BackgroundObtaining de novo chromosome-level genome assemblies greatly enhances conservation and evolutionary biology studies. For many research teams, long-read sequencing technologies (that produce highly contiguous assemblies) remain unaffordable or unpractical. For the groups that display high synteny conservation, these limitations can be overcome...

We have developed the regional principal components (rPCs) method, a novel approach for summarizing gene-level methylation. rPCs address the challenge of deciphering complex epigenetic mechanisms in diseases like Alzheimer's disease (AD). In contrast to averaging, rPCs leverage principal components analysis to capture complex methylation patterns across...

Mid-density targeted genotyping-by-sequencing (GBS) combines trait-specific markers with thousands of genomic markers at an attractive price for linkage mapping and genomic selection. A 2.5K targeted GBS assay for potato was developed using the DArTagTM technology and later expanded to 4K targets. Genomic markers were selected from the potato InfiniumTM...

Despite recent advances in sequencing technologies, genome-scale datasets continue to have missing bases and genomic segments. Such incomplete datasets can undermine downstream analyses, such as disease risk prediction and association studies. Consequently, the imputation of missing information is a common pre-processing step for which many methodologies...

We show much-improved accuracy of inference of GRN (gene regulatory network) structure resulting from the use of an epigenomic prior network. We also find that DNAme data are very effective for inferring the epigenomic prior network, recapitulating known epigenomic network structure found previously from chromatin accessibility data, and in some cases...

The identification of sites of DNA replication initiation in mammalian cells has been challenging. Here, we present unbiased detection of replication initiation events in human cells using BrdU incorporation and single-molecule nanopore sequencing. Increases in BrdU incorporation allow us to measure DNA replication dynamics, including identification...