Methods, software, and public datasets

Core Lab Resources

JTK_CYCLE

Nonparametric rhythmicity detection for genome-scale time-series data.

Publication

PSEA

Phase Set Enrichment Analysis for interpreting rhythmic pathways and coordinated gene sets.

Publication

MetaCycle

Integrated rhythmicity analysis that combines complementary periodicity algorithms.

Publication • GitHub

CYCLOPS / CYCLOPS2

Computational recovery of temporal order in unordered human transcriptomic datasets, with recent methods work extending the framework to newer integration challenges.

CYCLOPS • CYCLOPS2

CircaDB

Searchable mammalian circadian gene-expression profiles for bench and computational investigators.

Explore CircaDB • Publication

Gene Atlas

One of the earliest comprehensive maps of gene expression across mammalian tissues and a foundational functional genomics resource.

Publication

Public Datasets and Reference Resources

Gene Atlas

The Gene Atlas is one of the earliest comprehensive maps of gene expression across mammalian tissues and remains one of the lab’s most influential functional genomics resources.

Publication

Circadian Atlas

The multi-organ mouse circadian atlas that established the breadth and tissue specificity of rhythmic transcription.

Publication

Human Circadian Resource

The published human tissue resource built from CYCLOPS-ordered transcriptomic data with applications to circadian medicine.

Publication

Gene Wiki

Open community annotation for human genes, developed to broaden access to functional genomic knowledge.

Publication

Practical Use

• Use JTK_CYCLE or MetaCycle for rhythmicity detection in structured time-series experiments.
• Use PSEA for questions about pathway timing rather than isolated genes.
• Use CYCLOPS when samples lack collection times but still preserve circadian structure.
• Use CircaDB and the circadian atlas to move from a gene or tissue to a published rhythmic-expression context.