Guest Editors:

Lenny Heath
Héctor Corrada Bravo
Michael Mahoney
Michael Schatz

Special Issue Papers

Scanning the Issue: Bioinformatics of DNA

By L. S. Heath, H. C. Bravo, M. Caccamo, and M. Schatz

Building and Improving Reference Genome Assemblies

By K. M. Steinberg, V. A. Schneider, C. Alkan, M. J. Montague, W. C. Warren, D. M. Church, and R. K. Wilson

This paper reviews the problems and algorithms of assembling a complete genome from millions of short DNA sequencing reads.

Short Read Mapping: An Algorithmic Tour

By S. Canzar and S. L. Salzberg

This paper discusses the challenge of mapping short DNA reads to an existing target genome, covering the approaches and the current tools for addressing this problem.

Reading the Underlying Information From Massive Metagenomic Sequencing Data

By X. Zhang, S. Liu, H. Cui, and T. Chen

This paper addresses the computational processing of metagenomic data, describing the typical pipeline of a variety of software tools for the task and the current state of the art.

De Novo Annotation of Transposable Elements: Tackling the Fat Genome Issue

By V. Jamilloux, J. Daron, F. Choulet, and H. Quesneville

This paper introduces a computational method for annotating an important class of repetitive sequences, called transposable elements, in the wheat genome.

A Novel Pathway Analysis Approach Based on the Unexplained Disregulation of Genes

By S. Ansari, C. Voichita, M. Donato, R. Tagett, and S. Draghici

This paper describes a new computational analysis method for gene expression data that utilizes all the data effectively for identifying the dynamics of biological pathways.

DANUBE: Data-Driven Meta-ANalysis Using UnBiased Empirical Distributions—Applied to Biological Pathway Analysis

By T. Nguyen, C. Mitrea, R. Tagett, and S. Draghici

This paper proposes DANUBE, a new unbiased method of statistical meta-analysis that is applied to combine the results of multiple experiments performed for the same biological condition.

Linking Statistical and Ecological Theory: Hubbell's Unified Neutral Theory of Biodiversity as a Hierarchical Dirichlet Process

By K. Harris, T. L. Parsons, U. Z. Ijaz, L. Lahti, I. Holmes, and C. Quince

This paper addresses the issue of a species occupying a specific ecological niche by introducing a new algorithmic model that overcomes shortcomings of the traditional neutral models.

Bridging Histology and Bioinformatics—Computational Analysis of Spatially Resolved Transcriptomics

By M. Mignardi, O. Ishaq, X. Qian, and C. Wählby

This paper reviews image processing techniques for measuring gene expression in different regions of tissue samples.

A Parallel Algorithm for N-Way Interval Set Intersection

By R. M. Layer and A. R. Quinlan

This paper proposes a parallel algorithm for computing the intersection of multiple sets of genomic sequences.

Manual for Using Homomorphic Encryption for Bioinformatics

By N. Dowlin, R. Gilad-Bachrach, K. Laine, K. Lauter, M. Naehrig, and J. Wernsing

This paper provides a new homomorphic encryption algorithm and associated software for bioinformatics to enhance the security and privacy associated with computing on human genomes.