Looking for a Straw in a Haystack by Bridging the Cracks Between Individual Judgments: Narrowing the Knowledge Gap To Anticipate Surprises by Transforming Risk Assessors' Small Worlds Into Large Worlds. [PDF]
Risk AnalABSTRACT The world is constantly changing, yet a risk assessment is based on the knowledge available at one point in time. There will therefore be a gap between the range of possibilities known or conceivable to the assessor at that time and all the possibilities that could occur over infinite time.
Derbyshire J, Aven T.
europepmc +2 more sources
Independence number of de Bruijn graphs
Discrete Mathematics, 2006 zbMATH Open Web Interface contents unavailable due to conflicting licenses.
Nicolas Lichiardopol
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Identifying and classifying trait linked polymorphisms in non-reference species by walking coloured de bruijn graphs. [PDF]
PLoS ONE, 2013 Single Nucleotide Polymorphisms are invaluable markers for tracing the genetic basis of inheritable traits and the ability to create marker libraries quickly is vital for timely identification of target genes. Next-generation sequencing makes it possible
Richard M Leggett +7 more
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On the domination number of $t$-constrained de Bruijn graphs [PDF]
Discrete Mathematics & Theoretical Computer Science, 2022 Motivated by the work on the domination number of directed de Bruijn graphs and some of its generalizations, in this paper we introduce a natural generalization of de Bruijn graphs (directed and undirected), namely $t$-constrained de Bruijn graphs, where
Tiziana Calamoneri +2 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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What do Eulerian and Hamiltonian cycles have to do with genome assembly?
PLoS Computational Biology, 2021 Many students are taught about genome assembly using the dichotomy between the complexity of finding Eulerian and Hamiltonian cycles (easy versus hard, respectively).
Paul Medvedev, Mihai Pop
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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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RGFA: powerful and convenient handling of assembly graphs [PDF]
PeerJ, 2016 The “Graphical Fragment Assembly” (GFA) is an emerging format for the representation of sequence assembly graphs, which can be adopted by both de Bruijn graph- and string graph-based assemblers. Here we present RGFA, an implementation of the proposed GFA
Giorgio Gonnella, Stefan Kurtz
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MetaVelvet-DL: a MetaVelvet deep learning extension for de novo metagenome assembly
BMC Bioinformatics, 2021 Background The increasing use of whole metagenome sequencing has spurred the need to improve de novo assemblers to facilitate the discovery of unknown species and the analysis of their genomic functions.
Kuo-ching Liang, Yasubumi Sakakibara
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