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.
2024
Kristyn Galbraith, Jonathan Serrano, Guomiao Shen, Ivy Tran, Cheyanne C. Slocum, Courtney Ketchum, Zied Abdullaev, Rust Turakulov, Tejus Bale, Marc Ladanyi, Purvil Sukhadia, Michael Zaidinski, Kerry Mullaney, Sara DiNapoli, Benjamin L. Liechty, Marissa Barbaro, Jeffrey C. Allen, Sharon L. Gardner, Jeffrey Wisoff, David Harter, Eveline Teresa Hidalgo, John G. Golfinos, Daniel A. Orringer, Kenneth Aldape, Jamal Benhamida, Kazimierz O. Wrzeszczynski, George Jour, Matija Snuderl, Impact of rare and multiple concurrent gene fusions on diagnostic DNA methylation classifier in brain tumors, Molecular Cancer Research. DOI: 10.1158/1541-7786.MCR-23-0627
Markku Miettinen, Zied Abdullaev, Rust Turakulov, Martha Quezado,Alejandro Luiña Contreras, Christian A. Curcio, Janusz Rys, Malgorzata Chlopek, Jerzy Lasota, Kenneth D. Aldape, Assessment of the utility of the sarcoma DNA methylation classifier In surgical pathology. American Journal of Surgical Pathology. DOI: 10.1097/PAS.0000000000002138
Katherine J Aney, Woo-Jeong Jeong, Andres F Vallejo, Cassandra Burdziak, Ethan Chen, Austin Wang, Pal Koak, Kellie Wise, Kirk Jensen, Dana Pe'er, Stephanie K Dougan, Luciano Martelotto, Sahar Nissim, A novel approach for pancreas transcriptomics reveals the cellular landscape in homeostasis and acute pancreatitis. Gastroenterology. DOI: 10.1053/j.gastro.2024.01.043
Aaron L Phillips, Scott Ferguson, Rachel A Burton, Nathan S Watson-Haigh, CLAW: an automated Snakemake workflow for the assembly of chloroplast genomes from long-read data. PLoS Computational Biology. DOI: 10.1371/journal.pcbi.1011870
Stephen J. Trueman, Mark G. Penter, Kátia Sampaio Malagodi-Braga, Joel Nichols, Anushika L. De Silva, Adalgisa Thayne Munhoz Ramos, Leonardo Massaharu Moriya, Steven M. Ogbourne, David Hawkes, Trent Peters, Naga Kasinadhuni, Shahla Hosseini Bai, Helen M. Wallace and Wiebke Kämper, High outcrossing levels among global macadamia cultivars: implications for nut quality, orchard designs and pollinator management, Horticulture. DOI: 10.3390/horticulturae10030203
Benjamin Mayne, David Chandler, Christopher Noune, Thomas Espinoza, David Roberts, Chloe Anderson, Oliver Berry, Increased scalability and sequencing quality of an epigenetic age prediction assay, PLoS One, DOI: 10.1371/journal.pone.0297006
Anushika L. De Silva, Wiebke Kämper, Steven M. Ogbourne, Joel Nichols, Jack W. L. Royle, Trent Peters, David Hawkes, Shahla Hosseini Bai, Helen M. Wallace and Stephen J. Trueman, MassARRAY and SABER Analyses of SNPs in embryo DNA reveal the abscission of self-fertilised progeny during fruit development of Macadamia (Macadamia integrifolia Maiden & Betche), International Journal of Molecular Sciences. DOI: 10.3390/ijms25126419
Danh-Tai Hoang, Eldad D. Shulman, Rust Turakulov, Zied Abdullaev, Omkar Singh, Emma M. Campagnolo, H. Lalchungnunga, Eric A. Stone, MacLean P. Nasrallah, Eytan Ruppin & Kenneth Aldape, Prediction of DNA methylation-based tumor types from histopathology in central nervous system tumors with deep learning. Nature Medicine, DOI: 10.1038/s41591-024-02995-8
Sally Potter, Craig Moritz, Maxine P Piggott, Jason G Bragg, Ana C Afonso Silva, Ke Bi, Christiana McDonald-Spicer, Rustamzhon Turakulov, Mark D B Eldridge, Museum skins enable identification of introgression associated with cytonuclear discordance, Systematic Biology. DOI: 10.1093/sysbio/syae016
Karisa C. Schreck, Roy E. Strowd, Louis B. Nabors, Benjamin M. Ellingson, Michael Chang, Sze K. Tan, Zied Abdullaev, Rust Turakulov, Kenneth Aldape, Neeraja Danda, Serena Desideri, Joy Fisher, Michaella Iacoboni, Trisha Surakus, Michelle A. Rudek, Chetan Bettegowda, Stuart A. Grossman, Xiaobu Ye, Response rate and molecular correlates to encorafenib and binimetinib in BRAF-V600E mutant high-grade glioma, Clinical Cancer Research. DOI: 10.1158/1078-0432.CCR-23-3241
K. M. Sumby, J. R. Stephen, J. J. Austin, R. K. Schilling, T. R. Cavagnaro, A novel method to assess the integrity of frozen archival DNAsamples: alpha-diversity ratios of short- and long-read 16SrRNA gene sequences, Methods in Ecology and Evolution. DOI: 10.1111/2041-210X.14411
Widad Abou Chaar, Anirudh N. Eranki, Hannah A. Stevens, Sonya L. Watson MS, Darice Y. Wong, Veronica S. Avila, Megan Delfeld, Alexander J. Gary, Sanjukta Tawde MS, Malia Triebold MS, Marcello Cherchi, Tao Xie, Paul J. Lockhart, Melanie Bahlo, David Pellerin, MSc, Marie-Josée Dicaire, Matt Danzi, Stephan Zuchner, Bernard C. Brais, Susan Perlman, Margit Burmeister, Henry Paulson, Sharan Srinivasan, Lawrence Schut, Matthew Bower MS, Khalaf Bushara, Chuanhong Liao MS, Vikram G. Shakkottai, John Collins, H. Brent Clark, Soma Das, Brent L. Fogel, Christopher M. Gomez, Clinical, radiological and pathological features of a large American cohort of spinocerebellar ataxia (SCA27B), Annals of Neurology. DOI: 10.1002/ana.27060
2023
Lina Herliana, Julian G Schwerdt, Tycho R Neumann, Anita Severn-Ellis, Jana L Phan, James M Cowley, Neil J Shirley, Matthew R Tucker, Tina Bianco-Miotto, Jacqueline Batley, Nathan S Watson-Haigh, Rachel A Burton, A chromosome-level genome assembly of Plantago ovata, Scientific Reports. DOI: 10.1038/s41598-022-25078-5
Na Sai, James Paul Bockman, Hao Chen, Nathan Watson-Haigh, Bo Xu, Xueying Feng, Adriane Piechatzek, Chunhua Shen, Matthew Gilliham, SAI: an efficient and user-friendly tool for measurement of stomatal pores and density using deep computer vision. New Phytologist. DOI: 10.1111/nph.18765
Scott A Oliphant, Nathan S Watson-Haigh, Krista M Sumby, Jennifer M Gardner, Vladimir Jiranek,Fructilactobacillus cliffordii sp. nov., Fructilactobacillus hinvesii sp. nov., Fructilactobacillus myrtifloralis sp. nov., Fructilactobacillus carniphilus sp. nov. and Fructobacillus americanaquae sp. nov., five novel lactic acid bacteria isolated from insects or flowers of Kangaroo Island, South Australia, International Journal of Systematic and Evolutionary Microbiology. DOI: 10.1099/ijsem.0.005730
Andrew Chen, Jiaman Sun, Guillaume Martin, Lesley-Ann Gray, Eva Hřibová, Pavla Christelová, Nabila Yahiaoui, Steve Rounsley, Rebecca Lyons, Jacqueline Batley, Ning Chen, Sharon Hamill, Subash K. Rai, Lachlan Coin, Brigitte Uwimana, Angelique D’Hont, Jaroslav Doležel, David Edwards, Rony Swennen and Elizabeth A. B. Aitken, Identification of a major QTL-controlling resistance to the subtropical race 4 of Fusarium oxysporum f. sp. cubense in Musa acuminata ssp. malaccensis, Pathogens. DOI: 10.3390/pathogens12020289
Tracy L Leong, Christian Aloe, Savreet Aujla, Hao Wang, Velimir Gayevskiy, Marie-Liesse Asselin-Labat, Lesley-Ann Gray, Daniel Steinfort, Steven Bozinovski, Heterogeneity of tumour mutational burden in metastatic NSCLC demonstrated by endobronchial ultrasound sampling, Frontiers in Oncology. DOI: 10.3389/fonc.2023.1150349
Andre Mu, William P. Klare, Sarah L. Baines, C. N. Ignatius Pang, Romain Guérillot, Nichaela Harbison-Price, Nadia Keller, Jonathan Wilksch, Nguyen Thi Khanh Nhu, Minh-Duy Phan, Bernhard Keller, Brunda Nijagal, Dedreia Tull, Saravanan Dayalan, Hwa Huat Charlie Chua, Dominik Skoneczny, Jason Koval, Abderrahman Hachani, Anup D. Shah, Nitika Neha, Snehal Jadhav, Sally R. Partridge, Amanda J. Cork, Kate Peters, Olivia Bertolla, Stephan Brouwer, Steven J. Hancock, Laura Álvarez-Fraga, David M. P. De Oliveira, Brian Forde, Ashleigh Dale, Warasinee Mujchariyakul, Calum J. Walsh, Ian Monk, Anna Fitzgerald, Mabel Lum, Carolina Correa-Ospina, Piklu Roy Chowdhury, Robert G. Parton, James De Voss, James Beckett, Francois Monty, Jessica McKinnon, Xiaomin Song, John R. Stephen, Marie Everest, Matt I. Bellgard, Matthew Tinning, Michael Leeming, Dianna Hocking, Leila Jebeli, Nancy Wang, Nouri Ben Zakour, Serhat A. Yasar, Stefano Vecchiarelli, Tonia Russell, Thiri Zaw, Tyrone Chen, Don Teng, Zena Kassir, Trevor Lithgow, Adam Jenney, Jason N. Cole, Victor Nizet, Tania C. Sorrell, Anton Y. Peleg, David L. Paterson, Scott A. Beatson, Jemma Wu, Mark P. Molloy, Anna E. Syme, Robert J. A. Goode, Adam A. Hunter, Grahame Bowland, Nicholas P. West, Marc R. Wilkins, Steven P. Djordjevic, Mark R. Davies, Torsten Seemann, Benjamin P. Howden, Dana Pascovici, Sonika Tyagi, Ralf B. Schittenhelm, David P. De Souza, Malcolm J. McConville, Jonathan R. Iredell, Stuart J. Cordwell, Richard A. Strugnell, Timothy P. Stinear, Mark A. Schembri & Mark J. Walker, Integrative omics identifies conserved and pathogen-specific responses of sepsis-causing bacteria, Nature Communications. DOI: 10.1038/s41467-023-37200-w
Yasmin L. Jayasinghe, Sepehr N. Tabrizi, Matthew Stevens, Trishe Y-M. Leong, Jan Pyman, Sonia R. Grover, Suzanne M. Garland, and the Early-Onset Cervical Cancer (EOCC) Study Group, Pre-vaccination human papillomavirus genotypes and HPV16 variants among women aged 25 years or less with cervical cancer, Pathogens. DOI: 10.3390/pathogens12030451
Leire Moya, Carina Walpole, Fiona Rae, Srilakshmi Srinivasan, Inge Seim, John Lai, David Nicol, Elizabeth D. Williams, Judith A. Clements & Jyotsna Batra, Characterisation of cell lines derived from prostate cancer patients with localised disease, Prostate Cancer and Prostatic Diseases. DOI: 10.1038/s41391-023-00679-x
John Lai, Chi Kuen Wong, Daniel F. Schmidt, Miroslaw K. Kapuscinski, Karen Alpen, Robert J. MacInnis, Daniel D. Buchanan, Aung K. Win, Jane C. Figueiredo, Andrew T. Chan, Tabitha A. Harrison, Michael Hoffmeister, Emily White, Loic Le Marchand, Rish K. Pai, Ulrike Peters, John L. Hopper, Mark A. Jenkins, Enes Makalic, Using DEPendency of association on the number of Top Hits (DEPTH) as a complementary tool to identify novel colorectal cancer susceptibility loci, Cancer Epidemiology Biomarkers & Prevention, DOI: 10.1158/1055-9965.EPI-22-1209
2022
Hui Liu, Daniel Mullan, Shancen Zhao, Yong Zhang, Jun Ye, Yong Wang, Aimin Zhang, Xiaoqing Zhao, Guannan Liu, Chi Zhang, Kenneth Chan, Zhanyuan Lu, Guijun Yan, Genomic regions controlling yield-related traits in spring wheat: a mini review and a case study for rainfed environments in Australia and China. Genomics. DOI: 10.1016/j.ygeno.2022.110268
Amy Li, K. Campbell, S. Lal, Y. Ge, A. Keogh, P. S. Macdonald, Peter Lau, John Lai, W. A. Linke, J. Van der Velden, A. Field, B. Martinac, M. Grosser & Cristobal dos Remedios, Peripartum cardiomyopathy: a global effort to find the cause and cure for the rare and little understood disease. Biophysical Reviews, DOI: 10.1007/s12551-022-00930-0
Stephen J Trueman, Wiebke Kämper, Joel Nichols, Steven M Ogbourne, David Hawkes, Trent Peters, Shahla Hosseini Bai, Helen M Wallace, Pollen limitation and xenia effects in a cultivated mass-flowering tree, Macadamia integrifolia (Proteaceae). Annals of Botany. DOI: 10.1093/aob/mcab112
Roger Huerlimann, Jeff A Cowley, Nicholas M Wade, Yinan Wang, Naga Kasinadhuni, Chon-Kit Kenneth Chan, Jafar S Jabbari, Kirby Siemering, Lavinia Gordon, Matthew Tinning, Juan D Montenegro, Gregory E Maes, Melony J Sellars, Greg J Coman, Sean McWilliam, Kyall R Zenger, Mehar S Khatkar, Herman W Raadsma, Dallas Donovan, Gopala Krishna, Dean R Jerry, Genome assembly of the Australian black tiger shrimp (Penaeus monodon) reveals a novel fragmented IHHNV EVE sequence. Genes Genomes Genetics. DOI: 10.1093/g3journal/jkac034
Vanessa S Tamlin, Cynthia D K Bottema, Lucy Woolford, Elizabeth C Dobson, Allan E Kessell, Anne E Peaston, Canine mast cell tumours part I: Clinical and survival outcomes, Veterinary Medicine and Science. DOI: 10.1002/vms3.812
Angela Pizzolla, Simon Paul Keam, Ismael A Vergara, Franco Caramia, Niko Thio, Minyu Wang, Nikolce Kocovski, Daniela Tantalo, Jafar Jabbari, George Au-Yeung, Shahneen Sandhu, David E Gyorki, Alison Weppler, Maurizio Perdicchio, Grant A McArthur, Anthony T Papenfuss and Paul Joseph Neeson, Tissue-resident memory T cells from a metastatic vaginal melanoma patient are tumor-responsive T cells and increase after anti-PD-1 treatment. Journal of ImmunoTherapy of Cancer. DOI: 10.1136/jitc-2022-004574
Lina Herliana, Julian G Schwerdt, Tycho R Neumann, Anita Severn-Ellis, Jana L Phan, James M Cowley, Neil J Shirley, Matthew R Tucker, Tina Bianco-Miotto, Jacqueline Batley, Nathan S Watson-Haigh, Rachel A Burton, The complete genome sequence of elite bread wheat cultivar, "Sonmez", F1000 Research. DOI: 10.12688/f1000research.121637.1
Aaron L. Phillips, Scott Ferguson, Nathan S. Watson-Haigh, Ashley W. Jones, Justin O. Borevitz, Rachel A. Burton & Brian J. Atwell, The first long-read nuclear genome assembly of Oryza australiensis, a wild rice from northern Australia. Scientific Reports. DOI: 10.1038/s41598-022-14893-5
Scott A Oliphant, Nathan S Watson-Haigh, Krista M Sumby, Jennifer Gardner, Scott Groom, Vladimir Jiranek, Apilactobacillus apisilvae sp. nov., Nicolia spurrieriana gen. nov. sp. nov., Bombilactobacillus folatiphilus sp. nov. and Bombilactobacillus thymidiniphilus sp. nov., four new lactic acid bacterial isolates from stingless bees Tetragonula carbonaria and Austroplebeia australis. International Journal of Systematic and Evolutionary Microbiology. DOI: 10.1099/ijsem.0.005588
Brianna N Maslen, Lesley A Gray, Seyed A Ghorashi, Jason D White, Michael A Campbell, Sameer D Pant, Temporal changes in the faecal microbiota of beef cattle on feedlot placement, Animals. DOI: 10.3390/ani12192500
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. DOI: 10.1093/jncics/pkab022.
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. DOI: 10.1186/s13059-021-02552-3
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. DOI: 10.1002/cbf.3653
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. DOI: 10.1186/s13059-021-02525-6
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. DOI: 10.1186/s13104-021-05750-1
Ana Cristina Vargas, Lesley-Ann Gray, Christine L. White, Fiona M. Maclean, Peter Grimison, Nima Mesbah Ardakani, Fiona Bonar, Elizabeth M. Algar, Alison L. Cheah, Peter Russell, Annabelle Mahar & Anthony J. Gill Genome wide methylation profiling of selected matched soft tissue sarcomas identifies methylation changes in metastatic and recurrent disease, Scientific Reports. DOI: 10.1038/s41598-020-79648-6
Jessamine E. Hazlewood , Troy Dumenil, Thuy T. Le, Andrii Slonchak, Stephen H. Kazakoff, Ann-Marie Patch, Lesley-Ann Gray, Paul M. Howley, Liang Liu, John D. Hayball, Kexin Yan, Daniel J. Rawle, Natalie A. Prow, Andreas Suhrbier, Injection site vaccinology of a recombinant vaccinia-based vector reveals diverse innate immune signatures, PLoS Pathogens. DOI: 10.1371/journal.ppat.1009215
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, DOI: 10.1186/s42523-020-0021-3
Hashmath Inayath Hussain, Naga Kasinadhuni & Tony Arioli, The effect of seaweed extract on tomato plant growth, productivity and soil. Journal of Applied Phycology. DOI: 10.1007/s10811-021-02387-2
Wiebke Kämper, Stephen J. Trueman, Jade Cooke, Naga Kasinadhuni, Aaron J. Brunton, Steven M. Ogbourne, Single-nucleotide polymoprhism that uniquely identify cultivars of avocado (Persea americana), Applications in Plant Science. DOI: 10.1002/aps3.11440
Wiebke Kämper, Steven M Ogbourne, David Hawkes, Stephen J Trueman, SNP markers reveal relationships between fruit paternity, fruit quality and distance from a cross-pollen source in avocado orchards, Scientific Reports. DOI: 10.1038/s41598-021-99394-7
Jerzy H. Czembor, Elzbieta Czembor, Radoslaw Suchecki and Nathan S. Watson-Haigh, Genome-wide association study for powdery mildew and rusts adult plant resistance in European spring barley from Polish gene bank, Agronomy. DOI: 10.3390/agronomy12010007
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.
Matthew N. Nelson, Jafar S. Jabbari, Rust Turakulov, Aneeta Pradhan, Maria Pazos-Navarro, Jacob S. Stai, Steven B. Cannon and Daniel Real, The first genetic map for a Psoraleoid legume (Bituminaria bituminosa) reveals highly conserved synteny with Phaseoloid legumes, Plants. DOI: 10.3390/plants9080973
Natalee D. Newton, Agathe M. G. Colmant , Caitlin A. O’Brien, Emma Ledger, Devina Paramitha, Helle Bielefeldt-Ohmann, Daniel Watterson, Breeanna J. McLean, Sonja Hall-Mendelin, David Warrilow, Andrew F. van den Hurk, Wenjun Liu, Christina Hoare, Joanne R. Kizu, Penelope J. Gauci, John Haniotis, Stephen L. Doggett, Babak Shaban, Cheryl A. Johansen, Roy A. Hall and Jody Hobson-Peters, Genetic morphological and antigenic relationships between mesonivirus isolates from Australian mosquitoes and evidence for their horizontal transmission, Viruses. DOI: 10.3390/v12101159
Carolin K Scriba, Sarah J Beecroft, Joshua S Clayton, Andrea Cortese, Roisin Sullivan, Wai Yan Yau, Natalia Dominik, Miriam Rodrigues, Elizabeth Walker, Zoe Dyer, Teddy Y Wu, Mark R Davis, David C Chandler, Ben Weisburd, Henry Houlden, Mary M Reilly, Nigel G Laing, Phillipa J Lamont, Richard H Roxburgh, Gianina Ravenscroft, A novel RFC1 repeat motif (ACAGG) in two Asia-Pacific CANVAS families, Brain. DOI: 10.1093/brain/awaa263
Tongted P Das, David A Kipp, David S Kliman, Sushrut S Patil, David J Curtis, Maureen E O'Brien, Michael I Swain, Jacqueline M L Widjaja, Jade L Cooke, Melinda N Ziino, Andrew Spencer, Important factors in implementation of lineage-specific chimerism analysis for routine use, Bone Marrow Transplantation. DOI: 10.1038/s41409-020-01089-6
Ann E. Frazier, Alison G. Compton, Yoshihito Kishita, Daniella H. Hock, AnneMarie E. Welch, Sumudu S.C. Amaraseker, Rocio Rius, Luke E. Formosa, Atsuko Imai-Okazaki, David Francis, Min Wang, Nicole J. Lake, Simone Tregoning, Jafar S. Jabbari, Alexis Lucattini, Kazuhiro R. Nitta, Akira Ohtake, Kei Murayama, David J. Amor, George McGillivray, Flora Y. Wong, Marjo S. van der Knaap, R. Jeroen Vermeulen, Esko J. Wiltshire, Janice M. Fletcher, Barry Lewis, Gareth Baynam, Carolyn Ellaway, Shanti Balasubramaniam, Kaustuv Bhattacharya, Mary-Louise Freckmann, Susan Arbuckle, Michael Rodriguez, Ryan J. Taft, Simon Sadedin, Mark J. Cowley, André E. Minoche, Sarah E. Calvo, Vamsi K. Mootha, Michael T. Ryan, Yasushi Okazaki, David A. Stroud, Cas Simons, John Christodoulou, David R. Thorburn, Fatal perinatal mitochondrial cardiac failure caused by recurrent de novo duplications in the ATAD3 locus, Med. DOI: 10.1016/j.medj.2020.06.004
Dhamidhu Eratne, Amy Schneider, Ella Lynch, Melissa Martyn, Dennis Velakoulis, Michael Fahey, Patrick Kwan, Richard Leventer, Haloom Rafehi, Belinda Chong, Zornitza Stark, Sebastian Lunke, Dean G. Phelan, Melanie O'Keefe, Kirby Siemering, Kirsty West, Adrienne Sexton, Anna Jarmolowicz, Jessica A. Taylor, Joshua Schultz, Rebecca Purvis, Eloise Uebergang, Heather Chalinor, Belinda Creighton, Nikki Gelfand, Tamar Saks, Yael Prawer, Yana Smagarinsky, Tianxin Pan, Ilias Goranitis, Zanfina Ademi, Clara Gaff, Aamira Huq, Maie Walsh, Paul A. James, Emma I. Krzesinski, Mathew Wallis, Chloe A. Stutterd, Melanie Bahlo, Martin B. Delatycki, Samuel F. Berkovic, The clinical utility of exome sequencing and extended bioinformatic analyses in adolescents and adults with a broad range of neurological phenotypes: An Australian perspective, Journal of the Neurological Sciences. DOI: 10.1016/j.jns.2020.117260
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.
