Mark F. Richardson

Is developmental plasticity triggered by DNA methylation changes in the invasive cane toad (Rhinella marina)?

The paper investigates whether DNA methylation changes mediate developmental plasticity in cane toad tadpoles exposed to cannibal or alarm cues, finding distinct methylation patterns for each cue type.

Brain transcriptome analysis reveals gene expression differences associated with dispersal behaviour between range-front and range-core populations of invasive cane toads in Australia

The paper compares brain transcriptomes of invasive cane toads from different populations to identify gene expression differences linked to dispersal behaviour during range expansion.

Inherent population structure determines the importance of filtering parameters for reduced representation sequencing analyses

The paper shows that filtering parameter choices in reduced representation sequencing analyses impact population structure detection, depending on the inherent genetic differentiation of the dataset.

A field guide for the compositional analysis of any-omics data

This paper provides a guide for applying compositional data analysis to NGS count data, emphasizing log-ratio transformations and addressing limitations of conventional normalization methods.

Differential expression analysis of log-ratio transformed counts: benchmarking methods for RNA-Seq data

The paper benchmarks ALDEx2, a log-ratio transformation method, against conventional RNA-Seq differential expression tools, showing it has high precision and comparable performance on real data.

Understanding sequencing data as compositions: anoutlook and review

This paper reviews compositional data analysis principles and discusses their application to sequencing data, highlighting challenges and future directions.

propr: An R-package for Identifying Proportionally Abundant Features Using Compositional Data Analysis

The paper introduces an R package for analyzing compositional data by implementing two proportionality measures and discussing their application to genomic data.

Best Practice Data Life Cycle Approaches for the Life Sciences

The paper provides best practice data life cycle approaches for life sciences researchers focusing on omics datasets and computational data analysis.