Selected publications

HIF-2alpha, Hypoxia, and Molecular Clock Mechanisms

• 1997 bHLH-PAS family paper. Hogenesch JB, Chan WK, Jackiw VH, Brown RC, Gu YZ, Pray-Grant M, Perdew GH, Bradfield CA. Characterization of a subset of the basic-helix-loop-helix-PAS superfamily that interacts with components of the dioxin signaling pathway. J Biol Chem. 1997.
• BMAL1 / MOP3. Hogenesch JB, Gu YZ, Jain S, Bradfield CA. The basic-helix-loop-helix-PAS orphan MOP3 forms transcriptionally active complexes with circadian and hypoxia factors. Proc Natl Acad Sci U S A. 1998.
• BMAL2 / MOP9. Hogenesch JB, Gu YZ, Moran SM, Shimomura K, Radcliffe LA, Takahashi JS, Bradfield CA. The basic helix-loop-helix-PAS protein MOP9 is a brain-specific heterodimeric partner of circadian and hypoxia factors. J Neurosci. 2000.
• RORA / RORE loop. Sato TK, Panda S, Miraglia LJ, Reyes TM, Rudic RD, McNamara P, Naik KA, FitzGerald GA, Kay SA, Hogenesch JB. A functional genomics strategy reveals Rora as a component of the mammalian circadian clock. Neuron. 2004.
• CHRONO. Anafi RC, Lee Y, Sato TK, Venkataraman A, Ramanathan C, Kavakli IH, Hughes ME, Baggs JE, Growe J, Liu AC, Kim J, Hogenesch JB. Machine learning helps identify CHRONO as a circadian clock component. PLoS Biol. 2014.

Genome-scale Circadian Transcription

• Genome-scale circadian transcription. Panda S, Antoch MP, Miller BH, Su AI, Schook AB, Straume M, Schultz PG, Kay SA, Takahashi JS, Hogenesch JB. Coordinated transcription of key pathways in the mouse by the circadian clock. Cell. 2002.
• Gene Atlas. Su AI, Wiltshire T, Batalov S, Lapp H, Ching KA, Block D, Zhang J, Soden R, Hayakawa M, Kreiman G, Cooke MP, Walker JR, Hogenesch JB. A gene atlas of the mouse and human protein-encoding transcriptomes. Proc Natl Acad Sci U S A. 2004.
• Mammalian circadian transcriptome. Hughes ME, DiTacchio L, Hayes KR, Vollmers C, Pulivarthy S, Baggs JE, Panda S, Hogenesch JB. Harmonics of circadian gene transcription in mammals. PLoS Genet. 2009.
• Functional genomics clock modulators. Zhang EE, Liu AC, Hirota T, Miraglia LJ, Welch G, Pongsawakul PY, Liu X, Atwood A, Huss JW 3rd, Janes J, Su AI, Hogenesch JB, Kay SA. A genome-wide RNAi screen for modifiers of the circadian clock in human cells. Cell. 2009.
• Mouse organ atlas. Zhang R, Lahens NF, Ballance HI, Hughes ME, Hogenesch JB. A circadian gene expression atlas in mammals: implications for biology and medicine. Proc Natl Acad Sci U S A. 2014.
• Human circadian atlas. Ruben MD, Wu G, Smith DF, Schmidt RE, Francey LJ, Lee YY, Anafi RC, Hogenesch JB. A database of tissue-specific rhythmically expressed human genes has potential applications in circadian medicine. Sci Transl Med. 2018.

Algorithms and Public Resources

• Clock Gene Wiki. Huss JW 3rd, Orozco C, Goodale J, Wu C, Batalov S, Vickers TJ, Valafar F, Su AI, Hogenesch JB. Clock Gene Wikis available. PLoS Comput Biol. 2008.
• JTK_CYCLE. Hughes ME, Hogenesch JB, Kornacker K. JTK_CYCLE: an efficient nonparametric algorithm for detecting rhythmic components in genome-scale data sets. J Biol Rhythms. 2010.
• Gene Wiki. Huss JW 3rd, Lindenbaum P, Martone M, Roberts D, Pizarro A, Valafar F, Hogenesch JB, Su AI. The Gene Wiki: community intelligence applied to human gene annotation. Nucleic Acids Res. 2010.
• CircaDB. Pizarro A, Hayer K, Lahens NF, Hogenesch JB. CircaDB: a database of mammalian circadian gene expression profiles. Nucleic Acids Res. 2013.
• PSEA. Zhang R, Podtelezhnikov AA, Hogenesch JB, Anafi RC. Discovering biology in periodic data through phase set enrichment analysis (PSEA). J Biol Rhythms. 2016.
• MetaCycle. Wu G, Anafi RC, Hughes ME, Kornacker K, Hogenesch JB. MetaCycle: an integrated R package to evaluate periodicity in large scale data. Bioinformatics. 2016.
• CYCLOPS. Anafi RC, Francey LJ, Hogenesch JB, Kim J. CYCLOPS reveals human transcriptional rhythms in health and disease. Proc Natl Acad Sci U S A. 2017.
• CYCLOPS2. Anafi RC, Wu G, et al. CYCLOPS2: Navigating modern challenges in circadian data integration. J Biol Rhythms. 2025.

Human Circadian Biology and Circadian Medicine

• Dosing time matters. Ruben MD, Smith DF, FitzGerald GA, Hogenesch JB. Dosing time matters. Science. 2019.

Human Genetics and Rare Disease

• mTOR and Smith-Kingsmore syndrome. Liu AC, Shen Y, Serbinski CR, He H, Roman D, Endale M, Aschbacher-Smith L, King KA, Granadillo JL, López I, Krueger DA, Dye TJ, Smith DF, Hogenesch JB, Prada CE. Clinical and functional studies of MTOR variants in Smith-Kingsmore syndrome reveal deficits of circadian rhythm and sleep-wake behavior. HGG Adv. 2024.
• SHINE syndrome model. Tamir S, Paulose J, Nguyen A, Gadara D, Witt RM, Prasad B, Hogenesch JB. A patient-derived mouse model reproduces molecular, neurological, and sleep symptoms of SHINE syndrome. Hum Mol Genet. 2026.