Networks are one of the most common ways to represent biological systems as complex sets
of binary interactions or relations between different bioentities. In this article, we discuss the …

A central goal of systems biology is to elucidate the structural and functional architecture of
the cell. To this end, large and complex networks of molecular interactions are being rapidly …

In this paper, we propose BioHD, a novel genomic sequence searching platform based on
Hyper-Dimensional Computing (HDC) for hardware-friendly computation. BioHD transforms …

In this paper we survey methods for performing a comparative graph analysis and explain
the history, foundations and differences of such techniques of the last 50 years. While …

High-throughput experimental technologies are generating increasingly massive and
complex genomic data sets. The sheer enormity and heterogeneity of these data threaten to …

Sequence comparison and alignment has had an enormous impact on our understanding of
evolution, biology and disease. Comparison and alignment of biological networks will …

This handbook provides an up-to-date compendium of fundamental computer science
topics, techniques, and applications. Along with updating and revising many of the existing …

Motivation: High-throughput methods for detecting molecular interactions have produced
large sets of biological network data with much more yet to come. Analogous to sequence …

Motivation: Biological network alignment aims to identify similar regions between networks
of different species. Existing methods compute node similarities to rapidly identify from …

Currently, a huge amount of biological data can be naturally represented by graphs, eg,
protein interaction networks, gene regulatory networks, etc. The need for indexing large …