Publications | Hogenesch Lab

Full Publication List

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Nobel context

The official historical materials for the 2019 Nobel Prize in Physiology or Medicine on oxygen sensing name Hogenesch et al., 1997 in the HIF-2alpha branch of the field. The clock papers below also sit in the scientific arc recognized by the 2017 Nobel Prize in Physiology or Medicine.

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

Gene Atlas. 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.
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.