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  1. The classical gene and species tree reconciliation, used to infer the history of gene gain and loss explaining the evolution of gene families, assumes an independent evolution for each family. While this assum...

    Authors: Mattéo Delabre, Nadia El-Mabrouk, Katharina T. Huber, Manuel Lafond, Vincent Moulton, Emmanuel Noutahi and Miguel Sautie Castellanos

    Citation: Algorithms for Molecular Biology 2020 15:12

    Content type: Research

    Published on:

  2. Most modern seed-and-extend NGS read mappers employ a seeding scheme that requires extracting t non-overlapping seeds in each read in order to find all valid mappings under an edit distance threshold of t. As t g...

    Authors: Hongyi Xin, Mingfu Shao and Carl Kingsford

    Citation: Algorithms for Molecular Biology 2020 15:10

    Content type: Research

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  3. Transcriptomic structural variants (TSVs)—large-scale transcriptome sequence change due to structural variation - are common in cancer. TSV detection from high-throughput sequencing data is a computationally c...

    Authors: Yutong Qiu, Cong Ma, Han Xie and Carl Kingsford

    Citation: Algorithms for Molecular Biology 2020 15:9

    Content type: Research

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  4. In the field of genome rearrangement algorithms, models accounting for gene duplication lead often to hard problems. For example, while computing the pairwise distance is tractable in most duplication-free mod...

    Authors: Aniket C. Mane, Manuel Lafond, Pedro C. Feijao and Cedric Chauve

    Citation: Algorithms for Molecular Biology 2020 15:8

    Content type: Research

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  5. Non-parametric and semi-parametric resampling procedures are widely used to perform support estimation in computational biology and bioinformatics. Among the most widely used methods in this class is the stand...

    Authors: Wei Wang, Jack Smith, Hussein A. Hejase and Kevin J. Liu

    Citation: Algorithms for Molecular Biology 2020 15:7

    Content type: Research

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  6. Many of the commonly used methods for orthology detection start from mutually most similar pairs of genes (reciprocal best hits) as an approximation for evolutionary most closely related pairs of genes (recipr...

    Authors: Peter F. Stadler, Manuela Geiß, David Schaller, Alitzel López Sánchez, Marcos González Laffitte, Dulce I. Valdivia, Marc Hellmuth and Maribel Hernández Rosales

    Citation: Algorithms for Molecular Biology 2020 15:5

    Content type: Research

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  7. Recent large-scale community sequencing efforts allow at an unprecedented level of detail the identification of genomic regions that show signatures of natural selection. Traditional methods for identifying su...

    Authors: Jarno Alanko, Hideo Bannai, Bastien Cazaux, Pierre Peterlongo and Jens Stoye

    Citation: Algorithms for Molecular Biology 2020 15:2

    Content type: Research

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  8. Estimated gene trees are often inaccurate, due to insufficient phylogenetic signal in the single gene alignment, among other causes. Gene tree correction aims to improve the accuracy of an estimated gene tree ...

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

    Citation: Algorithms for Molecular Biology 2020 15:1

    Content type: Research

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  9. As the number of sequenced genomes grows, researchers have access to an increasingly rich source for discovering detailed evolutionary information. However, the computational technologies for inferring biologi...

    Authors: Hisanori Kiryu, Yuto Ichikawa and Yasuhiro Kojima

    Citation: Algorithms for Molecular Biology 2019 14:23

    Content type: Research

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  10. Genomic data analyses such as Genome-Wide Association Studies (GWAS) or Hi-C studies are often faced with the problem of partitioning chromosomes into successive regions based on a similarity matrix of high-re...

    Authors: Christophe Ambroise, Alia Dehman, Pierre Neuvial, Guillem Rigaill and Nathalie Vialaneix

    Citation: Algorithms for Molecular Biology 2019 14:22

    Content type: Research

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  11. The evolutionary distance between two genomes can be estimated by computing a minimum length sequence of operations, called genome rearrangements, that transform one genome into another. Usually, a genome is mode...

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

    Citation: Algorithms for Molecular Biology 2019 14:21

    Content type: Research

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  12. 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

    Content type: Software article

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  13. 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

    Content type: Research

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  14. 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

    Content type: Research

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  15. 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

    Content type: Research

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  16. 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

    Content type: Research

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  17. 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

    Content type: Research

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  18. 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

    Content type: Research

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  19. 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

    Content type: Research

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  20. 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

    Content type: Research

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  21. 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

    Content type: Research

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  22. 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

    Content type: Research

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  23. 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

    Content type: Software article

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  24. 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

    Content type: Research

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  25. 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

    Content type: Research

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  26. 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

    Content type: Research

    Published on:

  27. 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

    Content type: Research

    Published on:

  28. 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

    Content type: Research

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  29. 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

    Content type: Research

    Published on:

  30. 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

    Content type: Research

    Published on:

  31. 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

    Content type: Research

    Published on:

  32. 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

    Content type: Research

    Published on:

  33. 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

    Content type: Research

    Published on: