Publications
Genomic Characterization of Salmonella enterica serovar Weltevreden Associated with Human Diarrhea
J Zhang, Z Peng, K Chen, Z Zhan, H Shen, S Feng, H Gou, X Qu, M Ziemann, D Layton, X Wang, H Chen, B Wu, X Xu, M Liao
(2023), Vol. 11, pp. 1-14, Microbiology Spectrum, Washington, D.C., C1
Ishant Khurana, Harikrishnan Kaipananickal, Scott Maxwell, Sørine Birkelund, Anna Syreeni, Carol Forsblom, Jun Okabe, Mark Ziemann, Antony Kaspi, Haloom Rafehi, Anne Jørgensen, Keith Al-Hasani, Merlin Thomas, Guozhi Jiang, Andrea Luk, Heung Lee, Yu Huang, Yotsapon Thewjitcharoen, Soontaree Nakasatien, Thep Himathongkam, Christopher Fogarty, Rachel Njeim, Assaad Eid, Tine Hansen, Nete Tofte, Evy Ottesen, Ronald Ma, Juliana Chan, Mark Cooper, Peter Rossing, Per-Henrik Groop, Assam El-Osta
(2023), Vol. 133, pp. 1-18, Journal of Clinical Investigation, United States, C1-1
MicroRNA-101-3p Modulates Mitochondrial Metabolism via the Regulation of Complex II Assembly
Mark Ziemann, Sze Lim, Yilin Kang, Sona Samuel, Isabel Sanchez, Michael Gantier, Diana Stojanovski, Matthew McKenzie
(2022), Vol. 434, pp. 1-16, Journal of Molecular Biology, Amsterdam, The Netherlands, C1
Urgent need for consistent standards in functional enrichment analysis
K Wijesooriya, S Jadaan, K Perera, T Kaur, M Ziemann
(2022), Vol. 18, pp. 1-14, PLoS Computational Biology, San Francisco, Calif., C1
Methylomic and transcriptomic characterization of postoperative systemic inflammatory dysregulation
C Bain, P Myles, R Taylor, H Trahair, Y Lee, L Croft, P Peyton, T Painter, M Chan, S Wallace, T Corcoran, A Shaw, E Paul, M Ziemann, K Bozaoglu
(2022), Vol. 247, pp. 79-98, Translational Research: the journal of laboratory and clinical medicine, Amsterdam, The Netherlands, C1
M Ziemann, W Wu, X Deng, X Du
(2022), Vol. 13, Frontiers in Genetics, Switzerland, C1
H Burgin, A Sharpe, S Nie, M Ziemann, J Crameri, D Stojanovski, J Pitt, A Ohtake, K Murayama, M McKenzie
(2022), pp. 1-22, FEBS Journal, London, Eng., C1
Harrison Burgin, Jordan Crameri, Diana Stojanovski, M Sanchez, Mark Ziemann, Matthew McKenzie
(2022), Vol. 23, pp. 1-19, International Journal of Molecular Sciences, Basel, Switzerland, C1
Simon Royce, Paul Licciardi, Raymond Beh, Jane Bourke, Chantal Donovan, Andrew Hung, Ishant Khurana, Julia Liang, Scott Maxwell, Nadia Mazarakis, Eleni Pitsillou, Ya Siow, Kenneth Snibson, Mark Tobin, Katherine Ververis, Jitraporn Vongsvivut, Mark Ziemann, Chrishan Samuel, Mimi Tang, Assam El-Osta, Tom Karagiannis
(2022), Vol. 79, pp. 579-, Cellular and Molecular Life Sciences, Switzerland, C1
M Coughlan, M Ziemann, A Laskowski, T Woodruff, S Tan
(2022), Vol. 12, pp. 20278-, Scientific Reports, England, C1
M Felisbino, M Ziemann, I Khurana, J Okabe, K Al-Hasani, S Maxwell, K Harikrishnan, C de Oliveira, M Mello, A El-Osta
(2021), Vol. 11, Scientific Reports, England, C1-1
Sex-Specific Control of Human Heart Maturation by the Progesterone Receptor
C Sim, B Phipson, M Ziemann, H Rafehi, R Mills, K Watt, K Abu-Bonsrah, R Kalathur, H Voges, D Dinh, M Ter Huurne, C Vivien, A Kaspi, H Kaipananickal, A Hidalgo, L Delbridge, R Robker, P Gregorevic, C Dos Remedios, S Lal, A Piers, I Konstantinov, D Elliott, A El-Osta, A Oshlack, J Hudson, E Porrello
(2021), Vol. 143, pp. 1614-1628, Circulation, United States, C1
Processed foods drive intestinal barrier permeability and microvascular diseases
M Snelson, S Tan, R Clarke, C De Pasquale, V Thallas-Bonke, T Nguyen, S Penfold, B Harcourt, K Sourris, R Lindblom, M Ziemann, D Steer, A El-Osta, M Davies, L Donnellan, P Deo, N Kellow, M Cooper, T Woodruff, C Mackay, J Forbes, M Coughlan
(2021), Vol. 7, Science Advances, United States, C1
S Tan, R Lindblom, M Ziemann, A Laskowski, C Granata, M Snelson, V Thallas-Bonke, A El-Osta, C Baeza-Garza, S Caldwell, R Hartley, T Krieg, M Cooper, M Murphy, M Coughlan
(2021), Vol. 13, Nutrients, Switzerland, C1-1
Yap regulates skeletal muscle fatty acid oxidation and adiposity in metabolic disease
K Watt, D Henstridge, M Ziemann, C Sim, M Montgomery, D Samocha-Bonet, B Parker, G Dodd, S Bond, T Salmi, R Lee, R Thomson, A Hagg, J Davey, H Qian, R Koopman, A El-Osta, J Greenfield, M Watt, M Febbraio, B Drew, A Cox, E Porrello, K Harvey, P Gregorevic
(2021), Vol. 12, Nature Communications, England, C1
Gene name errors: Lessons not learned
M Abeysooriya, M Soria, M Kasu, M Ziemann
(2021), Vol. 17, PLoS Computational Biology, United States, C1
Activation of Hippo signaling pathway mediates mitochondria dysfunction and dilated cardiomyopathy in mice
W Wu, M Ziemann, K Huynh, G She, Z Pang, Y Zhang, T Duong, H Kiriazis, T Pu, R Bai, J Li, Y Zhang, M Chen, J Sadoshima, X Deng, P Meikle, X Du
(2021), Vol. 11, pp. 8993-9008, Theranostics, Sydney, N.S.W., C1
D Riddy, H Kammoun, A Murphy, S Bosnyak-Gladovic, R De La Fuente Gonzalez, J Merlin, M Ziemann, S Fabb, T Pierce, N Diepenhorst, P Rueda, A El-Osta, J Gautier, N Venteclef, W Charman, A Christopoulos, P Sexton, R Summers, M Febbraio, P Delerive, C Langmead
(2021), Vol. 9, BMJ Open Diabetes Research and Care, England, C1-1
Sih Tan, Mark Ziemann, Vicki Thallas-Bonke, Matthew Snelson, Vinod Kumar, Adrienne Laskowski, Tuong-Vi Nguyen, Kevin Huynh, Michele Clarke, Renata Libianto, Scott Baker, Alison Skene, David Power, Richard MacIsaac, Darren Henstridge, Rick Wetsel, Assam El-Osta, Peter Meikle, Scott Wilson, Josephine Forbes, Mark Cooper, Elif Ekinci, Trent Woodruff, Melinda Coughlan
(2020), Vol. 69, pp. 83-98, Diabetes, New York, N.Y., C1
Mitch: Multi-contrast pathway enrichment for multi-omics and single-cell profiling data
A Kaspi, M Ziemann
(2020), Vol. 21, BMC Genomics, England, C1
C Bain, M Ziemann, A Kaspi, A Khan, R Taylor, H Trahair, I Khurana, H Kaipananickal, S Wallace, A El-Osta, P Myles, K Bozaoglu
(2020), Vol. 7, pp. 2468-2478, ESC Heart Failure, England, C1
M Lopez Sanchez, N Van Bergen, L Kearns, M Ziemann, H Liang, A Hewitt, D Mackey, I Trounce
(2020), Vol. 54, pp. 113-121, Mitochondrion, Netherlands, C1
M Islam, H Gan, M Ziemann, H Hussain, T Arioli, D Cahill
(2020), Vol. 11, Frontiers in Plant Science, Switzerland, C1
Matthew McKenzie, Mark Ziemann
(2020), pp. 1-6, International Journal of Educational Research Open, Amsterdam, The Netherlands, C1
Nuclear response to divergent mitochondrial DNA genotypes modulates the interferon immune response
M Lopez Sanchez, M Ziemann, A Bachem, R Makam, J Crowston, C Pinkert, M McKenzie, S Bedoui, I Trounce
(2020), Vol. 15, pp. e0239804-, PloS one, United States, C1
M Nguyen, M Ziemann, H Kiriazis, Y Su, Z Thomas, Q Lu, D Donner, W Zhao, H Rafehi, J Sadoshima, J McMullen, A El-Osta, X Du
(2019), Vol. 316, pp. H45-H60, American Journal of Physiology - Heart and Circulatory Physiology, United States, C1-1
W Zhao, Q Lu, M Nguyen, Y Su, M Ziemann, L Wang, H Kiriazis, H Puthalakath, J Sadoshima, H Hu, X Du
(2019), Vol. 176, pp. 2465-2481, British Journal of Pharmacology, England, C1
Digital expression explorer 2: A repository of uniformly processed RNA sequencing data
M Ziemann, A Kaspi, A El-Osta
(2019), Vol. 8, GigaScience, United States, C1
Genomic DNA methylation distinguishes subtypes of human focal cortical dysplasia
K Kobow, M Ziemann, H Kaipananickal, I Khurana, A Mühlebner, M Feucht, J Hainfellner, T Czech, E Aronica, T Pieper, H Holthausen, M Kudernatsch, H Hamer, B Kasper, K Rössler, V Conti, R Guerrini, R Coras, I Blümcke, A El-Osta, A Kaspi
(2019), Vol. 60, pp. 1091-1103, Epilepsia, United States, C1-1
Sex-Based Mhrt Methylation Chromatinizes MeCP2 in the Heart
K Harikrishnan, J Okabe, P Mathiyalagan, A Khan, S Jadaan, G Sarila, M Ziemann, I Khurana, S Maxwell, X Du, A El-Osta
(2019), Vol. 17, pp. 288-301, iScience, United States, C1-1
RNA-seq-based identification of Star upregulation by islet amyloid formation
M Hogan, M Ziemann, H K N, H Rodriguez, A Kaspi, N Esser, A Templin, A El-Osta, S Kahn
(2019), Vol. 32, pp. 67-76, Protein Engineering, Design and Selection, England, C1-1
Lipoxins regulate the early growth response-1 network and reverse diabetic kidney disease
E Brennan, M Mohan, A McClelland, C Tikellis, M Ziemann, A Kaspi, S Gray, R Pickering, S Tan, S Tasadaque Ali-Shah, P Guiry, A El-Osta, K Jandeleit-Dahm, M Cooper, C Godson, P Kantharidis
(2018), Vol. 29, pp. 1437-1448, Journal of the American Society of Nephrology, United States, C1-1
S Hagiwara, K Sourris, M Ziemann, W Tieqiao, M Mohan, A McClelland, E Brennan, J Forbes, M Coughlan, B Harcourt, S Penfold, B Wang, G Higgins, R Pickering, A El-Osta, M Thomas, M Cooper, P Kantharidis
(2018), Vol. 67, pp. 960-973, Diabetes, United States, C1-1
A Kaspi, I Khurana, M Ziemann, T Connor, B Spolding, P Zimmet, K Walder, A El-Osta
(2018), Vol. 62, Molecular Nutrition and Food Research, Germany, C1
A Lipponen, A El-Osta, A Kaspi, M Ziemann, I Khurana, H Kn, V Navarro-Ferrandis, N Puhakka, J Paananen, A Pitkänen
(2018), Vol. 6, pp. 17-, Acta neuropathologica communications, England, C1-1
Age-related differential structural and transcriptomic responses in the hypertensive heart
F Marques, P Chu, M Ziemann, A Kaspi, H Kiriazis, X Du, A El-Osta, D Kaye
(2018), Vol. 9, Frontiers in Physiology, Switzerland, C1-1
Multicellular transcriptional analysis of mammalian heart regeneration
G Quaife-Ryan, C Sim, M Ziemann, A Kaspi, H Rafehi, M Ramialison, A El-Osta, J Hudson, E Porrello
(2017), Vol. 136, pp. 1123-1139, Circulation, United States, C1-1
H Rafehi, A Kaspi, M Ziemann, J Okabe, T Karagiannis, A El-Osta
(2017), Vol. 12, pp. 991-1003, Epigenetics, United States, C1-1
F Marques, E Nelson, P Chu, D Horlock, A Fiedler, M Ziemann, J Tan, S Kuruppu, N Rajapakse, A El-Osta, C Mackay, D Kaye
(2017), Vol. 135, pp. 964-977, Circulation, United States, C1-1
MeCP2 interacts with chromosomal microRNAs in brain
A Khan, M Ziemann, H Rafehi, S Maxwell, G Ciccotosto, A El-Osta
(2017), Vol. 12, pp. 1028-1037, Epigenetics, Abingdon, Eng., C1-1
I Khurana, A Kaspi, M Ziemann, T Block, T Connor, B Spolding, A Cooper, P Zimmet, A El-Osta, K Walder
(2017), Vol. 49, pp. S103-S104, Pathology, Amsterdam, The Netherlands, C1
I Khurana, A Kaspi, M Ziemann, T Block, T Connor, B Spolding, A Cooper, P Zimmet, A El-Osta, K Walder
(2016), Vol. 40, pp. 1079-1088, International Journal of Obesity, England, C1
Set7 mediated interactions regulate transcriptional networks in embryonic stem cells
Natasha Tuano, Jun Okabe, Mark Ziemann, Mark Cooper, Assam El-Osta
(2016), Vol. 44, pp. 9206-9217, Nucleic acids research, Oxford, Eng., C1-1
Gene name errors are widespread in the scientific literature
M Ziemann, Y Eren, A El-Osta
(2016), Vol. 17, Genome Biology, England, C1-1
Evaluation of microRNA alignment techniques
M Ziemann, A Kaspi, A El-Osta
(2016), Vol. 22, pp. 1120-1138, RNA, United States, C1-1
Etiology matters-Genomic DNA Methylation Patterns in Three Rat Models of Acquired Epilepsy
K Debski, A Pitkanen, N Puhakka, A Bot, I Khurana, K Harikrishnan, M Ziemann, A Kaspi, A El-Osta, K Lukasiuk, K Kobow
(2016), Vol. 6, Scientific Reports, England, C1-1
Current perspectives in Set7 mediated stem cell differentiation
Nazanin Karimnia, Haloom Rafehi, Natasha Tuano, Mark Ziemann, Harikrishnan K N, Jun Okabe, Assam El-Osta
(2016), Vol. 2, pp. 1-8, Non-coding RNA, Basel, Switzerland, C1-1
N Nejat, D Cahill, G Vadamalai, M Ziemann, J Rookes, N Naderali
(2015), Vol. 290, pp. 1899-1910, Molecular genetics and genomics, New York , N. Y., C1
Dynamic changes in the cardiac methylome during postnatal development
Choon Sim, Mark Ziemann, Antony Kaspi, K Harikrishnan, Jenny Ooi, Ishant Khurana, Lisa Chang, James Hudson, Assam El-Osta, Enzo Porrello
(2015), Vol. 29, pp. 1329-1343, FASEB journal, Bethesda, Md., C1-1
HDAC inhibition attenuates cardiac hypertrophy by acetylation and deacetylation of target genes
Jenny Ooi, Natasha Tuano, Haloom Rafehi, Xiao-Ming Gao, Mark Ziemann, Xiao-Jun Du, Assam El-Osta
(2015), Vol. 10, pp. 418-430, Epigenetics, Abingdon, Eng., C1-1
Annabelle Rodd, Katherine Ververis, Dheeshana Sayakkarage, Abdul Khan, Haloom Rafehi, Mark Ziemann, Shanon Loveridge, Ross Lazarus, Caroline Kerr, Trevor Lockett, Assam El-Osta, Tom Karagiannis, Louise Bennett
(2015), Vol. 6, pp. 2507-2524, Food & function, Cambridge, England, C1-1
Identification and expression analysis of the barley (Hordeum vulgare L.) aquaporin gene family
Runyararo Hove, Mark Ziemann, Mrinal Bhave
(2015), Vol. 10, pp. 1-21, PLOS One, San Francisco, Calif, C1-1
Development of novel activin-targeted therapeutics
Justin Chen, Kelly Walton, Sara Al-Musawi, Emily Kelly, Hongwei Qian, Mylinh La, Louis Lu, George Lovrecz, Mark Ziemann, Ross Lazarus, Assam El-Osta, Paul Gregorevic, Craig Harrison
(2015), Vol. 23, pp. 434-444, Molecular therapy, Amsterdam, The Netherlands, C1-1
A Kamboj, M Ziemann, M Bhave
(2015), Vol. 37, pp. 1-12, Acta physiologiae plantarum, Berlin, Germany, C1-1
Clinical applicability of methylome sequencing in a pilot study of ischemic stroke individuals
Mark Ziemann, K Harikrishnan, Ishant Khurana, Antony Kaspi, Samuel Keating, Deidre De Silva, Kyaw Moe, Assam El-Osta
(2015), Vol. 2, pp. 11-22, Methods in Next Generation Sequencing, Berlin, Germany, C1-1
Abiotic stress response in barley and the emergent roles of microRNAs
T Dang, M Ziemann, M Bhave
(2014), pp. 165-192, Barley: physical properties, genetic factors and environmental impacts on growth, Hauppage, N.Y., B1-1
Rapid development of non-alcoholic steatohepatitis in Psammomys obesus (Israeli Sand Rat)
B Spolding, T Connor, C Wittmer, L Abreu, A Kaspi, M Ziemann, G Kaur, A Cooper, S Morrison, S Lee, A Sinclair, Y Gibert, J Trevaskis, J Roth, A El-Osta, R Standish, K Walder
(2014), Vol. 9, pp. 1-7, PLoS one, San Francisco, Calif., C1
C Latouche, S Heywood, S Henry, M Ziemann, R Lazarus, A El-Osta, J Armitage, B Kingwell
(2014), Vol. 144, pp. 237-244, The Journal of Nutrition, Bethesda, Md, United States, C1
Non-referenced genome assembly from epigenomic short-read data
A Kaspi, M Ziemann, S Keating, I Khurana, T Connor, B Spolding, A Cooper, R Lazarus, K Walder, P Zimmet, A El-Osta
(2014), Vol. 9, pp. 1329-1338, Epigenetics, United States, C1
Deep sequencing reveals novel Set7 networks
Samuel Keating, Mark Ziemann, Jun Okabe, Abdul Khan, Aneta Balcerczyk, Assam El-Osta
(2014), Vol. 71, pp. 4471-4486, Cellular and molecular life sciences, Basel, Switzerland, C1-1
Vascular histone deacetylation by pharmacological HDAC inhibition
Haloom Rafehi, Aneta Balcerczyk, Sebastian Lunke, Antony Kaspi, Mark Ziemann, Harikrishnan Kn, Jun Okabe, Ishant Khurana, Jenny Ooi, Abdul Khan, Xiao-Jun Du, Lisa Chang, Izhak Haviv, Samuel Keating, Tom Karagiannis, Assam El-Osta
(2014), Vol. 24, pp. 1271-1284, Genome research, Cold Spring Harbor, N.Y., C1-1
Endothelial transcriptome in response to pharmacological methyltransferase inhibition
Jun Okabe, Ana Fernandez, Mark Ziemann, Samuel Keating, Aneta Balcerczyk, Assam El-Osta
(2014), Vol. 9, pp. 1755-1762, ChemMedChem, Weinheim, Germany, C1-1
Mark Ziemann, Antony Kaspi, Ross Lazarus, Assam El-Osta
(2013), Vol. 9, pp. 212-215, Bioinformation, [Singapore], C1-1
OrthoRBH: a streamlined pipeline for mining large gene family sequences in related species
Mark Ziemann, Atul Kamboj, Mrinal Bhave
(2013), Vol. 9, pp. 267-269, Bioinformation, [Singapore], C1-1
Deep sequencing reveals increased DNA methylation in chronic rat epilepsy
Katja Kobow, Antony Kaspi, K Harikrishnan, Katharina Kiese, Mark Ziemann, Ishant Khurana, Ina Fritzsche, Jan Hauke, Eric Hahnen, Roland Coras, Angelika Mühlebner, Assam El-Osta, Ingmar Blümcke
(2013), Vol. 126, pp. 741-756, Acta neuropathologica, New York, N. Y., C1-1
Analysis of the barley leaf transcriptome under salinity stress using mRNA-Seq
M Ziemann, A Kamboj, R Hove, S Loveridge, A El-Osta, M Bhave
(2013), Vol. 35, pp. 1915-1924, Acta physiologiae plantarum, New York, N. Y., C1-1
Antony Kaspi, Mark Ziemann, Haloom Rafehi, Ross Lazarus, Assam El-Osta
(2012), Vol. 94, pp. 2353-2359, Biochimie, Amsterdam, The Netherlands, C1-1
Haloom Rafehi, Andrea Smith, Aneta Balcerczyk, Mark Ziemann, Jenny Ooi, Shanon Loveridge, Emma Baker, Assam El-Osta, Tom Karagiannis
(2012), Vol. 7, pp. 343-355, Genes & nutrition, New York, N. Y., C1-1
Microparticles: major transport vehicles for distinct microRNAs in circulation
Philipp Diehl, Alba Fricke, Laura Sander, Johannes Stamm, Nicole Bassler, Nay Htun, Mark Ziemann, Thomas Helbing, Assam El-Osta, Jeremy Jowett, Karlheinz Peter
(2012), Vol. 93, pp. 633-644, Cardiovascular research, Oxford, Eng., C1-1
Haloom Rafehi, Katherine Ververis, Aneta Balcerczyk, Mark Ziemann, Jenny Ooi, Sean Hu, Faith Kwa, Shanon Loveridge, George Georgiadis, Assam El-Osta, Tom Karagiannis
(2012), Vol. 2, pp. 1-14, Pathobiology of aging and age-related diseases, Abingdon, Eng., C1-1
PPIase activities and interaction partners of FK506-binding proteins in the wheat thylakoid
Peter Gollan, Mark Ziemann, Mrinal Bhave
(2011), Vol. 143, pp. 385-395, Physiologia plantarum, Chichester, Eng., C1-1
Luciano Pirola, Aneta Balcerczyk, Richard Tothill, Izhak Haviv, Antony Kaspi, Sebastian Lunke, Mark Ziemann, Tom Karagiannis, Stephen Tonna, Adam Kowalczyk, Bryan Beresford-Smith, Geoff Macintyre, Ma Kelong, Zhang Hongyu, Jingde Zhu, Assam El-Osta
(2011), Vol. 21, pp. 1601-1615, Genome research, Cold Spring Harbor, N.Y., C1-1
Mark Ziemann, Mrinal Bhave, Sabine Zachgo
(2011), Vol. 38, pp. 25-34, Functional plant biology, Clayton, Vic., C1-1
Funded Projects at Deakin
Industry and Other Funding
Clinical Biomarker Shoulder Study: Transcriptomic differences between inflammatory conditions of the shoulder: osteoarthritis and rotator cuff tears -The SHOaW Study.
Dr Samuel James Lynskey, Prof Richard Page, Dr Stephen Gill, Prof Sean Mcgee, Dr Mark Ziemann, Dr Luba Sominsky
Australian Orthopaedic Association Research Foundation
- 2023: $10,000
Supervisions
No completed student supervisions to report