Genomic tools in biological invasions: current state and future frontiers

A McGaughran, MK Dhami, E Parvizi… - Genome biology and …, 2024 - academic.oup.com
Human activities are accelerating rates of biological invasions and climate-driven range
expansions globally, yet we understand little of how genomic processes facilitate the …

Accurate long-read de novo assembly evaluation with Inspector

Y Chen, Y Zhang, AY Wang, M Gao, Z Chong - Genome Biology, 2021 - Springer
Long-read de novo genome assembly continues to advance rapidly. However, there is a
lack of effective tools to accurately evaluate the assembly results, especially for structural …

[HTML][HTML] A new domestic cat genome assembly based on long sequence reads empowers feline genomic medicine and identifies a novel gene for dwarfism

RM Buckley, BW Davis, WA Brashear, FHG Farias… - PLoS …, 2020 - journals.plos.org
The domestic cat (Felis catus) numbers over 94 million in the USA alone, occupies
households as a companion animal, and, like humans, suffers from cancer and common and …

Haplotype threading: accurate polyploid phasing from long reads

SD Schrinner, RS Mari, J Ebler, M Rautiainen, L Seillier… - Genome biology, 2020 - Springer
Resolving genomes at haplotype level is crucial for understanding the evolutionary history of
polyploid species and for designing advanced breeding strategies. Polyploid phasing still …

Characterization of structural variation in Tibetans reveals new evidence of high-altitude adaptation and introgression

C Quan, Y Li, X Liu, Y Wang, J **, Y Lu, G Zhou - Genome biology, 2021 - Springer
Background Structural variation (SV) acts as an essential mutational force sha** the
evolution and function of the human genome. However, few studies have examined the role …

Personalized genome structure via single gamete sequencing

R Lyu, V Tsui, DJ McCarthy, W Crismani - Genome Biology, 2021 - Springer
Genetic maps have been fundamental to building our understanding of disease genetics
and evolutionary processes. The gametes of an individual contain all of the information …

Comprehensive characterization of copy number variation (CNV) called from array, long-and short-read data

K Lavrichenko, S Johansson, I Jonassen - BMC genomics, 2021 - Springer
Background SNP arrays, short-and long-read genome sequencing are genome-wide high-
throughput technologies that may be used to assay copy number variants (CNVs) in a …

CaBagE: A Ca s9-based Ba ck g round E limination strategy for targeted, long-read DNA sequencing

AD Wallace, TA Sasani, J Swanier, BL Gates… - PLoS …, 2021 - journals.plos.org
A substantial fraction of the human genome is difficult to interrogate with short-read DNA
sequencing technologies due to paralogy, complex haplotype structures, or tandem repeats …

Hidden biases in germline structural variant detection

MM Khayat, SME Sahraeian, S Zarate, A Carroll… - Genome biology, 2021 - Springer
Background Genomic structural variations (SV) are important determinants of genotypic and
phenotypic changes in many organisms. However, the detection of SV from next-generation …

Loss-of-function tolerance of enhancers in the human genome

D Xu, O Gokcumen, E Khurana - PLoS Genetics, 2020 - journals.plos.org
Previous studies have surveyed the potential impact of loss-of-function (LoF) variants and
identified LoF-tolerant protein-coding genes. However, the tolerance of human genomes to …