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Selected papers from WABI 2016

Edited by Martin C. Frith and Christian N.S. Pedersen 

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.

  1. Content type: Research

    Mixtures of beta distributions are a flexible tool for modeling data with values on the unit interval, such as methylation levels. However, maximum likelihood parameter estimation with beta distributions suffe...

    Authors: Christopher Schröder and Sven Rahmann

    Citation: Algorithms for Molecular Biology 2017 12:21

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  2. Content type: Research

    Isometric gene tree reconciliation is a gene tree/species tree reconciliation problem where both the gene tree and the species tree include branch lengths, and these branch lengths must be respected by the rec...

    Authors: Broňa Brejová, Askar Gafurov, Dana Pardubská, Michal Sabo and Tomáš Vinař

    Citation: Algorithms for Molecular Biology 2017 12:17

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  3. Content type: Research

    In this work, we present a new coarse grained representation of RNA dynamics. It is based on adjacency matrices and their interactions patterns obtained from molecular dynamics simulations. RNA molecules are w...

    Authors: Sven Jager, Benjamin Schiller, Philipp Babel, Malte Blumenroth, Thorsten Strufe and Kay Hamacher

    Citation: Algorithms for Molecular Biology 2017 12:15

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  4. Content type: Research

    The gene family-free framework for comparative genomics aims at providing methods for gene order analysis that do not require prior gene family assignment, but work directly on a sequence similarity graph. We ...

    Authors: Daniel Doerr, Metin Balaban, Pedro Feijão and Cedric Chauve

    Citation: Algorithms for Molecular Biology 2017 12:14

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  5. Content type: Research

    Cancer is an evolutionary process characterized by the accumulation of somatic mutations in a population of cells that form a tumor. One frequent type of mutations is copy number aberrations, which alter the n...

    Authors: Mohammed El-Kebir, Benjamin J. Raphael, Ron Shamir, Roded Sharan, Simone Zaccaria, Meirav Zehavi and Ron Zeira

    Citation: Algorithms for Molecular Biology 2017 12:13

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  6. Content type: Research

    Given a peptide as a string of amino acids, the masses of all its prefixes and suffixes can be found by a trivial linear scan through the amino acid masses. The inverse problem is the ideal ...

    Authors: Thomas Tschager, Simon Rösch, Ludovic Gillet and Peter Widmayer

    Citation: Algorithms for Molecular Biology 2017 12:12

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  7. Content type: Research

    In a computed protein multiple sequence alignment, the coreness of a column is the fraction of its substitutions that are in so-called core columns of the gold-standard reference alignment of its proteins. In ben...

    Authors: Dan DeBlasio and John Kececioglu

    Citation: Algorithms for Molecular Biology 2017 12:11

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  8. Content type: Research

    A basic task in bioinformatics is the counting of k-mers in genome sequences. Existing k-mer counting tools are most often optimized for small k < 32 and suffer from excessive memory resource consumption or degra...

    Authors: Marius Erbert, Steffen Rechner and Matthias Müller-Hannemann

    Citation: Algorithms for Molecular Biology 2017 12:9

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  9. Content type: Research

    Phylogenetic tree reconciliation is a widely-used method for inferring the evolutionary histories of genes and species. In the duplication-loss-coalescence (DLC) model, we seek a reconciliation that explains t...

    Authors: Daniel Bork, Ricson Cheng, Jincheng Wang, Jean Sung and Ran Libeskind-Hadas

    Citation: Algorithms for Molecular Biology 2017 12:6

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  10. Content type: Research

    The deviation of the observed frequency of a word w from its expected frequency in a given sequence x is used to determine whether or not the word is avoided. This concept is particularly useful in DNA linguisti...

    Authors: Yannis Almirantis, Panagiotis Charalampopoulos, Jia Gao, Costas S. Iliopoulos, Manal Mohamed, Solon P. Pissis and Dimitris Polychronopoulos

    Citation: Algorithms for Molecular Biology 2017 12:5

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  11. Content type: Research

    Rearrangements are large-scale mutations in genomes, responsible for complex changes and structural variations. Most rearrangements that modify the organization of a genome can be represented by the double cut...

    Authors: Diego P. Rubert, Pedro Feijão, Marília Dias Vieira Braga, Jens Stoye and Fábio Henrique Viduani Martinez

    Citation: Algorithms for Molecular Biology 2017 12:3

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