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Article
Open AccessThe complete sequence and comparative analysis of ape sex chromosomes
Apes possess two sex chromosomes—the male-specific Y chromosome and the X chromosome, which is present in both males and females. The Y chromosome is crucial for male reproduction, with deletions being linked ...
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Article
Pangenome graph construction from genome alignments with Minigraph-Cactus
Pangenome references address biases of reference genomes by storing a representative set of diverse haplotypes and their alignment, usually as a graph. Alternate alleles determined by variant callers can be us...
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Article
Open AccessIdentification of constrained sequence elements across 239 primate genomes
Noncoding DNA is central to our understanding of human gene regulation and complex diseases1,2, and measuring the evolutionary sequence constraint can establish the functional relevance of putative regulatory ele...
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Article
Open AccessA draft human pangenome reference
Here the Human Pangenome Reference Consortium presents a first draft of the human pangenome reference. The pangenome contains 47 phased, diploid assemblies from a cohort of genetically diverse individuals1. These...
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Article
Open AccessProgressive Cactus is a multiple-genome aligner for the thousand-genome era
New genome assemblies have been arriving at a rapidly increasing pace, thanks to decreases in sequencing costs and improvements in third-generation sequencing technologies1–3. For example, the number of vertebrat...
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Article
Open AccessGenoty** structural variants in pangenome graphs using the vg toolkit
Structural variants (SVs) remain challenging to represent and study relative to point mutations despite their demonstrated importance. We show that variation graphs, as implemented in the vg toolkit, provide a...
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Article
Variation graph toolkit improves read map** by representing genetic variation in the reference
Reducing read map** bias and improving complex variant detection with a highly scalable computational toolkit that implements variation graphs.
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Chapter and Conference Paper
Superbubbles, Ultrabubbles and Cacti
A superbubble is a type of directed acyclic subgraph with single distinct source and sink vertices. In genome assembly and genetics, the possible paths through a superbubble can be considered to represent the ...
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Article
Open AccessRepresenting and decomposing genomic structural variants as balanced integer flows on sequence graphs
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 ...
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Article
Open AccessA call for benchmarking transposable element annotation methods
DNA derived from transposable elements (TEs) constitutes large parts of the genomes of complex eukaryotes, with major impacts not only on genomic research but also on how organisms evolve and function. Althoug...
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Article
Open AccessA unifying model of genome evolution under parsimony
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 ...
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Chapter and Conference Paper
Building a Pangenome Reference for a Population
A reference genome is a high quality individual genome that is used as a coordinate system for the genomes of a population, or genomes of closely related subspecies. Given a set of genomes partitioned by homol...
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Chapter and Conference Paper
A Probabilistic Model for Sequence Alignment with Context-Sensitive Indels
Probabilistic approaches for sequence alignment are usually based on pair Hidden Markov Models (HMMs) or Stochastic Context Free Grammars (SCFGs). Recent studies have shown a significant correlation between th...
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Chapter and Conference Paper
NAPX: A Polynomial Time Approximation Scheme for the Noah’s Ark Problem
The Noah’s Ark Problem (NAP) is an NP-Hard optimization problem with relevance to ecological conservation management. It asks to maximize the phylogenetic diversity (PD) of a set of taxa given a fixed budget, ...
