Yun S. Song

2 months ago | biorxiv.org | Yun Deng |Yun S. Song |Rasmus Nielsen

AbstractInference of Ancestral Recombination Graphs (ARGs) is of central interest in the analysis of genomic variation. ARGs can be specified in terms of topologies and coalescence times.

Jan 2, 2025 | nature.com | Yun S. Song

AbstractProtein language models have demonstrated remarkable performance in predicting the effects of missense variants but DNA language models have not yet shown a competitive edge for complex genomes such as that of humans. This limitation is particularly evident when dealing with the vast complexity of noncoding regions that comprise approximately 98% of the human genome.

Nov 18, 2024 | nature.com | Yun S. Song |Heon-Jeong Lee |Chul-Hyun Cho |Jae Kyoung Kim |Dongju Lim |Jung-Been Lee | +3 more

Wearable devices enable passive collection of sleep, heart rate, and step-count data, offering potential for mood episode prediction in mood disorder patients. However, current models often require various data types, limiting real-world application. Here, we develop models that predict future episodes using only sleep-wake data, easily gathered through smartphones and wearables when trained on an individual’s sleep-wake history and past mood episodes. Using mathematical modeling to longitudinal data from 168 patients (587 days average clinical follow-up, 267 days wearable data), we derived 36 sleep and circadian rhythm features. These features enabled accurate next-day predictions for depressive, manic, and hypomanic episodes (AUCs: 0.80, 0.98, 0.95). Notably, daily circadian phase shifts were the most significant predictors: delays linked to depressive episodes, advances to manic episodes. This prospective observational cohort study (ClinicalTrials.gov: NCT03088657, 2017-3-23) shows sleep-wake data, combined with prior mood episode history, can effectively predict mood episodes, enhancing mood disorder management.

Oct 2, 2024 | biorxiv.org | Yun Deng |Rasmus Nielsen |Yun S. Song

AbstractIt was recently reported that a severe ancient bottleneck occurred around 900 thousand years ago in the ancestry of African populations, while this signal is absent in non-African populations. Here, we present evidence to show that this finding is likely a statistical artifact. Competing Interest StatementThe authors have declared no competing interest.

Mar 16, 2024 | biorxiv.org | Yun Deng |Rasmus Nielsen |Yun S. Song

AbstractThe Ancestral Recombination Graph (ARG), which describes the full genealogical history of a sample of genomes, is a vital tool in population genomics and biomedical research. Recent advancements have increased ARG reconstruction scalability to tens or hundreds of thousands of genomes, but these methods rely on heuristics, which can reduce accuracy, particularly in the presence of model misspecification.