Artificial intelligence in molecular medicine

B Gomes, EA Ashley - New England Journal of Medicine, 2023 - Mass Medical Soc
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A guide for the diagnosis of rare and undiagnosed disease: beyond the exome

S Marwaha, JW Knowles, EA Ashley - Genome medicine, 2022 - Springer
Rare diseases affect 30 million people in the USA and more than 300–400 million
worldwide, often causing chronic illness, disability, and premature death. Traditional …

The complete sequence of a human Y chromosome

A Rhie, S Nurk, M Cechova, SJ Hoyt, DJ Taylor… - Nature, 2023 - nature.com
The human Y chromosome has been notoriously difficult to sequence and assemble
because of its complex repeat structure that includes long palindromes, tandem repeats and …

The complete sequence of a human genome

S Nurk, S Koren, A Rhie, M Rautiainen, AV Bzikadze… - Science, 2022 - science.org
Since its initial release in 2000, the human reference genome has covered only the
euchromatic fraction of the genome, leaving important heterochromatic regions unfinished …

A complete reference genome improves analysis of human genetic variation

S Aganezov, SM Yan, DC Soto, M Kirsche, S Zarate… - Science, 2022 - science.org
Compared to its predecessors, the Telomere-to-Telomere CHM13 genome adds nearly 200
million base pairs of sequence, corrects thousands of structural errors, and unlocks the most …

Ultrarapid nanopore genome sequencing in a critical care setting

JE Gorzynski, SD Goenka, K Shafin… - … England Journal of …, 2022 - Mass Medical Soc
Genetic Diagnoses in Critical Care Because a genetic diagnosis can guide clinical
management and improve prognosis in critically ill patients, much effort has gone into …

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 …

Assembly of 43 human Y chromosomes reveals extensive complexity and variation

P Hallast, P Ebert, M Loftus, F Yilmaz, PA Audano… - Nature, 2023 - nature.com
The prevalence of highly repetitive sequences within the human Y chromosome has
prevented its complete assembly to date and led to its systematic omission from genomic …

Scalable Nanopore sequencing of human genomes provides a comprehensive view of haplotype-resolved variation and methylation

M Kolmogorov, KJ Billingsley, M Mastoras… - Nature …, 2023 - nature.com
Long-read sequencing technologies substantially overcome the limitations of short-reads
but have not been considered as a feasible replacement for population-scale projects, being …

Symphonizing pileup and full-alignment for deep learning-based long-read variant calling

Z Zheng, S Li, J Su, AWS Leung, TW Lam… - Nature Computational …, 2022 - nature.com
Deep learning-based variant callers are becoming the standard and have achieved superior
single nucleotide polymorphisms calling performance using long reads. Here we present …