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  1. Content type: Software article

    Full Bayesian inference for detecting copy number variants (CNV) from whole-genome sequencing (WGS) data is still largely infeasible due to computational demands. A recently introduced approach to perform Forw...

    Authors: John Wiedenhoeft, Alex Cagan, Rimma Kozhemyakina, Rimma Gulevich and Alexander Schliep

    Citation: Algorithms for Molecular Biology 2019 14:20

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  2. Content type: Research

    We introduce a new dissimilarity measure between a pair of “clonal trees”, each representing the progression and mutational heterogeneity of a tumor sample, constructed by the use of single cell or bulk high t...

    Authors: Nikolai Karpov, Salem Malikic, Md. Khaledur Rahman and S. Cenk Sahinalp

    Citation: Algorithms for Molecular Biology 2019 14:17

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  3. Content type: Research

    The area of genome rearrangements has given rise to a number of interesting biological, mathematical and algorithmic problems. Among these, one of the most intractable ones has been that of finding the median ...

    Authors: Leonid Chindelevitch, Sean La and Joao Meidanis

    Citation: Algorithms for Molecular Biology 2019 14:16

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  4. Content type: Research

    High-throughput sequencing technologies have led to explosive growth of genomic databases; one of which will soon reach hundreds of terabytes. For many applications we want to build and store indexes of these ...

    Authors: Christina Boucher, Travis Gagie, Alan Kuhnle, Ben Langmead, Giovanni Manzini and Taher Mun

    Citation: Algorithms for Molecular Biology 2019 14:13

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  5. Content type: Research

    We study the problem of identifying differentially mutated subnetworks of a large gene–gene interaction network, that is, subnetworks that display a significant difference in mutation frequency in two sets of ...

    Authors: Morteza Chalabi Hajkarim, Eli Upfal and Fabio Vandin

    Citation: Algorithms for Molecular Biology 2019 14:10

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  6. Content type: Research

    With long reads getting even longer and cheaper, large scale sequencing projects can be accomplished without short reads at an affordable cost. Due to the high error rates and less mature tools, de novo assemb...

    Authors: Riku Walve, Pasi Rastas and Leena Salmela

    Citation: Algorithms for Molecular Biology 2019 14:8

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  7. Content type: Research

    Sequencing technologies produce larger and larger collections of biosequences that have to be stored in compressed indices supporting fast search operations. Many compressed indices are based on the Burrows–Wh...

    Authors: Lavinia Egidi, Felipe A. Louza, Giovanni Manzini and Guilherme P. Telles

    Citation: Algorithms for Molecular Biology 2019 14:6

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  8. Content type: Research

    Network connectivity problems are abundant in computational biology research, where graphs are used to represent a range of phenomena: from physical interactions between molecules to more abstract relationship...

    Authors: Jimmy Wu, Alex Khodaverdian, Benjamin Weitz and Nir Yosef

    Citation: Algorithms for Molecular Biology 2019 14:5

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  9. Content type: Research

    Sequencing technologies keep on turning cheaper and faster, thus putting a growing pressure for data structures designed to efficiently store raw data, and possibly perform analysis therein. In this view, ther...

    Authors: Nicola Prezza, Nadia Pisanti, Marinella Sciortino and Giovanna Rosone

    Citation: Algorithms for Molecular Biology 2019 14:3

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  10. Content type: Research

    Absolute fast converging (AFC) phylogeny estimation methods are ones that have been proven to recover the true tree with high probability given sequences whose lengths are polynomial in the number of number of...

    Authors: Qiuyi Zhang, Satish Rao and Tandy Warnow

    Citation: Algorithms for Molecular Biology 2019 14:2

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  11. Content type: Research

    A key factor in computational drug design is the consistency and reliability with which intermolecular interactions between a wide variety of molecules can be described. Here we present a procedure to efficien...

    Authors: Martin S. Engler, Bertrand Caron, Lourens Veen, Daan P. Geerke, Alan E. Mark and Gunnar W. Klau

    Citation: Algorithms for Molecular Biology 2019 14:1

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  12. 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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  13. 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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  14. 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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  15. 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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  16. 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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  17. 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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  18. 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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  19. 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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  20. 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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  21. 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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  22. 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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  23. 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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  24. 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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  25. 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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  26. 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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  27. 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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  28. 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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  29. 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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  30. 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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  31. 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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  32. 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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  33. 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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  34. 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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  35. 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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