WAVECLOCK: wavelet analysis of circadian oscillation. - Tom S. Price; Julie E. Baggs; Anne M. Curtis; Garret A. FitzGerald; John B. Hogenesch (Bioinform., 2008)

NetAtlas: A Cytoscape Plugin to Examine Signaling Networks Based on Tissue Gene Expression. - Longlong Yang; John R. Walker; John B. Hogenesch; Russell S. Thomas (Silico Biol., 2008)

The Gene Wiki: community intelligence applied to human gene annotation. - Jon W. Huss III; Pierre Lindenbaum; Michael Martone; Donabel Roberts; Angel D. Pizarro; Faramarz Valafar; John B. Hogenesch; Andrew I. Su (Nucleic Acids Res., 2010)

Comparative analysis of RNA-Seq alignment algorithms and the RNA-Seq unified mapper (RUM). - Gregory R. Grant; Michael H. Farkas; Angel D. Pizarro; Nicholas F. Lahens; Jonathan Schug; Brian P. Brunk; Christian J. Stoeckert Jr.; John B. Hogenesch; Eric A. Pierce (Bioinform., 2011)

Design and analysis of large-scale biological rhythm studies: a comparison of algorithms for detecting periodic signals in biological data. - Anastasia Deckard; Ron C. Anafi; John B. Hogenesch; Steven B. Haase; John Harer (Bioinform., 2013)

CircaDB: a database of mammalian circadian gene expression profiles. - Angel D. Pizarro; Katharina Hayer; Nicholas F. Lahens; John B. Hogenesch (Nucleic Acids Res., 2013)

Benchmark analysis of algorithms for determining and quantifying full-length mRNA splice forms from RNA-seq data. - Katharina E. Hayer; Angel D. Pizarro; Nicholas F. Lahens; John B. Hogenesch; Gregory R. Grant (Bioinform., 2015)

MetaCycle: an integrated R package to evaluate periodicity in large scale data. - Gang Wu; Ron C. Anafi; Michael Hughes; Karl Kornacker; John B. Hogenesch (Bioinform., 2016)

Normalized coefficient of variation (nCV): a method to evaluate circadian clock robustness in population scale data. - Gang Wu; Lauren J. Francey; Marc D. Ruben; John B. Hogenesch (Bioinform., 2021)

An in silico genome-wide screen for circadian clock strength in human samples. - Gang Wu; Marc D. Ruben; Lauren J. Francey; Yin Yeng Lee; Ron C. Anafi; John B. Hogenesch (Bioinform., 2022)