Variation graphs

Part 1 of ebook "Statistics and analysis of shapes" provides readers with contents including: medial axis computation and evolution; shape variation of medial axis representations via principal geodesic analysis on symmetric spaces; 2D shape modeling using skeletal graphs in a morse theoretic framework; matching with shape contexts;...

175p mothoiphong 28-06-2024 2 1   Download

Optimal integration of transcriptomics data and associated spatial information is essential towards fully exploiting spatial transcriptomics to dissect tissue heterogeneity and map out intercellular communications.

15p vicwell 29-02-2024 5 2   Download

Part 2 book "Beginning and intermediate algebra" includes content: Writing equations of lines, functions, and variation; radicals and rational exponents; quadratic functions, inequalities, and algebra of functions; exponential and logarithmic functions; conic sections and more graphing; more on systems of equations and inequalities; miscellaneous topics.

486p muasambanhan07 08-02-2024 3 0   Download

Part 1 of ebook "Electrical and electronic principles and technology (Sixth edition)" provides readers with contents including: revision of some basic mathematics; some mathematics revision; further mathematics revision; basic electrical and electronic engineering principles; units associated with basic electrical quantities; an introduction to electric circuits; resistance variation; batteries and alternative sources of energy; series and parallel networks;...

261p hanlinhchi 29-08-2023 14 6   Download

Ebook College algebra (3rd edition): Part 1 includes the following content: Chapter 0: prerequisites and review; chapter 1: equations and inequalities; chapter 2: graphs; chapter 3: functions and their graphs. Please refer to the documentation for more details.

394p runthenight03 07-12-2022 10 5   Download

Accurate detection and genotyping of structural variations (SVs) from short-read data is a long-standing area of development in genomics research and clinical sequencing pipelines. We introduce Paragraph, an accurate genotyper that models SVs using sequence graphs and SV annotations.

13p vielonmusk 30-01-2022 11 0   Download

Efficiently scaling genomic variant search indexes to thousands of samples is computationally challenging due to the presence of multiple coordinate systems to avoid reference biases. We present VariantStore, a system that indexes genomic variants from multiple samples using a variation graph and enables variant queries across any sample-specific coordinate system.

25p viarchimedes 26-01-2022 16 0   Download

Genome graphs allow very general representations of genetic variation; depending on the model and implementation, variation at different length-scales (single nucleotide polymorphisms (SNPs), structural variants) and on different sequence backgrounds can be incorporated with different levels of transparency.

27p viarchimedes 26-01-2022 11 0   Download

The current bovine genomic reference sequence was assembled from a Hereford cow. The resulting linear assembly lacks diversity because it does not contain allelic variation, a drawback of linear references that causes reference allele bias.

27p viarchimedes 26-01-2022 6 0   Download

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.

28p viarchimedes 26-01-2022 8 0   Download

During the last decade, the analysis of ancient DNA (aDNA) sequence has become a powerful tool for the study of past human populations. However, the degraded nature of aDNA means that aDNA molecules are short and frequently mutated by post-mortem chemical modifications.

18p viarchimedes 26-01-2022 7 0   Download

The practical use of graph-based reference genomes depends on the ability to align reads to them. Performing substring queries to paths through these graphs lies at the core of this task. The combination of increasing pattern length and encoded variations inevitably leads to a combinatorial explosion of the search space.

16p viarchimedes 26-01-2022 14 0   Download

Genomes computationally inferred from large metagenomic data sets are often incomplete and may be missing functionally important content and strain variation. We introduce an information retrieval system for large metagenomic data sets that exploits the sparsity of DNA assembly graphs to efficiently extract subgraphs surrounding an inferred genome.

16p viarchimedes 26-01-2022 6 0   Download

Microbiomes play vital roles in shaping environments and stabilize them based on their compositions and inter-species relationships among its species. Variations in microbial properties have been reported to have significant impact on their host environment.

13p viansan2711 30-07-2021 14 1   Download

Parsimony and maximum likelihood methods of phylogenetic tree estimation and parsimony methods for genome rearrangements are central to the study of genome evolution yet to date they have largely been pursued in isolation.

31p vikentucky2711 26-11-2020 13 1   Download

The study of genomic variation has provided key insights into the functional role of mutations. Predominantly, studies have focused on single nucleotide variants (SNV), which are relatively easy to detect and can be described with rich mathematical models.

16p vioklahoma2711 19-11-2020 8 0   Download

During cancer progression genomes undergo point mutations as well as larger segmental changes. The latter include, among others, segmental deletions duplications, translocations and inversions.The result is a highly complex, patient-specific cancer karyotype.

14p viconnecticut2711 29-10-2020 9 2   Download

Cancer as a worldwide problem is driven by genomic alterations. With the advent of high-throughput sequencing technology, a huge amount of genomic data generates at every second which offer many valuable cancer information and meanwhile throw a big challenge to those investigators.

17p vijisoo2711 27-10-2020 12 0   Download

Genome graph is an emerging approach for representing structural variants on genomes with branches. For example, representing structural variants of cancer genomes as a genome graph is more natural than representing such genomes as differences from the linear reference genome.

14p vicolorado2711 23-10-2020 10 1   Download

Protein-protein interactions (PPIs) are central to many biological processes. Considering that the experimental methods for identifying PPIs are time-consuming and expensive, it is important to develop automated computational methods to better predict PPIs.

16p vicolorado2711 22-10-2020 11 0   Download