Museum of spatial transcriptomics

L Moses, L Pachter - Nature methods, 2022 - nature.com
The function of many biological systems, such as embryos, liver lobules, intestinal villi, and
tumors, depends on the spatial organization of their cells. In the past decade, high …

Taming transposable elements in vertebrates: from epigenetic silencing to domestication

MV Almeida, G Vernaz, ALK Putman, EA Miska - Trends in Genetics, 2022 - cell.com
Transposable element (TE)-derived sequences are ubiquitous in most eukaryotic genomes
known to date. Because their expression and mobility can lead to genomic instability …

Semi-automated assembly of high-quality diploid human reference genomes

ED Jarvis, G Formenti, A Rhie, A Guarracino, C Yang… - Nature, 2022 - nature.com
The current human reference genome, GRCh38, represents over 20 years of effort to
generate a high-quality assembly, which has benefitted society,. However, it still has many …

The complete reference genome for grapevine (Vitis vinifera L.) genetics and breeding

X Shi, S Cao, X Wang, S Huang, Y Wang… - Horticulture …, 2023 - academic.oup.com
Grapevine is one of the most economically important crops worldwide. However, the
previous versions of the grapevine reference genome tipically consist of thousands of …

Continuous synthesis of E. coli genome sections and Mb-scale human DNA assembly

JF Zürcher, AA Kleefeldt, LFH Funke, J Birnbaum… - Nature, 2023 - nature.com
Whole-genome synthesis provides a powerful approach for understanding and expanding
organism function,–. To build large genomes rapidly, scalably and in parallel, we need (1) …

Complete vertebrate mitogenomes reveal widespread repeats and gene duplications

G Formenti, A Rhie, J Balacco, B Haase, J Mountcastle… - Genome biology, 2021 - Springer
Background Modern sequencing technologies should make the assembly of the relatively
small mitochondrial genomes an easy undertaking. However, few tools exist that address …

Scalable, accessible and reproducible reference genome assembly and evaluation in Galaxy

D Larivière, L Abueg, N Brajuka, C Gallardo-Alba… - Nature …, 2024 - nature.com
The Earth BioGenome Project aims to produce reference genomes for all~ 1.8 million known
eukaryotic species over the next decade 1–4. Achieving this goal will require the current …

[LLIBRE][B] Genomes 5

TA Brown - 2023 - taylorfrancis.com
Genomes 5 has been completely revised and updated. It is a thoroughly modern textbook
about genomes and how they are investigated. As with previous Genomes editions …

Pangenome graphs and their applications in biodiversity genomics

S Secomandi, GR Gallo, R Rossi… - Nature Genetics, 2025 - nature.com
Complete datasets of genetic variants are key to biodiversity genomic studies. Long-read
sequencing technologies allow the routine assembly of highly contiguous, haplotype …

Data Storage Using DNA

S Wang, X Mao, F Wang, X Zuo, C Fan - Advanced Materials, 2024 - Wiley Online Library
The exponential growth of global data has outpaced the storage capacities of current
technologies, necessitating innovative storage strategies. DNA, as a natural medium for …