On the origin and evolution of SARS-CoV-2

D Singh, SV Yi - Experimental & molecular medicine, 2021 - nature.com
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is responsible for the
ongoing global outbreak of a coronavirus disease (herein referred to as COVID-19). Other …

Transposable elements shape the evolution of mammalian development

AD Senft, TS Macfarlan - Nature Reviews Genetics, 2021 - nature.com
Transposable elements (TEs) promote genetic innovation but also threaten genome stability.
Despite multiple layers of host defence, TEs actively shape mammalian-specific …

Liftoff: accurate mapping of gene annotations

A Shumate, SL Salzberg - Bioinformatics, 2021 - academic.oup.com
Motivation Improvements in DNA sequencing technology and computational methods have
led to a substantial increase in the creation of high-quality genome assemblies of many …

GENESPACE tracks regions of interest and gene copy number variation across multiple genomes

JT Lovell, A Sreedasyam, ME Schranz, M Wilson… - elife, 2022 - elifesciences.org
The development of multiple chromosome-scale reference genome sequences in many
taxonomic groups has yielded a high-resolution view of the patterns and processes of …

A global catalog of whole-genome diversity from 233 primate species

LFK Kuderna, H Gao, MC Janiak, M Kuhlwilm, JD Orkin… - Science, 2023 - science.org
The rich diversity of morphology and behavior displayed across primate species provides an
informative context in which to study the impact of genomic diversity on fundamental …

The landscape of tolerated genetic variation in humans and primates

H Gao, T Hamp, J Ede, JG Schraiber, J McRae… - Science, 2023 - science.org
Personalized genome sequencing has revealed millions of genetic differences between
individuals, but our understanding of their clinical relevance remains largely incomplete. To …

MUMmer4: A fast and versatile genome alignment system

G Marçais, AL Delcher, AM Phillippy… - PLoS computational …, 2018 - journals.plos.org
The MUMmer system and the genome sequence aligner nucmer included within it are
among the most widely used alignment packages in genomics. Since the last major release …

Human-specific genetics: new tools to explore the molecular and cellular basis of human evolution

AA Pollen, U Kilik, CB Lowe, JG Camp - Nature Reviews Genetics, 2023 - nature.com
Our ancestors acquired morphological, cognitive and metabolic modifications that enabled
humans to colonize diverse habitats, develop extraordinary technologies and reshape the …

[HTML][HTML] Long walk to genomics: History and current approaches to genome sequencing and assembly

AM Giani, GR Gallo, L Gianfranceschi… - Computational and …, 2020 - Elsevier
Genomes represent the starting point of genetic studies. Since the discovery of DNA
structure, scientists have devoted great efforts to determine their sequence in an exact way …

[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 …