amanda J., Huang, Ni, Bartolome-Casado, Raquel, Li, Ruoyan, Koplev, Simon, Nilsen, Hogne R., Moy, Madelyn, Cakir, Batuhan, Polanski, Krzysztof, Gudiño, Victoria, Melón-Ardanaz, Elisa, Sumanaweera, Dinithi, Dimitrov, Daniel, Milchsack, Lisa Marie, FitzPatrick, Michael E. B., Provine, Nicholas M., Boccacino, Jacqueline M., Dann, Emma, Predeus, Alexander V., To, Ken, Prete, Martin, Chapman, Jonathan A., Masi, Andrea C., Stephenson, Emily, Engelbert, Justin, Lobentanzer, Sebastian, Perera, Shani, Richardson, Laura, Kapuge, Rakeshlal, Wilbrey-Clark, Anna, Semprich, Claudia I., Ellams, Sophie, Tudor, Catherine, Joseph, Philomeena, Garrido-Trigo, Alba, Corraliza, Ana M., Oliver, Thomas R. W., Hook, C. Elizabeth, James, Kylie R., Mahbubani, Krishnaa T., Saeb-Parsy, Kourosh, Zilbauer, Matthias, Saez-Rodriguez, Julio, Høivik, Marte Lie, Bækkevold, Espen S., Stewart, Christopher J., Berrington, Janet E., Meyer, Kerstin B., Klenerman, Paul, Salas, Azucena, Haniffa, Muzlifah, Jahnsen, Frode L., Elmentaite, Rasa, and Teichmann, Sarah A.

Published
2024
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5. An integrated cell atlas of the lung in health and disease

Author

Sikkema, Lisa, Ramírez-Suástegui, Ciro, Strobl, Daniel C, Gillett, Tessa E, Zappia, Luke, Madissoon, Elo, Markov, Nikolay S, Zaragosi, Laure-Emmanuelle, Ji, Yuge, Ansari, Meshal, Arguel, Marie-Jeanne, Apperloo, Leonie, Banchero, Martin, Bécavin, Christophe, Berg, Marijn, Chichelnitskiy, Evgeny, Chung, Mei-i, Collin, Antoine, Gay, Aurore CA, Gote-Schniering, Janine, Hooshiar Kashani, Baharak, Inecik, Kemal, Jain, Manu, Kapellos, Theodore S, Kole, Tessa M, Leroy, Sylvie, Mayr, Christoph H, Oliver, Amanda J, von Papen, Michael, Peter, Lance, Taylor, Chase J, Walzthoeni, Thomas, Xu, Chuan, Bui, Linh T, De Donno, Carlo, Dony, Leander, Faiz, Alen, Guo, Minzhe, Gutierrez, Austin J, Heumos, Lukas, Huang, Ni, Ibarra, Ignacio L, Jackson, Nathan D, Kadur Lakshminarasimha Murthy, Preetish, Lotfollahi, Mohammad, Tabib, Tracy, Talavera-López, Carlos, Travaglini, Kyle J, Wilbrey-Clark, Anna, Worlock, Kaylee B, Yoshida, Masahiro, van den Berge, Maarten, Bossé, Yohan, Desai, Tushar J, Eickelberg, Oliver, Kaminski, Naftali, Krasnow, Mark A, Lafyatis, Robert, Nikolic, Marko Z, Powell, Joseph E, Rajagopal, Jayaraj, Rojas, Mauricio, Rozenblatt-Rosen, Orit, Seibold, Max A, Sheppard, Dean, Shepherd, Douglas P, Sin, Don D, Timens, Wim, Tsankov, Alexander M, Whitsett, Jeffrey, Xu, Yan, Banovich, Nicholas E, Barbry, Pascal, Duong, Thu Elizabeth, Falk, Christine S, Meyer, Kerstin B, Kropski, Jonathan A, Pe’er, Dana, Schiller, Herbert B, Tata, Purushothama Rao, Schultze, Joachim L, Teichmann, Sara A, Misharin, Alexander V, Nawijn, Martijn C, Luecken, Malte D, and Theis, Fabian J

Subjects
Biomedical and Clinical Sciences, Health Sciences, Lung, Genetics, 2.1 Biological and endogenous factors, 1.1 Normal biological development and functioning, Generic health relevance, Respiratory, Good Health and Well Being, Humans, COVID-19, Pulmonary Fibrosis, Lung Neoplasms, Macrophages, Lung Biological Network Consortium, Medical and Health Sciences, Immunology, Biomedical and clinical sciences, Health sciences
Abstract

Single-cell technologies have transformed our understanding of human tissues. Yet, studies typically capture only a limited number of donors and disagree on cell type definitions. Integrating many single-cell datasets can address these limitations of individual studies and capture the variability present in the population. Here we present the integrated Human Lung Cell Atlas (HLCA), combining 49 datasets of the human respiratory system into a single atlas spanning over 2.4 million cells from 486 individuals. The HLCA presents a consensus cell type re-annotation with matching marker genes, including annotations of rare and previously undescribed cell types. Leveraging the number and diversity of individuals in the HLCA, we identify gene modules that are associated with demographic covariates such as age, sex and body mass index, as well as gene modules changing expression along the proximal-to-distal axis of the bronchial tree. Mapping new data to the HLCA enables rapid data annotation and interpretation. Using the HLCA as a reference for the study of disease, we identify shared cell states across multiple lung diseases, including SPP1+ profibrotic monocyte-derived macrophages in COVID-19, pulmonary fibrosis and lung carcinoma. Overall, the HLCA serves as an example for the development and use of large-scale, cross-dataset organ atlases within the Human Cell Atlas.

Published
2023

7. A spatially resolved atlas of the human lung characterizes a gland-associated immune niche

Author

Madissoon, Elo, Oliver, Amanda J., Kleshchevnikov, Vitalii, Wilbrey-Clark, Anna, Polanski, Krzysztof, Richoz, Nathan, Ribeiro Orsi, Ana, Mamanova, Lira, Bolt, Liam, Elmentaite, Rasa, Pett, J. Patrick, Huang, Ni, Xu, Chuan, He, Peng, Dabrowska, Monika, Pritchard, Sophie, Tuck, Liz, Prigmore, Elena, Perera, Shani, Knights, Andrew, Oszlanczi, Agnes, Hunter, Adam, Vieira, Sara F., Patel, Minal, Lindeboom, Rik G. H., Campos, Lia S., Matsuo, Kazuhiko, Nakayama, Takashi, Yoshida, Masahiro, Worlock, Kaylee B., Nikolić, Marko Z., Georgakopoulos, Nikitas, Mahbubani, Krishnaa T., Saeb-Parsy, Kourosh, Bayraktar, Omer Ali, Clatworthy, Menna R., Stegle, Oliver, Kumasaka, Natsuhiko, Teichmann, Sarah A., and Meyer, Kerstin B.

Published
2023
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8. Enterotoxins can support CAR T cells against solid tumors

Author

von Scheidt, Bianca, Wang, Minyu, Oliver, Amanda J., Chan, Jack D., Jana, Metta K., Ali, Aesha I., Clow, Fiona, Fraser, John D., Quinn, Kylie M., Darcy, Phillip K., Kershaw, Michael H., and Slaney, Clare Y.

Published
2019

9. MAIT cells regulate NK cell-mediated tumor immunity

Author

Petley, Emma V., Koay, Hui-Fern, Henderson, Melissa A., Sek, Kevin, Todd, Kirsten L., Keam, Simon P., Lai, Junyun, House, Imran G., Li, Jasmine, Zethoven, Magnus, Chen, Amanda X. Y., Oliver, Amanda J., Michie, Jessica, Freeman, Andrew J., Giuffrida, Lauren, Chan, Jack D., Pizzolla, Angela, Mak, Jeffrey Y. W., McCulloch, Timothy R., Souza-Fonseca-Guimaraes, Fernando, Kearney, Conor J., Millen, Rosemary, Ramsay, Robert G., Huntington, Nicholas D., McCluskey, James, Oliaro, Jane, Fairlie, David P., Neeson, Paul J., Godfrey, Dale I., Beavis, Paul A., and Darcy, Phillip K.

Published
2021
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10. Early human lung immune cell development and its role in epithelial cell fate

Author

Barnes, Josephine L., primary, Yoshida, Masahiro, additional, He, Peng, additional, Worlock, Kaylee B., additional, Lindeboom, Rik G.H., additional, Suo, Chenqu, additional, Pett, J. Patrick, additional, Wilbrey-Clark, Anna, additional, Dann, Emma, additional, Mamanova, Lira, additional, Richardson, Laura, additional, Polanski, Krzysztof, additional, Pennycuick, Adam, additional, Allen-Hyttinen, Jessica, additional, Herczeg, Iván T., additional, Arzili, Romina, additional, Hynds, Robert E., additional, Teixeira, Vitor H., additional, Haniffa, Muzlifah, additional, Lim, Kyungtae, additional, Sun, Dawei, additional, Rawlins, Emma L., additional, Oliver, Amanda J., additional, Lyons, Paul A., additional, Marioni, John C., additional, Ruhrberg, Christiana, additional, Tuong, Zewen Kelvin, additional, Clatworthy, Menna R., additional, Reading, James L., additional, Janes, Sam M., additional, Teichmann, Sarah A., additional, Meyer, Kerstin B., additional, and Nikolić, Marko Z., additional

Published
2023
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11. Expression profiling of cerebrospinal fluid identifies dysregulated antiviral mechanisms in multiple sclerosis.

Author

Ban, Maria, Bredikhin, Danila, Huang, Yuanhua, Bonder, Marc Jan, Katarzyna, Kania, Oliver, Amanda J, Wilson, Nicola K, Coupland, Paul, Hadfield, James, Göttgens, Berthold, Madissoon, Elo, Stegle, Oliver, and Sawcer, Stephen

Subjects
GENE expression, MULTIPLE sclerosis, CEREBROSPINAL fluid, LOCUS (Genetics), AUTOIMMUNE diseases, RNA splicing
Abstract

Despite the overwhelming evidence that multiple sclerosis is an autoimmune disease, relatively little is known about the precise nature of the immune dysregulation underlying the development of the disease. Reasoning that the CSF from patients might be enriched for cells relevant in pathogenesis, we have completed a high-resolution single-cell analysis of 96 732 CSF cells collected from 33 patients with multiple sclerosis (n = 48 675) and 48 patients with other neurological diseases (n = 48 057). Completing comprehensive cell type annotation, we identified a rare population of CD8+ T cells, characterized by the upregulation of inhibitory receptors, increased in patients with multiple sclerosis. Applying a Multi-Omics Factor Analysis to these single-cell data further revealed that activity in pathways responsible for controlling inflammatory and type 1 interferon responses are altered in multiple sclerosis in both T cells and myeloid cells. We also undertook a systematic search for expression quantitative trait loci in the CSF cells. Of particular interest were two expression quantitative trait loci in CD8+ T cells that were fine mapped to multiple sclerosis susceptibility variants in the viral control genes ZC3HAV1 (rs10271373) and IFITM2 (rs1059091). Further analysis suggests that these associations likely reflect genetic effects on RNA splicing and cell-type specific gene expression respectively. Collectively, our study suggests that alterations in viral control mechanisms might be important in the development of multiple sclerosis. [ABSTRACT FROM AUTHOR]

Published
2024
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14. Supplementary Table S1 from Combined BRAF, MEK, and CDK4/6 Inhibition Depletes Intratumoral Immune-Potentiating Myeloid Populations in Melanoma

Author

Lelliott, Emily J., primary, Mangiola, Stefano, primary, Ramsbottom, Kelly M., primary, Zethoven, Magnus, primary, Lim, Lydia, primary, Lau, Peter K.H., primary, Oliver, Amanda J., primary, Martelotto, Luciano G., primary, Kirby, Laura, primary, Martin, Claire, primary, Patel, Riyaben P., primary, Slater, Alison, primary, Cullinane, Carleen, primary, Papenfuss, Anthony T., primary, Haynes, Nicole M., primary, McArthur, Grant A., primary, Oliaro, Jane, primary, and Sheppard, Karen E., primary

Published
2023
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15. Data from Combined BRAF, MEK, and CDK4/6 Inhibition Depletes Intratumoral Immune-Potentiating Myeloid Populations in Melanoma

Author

Lelliott, Emily J., primary, Mangiola, Stefano, primary, Ramsbottom, Kelly M., primary, Zethoven, Magnus, primary, Lim, Lydia, primary, Lau, Peter K.H., primary, Oliver, Amanda J., primary, Martelotto, Luciano G., primary, Kirby, Laura, primary, Martin, Claire, primary, Patel, Riyaben P., primary, Slater, Alison, primary, Cullinane, Carleen, primary, Papenfuss, Anthony T., primary, Haynes, Nicole M., primary, McArthur, Grant A., primary, Oliaro, Jane, primary, and Sheppard, Karen E., primary

Published
2023
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16. Supplementary Figures from Combined BRAF, MEK, and CDK4/6 Inhibition Depletes Intratumoral Immune-Potentiating Myeloid Populations in Melanoma

Author

Lelliott, Emily J., primary, Mangiola, Stefano, primary, Ramsbottom, Kelly M., primary, Zethoven, Magnus, primary, Lim, Lydia, primary, Lau, Peter K.H., primary, Oliver, Amanda J., primary, Martelotto, Luciano G., primary, Kirby, Laura, primary, Martin, Claire, primary, Patel, Riyaben P., primary, Slater, Alison, primary, Cullinane, Carleen, primary, Papenfuss, Anthony T., primary, Haynes, Nicole M., primary, McArthur, Grant A., primary, Oliaro, Jane, primary, and Sheppard, Karen E., primary

Published
2023
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17. Figure S4 from Macrophage-Derived CXCL9 and CXCL10 Are Required for Antitumor Immune Responses Following Immune Checkpoint Blockade

Author

House, Imran G., primary, Savas, Peter, primary, Lai, Junyun, primary, Chen, Amanda X.Y., primary, Oliver, Amanda J., primary, Teo, Zhi L., primary, Todd, Kirsten L., primary, Henderson, Melissa A., primary, Giuffrida, Lauren, primary, Petley, Emma V., primary, Sek, Kevin, primary, Mardiana, Sherly, primary, Gide, Tuba N., primary, Quek, Camelia, primary, Scolyer, Richard A., primary, Long, Georgina V., primary, Wilmott, James S., primary, Loi, Sherene, primary, Darcy, Phillip K., primary, and Beavis, Paul A., primary

Published
2023
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18. Supplementary Figure Legends from Macrophage-Derived CXCL9 and CXCL10 Are Required for Antitumor Immune Responses Following Immune Checkpoint Blockade

Author

House, Imran G., primary, Savas, Peter, primary, Lai, Junyun, primary, Chen, Amanda X.Y., primary, Oliver, Amanda J., primary, Teo, Zhi L., primary, Todd, Kirsten L., primary, Henderson, Melissa A., primary, Giuffrida, Lauren, primary, Petley, Emma V., primary, Sek, Kevin, primary, Mardiana, Sherly, primary, Gide, Tuba N., primary, Quek, Camelia, primary, Scolyer, Richard A., primary, Long, Georgina V., primary, Wilmott, James S., primary, Loi, Sherene, primary, Darcy, Phillip K., primary, and Beavis, Paul A., primary

Published
2023
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19. Supplementary Figure 7 from A Histone Deacetylase Inhibitor, Panobinostat, Enhances Chimeric Antigen Receptor T-cell Antitumor Effect Against Pancreatic Cancer

Author

Ali, Aesha I., primary, Wang, Minyu, primary, von Scheidt, Bianca, primary, Dominguez, Pilar M., primary, Harrison, Aaron J., primary, Tantalo, Daniela G.M., primary, Kang, Jian, primary, Oliver, Amanda J., primary, Chan, Jack D., primary, Du, Xin, primary, Bai, Yuchen, primary, Lee, Belinda, primary, Johnstone, Ricky W., primary, Darcy, Phillip K., primary, Kershaw, Michael H., primary, and Slaney, Clare Y., primary

Published
2023
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20. Supplementary Figure 3 from A Histone Deacetylase Inhibitor, Panobinostat, Enhances Chimeric Antigen Receptor T-cell Antitumor Effect Against Pancreatic Cancer

Author

Ali, Aesha I., primary, Wang, Minyu, primary, von Scheidt, Bianca, primary, Dominguez, Pilar M., primary, Harrison, Aaron J., primary, Tantalo, Daniela G.M., primary, Kang, Jian, primary, Oliver, Amanda J., primary, Chan, Jack D., primary, Du, Xin, primary, Bai, Yuchen, primary, Lee, Belinda, primary, Johnstone, Ricky W., primary, Darcy, Phillip K., primary, Kershaw, Michael H., primary, and Slaney, Clare Y., primary

Published
2023
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21. Supplementary Figure 4 from A Histone Deacetylase Inhibitor, Panobinostat, Enhances Chimeric Antigen Receptor T-cell Antitumor Effect Against Pancreatic Cancer

Author

Ali, Aesha I., primary, Wang, Minyu, primary, von Scheidt, Bianca, primary, Dominguez, Pilar M., primary, Harrison, Aaron J., primary, Tantalo, Daniela G.M., primary, Kang, Jian, primary, Oliver, Amanda J., primary, Chan, Jack D., primary, Du, Xin, primary, Bai, Yuchen, primary, Lee, Belinda, primary, Johnstone, Ricky W., primary, Darcy, Phillip K., primary, Kershaw, Michael H., primary, and Slaney, Clare Y., primary

Published
2023
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22. Supplementary Figure 1 from A Histone Deacetylase Inhibitor, Panobinostat, Enhances Chimeric Antigen Receptor T-cell Antitumor Effect Against Pancreatic Cancer

Author

Ali, Aesha I., primary, Wang, Minyu, primary, von Scheidt, Bianca, primary, Dominguez, Pilar M., primary, Harrison, Aaron J., primary, Tantalo, Daniela G.M., primary, Kang, Jian, primary, Oliver, Amanda J., primary, Chan, Jack D., primary, Du, Xin, primary, Bai, Yuchen, primary, Lee, Belinda, primary, Johnstone, Ricky W., primary, Darcy, Phillip K., primary, Kershaw, Michael H., primary, and Slaney, Clare Y., primary

Published
2023
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23. Supplementary Figure 8 from A Histone Deacetylase Inhibitor, Panobinostat, Enhances Chimeric Antigen Receptor T-cell Antitumor Effect Against Pancreatic Cancer

Author

Ali, Aesha I., primary, Wang, Minyu, primary, von Scheidt, Bianca, primary, Dominguez, Pilar M., primary, Harrison, Aaron J., primary, Tantalo, Daniela G.M., primary, Kang, Jian, primary, Oliver, Amanda J., primary, Chan, Jack D., primary, Du, Xin, primary, Bai, Yuchen, primary, Lee, Belinda, primary, Johnstone, Ricky W., primary, Darcy, Phillip K., primary, Kershaw, Michael H., primary, and Slaney, Clare Y., primary

Published
2023
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24. Supplementary Figure 5 from A Histone Deacetylase Inhibitor, Panobinostat, Enhances Chimeric Antigen Receptor T-cell Antitumor Effect Against Pancreatic Cancer

Author

Ali, Aesha I., primary, Wang, Minyu, primary, von Scheidt, Bianca, primary, Dominguez, Pilar M., primary, Harrison, Aaron J., primary, Tantalo, Daniela G.M., primary, Kang, Jian, primary, Oliver, Amanda J., primary, Chan, Jack D., primary, Du, Xin, primary, Bai, Yuchen, primary, Lee, Belinda, primary, Johnstone, Ricky W., primary, Darcy, Phillip K., primary, Kershaw, Michael H., primary, and Slaney, Clare Y., primary

Published
2023
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25. Supplementary Figure 6 from A Histone Deacetylase Inhibitor, Panobinostat, Enhances Chimeric Antigen Receptor T-cell Antitumor Effect Against Pancreatic Cancer

Author

Ali, Aesha I., primary, Wang, Minyu, primary, von Scheidt, Bianca, primary, Dominguez, Pilar M., primary, Harrison, Aaron J., primary, Tantalo, Daniela G.M., primary, Kang, Jian, primary, Oliver, Amanda J., primary, Chan, Jack D., primary, Du, Xin, primary, Bai, Yuchen, primary, Lee, Belinda, primary, Johnstone, Ricky W., primary, Darcy, Phillip K., primary, Kershaw, Michael H., primary, and Slaney, Clare Y., primary

Published
2023
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26. Supplementary Figure 2 from A Histone Deacetylase Inhibitor, Panobinostat, Enhances Chimeric Antigen Receptor T-cell Antitumor Effect Against Pancreatic Cancer

Author

Ali, Aesha I., primary, Wang, Minyu, primary, von Scheidt, Bianca, primary, Dominguez, Pilar M., primary, Harrison, Aaron J., primary, Tantalo, Daniela G.M., primary, Kang, Jian, primary, Oliver, Amanda J., primary, Chan, Jack D., primary, Du, Xin, primary, Bai, Yuchen, primary, Lee, Belinda, primary, Johnstone, Ricky W., primary, Darcy, Phillip K., primary, Kershaw, Michael H., primary, and Slaney, Clare Y., primary

Published
2023
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27. Gene-level alignment of single cell trajectories

Author

Sumanaweera, Dinithi, primary, Suo, Chenqu, additional, Cujba, Ana-Maria, additional, Muraro, Daniele, additional, Dann, Emma, additional, Polanski, Krzysztof, additional, Steemers, Alexander S., additional, Lee, Woochan, additional, Oliver, Amanda J., additional, Park, Jong-Eun, additional, Meyer, Kerstin B., additional, Dumitrascu, Bianca, additional, and Teichmann, Sarah A., additional

Published
2023
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28. A spatially resolved atlas of the human lung characterizes a gland-associated immune niche

Author

Madissoon, Elo, primary, Oliver, Amanda J., additional, Kleshchevnikov, Vitalii, additional, Wilbrey-Clark, Anna, additional, Polanski, Krzysztof, additional, Richoz, Nathan, additional, Ribeiro Orsi, Ana, additional, Mamanova, Lira, additional, Bolt, Liam, additional, Elmentaite, Rasa, additional, Pett, J. Patrick, additional, Huang, Ni, additional, Xu, Chuan, additional, He, Peng, additional, Dabrowska, Monika, additional, Pritchard, Sophie, additional, Tuck, Liz, additional, Prigmore, Elena, additional, Perera, Shani, additional, Knights, Andrew, additional, Oszlanczi, Agnes, additional, Hunter, Adam, additional, Vieira, Sara F., additional, Patel, Minal, additional, Lindeboom, Rik G. H., additional, Campos, Lia S., additional, Matsuo, Kazuhiko, additional, Nakayama, Takashi, additional, Yoshida, Masahiro, additional, Worlock, Kaylee B., additional, Nikolić, Marko Z., additional, Georgakopoulos, Nikitas, additional, Mahbubani, Krishnaa T., additional, Saeb-Parsy, Kourosh, additional, Bayraktar, Omer Ali, additional, Clatworthy, Menna R., additional, Stegle, Oliver, additional, Kumasaka, Natsuhiko, additional, Teichmann, Sarah A., additional, and Meyer, Kerstin B., additional

Published
2022
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29. Early human lung immune cell development and its role in epithelial cell fate

Author

Barnes, Josephine L., primary, He, Peng, additional, Yoshida, Masahiro, additional, Worlock, Kaylee B., additional, Lindeboom, Rik G.H., additional, Suo, Chenqu, additional, Pett, J. Patrick, additional, Wilbrey-Clark, Anna, additional, Dann, Emma, additional, Mamanova, Lira, additional, Richardson, Laura, additional, Oliver, Amanda J., additional, Pennycuick, Adam, additional, Allen-Hyttinen, Jessica, additional, Herczeg, Iván T., additional, Hynds, Robert E., additional, Teixeira, Vitor H., additional, Haniffa, Muzlifah, additional, Lim, Kyungtae, additional, Sun, Dawei, additional, Rawlins, Emma L., additional, Polanski, Krzysztof, additional, Lyons, Paul A., additional, Marioni, John C., additional, Tuong, Zewen Kelvin, additional, Clatworthy, Menna R., additional, Reading, James L., additional, Janes, Sam M., additional, Teichmann, Sarah A., additional, Meyer, Kerstin B., additional, and Nikolić, Marko Z., additional

Published
2022
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30. A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche

Author

Madissoon, Elo, primary, Oliver, Amanda J., additional, Kleshchevnikov, Vitalii, additional, Wilbrey-Clark, Anna, additional, Polanski, Krzysztof, additional, Orsi, Ana Ribeiro, additional, Mamanova, Lira, additional, Bolt, Liam, additional, Richoz, Nathan, additional, Elmentaite, Rasa, additional, Pett, J. Patrick, additional, Huang, Ni, additional, He, Peng, additional, Dabrowska, Monika, additional, Pritchard, Sophie, additional, Tuck, Liz, additional, Prigmore, Elena, additional, Knights, Andrew, additional, Oszlanczi, Agnes, additional, Hunter, Adam, additional, Vieira, Sara F., additional, Patel, Minal, additional, Georgakopoulos, Nikitas, additional, Mahbubani, Krishnaa, additional, Saeb-Parsy, Kourosh, additional, Clatworthy, Menna, additional, Bayraktar, Omer Ali, additional, Stegle, Oliver, additional, Kumasaka, Natsuhiko, additional, Teichmann, Sarah A., additional, and Meyer, Kerstin B., additional

Published
2021
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31. A Histone Deacetylase Inhibitor, Panobinostat, Enhances Chimeric Antigen Receptor T-cell Antitumor Effect Against Pancreatic Cancer

Author

Ali, Aesha I., primary, Wang, Minyu, additional, von Scheidt, Bianca, additional, Dominguez, Pilar M., additional, Harrison, Aaron J., additional, Tantalo, Daniela G.M., additional, Kang, Jian, additional, Oliver, Amanda J., additional, Chan, Jack D., additional, Du, Xin, additional, Bai, Yuchen, additional, Lee, Belinda, additional, Johnstone, Ricky W., additional, Darcy, Phillip K., additional, Kershaw, Michael H., additional, and Slaney, Clare Y., additional

Published
2021
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33. Combined BRAF, MEK, and CDK4/6 Inhibition Depletes Intratumoral Immune-Potentiating Myeloid Populations in Melanoma

Author

Lelliott, Emily J., primary, Mangiola, Stefano, additional, Ramsbottom, Kelly M., additional, Zethoven, Magnus, additional, Lim, Lydia, additional, Lau, Peter K.H., additional, Oliver, Amanda J., additional, Martelotto, Luciano G., additional, Kirby, Laura, additional, Martin, Claire, additional, Patel, Riyaben P., additional, Slater, Alison, additional, Cullinane, Carleen, additional, Papenfuss, Anthony T., additional, Haynes, Nicole M., additional, McArthur, Grant A., additional, Oliaro, Jane, additional, and Sheppard, Karen E., additional

Published
2021
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36. A Novel Inhaled Dry-Powder Formulation of Ribavirin Allows for Efficient Lung Delivery in Healthy Participants and Those with Chronic Obstructive Pulmonary Disease in a Phase 1 Study

Author

Dumont, Etienne F., primary, Oliver, Amanda J., additional, Ioannou, Chris, additional, Billiard, Julia, additional, Dennison, Jeremy, additional, van den Berg, Frans, additional, Yang, Shuying, additional, Chandrasekaran, Vijayalakshmi, additional, Young, Graeme C., additional, Lahiry, Anirban, additional, Starbuck, David C., additional, Harrell, Andrew W., additional, Georgiou, Alex, additional, Hopchet, Nathalie, additional, Gillies, Andy, additional, and Baker, Stephen J., additional

Published
2020
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37. Macrophage-Derived CXCL9 and CXCL10 Are Required for Antitumor Immune Responses Following Immune Checkpoint Blockade

Author

House, Imran G., primary, Savas, Peter, additional, Lai, Junyun, additional, Chen, Amanda X.Y., additional, Oliver, Amanda J., additional, Teo, Zhi L., additional, Todd, Kirsten L., additional, Henderson, Melissa A., additional, Giuffrida, Lauren, additional, Petley, Emma V., additional, Sek, Kevin, additional, Mardiana, Sherly, additional, Gide, Tuba N., additional, Quek, Camelia, additional, Scolyer, Richard A., additional, Long, Georgina V., additional, Wilmott, James S., additional, Loi, Sherene, additional, Darcy, Phillip K., additional, and Beavis, Paul A., additional

Published
2020
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38. Enhancing chimeric antigen receptor T‐cell immunotherapy against cancer using a nanoemulsion‐based vaccine targeting cross‐presenting dendritic cells

Author

Chan, Jack D, primary, Scheidt, Bianca, additional, Zeng, Bijun, additional, Oliver, Amanda J, additional, Davey, Ashleigh S, additional, Ali, Aesha I, additional, Thomas, Ranjeny, additional, Trapani, Joseph A, additional, Darcy, Phillip K, additional, Kershaw, Michael H, additional, Dolcetti, Riccardo, additional, and Slaney, Clare Y, additional

Published
2020
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40. Novel combination immunotherapy for pancreatic cancer: potent anti‐tumor effects with CD40 agonist and interleukin‐15 treatment

Author

Van Audenaerde, Jonas RM, primary, Marcq, Elly, additional, Scheidt, Bianca, additional, Davey, Ashleigh S, additional, Oliver, Amanda J, additional, De Waele, Jorrit, additional, Quatannens, Delphine, additional, Van Loenhout, Jinthe, additional, Pauwels, Patrick, additional, Roeyen, Geert, additional, Lardon, Filip, additional, Slaney, Clare Y, additional, Peeters, Marc, additional, Kershaw, Michael H, additional, Darcy, Phillip K, additional, and Smits, Evelien LJM, additional

Published
2020
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43. Tissue‐specific tumor microenvironments influence responses to immunotherapies

Author

Oliver, Amanda J, primary, Davey, Ashleigh S, additional, Keam, Simon P, additional, Mardiana, Sherly, additional, Chan, Jack D, additional, Scheidt, Bianca, additional, Beavis, Paul A, additional, House, Imran G, additional, Van Audernaerde, Jonas RM, additional, Darcy, Phillip K, additional, Kershaw, Michael H, additional, and Slaney, Clare Y, additional

Published
2019
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44. Cross‐talk between tumors at anatomically distinct sites.

Author

Oliver, Amanda J., Darcy, Phillip K., Trapani, Joseph A., Kershaw, Michael H., and Slaney, Clare Y.

Subjects
*EXTRACELLULAR vesicles, *TUMOR microenvironment, *CANCER cells, *TUMORS, *CANCER invasiveness
Abstract

Cancer tissue is not homogenous, and individual metastases at different anatomical locations can differ from the primary tumor and from one another in both their morphology and cellular composition, even within an individual patient. Tumors are composed of cancer cells and a range of other cell types, which, together with a variety of secreted molecules, collectively comprise the tumor microenvironment (TME). Cells of the TME can communicate with each other and with distant tissues in a form of molecular cross‐talk to influence their growth and function. Cross‐talk between cancer cells and local immune cells is well described and can lead to the induction of local immunosuppression. Recently, it has become apparent that tumors located remotely from each other, can engage in cross‐talk that can influence their responsiveness to various therapies, including immunotherapy. In this article, we review studies that describe how tumors systemically communicate with distant tissues through motile cells, extracellular vesicles, and secreted molecules that can affect their function. In addition, we summarize evidence from mouse studies and the clinic that indicate an ability of some tumors to influence the progression and therapeutic responses of other tumors in different anatomical locations. [ABSTRACT FROM AUTHOR]

Published
2021
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46. Reply

Author

Oliver, Amanda J., primary, Goldfrad, Caroline H., additional, Tomkins, Susan A., additional, and Grigg, Jonathan, additional

Published
2017
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47. Change in Lower Mississippi River secondary channels: An atlas of bathymetric and photographic data

Author

Guntren, Erin F.; Oliver, Amanda J. M.; Keevin, Thomas M., United States. Army. Corps of Engineers. St. Louis District; United States. Army. Corps of Engineers. Mississippi Valley Division; United States. Mississippi River Commission; Mississippi River Geomorphology and Potamology Program (U.S.); Engineer Research and Development Center (U.S.), Guntren, Erin F.; Oliver, Amanda J. M.; Keevin, Thomas M., and United States. Army. Corps of Engineers. St. Louis District; United States. Army. Corps of Engineers. Mississippi Valley Division; United States. Mississippi River Commission; Mississippi River Geomorphology and Potamology Program (U.S.); Engineer Research and Development Center (U.S.)

Abstract

Mississippi Valley Division US Army Engineer District, St. Louis Change in Lower Mississippi River Secondary Channels: An Atlas of Bathymetric and Photographic Data MRG&P Report No. 8 • June 2016 Mississippi River Geomorphology and Potamology Program MRG&P Report No. 8 June 2016 Change in Lower Mississippi River Secondary Channels: An Atlas of Bathymetric and Photographic Data Erin L. M. Guntren, Amanda J. M. Oliver, and Thomas M. Keevin US Army Engineer District, St. Louis 1222 Spruce Street St. Louis, MO 63103-2833 Donald C. Williams US Army Engineer Division, Mississippi Valley 1400 Walnut Street Vicksburg, MS 39180 Final report Approved for public release; distribution is unlimited. Under Secondary Channel Report, Project Number 96x3122 MRG&P Report No. 8 ii Abstract Historically, the Lower Mississippi River (LMR) flowed over 1,130 miles and had access to a 30- to 124-mile wide floodplain. Over time, a multitude of engineering activities undertaken to create safer navigation and reduce flood damage shortened the Lower Mississippi River by 140 miles and greatly reduced the floodplain. These engineering activities also included closing dike construction in secondary channels to divert more water to the main channel during low river stages. However, the importance of secondary channels to the overall river ecosystem has led to the removal or notching of many closing dikes to restore flow and connection at low river stages. As part of this overall effort to conserve and restore the function and value of secondary channels, this study provides information on the existing and long-term (1960s-2000s) trends of the channels’ areas and volume. To do this, bathymetric data and aerial photography were gathered from the New Orleans, Vicksburg, and Memphis Districts, U.S. Army Corps of Engineers. Secondary channels were located in the bathymetric files by looking for islands or bars with elevations > +5 ft Low Water Reference Plane. The secondary channels’ boundaries were th

Published
2016

49. Considerations for building and using integrated single-cell atlases.

Author

Hrovatin K, Sikkema L, Shitov VA, Heimberg G, Shulman M, Oliver AJ, Mueller MF, Ibarra IL, Wang H, Ramírez-Suástegui C, He P, Schaar AC, Teichmann SA, Theis FJ, and Luecken MD

Abstract

The rapid adoption of single-cell technologies has created an opportunity to build single-cell 'atlases' integrating diverse datasets across many laboratories. Such atlases can serve as a reference for analyzing and interpreting current and future data. However, it has become apparent that atlasing approaches differ, and the impact of these differences are often unclear. Here we review the current atlasing literature and present considerations for building and using atlases. Importantly, we find that no one-size-fits-all protocol for atlas building exists, but rather we discuss context-specific considerations and workflows, including atlas conceptualization, data collection, curation and integration, atlas evaluation and atlas sharing. We further highlight the benefits of integrated atlases for analyses of new datasets and deriving biological insights beyond what is possible from individual datasets. Our overview of current practices and associated recommendations will improve the quality of atlases to come, facilitating the shift to a unified, reference-based understanding of single-cell biology., Competing Interests: Competing interests: G.H. and H.W. are employees of Genentech whose views are their own and do not represent those of Genentech, Roche or affiliates. M.D.L. contracted for the Chan Zuckerberg Initiative, consults for CatalYm and received speaker fees from Pfizer and Janssen Pharmaceuticals. S.A.T. has consulted for or been a member of scientific advisory boards at Qiagen, Sanofi, GlaxoSmithKline and ForeSite Labs. S.A.T. is a cofounder and an equity holder of TransitionBio and EnsoCell and a SAB member of Element Biosciences and an independent non-executive director on the 10X Genomics board. S.A.T. is a part-time employee at GlaxoSmithKline. F.J.T. consults for Immunai, Singularity Bio B.V., CytoReason, Cellarity and Curie Bio Operations and has an ownership interest in Dermagnostix and Cellarity. The remaining authors declare no competing interests., (© 2024. Springer Nature America, Inc.)

Published
2024
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50. Gene-level alignment of single-cell trajectories.

Author

Sumanaweera D, Suo C, Cujba AM, Muraro D, Dann E, Polanski K, Steemers AS, Lee W, Oliver AJ, Park JE, Meyer KB, Dumitrascu B, and Teichmann SA

Abstract

Single-cell data analysis can infer dynamic changes in cell populations, for example across time, space or in response to perturbation, thus deriving pseudotime trajectories. Current approaches comparing trajectories often use dynamic programming but are limited by assumptions such as the existence of a definitive match. Here we describe Genes2Genes, a Bayesian information-theoretic dynamic programming framework for aligning single-cell trajectories. It is able to capture sequential matches and mismatches of individual genes between a reference and query trajectory, highlighting distinct clusters of alignment patterns. Across both real world and simulated datasets, it accurately inferred alignments and demonstrated its utility in disease cell-state trajectory analysis. In a proof-of-concept application, Genes2Genes revealed that T cells differentiated in vitro match an immature in vivo state while lacking expression of genes associated with TNF signaling. This demonstrates that precise trajectory alignment can pinpoint divergence from the in vivo system, thus guiding the optimization of in vitro culture conditions., (© 2024. The Author(s).)

Published
2024
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