Selected papers from WABI 2015

Edited by Mihai Pop and Helene Touzet

This collection of articles has not been sponsored and articles have undergone the journal’s standard peer-review process. The Guest Editors declare no competing interests.

View all collections published in Algorithms for Molecular Biology.

Analysis of gene copy number changes in tumor phylogenetics

Evolution of cancer cells is characterized by large scale and rapid changes in the chromosomal landscape. The fluorescence in situ hybridization (FISH) technique provides a way to measure the copy numbers of ...

Authors: Jun Zhou, Yu Lin, Vaibhav Rajan, William Hoskins, Bing Feng and Jijun Tang

Citation: Algorithms for Molecular Biology 2016 11:26

Content type: Research Published on: 22 September 2016
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An improved Four-Russians method and sparsified Four-Russians algorithm for RNA folding

The basic RNA secondary structure prediction problem or single sequence folding problem (SSF) was solved 35 years ago by a now well-known

Authors: Yelena Frid and Dan Gusfield

Citation: Algorithms for Molecular Biology 2016 11:22

Content type: Research Published on: 5 August 2016
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Towards sub-quadratic time and space complexity solutions for the dated tree reconciliation problem

Recent coevolutionary analysis has considered tree topology as a means to reduce the asymptotic complexity associated with inferring the complex coevolutionary interrelationships that arise between phylogeneti...

Authors: Benjamin Drinkwater and Michael A. Charleston

Citation: Algorithms for Molecular Biology 2016 11:15

Content type: Research Published on: 21 May 2016
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BicNET: Flexible module discovery in large-scale biological networks using biclustering

Despite the recognized importance of module discovery in biological networks to enhance our understanding of complex biological systems, existing methods generally suffer from two major drawbacks. First, there...

Authors: Rui Henriques and Sara C. Madeira

Citation: Algorithms for Molecular Biology 2016 11:14

Content type: Research Published on: 20 May 2016
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Models and algorithms for genome rearrangement with positional constraints

Traditionally, the merit of a rearrangement scenario between two gene orders has been measured based on a parsimony criteria alone; two scenarios with the same number of rearrangements are considered equally g...

Authors: Krister M. Swenson, Pijus Simonaitis and Mathieu Blanchette

Citation: Algorithms for Molecular Biology 2016 11:13

Content type: Research Published on: 17 May 2016
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Circular sequence comparison: algorithms and applications

Sequence comparison is a fundamental step in many important tasks in bioinformatics; from phylogenetic reconstruction to the reconstruction of genomes. Traditional algorithms for measuring approximation in seq...

Authors: Roberto Grossi, Costas S. Iliopoulos, Robert Mercas, Nadia Pisanti, Solon P. Pissis, Ahmad Retha and Fatima Vayani

Citation: Algorithms for Molecular Biology 2016 11:12

Content type: Research Published on: 10 May 2016

The Erratum to this article has been published in Algorithms for Molecular Biology 2016 11:21
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Jabba: hybrid error correction for long sequencing reads

Third generation sequencing platforms produce longer reads with higher error rates than second generation technologies. While the improved read length can provide useful information for downstream analysis, un...

Authors: Giles Miclotte, Mahdi Heydari, Piet Demeester, Stephane Rombauts, Yves Van de Peer, Pieter Audenaert and Jan Fostier

Citation: Algorithms for Molecular Biology 2016 11:10

Content type: Software article Published on: 3 May 2016
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Sparse RNA folding revisited: space-efficient minimum free energy structure prediction

RNA secondary structure prediction by energy minimization is the central computational tool for the analysis of structural non-coding RNAs and their interactions. Sparsification has been successfully applied to i...

Authors: Sebastian Will and Hosna Jabbari

Citation: Algorithms for Molecular Biology 2016 11:7

Content type: Research article Published on: 23 April 2016
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MissMax: alignment-free sequence comparison with mismatches through filtering and heuristics

Measuring sequence similarity is central for many problems in bioinformatics. In several contexts alignment-free techniques based on exact occurrences of substrings are faster, but also less accurate, than ali...

Authors: Cinzia Pizzi

Citation: Algorithms for Molecular Biology 2016 11:6

Content type: Research Published on: 21 April 2016
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The link between orthology relations and gene trees: a correction perspective

While tree-oriented methods for inferring orthology and paralogy relations between genes are based on reconciling a gene tree with a species tree, many tree-free methods are also available (usually based on se...

Authors: Manuel Lafond, Riccardo Dondi and Nadia El-Mabrouk

Citation: Algorithms for Molecular Biology 2016 11:4

Content type: Research Published on: 16 April 2016
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Bloom Filter Trie: an alignment-free and reference-free data structure for pan-genome storage

High throughput sequencing technologies have become fast and cheap in the past years. As a result, large-scale projects started to sequence tens to several thousands of genomes per species, producing a high nu...

Authors: Guillaume Holley, Roland Wittler and Jens Stoye

Citation: Algorithms for Molecular Biology 2016 11:3

Content type: Research Published on: 14 April 2016
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