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  1. 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

    Content type: Research

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  2. 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

    Content type: Research

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  3. 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

    Content type: Research

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  4. 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

    Content type: Research

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  5. 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

    Content type: Research

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  6. 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

    Content type: Research

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  7. 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

    Content type: Research

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  8. 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

    Content type: Research

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  9. 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

    Content type: Software article

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  10. 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

    Content type: Research

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  11. 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

    Content type: Research

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  12. 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

    Content type: Research

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  13. 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

    Content type: Research

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  14. 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

    Content type: Software article

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  15. 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

    Content type: Research

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  16. 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

    Content type: Research

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  17. 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

    Content type: Research

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  18. 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

    Content type: Research

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

  19. 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

    Content type: Research

    Published on:

  20. 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

    Content type: Research

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  21. 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

    Content type: Research

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  22. 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

    Content type: Research

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

  23. 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

    Content type: Research

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  24. 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

    Content type: Software article

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  25. 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

    Content type: Research

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  26. 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

    Content type: Research

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  27. 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

    Content type: Software article

    Published on:

  28. 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

    Content type: Research

    Published on:

  29. 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

    Content type: Software article

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  30. 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

    Content type: Software article

    Published on:

  31. 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

    Content type: Research

    Published on:

  32. 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

    Content type: Research

    Published on: