Skip to main content

Articles

Page 1 of 8

  1. Mutation trees are rooted trees in which nodes are of arbitrary degree and labeled with a mutation set. These trees, also referred to as clonal trees, are used in computational oncology to represent the mutati...

    Authors: Katharina Jahn, Niko Beerenwinkel and Louxin Zhang

    Citation: Algorithms for Molecular Biology 2021 16:9

    Content type: Research

    Published on:

  2. Advances in genome sequencing over the last years have lead to a fundamental paradigm shift in the field. With steadily decreasing sequencing costs, genome projects are no longer limited by the cost of raw seq...

    Authors: Thomas Gatter, Sarah von Löhneysen, Jörg Fallmann, Polina Drozdova, Tom Hartmann and Peter F. Stadler

    Citation: Algorithms for Molecular Biology 2021 16:8

    Content type: Research

    Published on:

  3. Genotype-phenotype maps provide a meaningful filtration of sequence space and RNA secondary structures are particular such phenotypes. Compatible sequences, which satisfy the base-pairing constraints of a give...

    Authors: Fenix W. Huang, Christopher L. Barrett and Christian M. Reidys

    Citation: Algorithms for Molecular Biology 2021 16:7

    Content type: Research

    Published on:

  4. Genome wide optical maps are high resolution restriction maps that give a unique numeric representation to a genome. They are produced by assembling hundreds of thousands of single molecule optical maps, which...

    Authors: Kingshuk Mukherjee, Massimiliano Rossi, Leena Salmela and Christina Boucher

    Citation: Algorithms for Molecular Biology 2021 16:6

    Content type: Research

    Published on:

  5. The probability of sequencing a set of RNA-seq reads can be directly modeled using the abundances of splice junctions in splice graphs instead of the abundances of a list of transcripts. We call this model gra...

    Authors: Cong Ma, Hongyu Zheng and Carl Kingsford

    Citation: Algorithms for Molecular Biology 2021 16:5

    Content type: Research

    Published on:

  6. A classical problem in comparative genomics is to compute the rearrangement distance, that is the minimum number of large-scale rearrangements required to transform a given genome into another given genome. Th...

    Authors: Diego P. Rubert, Fábio V. Martinez and Marília D. V. Braga

    Citation: Algorithms for Molecular Biology 2021 16:4

    Content type: Research

    Published on:

  7. With an increasing number of patient-derived xenograft (PDX) models being created and subsequently sequenced to study tumor heterogeneity and to guide therapy decisions, there is a similarly increasing need fo...

    Authors: Jens Zentgraf and Sven Rahmann

    Citation: Algorithms for Molecular Biology 2021 16:2

    Content type: Research

    Published on:

  8. Simultaneous alignment and folding (SA&F) of RNAs is the indispensable gold standard for inferring the structure of non-coding RNAs and their general analysis. The original algorithm, proposed by Sankoff, solv...

    Authors: Milad Miladi, Martin Raden, Sebastian Will and Rolf Backofen

    Citation: Algorithms for Molecular Biology 2020 15:19

    Content type: Research

    Published on:

  9. The construction of a suffix array for a collection of strings is a fundamental task in Bioinformatics and in many other applications that process strings. Related data structures, as the Longest Common Prefix...

    Authors: Felipe A. Louza, Guilherme P. Telles, Simon Gog, Nicola Prezza and Giovanna Rosone

    Citation: Algorithms for Molecular Biology 2020 15:18

    Content type: Software Article

    Published on:

  10. Data about herpesvirus microRNA motifs on human circular RNAs suggested the following statistical question. Consider independent random counts, not necessarily identically distributed. Conditioned on the sum, ...

    Authors: John L. Spouge, Joseph M. Ziegelbauer and Mileidy Gonzalez

    Citation: Algorithms for Molecular Biology 2020 15:17

    Content type: Research

    Published on:

  11. The history of gene families—which are equivalent to event-labeled gene trees—can to some extent be reconstructed from empirically estimated evolutionary event-relations containing pairs of orthologous, paralo...

    Authors: Manuel Lafond and Marc Hellmuth

    Citation: Algorithms for Molecular Biology 2020 15:16

    Content type: Research

    Published on:

  12. Identifying the secondary structure of an RNA is crucial for understanding its diverse regulatory functions. This paper focuses on how to enhance target identification in a Boltzmann ensemble of structures via...

    Authors: Thomas J. X. Li and Christian M. Reidys

    Citation: Algorithms for Molecular Biology 2020 15:15

    Content type: Research

    Published on:

  13. Cytoplasmic incompatibility (CI) relates to the manipulation by the parasite Wolbachia of its host reproduction. Despite its widespread occurrence, the molecular basis of CI remains unclear and theoretical models...

    Authors: Tiziana Calamoneri, Mattia Gastaldello, Arnaud Mary, Marie-France Sagot and Blerina Sinaimeri

    Citation: Algorithms for Molecular Biology 2020 15:14

    Content type: Research

    Published on:

  14. Association studies have been widely used to search for associations between common genetic variants observations and a given phenotype. However, it is now generally accepted that genes and environment must be...

    Authors: Florent Guinot, Marie Szafranski, Julien Chiquet, Anouk Zancarini, Christine Le Signor, Christophe Mougel and Christophe Ambroise

    Citation: Algorithms for Molecular Biology 2020 15:13

    Content type: Research

    Published on:

  15. 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:

  16. 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

    Published on:

  17. 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

    Published on:

  18. 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

    Published on:

  19. 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

    Published on:

  20. 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

    Published on:

  21. 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

    Published on:

  22. 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

    Published on:

  23. 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

    Published on:

  24. 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

    Published on:

  25. 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

    Published on:

  26. 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

    Published on:

  27. 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

    Published on:

  28. 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

    Published on:

  29. 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

    Published on:

  30. 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

    Published on:

  31. 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

    Published on:

  32. 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

    Published on:

  33. 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

    Published on: