Artificial intelligence in molecular medicine

B Gomes, EA Ashley - New England Journal of Medicine, 2023 - Mass Medical Soc
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Towards population-scale long-read sequencing

W De Coster, MH Weissensteiner… - Nature Reviews …, 2021 - nature.com
Long-read sequencing technologies have now reached a level of accuracy and yield that
allows their application to variant detection at a scale of tens to thousands of samples …

Towards generalist biomedical AI

T Tu, S Azizi, D Driess, M Schaekermann, M Amin… - NEJM AI, 2024 - ai.nejm.org
Background Medicine is inherently multimodal, requiring the simultaneous interpretation
and integration of insights between many data modalities spanning text, imaging, genomics …

A draft human pangenome reference

WW Liao, M Asri, J Ebler, D Doerr, M Haukness… - Nature, 2023 - nature.com
Abstract Here the Human Pangenome Reference Consortium presents a first draft of the
human pangenome reference. The pangenome contains 47 phased, diploid assemblies …

Haplotype-aware variant calling with PEPPER-Margin-DeepVariant enables high accuracy in nanopore long-reads

K Shafin, T Pesout, PC Chang, M Nattestad… - Nature …, 2021 - nature.com
Long-read sequencing has the potential to transform variant detection by reaching currently
difficult-to-map regions and routinely linking together adjacent variations to enable read …

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 …

DeepConsensus improves the accuracy of sequences with a gap-aware sequence transformer

G Baid, DE Cook, K Shafin, T Yun… - Nature …, 2023 - nature.com
Circular consensus sequencing with Pacific Biosciences (PacBio) technology generates
long (10–25 kilobases), accurate 'HiFi'reads by combining serial observations of a DNA …

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 …

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 …

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 …