Dr Quan Nguyen
Senior Research Fellow - Group Leader
Institute for Molecular Bioscience
Featured projects | Duration |
---|---|
Quantitative transcriptome analysis (CAGE) Genome Innovation Hub Collaborative Project (UQ infrastructure) |
2019 |
Spatial genomics technologies to study cancer and genetic diseases in tissue contexts Genome Innovation Hub Collaborative Project (UQ infrastructure) |
2019 |
HTS single cell CRISPR technology for experimental validation of population genetics and functional genomics discovery Genome Innovation Hub Collaborative Project (UQ infrastructure) |
2021 |
Developing new "spatial omics" capabilities Genome Innovation Hub Collaborative Project (UQ infrastructure) |
2021 |
Cas9 targeted enrichment for Nanopore sequencing Genome Innovation Hub Collaborative Project (UQ infrastructure) |
2023 |
Publications
Book Chapters
Crowhurst, Liam M., Mulay, Onkar, Palpant, Nathan and Nguyen, Quan H. (2021). scIVA: single cell database and tools for interactive visualisation and analysis. Practical guide to life science databases. (pp. 191-205) edited by Imad Abugessaisa and Takeya Kasukawa. Singapore: Springer. doi: 10.1007/978-981-16-5812-9_10
Nguyen, Quan and Carninci, Piero (2015). Expression specificity of disease-associated lncRNAs: toward personalized medicine. Long non-coding RNAs in human disease. (pp. 237-258) edited by Kevin V. Morris. Cham, Switerland: Springer International Publishing. doi: 10.1007/82_2015_464
Journal Articles
Patrick, 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
Chauquet, Solal, Willis, Emily F., Grice, Laura, Harley, Samuel B. R., Powell, Joseph E., Wray, Naomi R., Nguyen, Quan, Ruitenberg, Marc J., Shah, Sonia and Vukovic, Jana (2024). Exercise rejuvenates microglia and reverses T cell accumulation in the aged female mouse brain. Aging Cell, 23 (7) e14172, e14172. doi: 10.1111/acel.14172
Chen, Yibi, Dougan, Katherine E., Nguyen, Quan, Bhattacharya, Debashish and Chan, Cheong Xin (2024). Genome-wide transcriptome analysis reveals the diversity and function of long non-coding RNAs in dinoflagellates. NAR Genomics and Bioinformatics, 6 (1) lqae016, lqae016. doi: 10.1093/nargab/lqae016
Gillespie, 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
Ruitenberg, 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
Garmire, Lana X., Li, Yijun, Huang, Qianhui, Xu, Chuan, Teichmann, Sarah A., Kaminski, Naftali, Pellegrini, Matteo, Nguyen, Quan and Teschendorff, Andrew E. (2024). Challenges and perspectives in computational deconvolution of genomics data. Nature Methods, 21 (3), 1-10. doi: 10.1038/s41592-023-02166-6
Selvakumar, 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
Nguyen, 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
Liu, 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. doi: 10.1038/s41422-024-01026-y
Friedman, 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. (2023). HOPX-associated molecular programs control cardiomyocyte cell states underpinning cardiac structure and function. Developmental Cell, 59 (1), 91-107.e1. doi: 10.1016/j.devcel.2023.11.012
Pham, 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
Causer, 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, 89. doi: 10.1038/s41698-023-00444-2
Li, 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
Tan, 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
Marla, 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
Tu, 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
Vo, 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
Sun, 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
Pham, Duy and Nguyen, Quan (2023). Abstract LB076: A novel spatial trajectory inference method for detecting regional breast cancer progression from spatial transcriptomics data. Cancer Research, 83 (8_Supplement) LB076. doi: 10.1158/1538-7445.am2023-lb076
Sadeghirad, 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
Nguyen, 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
Thomson, 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
Latinne, 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-Basel, 15 (3) ARTN 790, 790. doi: 10.3390/v15030790
Shojaei, 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
Sathe, 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
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
Pham, Duy, Truong, Buu, Tran, Khai, Ni, Guiyan, Nguyen, Dat, Tran, Trang T. H., Tran, Mai H., Thuy, Duong Nguyen, Vo, Nam S. and Nguyen, Quan (2022). Assessing polygenic risk score models for applications in populations with under-represented genomics data: an example of Vietnam. Briefings in Bioinformatics, 23 (6) bbac459. doi: 10.1093/bib/bbac459
Nguyen, Dat Thanh, Tran, Trang T. H., Tran, Mai Hoang, Tran, Khai, Pham, Duy, Duong, Nguyen Thuy, Nguyen, Quan and Vo, Nam S. (2022). A comprehensive evaluation of polygenic score and genotype imputation performances of human SNP arrays in diverse populations. Scientific Reports, 12 (1) 17556, 1-13. doi: 10.1038/s41598-022-22215-y
Paragomi, Pedram, Dabo, Bashir, Pelucchi, Claudio, Bonzi, Rossella, Bako, Abdulaziz T., Sanusi, Nabila Muhammad, Nguyen, Quan H., Zhang, Zuo-Feng, Palli, Domenico, Ferraroni, Monica, Vu, Khanh Truong, Yu, Guo-Pei, Turati, Federica, Zaridze, David, Maximovitch, Dmitry, Hu, Jinfu, Mu, Lina, Boccia, Stefania, Pastorino, Roberta, Tsugane, Shoichiro, Hidaka, Akihisa, Kurtz, Robert C., Lagiou, Areti, Lagiou, Pagona, Camargo, M. Constanza, Curado, Maria Paula, Lunet, Nuno, Vioque, Jesus, Boffetta, Paolo ... Luu, Hung N. (2022). The association between peptic ulcer disease and gastric cancer: results from the Stomach Cancer Pooling (StoP) Project Consortium. Cancers, 14 (19) 4905, 1-14. doi: 10.3390/cancers14194905
Tran, M., Yoon, S., Teoh, M., Andersen, S., Lam, PY., Purdue, B. W., Raghubar, A., Hanson, S.J., Devitt, K., Jones, K., Walters, S., Monkman, J., Kulasinghe, A., Tuong, Z.K., Soyer, H.P., Frazer, I. H. and Nguyen, Q. (2022). A robust experimental and computational analysis framework at multiple resolutions, modalities and coverages. Frontiers in Immunology, 13 911873, 911873. doi: 10.3389/fimmu.2022.911873
Naval-Sanchez, Marina, Deshpande, Nikita, Tran, Minh, Zhang, Jingyu, Alhomrani, Majid, Alsanie, Walaa, Nguyen, Quan and Nefzger, Christian M. (2022). Benchmarking of ATAC Sequencing Data From BGI’s Low-Cost DNBSEQ-G400 Instrument for Identification of Open and Occupied Chromatin Regions. Frontiers in Molecular Biosciences, 9 900323, 1-15. doi: 10.3389/fmolb.2022.900323
Raghubar, Arti M., Pham, Duy T., Tan, Xiao, Grice, Laura F., Crawford, Joanna, Lam, Pui Yeng, Andersen, Stacey B., Yoon, Sohye, Teoh, Siok Min, Matigian, Nicholas A., Stewart, Anne, Francis, Leo, Ng, Monica S. Y., Healy, Helen G., Combes, Alexander N., Kassianos, Andrew J., Nguyen, Quan and Mallett, Andrew J. (2022). Spatially resolved transcriptomes of mammalian kidneys illustrate the molecular complexity and interactions of functional nephron segments. Frontiers in Medicine, 9 873923, 873923. doi: 10.3389/fmed.2022.873923
Nguyen, Dat Thanh, Nguyen, Quan Hoang, Duong, Nguyen Thuy and Vo, Nam S. (2022). LmTag: functional-enrichment and imputation-aware tag SNP selection for population-specific genotyping arrays. Briefings in Bioinformatics, 23 (4) bbac252, 1-12. doi: 10.1093/bib/bbac252
Su, Andrew, Lee, HoJoon, Tan, Xiao, Suarez, Carlos J., Andor, Noemi, Nguyen, Quan and Ji, Hanlee P. (2022). A deep learning model for molecular label transfer that enables cancer cell identification from histopathology images. npj Precision Oncology, 6 (1) 14, 14. doi: 10.1038/s41698-022-00252-0
Tuong, Zewen Kelvin, Loudon, Kevin W., Berry, Brendan, Richoz, Nathan, Jones, Julia, Tan, Xiao, Nguyen, Quan, George, Anne, Hori, Satoshi, Field, Sarah, Lynch, Andy G., Kania, Katarzyna, Coupland, Paul, Babbage, Anne, Grenfell, Richard, Barrett, Tristan, Warren, Anne Y., Gnanapragasam, Vincent, Massie, Charlie and Clatworthy, Menna R. (2021). Resolving the immune landscape of human prostate at a single-cell level in health and cancer. Cell Reports, 37 (12) 110132, 110132. doi: 10.1016/j.celrep.2021.110132
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 (2021). Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network. Nature Communications, 12 (1) 3297. doi: 10.1038/s41467-021-23143-7
Tuong, Zewen K., Lukowski, Samuel W., Nguyen, Quan H., Chandra, Janin, Zhou, Chenhao, Gillinder, Kevin, Bashaw, Abate A., Ferdinand, John R., Stewart, Benjamin J., Teoh, Siok Min, Hanson, Sarah J., Devitt, Katharina, Clatworthy, Menna R., Powell, Joseph E. and Frazer, Ian H. (2021). A model of impaired Langerhans cell maturation associated with HPV induced epithelial hyperplasia. iScience, 24 (11) 103326, 103326. doi: 10.1016/j.isci.2021.103326
Shen, Sophie, Sun, Yuliangzi, Matsumoto, Maika, Shim, Woo Jun, Sinniah, Enakshi, Wilson, Sean B., Werner, Tessa, Wu, Zhixuan, Bradford, Stephen T., Hudson, James, Little, Melissa H., Powell, Joseph, Nguyen, Quan and Palpant, Nathan J. (2021). Integrating single-cell genomics pipelines to discover mechanisms of stem cell differentiation. Trends in Molecular Medicine, 27 (12), 1135-1158. doi: 10.1016/j.molmed.2021.09.006
Tran, Ngan K., Lea, Rodney A., Holland, Samuel, Nguyen, Quan, Raghubar, Arti M., Sutherland, Heidi G., Benton, Miles C., Haupt, Larisa M., Blackburn, Nicholas B., Curran, Joanne E., Blangero, John, Mallett, Andrew J. and Griffiths, Lyn R. (2021). Multi-phenotype genome-wide association studies of the Norfolk Island isolate implicate pleiotropic loci involved in chronic kidney disease. Scientific reports, 11 (1) 19425, 19425. doi: 10.1038/s41598-021-98935-4
Lewis, Sabrina M., Asselin-Labat, Marie-Liesse, Nguyen, Quan, Berthelet, Jean, Tan, Xiao, Wimmer, Verena C., Merino, Delphine, Rogers, Kelly L. and Naik, Shalin H. (2021). Spatial omics and multiplexed imaging to explore cancer biology. Nature Methods, 18 (9), 997-1012. doi: 10.1038/s41592-021-01203-6
Thompson, Michael, Matsumoto, Maika, Ma, Tianqi, Senabouth, Anne, Palpant, Nathan J., Powell, Joseph E. and Nguyen, Quan (2021). scGPS: determining cell states and global fate potential of subpopulations. Frontiers in Genetics, 12 666771, 666771. doi: 10.3389/fgene.2021.666771
Sun, Xuan, Cao, Benjamin, Naval-Sanchez, Marina, Pham, Tony, Sun, Yu Bo Yang, Williams, Brenda, Heazlewood, Shen Y, Deshpande, Nikita, Li, Jinhua, Kraus, Felix, Rae, James, Nguyen, Quan, Yari, Hamed, Schröder, Jan, Heazlewood, Chad K, Fulton, Madeline, Hatwell-Humble, Jessica, Das Gupta, Kaustav, Kapetanovic, Ronan, Chen, Xiaoli, Sweet, Matthew J, Parton, Robert G, Ryan, Michael T, Polo, Jose M, Nefzger, Christian M and Nilsson, Susan K (2021). Nicotinamide riboside attenuates age-associated metabolic and functional changes in hematopoietic stem cells. Nature Communications, 12 (1) 2665, 1-17. doi: 10.1038/s41467-021-22863-0
Neavin, Drew, Nguyen, Quan, Daniszewski, Maciej S., Liang, Helena H., Chiu, Han Sheng, Wee, Yong Kiat, Senabouth, Anne, Lukowski, Samuel W., Crombie, Duncan E., Lidgerwood, Grace E., Hernández, Damián, Vickers, James C., Cook, Anthony L., Palpant, Nathan J., Pébay, Alice, Hewitt, Alex W. and Powell, Joseph E. (2021). Single cell eQTL analysis identifies cell type-specific genetic control of gene expression in fibroblasts and reprogrammed induced pluripotent stem cells. Genome Biology, 22 (1) 76, 1-19. doi: 10.1186/s13059-021-02293-3
Jogia, Trisha, Lübstorf, Tom, Jacobson, Esther, Scriven, Elissa, Atresh, Sridhar, Nguyen, Quan H., Liebscher, Thomas, Schwab, Jan M., Kopp, Marcel A., Walsham, James, Campbell, Kate E. and Ruitenberg, Marc J. (2021). Prognostic value of early leukocyte fluctuations for recovery from traumatic spinal cord injury. Clinical and Translational Medicine, 11 (1) e272, e272. doi: 10.1002/ctm2.272
Shim, Woo Jun, Sinniah, Enakshi, Xu, Jun, Vitrinel, Burcu, Alexanian, Michael, Andreoletti, Gaia, Shen, Sophie, Sun, Yuliangzi, Balderson, Brad, Boix, Carles, Peng, Guangdun, Jing, Naihe, Wang, Yuliang, Kellis, Manolis, Tam, Patrick P L, Smith, Aaron, Piper, Michael, Christiaen, Lionel, Nguyen, Quan, Bodén, Mikael and Palpant, Nathan J. (2020). Conserved epigenetic regulatory logic infers genes governing cell identity. Cell Systems, 11 (6), 625-639.e13. doi: 10.1016/j.cels.2020.11.001
Tan, Xiao, Su, Andrew T., Hajiabadi, Hamideh, Tran, Minh and Nguyen, Quan (2020). Applying machine learning for integration of multi-modal genomics data and imaging data to quantify heterogeneity in tumour tissues. Methods in Molecular Biology, 2190, 209-228. doi: 10.1007/978-1-0716-0826-5_10
Senabouth, Anne, Andersen, Stacey, Shi, Qianyu, Shi, Lei, Jiang, Feng, Zhang, Wenwei, Wing, Kristof, Daniszewski, Maciej, Lukowski, Samuel W., Hung, Sandy S. C., Nguyen, Quan, Fink, Lynn, Beckhouse, Anthony, Pébay, Alice, Hewitt, Alex W. and Powell, Joseph E. (2020). Comparative performance of the BGI and Illumina sequencing technology for single-cell RNA-sequencing. NAR Genomics and Bioinformatics, 2 (2) lqaa034, 1-10. doi: 10.1093/nargab/lqaa034
Pham, Duy, Tan, Xiao, Xu, Jun, Grice, Laura F., Lam, Pui Yeng, Raghubar, Arti, Vukovic, Jana, Ruitenberg, Marc J. and Nguyen, Quan (2020). stLearn integrating spatial location, tissue morphology and gene expression to find cell types, cell-cell interactions and spatial trajectories within undissociated tissues. Biorxiv, 1-18. doi: 10.1101/2020.05.31.125658v1
Willis, Emily F., MacDonald, Kelli P. A., Nguyen, Quan H., Garrido, Adahir Labrador, Gillespie, Ellen R., Harley, Samuel B. R., Bartlett, Perry F., Schroder, Wayne A., Yates, Abi G., Anthony, Daniel C., Rose-John, Stefan, Ruitenberg, Marc J. and Vukovic, Jana (2020). Repopulating Microglia Promote Brain Repair in an IL-6-Dependent Manner. Cell, 180 (5), 833-846.e16. doi: 10.1016/j.cell.2020.02.013
Xu, Jun, Falconer, Caitlin, Nguyen, Quan, Crawford, Joanna, McKinnon, Brett D., Mortlock, Sally, Senabouth, Anne, Andersen, Stacey, Chiu, Han Sheng, Jiang, Longda, Palpant, Nathan J., Yang, Jian, Mueller, Michael D., Hewitt, Alex W., Pébay, Alice, Montgomery, Grant W., Powell, Joseph E. and Coin, Lachlan J. M. (2019). Genotype-free demultiplexing of pooled single-cell RNA-seq. Genome Biology, 20 (1) 290, 290. doi: 10.1186/s13059-019-1852-7
Alquicira-Hernandez, Jose, Sathe, Anuja, Ji, Hanlee P., Nguyen, Quan and Powell, Joseph E. (2019). scPred: accurate supervised method for cell-type classification from single-cell RNA-seq data. Genome Biology, 20 (1) 264. doi: 10.1186/s13059-019-1862-5
Tan, Xiao, Su, Andrew, Tran, Minh and Nguyen, Quan (2019). SpaCell: integrating tissue morphology and spatial gene expression to predict disease cells. Bioinformatics, 36 (7), 2293-2294. doi: 10.1093/bioinformatics/btz914
Lukowski, Samuel W., Lo, Camden Y., Sharov, Alexei A., Nguyen, Quan, Fang, Lyujie, Hung, Sandy S. C., Zhu, Ling, Zhang, Ting, Grünert, Ulrike, Nguyen, Tu, Senabouth, Anne, Jabbari, Jafar S., Welby, Emily, Sowden, Jane C., Waugh, Hayley S., Mackey, Adrienne, Pollock, Graeme, Lamb, Trevor D., Wang, Peng-Yuan, Hewitt, Alex W., Gillies, Mark C., Powell, Joseph E. and Wong, Raymond C. B. (2019). A single-cell transcriptome atlas of the adult human retina. The EMBO Journal, 38 (18) e100811, e100811. doi: 10.15252/embj.2018100811
Senabouth, Anne, Lukowski, Samuel W., Hernandez, Jose Alquicira, Andersen, Stacey B., Mei, Xin, Nguyen, Quan H. and Powell, Joseph E. (2019). ascend: R package for analysis of single-cell RNA-seq data. GigaScience, 8 (8) giz087. doi: 10.1093/gigascience/giz087
Friedman, Clayton E., Nguyen, Quan, Lukowski, Samuel W., Helfer, Abbigail, Chiu, Han Sheng, Miklas, Jason, Levy, Shiri, Suo, Shengbao, Han, Jing-Dong Jackie, Osteil, Pierre, Peng, Guangdun, Jing, Naihe, Baillie, Greg J., Senabouth, Anne, Christ, Angelika N., Bruxner, Timothy J., Murry, Charles E., Wong, Emily S., Ding, Jun, Wang, Yuliang, Hudson, James, Ruohola-Baker, Hannele, Bar-Joseph, Ziv, Tam, Patrick P.L., Powell, Joseph E. and Palpant, Nathan J. (2018). Single-cell transcriptomic analysis of cardiac differentiation from human PSCs reveals HOPX-dependent cardiomyocyte maturation. Cell Stem Cell, 23 (4), 586-598. doi: 10.1016/j.stem.2018.09.009
Daniszewski, Maciej, Nguyen, Quan, Chy, Hun S., Singh, Vikrant, Crombie, Duncan E., Kulkarni, Tejal, Liang, Helena H., Sivakumaran, Priyadharshini, Lidgerwood, Grace E., Hernández, Damián, Conquest, Alison, Rooney, Louise A., Chevalier, Sophie, Andersen, Stacey B., Senabouth, Anne, Vickers, James C., Mackey, David A., Craig, Jamie E., Laslett, Andrew L., Hewitt, Alex W., Powell, Joseph E. and Pébay, Alice (2018). Single-cell profiling identifies key pathways expressed by iPSCs cultured in different commercial media. iScience, 7, 30-39. doi: 10.1016/j.isci.2018.08.016
Lukowski, S. W., Tuong, Z. K., Noske, K., Senabouth, A., Nguyen, Q. H., Andersen, S. B., Soyer, H. P., Frazer, I. H. and Powell, J. E. (2018). Detection of HPV E7 transcription at single-cell resolution in epidermis. The Journal of Investigative Dermatology, 138 (12), 2558-2567. doi: 10.1016/j.jid.2018.06.169
Nguyen, Quan H., Lukowski, Samuel W., Chiu, Han Sheng, Senabouth, Anne, Bruxner, Timothy J.C., Christ, Angelika N., Palpant, Nathan J. and Powell, Joseph E. (2018). Single-cell RNA-seq of human induced pluripotent stem cells reveals cellular heterogeneity and cell state transitions between subpopulations. Genome Research, 28 (7), 1053-1066. doi: 10.1101/gr.223925.117
Nguyen, Quan, Aguado, Julio, Iannelli, Fabio, Suzuki, Ana Maria, Rossiello, Francesca, D'Adda Di Fagagna, Fabrizio and Carninci, Piero (2018). Target-enrichment sequencing for detailed characterization of small RNAs. Nature Protocols, 13 (4), 768-786. doi: 10.1038/nprot.2018.001
Nguyen, Quan H., Tellam, Ross L., Naval-Sanchez, Marina, Porto-Neto, Laercio R., Barendse, William, Reverter, Antonio, Hayes, Benjamin, Kijas, James and Dalrymple, Brian P. (2018). Mammalian genomic regulatory regions predicted by utilizing human genomics, transcriptomics, and epigenetics data. Gigascience, 7 (3), 1-17. doi: 10.1093/gigascience/gix136
Daniszewski, Maciej, Senabouth, Anne, Nguyen, Quan H., Crombie, Duncan E., Lukowski, Samuel W., Kulkarni, Tejal, Sluch, Valentin M., Jabbari, Jafar S., Chamling, Xitiz, Zack, Donald J., Pébay, Alice, Powell, Joseph E. and Hewitt, Alex W. (2018). Single cell RNA sequencing of stem cell-derived retinal ganglion cells. Scientific Data, 5 (1) 180013, 1-9. doi: 10.1038/sdata.2018.13
Naval-Sanchez, Marina, Nguyen, Quan, McWilliam, Sean, Porto-Neto, Laercio R., Tellam, Ross, Vuocolo, Tony, Reverter, Antonio, Perez-Enciso, Miguel, Brauning, Rudiger, Clarke, Shannon, McCulloch, Alan, Zamani, Wahid, Naderi, Saeid, Rezaei, Hamid Reza, Pompanon, Francois, Taberlet, Pierre, Worley, Kim C., Gibbs, Richard A., Muzny, Donna M., Jhangiani, Shalini N., Cockett, Noelle, Daetwyler, Hans and Kijas, James (2018). Sheep genome functional annotation reveals proximal regulatory elements contributed to the evolution of modern breeds. Nature Communications, 9 (1) 859. doi: 10.1038/s41467-017-02809-1
Iannelli, Fabio, Galbiati, Alessandro, Capozzo, Ilaria, Nguyen, Quan, Magnuson, Brian, Michelini, Flavia, D'Alessandro, Giuseppina, Cabrini, Matteo, Roncador, Marco, Francia, Sofia, Crosetto, Nicola, Ljungman, Mats, Carninci, Piero and di Fagagna, Fabrizio d'Adda (2017). A damaged genome's transcriptional landscape through multilayered expression profiling around in situ-mapped DNA double-strand breaks. Nature Communications, 8 (1) 15656, 15656. doi: 10.1038/ncomms15656
Rossiello, Francesca, Aguado, Julio, Sepe, Sara, Iannelli, Fabio, Nguyen, Quan, Pitchiaya, Sethuramasundaram, Carninci, Piero and Di Fagagna, Fabrizio d’Adda (2017). DNA damage response inhibition at dysfunctional telomeres by modulation of telomeric DNA damage response RNAs. Nature Communications, 8 (1) 13980, 13980. doi: 10.1038/ncomms13980
Nguyen, Quan, Tran, Trinh Tb, Chan, Leslie C. L., Nielsen, Lars K. and Reid, Steven (2016). In vitro production of baculoviruses: identifying host and virus genes associated with high productivity. Applied Microbiology and Biotechnology, 100 (21), 1-15. doi: 10.1007/s00253-016-7774-3
Hoang, M. H., Namirembe, S., van Noordwijk, M., Catacutan, D., Öborn, I., Perez-Teran, A. S., Nguyen, H. Q. and Dumas-Johansen, M. K. (2014). Farmer portfolios, strategic diversity management and climate-change adaptation - implications for policy in Vietnam and Kenya. Climate and Development, 6 (3), 216-225. doi: 10.1080/17565529.2013.857588
Nguyen,Quan, Nielsen, Lars K. and Reid, Steven (2013). Genome scale transcriptomics of baculovirus-insect interactions. Viruses, 5 (11), 2721-2747. doi: 10.3390/v5112721
Nguyen, Quan, Chan, Leslie C. L., Nielsen, Lars K. and Reid, Steven (2013). Genome scale analysis of differential mRNA expression of Helicoverpa zea insect cells infected with a H. armigera baculovirus. Virology, 444 (1-2), 158-170. doi: 10.1016/j.virol.2013.06.004
Nguyen, Quan, Hoang, Minh Ha, Oborn, Ingrid and Noordwijk, Meine (2013). Multipurpose agroforestry as a climate change resiliency option for farmers: an example of local adaptation in Vietnam. Climatic Change, 117 (1-2), 241-257. doi: 10.1007/s10584-012-0550-1
Nguyen, Quan, Palfreyman, Robin W., Chan, Leslie C. L., Reid, Steven and Nielsen, Lars K. (2012). Transcriptome sequencing of and microarray development for a Helicoverpa zea cell line to investigate in vitro insect cell-baculovirus interactions. PLoS One, 7 (5) e36324, e36324.1-e36324.15. doi: 10.1371/journal.pone.0036324
Jiang, Xiao-Xia, Nguyen, Quan, Chou, YuChia, Wang, Tao, Nandakumar, Vijayalakshmi, Yates, Peter, Jones, Lindsey, Wang, Lifeng, Won, Haejung, Lee, Hye-Ra, Jung, Jae U., Müschen, Markus, Huang, Xue F. and Chen, Si-Yi (2011). Control of B cell development by the histone H2A deubiquitinase MYSM1. Immunity, 35 (6), 883-896. doi: 10.1016/j.immuni.2011.11.010
Nguyen, Quan, Qi, Ying Mei, Wu, Yang, Chan, Leslie C. L., Nielsen, Lars K. and Reid, Steven (2011). In vitro production of Helicoverpa baculovirus biopesticides: Automated selection of insect cell clones for manufacturing and systems biology studies. Journal of Virological Methods, 175 (2), 197-205. doi: 10.1016/j.jviromet.2011.05.011
Veldhuyzen, WF, Nguyen, Q, McMaster, G and Lawrence, DS (2003). A Light-Activated Probe of Intracellular Protein Kinase Activity. Journal of the American Chemical Society, 125 (44), 13358-13359. doi: 10.1021/ja037801x
Gingrich, JC, Davis, DR and Nguyen, Q (2000). Multiplex detection and quantitation of proteins on Western blots using fluorescent probes. Biotechniques, 29 (3), 636-642.
Conference Papers
Kordowski, Anja, Mulay, Onkar, Harris, Lachlan, Nguyen, Quan H and Day, Bryan W. (2024). Spatial Transcriptomic Sequencing Of A DIPG Patient Tumour Resource. 2024 International Symposium on Pediatric Neuro-Oncology (ISPNO), Philadelphia, PA United States, 29 June – 2 July 2024. Cary, NC United States: Oxford University Press. doi: 10.1093/neuonc/noae064.102
Wichmann, Ignacio A., Huang, Robert J., Su, Andrew, Sathe, Anuja, Shum, Miranda V., Grimes, Susan M., Meka, Rithika, Almeda, Alison, Bai, Xiangqi, Shen, Jeanne, Nguyen, Quan, Amieva, Manuel, Hwang, Joo Ha and Ji, Hanlee P. (2024). A spatially mapped gene expression signature for intestinal stem-like cells identifies high-risk precursors of gastric cancer. American Association for Cancer Research Annual Meeting 2024, San Diego, CA United States, 5-10 April 2024. Philadelphia, PA United States: American Association for Cancer Research. doi: 10.1158/1538-7445.am2024-1140
Zhou, 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
Tan, 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
Su, 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
Zhang, 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.
Grice, Laura, Ni, Guiyan, Jin, Xinnan, Tran, Minh, Killingbeck, Emily, Gregory, Mark, Mulay, Onkar, Teoh, Siok-Min, Kulasinghe, Arutha, Leon, Michael, Murphy, Sarah, Warren, Sarah, Kim, Youngmi and Nguyen, Quan (2022). Abstract 3817: A single-cell, spatial multiomics atlas and cellular interactome of all major skin cancer types. American Association for Cancer Research Annual Meeting, Philadelphia, PA, United States, 8-13 April 2022. Philadelphia, PA, United States: American Association for Cancer Research. doi: 10.1158/1538-7445.am2022-3817
Vo, Tuan, Balderson, Brad, Jones, Kahli, Crawford, Joanna, Millar, Amanda, Tolson, Elissa, Ruitenberg, Marc, Robertson, Thomas, Bhuva, Dharmesh, Davis, Melissa, Wainwright, Brandon, Nguyen, Quan and Genovesi, Laura (2022). MEDB-06. Spatial transcriptomic analysis of Sonic Hedgehog Medulloblastoma identifies that loss of heterogeneity and induced differentiation underlies the response to CDK4/6 inhibition. International Symposium on Pediatric Neuro-Oncology, Hamburg, Germany, 12–15 June 2022. Cary, NC, United States: Oxford University Press. doi: 10.1093/neuonc/noac079.381
Selvakumar, D., Clayton, Z., Prowse, A., Dingwall, S., George, J., Shah, H., Paterson, H., Jeyaprakesh, P., Wu, Z., Campbell, T., Kotake, Y., Turnbull, S., Nguyen, Q., Grieve, S., Palpant, N., Pathan, F., Kizana, E., Kumar, S., Gray, P. and Chong, J. (2022). Cellular heterogeneity of pluripotent stem cell derived cardiomyocyte grafts is mechanistically linked to treatable arrhythmias. 70th Annual Scientific Meeting of the Cardiac Society of Australia and New Zealand, Gold Coast, QLD Australia, 11-14 August 2022. Chatswood, NSW Australia: Elsevier. doi: 10.1016/j.hlc.2022.06.004
Tran, Minh, Su, Andrew, Lee, HoJoon, Cruz, Richard, Pflieger, Lance, Dean, Ashely, Nguyen, Quan, Ji, Hanlee P. and Rhodes, Terence (2021). Understanding the tumour immune microenvironment of stage III colorectal cancer using multiplexed imaging mass cytometry. Royal College of Pathologists of Australasia - Pathology Update 2021, Sydney, NSW Australia, 2-4 July 2021. Oxford, United Kingdom: Elsevier. doi: 10.1016/j.pathol.2021.06.063
Tran, Minh, Su, Andrew, Lee, HoJoon, Cruz, Richard, Pflieger, Lance, Dean, Ashely, Nguyen, Quan, Ji, Hanlee and Rhodes, Terence (2020). 665 Spatial single-cell analysis of colorectal cancer tumour using multiplexed imaging mass cytometry. 35th Anniversary Annual Meeting (SITC 2020), Virtual, 11-14 November 2020. London, United Kingdom: BMJ Group. doi: 10.1136/jitc-2020-sitc2020.0665
Raghubar, Arti M., Pham, Duy T., Tan, Xiao, Grice, Laura F., Lam, Pui Yeng, Crawford, Joanna, Andersen, Stacey, Yoon, Sohye, Holland, Samuel E., Francis, Leo, Combes, Alexander N., Kassianos, Andrew J., Healy, Helen G., Nguyen, Quan and Mallett, Andrew J. (2020). Spatial Transcriptomics (ST): Integrating Molecular Profiles with Histomorphology in Kidney Tissue Sections. Kidney Week, Online, 19-25 October 2020. Washington, DC United States: American Society of Nephrology. doi: 10.1681/asn.20203110s112b
Nguyen, Quan H., Lukowski, Samuel W., Chiu, Han S., Friedman, Clayton E., Senabouth, Anne, Crowhurst, Liam, Bruxner, Timothy J. C., Christ, Angelika N., Hudson, James, Ding, Jun, Bar-Joseph, Ziv, Tam, Patrick P. L., Palpant, Nathan J. and Powell, Joseph E. (2018). Genetic networks modulating cell fate specification and contributing to cardiac disease risk in hiPSC-derived cardiomyocytes at single cell resolution. Human Genome Meeting 2018, Yokohama, Japan, 12-15 March 2018. London, United Kingdom: Henry Stewart Publications LLP. doi: 10.1186/s40246-018-0138-6
Nguyen, Q., Tellam, R. L., Kijas, J., Barendse, W. and Dalrymple, B. P. (2016). Predicting regulatory SNPs within enhancers and promoters in cattle. Functional Annotation of Animal Genomes (FAANG) Joint ASAS-ISAG Symposium, Salt Lake City, Utah, United States, July 23 2016. Cary, NC United States: Oxford University Press (OUP). doi: 10.2527/jas2016.94supplement432a
Sanchez, M. Naval, Brauning, R., Clarke, S. M., Nguyen, Q., McCulloch, A., Cockett, N. E., Zamani, W., Pompanon, F., Taberlet, P., McWilliam, S., Daetwyler, H. and Kijas, J. (2016). S0125 Changing patterns of genomic variability following domestication of sheep. Cary, NC, United States: Oxford University Press. doi: 10.2527/jas2016.94supplement413x
Nguyen, Quan, Prasath, Daniel B., Palfreyman, Robin W., Nielsen, Lars K., Chan, Leslie C. L. and Reid, Steven (2011). Optimising in vitro production of baculovirus biopesticides – a transcriptomics approach to establish a platform for expression analysis and bioengineering of virus and insect cells. Chemeca 2011: Australasian Conference on Chemical Engineering, Sydney, Australia, 18-21 September 2011. Barton, ACT, Australia: Engineers Australia.
Thesis
Nguyen, Hoang Quan (2013). Genome-scale transcriptomic study of Helicoverpa Zea host cells and H. armigera baculovirus infections in vitro. PhD Thesis, Australian Institute For Bioengineering and Nanotechnology, The University of Queensland.
Data Collections
Jiang, Yuanhao, Nguyen, Quan and Tan, Xiao (2024). DeepHis2Exp. The University of Queensland. (Dataset) doi: 10.48610/3e7a235
Andrew 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
Xiao Tan, Onkar Mulay and Quan Nguyen (2023). STimage dataset. The University of Queensland. (Dataset) doi: 10.48610/4fb74a9
Tan, 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