Results 21 to 30 of about 141,521 (289)
Fast and accurate genomic analyses using genome graphs [PDF]
Nature Genetics, 2017 Abstract The human reference genome serves as the foundation for genomics by providing a scaffold for alignment of sequencing reads, but currently only reflects a single consensus haplotype, which impairs read alignment and downstream analysis accuracy. Reference genome structures incorporating known genetic variation have been shown to
Goran Rakocevic +24 more
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Identifying genes targeted by disease-associated non-coding SNPs with a protein knowledge graph.
PLoS ONE, 2022 Genome-wide association studies (GWAS) have identified many single nucleotide polymorphisms (SNPs) that play important roles in the genetic heritability of traits and diseases.
Wytze J Vlietstra +4 more
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GraphAligner: rapid and versatile sequence-to-graph alignment
Genome Biology, 2020 Genome graphs can represent genetic variation and sequence uncertainty. Aligning sequences to genome graphs is key to many applications, including error correction, genome assembly, and genotyping of variants in a pangenome graph.
Mikko Rautiainen, Tobias Marschall
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On characterizing proper max-point-tolerance graphs
AKCE International Journal of Graphs and Combinatorics, 2023 Max-point-tolerance graphs (MPTG) were introduced by Catanzaro et al. in 2017 as a generalization of interval graphs. This graph class has many practical applications in the study of the human genome as well as in signal processing for networks. The same
Sanchita Paul
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Toward Recovering Allele-specific Cancer Genome Graphs. [PDF]
J Comput Biol, 2018 Integrated analysis of structural variants (SVs) and copy number alterations in aneuploid cancer genomes is key to understanding tumor genome complexity.
Rajaraman A, Ma J.
europepmc +3 more sources
, 2017 Abstract There is increasing recognition that a single, monoploid reference genome is a poor universal reference structure for human genetics, because it represents only a tiny fraction of human variation. Adding this missing variation results in a structure that can be described as a mathematical graph: a genome graph.
Novak, Adam M. +23 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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GenomicKB: a knowledge graph for the human genome
Nucleic Acids Research, 2022 AbstractGenomic Knowledgebase (GenomicKB) is a graph database for researchers to explore and investigate human genome, epigenome, transcriptome, and 4D nucleome with simple and efficient queries. The database uses a knowledge graph to consolidate genomic datasets and annotations from over 30 consortia and portals, including 347 million genomic entities,
Fan Feng +8 more
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Draft genome sequence of "Candidatus Cronobacter colletis" NCTC 14934T, a new species in the genus Cronobacter [PDF]
, 2014 Members of the Cronobacter genus are associated with serious infections in neonates.
Forsythe, S +7 more
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Cactus Graphs for Genome Comparisons
Journal of Computational Biology, 2010 Abstract We introduce a data structure, analysis, and visualization scheme called a cactus graph for comparing sets of related genomes. In common with multi-break point graphs and A-Bruijn graphs, cactus graphs can represent duplications and general genomic rearrangements, but additionally, they naturally ...
Benedict Paten +6 more
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