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2023 Journal Article Global analysis of transcription start sites and enhancers in endometrial stromal cells and differences associated with endometriosisMarla, Sushma, Mortlock, Sally, Yoon, Sohye, Crawford, Joanna, Andersen, Stacey, Mueller, Michael D., McKinnon, Brett, Nguyen, Quan and Montgomery, Grant W. (2023). Global analysis of transcription start sites and enhancers in endometrial stromal cells and differences associated with endometriosis. Cells, 12 (13) 1736, 1-22. doi: 10.3390/cells12131736 |
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2023 Journal Article In vivo inhibition of nuclear ACE2 translocation protects against SARS-CoV-2 replication and lung damage through epigenetic imprintingTu, Wen Juan, Melino, Michelle, Dunn, Jenny, McCuaig, Robert D., Bielefeldt-Ohmann, Helle, Tsimbalyuk, Sofiya, Forwood, Jade K., Ahuja, Taniya, Vandermeide, John, Tan, Xiao, Tran, Minh, Nguyen, Quan, Zhang, Liang, Nam, Andy, Pan, Liuliu, Liang, Yan, Smith, Corey, Lineburg, Katie, Nguyen, Tam H., Sng, Julian D. J., Tong, Zhen Wei Marcus, Chew, Keng Yih, Short, Kirsty R., Le Grand, Roger, Seddiki, Nabila and Rao, Sudha (2023). In vivo inhibition of nuclear ACE2 translocation protects against SARS-CoV-2 replication and lung damage through epigenetic imprinting. Nature Communications, 14 (1) 3680, 3680. doi: 10.1038/s41467-023-39341-4 |
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2023 Other Outputs Deep spatial-omics analysis of head & neck carcinomas provides alternative therapeutic targets and rational for treatment failureAndrew Causer, Xiao Tan, Xuehan Lu, Philip Moseley, Min Teoh, Natalie Molotkov, Margaret McGrath, Taehyun Kim, Peter Simpson, Christopher Perry, Ian Frazer, Benedict Panizza, Rahul Ladwa, Quan Nguyen and Jazmina L Gonzalez-Cruz (2023). Deep spatial-omics analysis of head & neck carcinomas provides alternative therapeutic targets and rational for treatment failure. The University of Queensland. (Dataset) doi: 10.48610/698bb9e |
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2023 Journal Article Spatial transcriptomic analysis of Sonic hedgehog medulloblastoma identifies that the loss of heterogeneity and promotion of differentiation underlies the response to CDK4/6 inhibitionVo, Tuan, Balderson, Brad, Jones, Kahli, Ni, Guiyan, Crawford, Joanna, Millar, Amanda, Tolson, Elissa, Singleton, Matthew, Kojic, Marija, Robertson, Thomas, Walters, Shaun, Mulay, Onkar, Bhuva, Dharmesh D., Davis, Melissa J., Wainwright, Brandon J., Nguyen, Quan and Genovesi, Laura A. (2023). Spatial transcriptomic analysis of Sonic hedgehog medulloblastoma identifies that the loss of heterogeneity and promotion of differentiation underlies the response to CDK4/6 inhibition. Genome Medicine, 15 (1) 29, 29. doi: 10.1186/s13073-023-01185-4 |
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2023 Journal Article Inferring cell diversity in single cell data using consortium-scale epigenetic data as a biological anchor for cell identitySun, Yuliangzi, Shim, Woo Jun, Shen, Sophie, Sinniah, Enakshi, Pham, Duy, Su, Zezhuo, Mizikovsky, Dalia, White, Melanie D., Ho, Joshua W. K., Nguyen, Quan, Bodén, Mikael and Palpant, Nathan J (2023). Inferring cell diversity in single cell data using consortium-scale epigenetic data as a biological anchor for cell identity. Nucleic Acids Research, 51 (11), e62-e62. doi: 10.1093/nar/gkad307 |
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2023 Conference Publication 275 Spatial transcriptomics of early invasive melanomas reveals molecular determinants of patient survivalZhou, C., Tan, S. X., Kao, Y., Claeson, M., Brown, S., Lambie, D., Whiteman, D., Soyer, H., Stark, M., Nguyen, Q. and Khosrotehrani, K. (2023). 275 Spatial transcriptomics of early invasive melanomas reveals molecular determinants of patient survival. 1st International Societies for Investigative Dermatology Meeting (ISID 2023), Tokyo, Japan, 10 - 13 May 2023. Oxford, United Kingdom: Elsevier. doi: 10.1016/j.jid.2023.03.279 |
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2023 Conference Publication A novel spatial trajectory inference method for detecting regional breast cancer progression from spatial transcriptomics dataPham, Duy and Nguyen, Quan (2023). A novel spatial trajectory inference method for detecting regional breast cancer progression from spatial transcriptomics data. AACR Annual Meeting 2023, Orlando, FL United States, 14-19 April 2023. Philadelphia, PA United States: American Association for Cancer Research. doi: 10.1158/1538-7445.am2023-lb076 |
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2023 Conference Publication Abstract 3116: Spatial single-cell atlas of stage III colorectal cancerSu, Andrew, Tran, Minh, Lee, HoJoon, Sathe, Anuja, Bai, Xiangqi, Cruz, Richard, Pflieger, Lance, Nguyen, Quan, Ji, Hanlee P. and Rhodes, Terence (2023). Abstract 3116: Spatial single-cell atlas of stage III colorectal cancer. AACR Annual Meeting 2023, Orlando, FL United States, 14-19 April 2023. Philadelphia, PA United States: American Association for Cancer Research. doi: 10.1158/1538-7445.am2023-3116 |
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2023 Conference Publication Applying spatial omics and computational integrative analyses to study drug responses and cancer immune cell interactionsTan, Xiao, Causer, Andrew, Vo, Tuan Quang Anh, Ma, Ning, Cheikh, Bassem Ben, Genovesi, Laura, Gonzalez-Cruz, Jazmina, Nguyen, Quan and Braubach, Oliver (2023). Applying spatial omics and computational integrative analyses to study drug responses and cancer immune cell interactions. AACR Annual Meeting 2023, Orlando, FL United States, 14-19 April 2023. Philadelphia, PA United States: American Association for Cancer Research. doi: 10.1158/1538-7445.am2023-4703 |
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2023 Journal Article Compartmentalized spatial profiling of the tumor microenvironment in head and neck squamous cell carcinoma identifies immune checkpoint molecules and tumor necrosis factor receptor superfamily members as biomarkers of response to immunotherapySadeghirad, Habib, Liu, Ning, Monkman, James, Ma, Ning, Cheikh, Bassem Ben, Jhaveri, Niyati, Tan, Chin Wee, Warkiani, Majid Ebrahimi, Adams, Mark N., Nguyen, Quan, Ladwa, Rahul, Braubach, Oliver, O’Byrne, Ken, Davis, Melissa, Hughes, Brett G. M. and Kulasinghe, Arutha (2023). Compartmentalized spatial profiling of the tumor microenvironment in head and neck squamous cell carcinoma identifies immune checkpoint molecules and tumor necrosis factor receptor superfamily members as biomarkers of response to immunotherapy. Frontiers in Immunology, 14 1135489, 1-16. doi: 10.3389/fimmu.2023.1135489 |
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2023 Journal Article One health surveillance highlights circulation of viruses with zoonotic potential in bats, pigs, and humans in Viet NamLatinne, Alice, Nga, Nguyen Thi Thanh, Long, Nguyen Van, Ngoc, Pham Thi Bich, Thuy, Hoang Bich, Long, Pham Thanh, Phuong, Nguyen Thanh, Quang, Le Tin Vinh, Tung, Nguyen, Nam, Vu Sinh, Duoc, Vu Trong, Thinh, Nguyen Duc, Schoepp, Randal, Ricks, Keersten, Inui, Ken K., Padungtod, Pawin, Johnson, Christine, Mazet, Jonna A. K. H., Walzer, Chris E., Olson, Sarah and Fine, Amanda (2023). One health surveillance highlights circulation of viruses with zoonotic potential in bats, pigs, and humans in Viet Nam. Viruses, 15 (3) 790, 1-24. doi: 10.3390/v15030790 |
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2023 Journal Article Fragment length profiles of cancer mutations enhance detection of circulating tumor DNA in patients with early-stage hepatocellular carcinomaNguyen, Van-Chu, Nguyen, Trong Hieu, Phan, Thanh Hai, Tran, Thanh-Huong Thi, Pham, Thu Thuy Thi, Ho, Tan Dat, Nguyen, Hue Hanh Thi, Duong, Minh-Long, Nguyen, Cao Minh, Nguyen, Que-Tran Bui, Bach, Hoai-Phuong Thi, Kim, Van-Vu, Pham, The-Anh, Nguyen, Bao Toan, Nguyen, Thanh Nhan Vo, Huynh, Le Anh Khoa, Tran, Vu Uyen, Tran, Thuy Thi Thu, Nguyen, Thanh Dang, Phu, Dung Thai Bieu, Phan, Boi Hoan Huu, Nguyen, Quynh-Tho Thi, Truong, Dinh-Kiet, Do, Thanh-Thuy Thi, Nguyen, Hoai-Nghia, Phan, Minh-Duy, Giang, Hoa and Tran, Le Son (2023). Fragment length profiles of cancer mutations enhance detection of circulating tumor DNA in patients with early-stage hepatocellular carcinoma. BMC Cancer, 23 (1) 233, 1-17. doi: 10.1186/s12885-023-10681-0 |
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2023 Journal Article Functional genomics analysis identifies loss of HNF1B function as a cause of Mayer-Rokitansky-Küster-Hauser syndromeThomson, Ella, Tran, Minh, Robevska, Gorjana, Ayers, Katie, van der Bergen, Jocelyn, Bhaskaran, Prarthna Gopalakrishnan, Haan, Eric, Cereghini, Silvia, Vash-Margita, Alla, Margetts, Miranda, Hensley, Alison, Nguyen, Quan, Sinclair, Andrew, Koopman, Peter and Pelosi, Emanuele (2023). Functional genomics analysis identifies loss of HNF1B function as a cause of Mayer-Rokitansky-Küster-Hauser syndrome. Human Molecular Genetics, 32 (6), 1032-1047. doi: 10.1093/hmg/ddac262 |
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2023 Conference Publication Adversarial online multi-task reinforcement learningNguyen, Quan and Mehta, Nishant A. (2023). Adversarial online multi-task reinforcement learning. 34th International Conference on Algorithmic Learning Theory (ALT), Singapore, Singapore, 20-23 February 2023. San Diego, CA USA: Journal of Machine Learning Research. |
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2023 Other Outputs STimage datasetXiao Tan, Onkar Mulay and Quan Nguyen (2023). STimage dataset. The University of Queensland. (Dataset) doi: 10.48610/4fb74a9 |
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2023 Journal Article IFI27 transcription is an early predictor for COVID-19 outcomes, a multi-cohort observational studyShojaei, Maryam, Shamshirian, Amir, Monkman, James, Grice, Laura, Tran, Minh, Tan, Chin Wee, Teo, Siok Min, Rodrigues Rossi, Gustavo, McCulloch, Timothy R., Nalos, Marek, Raei, Maedeh, Razavi, Alireza, Ghasemian, Roya, Gheibi, Mobina, Roozbeh, Fatemeh, Sly, Peter D., Spann, Kirsten M., Chew, Keng Yih, Zhu, Yanshan, Xia, Yao, Wells, Timothy J., Senegaglia, Alexandra Cristina, Kuniyoshi, Carmen Lúcia, Franck, Claudio Luciano, dos Santos, Anna Flavia Ribeiro, Noronha, Lucia de, Motamen, Sepideh, Valadan, Reza, Amjadi, Omolbanin ... Tang, Benjamin (2023). IFI27 transcription is an early predictor for COVID-19 outcomes, a multi-cohort observational study. Frontiers in Immunology, 13 1060438, 1-14. doi: 10.3389/fimmu.2022.1060438 |
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2023 Other Outputs A robust Platform for Integrative Spatial Multi-omics Analysis to Map Immune Responses to SARS-CoV-2 infection in Lung TissuesTan, Xiao and Nguyen, Quan (2023). A robust Platform for Integrative Spatial Multi-omics Analysis to Map Immune Responses to SARS-CoV-2 infection in Lung Tissues. The University of Queensland. (Dataset) doi: 10.48610/1bfc10c |
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2023 Journal Article Colorectal cancer metastases in the liver establish immunosuppressive spatial networking between tumor associated SPP1+ macrophages and fibroblastsSathe, Anuja, Mason, Kaishu, Grimes, Susan M., Zhou, Zilu, Lau, Billy T., Bai, Xiangqi, Su, Andrew, Tan, Xiao, Lee, HoJoon, Suarez, Carlos J., Nguyen, Quan, Poultsides, George, Zhang, Nancy R. and Ji, Hanlee P. (2023). Colorectal cancer metastases in the liver establish immunosuppressive spatial networking between tumor associated SPP1+ macrophages and fibroblasts. Clinical Cancer Research, 29 (1), 244-260. doi: 10.1158/1078-0432.ccr-22-2041 |
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2022 Journal Article Author Correction: Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network (Nature Communications, (2021), 12, 1, (3297), 10.1038/s41467-021-23143-7)Grapotte, Mathys, Saraswat, Manu, Bessière, Chloé, Menichelli, Christophe, Ramilowski, Jordan A., Severin, Jessica, Hayashizaki, Yoshihide, Itoh, Masayoshi, Tagami, Michihira, Murata, Mitsuyoshi, Kojima-Ishiyama, Miki, Noma, Shohei, Noguchi, Shuhei, Kasukawa, Takeya, Hasegawa, Akira, Suzuki, Harukazu, Nishiyori-Sueki, Hiromi, Frith, Martin C., Abugessaisa, Imad, Aitken, Stuart, Aken, Bronwen L., Alam, Intikhab, Alam, Tanvir, Alasiri, Rami, Alhendi, Ahmad M. N., Alinejad-Rokny, Hamid, Alvarez, Mariano J., Andersson, Robin, Arakawa, Takahiro ... Lecellier, Charles-Henri (2022). Author Correction: Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network (Nature Communications, (2021), 12, 1, (3297), 10.1038/s41467-021-23143-7). Nature Communications, 13 (1) 1200. doi: 10.1038/s41467-022-28758-y |
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2022 Conference Publication Exploratory data analysis of TCGA skin cutaneous melanoma RNA-seq dataZhang, Min, Arief, Vivi, McLachlan, Geoffrey, Nguyen, Quan and Basford, Kaye (2022). Exploratory data analysis of TCGA skin cutaneous melanoma RNA-seq data. Australasian Applied Statistics Conference (AASC), Inverloch, VIC Australia, 28 November - 2 December 2022. |
