We introduce Sailfish, a computational method for quantifying the abundance of previously
annotated RNA isoforms from RNA-seq data. Because Sailfish entirely avoids map** …

The Bloom filter provides fast approximate set membership while using little memory.
Engineers often use these filters to avoid slow operations such as disk or network accesses …

Algorithms are at the heart of every nontrivial computer application, and algorithmics is a
modern and active area of computer science. Every computer scientist and every …

Encrypted multi-map (EMM), as a special case of structured encryption, has attracted
extensive attention recently. However, most of EMM constructions reveal the real volumes of …

Metagenomic long-read sequencing is gaining popularity for various applications, including
pathogen detection and microbiome studies. To analyze the large data created in those …

Minimal perfect hash functions provide space-efficient and collision-free hashing on static
sets. Existing algorithms and implementations that build such functions have practical …

A hash function h, ie, a function from the set U of all keys to the range range [m]={0,..., m− 1}
is called a perfect hash function (PHF) for a subset S⊆ U of size n≤ m if h is 1-1 on S. The …

The primary goal of this article is to survey state-of-the-art indexing methods for approximate
dictionary searching. To improve understanding of the field, we introduce a taxonomy that …

Bloom and cuckoo filters provide fast approximate set membership while using little memory.
Engineers use them to avoid expensive disk and network accesses. The recently introduced …

Three-dimensional geometric data play fundamental roles in many computer vision
applications. However, their scale-dependent nature, ie the relative variation in the spatial …