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.
Mark A Jenkins, Daniel D Buchanan, John Lai, Enes Makalic, Gillian S Dite, Aung K Win, Mark Clendenning, Ingrid M Winship, Richard B Hayes, Jeroen R Huyghe, Ulrike Peters, Steven Gallinger, Loïc Le Marchand, Jane C Figueiredo, Rish K Pai, Polly A Newcomb, James M Church, Graham, (2021), Assessment of a Polygenic Risk Score for Colorectal Cancer to Predict Risk of Lynch Syndrome Colorectal Cancer, JNCI Cancer Spectrum.
Yue You, Luyi Tian, Shian Su, Xueyi Dong, Jafar S Jabbari, Peter F Hickey, Matthew E Ritchie, (2021), Benchmarking UMI-based single-cell RNA-seq preprocessing workflows, Genome Biology.
Mesalie Feleke, Samuel Bennett, Jiazhi Chen, David Chandler, Xiaoyong Hu, Jiake Xu (2021), Biological insights into the rapid tissue regeneration of freshwater crayfish and crustaceans, Cell Biochemistry and Function.
Luyi Tian, Jafar S Jabbari, Rachel Thijssen, Quentin Gouil, Shanika L Amarasinghe, Oliver Voogd, Hasaru Kariyawasam, Mei R M Du, Jakob Schuster, Changqing Wang, Shian Su, Xueyi Dong, Charity W Law, Alexis Lucattini, Yair David Joseph Prawer, Coralina Collar-Fernández, Jin D Chung, (2021), Comprehensive characterization of single-cell full-length isoforms in human and mouse with long-read sequencing, Genome Biology
Elzbieta Czembor, Jerzy H Czembor, Radoslaw Suchecki, Nathan S Watson-Haigh, (2021), DArT-based evaluation of soybean germplasm from Polish Gene Bank, (2021) BMC Research Notes
2021
Yuxuan Yuan, Philipp E Bayer, Robyn Anderson, HueyTyng Lee, Chon-Kit Kenneth Chan, Ruolan Zhao, Jacqueline Batley, David Edwards (2020). RefKA: A fast and efficient long-read genome assembly approach for large and complex genomes, bioRxiv, 18 April 2020.
Bashar M. Thejer, Partho P. Adhikary, Sarah L. Teakel, Johnny Fang, Paul A. Weston, Saliya Gurusinghe, Ayad G. Anwer, Martin Gosnell, Jalal A. Jazayeri, Marina Ludescher, Lesley-Ann Gray et. al. (2020). PGRMC1 effects on metabolism, genomic mutation and CpG methylation imply crucial roles in animal biology and disease, BMC Molecular and Cell Biology 21:26, 15 April 2020.
Heather G. Mack, Tanya Kowalski, Alexis Lucattini, Rc Andrew Symons, Ian Wicks & Anthony Jh Hall (2020). Genetic susceptibility to hydroxychloroquine retinal toxicity, Ophthalmic Genetics, 41:2, 159-170, 13 April 2020.
Md. Abdullah Al Mamun, Mark Sandeman, Phil Rayment, Phillip Brook-Carter, Emily Scholes, Naga Kasinadhuni, David Piedrafita, and Andrew R. Greenhill. Variation in gut bacterial composition is associated with Haemonchus contortus parasite infection of sheep, Animal Microbiome (2020) 2:3, 5 February 2020.
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.
2016
Monica Molano, Sepehr N. Tabrizi, Suzanne M. Garland, Jennifer M. Roberts, Dorothy A. Machalek, Samuel Phillips, David Chandler, Richard J. Hillman, Andrew E. Grulich, Fengyi Jin, I. Mary Poynten, David J. Templeton, Alyssa M. Cornall, SPANC Study Team (2016). CpG Methylation Analysis of HPV16 in Laser Capture Microdissected Archival Tissue and Whole Tissue Sections from High Grade Anal Squamous Intraepithelial Lesions: A Potential Disease Biomarker. Plos One, 11 (8), 1-15.
Danqing Yin, Matthew E. Ritchie, Jafar S. Jabbari, Tamara Beck, Marnie E. Blewitt & Andrew Keniry (2016). High concordance between Illumina HiSeq2500 and NextSeq500 for reduced representation bisulfite sequencing (RRBS). Genomics Data, 10, 97-100.
Alexa BR McIntyre, Lindsay Rizzardi, Angela M Yu, Noah Alexander, Gail L Rosen, Douglas J Botkin, Sarah E Stahl, Kristen K John, Sarah L Castro-Wallace, Ken McGrath, Aaron S Burton, Andrew P Feinberg and Christopher E Mason (2016). Nanopore sequencing in microgravity. NPJ Microgravity, 2 (1), 16035.
Nicholas M. Murphy, Matthew Burton, David R. Powell, Fernando J. Rossello, Don Cooper, Abha Chopra, Ming Je Hsieh, David C. Sayer, Lavinia Gordon, Mark D Pertile, Brian D. Tait, Helen R. Irving & Colin W. Pouton (2016). Haplotyping the human leukocyte antigen system from single chromosomes. Scientific Reports, 6 (1), 30381.
Jackson N. Reilly, Eileen A. McLaughlin, Simone J. Stanger, Amanda L. Anderson, Kate Hutcheon, Kiralee Church, Bettina P. Mihalas, Sonika Tyagi, Janet E. Holt, Andrew L. Eamens & Brett Nixon (2016). Characterisation of mouse epididymosomes reveals a complex profile of microRNAs and a potential mechanism for modification of the sperm epigenome. Scientific Reports, 6 (August), 31794.
Zornitza Stark, Tiong Y. Tan, Belinda Chong, Gemma R. Brett, Patrick Yap, Maie Walsh, Alison Yeung, Heidi Peters, Dylan Mordaunt, Shannon Cowie, David J. Amor, Ravi Savarirayan, George McGillivray, Lilian Downie, Paul G. Ekert, Christiane Theda, Paul A. James, Joy Yaplito-Lee, Monique M. Ryan, Richard J. Leventer, Emma Creed, Ivan Macciocca, Katrina M. Bell, Alicia Oshlack, Simon Sadedin, Peter Georgeson, Charlotte Anderson, Natalie Thorne, Melbourne Genomics Health Alliance, Clara Gaff, Susan M. White (2016). A prospective evaluation of whole-exome sequencing as a first-tier molecular test in infants with suspected monogenic disorders. Genetics in Medicine, 18 (11), 1090-1096.
2015
Chanyarat Paungfoo-Lonhienne, Yun Kit Yeoh, Naga Rup Pinaki Kasinadhuni, Thierry G. A. Lonhienne, Nicole Robinson, Philip Hugenholtz, Mark A. Ragan & Susanne Schmidt (2015). Nitrogen fertilizer dose alters fungal communities in sugarcane soil and rhizosphere. Scientific Reports, 5: 8678, 2 March 2015.
Richard Saffery and Lavinia Gordon (2015). Time for a standardized system of reporting sites of genomic methylation. Genome Biology, 30 April 2015.
Simon P. Sadedin, Harriet Dashnow, Paul A. James, Melanie Bahlo, Denis C. Bauer, Andrew Lonie, Sebastian Lunke, Ivan Macciocca, Jason P. Ross, Kirby R. Siemering, Zornitza Stark, Susan M. White, Melbourne Genomics Health Alliance, Graham Taylor, Clara Gaff1, Alicia Oshlack and Natalie P. Thorne (2015). Cpipe: a shared variant detection pipeline designed for diagnostic settings. Genome Medicine, 7:68, 10 July 2015.
Owen Stock, Lavinia Gordon, Jada Kapoor, Susan P. Walker, Clare Whitehead, Tu’uhevaha J. Kaitu’u-Lino, Gabrielle Pell, Natalie J. Hannan and Stephen Tong (2015). Chorioamnionitis Occurring in Women With Preterm Rupture of the Fetal Membranes Is Associated With a Dynamic Increase in mRNAs Coding Cytokines in the Maternal Circulation. Reproductive Sciences, Vol. 22(7) 852-859, July 2015.
Brett Nixon, Simone J. Stanger, Bettina P. Mihalas, Jackson N. Reilly, Amanda L. Anderson, Matthew D. Dun, Sonika Tyagi, Janet E. Holt, Eileen A. McLaughlin (2015). Next Generation Sequencing Analysis Reveals Segmental Patterns of microRNA Expression in Mouse Epididymal Epithelial Cells. PLoS ONE 10(8):e0135605, 13 August 2015.
Brett Nixon, Simone J. Stanger, Bettina P. Mihalas, Jackson N. Reilly, Amanda L. Anderson, Sonika Tyagi, Janet E. Holt, and Eileen A. McLaughlin (2015). The MicroRNA Signature of Mouse Spermatozoa Is Substantially Modified During Epididymal Maturation. Biology of Reproduction, 93(4):91, 1–20, 2 September 2015.
Amanda L. Anderson, Simone J. Stanger, Bettina P. Mihalas, Sonika Tyagi, Janet E. Holt, Eileen A. McLaughlin, Brett Nixon (2015). Assessment of microRNA expression in mouse epididymal epithelial cells and spermatozoa by next generation sequencing. Genomics Data, 6 (2015) 208–211, 18 September 2015.
Teodora Chamova, Velina Guergueltcheva, Mariana Gospodinova, Sabine Krause, Sebahattin Cirak, Ara Kaprelyan, Lyudmila Angelova, Violeta Mihaylova, Stoyan Bichev, David Chandler, Emanuil Naydenov, Margarita Grudkova, Presian Djukmedzhiev, Thomas Voit, Oksana Pogoryelova, Hanns Lochmüller, Hans H. Goebel, Melanie Bahlo, Luba Kalaydjieva, Ivailo Tournev. GNE myopathy in Roma patients homozygous for the p.I618T founder mutation. Neuromuscular Disorders 25 (2015) 713–718, September 2015.
