Skip to main content

Articles

Page 2 of 10

  2. We present a new method and software tool called rowbowt that applies a pangenome index to the problem of inferring genotypes from short-read sequencing data. The method uses a novel indexing structure called the...

    Authors: Taher Mun, Naga Sai Kavya Vaddadi and Ben Langmead
    Citation: Algorithms for Molecular Biology 2023 18:2
    Content type: Software Published on:

  5. Scaffolding is a bioinformatics problem aimed at completing the contig assembly process by determining the relative position and orientation of these contigs. It can be seen as a paths and cycles cover problem...

    Authors: Tom Davot, Annie Chateau, Rohan Fossé, Rodolphe Giroudeau and Mathias Weller
    Citation: Algorithms for Molecular Biology 2022 17:16
    Content type: Research Published on:

  8. The early development of a zygote can be mathematically described by a developmental tree. To compare developmental trees of different species, we need to define distances on trees. If children cells after a d...

    Authors: Yue Wang
    Citation: Algorithms for Molecular Biology 2022 17:13
    Content type: Research Published on:

  9. Cell signaling pathways, which are a series of reactions that start at receptors and end at transcription factors, are basic to systems biology. Properly modeling the reactions in such pathways requires directed ...

    Authors: Spencer Krieger and John Kececioglu
    Citation: Algorithms for Molecular Biology 2022 17:12
    Content type: Research Published on:

    The Correction to this article has been published in Algorithms for Molecular Biology 2022 17:17

  10. 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
    Content type: Research Published on:

  11. 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
    Content type: Research Published on:

  16. 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
    Content type: Research Published on:

  17. The increasing availability of high-quality genome assemblies raised interest in the characterization of genomic architecture. Major architectural elements, such as common repeats and segmental duplications (S...

    Authors: Hamza Išerić, Can Alkan, Faraz Hach and Ibrahim Numanagić
    Citation: Algorithms for Molecular Biology 2022 17:4
    Content type: Research Published on:

  18. 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
    Content type: Research Published on:

  21. 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
    Content type: Software article Published on:

  22. 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
    Content type: Research Published on:

  23. 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
    Content type: Research Published on:

  24. 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
    Content type: Research Published on:

  25. 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
    Content type: Research Published on:

  26. 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
    Content type: Software Article Published on:

  27. 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
    Content type: Research Published on:

  28. 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
    Content type: Research Published on:

  29. 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
    Content type: Research Published on:

  30. 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
    Content type: Research Published on:

  31. 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
    Content type: Research Published on:

  33. 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
    Content type: Research Published on:

  34. 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
    Content type: Research Published on:

  35. 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
    Content type: Research Published on:

  36. 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
    Content type: Research Published on:

  37. 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:

  38. 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:

  39. 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:

  40. 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:

  41. 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:

  42. 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:

  44. 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:

  46. 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:

  47. 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:

  48. 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:

  49. 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:

  50. 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:
  • ISSN: 1748-7188 (electronic)

Algorithms for Molecular Biology

ISSN: 1748-7188