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  1. Research

    Algorithms for matching partially labelled sequence graphs

    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 ...

    William R. Taylor

    Algorithms for Molecular Biology 2017 12:24

    Published on: 25 September 2017

  2. Research

    Partially local three-way alignments and the sequence signatures of mitochondrial genome rearrangements

    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...

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

    Algorithms for Molecular Biology 2017 12:22

    Published on: 23 August 2017

  3. Research

    ASP-based method for the enumeration of attractors in non-deterministic synchronous and asynchronous multi-valued networks

    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 ...

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

    Algorithms for Molecular Biology 2017 12:20

    Published on: 15 August 2017

  4. Research

    Isometric gene tree reconciliation revisited

    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...

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

    Algorithms for Molecular Biology 2017 12:17

    Published on: 13 June 2017

  5. Research

    StreAM-\(T_g\): algorithms for analyzing coarse grained RNA dynamics based on Markov models of connectivity-graphs

    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...

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

    Algorithms for Molecular Biology 2017 12:15

    Published on: 30 May 2017

  6. Research

    The gene family-free median of three

    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 ...

    Daniel Doerr, Metin Balaban, Pedro Feijão and Cedric Chauve

    Algorithms for Molecular Biology 2017 12:14

    Published on: 26 May 2017

  7. Research

    Complexity and algorithms for copy-number evolution problems

    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...

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

    Algorithms for Molecular Biology 2017 12:13

    Published on: 16 May 2017

  8. Research

    Core column prediction for protein multiple sequence alignments

    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...

    Dan DeBlasio and John Kececioglu

    Algorithms for Molecular Biology 2017 12:11

    Published on: 19 April 2017

  9. Research

    Aligning coding sequences with frameshift extension penalties

    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...

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

    Algorithms for Molecular Biology 2017 12:10

    Published on: 31 March 2017

  10. Research

    Gerbil: a fast and memory-efficient k-mer counter with GPU-support

    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...

    Marius Erbert, Steffen Rechner and Matthias Müller-Hannemann

    Algorithms for Molecular Biology 2017 12:9

    Published on: 31 March 2017

  11. Software article

    The feasibility of genome-scale biological network inference using Graphics Processing Units

    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...

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

    Algorithms for Molecular Biology 2017 12:8

    Published on: 20 March 2017

  12. Research

    On the computational complexity of the maximum parsimony reconciliation problem in the duplication-loss-coalescence model

    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...

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

    Algorithms for Molecular Biology 2017 12:6

    Published on: 14 March 2017

  13. Research

    On avoided words, absent words, and their application to biological sequence analysis

    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...

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

    Algorithms for Molecular Biology 2017 12:5

    Published on: 14 March 2017

  14. Research

    Approximating the DCJ distance of balanced genomes in linear time

    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...

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

    Algorithms for Molecular Biology 2017 12:3

    Published on: 9 March 2017

  15. Research

    Playing hide and seek with repeats in local and global de novo transcriptome assembly of short RNA-seq reads

    The main challenge in de novo genome assembly of DNA-seq data is certainly to deal with repeats that are longer than the reads. In de novo transcriptome assembly of RNA-seq reads, on the other hand, this prob...

    Leandro Lima, Blerina Sinaimeri, Gustavo Sacomoto, Helene Lopez-Maestre, Camille Marchet, Vincent Miele, Marie-France Sagot and Vincent Lacroix

    Algorithms for Molecular Biology 2017 12:2

    Published on: 22 February 2017

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