Host–transposon interactions: conflict, cooperation, and cooption

RL Cosby, NC Chang, C Feschotte - Genes & development, 2019 - genesdev.cshlp.org
Transposable elements (TEs) are mobile DNA sequences that colonize genomes and
threaten genome integrity. As a result, several mechanisms appear to have emerged during …

Nuclear actin filaments in DNA repair dynamics

CP Caridi, M Plessner, R Grosse, I Chiolo - Nature cell biology, 2019 - nature.com
Recent development of innovative tools for live imaging of actin filaments (F-actin) enabled
the detection of surprising nuclear structures responding to various stimuli, challenging …

BUSCO: assessing genomic data quality and beyond

M Manni, MR Berkeley, M Seppey… - Current …, 2021 - Wiley Online Library
Abstract Evaluation of the quality of genomic “data products” such as genome assemblies or
gene sets is of critical importance in order to recognize possible issues and correct them …

HiCanu: accurate assembly of segmental duplications, satellites, and allelic variants from high-fidelity long reads

S Nurk, BP Walenz, A Rhie, MR Vollger… - Genome …, 2020 - genome.cshlp.org
Complete and accurate genome assemblies form the basis of most downstream genomic
analyses and are of critical importance. Recent genome assembly projects have relied on a …

SyRI: finding genomic rearrangements and local sequence differences from whole-genome assemblies

M Goel, H Sun, WB Jiao, K Schneeberger - Genome biology, 2019 - Springer
Genomic differences range from single nucleotide differences to complex structural
variations. Current methods typically annotate sequence differences ranging from SNPs to …

Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation

S Koren, BP Walenz, K Berlin, JR Miller… - Genome …, 2017 - genome.cshlp.org
Long-read single-molecule sequencing has revolutionized de novo genome assembly and
enabled the automated reconstruction of reference-quality genomes. However, given the …

The enormous repetitive Antarctic krill genome reveals environmental adaptations and population insights

C Shao, S Sun, K Liu, J Wang, S Li, Q Liu, BE Deagle… - Cell, 2023 - cell.com
Antarctic krill (Euphausia superba) is Earth's most abundant wild animal, and its enormous
biomass is vital to the Southern Ocean ecosystem. Here, we report a 48.01-Gb chromosome …

FlyBase at 25: looking to the future

LS Gramates, SJ Marygold, G Santos… - Nucleic acids …, 2016 - academic.oup.com
Abstract Since 1992, FlyBase (flybase. org) has been an essential online resource for the
Drosophila research community. Concentrating on the most extensively studied species …

Nuclear F-actin and myosins drive relocalization of heterochromatic breaks

CP Caridi, C D'Agostino, T Ryu, G Zapotoczny… - Nature, 2018 - nature.com
Heterochromatin mainly comprises repeated DNA sequences that are prone to ectopic
recombination. In Drosophila cells,'safe'repair of heterochromatic double-strand breaks by …

SMARTdenovo: a de novo assembler using long noisy reads

H Liu, S Wu, A Li, J Ruan - Gigabyte, 2021 - pmc.ncbi.nlm.nih.gov
Long-read single-molecule sequencing has revolutionized de novo genome assembly and
enabled the automated reconstruction of reference-quality genomes. It has also been widely …