Full-text indexes provide fast substring search over large text collections. A serious problem
of these indexes has traditionally been their space consumption. A recent trend is to develop …

Innovations in Next-Generation Sequencing are enabling generation of DNA sequence data
at ever faster rates and at very low cost. For example, the Illumina NovaSeq 6000 sequencer …

Cells are the fundamental units of biological systems and exhibit unique development
trajectories and molecular features. Our exploration of how the genomes orchestrate the …

Motivation The growing use of next-generation sequencing and enlarged sequencing
throughput require efficient short-read alignment, where seeding is one of the major …

Motivation: A new protocol for sequencing the messenger RNA in a cell, known as RNA-
Seq, generates millions of short sequence fragments in a single run. These fragments, or …

Bowtie is an ultrafast, memory-efficient alignment program for aligning short DNA sequence
reads to large genomes. For the human genome, Burrows-Wheeler indexing allows Bowtie …

The suffix tree is one of the most important data structures in string processing and
comparative genomics. However, the space consumption of the suffix tree is a bottleneck in …

The proliferation of online text, such as on the World Wide Web and in databases, motivates
the need for space-efficient index methods that support fast search. Consider a text T of n …

Recent years have witnessed a dramatic increase of interest in sophisticated string matching
problems, especially in information retrieval and computational biology. This book presents …

Low-cost DNA sequencing technologies have expanded the role for direct nucleic acid
sequencing in the analysis of genomes, transcriptomes, and the metagenomes of whole …