Dr Mark Ziemann

STAFF PROFILE

Position

Lecturer in Biotechnology and Bioinformatics

Faculty

Faculty of Sci Eng & Built Env

Department

School of Life & Env. Sciences

Campus

Geelong Waurn Ponds Campus

Contact

m.ziemann@deakin.edu.au
+61 3 522 78965

Publications

Filter by

2019

Galectin-3 deficiency ameliorates fibrosis and remodeling in dilated cardiomyopathy mice with enhanced Mst1 signaling

My-Nhan Nguyen, Mark Ziemann, Helen Kiriazis, Yidan Su, Zara Thomas, Qun Lu, Daniel Donner, Wei-Bo Zhao, Haloom Rafehi, Junichi Sadoshima, Julie McMullen, Assam El-Osta, Xiao-Jun Du

(2019), Vol. 316, pp. H45-H60, American journal of physiology. Heart and circulatory physiology, Bethesda, Md., C1-1

journal

Stimulation of ?-adrenoceptors up-regulates cardiac expression of galectin-3 and BIM through the Hippo signalling pathway

Wei-Bo Zhao, Qun Lu, My-Nhan Nguyen, Yidan Su, Mark Ziemann, Li-Na Wang, Helen Kiriazis, Hamsa Puthalakath, Junichi Sadoshima, Hou-Yuan Hu, Xiao-Jun Du

(2019), Vol. 176, pp. 2465-2481, British journal of pharmacology, Chichester, Eng., C1

journal

Digital expression explorer 2: a repository of uniformly processed RNA sequencing data

Mark Ziemann, Antony Kaspi, Assam El-Osta

(2019), Vol. 8, Gigascience, Oxford, Eng., C1

journal

Genomic DNA methylation distinguishes subtypes of human focal cortical dysplasia

K Kobow, M Ziemann, H Kaipananickal, I Khurana, A Mhlebner, M Feucht, J Hainfellner, T Czech, E Aronica, T Pieper, H Holthausen, M Kudernatsch, H Hamer, B Kasper, K Rssler, V Conti, R Guerrini, R Coras, I Blmcke, A El-Osta, A Kaspi

(2019), Vol. 60, pp. 1091-1103, Epilepsia, Chichester, Eng., C1-1

journal

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, Amsterdam, The Netherlands, C1-1

journal

RNA-seq-based identification of Star upregulation by islet amyloid formation

Meghan Hogan, Mark Ziemann, Harikrishnan K N, Hanah Rodriguez, Antony Kaspi, Nathalie Esser, Andrew Templin, Assam El-Osta, Steven Kahn

(2019), pp. 1-10, Protein engineering, design and selection, Oxford, Eng., C1-1

journal
2018

Lipoxins regulate the early growth response-1 network and reverse diabetic Kidney disease

Eoin Brennan, Muthukumar Mohan, Aaron McClelland, Christos Tikellis, Mark Ziemann, Antony Kaspi, Stephen Gray, Raelene Pickering, Sih Tan, Syed Ali-Shah, Patrick Guiry, Assam El-Osta, Karin Jandeleit-Dahm, Mark Cooper, Catherine Godson, Phillip Kantharidis

(2018), Vol. 29, pp. 1437-1448, Journal of the American Society of Nephrology, Gainesville, Fla., C1-1

journal

RAGE deletion confers renoprotection by reducing responsiveness to transforming growth factor-? and increasing resistance to apoptosis

Shinji Hagiwara, Karly Sourris, Mark Ziemann, Wu Tieqiao, Muthukumar Mohan, Aaron McClelland, Eoin Brennan, Josephine Forbes, Melinda Coughlan, Brooke Harcourt, Sally Penfold, Bo Wang, Gavin Higgins, Raelene Pickering, Assam El-Osta, Merlin Thomas, Mark Cooper, Phillip Kantharidis

(2018), Vol. 67, pp. 960-973, Diabetes, Arlington, Va., C1-1

journal

Diet during pregnancy is implicated in the regulation of hypothalamic RNA methylation and risk of obesity in offspring

Antony Kaspi, Ishant Khurana, Mark Ziemann, Timothy Connor, Briana Spolding, Paul Zimmet, Ken Walder, Assam El-Osta

(2018), Vol. 62, pp. 1-10, Molecular nutrition and food research, Weinheim, Germany, C1

journal

Transcription factors Tp73, Cebpd, Pax6, and Spi1 rather than DNA methylation regulate chronic transcriptomics changes after experimental traumatic brain injury

Anssi Lipponen, Assam El-Osta, Antony Kaspi, Mark Ziemann, Ishant Khurana, Harikrishnan Kn, Vicente Navarro-Ferrandis, Noora Puhakka, Jussi Paananen, Asla Pitknen

(2018), Vol. 6, pp. 1-16, Acta neuropathologica communications, London, Eng., C1-1

journal

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, pp. 1-13, Frontiers in physiology, Lausanne, Switzerland, C1-1

journal
2017

Multicellular transcriptional analysis of mammalian heart regeneration

Gregory Quaife-Ryan, Choon Sim, Mark Ziemann, Antony Kaspi, Haloom Rafehi, Mirana Ramialison, Assam El-Osta, James Hudson, Enzo Porrello

(2017), Vol. 136, pp. 1123-1139, Circulation, Philadelphia, Pa., C1-1

journal

Systems approach to the pharmacological actions of HDAC inhibitors reveals EP300 activities and convergent mechanisms of regulation in diabetes

Haloom Rafehi, Antony Kaspi, Mark Ziemann, Jun Okabe, Tom Karagiannis, Assam El-Osta

(2017), Vol. 12, pp. 991-1003, Epigenetics, Abingdon, Eng., C1-1

journal

High-fiber diet and acetate supplementation change the gut microbiota and prevent the development of hypertension and heart failure in hypertensive mice

Francine Marques, Erin Nelson, Po-Yin Chu, Duncan Horlock, April Fiedler, Mark Ziemann, Jian Tan, Sanjaya Kuruppu, Niwanthi Rajapakse, Assam El-Osta, Charles Mackay, David Kaye

(2017), Vol. 135, pp. 964-977, Circulation, Philadelphia, Pa., C1-1

journal

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

journal
2016

DNA methylation regulates hypothalamic gene expression linking parental diet during pregnancy to the offspring's risk of obesity in Psammomys obesus

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, London, Eng., C1

journal

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

journal

Gene name errors are widespread in the scientific literature

Mark Ziemann, Yotam Eren, Assam El-Osta

(2016), Vol. 17, pp. 1-3, Genome biology, London, Eng., C1-1

journal

Evaluation of microRNA alignment techniques

Mark Ziemann, Antony Kaspi, Assam El-Osta

(2016), Vol. 22, pp. 1120-1138, RNA, Cold Spring Harbor, N.Y., C1-1

journal

Etiology matters - genomic DNA methylation patterns in three rat models of acquired epilepsy

Konrad D?bski, Asla Pitkanen, Noora Puhakka, Anna Bot, Ishant Khurana, K Harikrishnan, Mark Ziemann, Antony Kaspi, Assam El-Osta, Katarzyna Lukasiuk, Katja Kobow

(2016), Vol. 6, pp. 1-14, Scientific reports, London, Eng., C1-1

journal

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

journal
2015

Transcriptomics-based analysis using RNA-Seq of the coconut (Cocos nucifera) leaf in response to yellow decline phytoplasma infection

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

journal

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

journal

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

journal

RNA sequencing supports distinct reactive oxygen species-mediated pathways of apoptosis by high and low size mass fractions of Bay leaf (Lauris nobilis) in HT-29 cells

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

journal

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

journal

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

journal

Identification of salt-tolerant barley varieties by a consolidated physiological and molecular approach

A Kamboj, M Ziemann, M Bhave

(2015), Vol. 37, pp. 1-12, Acta physiologiae plantarum, Berlin, Germany, C1-1

journal
2014

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

journal

Maternal overnutrition programs changes in the expression of skeletal muscle genes that are associated with insulin resistance and defects of oxidative phosphorylation in adult male rat offspring.

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

journal

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, C1

journal

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

chapter

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

journal

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

journal

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

journal
2013

Motif analysis in DNAse hypersensitivity regions uncovers distal cis elements associated with gene expression

Mark Ziemann, Antony Kaspi, Ross Lazarus, Assam El-Osta

(2013), Vol. 9, pp. 212-215, Bioinformation, [Singapore], C1-1

journal

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

journal

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 Mhlebner, Assam El-Osta, Ingmar Blmcke

(2013), Vol. 126, pp. 741-756, Acta neuropathologica, New York, N. Y., C1-1

journal

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

journal
2012

A pipeline for the identification and characterization of chromatin modifications derived from ChIP-Seq datasets

Antony Kaspi, Mark Ziemann, Haloom Rafehi, Ross Lazarus, Assam El-Osta

(2012), Vol. 94, pp. 2353-2359, Biochimie, Amsterdam, The Netherlands, C1-1

journal

Investigation into the biological properties of the olive polyphenol, hydroxytyrosol: mechanistic insights by genome-wide mRNA-Seq analysis

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

journal

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

journal

Investigation of the biological properties of Cinnulin PF in the context of diabetes: mechanistic insights by genome-wide mRNA-Seq analysis

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

journal
2011

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

journal

Genome-wide analysis distinguishes hyperglycemia regulated epigenetic signatures of primary vascular cells

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

journal

Bioinformatic studies of the wheat glutaredoxin gene family and functional analysis of the ROXY1 orthologues

Mark Ziemann, Mrinal Bhave, Sabine Zachgo

(2011), Vol. 38, pp. 25-34, Functional plant biology, Clayton, Vic., C1-1

journal

Funded Projects at Deakin

No Funded Projects at Deakin found

Supervisions

No completed student supervisions to report