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2024 Journal Article Single-cell RNA sequencing reveals peripheral blood leukocyte responses to spinal cord injury in mice with humanised immune systemsGillespie, Ellen R., Grice, Laura F., Courtney, Isabel G., Lao, Hong Wa, Jung, Woncheol, Ramkomuth, Sonny, Xie, Jacky, Brown, David A., Walsham, James, Radford, Kristen J., Nguyen, Quan H. and Ruitenberg, Marc J. (2024). Single-cell RNA sequencing reveals peripheral blood leukocyte responses to spinal cord injury in mice with humanised immune systems. Journal of Neuroinflammation, 21 (1) 63, 1-20. doi: 10.1186/s12974-024-03048-0 |
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2024 Journal Article Cellular neighborhood analysis in spatial omics reveals new tissue domains and cell subtypesRuitenberg, Marc J. and Nguyen, Quan H. (2024). Cellular neighborhood analysis in spatial omics reveals new tissue domains and cell subtypes. Nature Genetics, 56 (3), 362-364. doi: 10.1038/s41588-023-01646-x |
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2024 Journal Article Association of UGT1A1 gene variants, expression levels, and enzyme concentrations with 2,3,7,8-TCDD exposure in individuals exposed to Agent Orange/DioxinQuang, Ha Van, Vuong, Nguyen Ba, Trang, Bui Ngoc Linh, Toan, Nguyen Linh and Tong, Hoang Van (2024). Association of UGT1A1 gene variants, expression levels, and enzyme concentrations with 2,3,7,8-TCDD exposure in individuals exposed to Agent Orange/Dioxin. Scientific Reports, 14 (1) 3315. doi: 10.1038/s41598-024-54004-0 |
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2024 Journal Article Cellular heterogeneity of pluripotent stem cell-derived cardiomyocyte grafts is mechanistically linked to treatable arrhythmiasSelvakumar, Dinesh, Clayton, Zoe E., Prowse, Andrew, Dingwall, Steve, Kim, Sul Ki, Reyes, Leila, George, Jacob, Shah, Haisam, Chen, Siqi, Leung, Halina H. L., Hume, Robert D., Tjahjadi, Laurentius, Igoor, Sindhu, Skelton, Rhys J. P., Hing, Alfred, Paterson, Hugh, Foster, Sheryl L., Pearson, Lachlan, Wilkie, Emma, Marcus, Alan D., Jeyaprakash, Prajith, Wu, Zhixuan, Chiu, Han Shen, Ongtengco, Cherica Felize J., Mulay, Onkar, McArthur, Jeffrey R., Barry, Tony, Lu, Juntang, Tran, Vu ... Chong, James J. H. (2024). Cellular heterogeneity of pluripotent stem cell-derived cardiomyocyte grafts is mechanistically linked to treatable arrhythmias. Nature Cardiovascular Research, 3 (2), 145-165. doi: 10.1038/s44161-023-00419-3 |
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2024 Journal Article HOPX-associated molecular programs control cardiomyocyte cell states underpinning cardiac structure and functionFriedman, Clayton E., Cheetham, Seth W., Negi, Sumedha, Mills, Richard J., Ogawa, Masahito, Redd, Meredith A., Chiu, Han Sheng, Shen, Sophie, Sun, Yuliangzi, Mizikovsky, Dalia, Bouveret, Romaric, Chen, Xiaoli, Voges, Holly K., Paterson, Scott, De Angelis, Jessica E., Andersen, Stacey B., Cao, Yuanzhao, Wu, Yang, Jafrani, Yohaann M.A., Yoon, Sohye, Faulkner, Geoffrey J., Smith, Kelly A., Porrello, Enzo, Harvey, Richard P., Hogan, Benjamin M., Nguyen, Quan, Zeng, Jian, Kikuchi, Kazu, Hudson, James E. and Palpant, Nathan J. (2024). HOPX-associated molecular programs control cardiomyocyte cell states underpinning cardiac structure and function. Developmental Cell, 59 (1), 91-107.e6. doi: 10.1016/j.devcel.2023.11.012 |
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2024 Journal Article Clinicopathologic characteristics of thyroid microcarcinoma: findings from a hospital-based study in VietnamNguyen, Bay Quang, Vu, Hai Thi, Nguyen, Linh My Thi, Nguyen, Quan H., Paragomi, Pedram and Luu, Hung N. (2024). Clinicopathologic characteristics of thyroid microcarcinoma: findings from a hospital-based study in Vietnam. Discovery Medicine, 36 (180), 209-216. doi: 10.24976/discov.med.202436180.20 |
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2024 Journal Article The 1% gift to humanity: The Human Genome Project IILiu, Weibin, Li, Yan, Patrinos, George P., Xu, Shuhua, Thong, Meow-Keong, Chen, Zhengming, Crawley, Francis P., Li, Liming, Ekmekci, Perihan Elif, Drmanac, Radoje, Cheong, Weiyang, Benamouzig, Robert, Nguyen, Quan, Volchkov, Pavel, Reichardt, Juergen K. V., Carninci, Piero, Majumder, Partha, Jin, Xin, Church, George, Wang, Jian and Xu, Xun (2024). The 1% gift to humanity: The Human Genome Project II. Cell Research, 34 (11), 747-750. doi: 10.1038/s41422-024-01026-y |
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2023 Journal Article Robust mapping of spatiotemporal trajectories and cell–cell interactions in healthy and diseased tissuesPham, Duy, Tan, Xiao, Balderson, Brad, Xu, Jun, Grice, Laura F., Yoon, Sohye, Willis, Emily F., Tran, Minh, Lam, Pui Yeng, Raghubar, Arti, Kalita-de Croft, Priyakshi, Lakhani, Sunil, Vukovic, Jana, Ruitenberg, Marc J. and Nguyen, Quan H. (2023). Robust mapping of spatiotemporal trajectories and cell–cell interactions in healthy and diseased tissues. Nature Communications, 14 (1) 7739, 1-25. doi: 10.1038/s41467-023-43120-6 |
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2023 Journal Article Deep spatial-omics analysis of Head & Neck carcinomas provides alternative therapeutic targets and rationale for treatment failureCauser, Andrew, Tan, Xiao, Lu, Xuehan, Moseley, Philip, Teoh, Siok M., Molotkov, Natalie, McGrath, Margaret, Kim, Taehyun, Simpson, Peter T., Perry, Christopher, Frazer, Ian H., Panizza, Benedict, Ladwa, Rahul, Nguyen, Quan and Gonzalez-Cruz, Jazmina L. (2023). Deep spatial-omics analysis of Head & Neck carcinomas provides alternative therapeutic targets and rationale for treatment failure. n p j Precision Oncology, 7 (1) 89, 1-13. doi: 10.1038/s41698-023-00444-2 |
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2023 Journal Article Tolerogenic dendritic cells protect against acute kidney injuryLi, Jennifer S.Y., Robertson, Harry, Trinh, Katie, Raghubar, Arti M., Nguyen, Quan, Matigian, Nicholas, Patrick, Ellis, Thomson, Angus W., Mallett, Andrew J. and Rogers, Natasha M. (2023). Tolerogenic dendritic cells protect against acute kidney injury. Kidney International, 104 (3), 492-507. doi: 10.1016/j.kint.2023.05.008 |
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2023 Journal Article A robust platform for integrative spatial multi‐omics analysis to map immune responses to SARS‐CoV‐2 infection in lung tissuesTan, Xiao, Grice, Laura F., Tran, Minh, Mulay, Onkar, Monkman, James, Blick, Tony, Vo, Tuan, Almeida, Ana Clara, da Silva Motta, Jarbas, Fernandes de Moura, Karen, Machado‐Souza, Cleber, Souza‐Fonseca‐Guimaraes, Paulo, Baena, Cristina Pellegrino, de Noronha, Lucia, Guimaraes, Fernanda Simoes Fortes, Luu, Hung N., Drennon, Tingsheng, Williams, Stephen, Stern, Jacob, Uytingco, Cedric, Pan, Liuliu, Nam, Andy, Cooper, Caroline, Short, Kirsty, Belz, Gabrielle T., Souza‐Fonseca‐Guimaraes, Fernando, Kulasinghe, Arutha 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. Immunology, 170 (3), 401-418. doi: 10.1111/imm.13679 |
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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 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 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 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 |
