Comparative phylogenomic analyses based on a new reference-quality human Ascaris genome assembly reveals a pig/human interbred species complex with implications for Ascaris control worldwide.
Cognate site identification uncovers the impact of combinatorial dimerization in specifying new DNA binding sites for human bZIP transcription factors and comprehensive specificity landscapes predict the impact of SNPs on bZIP binding at previously unannotated regulatory loci.
Bulk whole genome sequencing data can be used to study the genetic variation present in pathogenic bacterial populations over the time-course of a single infection within a host.
Compiling public datasets into a single, centralised repository and linking directly to analytical software completely transforms the scale and scope of causal inference across the phenome.
Fully assembled DNA methylomes from phylogeographically diverse clinical Mycobacterium tuberculosis complex isolates reveals 'intercellular mosaic methylation' as a source of epigenetic diversity.
Associations can be mapped using k-mer frequencies in sequencing reads without prior sequencing of a reference genome enabling detection of associations to variants of multiple types and outside of the reference.
Variation in the rate of mixed infections by malaria parasites and the relatedness structure among infecting strains reveals diversity in local epidemiological processes.
The coalescent history of a population can be learned just from the present genomic diversity, without having detailed prior knowledge of the pattern of recombination or the forces driving coalescence.
Selection by national-level antibiotic consumption and vaccination trends drives atypical recombinations, frequently resulting in interspecies sequence exchange at many sites across a bacterial species’ chromosome.
