The Power of Partnership

As part of the Australian genomics community, we work with a wide variety of organisations throughout Australia and beyond. This includes partnerships with our funding bodies, host institutes, and the greater research community. These partnerships and connections allow us to uphold our mission of being a key enabler of genomics research in Australia.

We are proud to be co-authors on such impressive papers over the years.

Where appropriate, please acknowledge the contributions of AGRF in your publications, simply by including the following sentence in your ‘Acknowledgements’ section: The authors wish to acknowledge the use of the services and facilities of AGRF.

2020

2019

Russell J. Diefenbach, Jenny H. Lee, David Chandler, Yinan Wang, Christian Pflueger, Georgina V. Long, Richard A. Scolyer, Matteo S. Carlino, Alexander M. Menzies, Richard F. Kefford and Helen Rizos (2019). Hypermethylation of Circulating Free DNA in Cutaneous Melanoma. Applied Sciences, 9 5074. 25 November 2019.

Jafar S. Jabbari, Luyi Tian. Massively parallel long-read sequencing of single cell RNA isoforms. (2019). Human Cell Atlas Method Development Community. Protocols.io. 7 November 2019.

Chon-Kit Kenneth Chan, Nedeljka Rosic, Michał T. Lorenc, Paul Visendi, Meng Lin, Paulina Kaniewska, Brett J. Ferguson, Peter M. Gresshoff, Jacqueline Batley, David Edwards (2018). A differential k-mer analysis pipeline for comparing RNA-Seq transcriptome and meta-transcriptome datasets without a reference. Functional & Integrative Genomics. March 2019, Volume 19, Issue 2, pp 363–371.

Bryan K. Ward, David Chandler et al. (2019). Implications of Androgen Receptor Hyperstimulation by the FKBP51 L119P Mutation: No Evidence for Early Emergence of L119P in Prostate Cancer. Journal of Steroids and Hormonal Science, 2019, 10:1.

Hua Ying, David C Hayward, Ira Cooke, Weiwen Wang, Aurelie Moya, Kirby R Siemering, Susanne Sprungala, Eldon E Ball, Sylvain Forêt, David J Miller (2019). The Whole-Genome Sequence of the Coral Acropora millepora. Genome Biology and Evolution Volume 11, Issue 5, May 2019, Pages 1374–1379.

Luyi Tian, Xueyi Dong, Saskia Freytag, Kim-Anh Lê Cao, Shian Su, Abolfazl JalalAbadi, Daniela Amann-Zalcenstein, Tom S. Weber, Azadeh Seidi, Jafar S. Jabbari, Shalin H. Naik & Matthew E. Ritchie (2019). Benchmarking single cell RNA-sequencing analysis pipelines using mixture control experiments. Nature Methods, 16, 479–487.

Trzaskowski M, Mehta D, Peyrot WJ, Hawkes D. et. al. (2019). Quantifying between-cohort and between-sex genetic heterogeneity in major depressive disorder. American Journal of Human Genetics, Sep;180(6):439-447.

Delay C, Chapman K, Taleski M, Wang Y, Tyagi S, Xiong Y, Imin N, Djordjevic MA. (2019). CEP3 levels affect starvation-related growth responses of the primary root. Journal of Experimental Botany, 2019 Sep 24;70(18):4763-4774.

Dang THY, Tyagi S, D'Cunha G, Bhave M, Crawford R, Ivanova EP. (2019). Computational prediction of microRNAs in marine bacteria of the genus Thalassospira. PloS One, March 12;14(3):e0212996.

Gigante S, Gouil Q, Lucattini A, Keniry A, Beck T, Tinning M, Gordon L, Woodruff C, Speed TP, Blewitt ME, Ritchie ME. (2019). Using long-read sequencing to detect imprinted DNA methylation. Nucleic Acids Research, May 7;47(8):e46.

Samuel W Lukowski, Camden Y Lo, Alexei A Sharov, Quan Nguyen, Lyujie Fang, Sandy SC Hung, Ling Zhu, Ting Zhang, Ulrike Grünert, Tu Nguyen, Anne Senabouth, Jafar S Jabbari et. al. (2019). A single‐cell transcriptome atlas of the adult human retina. The EMBO Journal, Volume 38, Issue 18.

M.A.A. Mamun, M. Sandeman,  P. Rayment, P. Brook‐Carter, E. Scholes,  N. Kasinadhuni, D. Piedrafita, A.R. Greenhill. (2019). The composition and stability of the faecal microbiota of Merino sheep. Journal of Applied Microbiology, Sep 28, 2019.

2018

Daniszewski, M., Senabouth, A., Nguyen, Q. H., Crombie, D. E., Lukowski, S. W., Kulkarni, T., Sluch, V. M., Jabbari, J. S., Chamling, X., Zack, D. J., Pébay, A., Powell, J. E., Hewitt, A. (2018). Single cell RNA sequencing of stem cell-derived retinal ganglion cells. Scientific Data. 5(Feb), 1–9.

Bayer, P. E., Golicz, A. A., Tirnaz, S., Chan, C.K.K., Edwards, D., Batley, J. (2018). Variation in abundance of predicted resistance genes in the Brassica oleracea pangenome. Plant Biotechnology. 7(5), 1–12.

Del Rosario Herrera, M., Jara Vidalon, L., Montenegro, J. D., Riccio, C., Guzman, F., Bartolini, I., Ghislain, M. (2018). Molecular and genetic characterization of the Ryadg locus on chromosome XI from Andigena potatoes conferring extreme resistance to potato virus Y. Theoretical and Applied Genetics. 131(9), 1925–1938.

Riekkola, L., Zerbini, A., Andrews, O., Andrews-Goff, V., Baker, C. S., Chandler, D., Childerhouse, S., Clapham, P., Dodémont, R., Donnelly, D., Friedlaender, A., Gallego, R., Garrigue, C., Ivashchenko, Y., Jarman, S., Lindsay, R., Pallin, L., Robbins, J., Steel, D., Tremlett, J., Vindenes, S., Constantine, R. (2018). Application of a multi-disciplinary approach to reveal population structure and Southern Ocean feeding grounds of humpback whales. Ecological Indicators. 89(Jun), 455–465.

Griffin, P. C., Khadake, J., LeMay, K. S., Lewis, S. E., Orchard, S., Pask, A., Pope, B., Roessner, U., Russell, K., Seemann, T., Treloar, A., Tyagi, S., Christiansen, J. H., Dayalan, S., Gladman, S., Hangartner, S. B., Hayden, H. L., Ho, W. W. H., Keeble-Gagnère, G., Korhonen, P. K., Neish, P., Prestes, P. R., Richardson, M. F., Watson-Haigh, N. S., Wyres, K. L.,. Young, N. D., Schneider, M. V. (2018). Best practice data life cycle approaches for the life sciences. F1000Research. 6(Jun), 1–22.

Armin Scheben, Brent Verpaalen, Cynthia T. Lawley, Chon‐Kit K. Chan, Philipp E. Bayer, Jacqueline Batley, David Edwards. (2018). CropSNPdb: a database of SNP array data for Brassica crops and hexaploid bread wheat. The Plant Journal. Volume98, Issue 1, April 2019, pages 142-152.

2017

Boutilier, J., Taylor, R., Ram, R., McNamara, E., Nguyen, Q., Goullée, H., Chandler, D., Mehta, M., Balmer, L., Laing, N., Morahan, G., Nowak, K. (2017). Variable cardiac a-actin (Actc1) expression in early adult skeletal muscle correlates with promoter methylation. Miochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms. 1860(10), 1025-1036.

Xie, H., Konate, M., Sai, N., Tesfamicael, K. G., Cavagnaro, T., Gilliham, M., Breen, J., Metcalfe, A., Stephen, J. R., De Bei, R., Collins, C., Lopez, C. M. R. (2017). Global DNA Methylation patterns can play a role in defining terroir in grapevine (Vitis vinifera cv. Shiraz). Frontiers in Plant Science. 8(Oct), 1–16.

Pal, B., Chen, Y., Vaillant, F., Jamieson, P., Gordon, L., Rios, A. C., Wilcox, S., Fu, N., Liu, K. H., Jackling, F. C., Davis, M. J., Lindeman, G. J., Smyth, G. K., Visvader, J. E. (2017). Construction of developmental lineage relationships in the mouse mammary gland by single-cell RNA profiling. Nature Communications. 8(1), 1–13.

Ray Tobler, Adam Rohrlach, Julien Soubrier, Pere Bover, Bastien Llamas, Jonathan Tuke, Nigel Bean, Ali Abdullah-Highfold, Shane Agius, Amy O’Donoghue, Isabel O’Loughlin, Peter Sutton, Fran Zilio, Keryn Walshe, Alan N. Williams, Chris S.M. Turney, Matthew Williams, Stephen M. Richards, Robert J. Mitchell, Emma Kowal, John R. Stephen, Lesley Williams, Wolfgang Haak & Alan Cooper (2017). Aboriginal mitogenomes reveal 50,000 years of regionalism in Australia. Nature, 544 (7649), 180-184.

Michael Lynch, Ken McGrath, Karthik Raj, Philippa McLaren, Karen Payne, Richard McCoy, & Urs Giger (2017). Hereditary factor VII deficiency in Asian Elephant (Elephas Maximus) caused by a F7 missense mutation. Journal of Wildlife Diseases, 53 (2), 248-257.

Paloma S. Moreno, Josef Wagner, Caroline S. Mansfield, Matthew Stevens, James R. Gilkerson, Carl D. Kirkwood (2017). Characterisation of the canine faecal virome in healthy dogs and dogs with acute diarrhea using shotgun metagenomics. PLoS One, 12 (6), 1-16.

Mike J. Wilkinson, Claudia Szabo, Caroline S. Ford, Yuval Yarom, Adam E. Croxford, Amanda Camp & Paul Gooding (2017). Replacing Sanger with Next Generation Sequencing to improve coverage and quality of reference DNA barcodes for plants. Scientific Reports, 7 (November), 46040.

Nathan S. Watson-Haigh, Jerico Revote, Radosław Suchecki, Sonika Tyagi, Susan M. Corley, Catherine A. Shang and Annette McGrath (2017). Towards an open, collaborative, reusable framework for sharing hands-on bioinformatics training workshops. Briefings in Bioinformatics, 18 (2), 348-355.