Big data in public health: terminology, machine learning, and privacy

SJ Mooney, V Pejaver - Annual review of public health, 2018 - annualreviews.org
The digital world is generating data at a staggering and still increasing rate. While these “big
data” have unlocked novel opportunities to understand public health, they hold still greater …

Genome interpretation using in silico predictors of variant impact

P Katsonis, K Wilhelm, A Williams, O Lichtarge - Human genetics, 2022 - Springer
Estimating the effects of variants found in disease driver genes opens the door to
personalized therapeutic opportunities. Clinical associations and laboratory experiments …

Calibration of computational tools for missense variant pathogenicity classification and ClinGen recommendations for PP3/BP4 criteria

V Pejaver, AB Byrne, BJ Feng, KA Pagel… - The American Journal of …, 2022 - cell.com
Summary Recommendations from the American College of Medical Genetics and Genomics
and the Association for Molecular Pathology (ACMG/AMP) for interpreting sequence variants …

Updated benchmarking of variant effect predictors using deep mutational scanning

BJ Livesey, JA Marsh - Molecular systems biology, 2023 - embopress.org
The assessment of variant effect predictor (VEP) performance is fraught with biases
introduced by benchmarking against clinical observations. In this study, building on our …

Functional EPAS1/HIF2A missense variant is associated with hematocrit in Andean highlanders

ES Lawrence, W Gu, RJ Bohlender… - Science …, 2024 - science.org
Hypoxia-inducible factor pathway genes are linked to adaptation in both human and
nonhuman highland species. EPAS1, a notable target of hypoxia adaptation, is associated …

Unsupervised and semi‐supervised learning: The next frontier in machine learning for plant systems biology

J Yan, X Wang - The Plant Journal, 2022 - Wiley Online Library
Advances in high‐throughput omics technologies are leading plant biology research into the
era of big data. Machine learning (ML) performs an important role in plant systems biology …

MetaRNN: differentiating rare pathogenic and rare benign missense SNVs and InDels using deep learning

C Li, D Zhi, K Wang, X Liu - Genome Medicine, 2022 - Springer
Multiple computational approaches have been developed to improve our understanding of
genetic variants. However, their ability to identify rare pathogenic variants from rare benign …

How chromosomal inversions reorient the evolutionary process

EL Berdan, NH Barton, R Butlin… - Journal of …, 2023 - Wiley Online Library
Inversions are structural mutations that reverse the sequence of a chromosome segment
and reduce the effective rate of recombination in the heterozygous state. They play a major …

Positive-unlabeled learning in bioinformatics and computational biology: a brief review

F Li, S Dong, A Leier, M Han, X Guo, J Xu… - Briefings in …, 2022 - academic.oup.com
Conventional supervised binary classification algorithms have been widely applied to
address significant research questions using biological and biomedical data. This …

Interpreting protein variant effects with computational predictors and deep mutational scanning

BJ Livesey, JA Marsh - Disease Models & Mechanisms, 2022 - journals.biologists.com
Computational predictors of genetic variant effect have advanced rapidly in recent years.
These programs provide clinical and research laboratories with a rapid and scalable method …