sam.buckberry@telethonkids.org.au
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I am a biologist who works at the intersection of epigenetics, genomics, bioinformatics, medical research and public health.
I currently lead the Epigenetics program in Indigenous Genomics at the Telethon Kids Institute. Here, my research is focused on using genomics technologies and cutting-edge data analytics to advance chronic disease prediction, prevention, and treatment. I also work on innovating ways to implement best practices in indigenous data sovereignty, privacy and security into state-of-the-art data systems for public and precision health.
From 2015-2021, I was a post-doctoral researcher in the Lister Lab, where my research focused on DNA methylation and its role in epigenetic gene regulation. This included characterising the epigenome in stem cell reprogramming and human brain development and ageing. I worked extensively with whole genome DNA methylation, ATAC-seq, ChIP-seq and RNA-seq data and developed customised analysis frameworks.
I am impact-focused and enjoy developing bespoke analysis frameworks for complex biological questions. I have broad experience in molecular and cell biology, scientific programming, high-performance computing, statistics and data visualisation.
Head,
Epigenetics | Indigenous Genomics
Telethon Kids Institute
Senior
Lecturer | Australian National University
ANU College of Health and Medicine
Doctor of Philosophy (2012-2015)
The University of Adelaide
Thesis: An integrative analysis of the human placental
transcriptome.
Awarded the Dean’s commendation for doctoral thesis
excellence.
Bachelor of Health Science - Honours (2011)
The University of Adelaide
Awawrded first class honours
Bachelor of Science (2008-2010)
Flinders University
Extended Major in Biological Sciences
Awarded the Chancellor’s Commendation
Head,
Epigenetics | Indigenous Genomics
Black Ochre Data Labs
Postdoctoral Research Fellow
Lister Lab | Epigenetics and
Genomics
Australasian Genomics Technology Association (AGTA) - Executive Committee (2017-)
WA Department of Health Human Research Ethics Committee (2020-)
Grant reviewer: NHMRC, New Zealand Heart Foundation, WA Department of Health
Journal reviewer: BMC Genomics, Genome Research, Clinical Epigenetics, Molecular Therapy, Oncogenesis, Placenta, F1000 Research, Scientific Reports, among others.
STEM mentor: School of Indigenous Studies, The University of Western Australia (2018)
MRFF Early to Mid-Career Researchers: The missing heritability of human disease: discovery to implementation (2022-2027) $4,877,532
MRFF Genomics Health Futures Mission Grant (2022-2024) Establishing epigenetic biomarkers in Indigenous Australians for precision health $991,506
WA Department of Health Merit Award (2020) BUCKBERRY S (CIA) $95,000
NHMRC-ARC Dementia Research Development Fellowship Grant (2016-2019): The Role of the neuronal methylome in natural brain ageing and the progression of Alzheimer’s Disease (APP1111206). BUCKBERRY S (CIA) $584,644
Robinson Research Institute Seed Funding (2015-2016): A multi-faceted approach to understanding the consequences of diabetes in early pregnancy. $25,000
Robinson Research Institute Seed Funding (2014-2015): Investigating new mechanisms regulating transcription in the pre-implantation embryo. $25,000
Buckberry S, Liu X, Polo JM & Lister R. Methods of Reprogramming a Cell. International patent PCT/AU2019/051296 World Intellectual Property Organization (WIPO)
Buckberry S A ‘memory wipe’ for stem cells may be the key to better therapies. The Conversation 17 Aug 2023 (re-published >25 outlets)
Using Big Data to Understand the Human Brain Pint of Science Festival (2018).
Buckberry S & Roberts CT. Why are males more at risk in the womb? Australasian Science, November 2014 (cover story)
Buckberry S, Liu X, Poppe D, Tan JP, Sun G, Chen J, Nguyen TV, de Mendoza A, Pflueger J, Frazer T, Vargas-Landín DB, Paynter JM, Smits N, Liu N, Ouyang JF, Rossello FJ, Chy HS, Rackham OJL, Laslett AL, Breen J, Faulkner GJ, Nefzger CM, Polo JM & Lister R (2023). Transient naive reprogramming corrects hiPS cells functionally and epigenetically. Nature 620, 863–872
Herring CA, Simmons RK, Freytag S, Poppe D, Moffet JJD, Pflueger J, Buckberry S, Vargas-Landin DB, Clément O, Echeverría EG, Sutton GJ, Alvarez-Franco A, Hou R, Pflueger C, McDonald K, Polo JM, Forrest ARR, Nowak AK, Voineagu I, Martelotto L & Lister R (2022). Human prefrontal cortex gene regulatory dynamics from gestation to adulthood at single-cell resolution. Cell 185, 4428–4447.e28.
de Mendoza A, Nguyen TV, Ford E, Poppe D, Buckberry, S, Pflueger J, Grimmer MR, Stolzenburg S, Bogdanovic O, Oshlack A, Farnham PJ, Blancafort P & Lister R (2022). Large-scale manipulation of promoter DNA methylation reveals context-specific transcriptional responses and stability. Genome Biology 23, 163
Grubman A, Choo XY, Chew G, Ouyang JF, Sun G, Croft NP, Rossello FJ, Simmons R, Buckberry S, Landin, DV, Pflueger J, Vandekolk TH, Abay Z, Zhou Y, Liu X, Chen J, Larcombe M, Haynes JM, McLean C, Williams S, Chai SY, Wilson T, Lister R, Pouton CW, Purcell AW, Rackham OJL, Petretto E & Polo JM (2021). Transcriptional signature in microglia associated with AB plaque phagocytosis. Nature Communications. 12, 3015
de Mendoza A, Poppe D, Buckberry S, Pflueger J, Albertin CB, Daish T, Bertrand S, de la Calle-Mustienes E, Gómez-Skarmeta JL, Nery JR, Ecker JR, Baer B, Ragsdale CW, Grützner F, Escriva H, Venkatesh B, Bogdanovic O & Lister R (2021). The emergence of the brain non-CpG methylation system in vertebrates. Nature Ecology & Evolution
Liu X, Ouyang JF, Rossello FJ, Tan JP, Davidson KC, Valdes DS, Schröder J, Sun YBY, Chen J, Knaupp AS, Sun G, Chy HS, Huang Z, Pflueger J, Firas J, Tano V, Buckberry S, Paynter J.M, Larcombe MR, Poppe D, Choo XY, O’Brien CM, Pastor WA, Chen D, Leichter AL, Naeem H, Tripathi P, Das PP, Grubman A, Powell DR, Laslett AL, David L, Nilsson SK, Clark AT, Lister R, Nefzger CM, Martelotto LG, Rackham OJL & Polo JM (2020). Reprogramming roadmap reveals route to human induced trophoblast stem cells. Nature 586, 101–107
Grubman A, Chew G, Ouyang JF, Sun G, Choo XY, McLean C, Simmons R, Buckberry S, Landin DV, Poppe D, Pflueger J, Lister R, Rackham OJ, Petretto E and Polo JM (2019). A single-cell atlas of entorhinal cortex from individuals with Alzheimer’s disease reveals cell-type-specific gene expression regulation. Nature Neuroscience 22:2087–2097
de Mendoza A, Hatleberg WL, Pang K, Leininger S, Bogdanovic O, Pflueger J, Buckberry S, Technau U, Hejnol A, Adamska M, Degnan BM, Degnan SM and Lister R (2019). Convergent evolution of a vertebrate-like methylome in a marine sponge. Nature Ecology and Evolution 3;10:1464-1473
de Mendoza A, Bonnet A, Vargas-Landin DB, Ji N, Hong F, Yang F, Li L, Hori K, Pflueger J, Buckberry S, Ohta H, Rosic N, Lesage P, Lin S and Lister R (2018). Recurrent acquisition of cytosine methyltransferases into eukaryotic retrotransposons. Nature Communications 9;1:1341
Stuart T, Buckberry S, Lister R (2018). Approaches for the Analysis and Interpretation of Whole Genome Bisulfite Sequencing Data. Methods in Molecular Biology 1767:299-310 - Book chapter
Mayne BT, Leemaqz SY, Buckberry S, Rodriguez Lopez CM, Roberts CT, Bianco-Miotto T and Breen J (2018). msgbsR: An R package for analysing methylation-sensitive restriction enzyme sequencing data. Scientific Reports 8;1:2190
Knaupp AS1, Buckberry S1, Pflueger J, Lim SM, Ford E, Larcombe MR, Rossello FJ, de Mendoza A, Alaei S, Firas J, Holmes ML, Nair SS, Clark SJ, Nefzger CM, Lister R and Polo JM (2017). Transient and permanent reconfiguration of chromatin and transcription factor occupancy drive reprogramming. Cell Stem Cell 21, 1-12 1Co-first author
Nefzger CM, Rossello FJ, Chen J, Liu X, Knaupp AS, Firas J, Paynter J, Pflueger J, Buckberry S, Lim SM, Williams B, Alaei S, Keshav Faye-Chauhan K, Nilsson SK, Lister R, Ramialison M, Powel DR, Rackham OJL and Polo JM (2017). Cell type of origin dictates the route to pluripotency. Cell Reports 21
Wilson RL, Leemaqz SY, Goh Z, McAninch D, Jankovic-Karasoulos T, Leghi GE, Phillips JA, Colafella KM, Tran C, O’Leary S, Buckberry S, Pederson S, Robertson SA, Bianco-Miotto T, Roberts CT (2017). Zinc is a critical regulator of placental morphogenesis and maternal hemodynamics during pregnancy in mice. Scientific Reports 9;7(1):15137
Valensisi C, Andrus C, Buckberry S, Doni Jayavelu N, Lund RJ, Lister R and Hawkins RD (2017). Epigenomic Landscapes of hESC-Derived Neural Rosettes: Modeling Neural Tube Formation and Diseases. Cell Reports 8:20
Lumb R, Buckberry S, Secker G, Lawrence D and Schwarz Q (2017). Transcriptome profiling reveals expression signatures of cranial neural crest cells arising from different axial levels. BMC Developmental Biology 17:5
Buckberry S, Bianco-Miotto T, Bent SJ, Clifton V, Shoubridge C, Shankar K and Roberts CT (2017). Placental transcriptome co-expression analysis reveals conserved regulatory programs across gestation. BMC Genomics 18:10
Mayne B, Bianco-Miotto T, Buckberry S, Breen J, Clifton V, Shoubridge C, Roberts CT (2016). Large scale gene expression meta-analysis reveals tissue-specific, sex-biased gene expression in humans. Frontiers in Genetics
Highet AR, Buckberry S, Mayne BT, Khoda SM, Bianco-Miotto T, Roberts CT (2016). First trimester trophoblasts forming endothelial-like tubes in vitro emulate a ‘blood vessel development’ gene expression profile. Gene Expression Patterns
Bianco-Miotto T, Mayne B, Buckberry S, Breen J, Rodriguez Lopez C, Roberts CT (2016). Recent progress towards understanding the role of DNA methylation in human placental development. Reproduction
Highet HR, Khoda SM, Buckberry S, Leemaqz S, Bianco-Miotto T, Harrington E, Ricciardelli C & Roberts CT (2015). Hypoxia induced HIF-1/HIF-2 activity alters trophoblast transcriptional regulation and promotes invasion. European Journal of Cell Biology 94(12):589-602.
Buckberry S, Spronk F, Wilson RL, Laurence JA, Bianco-Miotto T, Leemaqz S, O’Leary S, Anderson PH & Roberts CT (2015). The effect of Vdr gene ablation on global gene expression in the mouse placenta. Genomics Data 6:72-73
Wilson RL1, Buckberry S1, Spronk F1, Laurence JA, Leemaqz S, O’Leary S, Bianco-Miotto T, Du J, Anderson PH & Roberts CT (2015). Vitamin D Receptor Gene Ablation in the Conceptus Has Limited Effects on Placental Morphology, Function and Pregnancy Outcome. PLoS ONE 10(6):e0131287. 1These authors contributed equally to this work.
Buckberry S, Bianco-Miotto T, Bent SJ, Dekker GA & Roberts CT (2014). Integrative transcriptome meta-analysis reveals widespread sex-biased gene expression at the human fetal–maternal interface. Molecular Human Reproduction 20(8):810-9
Buckberry S, Bent SJ, Bianco-Miotto T & Roberts CT (2014). MassiR: a method for predicting the sex of samples in gene expression microarray datasets. Bioinformatics 30(14):2084-5
Buckberry S, Bianco-Miotto T & Roberts CT (2014). Imprinted and X-linked non-coding RNAs as potential regulators of human placental function, Epigenetics 9(1):81-9
Gatford KL, Heinemann GK, Thompson SD, Zhang JV, Buckberry S, Owens J, Dekker GA & Roberts CT (2014). Circulating IGF1 and IGF2 and SNP genotypes in pregnant and non-pregnant women and men. Endocrine Connections 3(3):138–149
Buckberry S, Bianco-Miotto T, Hiendleder S & Roberts CT (2012). Quantitative Allele-Specific Expression and DNA Methylation Analysis of H19, IGF2 and IGF2R in the Human Placenta across Gestation Reveals H19 Imprinting Plasticity. PLoS ONE 7(12):e51210
Buckberry S & Burke da Silva K (2012). Evolution: improving the understanding of undergraduate students with an active pedagogical approach. Evolution, Education & Outreach 5(2):266-273
Invited pannelist - AusBioTech 2022 Extract maximum value from your data with high-performance computing.
Overcoming the epigenetic barriers to cellular reprogramming. South Australia Health and Medical Research Institute 2019. Adelaide, Australia. Invited presentation.
Profiling the shifting epigenetic landscape during human reprogramming. People’s Choice Award, Epigenetics Consortium of South Australia Annual Research Meeting 2019. Adelaide Australia. Invited presentation.
Characterising epigenome dynamics during the reprogramming of somatic cells to iPS cells. Lorne Genome Conference 2017. Lorne, Australia.
Characterising epigenome dynamics during the reprogramming of somatic cells to iPS cells. Best ECR oral presentation, Australasian Genomic Technologies Association (AGTA) Conference 2016. Auckland, New Zealand.
Moving towards integrative epigenomic analyses. International Federation of Placenta Associations (IFPA) Conference 2015. Brisbane, Australia. Invited presentation.
Integrative analysis of placental transcriptome organization reveals highly conserved regulatory programs and points toward a preeclampsia gene cluster. New investigator award session. International Federation of Placenta Associations (IFPA) Conference 2015. Brisbane, Australia.
Integrative transcriptome meta-analysis reveals widespread sex-biased gene expression patterns in human extra-embryonic tissue. Promega PhD Student Award, Lorne Genome Conference 2014. Lorne Victoria, Australia.
What can big data tell us about big tummies? Robinson Research Institute Symposium 2014. Adelaide, Australia. Invited presentation.
Using RNA sequencing to comprehensively profile the transcriptomes of reproductive tissues. Society for Reproductive Biology Conference 2014. Melbourne, Australia. Invited presentation.
Sexual inequality begins in utero with genome-wide differences in the human placental transcriptome. ANZPRA new investigator award session, Society for Reproductive Biology Conference 2013. Sydney, Australia.
Using RNA sequencing to quantify placental transcriptomes. Methods in Reproductive Biology Symposium 2013. Mercy Hospital for Women, Melbourne, Australia. Invited presentation.
Sex-biased gene expression at the human fetal-maternal interface. Australian Society for Medical Research Annual Meeting 2013. Adelaide, Australia.
Quantitative allele-specific expression analysis reveals imprinting plasticity of the H19 lincRNA. ANZPRA new investigator award session, Society for Reproductive Biology Conference 2012. Gold Coast, Australia.
Allele-specific expression of H19 and IGF2 in the human placenta across gestation. Honours award session, Australian Society for Medical Research Annual Meeting 2012. Adelaide, Australia.
Lecturer, Masters of Biotechnology, School of Chemistry and Biochemistry, The University of Western Australia (2019, 2020, 2021).
Lecturer, The Objectives and Applications of Genomics 2017 (SCIE4001). School of Chemistry and Biochemistry, The University of Western Australia (2017).
Teaching Assistant for RNA-Seq analysis workshops at BioInfoSummer Conference 2013, Australian Mathematical Sciences Institute and the University of Adelaide.
Teaching Assistant for the Bioinformatics Workshops 2013, the University of Adelaide.
Tutor and Coordinator for undergraduate biology Peer Assisted Study Sessions (PASS), Flinders University (2010–2011).