Publications

Oliva A, Kaphle A, Reguant R, Sng LM, Twine NA, Malakar Y, Wickramarachchi A, Keller M, Ranbaduge T, Chan EK, Breen J, Buckberry S, Guennewig B, Haas M, Brown A, Cowley MJ, Thorne N, Jain Y, Bauer DC

Future-proofing genomic data and consent management: a comprehensive review of technology innovations

GigaScience 13, giae021

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

Transient naive reprogramming corrects hiPS cells functionally and epigenetically

Nature 620, 863–872

Khurana I, Howard NJ, Maxwell S, Du Preez A, Kaipananickal H, Breen J, Buckberry S, Okabe J, Al-Hasani K, Nakasatien S, Himathongkam T, Cooper ME, Maple-Brown L, Thewjitcharoen Y, Brown A & El-Osta A

Circulating epigenomic biomarkers correspond with kidney disease susceptibility in high-risk populations with type 2 diabetes mellitus

Diabetes Research and Clinical Practice 204, 110918

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

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

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

Transcriptional signature in microglia associated with Aβ 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

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 JM, 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

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 & Polo JM

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 & Lister R

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 & Lister R

Recurrent acquisition of cytosine methyltransferases into eukaryotic retrotransposons

Nature Communications 9(1), 1341

Stuart T, Buckberry S, Lister R

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 & Breen J

msgbsR: An R package for analysing methylation-sensitive restriction enzyme sequencing data

Scientific Reports 8(1), 2190

Knaupp AS*, Buckberry S*, 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 & Polo JM

Transient and permanent reconfiguration of chromatin and transcription factor occupancy drive reprogramming

Cell Stem Cell 21, 1–12 — *Co-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, Faye-Chauhan K, Nilsson SK, Lister R, Ramialison M, Powell DR, Rackham OJL & Polo JM

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

Zinc is a critical regulator of placental morphogenesis and maternal hemodynamics during pregnancy in mice

Scientific Reports 7(1), 15137

Valensisi C, Andrus C, Buckberry S, Doni Jayavelu N, Lund RJ, Lister R & Hawkins RD

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 & Schwarz Q

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 & Roberts CT

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

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

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

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

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

The effect of Vdr gene ablation on global gene expression in the mouse placenta

Genomics Data 6, 72–73

Wilson RL*, Buckberry S*, Spronk F*, Laurence JA, Leemaqz S, O'Leary S, Bianco-Miotto T, Du J, Anderson PH & Roberts CT

Vitamin D Receptor Gene Ablation in the Conceptus Has Limited Effects on Placental Morphology, Function and Pregnancy Outcome

PLoS ONE 10(6), e0131287 — *Equal contribution

Buckberry S, Bianco-Miotto T, Bent SJ, Dekker GA & Roberts CT

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

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

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

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

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

Evolution: improving the understanding of undergraduate students with an active pedagogical approach

Evolution, Education & Outreach 5(2), 266–273