Publications

Alex de Mendoza, Daniel Poppe, Sam Buckberry, Jahnvi Pflueger, Caroline B Albertin, Tasman Daish, Stephanie Bertrand, Elisa de la Calle-Mustienes, José Luis Gómez-Skarmeta, Joseph R Nery, Joseph R Ecker, Boris Baer, Clifton W Ragsdale, Frank Grützner, Hector Escriva, Byrappa Venkatesh, Ozren Bogdanovic, Ryan Lister (2021). The emergence of the brain non-CpG methylation system in vertebrates. Nature ecology & evolution.

Xiaodong Liu, John F Ouyang, Fernando J Rossello, Jia Ping Tan, Kathryn C Davidson, Daniela S Valdes, Jan Schröder, Yu B Y Sun, Joseph Chen, Anja S Knaupp, Guizhi Sun, Hun S Chy, Ziyi Huang, Jahnvi Pflueger, Jaber Firas, Vincent Tano, Sam Buckberry, Jacob M Paynter, Michael R Larcombe, Daniel Poppe, Xin Yi Choo, Carmel M O'Brien, William A Pastor, Di Chen, Anna L Leichter, Haroon Naeem, Pratibha Tripathi, Partha P Das, Alexandra Grubman, David R Powell, Andrew L Laslett, Laurent David, Susan K Nilsson, Amander T Clark, Ryan Lister, Christian M Nefzger, Luciano G Martelotto, Owen J L Rackham, Jose M Polo (2020). Reprogramming roadmap reveals route to human induced trophoblast stem cells. Nature.

Alexandra Grubman, Gabriel Chew, John F Ouyang, Guizhi Sun, Xin Yi Choo, Catriona McLean, Rebecca K Simmons, Sam Buckberry, Dulce B Vargas-Landin, Daniel Poppe, Jahnvi Pflueger, Ryan Lister, Owen J L Rackham, Enrico Petretto, Jose M Polo (2019). A single-cell atlas of entorhinal cortex from individuals with Alzheimer's disease reveals cell-type-specific gene expression regulation. Nature neuroscience.

Alex de Mendoza, William L Hatleberg, Kevin Pang, Sven Leininger, Ozren Bogdanovic, Jahnvi Pflueger, Sam Buckberry, Ulrich Technau, Andreas Hejnol, Maja Adamska, Bernard M Degnan, Sandie M Degnan, Ryan Lister (2019). Convergent evolution of a vertebrate-like methylome in a marine sponge. Nature ecology & evolution.

Alex de Mendoza, Amandine Bonnet, Dulce B Vargas-Landin, Nanjing Ji, Hongfei Li, Feng Yang, Ling Li, Koichi Hori, Jahnvi Pflueger, Sam Buckberry, Hiroyuki Ohta, Nedeljka Rosic, Pascale Lesage, Senjie Lin, Ryan Lister (2018). Recurrent acquisition of cytosine methyltransferases into eukaryotic retrotransposons. Nature communications.

Benjamin T Mayne, Shalem Y Leemaqz, Sam Buckberry, Carlos M Rodriguez Lopez, Claire T Roberts, Tina Bianco-Miotto, James Breen (2018). msgbsR: An R package for analysing methylation-sensitive restriction enzyme sequencing data. Scientific reports.

Tim Stuart, Sam Buckberry, Ryan Lister (2018). Approaches for the Analysis and Interpretation of Whole Genome Bisulfite Sequencing Data. Epigenome Editing: Methods and Protocols.

Anja S Knaupp, Sam Buckberry, Jahnvi Pflueger, Sue Mei Lim, Ethan Ford, Michael R Larcombe, Fernando J Rossello, Alex de Mendoza, Sara Alaei, Jaber Firas, Melissa L Holmes, Shalima S Nair, Susan J Clark, Christian M Nefzger, Ryan Lister, Jose M Polo (2017). Transient and Permanent Reconfiguration of Chromatin and Transcription Factor Occupancy Drive Reprogramming. Cell Stem Cell.

Christian M Nefzger, Fernando J Rossello, Joseph Chen, Xiaodong Liu, Anja S Knaupp, Jaber Firas, Jacob M Paynter, Jahnvi Pflueger, Sam Buckberry, Sue Mei Lim, Brenda Williams, Sara Alaei, Keshav Faye-Chauhan, Enrico Petretto, Susan K Nilsson, Ryan Lister, Mirana Ramialison, David R Powell, Owen J L Rackham, Jose M Polo (2017). Cell Type of Origin Dictates the Route to Pluripotency. Cell reports.

Rebecca L Wilson, Shalem Y Leemaqz, Zona Goh, Dale McAninch, Tanja Jankovic-Karasoulos, Gabriela E Leghi, Jessica A Phillips, Katrina Mirabito Colafella, Cuong Tran, Sean O'Leary, Sam Buckberry, Stephen Pederson, Sarah A Robertson, Tina Bianco-Miotto, Claire T Roberts (2017). Zinc is a critical regulator of placental morphogenesis and maternal hemodynamics during pregnancy in mice. Scientific reports.

Cristina Valensisi, Colin Andrus, Sam Buckberry, Naresh Doni Jayavelu, Riikka J Lund, Ryan Lister, R David Hawkins (2017). Epigenomic Landscapes of hESC-Derived Neural Rosettes: Modeling Neural Tube Formation and Diseases. Cell reports.

Rachael Lumb, Sam Buckberry, Genevieve Secker, David Lawrence, Quenten Schwarz (2017). Transcriptome profiling reveals expression signatures of cranial neural crest cells arising from different axial levels. BMC developmental biology.

Sam Buckberry, Tina Bianco-Miotto, Stephen J Bent, Vicki Clifton, Cheryl Shoubridge, Kartik Shankar, Claire T Roberts (2017). Placental transcriptome co-expression analysis reveals conserved regulatory programs across gestation. BMC genomics.

T Bianco-Miotto, C Blundell, S Buckberry, L Chamley, S Chong, E Cottrell, P Dawson, C Hanna, O Holland, R M Lewis, K Moritz, L Myatt, A V Perkins, T Powell, R Saffery, A Sferruzzi-Perri, C Sibley, D Simmons, P F O'Tierney-Ginn (2016). IFPA meeting 2015 workshop report I: placental mitochondrial function, transport systems and epigenetics. Placenta.

Benjamin T Mayne, Tina Bianco-Miotto, Sam Buckberry, James Breen, Vicki Clifton, Cheryl Shoubridge, Claire T Roberts (2016). Large Scale Gene Expression Meta-Analysis Reveals Tissue-Specific, Sex-Biased Gene Expression in Humans. Frontiers in genetics.

Tina Bianco-Miotto, Benjamin T Mayne, Sam Buckberry, James Breen, Carlos M Rodriguez Lopez, Claire T Roberts (2016). Recent progress towards understanding the role of DNA methylation in human placental development. Reproduction.

Amanda R Highet, Sam Buckberry, Benjamin T Mayne, Sultana M Khoda, Tina Bianco-Miotto, Claire T Roberts (2016). First trimester trophoblasts forming endothelial-like tubes in vitro emulate a 'blood vessel development' gene expression profile. Gene expression patterns: GEP.

Sam Buckberry, Fleur Spronk, Rebecca L Wilson, Jessica A Laurence, Tina Bianco-Miotto, Shalem Leemaqz, Sean O'Leary, Paul H Anderson, Claire T Roberts (2015). The effect of Vdr gene ablation on global gene expression in the mouse placenta. Genomics data.

Amanda R Highet, Sultana M Khoda, Sam Buckberry, Shalem Leemaqz, Tina Bianco-Miotto, Elaine Harrington, Carmela Ricciardelli, Claire T Roberts (2015). Hypoxia induced HIF-1/HIF-2 activity alters trophoblast transcriptional regulation and promotes invasion. European journal of cell biology.

Rebecca L Wilson, Sam Buckberry, Fleur Spronk, Jessica A Laurence, Shalem Leemaqz, Sean O'Leary, Tina Bianco-Miotto, Jing Du, Paul H Anderson, Claire T Roberts (2015). Vitamin D Receptor Gene Ablation in the Conceptus Has Limited Effects on Placental Morphology, Function and Pregnancy Outcome. PloS one.

Sam Buckberry, Claire Roberts (2015). Why are males more at risk in the womb?. Australasian Science.

K L Gatford, G K Heinemann, S D Thompson, J V Zhang, S Buckberry, J A Owens, G A Dekker, C T Roberts, SCOPE Consortium (2014). Circulating IGF1 and IGF2 and SNP genotypes in men and pregnant and non-pregnant women. Endocrine connections.

Sam Buckberry, Tina Bianco-Miotto, Stephen J Bent, Gustaaf A Dekker, Claire T Roberts (2014). Integrative transcriptome meta-analysis reveals widespread sex-biased gene expression at the human fetal-maternal interface. Molecular human reproduction.

Sam Buckberry, Stephen J Bent, Tina Bianco-Miotto, Claire T Roberts (2014). massiR: a method for predicting the sex of samples in gene expression microarray datasets. Bioinformatics.

Sam Buckberry, Tina Bianco-Miotto, Claire T Roberts (2014). Imprinted and X-linked non-coding RNAs as potential regulators of human placental function. Epigenetics: official journal of the DNA Methylation Society.

Sam Buckberry, Tina Bianco-Miotto, Stefan Hiendleder, Claire T Roberts (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.

Sam Buckberry, Tina Bianco-Miotto, Stefan Hiendleder, Claire T Roberts (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.

Sam Buckberry, Karen Burke da Silva (2012). Evolution: Improving the Understanding of Undergraduate Biology Students with an Active Pedagogical Approach. Evolution: Education and Outreach.