The University of Queensland

SMCHD1 has separable roles in chromatin architecture and gene silencing that could be targeted in disease

Tapia del Fierro, Andres, den Hamer, Bianca, Benetti, Natalia, Jansz, Natasha, Chen, Kelan, Beck, Tamara, Vanyai, Hannah, Gurzau, Alexandra D., Daxinger, Lucia, Xue, Shifeng, Ly, Thanh Thao Nguyen, Wanigasuriya, Iromi, Iminitoff, Megan, Breslin, Kelsey, Oey, Harald, Krom, Yvonne D., van der Hoorn, Dinja, Bouwman, Linde F., Johanson, Timothy M., Ritchie, Matthew E., Gouil, Quentin A., Reversade, Bruno, Prin, Fabrice, Mohun, Timothy, van der Maarel, Silvère M., McGlinn, Edwina, Murphy, James M., Keniry, Andrew, de Greef, Jessica C. and Blewitt, Marnie E. (2023). SMCHD1 has separable roles in chromatin architecture and gene silencing that could be targeted in disease. Nature Communications, 14 (1) 5466, 1-22. doi: 10.1038/s41467-023-40992-6

Distinct HOX gene family DNA methylation profiles in histologically normal skin dependent on dermoscopic pattern of adjacent nevi

Muse, Meghan E., Schaider, Helmut, Oey, Harald, Soyer, H. Peter, Christensen, Brock C. and Stark, Mitchell S. (2023). Distinct HOX gene family DNA methylation profiles in histologically normal skin dependent on dermoscopic pattern of adjacent nevi. Journal of Investigative Dermatology, 143 (9), 1830-1834. doi: 10.1016/j.jid.2023.03.1653

The role of MORC3 in silencing transposable elements in mouse embryonic stem cells

Desai, Varsha P., Chouaref, Jihed, Wu, Haoyu, Pastor, William A., Kan, Ryan L., Oey, Harald M., Li, Zheng, Ho, Jamie, Vonk, Kelly K. D., San Leon Granado, David, Christopher, Michael A., Clark, Amander T., Jacobsen, Steven E. and Daxinger, Lucia (2021). The role of MORC3 in silencing transposable elements in mouse embryonic stem cells. Epigenetics and Chromatin, 14 (1) 49, 49. doi: 10.1186/s13072-021-00420-9

Radiomics biomarkers correlate with CD8 expression and predict immune signatures in melanoma patients

Aoude, Lauren G., Wong, Bernadette, Bonazzi, Vanessa F, Brosda, Sandra, Walters, Shaun B., Koufariotis, Lambros T., Naeini, Marjan M., Pearson, John V, Oey, Harald, Patel, Kalpana, Bradford, Julia J., Bloxham, Conor J, Atkinson, Victoria, Law, Phillip, Strutton, Geoffrey, Bayley, Gerard, Yang, Samuel, Smithers, B. Mark, Waddell, Nicola, Miles, Kenneth and Barbour, Andrew P. (2021). Radiomics biomarkers correlate with CD8 expression and predict immune signatures in melanoma patients. Molecular Cancer Research, 19 (6) molcanres.1038.2020, 950-956. doi: 10.1158/1541-7786.mcr-20-1038

EBV-associated primary CNS lymphoma occurring after immunosuppression is a distinct immunobiological entity

Gandhi, Maher K., Hoang, Thanh, Law, Soi C., Brosda, Sandra, O'Rourke, Kacey, Tobin, Joshua W. D., Vari, Frank, Murigneux, Valentine, Fink, J. Lynn, Gunawardana, Jay, Gould, Clare M., Oey, Harald, Bednarska, Karolina, Delecluse, Susanne, Trappe, Ralf Ulrich, de Long, Lilia Merida, Sabdia, Muhammed Bilal, Bhagat, Govind, Hapgood, Greg, Blyth, Emily, Clancy, Leighton E., Wight, Joel, Hawkes, Eliza A., Rimsza, Lisa M., Maguire, Alanna, Bojarczuk, Kamil, Chapuy, Bjoern and Keane, Colm (2021). EBV-associated primary CNS lymphoma occurring after immunosuppression is a distinct immunobiological entity. Blood, 137 (11), 1468-1477. doi: 10.1182/blood.2020008520

Pathogenic germline variants are associated with poor survival in stage III/IV melanoma patients

Aoude, Lauren G., Bonazzi, Vanessa F., Brosda, Sandra, Patel, Kalpana, Koufariotis, Lambros T., Oey, Harald, Nones, Katia, Wood, Scott, Pearson, John V., Lonie, James M., Arneil, Melissa, Atkinson, Victoria, Smithers, B. Mark, Waddell, Nicola and Barbour, Andrew P. (2020). Pathogenic germline variants are associated with poor survival in stage III/IV melanoma patients. Scientific Reports, 10 (1) 17687, 17687. doi: 10.1038/s41598-020-74956-3

Chromosome arm aneuploidies shape tumour evolution and drug response

Shukla, Ankit, Nguyen, Thu H. M., Moka, Sarat B., Ellis, Jonathan J., Grady, John P., Oey, Harald, Cristino, Alexandre S., Khanna, Kum Kum, Kroese, Dirk P., Krause, Lutz, Dray, Eloise, Fink, J. Lynn and Duijf, Pascal H. G. (2020). Chromosome arm aneuploidies shape tumour evolution and drug response. Nature Communications, 11 (1) 449, 449. doi: 10.1038/s41467-020-14286-0

Targeting an adenosine-mediated “don’t eat me signal” augments anti-lymphoma immunity by anti-CD20 monoclonal antibody

Nakamura, Kyohei, Casey, Mika, Oey, Harald, Vari, Frank, Stagg, John, Gandhi, Maher K. and Smyth, Mark J. (2020). Targeting an adenosine-mediated “don’t eat me signal” augments anti-lymphoma immunity by anti-CD20 monoclonal antibody. Leukemia, 34 (10), 2708-2721. doi: 10.1038/s41375-020-0811-3

Whole-genome sequencing of human malignant mesothelioma tumours and cell lines

Oey, Harald, Daniels, Marissa, Relan, Vandana, Chee, Tian Mun, Davidson, Morgan R., Yang, Ian A., Ellis, Jonathan J., Fong, Kwun M., Krause, Lutz and Bowman, Rayleen V. (2019). Whole-genome sequencing of human malignant mesothelioma tumours and cell lines. Carcinogenesis, 40 (6), 724-734. doi: 10.1093/carcin/bgz066

Whole-genome sequence of the bovine blood fluke Schistosoma bovis supports interspecific hybridization with S. haematobium

Oey, Harald, Zakrzewski, Martha, Gravermann, Kerstin, Young, Neil D., Korhonen, Pasi K., Gobert, Geoffrey N., Nawaratna, Sujeevi, Hasan, Shihab, Martínez, David M., You, Hong, Lavin, Martin, Jones, Malcolm K., Ragan, Mark A., Stoye, Jens, Oleaga, Ana, Emery, Aidan M., Webster, Bonnie, Rollinson, David, Gasser, Robin B., McManus, Donald P. and Krause, Lutz (2019). Whole-genome sequence of the bovine blood fluke Schistosoma bovis supports interspecific hybridization with S. haematobium. PLOS Pathogens, 15 (1) e1007513, e1007513. doi: 10.1371/journal.ppat.1007513

Whole-genome sequence of the oriental lung fluke Paragonimus westermani

Oey, Harald, Zakrzewski, Martha, Narain, Kanwar, Devi, K Rekha, Agatsuma, Takeshi, Nawaratna, Sujeevi, Gobart, Geoffrey, Jones, Malcolm, Ragan, Mark A, McManus, Donald P and Krause, Lutz (2018). Whole-genome sequence of the oriental lung fluke Paragonimus westermani. GigaScience, 8 (1). doi: 10.1093/gigascience/giy146

Identification of the CIMP-like subtype and aberrant methylation of members of the chromosomal segregation and spindle assembly pathways in esophageal adenocarcinoma

Krause, Lutz, Nones, Katia , Loffler, Kelly A., Nancarrow, Derek, Oey, Harald , Tang, Yue Hang, Wayte, Nicola J., Patch, Ann Marie, Patel, Kalpana , Brosda, Sandra, Manning, Suzanne, Lampe, Guy, Clouston, Andrew, Thomas, Janine, Stoye, Jens, Hussey, Damian J., Watson, David I., Lord, Reginald V., Phillips, Wayne A., Gotley, David, Smithers, B. Mark, Whiteman, David C., Hayward, Nicholas K., Grimmond, Sean M., Waddell, Nicola and Barbour, Andrew P. (2016). Identification of the CIMP-like subtype and aberrant methylation of members of the chromosomal segregation and spindle assembly pathways in esophageal adenocarcinoma. Carcinogenesis, 37 (4), 356-365. doi: 10.1093/carcin/bgw018

Wiz binds active promoters and CTCF-binding sites and is required for normal behaviour in the mouse

Isbel, Luke, Prokopuk, Lexie, Wu, Haoyu, Daxinger, Lucia, Oey, Harald, Spurling, Alex, Lawther, Adam J., Hale, Matthew W. and Whitelaw, Emma (2016). Wiz binds active promoters and CTCF-binding sites and is required for normal behaviour in the mouse. eLife, 5 (JULY) e15082. doi: 10.7554/eLife.15082

Hypomethylation of ERVs in the sperm of mice haploinsufficient for the histone methyltransferase Setdb1 correlates with a paternal effect on phenotype

Daxinger, Lucia, Oey, Harald, Isbel, Luke, Whitelaw, Nadia C., Youngson, Neil A., Spurling, Alex, Vonk, Kelly K. D. and Whitelaw, Emma (2016). Hypomethylation of ERVs in the sperm of mice haploinsufficient for the histone methyltransferase Setdb1 correlates with a paternal effect on phenotype. Scientific Reports, 6 (1) 25004, e25004.1-e25004.10. doi: 10.1038/srep25004

Genetic and epigenetic variation among inbred mouse littermates: Identification of inter-individual differentially methylated regions

Oey, Harald, Isbel, Luke, Hickey, Peter, Ebaid, Basant and Whitelaw, Emma (2015). Genetic and epigenetic variation among inbred mouse littermates: Identification of inter-individual differentially methylated regions. Epigenetics and Chromatin, 8 (54) 47, 54. doi: 10.1186/s13072-015-0047-z

The recently identified modifier of murine metastable epialleles, Rearranged L-Myc Fusion, is involved in maintaining epigenetic marks at CpG island shores and enhancers

Harten, Sarah K., Oey, Harald, Bourke, Lauren M., Bharti, Vandhana, Isbel, Luke, Daxinger, Lucia, Faou, Pierre, Robertson, Neil, Matthews, Jacqueline M. and Whitelaw, Emma (2015). The recently identified modifier of murine metastable epialleles, Rearranged L-Myc Fusion, is involved in maintaining epigenetic marks at CpG island shores and enhancers. BMC Biology, 13 (21) 21, 1-15. doi: 10.1186/s12915-015-0128-2

Identification of novel hypomorphic and null mutations in Klf1 derived from a genetic screen for modifiers of α-globin transgene variegation

Sorolla, Anabel, Tallack, Michael R., Oey, Harald, Harten, Sarah K., Daxinger, Lucia Clemens, Magor, Graham W., Combes, Alex N., Ilsley, Melissa, Whitelaw, Emma and Perkins, Andrew C. (2015). Identification of novel hypomorphic and null mutations in Klf1 derived from a genetic screen for modifiers of α-globin transgene variegation. Genomics, 105 (2), 116-122. doi: 10.1016/j.ygeno.2014.09.013

Trim33 Binds and Silences a Class of Young Endogenous Retroviruses in the Mouse Testis; a Novel Component of the Arms Race between Retrotransposons and the Host Genome

Isbel, Luke, Srivastava, Rahul, Oey, Harald, Spurling, Alex, Daxinger, Lucia, Puthalakath, Hamsa and Whitelaw, Emma (2015). Trim33 Binds and Silences a Class of Young Endogenous Retroviruses in the Mouse Testis; a Novel Component of the Arms Race between Retrotransposons and the Host Genome. PLoS Genetics, 11 (12) e1005693, 1-25. doi: 10.1371/journal.pgen.1005693

On the meaning of the word 'epimutation'

Oey, H. and Whitelaw, E. (2014). On the meaning of the word 'epimutation'. Trends in Genetics, 30 (12), 519-520. doi: 10.1016/j.tig.2014.08.005

An ENU mutagenesis screen identifies novel and known genes involved in epigenetic processes in the mouse

Daxinger, Lucia, Harten, Sarah K., Oey, Harald, Epp, Trevor, Isbel, Luke, Huang, Edward, Whitelaw, Nadia, Apedaile, Anwyn, Sorolla, Anabel, Yong, Joan, Bharti, Vandhana, Sutton, Joanne, Ashe, Alyson, Pang, Zhenyi, Wallace, Nathan, Gerhardt, Daniel J., Blewitt, Marnie E., Jeddeloh, Jeffrey A. and Whitelaw, Emma (2013). An ENU mutagenesis screen identifies novel and known genes involved in epigenetic processes in the mouse. Genome Biology, 14 (9) R96. doi: 10.1186/gb-2013-14-9-r96

A forward genetic screen identifies eukaryotic translation initiation factor 3, subunit h (eiF3h), as an enhancer of variegation in the mouse

Daxinger, Lucia, Oey, Harald, Apedaile, Anwyn, Sutton, Joanne, Ashe, Alyson and Whitelaw, Emma (2012). A forward genetic screen identifies eukaryotic translation initiation factor 3, subunit h (eiF3h), as an enhancer of variegation in the mouse. G3: Genes, Genomes, Genetics, 2 (11), 1393-1396. doi: 10.1534/g3.112.004036

Commentary: Gartner's 'third component': still an open question

Oey, Harald and Whitelaw, Emma (2012). Commentary: Gartner's 'third component': still an open question. International Journal of Epidemiology, 41 (2) dys009, 356-358. doi: 10.1093/ije/dys009

The characterisation of piRNA-related 19mers in the mouse

Oey, Harald M., Youngson, Neil A. and Whitelaw, Emma (2011). The characterisation of piRNA-related 19mers in the mouse. BMC Genomics, 12 (1) 315. doi: 10.1186/1471-2164-12-315

Nuclear-localized tiny RNAs are associated with transcription initiation and splice sites in metazoans

Taft, Ryan, Simons, Cas, Nahkuri, Satu, Oey, Harald, Korbie, Darren J., Mercer, Timothy R., Holst, Jeff, Ritchie, William, Wong, Justin J-L., Rasko, John E. J., Rokhsar, Daniel S., Degnan, Bernard M. and Mattick, John S. (2010). Nuclear-localized tiny RNAs are associated with transcription initiation and splice sites in metazoans. Nature Structural and Molecular Biology, 17 (8), 1030-1035. doi: 10.1038/nsmb.1841

Pseudogenes and the electron transport chain

Oey, H. M., Maguire D. J. and McCabe, M. (2008). Pseudogenes and the electron transport chain. Advances in Experimental Medicine & Biology, 599, 101-107. doi: 10.1007/978-0-387-71764-7

EBV+ CNS lymphomas have a distinctive tumor microenvironment and genetic profile, which is amenable to combination 3rd party EBV-specific CTL and Ibrutinib therapy

Gandhi, M.K., Hoang, T., Tobin, J.W., Law, S.C., Talaulikar, D., Jain, S., Vari, F., Murigneux, V., Fink, L., Gunawardana, J., Gould, C., Oey, H., Delecluse, S., Trappe, R.U., Merida de Long, L., Sabdia, M.B., Bhagat, G., Hapgood, G., Blyth, E., Clancy, L., Casey, J., Wight, J., Hawkes, E. and Keane, C. (2019). EBV+ CNS lymphomas have a distinctive tumor microenvironment and genetic profile, which is amenable to combination 3rd party EBV-specific CTL and Ibrutinib therapy. 15th International Conference on Malignant Lymphoma, Lugano, Switzerland, 18–22 June 2019. Oxford, United Kingdom: John Wiley & Sons. doi: 10.1002/hon.91_2629

B2M Gene Expression Reflects an Immunologically Active Tumor Microenvironment in DLBCL

Gould, Clare, Keane, Colm, Murigneux, Valentine, Oey, Harald, Ellis, Jonathan, Birch, Simone, Gunawardana, Jay, Talaulikar, Dipti, Hertzberg, Mark S., Jones, Kimberley and Gandhi, Maher K. (2019). B2M Gene Expression Reflects an Immunologically Active Tumor Microenvironment in DLBCL. ASH Annual Meeting, Orlando, FL, United States, 7-10 December 2019. Washington, DC, United States: American Society of Hematology. doi: 10.1182/blood-2019-126537

Fusion genes identified from whole genome and whole transcriptome sequencing of malignant pleural mesothelioma tumours

Chee, T. M., Oey, H., Fong, K., Yang, I., Krause, L. and Bowman, R. (2019). Fusion genes identified from whole genome and whole transcriptome sequencing of malignant pleural mesothelioma tumours. IASLC 2019 World Conference on Lung Cancer, Barcelona, Spain, 7-10 September 2019. New York, NY, United States: Elsevier . doi: 10.1016/j.jtho.2019.08.697

Characterisation of novel hypomorphic and null mutations in klf1 derived from a genetic screen for modifiers of a-globin transgene variegation

Huang, Stephen, Gillinder, Kevin R., Ilsley, Melissa, Magor, Graham, Tallack, Michael, Sorolla, Anabel, Oey, Harald, Harten, Sarah, Clemens-Daxinger, Lucia, Whitelaw, Emma and Perkins, Andrew C. (2015). Characterisation of novel hypomorphic and null mutations in klf1 derived from a genetic screen for modifiers of a-globin transgene variegation. 57th Annual Meeting of the American Society of Hematology, Orlando, FL, United States, 5-8 December 2015. Washington, DC, United States: American Society of Hematology.

ALU sequences in the human respirome

Maguire, David J., Oey, Harald and McCabe, Michael (2006). ALU sequences in the human respirome. Oxygen Transport to Tissue XXVII 32nd annual meeting of the International Society on Transport to Tissue, Bari, Italy, 21-26 August 20004. New York, NY, United States: Springer New York. doi: 10.1007/0-387-29540-2_12