Genome sequencing and analysis allow researchers to decode the functional information
hidden in DNA sequences as well as to study cell to cell variation within a cell population …

Increases in the cohort size in long-read sequencing projects necessitate more efficient
software for quality assessment and processing of sequencing data from Oxford Nanopore …

Metabolomics has evolved as a discipline from a discovery and functional genomics tool,
and is now a cornerstone in the era of big data-driven precision medicine. Sample …

Whole-genome sequencing using sequencing technologies such as Illumina enables the
accurate detection of small-scale variants but provides limited information about haplotypes …

In 2020, we identified cancer-specific microbial signals in The Cancer Genome Atlas
(TCGA). Multiple peer-reviewed papers independently verified or extended our findings …

Molecular sequence data from rapidly evolving organisms are often sampled at different
points in time. Sampling times can then be used for molecular clock calibration. The root-to …

Nanopore sequencing is now routinely used in a variety of genomics applications, including
whole genome assembly (Jain et al., 2018) and real-time infectious disease surveillance …

The lack of population-scale databases hampers research and diagnostics for medically
relevant tandem repeats and repeat expansions. We attempt to fill this gap using our …

Seed-chain-extend with k-mer seeds is a powerful heuristic technique for sequence
alignment used by modern sequence aligners. Although effective in practice for both runtime …

Motivation Efficiently aligning sequences is a fundamental problem in bioinformatics. Many
recent algorithms for computing alignments through Smith–Waterman–Gotoh dynamic …