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  1. Reconstructing the genome of a species from short fragments is one of the oldest bioinformatics problems. Metagenomic assembly is a variant of the problem asking to reconstruct the circular genomes of all bact...

    Authors: Nidia Obscura Acosta, Veli Mäkinen and Alexandru I. Tomescu
    Citation: Algorithms for Molecular Biology 2018 13:3
  2. In the absence of horizontal gene transfer it is possible to reconstruct the history of gene families from empirically determined orthology relations, which are equivalent to event-labeled gene trees. Knowledge o...

    Authors: Nikolai Nøjgaard, Manuela Geiß, Daniel Merkle, Peter F. Stadler, Nicolas Wieseke and Marc Hellmuth
    Citation: Algorithms for Molecular Biology 2018 13:2
  3. 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
  4. 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
  5. 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
  6. 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
  7. 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
  8. 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
  9. 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
  10. 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
  11. 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
  12. 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
  13. 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
  14. 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
  15. 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
  16. 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
  17. 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
  18. 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
  19. 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
  20. 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
  21. 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
  22. 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
  23. 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...

    Authors: Leandro Lima, Blerina Sinaimeri, Gustavo Sacomoto, Helene Lopez-Maestre, Camille Marchet, Vincent Miele, Marie-France Sagot and Vincent Lacroix
    Citation: Algorithms for Molecular Biology 2017 12:2
  24. 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 ...

    Authors: S. Srivastava, S. B. Lal, D. C. Mishra, U. B. Angadi, K. K. Chaturvedi, S. N. Rai and A. Rai
    Citation: Algorithms for Molecular Biology 2016 11:27
  25. 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
  26. What an organism needs at least from its environment to produce a set of metabolites, e.g. target(s) of interest and/or biomass, has been called a minimal precursor set. Early approaches to enumerate all minimal ...

    Authors: Ricardo Andrade, Martin Wannagat, Cecilia C. Klein, Vicente Acuña, Alberto Marchetti-Spaccamela, Paulo V. Milreu, Leen Stougie and Marie-France Sagot
    Citation: Algorithms for Molecular Biology 2016 11:25
  27. Pyrosequencing Allele Quantification (AQ) is a cost-effective DNA sequencing method that can be used for detecting somatic mutations in formalin-fixed paraffin-embedded (FFPE) samples. The method displays a lo...

    Authors: Jerome Ambroise, Jamal Badir, Louise Nienhaus, Annie Robert, Anne-France Dekairelle and Jean-Luc Gala
    Citation: Algorithms for Molecular Biology 2016 11:24
  28. Recently, Marcus et al. (Bioinformatics 30:3476–83, 2014) proposed to use a compressed de Bruijn graph to describe the relationship between the genomes of many individuals/strains of the same or closely related s...

    Authors: Timo Beller and Enno Ohlebusch
    Citation: Algorithms for Molecular Biology 2016 11:20

    The Erratum to this article has been published in Algorithms for Molecular Biology 2016 11:28

  29. Metagenomics enables the analysis of bacterial population composition and the study of emergent population features, such as shared metabolic pathways. Recently, we have shown that metagenomics datasets can be...

    Authors: Elizabeth T. Hobbs, Talmo Pereira, Patrick K. O’Neill and Ivan Erill
    Citation: Algorithms for Molecular Biology 2016 11:19
  30. Superpositioning is an important problem in structural biology. Determining an optimal superposition requires a one-to-one correspondence between the atoms of two proteins structures. However, in practice, som...

    Authors: Jianbo Lu, Guoliang Xu, Shihua Zhang and Benzhuo Lu
    Citation: Algorithms for Molecular Biology 2016 11:18
  31. Identification of splice sites is essential for annotation of genes. Though existing approaches have achieved an acceptable level of accuracy, still there is a need for further improvement. Besides, most of th...

    Authors: Prabina Kumar Meher, Tanmaya Kumar Sahu, A. R. Rao and S. D. Wahi
    Citation: Algorithms for Molecular Biology 2016 11:16
  32. 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

    The Erratum to this article has been published in Algorithms for Molecular Biology 2016 11:21

  33. The mutual exclusivity of somatic genome alterations (SGAs), such as somatic mutations and copy number alterations, is an important observation of tumors and is widely used to search for cancer signaling pathw...

    Authors: Songjian Lu, Gunasheil Mandava, Gaibo Yan and Xinghua Lu
    Citation: Algorithms for Molecular Biology 2016 11:11
  34. 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