Bioinformatics of DNA
Volume 105, Issue 3 | March 2017
Guest Editors:
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.
Point of View
Spent Nuclear Fuel is not the Problem
By Per F. Peterson
An Enduring Problem: Radioactive Waste From Nuclear Energy
By M. V. Ramana
