Genome Innovation Hub

Stacey Andersen

Operations Manager
Genome Innovation Hub
Stacey Andersen

Expertise

- Single cell sequencing

- PacBio long read sequencing

- Short read sequencing

Researcher biography

After completing a Bachelor of Biomedical Science with Honours at Griffith University and subsequent lab experience at the Eskitis Institute for Cell and Molecular Therapies, Stacey joined UQ in 2010 to work in Professor Lars Nielsen’s group at the AIBN. In this role she investigated cell fate determination at the single cell level, and based on this experience was recruited to the laboratory of Associate Professor Joseph Powell at the IMB in 2017 to further develop single cell sequencing techniques. Here she was instrumental in expanding the single cell transcriptomics repertoire in the Powell laboratory, promoting collaborations within UQ and extending to the broader scientific community. After working on a project combining CRISPR/Cas9-mediated genome editing with single cell sequencing in the lab of Dr Nathan Palpant (IMB), Stacey joined the Genome Innovation Hub in 2019, initially holding a dual appointment with the IMB sequencing facility. After contributing to various projects in single cell, long read, and short read sequencing, she moved to the position of Operations Manager in 2022.

Featured projects Duration
Single-cell transcriptome and chromatin profiling in plant cells
Genome Innovation Hub Collaborative Project (UQ infrastructure)
 2020
Combining novel scSLAM-seq technology with 10x Genomics Chromium to track microchanges in newly synthesised RNA
Genome Innovation Hub Collaborative Project (UQ infrastructure)
 2020
Simultaneous identification of RNA-chromatin interactions and transcriptomes in single cells
Genome Innovation Hub Collaborative Project (UQ infrastructure)
 2020
Culture-independent metagenomic diagnostics
Genome Innovation Hub Collaborative Project (UQ infrastructure)
 2021
Genome-Phaser: protocol for fully phasing whole genome variants using haplotagging
Genome Innovation Hub Collaborative Project (UQ infrastructure)
 2021
RNA velocity quantification of single-cell transcriptomics
Genome Innovation Hub Collaborative Project (UQ infrastructure)
 2021
Expanding the scope of multimodal single cell sequencing
Genome Innovation Hub Collaborative Project (UQ infrastructure)
 2021
HTS single cell CRISPR technology for experimental validation of population genetics and functional genomics discovery
Genome Innovation Hub Collaborative Project (UQ infrastructure)
 2021
Enabling population scale epigenomics for crop improvement
Genome Innovation Hub Collaborative Project (UQ infrastructure)
 2021
Guide RNA design in non-model organisms
Genome Innovation Hub Collaborative Project (UQ infrastructure)
 2023
Developing a next generation single-cell transcriptomic tool
Genome Innovation Hub Collaborative Project (UQ infrastructure)
 2023
Quantitative transcriptome analysis (CAGE)
Genome Innovation Hub Collaborative Project (UQ infrastructure)
 2019
Discovery of new regulatory networks with long-read transcriptomics
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
Understanding host-pathogen interactions through development of new co-transcriptomic single cell RNA sequencing technologies
Genome Innovation Hub Collaborative Project (UQ infrastructure)
 2020

Publications

Book Chapter (1)
Journal Articles (23)
Conference Paper (1)
Data Collection (1)

Book Chapter

Raghubar, Arti M., Crawford, Joanna, Jones, Kahli, Lam, Pui Y., Andersen, Stacey B., Matigian, Nicholas A., Ng, Monica S Y, Healy, Helen, Kassianos, Andrew J. and Mallett, Andrew J. (2023). Spatial transcriptomics in kidney tissue. Kidney research: experimental protocols. (pp. 233-282) edited by Tim D. Hewitson, Nigel D. Toussaint and Edward R. Smith. New York, NY USA: Humana New York. doi: 10.1007/978-1-0716-3179-9_17

Journal Articles

Nhu, Nguyen Thi Khanh, Phan, Minh-Duy, Hancock, Steven J., Peters, Kate M., Alvarez-Fraga, Laura, Forde, Brian M., Andersen, Stacey B., Miliya, Thyl, Harris, Patrick N. A., Beatson, Scott A., Schlebusch, Sanmarie, Bergh, Haakon, Turner, Paul, Brauner, Annelie, Westerlund-Wikström, Benita, Irwin, Adam D. and Schembri, Mark A (2024). High-risk Escherichia coli clones that cause neonatal meningitis and association with recrudescent infection. eLife, 12 ARTN RP91853. doi: 10.7554/elife.91853.3
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
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
Nguyen, Loan T., Jung, Hyungtaek, Ma, Jun, Andersen, Stacey and Ross, Elizabeth (2023). Long-read Pore-C shows the 3D structure of the cattle genome. Animal Production Science, 63 (11), 1-11. doi: 10.1071/an22479
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
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
Yazar, Seyhan, Alquicira-Hernandez, Jose, Wing, Kristof, Senabouth, Anne, Gordon, M. Grace, Andersen, Stacey, Lu, Qinyi, Rowson, Antonia, Taylor, Thomas R. P., Clarke, Linda, Maccora, Katia, Chen, Christine, Cook, Anthony L., Ye, Chun Jimmie, Fairfax, Kirsten A., Hewitt, Alex W. and Powell, Joseph E. (2022). Single-cell eQTL mapping identifies cell type–specific genetic control of autoimmune disease. Science, 376 (6589) abf3041, eabf3041-+. doi: 10.1126/science.abf3041
Rødahl, Inga, Gotley, James, Andersen, Stacey B., Yu, Meihua, Mehdi, Ahmed M., Christ, Angelika N., Hamilton-Williams, Emma E., Frazer, Ian H., Lukowski, Samuel W. and Chandra, Janin (2021). Acquisition of murine splenic myeloid cells for protein and gene expression profiling by advanced flow cytometry and CITE-seq. STAR Protocols, 2 (4) 100842, 1-27. doi: 10.1016/j.xpro.2021.100842
Lukowski, Samuel W., Rodahl, Inga, Kelly, Samuel, Yu, Meihua, Gotley, James, Zhou, Chenhao, Millard, Susan, Andersen, Stacey B., Christ, Angelika N., Belz, Gabrielle, Frazer, Ian H. and Chandra, Janin (2021). Absence of Batf3 reveals a new dimension of cell state heterogeneity within conventional dendritic cells. iScience, 24 (5) 102402, 1-21. doi: 10.1016/j.isci.2021.102402
Schwaber, Jessica L., Korbie, Darren, Andersen, Stacey, Lin, Erica, Chrysanthopoulos, Panagiotis K., Trau, Matt and Nielsen, Lars K. (2021). Network mapping of primary CD34+ cells by Ampliseq based whole transcriptome targeted resequencing identifies unexplored differentiation regulatory relationships. PLoS ONE, 16 (2 ) e0246107, e0246107. doi: 10.1371/journal.pone.0246107
Engel, Jessica A., Lee, Hyun Jae, Williams, Cameron G., Kuns, Rachel, Olver, Stuart, Lansink, Lianne Im, Soon, Megan Sf, Andersen, Stacey B., Powell, Joseph E., Svensson, Valentine, Teichmann, Sarah A., Hill, Geoffrey R., Varelias, Antiopi, Koyama, Motoko and Haque, Ashraful (2020). Single-cell transcriptomics of alloreactive CD4+ T cells over time reveals divergent fates during gut graft-versus-host disease. JCI Insight, 5 (13) 137990. doi: 10.1172/jci.insight.137990
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
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
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
Lukowski, Samuel W., Patel, Jatin, Andersen, Stacey B., Sim, Seen-Ling, Wong, Ho Yi, Tay, Joshua, Winkler, Ingrid, Powell, Joseph E. and Khosrotehrani, Kiarash (2019). Single-cell transcriptional profiling of aortic endothelium identifies a hierarchy from endovascular progenitors to differentiated cells. Cell Reports, 27 (9), 2748-2758. doi: 10.1016/j.celrep.2019.04.102
Schwaber, Jessica, Andersen, Stacey and Nielsen, Lars (2019). Shedding light: the importance of reverse transcription efficiency standards in data interpretation. Biomolecular Detection and Quantification, 17 100077, 100077. doi: 10.1016/j.bdq.2018.12.002
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
Deveson, Ira W., Chen, Wendy Y., Wong, Ted, Hardwick, Simon A., Andersen, Stacey B., Nielsen, Lars K., Mattick, John S. and Mercer, Tim R. (2016). Representing genetic variation with synthetic DNA standards. Nature Methods, 13 (9), 784-791. doi: 10.1038/nmeth.3957
Hardwick, Simon A., Chen, Wendy Y., Wong, Ted, Deveson, Ira W., Blackburn, James, Andersen, Stacey B., Nielsen, Lars K., Mattick, John S. and Mercer, Tim R. (2016). Spliced synthetic genes as internal controls in RNA sequencing experiments. Nature Methods, 13 (9), 792-798. doi: 10.1038/nmeth.3958
Mercer, Tim R., Clark, Michael B., Anderson, Stacey B., Brunck, Marion E., Haerty, Wilifried, Crawford, Joanna, Taft, Ryan J., Nielsen, Lars K., Dinger, Marcel E. and Mattick, John S. (2015). Genome-wide discovery of human splicing branchpoints. Genome Research, 25 (2), 290-303. doi: 10.1101/gr.182899.114
Osborne, Geoffrey W., Andersen, Stacey B. and Battye, Francis L. (2015). Development of a novel cell sorting method that samples population diversity in flow cytometry. Cytometry Part A, 87 (11), 1047-1051. doi: 10.1002/cyto.a.22678
Brunck, Marion E. G., Andersen, Stacey B., Timmins, Nicholas E., Osborne, Geoffrey W. and Nielsen, Lars K. (2014). Absolute counting of neutrophils in whole blood using flow cytometry. Cytometry Part A, 85 (12), 1057-1064. doi: 10.1002/cyto.a.22503

Conference Paper

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

Data Collection

Ngo, Shyuan, Power, Dominique, Andersen, Stacey, Taherian Fard, Atefeh, Chang, Jeryn and Steyn, Frederik (2022). snrRNA-seq_muscle_dataset. The University of Queensland. (Dataset) doi: 10.48610/0106c8e

Areas of research

Cells
Genomics
Short read/Next Gen sequencing
Transcriptomics