Results 11 to 20 of about 3,685 (173)
The directed genus of the de Bruijn graph
Discrete Mathematics, 2009 zbMATH Open Web Interface contents unavailable due to conflicting licenses.
Alfred W. Hales, Nora Hartsfield
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An Efficient, Scalable, and Exact Representation of High-Dimensional Color Information Enabled Using de Bruijn Graph Search [PDF]
Journal of Computational Biology, 2020 Prashant Pandey +2 more
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The improved de Bruijn graph for multitask learning: predicting functions, subcellular localization, and interactions of noncoding RNAs [PDF]
Briefings in BioinformaticsLiwei Liu, Yuxiao Wei
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Buffering updates enables efficient dynamic de Bruijn graphs
Computational and Structural Biotechnology Journal, 2021 Motivation: The de Bruijn graph has become a ubiquitous graph model for biological data ever since its initial introduction in the late 1990s. It has been used for a variety of purposes including genome assembly (Zerbino and Birney, 2008; Bankevich et al.
Jarno Alanko +4 more
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A New Approach to Determine the Minimal Polynomials of Binary Modified de Bruijn Sequences
Mathematics, 2022 A binary modified de Bruijn sequence is an infinite and periodic binary sequence derived by removing a zero from the longest run of zeros in a binary de Bruijn sequence.
Musthofa +3 more
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On the Representation of De Bruijn Graphs [PDF]
Journal of Computational Biology, 2014 Abstract The de Bruijn graph plays an important role in bioinformatics, especially in the context of de novo assembly. However, the representation of the de Bruijn graph in memory is a computational bottleneck for many assemblers.
Chikhi, Rayan +4 more
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Edge minimization in de Bruijn graphs [PDF]
Information and Computation, 2020 This paper introduces the de Bruijn graph edge minimization problem, which is related to the compression of de Bruijn graphs: find the order-k de Bruijn graph with minimum edge count among all orders. We describe an efficient algorithm that solves this problem.
Uwe Baier +3 more
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Bifrost: highly parallel construction and indexing of colored and compacted de Bruijn graphs
Genome Biology, 2020 Memory consumption of de Bruijn graphs is often prohibitive. Most de Bruijn graph-based assemblers reduce the complexity by compacting paths into single vertices, but this is challenging as it requires the uncompacted de Bruijn graph to be available in ...
Guillaume Holley, Páll Melsted
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Applications of de Bruijn graphs in microbiome research
iMeta, 2022 High‐throughput sequencing has become an increasingly central component of microbiome research. The development of de Bruijn graph‐based methods for assembling high‐throughput sequencing data has been an important part of the broader adoption of ...
Keith Dufault‐Thompson, Xiaofang Jiang
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Cutwidth of the de Bruijn graph [PDF]
RAIRO - Theoretical Informatics and Applications, 1995 Summary: We establish an optimal upper bound on the cutwidth of the general de Bruijn graph. Our upper bound is essentially based on a new relation between the cutwidth and the area of the VLSI layout of a graph. The relation is interesting for itself as it generalizes the known relation between the area and the bisection width of graphs of bounded ...
André Raspaud +2 more
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