The recent boom in microfluidics and combinatorial indexing strategies, combined with low
sequencing costs, has empowered single-cell sequencing technology. Thousands—or even …

Cancer is generally characterized by acquired genomic aberrations in a broad spectrum of
types and sizes, ranging from single nucleotide variants to structural variants (SVs). At least …

Motivation: Cellular processes cause changes over time. Observing and measuring those
changes over time allows insights into the how and why of regulation. The experimental …

The human genome is diploid, which requires assigning heterozygous single nucleotide
polymorphisms (SNPs) to the two copies of the genome. The resulting haplotypes, lists of SNPs …

Small insertions and deletions (indels) and large structural variations (SVs) are major
contributors to human genetic diversity and disease. However, mutation rates and characteristics …

Virus populations can display high genetic diversity within individual hosts. The intra-host
collection of viral haplotypes, called viral quasispecies, is an important determinant of virulence…

A viral quasispecies, the ensemble of viral strains populating an infected person, can be
highly diverse. For optimal assessment of virulence, pathogenesis, and therapy selection, …

Motivation: Next-generation sequencing techniques have facilitated a large-scale analysis
of human genetic variation. Despite the advances in sequencing speed, the computational …

Motivation: The problem of finding remote homologues of a given protein sequence via
alignment methods is not fully solved. In fact, the task seems to become more difficult with more …

Circulating microRNAs (miRNA) are small noncoding RNA molecules that can be detected
in bodily fluids without the need for major invasive procedures on patients. miRNAs have …