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Algorithms for Molecular Biology

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  1. Content type: Research

    Various approaches to alignment-free sequence comparison are based on the length of exact or inexact word matches between pairs of input sequences. Haubold et al. (J Comput Biol 16:1487–1500, 2009) showed how the...

    Authors: Burkhard Morgenstern, Svenja Schöbel and Chris-André Leimeister

    Citation: Algorithms for Molecular Biology 2017 12:27

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  2. Content type: Research

    Suffix arrays, augmented by additional data structures, allow solving efficiently many string processing problems. The external memory construction of the generalized suffix array for a string collection is a ...

    Authors: Felipe A. Louza, Guilherme P. Telles, Steve Hoffmann and Cristina D. A. Ciferri

    Citation: Algorithms for Molecular Biology 2017 12:26

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  3. Content type: Research

    Multiple sequence alignment (MSA) plays a key role in biological sequence analyses, especially in phylogenetic tree construction. Extreme increase in next-generation sequencing results in shortage of efficient...

    Authors: Shixiang Wan and Quan Zou

    Citation: Algorithms for Molecular Biology 2017 12:25

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  4. Content type: Research

    In order to find correlated pairs of positions between proteins, which are useful in predicting interactions, it is necessary to concatenate two large multiple sequence alignments such that the sequences that ...

    Authors: William R. Taylor

    Citation: Algorithms for Molecular Biology 2017 12:24

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  5. Content type: Research

    Genomic DNA frequently undergoes rearrangement of the gene order that can be localized by comparing the two DNA sequences. In mitochondrial genomes different mechanisms are likely at work, at least some of whi...

    Authors: Marwa Al Arab, Matthias Bernt, Christian Höner zu Siederdissen, Kifah Tout and Peter F. Stadler

    Citation: Algorithms for Molecular Biology 2017 12:22

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  6. 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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  7. Content type: Research

    This paper addresses the problem of finding attractors in biological regulatory networks. We focus here on non-deterministic synchronous and asynchronous multi-valued networks, modeled using automata networks ...

    Authors: Emna Ben Abdallah, Maxime Folschette, Olivier Roux and Morgan Magnin

    Citation: Algorithms for Molecular Biology 2017 12:20

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  8. Content type: Research

    Numerous cellular differentiation processes can be captured using discrete qualitative models of biological regulatory networks. These models describe the temporal evolution of the state of the network subject...

    Authors: Louis Fippo Fitime, Olivier Roux, Carito Guziolowski and Loïc Paulevé

    Citation: Algorithms for Molecular Biology 2017 12:19

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  9. 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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  10. 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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  11. 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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  12. 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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  13. 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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  14. 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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  15. Content type: Research

    Frameshift translation is an important phenomenon that contributes to the appearance of novel coding DNA sequences (CDS) and functions in gene evolution, by allowing alternative amino acid translations of gene...

    Authors: Safa Jammali, Esaie Kuitche, Ayoub Rachati, François Bélanger, Michelle Scott and Aïda Ouangraoua

    Citation: Algorithms for Molecular Biology 2017 12:10

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  16. 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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  17. Content type: Software article

    Systems research spanning fields from biology to finance involves the identification of models to represent the underpinnings of complex systems. Formal approaches for data-driven identification of network int...

    Authors: Raghuram Thiagarajan, Amir Alavi, Jagdeep T. Podichetty, Jason N. Bazil and Daniel A. Beard

    Citation: Algorithms for Molecular Biology 2017 12:8

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  18. 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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  19. 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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