Matthew D. MacManes

Evolution and Diversification of the Aposematic Poison Frog, Oophaga pumilio, in Bocas del Toro

This study identifies genetic factors underlying color and pattern variation in Oophaga pumilio frogs from Bocas del Toro, finding key genes involved in different polymorphisms and evidence of selective sweeps.

Impacts of dietary fat on multi tissue gene expression in the desert-adapted cactus mouse

This study examines how dietary fat affects gene expression in five tissues and phenotypes of desert-adapted cactus mice, revealing impacts on immune function, circadian regulation, and mitochondrial function.

When the tap runs dry: The multi-tissue gene expression and physiological responses of water deprived Peromyscus eremicus

This study examines gene expression and physiological responses to water deprivation in the desert cactus mouse, identifying key pathways and adaptive mechanisms.

Signal, bias, and the role of transcriptome assembly quality in phylogenomic inference

The paper evaluates how transcriptome assembly quality affects phylogenomic analyses by comparing high- and low-quality assemblies in craniates.

Stress-mediated convergence of splicing landscapes in male and female Rock Doves

The paper examines how stress affects alternative splicing in the HPG axis of male and female rock doves, finding reduced sex differences in splicing after stress and a convergence in splicing patterns.

Higher quality de novo genome assemblies from degraded museum specimens: a linked-read approach to museomics

This study compares de novo genome assembly quality from degraded museum specimens using short-read and linked-read sequencing, finding linked-read provides higher quality assemblies.

The Oyster River Protocol: A Multi Assembler and Kmer Approach For de novo Transcriptome Assembly

The Oyster River Protocol improves de novo transcriptome assembly by combining multiple assemblers and kmer approaches, resulting in higher quality assemblies with better mapping rates and TransRate scores.

Sex-biased transcriptomic response of the reproductive axis to stress

The paper investigates how stress affects the HPG axis transcriptome in rock doves, finding females show more differential gene expression than males.

Transcriptomic analyses reveal tissue-specific selection on genes related to apoptotic processes in the subterranean rodent, Ctenomys sociabilis

The paper identifies genes under positive selection in Ctenomys sociabilis, particularly in spleen and liver, related to immune response and detoxification.

Widespread patterns of sexually dimorphic gene expression in an avian hypothalamic-pituitary-gonadal (HPG) axis

This study identifies sex-biased gene expression patterns in the HPG axis of rock doves, revealing tissue-specific differences in reproductive-related genes.

Severe acute dehydration in a desert rodent elicits a transcriptional response that effectively prevents kidney injury

The paper investigates the transcriptional response of desert rodents to acute dehydration and finds it prevents kidney injury.

Physiological and biochemical changes associated with experimental dehydration in the desert adapted cactus mouse, Peromyscus eremicus

The paper establishes baseline values for water intake and serum electrolytes in cactus mice under desert conditions and examines their response to acute dehydration.

Establishing evidenced-based best practice for the de novo assembly and evaluation of transcriptomes from non-model organisms

The paper establishes best practices for de novo transcriptome assembly in non-model organisms through benchmarking and open-source tools.

Optimizing error correction of RNAseq reads

This paper evaluates read correction tools for transcriptome-derived Illumina reads, showing that correction quality depends on sequencing depth, hardware, and experimental goals.