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Research
The history of gene families—which are equivalent to event-labeled gene trees—can be reconstructed from empirically estimated evolutionary event-relations containing pairs of orthologous, paralogous or xenologous...
Algorithms for Molecular Biology 2017 12:23
Published on: 29 August 2017
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...
Algorithms for Molecular Biology 2017 12:22
Published on: 23 August 2017
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...
Algorithms for Molecular Biology 2017 12:21
Published on: 18 August 2017
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 ...
Algorithms for Molecular Biology 2017 12:20
Published on: 15 August 2017
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...
Algorithms for Molecular Biology 2017 12:19
Published on: 20 July 2017
Research
We present a generalization of the positional Burrows–Wheeler transform, or PBWT, to genome graphs, which we call the gPBWT. A genome graph is a collapsed representation of a set of genomes described as a grap...
Algorithms for Molecular Biology 2017 12:18
Published on: 11 July 2017
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...
Algorithms for Molecular Biology 2017 12:17
Published on: 13 June 2017
Research
Combinatorial works on genome rearrangements have so far ignored the influence of intergene sizes, i.e. the number of nucleotides between consecutive genes, although it was recently shown decisive for the accu...
Algorithms for Molecular Biology 2017 12:16
Published on: 5 June 2017
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...
Algorithms for Molecular Biology 2017 12:15
Published on: 30 May 2017
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 ...
Algorithms for Molecular Biology 2017 12:14
Published on: 26 May 2017
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...
Algorithms for Molecular Biology 2017 12:13
Published on: 16 May 2017
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 ...
Algorithms for Molecular Biology 2017 12:12
Published on: 11 May 2017
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...
Algorithms for Molecular Biology 2017 12:11
Published on: 19 April 2017
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...
Algorithms for Molecular Biology 2017 12:10
Published on: 31 March 2017
Research
Algorithms for Molecular Biology 2017 12:9
Published on: 31 March 2017
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...
Algorithms for Molecular Biology 2017 12:8
Published on: 20 March 2017
Research
Semi-labeled trees generalize ordinary phylogenetic trees, allowing internal nodes to be labeled by higher-order taxa. Taxonomies are examples of semi-labeled trees. Suppose we are given collection
Algorithms for Molecular Biology 2017 12:7
Published on: 16 March 2017
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...
Algorithms for Molecular Biology 2017 12:6
Published on: 14 March 2017
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...
Algorithms for Molecular Biology 2017 12:5
Published on: 14 March 2017
Research
Given a gene family, the relations between genes (orthology/paralogy), are represented by a relation graph, where edges connect pairs of orthologous genes and “missing” edges represent paralogs. While a gene t...
Algorithms for Molecular Biology 2017 12:4
Published on: 11 March 2017
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...
Algorithms for Molecular Biology 2017 12:3
Published on: 9 March 2017
Research
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...
Algorithms for Molecular Biology 2017 12:2
Published on: 22 February 2017
Research
Spaced seeds, also named gapped q-grams, gapped k-mers, spaced q-grams, have been proven to be more sensitive than contiguous seeds (contiguous q-grams, contiguous k-mers) in nucleic a...
Algorithms for Molecular Biology 2017 12:1
Published on: 14 February 2017
Erratum
Algorithms for Molecular Biology 2016 11:28
Published on: 28 November 2016
The original article was published in Algorithms for Molecular Biology 2016 11:20
Software article
Protein structure comparison play important role in in silico functional prediction of a new protein. It is also used for understanding the evolutionary relationships among proteins. A variety of methods have ...
Algorithms for Molecular Biology 2016 11:27
Published on: 29 September 2016
