Travis C. Glenn

The paper optimizes genome assembly and variant discovery for Dermacentor reticulatus ticks using Oxford Nanopore sequencing, identifying workflow parameters that yield high-quality assemblies and genetic insights.

The paper develops and validates a set of 100,000 RNA baits (CryptoCap_100k) to enrich Cryptosporidium DNA from clinical and environmental samples, improving read mapping, coverage, and variant analysis while reducing costs.

The paper evaluates 54 tick genome assemblies, identifies 34 high-quality ones, and recommends long-read sequencing and Hi-C scaffolding to improve tick genomic resources.

This study evaluates methods for inferring large-scale avian phylogenies, finding that fast tree search approaches balance computational efficiency and accuracy.

The paper examines local adaptation in five song sparrow subspecies in Alaska, finding evidence of positive selection in two genes and a novel phylogeny suggesting M. m. maxima colonized earliest.

The paper develops a method to detect and identify minority Cryptosporidium species in mixed infections using amplicon sequencing and DADA2, demonstrating sensitivity to low-abundance variants.

The paper develops a duplex PCR assay to determine the sex and mating status of Ixodes scapularis ticks using DNA sequence markers identified through whole-genome resequencing and restriction site-associated DNA sequencing.

This study identifies polycistronic mRNA expression in Cryptosporidium parvum using long-read RNA-seq and ATAC-seq, revealing a novel gene regulation mechanism in apicomplexan parasites.

The paper presents a chromosome-level genome assembly and annotation of Cryptosporidium meleagridis, revealing 3,923 protein-coding genes and high completeness.

This paper compares three amplicon sequencing methods for SARS-CoV-2 variant detection in wastewater, finding ARTIC V4 most accurate for variant identification and abundance estimation.

The paper generates high-quality genome assemblies for Ixodes ricinus and identifies transposable elements as major drivers of genome evolution in ticks.

The paper compares phylogenomic methods using a well-resolved bird species tree, finding that ML concatenation performs best, while METAL shows promise with large datasets.

This study evaluates MDA's effectiveness for genome assembly with ONT sequencing, showing high-quality results from low DNA input and introducing a tool to mitigate concatemeric sequences.

The paper presents a gapless telomere-to-telomere genome assembly of Cryptosporidium parvum IOWA, annotated with reference gene IDs and RNA evidence.

The paper estimates intercontinental movement rates between Eurasian and North American waterbirds, identifying species at highest risk for avian influenza spread.

The paper develops Haplo-ST, an open-source tool for whole-genome MLST of Listeria monocytogenes, showing it can differentiate isolates from different environments with high sensitivity.

The paper presents a high-quality genome assembly of the song sparrow, Melospiza melodia, using Illumina sequencing and provides gene annotations and functional insights.

This paper presents a high-quality genome assembly of the saltwater crocodile and identifies genes under positive selection in crocodilians.

Adapterama II introduces a flexible and cost-effective method for amplicon sequencing on Illumina platforms using fusion primers and quadruple indexing.

The paper introduces a low-cost, highly multiplexed RADseq library preparation method called 2RAD/3RAD, which improves efficiency and compatibility with sequencing platforms.

The paper introduces dual-indexing systems to reduce NGS start-up, buy-in, and sample preparation costs by enabling combinatorial indexing of Illumina libraries.

The paper develops TGBS, a targeted bisulfite sequencing method, to analyze methylation changes in p21 across human and rat cells, showing differential methylation and response to 5-Aza treatment.