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  1. 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

  2. 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
  3. 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
  4. 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
  5. 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

  6. 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
  7. 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
  8. A large class of RNA secondary structure prediction programs uses an elaborate energy model grounded in extensive thermodynamic measurements and exact dynamic programming algorithms. External experimental evid...

    Authors: Ronny Lorenz, Ivo L. Hofacker and Peter F. Stadler
    Citation: Algorithms for Molecular Biology 2016 11:8
  9. Hash tables constitute a widely used data structure for indexing genomes that provides a list of genomic positions for each possible oligomer of a given size. The offset array in a hash table grows exponential...

    Authors: Thomas D. Wu
    Citation: Algorithms for Molecular Biology 2016 11:5
  10. In this paper we propose a method and discuss its computational implementation as an integrated tool for the analysis of viral genetic diversity on data generated by high-throughput sequencing. The main motiva...

    Authors: Jean P. Zukurov, Sieberth do Nascimento-Brito, Angela C. Volpini, Guilherme C. Oliveira, Luiz Mario R. Janini and Fernando Antoneli
    Citation: Algorithms for Molecular Biology 2016 11:2
  11. The accurate annotation of genes in newly sequenced genomes remains a challenge. Although sophisticated comparative pipelines are available, computationally derived gene models are often less than perfect. Thi...

    Authors: Henrike Indrischek, Nicolas Wieseke, Peter F. Stadler and Sonja J. Prohaska
    Citation: Algorithms for Molecular Biology 2016 11:1
  12. Markov chains are a common framework for individual-based state and time discrete models in evolution. Though they played an important role in the development of basic population genetic theory, the analysis o...

    Authors: Katja Reichel, Valentin Bahier, Cédric Midoux, Nicolas Parisey, Jean-Pierre Masson and Solenn Stoeckel
    Citation: Algorithms for Molecular Biology 2015 10:31
  13. A number of alignment tools have been developed to align sequencing reads to the human reference genome. The scale of information from next-generation sequencing (NGS) experiments, however, is increasing rapid...

    Authors: Jongpill Choi, Kiejung Park, Seong Beom Cho and Myungguen Chung
    Citation: Algorithms for Molecular Biology 2015 10:30
  14. The rational, in silico prediction of gene-knockouts to turn organisms into efficient cell factories is an essential and computationally challenging task in metabolic engineering. Elementary flux mode analys...

    Authors: Govind Nair, Christian Jungreuthmayer, Michael Hanscho and Jürgen Zanghellini
    Citation: Algorithms for Molecular Biology 2015 10:29
  15. Lateral, or Horizontal, Gene Transfers are a type of asymmetric evolutionary events where genetic material is transferred from one species to another. In this paper we consider LGT networks, a general model of p...

    Authors: Gabriel Cardona, Joan Carles Pons and Francesc Rosselló
    Citation: Algorithms for Molecular Biology 2015 10:28
  16. Detecting protein complexes within protein–protein interaction (PPI) networks is a major step toward the analysis of biological processes and pathways. Identification and characterization of protein complexes ...

    Authors: Sanghamitra Bandyopadhyay, Sumanta Ray, Anirban Mukhopadhyay and Ujjwal Maulik
    Citation: Algorithms for Molecular Biology 2015 10:24
  17. Knowledge of interaction types in biological networks is important for understanding the functional organization of the cell. Currently information-based approaches are widely used for inferring gene regulator...

    Authors: Pegah Khosravi, Vahid H Gazestani, Leila Pirhaji, Brian Law, Mehdi Sadeghi, Bahram Goliaei and Gary D Bader
    Citation: Algorithms for Molecular Biology 2015 10:23

    The Erratum to this article has been published in Algorithms for Molecular Biology 2015 10:25

  18. Pareto optimization combines independent objectives by computing the Pareto front of its search space, defined as the set of all solutions for which no other candidate solution scores better under all objectives....

    Authors: Cédric Saule and Robert Giegerich
    Citation: Algorithms for Molecular Biology 2015 10:22
  19. The increase of protein–protein interaction (PPI) data of different species makes it possible to identify common subnetworks (conserved protein complexes) across species via local alignment of their PPI networ...

    Authors: Wei Peng, Jianxin Wang, Fangxiang Wu and Pan Yi
    Citation: Algorithms for Molecular Biology 2015 10:21
  20. The problem of enumerating bubbles with length constraints in directed graphs arises in transcriptomics where the question is to identify all alternative splicing events present in a sample of mRNAs sequenced ...

    Authors: Gustavo Sacomoto, Vincent Lacroix and Marie-France Sagot
    Citation: Algorithms for Molecular Biology 2015 10:20
  21. Analogous to genomic sequence alignment, biological network alignment identifies conserved regions between networks of different species. Then, function can be transferred from well- to poorly-annotated specie...

    Authors: Joseph Crawford, Yihan Sun and Tijana Milenković
    Citation: Algorithms for Molecular Biology 2015 10:19
  22. Resolution of repeats and scaffolding of shorter contigs are critical parts of genome assembly. Modern assemblers usually perform such steps by heuristics, often tailored to a particular technology for produci...

    Authors: Vladimír Boža, Broňa Brejová and Tomáš Vinař
    Citation: Algorithms for Molecular Biology 2015 10:18
  23. The core–periphery model for protein interaction (PPI) networks assumes that protein complexes in these networks consist of a dense core and a possibly sparse periphery that is adjacent to vertices in the core...

    Authors: Sharon Bruckner, Falk Hüffner and Christian Komusiewicz
    Citation: Algorithms for Molecular Biology 2015 10:16
  24. Autocatalytic sets are considered to be fundamental to the origin of life. Prior theoretical and computational work on the existence and properties of these sets has relied on a fast algorithm for detectingsel...

    Authors: Wim Hordijk, Joshua I Smith and Mike Steel
    Citation: Algorithms for Molecular Biology 2015 10:15
  25. Structural variation in genomes can be revealed by many (dis)similarity measures. Rearrangement operations, such as the so called double-cut-and-join (DCJ), are large-scale mutations that can create complex ch...

    Authors: Fábio V Martinez, Pedro Feijão, Marília DV Braga and Jens Stoye
    Citation: Algorithms for Molecular Biology 2015 10:13
  26. During evolution, global mutations may alter the order and the orientation of the genes in a genome. Such mutations are referred to as rearrangement events, or simply operations. In unichromosomal genomes, the...

    Authors: Gustavo Rodrigues Galvão, Orlando Lee and Zanoni Dias
    Citation: Algorithms for Molecular Biology 2015 10:12
  27. The body-bar Pebble Game (PG) algorithm is commonly used to calculate network rigidity properties in proteins and polymeric materials. To account for fluctuating interactions such as hydrogen bonds, an ensembl...

    Authors: Luis C González, Hui Wang, Dennis R Livesay and Donald J Jacobs
    Citation: Algorithms for Molecular Biology 2015 10:11
  28. Several sources of noise obfuscate the identification of single nucleotide variation (SNV) in next generation sequencing data. For instance, errors may be introduced during library construction and sequencing ...

    Authors: Steve Hoffmann, Peter F Stadler and Korbinian Strimmer
    Citation: Algorithms for Molecular Biology 2015 10:10
  29. This paper presents a constraint-based method for improving protein docking results. Efficient constraint propagation cuts over 95% of the search time for finding the configurations with the largest contact su...

    Authors: Ludwig Krippahl and Pedro Barahona
    Citation: Algorithms for Molecular Biology 2015 10:9
  30. Interaction sites on protein surfaces mediate virtually all biological activities, and their identification holds promise for disease treatment and drug design. Novel algorithmic approaches for the prediction ...

    Authors: Tristan T Aumentado-Armstrong, Bogdan Istrate and Robert A Murgita
    Citation: Algorithms for Molecular Biology 2015 10:7
  31. Alignment-free methods are increasingly used to calculate evolutionary distances between DNA and protein sequences as a basis of phylogeny reconstruction. Most of these methods, however, use heuristic distance...

    Authors: Burkhard Morgenstern, Bingyao Zhu, Sebastian Horwege and Chris André Leimeister
    Citation: Algorithms for Molecular Biology 2015 10:5
  32. The data volume generated by Next-Generation Sequencing (NGS) technologies is growing at a pace that is now challenging the storage and data processing capacities of modern computer systems. In this context an...

    Authors: Matteo Comin, Andrea Leoni and Michele Schimd
    Citation: Algorithms for Molecular Biology 2015 10:4