Endorsements by Mark Daniel Ziemann

0000-0002-7688-6974

Head of Bioinformatics, Life Sciences, Burnet Institute
Lecturer, School of Life and Environmental Science, Deakin University
MONASH UNIVERSITY
Genomics, Epigenetics, Systems biology, Epigenomic medicine, Molecular genetics

Genome Spot - Practical tips for genome analysis

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MONASH UNIVERSITY profile page

Endorsements

Red flags for paper mills need to go beyond the level of individual articles: a case study of Hindawi special issues
robustclearexciting
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A Reproducible Data Analysis Workflow with R Markdown, Git, Make, and Docker
robust
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Own works

Fast and Furious: Metabolic Pathways Fuelling Devil Facial Tumour Disease
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Target Selection, Homokaryotic Isolation, and Screening Methods for Gene Editing in the Destructive Global Pathogen, Phytophthora cinnamomi
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Skeletal muscle mitochondria contain nuclear-encoded RNA species prior to and following adaptation to exercise training in rats
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Direction-aware functional class scoring enrichment analysis of infinium DNA methylation data
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'QuickDASH' to find unique genes and biological processes associated with shoulder osteoarthritis: a prospective case-control study.
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Hippo pathway activation causes multiple lipid derangements in a murine model of cardiomyopathy.
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The transcriptomic signature of age and sex is not conserved in human primary myocytes
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Purification of mitochondria from skeletal muscle tissue for transcriptomic analyses reveals localization of nuclear‐encoded noncoding <scp>RNAs</scp>
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Purification of mitochondria from skeletal muscle tissue for transcriptomic analyses reveals localization of nuclear‐encoded noncoding RNAs
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Epigenetic Analysis of ST3GAL3 and other Sialic Acid Metabolism Genes in ADHD
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Sterol complex visualisation in Phytophthora cinnamomi and expression analysis of genes involved in sterol sensing, recruitment and conversion
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Viable protoplast isolation, organelle visualization and transformation of the globally distributed plant pathogen Phytophthora cinnamomi
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Novel Insights into Changes in Gene Expression within the Hypothalamus in Two Asthma Mouse Models: A Transcriptomic Lung–Brain Axis Study
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Direction-aware functional class scoring enrichment analysis of Infinium DNA methylation data
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Amyloid beta 42 alters cardiac metabolism and impairs cardiac function in male mice with obesity
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Two subtle problems with overrepresentation analysis
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A recipe for extremely reproducible enrichment analysis (and why we need it)
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The five pillars of computational reproducibility: bioinformatics and beyond
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A recipe for extremely reproducible enrichment analysis
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A recipe for extremely reproducible enrichment analysis v2
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The five pillars of computational reproducibility: Bioinformatics and beyond
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A recipe for extremely reproducible enrichment analysis v1
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Genomic Characterization of Salmonella enterica serovar Weltevreden Associated with Human Diarrhea.
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Reduced methylation corresponds with diabetic nephropathy risk in type 1 diabetes
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Reduced methylation correlates with diabetic nephropathy risk in type 1 diabetes
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Sulforaphane prevents and reverses allergic airways disease in mice via anti-inflammatory, antioxidant, and epigenetic mechanisms.
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Stimulating Mitochondrial Biogenesis with Deoxyribonucleosides Increases Functional Capacity in ECHS1-Deficient Cells.
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Loss of mitochondrial fatty acid β-oxidation protein short-chain Enoyl-CoA hydratase disrupts oxidative phosphorylation protein complex stability and function.
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Transcriptomic Analysis of Dysregulated Genes of the nDNA-mtDNA Axis in a Mouse Model of Dilated Cardiomyopathy.
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Purification of mitochondria from skeletal muscle tissue for transcriptomic analyses reveals localisation of nuclear-encoded non-coding RNAs
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Methylomic and transcriptomic characterization of postoperative systemic inflammatory dysregulation.
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Urgent need for consistent standards in functional enrichment analysis.
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Amyloid beta 42 alters cardiac metabolism and impairs cardiac function in obesity
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Valproic acid attenuates cellular senescence in diabetic kidney disease through the inhibition of complement C5a receptors
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Yap regulates skeletal muscle fatty acid oxidation and adiposity in metabolic disease
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MicroRNA-101-3p Modulates Mitochondrial Metabolism via the Regulation of Complex II Assembly.
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Deletion of GPR21 improves glucose homeostasis and inhibits the CCL2-CCR2 axis by divergent mechanisms
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Guidelines for reliable and reproducible functional enrichment analysis
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Gene name errors: Lessons not learned.
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Targeting Methylglyoxal in Diabetic Kidney Disease Using the Mitochondria-Targeted Compound MitoGamide
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Population genomics of Salmonella enterica serovar Weltevreden ST365, an emerging predominant causative agent of diarrheal disease
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Gene name errors: lessons not learned
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Sex-Specific Control of Human Heart Maturation by the Progesterone Receptor.
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Processed foods drive intestinal barrier permeability and microvascular diseases
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Valproic acid influences the expression of genes implicated with hyperglycaemia-induced complement and coagulation pathways.
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Activation of Hippo signaling pathway mediates mitochondria dysfunction and dilated cardiomyopathy in mice
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Sex-Specific Control of Human Heart Maturation by the Progesterone Receptor
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Sulforaphane prevents and reverses allergic airways disease in mice via anti-inflammatory, antioxidant and epigenetic mechanisms
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Nuclear response to divergent mitochondrial DNA genotypes modulates the interferon immune response
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Tallyup: the Docker pipeline driving the Digital Expression Explorer 2 resource
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Assessment of the web-based audience response system socrative for biomedical science revision classes
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OXPHOS bioenergetic compensation does not explain disease penetrance in Leber hereditary optic neuropathy.
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Phaeophyceaean (Brown Algal) Extracts Activate Plant Defense Systems in Arabidopsis thaliana Challenged With Phytophthora cinnamomi.
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DNA methylation patterns from peripheral blood separate coronary artery disease patients with and without heart failure.
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mitch: multi-contrast pathway enrichment for multi-omics and single-cell profiling data
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mitch
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Deficiency of Prebiotic Fibre and Insufficient Signalling Through Gut Metabolite Sensing Receptors Leads to Cardiovascular Disease.
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Deficiency of Prebiotic Fiber and Insufficient Signaling through Gut Metabolite-Sensing Receptors Leads to Cardiovascular Disease
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Complement C5a Induces Renal Injury in Diabetic Kidney Disease Via Disruption in Mitochondrial Metabolic Agility
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RNA-seq-based identification of Star upregulation by islet amyloid formation
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Sex-Based Mhrt Methylation Chromatinizes MeCP2 in the Heart
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Genomic DNA methylation distinguishes subtypes of human focal cortical dysplasia.
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Reply to "Letter to the Editor: Not all modified citrus pectins are the same: size does matter".
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Digital expression explorer 2: a repository of uniformly processed RNA sequencing data
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Stimulation of β-adrenoceptors up-regulates cardiac expression of galectin-3 and BIM through the Hippo signalling pathway.
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Galectin-3 deficiency ameliorates fibrosis and remodeling in dilated cardiomyopathy mice with enhanced Mst1 signaling
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Age-related differential structural and transcriptomic responses in the hypertensive heart
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Diet during Pregnancy is Implicated in the Regulation of Hypothalamic RNA Methylation and Risk of Obesity in Offspring
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Lipoxins regulate the early growth response-1 network and reverse diabetic kidney disease
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Lipoxins Regulate the Early Growth Response–1 Network and Reverse Diabetic Kidney Disease
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Valproic acid attenuates hyperglycemia-induced complement and coagulation cascade gene expression
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Additional file 1: of Transcription factors Tp73, Cebpd, Pax6, and Spi1 rather than DNA methylation regulate chronic transcriptomics changes after experimental traumatic brain injury
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Digital Expression Explorer 2: a repository of 4.5 trillion uniformly processed RNA-seq reads and counting
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RAGE deletion confers renoprotection by reducing responsiveness to transforming growth factor-β and increasing resistance to apoptosis
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Transcription factors Tp73, Cebpd, Pax6, and Spi1 rather than DNA methylation regulate chronic transcriptomics changes after experimental traumatic brain injury
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Yet Another Script For Processing Drop-Seq Data
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MeCP2 interacts with chromosomal microRNAs in brain
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Multicellular Transcriptional Analysis of Mammalian Heart Regeneration.
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Systems approach to the pharmacological actions of HDAC inhibitors reveals EP300 activities and convergent mechanisms of regulation in diabetes.
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Set7 regulates smooth muscle cell differentiation
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NET silencing by let-7i in posturaltachycardia syndrome
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High Fibre Diet and Acetate Supplementation Change the Gut Microbiota and Prevent the Development of Hypertension and Heart Failure in DOCA-Salt Hypertensive Mice
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How NGS is transforming medicine
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Minitalk: Gene Name Errors
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Multicellular Transcriptional Analysis of Mammalian Heart Regeneration
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The Accessible Chromatin Landscape of Murine and Human Cardiomyocyte Development
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The ENCODE Gene Set Hub
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Current perspectives in Set7 mediated stem cell differentiation
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Gene name errors are widespread in the scientific literature
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Regulation of hypothalamic gene expression by DNA methylation is influenced by parental diet during pregnancy and linked to offspring's risk of obesity
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Evaluation of microRNA alignment techniques
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DNA methylation regulates hypothalamic gene expression linking parental diet during pregnancy to the offspring's risk of obesity in Psammomys obesus
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Accuracy, speed and error tolerance of short DNA sequence aligners
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Etiology matters-Genomic DNA Methylation Patterns in Three Rat Models of Acquired Epilepsy
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Additional file 1: Table S1. of Gene name errors are widespread in the scientific literature
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Set7 mediated interactions regulate transcriptional networks in embryonic stem cells
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Dynamic changes in the cardiac methylome during postnatal development
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Clinical applicability of methylome sequencing in a pilot study of ischemic stroke individuals
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Development of novel activin-targeted therapeutics
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Digital Expression Explorer: A user-friendly repository of uniformly processed RNA-seq data
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Endurance exercise stimulates rapid changes in promoter histone acetylation in skeletal muscle
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HDAC inhibition attenuates cardiac hypertrophy by acetylation and deacetylation of target genes.
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Identification and expression analysis of the barley (Hordeum vulgare L.) aquaporin gene family
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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
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Transcriptomics-based analysis using RNA-Seq of the coconut (Cocos nucifera) leaf in response to yellow decline phytoplasma infection
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Rapid development of non-alcoholic steatohepatitis in Psammomys obesus (Israeli sand rat)
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Deep sequencing reveals novel Set7 networks
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Endothelial transcriptome in response to pharmacological methyltransferase inhibition
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Identification of salt-tolerant barley varieties by a consolidated physiological and molecular approach
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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
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Non-referenced genome assembly from epigenomic short-read data
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Vascular histone deacetylation by pharmacological HDAC inhibition
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Analysis of the barley leaf transcriptome under salinity stress using mRNA-Seq
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Deep sequencing reveals increased DNA methylation in chronic rat epilepsy
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Motif analysis in DNAse hypersensitivity regions uncovers distal cis elements associated with gene expression.
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OrthoRBH: A streamlined pipeline for mining large gene family sequences in related species.
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Creating reusable tools from scripts
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Microparticles: major transport vehicles for distinct microRNAs in circulation.
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A pipeline for the identification and characterization of chromatin modifications derived from ChIP-Seq datasets
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Investigation into the biological properties of the olive polyphenol, hydroxytyrosol: mechanistic insights by genome-wide mRNA-Seq analysis
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Investigation of the biological properties of Cinnulin PF in the context of diabetes
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PPIase activities and interaction partners of FK506-binding proteins in the wheat thylakoid.
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Genome-wide analysis distinguishes hyperglycemia regulated epigenetic signatures of primary vascular cells
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Bioinformatic studies of the wheat glutaredoxin gene family and functional analysis of the ROXY1 orthologues
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Glutaredoxin family genes in plant development
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Identification of plant cell wall mutants by means of a forward chemical genetic approach using hydrolases
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Nuclear activity of ROXY1, a glutaredoxin interacting with TGA factors, is required for petal development in arabidopsis thaliana
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Origin and diversification of land plant CC-type glutaredoxins.
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Evidence of physical interactions of puroindoline proteins using the yeast two-hybrid system
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