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Representing Variant Calling Format as Directed Acyclic Graphs to Enable the Use of Cloud Computing for Efficient and Cost Effective Genome Analysis [PDF]
, 2017 Ever since the completion of the Human Genome Project in 2003, the human genome has been represented as a linear sequence of 3.2 billion base pairs and is referred to as the "Reference Genome".
Ashiq Anjum, Rizos Sakellariou
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Breakpoint graphs and ancestral genome reconstructions [PDF]
Genome Research, 2009 Recently completed whole-genome sequencing projects marked the transition from gene-based phylogenetic studies to phylogenomics analysis of entire genomes. We developed an algorithm MGRA for reconstructing ancestral genomes and used it to study the rearrangement history of seven mammalian genomes: human, chimpanzee, macaque, mouse, rat, dog, and ...
Pavel Pevzner, Max A Alekseyev
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Goodbye reference, hello genome graphs
Nature Biotechnology, 2019Algorithms for building a variant-aware human graph genome enable fast and accurate genotyping without huge memory requirements.
Adam Ameur, Ameur Adam
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Graph-based pan-genomes: increased opportunities in plant genomics
Journal of Experimental Botany, 2022AbstractDue to the development of sequencing technology and the great reduction in sequencing costs, an increasing number of plant genomes have been assembled, and numerous genomes have revealed large amounts of variations. However, a single reference genome does not allow the exploration of species diversity, and therefore the concept of pan-genome ...
Shuo Wang +4 more
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Graph Modeling for Genomics and Epidemiology
2023The last decades have seen great leaps made in the development of RNA sequencing technologies, yielding lower cost and greater throughput of experiments, to the point where the scale of the data produced on a daily basis is staggering. While computational hardware is also continuously improving, famously (or perhaps infamously) described by Gordon ...
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Scalable Assembly for Massive Genomic Graphs
2017 17th IEEE/ACM International Symposium on Cluster, Cloud and Grid Computing (CCGRID), 2017Scientists increasingly want to assemble large genomes, metagenomes, and large numbers of individual genomes. In order to meet the demand for processing these huge datasets, parallel genome assembly is a vital step. Among all the parallel genome assemblers, de Bruijn graph based ones are most popular.
Jintao Meng 0001 +5 more
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Graph Data Modelling for Genomic Variants
2019 IEEE SmartWorld, Ubiquitous Intelligence & Computing, Advanced & Trusted Computing, Scalable Computing & Communications, Cloud & Big Data Computing, Internet of People and Smart City Innovation (SmartWorld/SCALCOM/UIC/ATC/CBDCom/IOP/SCI), 2019Genome variant analysis is performed on Variant Call Format (VCF) files. It can take days to process these files for genome analytics due to challenges such as loading the files for each user query and processing them to answer questions of interest. As data sizes grow, timely processing of this data is putting enormous pressure on the computational ...
Anjum, Ashiq, Aizad, Sanna
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The ‘Butterfly effect’ in Cayley graphs with applications to genomics
Journal of Mathematical Biology, 2011Suppose a finite set X is repeatedly transformed by a sequence of permutations of a certain type acting on an initial element x to produce a final state y. For example, in genomics applications, X could be a set of genomes and the permutations certain genome 'rearrangements' or, in group theory, X could be the set of configurations of a Rubik's cube ...
Moulton, Vincent, Steel, Mike
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From de Bruijn Graphs to Rectangle Graphs for Genome Assembly
2012Jigsaw puzzles were originally constructed by painting a picture on a rectangular piece of wood and further cutting it into smaller pieces with a jigsaw. The Jigsaw Puzzle Problem is to find an arrangement of these pieces that fills up the rectangle in such a way that neighboring pieces have "matching" boundaries with respect to color and texture ...
Nikolay Vyahhi +3 more
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Using Random Graphs in Population Genomics
2013I shall discuss the application of algorithmic and combinatorial tools in the area of population genomics, which has not been the traditional stomping ground for algorithmicists.
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