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  2. The Lomb–Scargle periodogram-b...

The Lomb–Scargle periodogram-based differentially expressed gene detection along pseudotime（Published in Nucleic Acids Research, July, 2026）

Journal Title
/掲載ジャーナル名		 Nucleic Acids Research
Publication Year and Month
/掲載年月		 July, 2026
Paper Title
/論文タイトル		 The Lomb–Scargle periodogram-based differentially expressed gene detection along pseudotime
DOI
/論文DOI		 10.1093/nar/gkag682
 Author of Waseda University
/本学の著者		 IUCHI, Hitoshi(Junior Researcher(Assistant Professor), Faculty of Science and Engineering, Waseda Research Institute for Science and Engineering):Lead Author
Related Websites
/関連Web		 –
Abstract
/抄録
Single-cell RNA sequencing has provided high-resolution snapshots of biological processes and has contributed to the understanding of cell dynamics. Trajectory inference has the potential to provide a quantitative representation of cell dynamics, and several trajectory inference algorithms have been developed. However, the downstream analysis of trajectory inference, such as the analysis of differentially expressed genes, remains challenging. Here, we present scLS, a Lomb–Scargle periodogram-based framework for two differential expression tests: a dynamic expression test for pseudotime-associated variation and a shifted expression test for condition-dependent differences in pseudotime-indexed expression trajectories. Because scLS operates in the frequency domain, it does not require specification of an explicit regression model and can be applied to inferred tree-structured trajectories without explicit branch assignment. We validated this approach using simulated data and real datasets, and our results showed that scLS achieved competitive performance and complementary sensitivity to transient or complex pseudotime-associated patterns. Our approach provides a computationally efficient first-pass screening framework that can be combined with lineage-aware analyses for detailed biological interpretation.
18 JULY 2026
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