List of works - Mark Ziemann

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

scientific article published on 13 June 2012

Accuracy, speed and error tolerance of short DNA sequence aligners

Activation of Hippo signaling pathway mediates mitochondria dysfunction and dilated cardiomyopathy in mice

scientific article published on 21 August 2021

Age-Related Differential Structural and Transcriptomic Responses in the Hypertensive Heart

scientific article published on 09 July 2018

Analysis of the barley leaf transcriptome under salinity stress using mRNA-Seq

article

Bioinformatic studies of the wheat glutaredoxin gene family and functional analysis of theROXY1orthologues

article

Clinical applicability of methylome sequencing in a pilot study of ischemic stroke individuals

Complement C5a Induces Renal Injury in Diabetic Kidney Disease Via Disruption in Mitochondrial Metabolic Agility

scientific article published on 17 October 2019

Creating reusable tools from scripts: the Galaxy Tool Factory

scientific article published on 28 September 2012

Current perspectives in Set7 mediated stem cell differentiation.

scientific article

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

scientific article published on 25 April 2016

Deep sequencing reveals increased DNA methylation in chronic rat epilepsy

scientific article

Deep sequencing reveals novel Set7 networks.

scientific article published on 30 May 2014

Deficiency of Prebiotic Fibre and Insufficient Signalling Through Gut Metabolite Sensing Receptors Leads to Cardiovascular Disease

scientific article published on 25 February 2020

Deletion of GPR21 improves glucose homeostasis and inhibits the CCL2-CCR2 axis by divergent mechanisms

scientific article published on 01 November 2021

Development of novel activin-targeted therapeutics

scientific article

Diet during Pregnancy is Implicated in the Regulation of Hypothalamic RNA Methylation and Risk of Obesity in Offspring

scientific article published on 07 June 2018

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

scientific article published on 01 April 2019

Dynamic changes in the cardiac methylome during postnatal development

scientific article published on 9 December 2014

Endothelial Transcriptome in Response to Pharmacological Methyltransferase Inhibition

article

Etiology matters - Genomic DNA Methylation Patterns in Three Rat Models of Acquired Epilepsy.

scientific article

Evaluation of microRNA alignment techniques.

scientific article published on 9 June 2016

Evidence of physical interactions of puroindoline proteins using the yeast two-hybrid system

article

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

scientific article published on 02 November 2018

Gene name errors are widespread in the scientific literature

scientific article

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

scientific article

Genomic DNA methylation distinguishes subtypes of human focal cortical dysplasia

scientific article published on 10 May 2019

HDAC inhibition attenuates cardiac hypertrophy by acetylation and deacetylation of target genes

scientific article

High-Fiber Diet and Acetate Supplementation Change the Gut Microbiota and Prevent the Development of Hypertension and Heart Failure in Hypertensive Mice.

scientific article

Identification and Expression Analysis of the Barley (Hordeum vulgare L.) Aquaporin Gene Family

scientific article published on 9 June 2015

Identification of plant cell wall mutants by means of a forward chemical genetic approach using hydrolases

scientific article published on 10 August 2009

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

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

scientific article

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

scientific article

Lipoxins Regulate the Early Growth Response-1 Network and Reverse Diabetic Kidney Disease.

scientific article published on 28 February 2018

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.

scientific article published on 31 December 2013

MeCP2 interacts with chromosomal microRNAs in brain

scientific article published in January 2017

Microparticles: major transport vehicles for distinct microRNAs in circulation

scientific article published on 18 January 2012

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

scientific article published on 21 February 2013

Multi-Cellular Transcriptional Analysis of Mammalian Heart Regeneration ⬇️

scientific article

NET silencing by let-7i in postural tachycardia syndrome

scientific article published on 23 March 2017

Non-referenced genome assembly from epigenomic short-read data

scientific article

Nuclear activity of ROXY1, a glutaredoxin interacting with TGA factors, is required for petal development in Arabidopsis thaliana

scientific article published on 13 February 2009

Nuclear response to divergent mitochondrial DNA genotypes modulates the interferon immune response

scientific article published on 08 October 2020

OrthoRBH: A streamlined pipeline for mining large gene family sequences in related species

scientific article published on 2 March 2013

PPIase activities and interaction partners of FK506-binding proteins in the wheat thylakoid

scientific article

RAGE Deletion Confers Renoprotection by Reducing Responsiveness to Transforming Growth Factor-β and Increasing Resistance to Apoptosis

scientific article published on 15 February 2018

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

scientific article published on 26 June 2015

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

scientific article published on 01 December 2019

Rapid development of non-alcoholic steatohepatitis in Psammomys obesus (Israeli sand rat)

scientific article

Reply to "Letter to the Editor: Not all modified citrus pectins are the same: size does matter"

scientific article published on 01 May 2019

Set7 mediated interactions regulate transcriptional networks in embryonic stem cells.

scientific article published on 20 July 2016

Set7 regulates smooth muscle cell differentiation

Sex-Based Mhrt Methylation Chromatinizes MeCP2 in the Heart

scientific article published on 27 June 2019

Sex-Specific Control of Human Heart Maturation by the Progesterone Receptor

scientific article published on 08 March 2021

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

scientific article published on 30 May 2019

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

scientific article published on 8 September 2017

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

scientific article published on 27 February 2018

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

scientific article published on 18 April 2015

Urgent need for consistent standards in functional enrichment analysis

scientific article published on 09 March 2022

Valproic acid attenuates hyperglycemia-induced complement and coagulation cascade gene expression

article

Valproic acid influences the expression of genes implicated with hyperglycaemia-induced complement and coagulation pathways

scientific article published on 25 January 2021

Vascular histone deacetylation by pharmacological HDAC inhibition

scientific article

Yap regulates skeletal muscle fatty acid oxidation and adiposity in metabolic disease

scientific article published on 17 May 2021

mitch: multi-contrast pathway enrichment for multi-omics and single-cell profiling data

scientific article published on 29 June 2020

List of works by Mark Ziemann

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

Accuracy, speed and error tolerance of short DNA sequence aligners

Activation of Hippo signaling pathway mediates mitochondria dysfunction and dilated cardiomyopathy in mice

Age-Related Differential Structural and Transcriptomic Responses in the Hypertensive Heart

Analysis of the barley leaf transcriptome under salinity stress using mRNA-Seq

Bioinformatic studies of the wheat glutaredoxin gene family and functional analysis of theROXY1orthologues

Clinical applicability of methylome sequencing in a pilot study of ischemic stroke individuals

Complement C5a Induces Renal Injury in Diabetic Kidney Disease Via Disruption in Mitochondrial Metabolic Agility

Creating reusable tools from scripts: the Galaxy Tool Factory

Current perspectives in Set7 mediated stem cell differentiation.

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

Deep sequencing reveals increased DNA methylation in chronic rat epilepsy

Deep sequencing reveals novel Set7 networks.

Deficiency of Prebiotic Fibre and Insufficient Signalling Through Gut Metabolite Sensing Receptors Leads to Cardiovascular Disease

Deletion of GPR21 improves glucose homeostasis and inhibits the CCL2-CCR2 axis by divergent mechanisms

Development of novel activin-targeted therapeutics

Diet during Pregnancy is Implicated in the Regulation of Hypothalamic RNA Methylation and Risk of Obesity in Offspring

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

Dynamic changes in the cardiac methylome during postnatal development

Endothelial Transcriptome in Response to Pharmacological Methyltransferase Inhibition

Etiology matters - Genomic DNA Methylation Patterns in Three Rat Models of Acquired Epilepsy.

Evaluation of microRNA alignment techniques.

Evidence of physical interactions of puroindoline proteins using the yeast two-hybrid system

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

Gene name errors are widespread in the scientific literature

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

Genomic DNA methylation distinguishes subtypes of human focal cortical dysplasia

HDAC inhibition attenuates cardiac hypertrophy by acetylation and deacetylation of target genes

High-Fiber Diet and Acetate Supplementation Change the Gut Microbiota and Prevent the Development of Hypertension and Heart Failure in Hypertensive Mice.

Identification and Expression Analysis of the Barley (Hordeum vulgare L.) Aquaporin Gene Family

Identification of plant cell wall mutants by means of a forward chemical genetic approach using hydrolases

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

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

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

Lipoxins Regulate the Early Growth Response-1 Network and Reverse Diabetic Kidney Disease.

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.

MeCP2 interacts with chromosomal microRNAs in brain

Microparticles: major transport vehicles for distinct microRNAs in circulation

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

Multi-Cellular Transcriptional Analysis of Mammalian Heart Regeneration ⬇️

NET silencing by let-7i in postural tachycardia syndrome

Non-referenced genome assembly from epigenomic short-read data

Nuclear activity of ROXY1, a glutaredoxin interacting with TGA factors, is required for petal development in Arabidopsis thaliana

Nuclear response to divergent mitochondrial DNA genotypes modulates the interferon immune response

OrthoRBH: A streamlined pipeline for mining large gene family sequences in related species

PPIase activities and interaction partners of FK506-binding proteins in the wheat thylakoid

RAGE Deletion Confers Renoprotection by Reducing Responsiveness to Transforming Growth Factor-β and Increasing Resistance to Apoptosis

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

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

Rapid development of non-alcoholic steatohepatitis in Psammomys obesus (Israeli sand rat)

Reply to "Letter to the Editor: Not all modified citrus pectins are the same: size does matter"

Set7 mediated interactions regulate transcriptional networks in embryonic stem cells.

Set7 regulates smooth muscle cell differentiation

Sex-Based Mhrt Methylation Chromatinizes MeCP2 in the Heart

Sex-Specific Control of Human Heart Maturation by the Progesterone Receptor

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

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

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

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

Urgent need for consistent standards in functional enrichment analysis

Valproic acid attenuates hyperglycemia-induced complement and coagulation cascade gene expression

Valproic acid influences the expression of genes implicated with hyperglycaemia-induced complement and coagulation pathways

Vascular histone deacetylation by pharmacological HDAC inhibition

Yap regulates skeletal muscle fatty acid oxidation and adiposity in metabolic disease

mitch: multi-contrast pathway enrichment for multi-omics and single-cell profiling data