Next-generation data filtering in the genomics era

W Hemstrom, JA Grummer, G Luikart… - Nature Reviews …, 2024 - nature.com
Genomic data are ubiquitous across disciplines, from agriculture to biodiversity, ecology,
evolution and human health. However, these datasets often contain noise or errors and are …

Genetic variation across and within individuals

Z Yu, THH Coorens, MM Uddin, KG Ardlie… - Nature Reviews …, 2024 - nature.com
Germline variation and somatic mutation are intricately connected and together shape
human traits and disease risks. Germline variants are present from conception, but they vary …

Analysis and benchmarking of small and large genomic variants across tandem repeats

AC English, E Dolzhenko, H Ziaei Jam… - Nature …, 2024 - nature.com
Tandem repeats (TRs) are highly polymorphic in the human genome, have thousands of
associated molecular traits and are linked to over 60 disease phenotypes. However, they …

Comprehensive genome analysis and variant detection at scale using DRAGEN

S Behera, S Catreux, M Rossi, S Truong, Z Huang… - Nature …, 2024 - nature.com
Research and medical genomics require comprehensive, scalable methods for the
discovery of novel disease targets, evolutionary drivers and genetic markers with clinical …

Implementing whole genome sequencing (WGS) in clinical practice: advantages, challenges, and future perspectives

P Brlek, L Bulić, M Bračić, P Projić, V Škaro, N Shah… - Cells, 2024 - mdpi.com
The integration of whole genome sequencing (WGS) into all aspects of modern medicine
represents the next step in the evolution of healthcare. Using this technology, scientists and …

The complete and fully-phased diploid genome of a male Han Chinese

C Yang, Y Zhou, Y Song, D Wu, Y Zeng, L Nie, P Liu… - Cell Research, 2023 - nature.com
Since the release of the complete human genome, the priority of human genomic study has
now been shifting towards closing gaps in ethnic diversity. Here, we present a fully phased …

Plant pangenomes for crop improvement, biodiversity and evolution

M Schreiber, M Jayakodi, N Stein… - Nature Reviews Genetics, 2024 - nature.com
Plant genome sequences catalogue genes and the genetic elements that regulate their
expression. Such inventories further research aims as diverse as map** the molecular …

Beyond the human genome project: the age of complete human genome sequences and pangenome references

DJ Taylor, JM Eizenga, Q Li, A Das… - Annual review of …, 2024 - annualreviews.org
The Human Genome Project was an enormous accomplishment, providing a foundation for
countless explorations into the genetics and genomics of the human species. Yet for many …

Benchmarking reveals superiority of deep learning variant callers on bacterial nanopore sequence data

MB Hall, RR Wick, LM Judd, AN Nguyen, EJ Steinig… - Elife, 2024 - elifesciences.org
Variant calling is fundamental in bacterial genomics, underpinning the identification of
disease transmission clusters, the construction of phylogenetic trees, and antimicrobial …

Multiple human population movements and cultural dispersal events shaped the landscape of Chinese paternal heritage

M Wang, Y Huang, K Liu, Z Wang… - Molecular Biology …, 2024 - academic.oup.com
Large-scale genomic projects and ancient DNA innovations have ushered in a new
paradigm for exploring human evolutionary history. However, the genetic legacy of …