Resources
Methods, software, and public datasets
The lab’s public-facing tools and datasets make rhythmic biology easier to analyze, compare, and reuse.
Recent Methods Highlight
CYCLOPS2 extends the lab’s work with Ron Anafi on reconstructing circadian structure from unordered human datasets and addresses newer challenges in circadian data integration.
Core Lab Resources
PSEA
Phase Set Enrichment Analysis for interpreting rhythmic pathways and coordinated gene sets.
MetaCycle
Integrated rhythmicity analysis that combines complementary periodicity algorithms.
CYCLOPS / CYCLOPS2
Computational recovery of temporal order in unordered human transcriptomic datasets, with recent methods work extending the framework to newer integration challenges.
CircaDB
Searchable mammalian circadian gene-expression profiles for bench and computational investigators.
Public Datasets and Reference Resources
Gene Atlas
The 2002 circadian transcription study and the expanded 2004 Gene Atlas established tissue-scale references for mammalian gene expression.
Circadian Atlas
The multi-organ mouse circadian atlas that established the breadth and tissue specificity of rhythmic transcription.
Human Circadian Resource
The published human tissue resource built from CYCLOPS-ordered transcriptomic data with applications to circadian medicine.
Gene Wiki
Open community annotation for human genes, developed to broaden access to functional genomic knowledge.
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.