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  1. Content type: Software article

    Motif analysis methods have long been central for studying biological function of nucleotide sequences. Functional genomics experiments extend their potential. They typically generate sequence lists ranked by ...

    Authors: Morten Muhlig Nielsen, Paula Tataru, Tobias Madsen, Asger Hobolth and Jakob Skou Pedersen

    Citation: Algorithms for Molecular Biology 2018 13:17

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  2. Content type: Research

    Superbubbles are distinctive subgraphs in direct graphs that play an important role in assembly algorithms for high-throughput sequencing (HTS) data. Their practical importance derives from the fact they are c...

    Authors: Fabian Gärtner, Lydia Müller and Peter F. Stadler

    Citation: Algorithms for Molecular Biology 2018 13:16

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  3. Content type: Research

    Genome sequences and genome annotation data have become available at ever increasing rates in response to the rapid progress in sequencing technologies. As a consequence the demand for methods supporting compa...

    Authors: Fabian Gärtner, Christian Höner zu Siederdissen, Lydia Müller and Peter F. Stadler

    Citation: Algorithms for Molecular Biology 2018 13:15

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  4. Content type: Research

    Liquid chromatography combined with tandem mass spectrometry is an important tool in proteomics for peptide identification. Liquid chromatography temporally separates the peptides in a sample. The peptides tha...

    Authors: Yves Frank, Tomas Hruz, Thomas Tschager and Valentin Venzin

    Citation: Algorithms for Molecular Biology 2018 13:14

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  5. Content type: Research

    One way to estimate the evolutionary distance between two given genomes is to determine the minimum number of large-scale mutations, or genome rearrangements, that are necessary to transform one into the other. I...

    Authors: Andre R. Oliveira, Guillaume Fertin, Ulisses Dias and Zanoni Dias

    Citation: Algorithms for Molecular Biology 2018 13:13

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  6. Content type: Research

    Most phylogenetic studies using molecular data treat gaps in multiple sequence alignments as missing data or even completely exclude alignment columns that contain gaps.

    Authors: Alexander Donath and Peter F. Stadler

    Citation: Algorithms for Molecular Biology 2018 13:12

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  7. Content type: Research

    The double cut and join (DCJ) model of genome rearrangement is well studied due to its mathematical simplicity and power to account for the many events that transform gene order. These studies have mostly been...

    Authors: Pijus Simonaitis and Krister M. Swenson

    Citation: Algorithms for Molecular Biology 2018 13:9

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  8. Content type: Research

    Patterns with wildcards in specified positions, namely spaced seeds, are increasingly used instead of k-mers in many bioinformatics applications that require indexing, querying and rapid similarity search, as the...

    Authors: Samuele Girotto, Matteo Comin and Cinzia Pizzi

    Citation: Algorithms for Molecular Biology 2018 13:8

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  9. Content type: Research

    An important task in a metagenomic analysis is the assignment of taxonomic labels to sequences in a sample. Most widely used methods for taxonomy assignment compare a sequence in the sample to a database of kn...

    Authors: Nidhi Shah, Stephen F. Altschul and Mihai Pop

    Citation: Algorithms for Molecular Biology 2018 13:7

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  10. Content type: Research

    For a combination of reasons (including data generation protocols, approaches to taxon and gene sampling, and gene birth and loss), estimated gene trees are often incomplete, meaning that they do not contain a...

    Authors: Sarah Christensen, Erin K. Molloy, Pranjal Vachaspati and Tandy Warnow

    Citation: Algorithms for Molecular Biology 2018 13:6

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  11. Content type: Research

    Microbial typing methods are commonly used to study the relatedness of bacterial strains. Sequence-based typing methods are a gold standard for epidemiological surveillance due to the inherent portability of s...

    Authors: João A. Carriço, Maxime Crochemore, Alexandre P. Francisco, Solon P. Pissis, Bruno Ribeiro-Gonçalves and Cátia Vaz

    Citation: Algorithms for Molecular Biology 2018 13:4

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  12. Content type: Research

    A profile-comparison method with position-specific scoring matrix (PSSM) is among the most accurate alignment methods. Currently, cosine similarity and correlation coefficients are used as scoring functions of...

    Authors: Kazunori D. Yamada

    Citation: Algorithms for Molecular Biology 2018 13:5

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  13. Content type: Research

    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

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  14. Content type: Research

    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

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  15. Content type: Research

    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

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  16. Content type: Research

    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

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  17. Content type: Research

    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

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  18. Content type: Research

    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

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  19. Content type: 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...

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

    Citation: Algorithms for Molecular Biology 2017 12:22

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  20. Content type: 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...

    Authors: Christopher Schröder and Sven Rahmann

    Citation: Algorithms for Molecular Biology 2017 12:21

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  21. Content type: 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 ...

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

    Citation: Algorithms for Molecular Biology 2017 12:20

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  22. Content type: 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...

    Authors: Louis Fippo Fitime, Olivier Roux, Carito Guziolowski and Loïc Paulevé

    Citation: Algorithms for Molecular Biology 2017 12:19

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  23. Content type: 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...

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

    Citation: Algorithms for Molecular Biology 2017 12:17

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  24. Content type: 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...

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

    Citation: Algorithms for Molecular Biology 2017 12:15

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  25. Content type: 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 ...

    Authors: Daniel Doerr, Metin Balaban, Pedro Feijão and Cedric Chauve

    Citation: Algorithms for Molecular Biology 2017 12:14

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  26. Content type: 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...

    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

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  27. Content type: 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 ...

    Authors: Thomas Tschager, Simon Rösch, Ludovic Gillet and Peter Widmayer

    Citation: Algorithms for Molecular Biology 2017 12:12

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  28. Content type: 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...

    Authors: Dan DeBlasio and John Kececioglu

    Citation: Algorithms for Molecular Biology 2017 12:11

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  29. Content type: 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...

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

    Citation: Algorithms for Molecular Biology 2017 12:10

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  30. Content type: Research

    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

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  31. Content type: 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...

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

    Citation: Algorithms for Molecular Biology 2017 12:8

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  32. Content type: 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...

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

    Citation: Algorithms for Molecular Biology 2017 12:6

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  33. Content type: 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...

    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

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  34. Content type: 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...

    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

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  35. Content type: 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...

    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

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  36. Content type: 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 ...

    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

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  37. Content type: Research

    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

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  38. Content type: Research

    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

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  39. Content type: Research

    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

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