PUBLICATIONS





Publications


Bailey MJ, Coon SL, Carter DA, Humphries A, Kim JS, Shi Q, Gaildrat P, Morin F, Ganguly S, Hogenesch JB, Weller JL, Rath MF, Mřller M, Baler R, Sugden D, Rangel ZG, Munson PJ, Klein DC.
Night/day changes in pineal expression of >600 genes: Central role of adrenergic/cAMP signaling
J Biol Chem. 2008 Dec 22. [Epub ahead of print]
PMID: 19103603 [PubMed - indexed for MEDLINE]

Price, T.S., Baggs, J.E., Curtis, A.M., Fitzgerald, G.A., and Hogenesch, J.B.
WAVECLOCK: Wavelet analysis of circadian oscillation. Bioinformatics (Oxford, England).
Bioinformatics. 2008 Dec 1;24(23):2794-5. Epub 2008 Oct 17.
PMID: 18931366 [PubMed - indexed for MEDLINE]

Takahashi JS, Shimomura K, Kumar V.
Searching for genes underlying behavior: lessons from circadian rhythms.
Science. 2008 Nov 7;322(5903):909-12.
PMID: 18988844 [PubMed - indexed for MEDLINE]

Nakamura TJ, Sellix MT, Menaker M, Block GD.
Estrogen directly modulates circadian rhythms of PER2 expression in the uterus.
Am J Physiol Endocrinol Metab. 2008 Nov;295(5):E1025-31. Epub 2008 Aug 26.
PMID: 18728223 [PubMed - indexed for MEDLINE]

Hogenesch, J.B., and Su, A.I.
Clock gene wikis available: join the "long tail".
J Biol Rhythms. 2008 Oct;23(5):456-7.
PMID: 18838611 [PubMed - indexed for MEDLINE]

Takahashi JS, Hong HK, Ko CH, McDearmon EL.
The genetics of mammalian circadian order and disorder: implications for physiology and disease.
Nat Rev Genet. 2008 Oct;9(10):764-75. Review.
PMID: 18802415 [PubMed - indexed for MEDLINE]

Green CB, Takahashi JS, Bass J.
The meter of metabolism.
Cell. 2008 Sep 5;134(5):728-42. Review.
PMID: 18775307 [PubMed - indexed for MEDLINE]

Doyle SE, Yoshikawa T, Hillson H, Menaker M.
Retinal pathways influence temporal niche.
Proc Natl Acad Sci U S A. 2008 Sep 2;105(35):13133-8. Epub 2008 Aug 11.
PMID: 18695249 [PubMed - indexed for MEDLINE]

Kumaki, Y., Ukai-Tadenuma, M., Uno, K.D., Nishio, J., Masumoto, K.H., Nagano, M., Komori, T., Shigeyoshi, Y., Hogenesch, J.B., and Ueda, H.R.
Analysis and synthesis of high-amplitude Cis-elements in the mammalian circadian clock.
Proc Natl Acad Sci U S A. 2008 Sep 30;105(39):14946-51.
PMID: 18815372 [PubMed - indexed for MEDLINE]

Yang, L., Walker, J.R., Hogenesch, J.B., and Thomas, R.S.
NetAtlas: a Cytoscape plugin to examine signaling networks based on tissue gene expression.
In Silico Biol. 2008;8(1):47-52.
PMID: 18430989 [PubMed - indexed for MEDLINE]

Vujovic N, Davidson AJ, Menaker M.
Sympathetic input modulates, but does not determine, phase of peripheral circadian oscillators
Am J Physiol Regul Integr Comp Physiol. 2008 Jul;295(1):R355-60. Epub 2008 Apr 23.
PMID: 18434440 [PubMed - indexed for MEDLINE]

O'Neill JS, Maywood ES, Chesham JE, Takahashi JS, Hastings MH.
cAMP-dependent signaling as a core component of the mammalian circadian pacemaker.
Science. 2008 May 16;320(5878):949-53.
PMID: 18487196 [PubMed - indexed for MEDLINE]

Wu C, Delano DL, Mitro N, Su SV, Janes J, McClurg P, Batalov S, Welch GL, Zhang J, Orth AP, Walker JR, Glynne RJ, Cooke MP, Takahashi JS, Shimomura K, Kohsaka A, Bass J, Saez E, Wiltshire T, Su AI.
Gene set enrichment in eQTL data identifies novel annotations and pathway regulators.
PLoS Genet. 2008 May 9;4(5):e1000070.
PMID: 18464898 [PubMed - indexed for MEDLINE]

McClurg P, Janes J, Wu C, Delano DL, Walker JR, Batalov S, Takahashi JS, Shimomura K, Kohsaka A, Bass J, Wiltshire T, Su AI.
Genomewide association analysis in diverse inbred mice: power and population structure.
Genetics. 2007 May;176(1):675-83. Epub 2007 Apr 3.
PMID: 17409088 [PubMed - indexed for MEDLINE]

Kwak Y, Lundkvist GB, Brask J, Davidson A, Menaker M, Kristensson K, Block GD.
Interferon-gamma alters electrical activity and clock gene expression in suprachiasmatic nucleus neurons.
J Biol Rhythms. 2008 Apr;23(2):150-9.
PMID: 18375864 [PubMed - indexed for MEDLINE]

Meng QJ, Logunova L, Maywood ES, Gallego M, Lebiecki J, Brown TM, Sládek M, Semikhodskii AS, Glossop NR, Piggins HD, Chesham JE, Bechtold DA, Yoo SH, Takahashi JS, Virshup DM, Boot-Handford RP, Hastings MH, Loudon AS.
Setting clock speed in mammals: the CK1 epsilon tau mutation in mice accelerates circadian pacemakers by selectively destabilizing PERIOD proteins.
Neuron. 2008 Apr 10;58(1):78-88.
PMID: 18400165 [PubMed - indexed for MEDLINE]

Roybal K, Theobold D, Graham A, DiNieri JA, Russo SJ, Krishnan V, Chakravarty S, Peevey J, Oehrlein N, Birnbaum S, Vitaterna MH, Orsulak P, Takahashi JS, Nestler EJ, Carlezon WA Jr, McClung CA.
Mania-like behavior induced by disruption of CLOCK.
Proc Natl Acad Sci U S A. 2007 Apr 10;104(15):6406-11. Epub 2007 Mar 22.
PMID: 17379666 [PubMed - indexed for MEDLINE]

Menaker M.
Circadian clocks: 50 years on
Cold Spring Harb Symp Quant Biol. 2007;72:655-9.
PMID: 18419325 [PubMed - indexed for MEDLINE]

Hughes, M., Deharo, L., Pulivarthy, S.R., Gu, J., Hayes, K., Panda, S., and Hogenesch, J.B.
High-resolution time course analysis of gene expression from pituitary.
Cold Spring Harb Symp Quant Biol. 2007;72:381-6.
PMID: 18419295 [PubMed - indexed for MEDLINE]

Ptácek LJ, Jones CR, Fu YH.
Novel insights from genetic and molecular characterization of the human clock.
Cold Spring Harb Symp Quant Biol. 2007;72:273-7.
PMID: 18419283 [PubMed - indexed for MEDLINE]

van der Schalie EA, Conte FE, Marz KE, Green CB.
Structure/function analysis of Xenopus cryptochromes 1 and 2 reveals differential nuclear localization mechanisms and functional domains important for interaction with and repression of CLOCK-BMAL1.
Mol Cell Biol. 2007 Mar;27(6):2120-9. Epub 2007 Jan 8
PMID: 17210647 [PubMed - indexed for MEDLINE]

Doyle S, Menaker M.
Circadian photoreception in vertebrates.
Cold Spring Harb Symp Quant Biol. 2007;72:499-508.
PMID: 18419310 [PubMed - indexed for MEDLINE]

Amelio, A.L., Miraglia, L.J., Conkright, J.J., Mercer, B.A., Batalov, S., Cavett, V., Orth, A.P., Busby, J., Hogenesch, J.B., and Conkright, M.D.
A coactivator trap identifies NONO (p54nrb) as a component of the cAMP-signaling pathway.
Proc Natl Acad Sci U S A. 2007 Dec 18;104(51):20314-9.
PMID: 18077367 [PubMed - indexed for MEDLINE]

Kozlov, S.V., Bogenpohl, J.W., Howell, M.P., Wevrick, R., Panda, S., Hogenesch, J.B., Muglia, L.J., Van Gelder, R.N., Herzog, E.D., and Stewart, C.L.
The imprinted gene Magel2 regulates normal circadian output.
Nat Genet. 2007 Oct;39(10):1266-72. Epub 2007 Sep 23.
PMID: 17893678 [PubMed - indexed for MEDLINE]

Bartell PA, Miranda-Anaya M, McIvor W, Menaker M.
Interactions between dopamine and melatonin organize circadian rhythmicity in the retina of the green iguana.
J Biol Rhythms. 2007 Dec;22(6):515-23.
PMID: 18057326 [PubMed - indexed for MEDLINE]

Halsey, T.A., Yang, L., Walker, J.R., Hogenesch, J.B., and Thomas, R.S.
A functional map of NFkappaB signaling identifies novel modulators and multiple system controls.
Genome Biology 2007; 8(6): R104.
PMID: 17553156 [PubMed - indexed for MEDLINE]

McCarthy JJ, Andrews JL, McDearmon EL, Campbell KS, Barber BK, Miller BH, Walker JR, Hogenesch JB, Takahashi JS, Esser KA.
Identification of the circadian transcriptome in adult mouse skeletal muscle.
Physiol Genomics. 2007 Sep 19;31(1):86-95. Epub 2007 Jun 5.
PMID: 17550994 [PubMed - indexed for MEDLINE]

Liu AC, Welsh DK, Ko CH, Tran HG, Zhang EE, Priest AA, Buhr ED, Singer O, Meeker K, Verma IM, Doyle FJ 3rd, Takahashi JS, Kay SA.
Intercellular coupling confers robustness against mutations in the SCN circadian clock network.
Cell. 2007 May 4;129(3):605-16.
PMID: 17482552 [PubMed - indexed for MEDLINE]

Siepka SM, Yoo SH, Park J, Song W, Kumar V, Hu Y, Lee C, Takahashi JS.
Circadian mutant Overtime reveals F-box protein FBXL3 regulation of cryptochrome and period gene expression.
Cell. 2007 Jun 1;129(5):1011-23. Epub 2007 Apr 26.
PMID: 17462724 [PubMed - indexed for MEDLINE]
  Comment in: Cell. 2007 Jun 1;129(5):857-9.
Circadian mutant Overtime reveals F-box protein FBXL3 regulation of cryptochrome and period gene expression. Siepka SM, Yoo SH, Park J, Song W, Kumar V, Hu Y, Lee C, Takahashi JS. Howard Hughes Medical Institute, Northwestern University, 2205 Tech Drive, Evanston, IL 60208, USA.

Boothroyd CE, Wijnen H, Naef F, Saez L, Young MW.
Integration of light and temperature in the regulation of circadian gene expression in Drosophila.
PLoS Genet. 2007 Apr 6;3(4):e54.
PMID: 17411344 [PubMed - indexed for MEDLINE]

Miller BH, McDearmon EL, Panda S, Hayes KR, Zhang J, Andrews JL, Antoch MP, Walker JR, Esser KA, Hogenesch JB, Takahashi JS.
Circadian and CLOCK-controlled regulation of the mouse transcriptome and cell proliferation.
Proc Natl Acad Sci U S A. 2007 Feb 27;104(9):3342-7. Epub 2007 Feb 20.
PMID: 17360649 [PubMed - indexed for MEDLINE]

Kornmann B, Schaad O, Bujard H, Takahashi JS, Schibler U.
System-driven and oscillator-dependent circadian transcription in mice with a conditionally active liver clock.
PLoS Biol. 2007 Feb;5(2):e34.
PMID: 17298173 [PubMed - indexed for MEDLINE]

Hong HK, Chong JL, Song W, Song EJ, Jyawook AA, Schook AC, Ko CH, Takahashi JS.
Inducible and reversible Clock gene expression in brain using the tTA system for the study of circadian behavior.
PLoS Genet. 2007 Feb 23;3(2):e33. Epub 2007 Jan 5.
PMID: 17319750 [PubMed - indexed for MEDLINE]

Xu Y, Toh KL, Jones CR, Shin JY, Fu YH, Ptacek LJ.
Modeling of a human circadian mutation yields insights into clock regulation by PER2.
Cell. 2007 Jan 12;128(1):59-70.
PMID: 17218255 [PubMed - indexed for MEDLINE]

Mignot E, Takahashi JS.
A circadian sleep disorder reveals a complex clock.
Cell. 2007 Jan 12;128(1):22-3.
PMID: 17218251 [PubMed - indexed for MEDLINE]
  Comment in: Cell. 2007 Jun 1;129(5):1011-23.
Modeling of a human circadian mutation yields insights into clock regulation by PER2. Xu Y, Toh KL, Jones CR, Shin JY, Fu YH, Ptácek LJ. Department of Neurology, University of California, San Francisco, San Francisco, CA 94158.


McDearmon EL, Patel KN, Ko CH, Walisser JA, Schook AC, Chong JL, Wilsbacher LD, Song EJ, Hong HK, Bradfield CA, Takahashi JS.
Dissecting the functions of the mammalian clock protein BMAL1 by tissue-specific rescue in mice.
Science. 2006 Nov 24;314(5803):1304-8.
PMID: 17124323 [PubMed - indexed for MEDLINE]


Davidson AJ, Yamazaki S, Arble DM, Menaker M, Block GD.
Resetting of central and peripheral circadian oscillators in aged rats.
Neurobiol Aging. 2008 Mar;29(3):471-7. Epub 2006 Nov 28.
PMID: 17129640 [PubMed - indexed for MEDLINE]


Wijnen H, Young MW.
Interplay of circadian clocks and metabolic rhythms.
Annu Rev Genet. 2006;40:409-48. Review.
PMID: 17094740 [PubMed - indexed for MEDLINE]

Siepka SM, Yoo SH, Park J, Lee C, Takahashi JS.
Genetics and neurobiology of circadian clocks in mammals.
Cold Spring Harb Symp Quant Biol. 2007;72:251-9. Review.
PMID: 18419282 [PubMed - indexed for MEDLINE]

Ko CH, Takahashi JS.
Molecular components of the mammalian circadian clock.
Hum Mol Genet. 2006 Oct 15;15 Spec No 2:R271-7. Review.
PMID: 16987893 [PubMed - indexed for MEDLINE]

Doyle SE, Castrucci AM, McCall M, Provencio I, Menaker M  
Non-visual light responses in the Rpe65 knockout mouse: rod loss restores sensitivity to the melanopsin system.
Proc Natl Acad Sci U S A. 2006 Jul 5;103(27):10432-7.
PMID: 16788070 [PubMed - indexed for MEDLINE]

Green CB, Takahashi JS.
Xenobiotic metabolism in the fourth dimension: PARtners in time.
Cell Metab. 2006 Jul;4(1):3-4. Review.
PMID: 16814725 [PubMed - indexed for MEDLINE]

Meredith AL, Wiler SW, Miller BH, Takahashi JS, Fodor AA, Ruby NF, Aldrich RW.
BK calcium-activated potassium channels regulate circadian behavioral rhythms and pacemaker output.
Nat Neurosci. 2006 Aug;9(8):1041-9. Epub 2006 Jul 16. Erratum in: Nat Neurosci. 2006 Sep;9(9):1193.
PMID: 16845385 [PubMed - indexed for MEDLINE]

Tu DC, Owens LA, Anderson L, Golczak M, Doyle SE, McCall M, Menaker M, Palczewski K, Van Gelder RN 
Inner retinal photoreception independent of the visual retinoid cycle.
Proc Natl Acad Sci U S A. 2006 Jul 5;103(27):10426-31..
PMID: 16788071 [PubMed - indexed for MEDLINE]

Numano R, Yamazaki S, Umeda N, Sujino M, Takahashi R, Ueda M, Mori A, Yamada K,  Sakaki Y, Inouye ST,  Menaker M, Tei H.
Constitutive expression of the Period1 gene impairs behavioral and molecular circadian rhythms.
Proc Natl Acad Sci U S A. 2006 Mar 7;103(10):3716-21.
PMID: 16537451 [PubMed - indexed for MEDLINE]

Miller BH, Olson SL, Levine JE, Turek FW, Horton TH, Takahashi JS.
Vasopressin regulation of the proestrous luteinizing hormone surge in wild-type and Clock mutant mice.
Biol Reprod. 2006 Nov;75(5):778-84. Epub 2006 Jul 26.
PMID: 16870944 [PubMed - indexed for MEDLINE]

Vitaterna MH, Ko CH, Chang AM, Buhr ED, Fruechte EM, Schook A, Antoch MP, Turek FW, Takahashi JS.
The mouse Clock mutation reduces circadian pacemaker amplitude and enhances efficacy of resetting stimuli and phase-response curve amplitude.
Proc Natl Acad Sci U S A. 2006 Jun 13;103(24):9327-32. Epub 2006 Jun 5.
PMID: 16754844 [PubMed - indexed for MEDLINE]
Davidson AJ, Straume M, Block GD, Menaker M.
Daily timed meals dissociate circadian rhythms in hepatoma and healthy host liver
Int J Cancer. 2006 Apr 1;118(7):1623-7.
PMID: 16231323 [PubMed - indexed for MEDLINE]

Sato TK, Yamada RG, Ukai H, Baggs JE, Miraglia LJ, Kobayashi TJ, Welsh DK, Kay SA, Ueda HR, Hogenesch JB.
Feedback repression is required for mammalian circadian clock function.
Nat Genet. 2006 Mar;38(3):312-9. Epub 2006 Feb 12.
PMID: 16474406 [PubMed - indexed for MEDLINE]


Menaker M.
Circadian organization in the real world.
Proc Natl Acad Sci U S A. 2006 Feb 28;103(9):3015-6.
PMID: 16492750 [PubMed - indexed for MEDLINE]

Pieper AA, Wu X, Han TW, Estill SJ, Dang Q, Wu LC, Reece-Fincanon S, Dudley CA, Richardson JA, Brat DJ, McKnight SL. 2005. The neuronal PAS domain protein 3 transcription factor controls FGF-mediated adult hippocampal neurogenesis in mice. Proceedings of the National Academy of Sciences of the United States of America 102(39):14052-7.
Wu X, Alexander PB, He Y, Kikkawa M, Vogel P, McKnight SL. 2005.Mammalian sprouty proteins assemble into large monodisperse particles having the properties of intracellular nanobatteries. Proceedings of the National Academy of Sciences of the United States of America 102(39):14058-14062.
Tataroglu Ö, Davidson AJ, Benvenuto LJ, Menaker M. 2006.
The methamphetamine-sensitive circadian oscillator (MASCO) in mice. Journal of Biological Rhythms 21(3):185-194.
Franken P, Dudley CA, Estill SJ, Barakat M, Thomason R, O’Hara BF, McKnight SL. 2006. NPAS2 as a transcriptional regulator of non-rapid eye movement sleep: Genotype and sex interactions. Proceedings of the National Academy of Sciences of the United States of America 103(18):7118-7123

van der Schalie E, Green CB.
Quick Guide: Cryptochromes.
Curr Biol. 2005 Oct 11;15(19):R785.
PMID: 16213804 [PubMed - indexed for MEDLINE]

Ptacek LJ, Jones CR, Fu YH.
Genetic approaches to human behavior.
Methods Enzymol. 2005; 393:239-50.
PMID: 15817292 [PubMed - indexed for MEDLINE]