Hardware accelerators are becoming increasingly commonplace in delivering high
performance computing solutions at a fraction of the cost of conventional supercomputers …

To tackle the exponentially increasing throughput of Next-Generation Sequencing (NGS),
most of the existing short-read aligners can be configured to favor speed in trade of accuracy …

The recent advent of high-throughput sequencing machines producing big amounts of short
reads has boosted the interest in efficient string searching techniques. As of today, many …

General Purpose Graphic Processing Units (GPGPUs) constitute an inexpensive resource
for computing-intensive applications that could exploit an intrinsic fine-grain parallelism. This …

New and emerging applications can change the mix of operations commonly used within
computer architectures. It is sometimes surprising when instruction-set architecture (ISA) …

Spurred by a widening gap between hardware accelerators and traditional processors,
numerous bioinformatics applications have harnessed the computing power of GPUs and …

Automated software diversity promises to reduce an attacker's ability to reuse exploits across
application instances. However, many questions remain regarding the efficacy of and …

One embodiment of the present invention sets forth a method for aligning a plurality of sets
of base pairs with a reference genome. The method includes the steps of generat ing a …

The FM-index is a data structure which is seeing more and more pervasive use, in particular
in the field of high-throughput bioinformatics. Algorithms based on it show a pseudo-random …

This thesis studies problems related to compressed full-text indexes. A fulltext index is a data
structure for indexing textual (sequence) data, so that the occurrences of any query string in …