Journal Articles
Stary, Victoria, Pandey, Ram V., List, Julia, Kleissl, Lisa, Deckert, Florian, Kabiljo, Julijan, Laengle, Johannes, Gerakopoulos, Vasileios, Oehler, Rudolf, Watzke, Lukas, Farlik, Matthias, Lukowski, Samuel W., Vogt, Anne B., Stary, Georg, Stockinger, Hannes, Bergmann, Michael and Pilat, Nina (2024). Dysfunctional tumor-infiltrating Vδ1 + T lymphocytes in microsatellite-stable colorectal cancer. Nature Communications, 15 (1) 6949, 6949. doi: 10.1038/s41467-024-51025-1
Shamanskiy, Victor, Mikhailova, Alina A., Tretiakov, Evgenii O., Ushakova, Kristina, Mikhailova, Alina G., Oreshkov, Sergei, Knorre, Dmitry A., Ree, Natalia, Overdevest, Jonathan B., Lukowski, Samuel W., Gostimskaya, Irina, Yurov, Valerian, Liou, Chia-Wei, Lin, Tsu-Kung, Kunz, Wolfram S., Reymond, Alexandre, Mazunin, Ilya, Bazykin, Georgii A., Fellay, Jacques, Tanaka, Masashi, Khrapko, Konstantin, Gunbin, Konstantin and Popadin, Konstantin (2023). Secondary structure of the human mitochondrial genome affects formation of deletions. BMC Biology, 21 (1) 103, 1-13. doi: 10.1186/s12915-023-01606-1
McKinnon, Brett D., Lukowski, Samuel W., Mortlock, Sally, Crawford, Joanna, Atluri, Sharat, Subramaniam, Sugarniya, Johnston, Rebecca L., Nirgianakis, Konstantinos, Tanaka, Keisuke, Amoako, Akwasi, Mueller, Michael D. and Montgomery, Grant W. (2022). Altered differentiation of endometrial mesenchymal stromal fibroblasts is associated with endometriosis susceptibility. Communications Biology, 5 (1) 600, 600. doi: 10.1038/s42003-022-03541-3
Krueger, Annika, Zaugg, Julian, Chisholm, Sarah, Linedale, Richard, Lachner, Nancy, Teoh, Siok Min, Tuong, Zewen K., Lukowski, Samuel W., Morrison, Mark, Soyer, H. Peter, Hugenholtz, Philip, Hill, Michelle M. and Frazer, Ian H. (2022). Secreted toxins from Staphylococcus aureus strains isolated from keratinocyte skin cancers mediate pro-tumorigenic inflammatory responses in the skin. Frontiers in Microbiology, 12 789042, 789042. doi: 10.3389/fmicb.2021.789042
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
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
Vilar, Rui, Lukowski, Samuel W., Garieri, Marco, Di Sanza, Corinne, Neerman-Arbez, Marguerite and Fish, Richard J. (2021). Chemical Modulators of Fibrinogen Production and Their Impact on Venous Thrombosis. Thrombosis and Haemostasis, 121 (4), 433-448. doi: 10.1055/s-0040-1718414
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
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
Zhou, Chenhao, Tuong, Zewen Kelvin, Lukowski, Samuel Wieslaw, Chandra, Janin and Frazer, Ian H. (2021). Antigen nonspecific induction of distinct regulatory T cell states in oncogene-driven hyperproliferative skin. ImmunoHorizons, 5 (2), 102-116. doi: 10.4049/immunohorizons.2100006
Budhwani, Megha, Lukowski, Samuel W., Porceddu, Sandro V., Frazer, Ian H. and Chandra, Janin (2020). Dysregulation of stemness pathways in HPV mediated cervical malignant transformation identifies potential oncotherapy targets. Frontiers in Cellular and Infection Microbiology, 10 307, 307. doi: 10.3389/fcimb.2020.00307
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
Mortlock, Sally, Kendarsari, Raden I., Fung, Jenny N., Gibson, Greg, Yang, Fei, Restuadi, Restuadi, Girling, Jane E., Holdsworth-Carson, Sarah J., Teh, Wan Tinn, Lukowski, Samuel W., Healey, Martin, Qi, Ting, Rogers, Peter A. W., Yang, Jian, McKinnon, Brett and Montgomery, Grant W. (2020). Tissue specific regulation of transcription in endometrium and association with disease. Human Reproduction, 35 (2), 377-393. doi: 10.1093/humrep/dez279
Byrne, Adam J., Powell, Joseph E., O’Sullivan, Brendan J., Ogger, Patricia P., Hoffland, Ashley, Cook, James, Bonner, Katie L., Hewitt, Richard J., Wolf, Simone, Ghai, Poonam, Walker, Simone A., Lukowski, Samuel W., Molyneaux, Philip L., Saglani, Sejal, Chambers, Daniel C., Maher, Toby M. and Lloyd, Clare M. (2020). Dynamics of human monocytes and airway macrophages during healthy aging and after transplant. The Journal of Experimental Medicine, 217 (3) e20191236. doi: 10.1084/jem.20191236
Devitt, Katharina, Hanson, Sarah J., Tuong, Zewen K., McMeniman, Erin, Soyer, H. Peter, Frazer, Ian H. and Lukowski, Samuel W. (2019). Single-cell RNA sequencing reveals cell type-specific HPV expression in hyperplastic skin lesions. Virology, 537, 14-19. doi: 10.1016/j.virol.2019.08.007
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
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
Mortlock, Sally, Restuadi, Restuadi, Levien, Rupert, Girling, Jane E., Holdsworth-Carson, Sarah J., Healey, Martin, Zhu, Zhihong, Qi, Ting, Wu, Yang, Lukowski, Samuel W., Rogers, Peter A. W., Yang, Jian, McRae, Allan F., Fung, Jenny N. and Montgomery, Grant W. (2019). Genetic regulation of methylation in human endometrium and blood and gene targets for reproductive diseases. Clinical Epigenetics, 11 (1) 49, 49. doi: 10.1186/s13148-019-0648-7
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
Chambers, Daniel C., Carew, Alan M., Lukowski, Samuel W. and Powell, Joseph E. (2018). Transcriptomics and single-cell RNA-sequencing. Respirology, 24 (1), 29-36. doi: 10.1111/resp.13412
Fung, Jenny N., Mortlock, Sally, Girling, Jane E., Holdsworth-Carson, Sarah J., Teh, Wan Tinn, Zhu, Zhihong, Lukowski, Samuel W., McKinnon, Brett D., McRae, Allan, Yang, Jian, Healey, Martin, Powell, Joseph E., Rogers, Peter A. W. and Montgomery, Grant W (2018). Genetic regulation of disease risk and endometrial gene expression highlights potential target genes for endometriosis and polycystic ovarian syndrome. Scientific Reports, 8 (1) 11424, 11424. doi: 10.1038/s41598-018-29462-y
Ramnath, Divya, Irvine, Katharine M., Lukowski, Samuel W., Horsfall, Leigh U., Loh, Zhixuan, Clouston, Andrew D., Patel, Preya J., Fagan, Kevin J., Iyer, Abishek, Lampe, Guy, Stow, Jennifer L., Schroder, Kate, Fairlie, David P., Powell, Joseph E., Powell, Elizabeth E. and Sweet, Matthew J. (2018). Hepatic expression profiling identifies steatosis-independent and steatosis-driven advanced fibrosis genes. JCI Insight, 3 (14) ARTN e120274. doi: 10.1172/jci.insight.120274
De Smit, Elisabeth, Lukowski, Samuel W., Anderson, Lisa, Senabouth, Anne, Dauyey, Kaisar, Song, Sharon, Wyse, Bruce, Wheeler, Lawrie, Chen, Christine Y., Cao, Khoa, Wong Ten Yuen, Amy, Shuey, Neil, Clarke, Linda, Lopez Sanchez, Isabel, Hung, Sandy S. C., Pébay, Alice, Mackey, David A., Brown, Matthew A., Hewitt, Alex W. and Powell, Joseph E. (2018). Longitudinal expression profiling of CD4+ and CD8+ cells in patients with active to quiescent giant cell arteritis. BMC Medical Genomics, 11 (1) 61, 61. doi: 10.1186/s12920-018-0376-4
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
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
Popadin, Konstantin, Peischl, Stephan, Garieri, Marco, Sailani, M. Reza, Letourneau, Audrey, Santoni, Federico, Lukowski, Samuel W., Bazykin, Georgii A., Nikolaev, Sergey, Meyer, Diogo, Excoffier, Laurent, Reymond, Alexandre and Antonarakis, Stylianos E. (2018). Slightly deleterious genomic variants and transcriptome perturbations in Down syndrome embryonic selection. Genome Research, 28 (1), 1-10. doi: 10.1101/gr.228411.117
Lukowski, Samuel W., Lloyd-Jones, Luke R., Holloway, Alexander, Kirsten, Holger, Hemani, Gibran, Yang, Jian, Small, Kerrin, Zhao, Jing, Metspalu, Andres, Dermitzakis, Emmanouil T., Gibson, Greg, Spector, Timothy D., Thiery, Joachim, Scholz, Markus, Montgomery, Grant W., Esko, Tonu, Visscher, Peter M. and Powell, Joseph E. (2017). Genetic correlations reveal the shared genetic architecture of transcription in human peripheral blood. Nature Communications, 8 (483) 483, 483. doi: 10.1038/s41467-017-00473-z
Fung, Jenny N., Girling, Jane E., Lukowski, Samuel W., Sapkota, Yadav, Wallace, Leanne, Holdsworth-Carson, Sarah J., Henders, Anjali K., Healey, Martin, Rogers, Peter A. W., Powell, Joseph E. and Montgomery, Grant W. (2017). The genetic regulation of transcription in human endometrial tissue. Human Reproduction, 32 (4), 893-904. doi: 10.1093/humrep/dex006
Irvine, Katharine M., Xuan Banh, Gadd, Victoria L., Wojcik, Kyle K., Ariffin, Juliana K., Jose, Sara, Lukowski, Samuel, Baillie, Gregory J., Sweet, Matthew J. and Powell, Elizabeth E. (2016). CRIg-expressing peritoneal macrophages are associated with disease severity in patients with cirrhosis and ascites. JCI Insight, 1 (8) e86914, e86914. doi: 10.1172/jci.insight.86914
Casini, A., Sokollik, C., Lukowski, S. W., Lurz, E., Rieubland, C., de Moerloose, P. and Neerman-Arbez, M. (2015). Hypofibrinogenemia and liver disease: A new case of Aguadilla fibrinogen and review of the literature. Haemophilia, 21 (6), 820-827. doi: 10.1111/hae.12719
Lukowski, Samuel W., Fish, Richard J., Martin-Levilain, Juliette, Gonelle-Gispert, Carmen, Buehler, Leo H., Maechler, Pierre, Dermitzakis, Emmanouil T. and Neerman-Arbez, Marguerite (2015). Integrated analysis of mRNA and miRNA expression in response to interleukin-6 in hepatocytes. Genomics, 106 (2), 107-115. doi: 10.1016/j.ygeno.2015.05.001
Ng, Preston S. K., Boehm, Raphael, Hartley-Tassell, Lauren E., Steen, Jason A., Wang, Hui, Lukowski, Samuel W., Hawthorne, Paula L., Trezise, Ann E. O., Coloe, Peter J., Grimmond, Sean M., Haselhorst, Thomas, von Itzstein, Mark, Paton, Adrienne W., Paton, James C. and Jennings, Michael P. (2014). Ferrets exclusively synthesize Neu5Ac and express naturally humanized influenza A virus receptors. Nature Communications, 5 (5750) 5750, 1-9. doi: 10.1038/ncomms6750
Popadin, Konstantin Y., Gutierrez-Arcelus, Maria, Lappalainen, Tuuli, Buil, Alfonso, Steinberg, Julia, Nikolaev, Sergey I., Lukowski, Samuel W., Bazykin, Georgii A., Seplyarskiy, Vladimir B., Ioannidis, Panagiotis, Zdobnov, Evgeny M., Dermitzakis, Emmanouil T. and Antonarakis, Stylianos E. (2014). Gene age predicts the strength of purifying selection acting on gene expression variation in humans. American Journal of Human Genetics, 95 (6), 660-674. doi: 10.1016/j.ajhg.2014.11.003
Lukowski, Samuel W., Rothnagel, Joseph A. and Trezise, Ann E. O. (2014). CFTR mRNA expression is regulated by an upstream open reading frame and RNA secondary structure in its 5' untranslated region. Human Molecular Genetics, 24 (4) ddu501, 899-912. doi: 10.1093/hmg/ddu501
Casini, A., Lukowski, S., Quintard, V. Louvain, Crutu, A., Zak, M., Regazzoni, S., de Moerloose, P. and Neerman-Arbez, M. (2014). FGB mutations leading to congenital quantitative fibrinogen deficiencies: an update and report of four novel mutations. Thrombosis Research, 133 (5), 868-874. doi: 10.1016/j.thromres.2014.01.022
Phan, Minh-Duy, Peters, Kate M., Sarkar, Sohinee, Lukowski, Samuel W., Allsopp, Luke P., Moriel, Danilo Gomes, Achard, Maud E. S., Totsika, Makrina, Marshall, Vikki M., Upton, Mathew, Beatson, Scott A. and Schembri, Mark A. (2013). The serum resistome of a globally disseminated multidrug resistant uropathogenic Escherichia coli clone. PloS Genetics, 9 (10) e1003834, e1003834.1-e1003834.18. doi: 10.1371/journal.pgen.1003834
Lukowski, Samuel W., Bombieri, Christina and Trezise, Ann E. O. (2011). Disrupted posttranscriptional regulation of the cystic fibrosis transmembrane conductance regulator (CFTR) by a 5′UTR mutation is associated with a cftr-related disease. Human Mutation, 32 (10), E2266-E2282. doi: 10.1002/humu.21545
Conference Papers
Wong, Raymond, Nguyen, Tu, Fang, Lyujie, Lukowski, Sam, Lo, Camden, Hung, Sandy, Luu, Chi D., Gillies, Mark C. and Hewitt, Alex W. (2020). Towards retinal regeneration: Reprogramming retinal glial cells into photoreceptors using CRISPRa. Annual Meeting of the Association-for-Research-in-Vision-and-Ophthalmology (ARVO), Electr Network, May 01-07, 2020. ROCKVILLE: ASSOC RESEARCH VISION OPHTHALMOLOGY INC.
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
Lukowski, Samuel L., Bombieri, Cristina, Castellani, Carlo, Pignatti , Pier Franco and Trezise, Ann E. O. (2009). A new mechanism of Cystic Fibrosis-related disease : Disruption of the post-transcriptional regulation of the CFTR gene. 30th Annual Lorne Conference on the Organization and Expression of the Genome, Lorne, Victoria, Australia, 15-18 February, 2009.
Lukowski, Sam W. and Trezise, Ann E. O. (2008). Novel UTR elements post-transcriptionally regulate CFTR translation. 29th Lorne Genome Conference on the Organization and Expression of the Genome, Lorne, Australia, 17-21 February 2008.
Lukowski, Sam W., Bombieri, Cristina, Castellani, Carlo, Pignatti, Pier Franco and Trezise, Ann E. O. (2007). Mutations in the 5'Untranslated Region of the Cystic Fibrosis Gene Alter Post-transcriptional Regulation and are Associated with Severe Chronic Lung Disease. 28th Annual Lorne Conference on the Organization and Expression of the Genome, Lorne, Victoria, 11-15 Feb 2007.
Lukowski, Sam W. and Trezise, Ann E.O. (2006). Post-transcriptional Regulation of the Cystic Fibrosis Gene. ComBio2006 (Combined Biological Societies) Conference, Brisbane, QLD, Australia, 24-28 Sep 2006.
Lukowski, S., Mattick, J. S. and Trezise, A. E. O. (2005). Uncovering the hidden layer Of RNA regulatory networks. 26th Annual Lorne Conference on the Organization and Expression of the Genome, Phillip Island, Victoria, 13-17 February 2005.
Lukowski, Sam W. and Trezise, Ann E.O. (2004). Post-transcriptional Regulation of the Cystic Fibrosis Gene. 27th Annual Lorne Conference on the Organization and Expression of the Genome, Lorne, Victoria, 12-15 Feb 2006.
Patent
Palpant, Nathan, Anderson, Stacey, Werner, Tessa, Lukowski, Samuel and Shen, Sophie (2022). Methods and compositions for multiplexing cell analysis. PCT/AU2022/051476.
Thesis
Lukowski, Samuel (2010). Post-transcriptional regulation of the cystic fibrosis transmembrane conductance regulator (CFTR) by the 5´ untranslated region. PhD Thesis, School of Chemistry and Molecular Biosciences, The University of Queensland.