Results 11 to 20 of about 141,521 (289)
Linearization of genome sequence graphs revisited [PDF]
iScience, 2021 Summary: The need to include the genetic variation within a population into a reference genome led to the concept of a genome sequence graph. Nodes of such a graph are labeled with DNA sequences occurring in represented genomes.
Anna Lisiecka, Norbert Dojer
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Genome-wide inference of ancestral recombination graphs. [PDF]
PLoS Genetics, 2014 The complex correlation structure of a collection of orthologous DNA sequences is uniquely captured by the "ancestral recombination graph" (ARG), a complete record of coalescence and recombination events in the history of the sample.
Matthew D Rasmussen +3 more
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Coordinates and intervals in graph-based reference genomes [PDF]
BMC Bioinformatics, 2017 Background It has been proposed that future reference genomes should be graph structures in order to better represent the sequence diversity present in a species.
Knut D. Rand +5 more
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Read Mapping on Genome Variation Graphs. [PDF]
, 2019 Genome variation graphs are natural candidates to represent a pangenome collection. In such graphs, common subsequences are encoded as vertices and the genomic variations are captured by introducing additional labeled vertices and directed edges. Unlike a linear reference, a reference graph allows a rich representation of the genomic diversities and ...
Naga Sai Kavya Vaddadi +2 more
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A variant selection framework for genome graphs. [PDF]
Bioinformatics, 2021 Abstract Motivation Variation graph representations are projected to either replace or supplement conventional single genome references due to their ability to capture population genetic diversity and reduce reference bias.
Jain C, Tavakoli N, Aluru S.
europepmc +5 more sources
Finding Cross Genome Patterns in Annotation Graphs [PDF]
, 2012 Annotation graph datasets are a natural representation of scientific knowledge. They are common in the life sciences where concepts such as genes and proteins are annotated with controlled vocabulary terms from ontologies. Scientists are interested in analyzing or mining these annotations, in synergy with the literature, to discover patterns.
Joseph Benik +5 more
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Hyperspectral Image Classification Using Deep Genome Graph-Based Approach
Sensors, 2021 Recently developed hybrid models that stack 3D with 2D CNN in their structure have enjoyed high popularity due to their appealing performance in hyperspectral image classification tasks. On the other hand, biological genome graphs have demonstrated their
Haron Tinega +4 more
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Bioinformatics, 2022 AbstractMotivationIntra-sample heterogeneity describes the phenomenon where a genomic sample contains a diverse set of genomic sequences. In practice, the true string sets in a sample are often unknown due to limitations in sequencing technology. In order to compare heterogeneous samples, genome graphs can be used to represent such sets of strings ...
Yutong Qiu, Carl Kingsford
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Frontiers in Genetics, 2023 Whole genome sequencing has revolutionized infectious disease surveillance for tracking and monitoring the spread and evolution of pathogens. However, using a linear reference genome for genomic analyses may introduce biases, especially when studies are ...
Zuyu Yang +12 more
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Viruses, 2020 Viruses represent important test cases for data federation due to their genome size and the rapid increase in sequence data in publicly available databases.
Joan Martí-Carreras +32 more
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