Plant NLR diversity: the known unknowns of pan-NLRomes

AC Barragan, D Weigel - The Plant Cell, 2021 - academic.oup.com
Plants and pathogens constantly adapt to each other. As a consequence, many members of
the plant immune system, and especially the intracellular nucleotide-binding site leucine …

Genome graphs and the evolution of genome inference

B Paten, AM Novak, JM Eizenga, E Garrison - Genome research, 2017 - genome.cshlp.org
The human reference genome is part of the foundation of modern human biology and a
monumental scientific achievement. However, because it excludes a great deal of common …

Progressive Cactus is a multiple-genome aligner for the thousand-genome era

J Armstrong, G Hickey, M Diekhans, IT Fiddes… - Nature, 2020 - nature.com
New genome assemblies have been arriving at a rapidly increasing pace, thanks to
decreases in sequencing costs and improvements in third-generation sequencing …

[HTML][HTML] Characterizing the major structural variant alleles of the human genome

PA Audano, A Sulovari, TA Graves-Lindsay… - Cell, 2019 - cell.com
In order to provide a comprehensive resource for human structural variants (SVs), we
generated long-read sequence data and analyzed SVs for fifteen human genomes. We …

Evaluation of GRCh38 and de novo haploid genome assemblies demonstrates the enduring quality of the reference assembly

VA Schneider, T Graves-Lindsay, K Howe… - Genome …, 2017 - genome.cshlp.org
The human reference genome assembly plays a central role in nearly all aspects of today's
basic and clinical research. GRCh38 is the first coordinate-changing assembly update since …

[PDF][PDF] Computational pan-genomics: status, promises and challenges

Briefings in bioinformatics, 2018 - academic.oup.com
Many disciplines, from human genetics and oncology to plant breeding, microbiology and
virology, commonly face the challenge of analyzing rapidly increasing numbers of genomes …

Genetic variation, comparative genomics, and the diagnosis of disease

EE Eichler - New England Journal of Medicine, 2019 - Mass Medical Soc
Uncharted Regions of the Human Genome The genome is not akin to a string of fixed length.
Many large segments of DNA may be present or absent—a major contributor to pathogenic …

Whole-genome alignment and comparative annotation

J Armstrong, IT Fiddes, M Diekhans… - Annual review of …, 2019 - annualreviews.org
Rapidly improving sequencing technology coupled with computational developments in
sequence assembly are making reference-quality genome assembly economical. Hundreds …

Estimating pangenomes with roary

F Sitto, FU Battistuzzi - Molecular biology and evolution, 2020 - academic.oup.com
A description of the genetic makeup of a species based on a single genome is often
insufficient because it ignores the variability in gene repertoire among multiple strains. The …

Kourami: graph-guided assembly for novel human leukocyte antigen allele discovery

H Lee, C Kingsford - Genome biology, 2018 - Springer
Accurate typing of human leukocyte antigen (HLA) is important because HLA genes play
important roles in immune responses and disease genesis. Previously available …