Variant calling and benchmarking in an era of complete human genome sequences

ND Olson, J Wagner, N Dwarshuis, KH Miga… - Nature Reviews …, 2023 - nature.com
Genetic variant calling from DNA sequencing has enabled understanding of germline
variation in hundreds of thousands of humans. Sequencing technologies and variant-calling …

Genomics in the long-read sequencing era

EL van Dijk, D Naquin, K Gorrichon, Y Jaszczyszyn… - Trends in Genetics, 2023 - cell.com
Long-read sequencing (LRS) technologies have provided extremely powerful tools to
explore genomes. While in the early years these methods suffered technical limitations, they …

Telomere-to-telomere assembly of diploid chromosomes with Verkko

M Rautiainen, S Nurk, BP Walenz, GA Logsdon… - Nature …, 2023 - nature.com
Abstract The Telomere-to-Telomere consortium recently assembled the first truly complete
sequence of a human genome. To resolve the most complex repeats, this project relied on …

How will generative AI disrupt data science in drug discovery?

JP Vert - Nature Biotechnology, 2023 - nature.com
In the short few months since the release of ChatGPT 1, 2, the potential for large language
models (LLMs) and generative artificial intelligence (AI) to disrupt fields as diverse as art …

High-throughput RNA isoform sequencing using programmed cDNA concatenation

AM Al'Khafaji, JT Smith, KV Garimella, M Babadi… - Nature …, 2024 - nature.com
Full-length RNA-sequencing methods using long-read technologies can capture complete
transcript isoforms, but their throughput is limited. We introduce multiplexed arrays isoform …

[HTML][HTML] Battery safety: Machine learning-based prognostics

J Zhao, X Feng, Q Pang, M Fowler, Y Lian… - Progress in Energy and …, 2024 - Elsevier
Lithium-ion batteries play a pivotal role in a wide range of applications, from electronic
devices to large-scale electrified transportation systems and grid-scale energy storage …

Applications of long-read sequencing to Mendelian genetics

FK Mastrorosa, DE Miller, EE Eichler - Genome medicine, 2023 - Springer
Advances in clinical genetic testing, including the introduction of exome sequencing, have
uncovered the molecular etiology for many rare and previously unsolved genetic disorders …

Gapless assembly of complete human and plant chromosomes using only nanopore sequencing

S Koren, Z Bao, A Guarracino, S Ou… - Genome …, 2024 - genome.cshlp.org
The combination of ultra-long (UL) Oxford Nanopore Technologies (ONT) sequencing reads
with long, accurate Pacific Bioscience (PacBio) High Fidelity (HiFi) reads has enabled the …

Applications of transformer-based language models in bioinformatics: a survey

S Zhang, R Fan, Y Liu, S Chen, Q Liu… - Bioinformatics …, 2023 - academic.oup.com
The transformer-based language models, including vanilla transformer, BERT and GPT-3,
have achieved revolutionary breakthroughs in the field of natural language processing …

Technology-enabled great leap in deciphering plant genomes

L Xie, X Gong, K Yang, Y Huang, S Zhang, L Shen… - Nature Plants, 2024 - nature.com
Plant genomes provide essential and vital basic resources for studying many aspects of
plant biology and applications (for example, breeding). From 2000 to 2020, 1,144 genomes …