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Structural variation in the 3D genome [PDF]
Nature Reviews Genetics, 2018 Structural and quantitative chromosomal rearrangements, collectively referred to as structural variation (SV), contribute to a large extent to the genetic diversity of the human genome and thus are of high relevance for cancer genetics, rare diseases and evolutionary genetics.
Malte Spielmann +2 more
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Structural variation in the sequencing era
Nature Reviews Genetics, 2019 Identifying structural variation (SV) is essential for genome interpretation but has been historically difficult due to limitations inherent to available genome technologies. Detection methods that use ensemble algorithms and emerging sequencing technologies have enabled the discovery of thousands of SVs, uncovering information about their ubiquity ...
Steve S Ho +2 more
exaly +4 more sources
Balancing selection on genomic deletion polymorphisms in humans
eLife, 2023 A key question in biology is why genomic variation persists in a population for extended periods. Recent studies have identified examples of genomic deletions that have remained polymorphic in the human lineage for hundreds of millennia, ostensibly owing
Alber Aqil +3 more
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Profiling variable-number tandem repeat variation across populations using repeat-pangenome graphs
Nature Communications, 2021 Variable number tandem repeats (VNTRs) are difficult to analyze by short-read sequencing in disease studies. Here, the authors describe a VNTR mapping strategy for short-read analyses using a repeat pangenome graph.
Tsung-Yu Lu +2 more
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Structure Tensor Total Variation [PDF]
SIAM Journal on Imaging Sciences, 2015 Summary: We introduce a novel generic energy functional that we employ to solve inverse imaging problems within a variational framework. The proposed regularization family, termed as structure tensor total variation (STV), penalizes the eigenvalues of the structure tensor and is suitable for both grayscale and vector-valued images.
Stamatios Lefkimmiatis +3 more
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Structural variations in papaya genomes [PDF]
BMC Genomics, 2021 Abstract Background Structural variations (SVs) are a type of mutations that have not been widely detected in plant genomes and studies in animals have shown their role in the process of domestication. An in-depth study of SVs will help us to further understand the impact of SVs on the phenotype and environmental ...
Zhenyang Liao +5 more
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The effects of common structural variants on 3D chromatin structure
BMC Genomics, 2020 Background Three-dimensional spatial organization of chromosomes is defined by highly self-interacting regions 0.1–1 Mb in size termed Topological Associating Domains (TADs).
Omar Shanta +3 more
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Journal of Fungi, 2022 Genome rearrangements in filamentous fungi are prevalent but little is known about the modalities of their evolution, in part because few complete genomes are available within a single genus.
Mathieu Quenu +10 more
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Symmetry and Variation of Hodge Structures [PDF]
Asian Journal of Mathematics, 2004 The main problem addressed in the paper is the Torelli problem for n-dimensional varieties of general type, more specifically for varieties with ample canonical bundle. It asks under which geometrical condition for a variety the period map for the Hodge structure of weight n is a local embedding.
Bauer , I. C., Catanese , F.
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Analysis of unmapped regions associated with long deletions in Korean whole genome sequences based on short read data [PDF]
Genomics & Informatics, 2019 While studies aimed at detecting and analyzing indels or single nucleotide polymorphisms within human genomic sequences have been actively conducted, studies on detecting long insertions/deletions are not easy to orchestrate.
Yuna Lee, Kiejung Park, Insong Koh
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