The third revolution in sequencing technology

EL Van Dijk, Y Jaszczyszyn, D Naquin, C Thermes - Trends in Genetics, 2018 - cell.com
Forty years ago the advent of Sanger sequencing was revolutionary as it allowed complete
genome sequences to be deciphered for the first time. A second revolution came when next …

Sequence, chromatin and evolution of satellite DNA

J Thakur, J Packiaraj, S Henikoff - International journal of molecular …, 2021 - mdpi.com
Satellite DNA consists of abundant tandem repeats that play important roles in cellular
processes, including chromosome segregation, genome organization and chromosome end …

Epigenetic patterns in a complete human genome

A Gershman, MEG Sauria, X Guitart, MR Vollger… - Science, 2022 - science.org
The completion of a telomere-to-telomere human reference genome, T2T-CHM13, has
resolved complex regions of the genome, including repetitive and homologous regions …

DeepSignal: detecting DNA methylation state from Nanopore sequencing reads using deep-learning

P Ni, N Huang, Z Zhang, DP Wang, F Liang… - …, 2019 - academic.oup.com
Abstract Motivation The Oxford Nanopore sequencing enables to directly detect methylation
states of bases in DNA from reads without extra laboratory techniques. Novel computational …

Non–B-form DNA tends to form in centromeric regions and has undergone changes in polyploid oat subgenomes

Q Liu, C Yi, Z Zhang, H Su, C Liu… - Proceedings of the …, 2023 - National Acad Sciences
Centromeres are the specialized regions of the chromosomes that direct faithful
chromosome segregation during cell division. Despite their functional conservation …

Recompleting the Caenorhabditis elegans genome

J Yoshimura, K Ichikawa, MJ Shoura, KL Artiles… - Genome …, 2019 - genome.cshlp.org
Caenorhabditis elegans was the first multicellular eukaryotic genome sequenced to
apparent completion. Although this assembly employed a standard C. elegans strain (N2), it …

What is speciation genomics? The roles of ecology, gene flow, and genomic architecture in the formation of species

CR Campbell, JW Poelstra… - Biological Journal of the …, 2018 - academic.oup.com
As is true of virtually every realm of the biological sciences, our understanding of speciation
is increasingly informed by the genomic revolution of the past decade. Investigators can ask …

The miR-430 locus with extreme promoter density forms a transcription body during the minor wave of zygotic genome activation

Y Hadzhiev, L Wheatley, L Cooper, F Ansaloni… - Developmental cell, 2023 - cell.com
In anamniote embryos, the major wave of zygotic genome activation starts during the mid-
blastula transition. However, some genes escape global genome repression, are activated …

Chromosome-scale assemblies reveal the structural evolution of African cichlid genomes

MA Conte, R Joshi, EC Moore, SP Nandamuri… - …, 2019 - academic.oup.com
Background African cichlid fishes are well known for their rapid radiations and are a model
system for studying evolutionary processes. Here we compare multiple, high-quality …

Cell cycle length governs heterochromatin reprogramming during early development in non-mammalian vertebrates

HS Fukushima, T Ikeda, S Ikeda, H Takeda - EMBO reports, 2024 - embopress.org
Heterochromatin marks such as H3K9me3 undergo global erasure and re-establishment
after fertilization, and the proper reprogramming of H3K9me3 is essential for early …