Mark Ziemann

Tissue-specific divergence in sex-biased DNA methylation across the lifespan

This study identifies tissue-specific sex-biased DNA methylation changes across the lifespan, showing that age-related methylation changes are widespread but sex effects are rare and tissue-specific.

Characterisation of vaginal Lactobacillus isolates from South African women towards the development of a biotherapeutic to optimise the vaginal microbiome

The paper characterizes vaginal Lactobacillus isolates from South African women to identify biotherapeutic candidates that can optimize the vaginal microbiome and reduce HIV risk.

The transcriptomic signature of age and sex is not conserved in human primary myocytes

The study compares the transcriptomic profiles of human muscle biopsies and their derived primary myocytes, finding minimal retention of age and sex-related gene expression patterns in culture.

Metabolic Pathways Fuelling Devil Facial Tumour Disease

This study compares the metabolic profiles of two transmissible cancers in Tasmanian devils, finding DFT2 has higher glycolytic activity and less metabolic flexibility than DFT1.

Skeletal muscle mitochondria contain nuclear-encoded RNA species prior to and following adaptation to exercise training in rats

This study identifies nuclear-encoded RNAs in mitochondria of rat skeletal muscle, with some miRNAs showing altered abundance after exercise training.

Direction-aware functional class scoring enrichment analysis of Infinium DNA methylation data

The paper introduces a directional functional class scoring method for Infinium DNA methylation data, showing improved performance in detecting pathway methylation differences in various biological contexts.

Guidelines for reliable and reproducible functional enrichment analysis

This paper identifies common methodological flaws in functional enrichment analysis and highlights the need for standardized practices to improve reliability and reproducibility.

Gene name errors: lessons not learned

The paper examines gene name errors in supplementary files and finds they persist despite prior warnings, with new software identifying higher error rates.

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

This study shows valproic acid reduces hyperglycemia-induced activation of complement and coagulation genes in hepatocytes.

Accuracy, speed and error tolerance of short DNA sequence aligners

This study evaluates the accuracy, speed, and error tolerance of six DNA sequence aligners using simulated reads, finding BWA aln most accurate overall and STAR fastest.