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  1. Phylogenetic networks are mathematical models of evolutionary processes involving reticulate events such as hybridization, recombination, or horizontal gene transfer. One of the crucial notions in phylogenetic...

    Authors: Marcin Wawerka, Dawid Dąbkowski, Natalia Rutecka, Agnieszka Mykowiecka and Paweł Górecki
    Citation: Algorithms for Molecular Biology 2022 17:11
  2. Commonly, sequence and structure elements are assumed to evolve congruently, such that homologous sequence positions correspond to homologous structural features. Assuming congruent evolution, alignments based on...

    Authors: Peter F. Stadler and Sebastian Will
    Citation: Algorithms for Molecular Biology 2022 17:10
  3. k-mer counting is a common task in bioinformatic pipelines, with many dedicated tools available. Many of these tools produce in output k-mer count tables containing both k-mers and counts, easily reaching tens of...

    Authors: Yoshihiro Shibuya, Djamal Belazzougui and Gregory Kucherov
    Citation: Algorithms for Molecular Biology 2022 17:5
  4. Every tumor is composed of heterogeneous clones, each corresponding to a distinct subpopulation of cells that accumulated different types of somatic mutations, ranging from single-nucleotide variants (SNVs) to...

    Authors: Palash Sashittal, Simone Zaccaria and Mohammed El-Kebir
    Citation: Algorithms for Molecular Biology 2022 17:3
  5. Pattern matching is a key step in a variety of biological sequence analysis pipelines. The FM-index is a compressed data structure for pattern matching, with search run time that is independent of the length o...

    Authors: Tim Anderson and Travis J. Wheeler
    Citation: Algorithms for Molecular Biology 2021 16:25
  6. In the comparative genomics field, one of the goals is to estimate a sequence of genetic changes capable of transforming a genome into another. Genome rearrangement events are mutations that can alter the gene...

    Authors: Klairton L. Brito, Andre R. Oliveira, Alexsandro O. Alexandrino, Ulisses Dias and Zanoni Dias
    Citation: Algorithms for Molecular Biology 2021 16:24
  7. The supertree problem, i.e., the task of finding a common refinement of a set of rooted trees is an important topic in mathematical phylogenetics. The special case of a common leaf set L is known to be solvable i...

    Authors: David Schaller, Marc Hellmuth and Peter F. Stadler
    Citation: Algorithms for Molecular Biology 2021 16:23
  8. A semi-labeled tree is a tree where all leaves as well as, possibly, some internal nodes are labeled with taxa. Semi-labeled trees encompass ordinary phylogenetic trees and taxonomies. Suppose we are given a c...

    Authors: David Fernández-Baca and Lei Liu
    Citation: Algorithms for Molecular Biology 2021 16:22
  9. The rearrangement distance is a method to compare genomes of different species. Such distance is the number of rearrangement events necessary to transform one genome into another. Two commonly studied events a...

    Authors: Gabriel Siqueira, Alexsandro Oliveira Alexandrino, Andre Rodrigues Oliveira and Zanoni Dias
    Citation: Algorithms for Molecular Biology 2021 16:21
  10. Repetitive elements contribute a large part of eukaryotic genomes. For example, about 40 to 50% of human, mouse and rat genomes are repetitive. So identifying and classifying repeats is an important step in ge...

    Authors: Fabian Hausmann and Stefan Kurtz
    Citation: Algorithms for Molecular Biology 2021 16:20
  11. Best match graphs (BMGs) are a class of colored digraphs that naturally appear in mathematical phylogenetics as a representation of the pairwise most closely related genes among multiple species. An arc connec...

    Authors: David Schaller, Manuela Geiß, Marc Hellmuth and Peter F. Stadler
    Citation: Algorithms for Molecular Biology 2021 16:19
  12. Analysis of chemical graphs is becoming a major research topic in computational molecular biology due to its potential applications to drug design. One of the major approaches in such a study is inverse quant...

    Authors: Naveed Ahmed Azam, Jianshen Zhu, Yanming Sun, Yu Shi, Aleksandar Shurbevski, Liang Zhao, Hiroshi Nagamochi and Tatsuya Akutsu
    Citation: Algorithms for Molecular Biology 2021 16:18
  13. Prediction of drug resistance and identification of its mechanisms in bacteria such as Mycobacterium tuberculosis, the etiological agent of tuberculosis, is a challenging problem. Solving this problem requires a ...

    Authors: Hooman Zabeti, Nick Dexter, Amir Hosein Safari, Nafiseh Sedaghat, Maxwell Libbrecht and Leonid Chindelevitch
    Citation: Algorithms for Molecular Biology 2021 16:17
  14. Gene clusters are groups of genes that are co-locally conserved across various genomes, not necessarily in the same order. Their discovery and analysis is valuable in tasks such as gene annotation and predicti...

    Authors: Galia R. Zimerman, Dina Svetlitsky, Meirav Zehavi and Michal Ziv-Ukelson
    Citation: Algorithms for Molecular Biology 2021 16:16
  15. In the context of biomarker discovery and molecular characterization of diseases, laser capture microdissection is a highly effective approach to extract disease-specific regions from complex, heterogeneous ti...

    Authors: Leonie Selbach, Tobias Kowalski, Klaus Gerwert, Maike Buchin and Axel Mosig
    Citation: Algorithms for Molecular Biology 2021 16:15
  16. Directed evolution (DE) is a technique for protein engineering that involves iterative rounds of mutagenesis and screening to search for sequences that optimize a given property, such as binding affinity to a ...

    Authors: Trevor S. Frisby and Christopher James Langmead
    Citation: Algorithms for Molecular Biology 2021 16:13
  17. One of the Grand Challenges in Science is the construction of the Tree of Life, an evolutionary tree containing several million species, spanning all life on earth. However, the construction of the Tree of Life i...

    Authors: Xilin Yu, Thien Le, Sarah A. Christensen, Erin K. Molloy and Tandy Warnow
    Citation: Algorithms for Molecular Biology 2021 16:12
  18. Genome assembly is one of the most important problems in computational genomics. Here, we suggest addressing an issue that arises in homology-based scaffolding, that is, when linking and ordering contigs to ob...

    Authors: Sven Schrinner, Manish Goel, Michael Wulfert, Philipp Spohr, Korbinian Schneeberger and Gunnar W. Klau
    Citation: Algorithms for Molecular Biology 2021 16:11
  19. K-mer based methods have become prevalent in many areas of bioinformatics. In applications such as database search, they often work with large multi-terabyte-sized datasets. Storing such large datasets is a de...

    Authors: Amatur Rahman, Rayan Chikhi and Paul Medvedev
    Citation: Algorithms for Molecular Biology 2021 16:10
  20. 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
  21. 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
  22. 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
  23. 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
  24. 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
  25. 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
  26. 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
  27. 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
  28. 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
  29. 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
  30. 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
  31. 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
  32. 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
  33. 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
  34. 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
  35. 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
  36. 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
  37. 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
  38. 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