Anafi RC, Francey LJ, Hogenesch JB, Kim J: CYCLOPS reveals human transcriptional rhythms in health and disease Proceedings of the National Academy of Sciences of the United States of America 114 (20): 5312-5317,2017.
Krishnaiah SY, Wu G, Altman B, Growe J, Rhoades SD, Coldren F, Venkataraman A, Olarerin-George AO, Francey LJ, Mukherjee S, Girish S, Selby CP, Cal S, Er U, Sianati B, Sengupta A, Anafi RC, Kavakli IH, Sancar A, Baur JA, Dang CV, Hogenesch JB, Weljie AM: Clock regulation of metabolites reveals coupling between transcription and metabolism Cell Metabolism 25 (4): 961-974.e4,2017.
Wu G, Anafi RC, Hughes ME, Kornacker K, Hogenesch JB: MetaCycle: an integrated R package to evaluate periodicity in large scale data. Bioinformatics 32 (21): 3351-3353,2016.
Zhang R, Podtelezhnikov AA, Hogenesch JB, Anafi RC: Discovering biology in periodic data through Phase Set Enrichment Analysis (PSEA) Journal of Biological Rhythms 31 (3): 244-257,2016.
Arnardottir ES, Nikonova EV, Shockley KR, Podtelezhnikov AA, Anafi RC, Tanis KQ, Maislin G, Stone DJ, Renger JJ, Winrow CJ, Pack AI: Blood-gene expression reveals reduced circadian rhythmicity in individuals resistant to sleep deprivation. Sleep 37 (10): 1589-1600,2014.
Anafi RC, Lee Y, Sato TK, Venkataraman A, Ramanathan C, Kavakli IH, Hughes ME, Baggs JE, Growe J, Liu AC, Kim J, Hogenesch J: Machine learning helps identify CHRONO as a circadian clock component. PLoS Biology 12 (4): e1001840,2014.
Deckard A, Anafi RC, Hogenesch JB, Haase SB, Harer J: Design and analysis of large-scale biological rhythm studies: a comparison of algorithms for detecting periodic signals in biological data Bioinformatics (Oxford, England) 29 (24): 3174-3180,2013.
Anafi RC, Pellegrino R, Shockley KR, Romer M, Tufik S, Pack A: Sleep is not just for the brain: transcriptional responses to sleep in peripheral tissues BMC Genomics 14 : 362,2013.
Schwartz BL, Anafi RC, Aliyeva M, Thompson-Figueroa JA, Allen GB, Lundblad LKA, Bates JHT: Effects of central airway shunting on the mechanical impedance of the mouse lung Annals of Biomedical Engineering 39 (1): 497-507,2011.
Anafi RC, Bates JHT: Balancing robustness against the dangers of multiple attractors in a Hopfield-type model of biological attractors PLoS One 5 (12): e14413,2010.