References(83)
[1]
MW Young, SA Kay. Time zones: a comparative genetics of circadian clocks. Nat Rev Genet. 2001, 2(9): 702-715.
[2]
PL Lowrey, JS Takahashi. Genetics of circadian rhythms in mammalian model organisms. In The Genetics of Circadian Rhythms. Amsterdam: Elsevier, 2011.
[3]
R Allada, BY Chung. Circadian organization of behavior and physiology in Drosophila. Annu Rev Physiol. 2010, 72: 605-624.
[4]
JA Mohawk, CB Green, JS Takahashi. Central and peripheral circadian clocks in mammals. Annu Rev Neurosci. 2012, 35: 445-462.
[5]
MH Hastings, AB Reddy, ES Maywood. A clockwork web: circadian timing in brain and periphery, in health and disease. Nat Rev Neurosci. 2003, 4(8): 649-661.
[6]
M Stratmann, U Schibler. Properties, entrainment, and physiological functions of mammalian peripheral oscillators. J Biol Rhythms. 2006, 21(6): 494-506.
[7]
E Slat, GM Freeman Jr, ED Herzog. The clock in the brain: neurons, glia, and networks in daily rhythms. Handb Exp Pharmacol. 2013(217): 105-123.
[8]
RJ Konopka, S Benzer. Clock mutants of drosophila melanogaster. Proc Natl Acad Sci U S A. 1971, 68(9): 2112-2116.
[9]
MH Vitaterna, DP King, AM Chang, et al. Mutagenesis and mapping of a mouse gene, Clock, essential for circadian behavior. Science. 1994, 264(5159): 719-725.
[10]
MP Antoch, EJ Song, AM Chang, et al. Functional identification of the mouse circadian Clock gene by transgenic BAC rescue. Cell. 1997, 89(4): 655-667.
[11]
DP King, Y Zhao, AM Sangoram, et al. Positional cloning of the mouse circadian clock gene. Cell. 1997, 89(4): 641-653.
[12]
R Allada, NE White, WV So, et al. A mutant Drosophila homolog of mammalian Clock disrupts circadian rhythms and transcription of period and timeless. Cell. 1998, 93(5): 791-804.
[13]
ZS Sun, U Albrecht, O Zhuchenko, et al. RIGUI, a putative mammalian ortholog of the Drosophila period gene. Cell. 1997, 90(6): 1003-1011.
[14]
H Tei, H Okamura, Y Shigeyoshi, et al. Circadian oscillation of a mammalian homologue of the Drosophila period gene. Nature. 1997, 389(6650): 512-516.
[15]
TA Bargiello, MW Young. Molecular genetics of a biological clock in Drosophila. Proc Natl Acad Sci U S A. 1984, 81(7): 2142-2146.
[16]
TA Bargiello, FR Jackson, MW Young. Restoration of circadian behavioural rhythms by gene transfer in Drosophila. Nature. 1984, 312(5996): 752-754.
[17]
P Reddy, WA Zehring, DA Wheeler, et al. Molecular analysis of the period locus in Drosophila melanogaster and identification of a transcript involved in biological rhythms. Cell. 1984, 38(3): 701-710.
[18]
WA Zehring, DA Wheeler, P Reddy, et al. P-element transformation with period locus DNA restores rhythmicity to mutant, arrhythmic Drosophila melanogaster. Cell. 1984, 39(2 Pt 1): 369-376.
[19]
MJ McDonald, M Rosbash. Microarray analysis and organization of circadian gene expression in Drosophila. Cell. 2001, 107(5): 567-578.
[20]
RA Akhtar, AB Reddy, ES Maywood, et al. Circadian cycling of the mouse liver transcriptome, as revealed by cDNA microarray, is driven by the suprachiasmatic nucleus. Curr Biol. 2002, 12(7): 540-550.
[21]
S Panda, MP Antoch, BH Miller, et al. Coordinated transcription of key pathways in the mouse by the circadian clock. Cell. 2002, 109(3): 307-320.
[22]
KF Storch, O Lipan, I Leykin, et al. Extensive and divergent circadian gene expression in liver and heart. Nature. 2002, 417(6884): 78-83.
[23]
HR Ueda, WB Chen, A Adachi, et al. A transcription factor response element for gene expression during circadian night. Nature. 2002, 418(6897): 534-539.
[24]
ME Hughes, KC Abruzzi, R Allada, et al. Guidelines for genome-scale analysis of biological rhythms. J Biol Rhythms. 2017, 32(5): 380-393.
[25]
M Hatori, S Gill, LS Mure, et al. Lhx1 maintains synchrony among circadian oscillator neurons of the SCN. Elife. 2014, 3: e03357.
[26]
WG Pembroke, A Babbs, KE Davies, et al. Temporal transcriptomics suggest that twin-peaking genes reset the clock. Elife. 2015, 4: e10518.
[27]
M Hughes, L Deharo, SR Pulivarthy, et al. High- resolution time course analysis of gene expression from pituitary. Cold Spring Harb Symp Quant Biol. 2007, 72: 381-386.
[28]
R Zhang, NF Lahens, HI Ballance, et al. A circadian gene expression atlas in mammals: implications for biology and medicine. Proc Natl Acad Sci USA. 2014, 111(45): 16219-16224.
[29]
M Ruben, MD Drapeau, D Mizrak, et al. A mechanism for circadian control of pacemaker neuron excitability. J Biol Rhythms. 2012, 27(5): 353-364.
[30]
E Nagoshi, K Sugino, , et al. Dissecting differential gene expression within the circadian neuronal circuit of Drosophila. Nat Neurosci. 2010, 13(1): 60-68.
[31]
JM Keil, A Qalieh, KY Kwan. Brain transcriptome databases: a user’s guide. J Neurosci. 2018, 38(10): 2399-2412.
[32]
Z Wang, M Gerstein, M Snyder. RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet. 2009, 10(1): 57-63.
[33]
ME Hughes, L DiTacchio, KR Hayes, et al. Harmonics of circadian gene transcription in mammals. PLoS Genet. 2009, 5(4): e1000442.
[34]
SY Krishnaiah, G Wu, BJ Altman, et al. Clock regulation of metabolites reveals coupling between transcription and metabolism. Cell Metab. 2017, 25(5): 1206.
[35]
SA Wen, DY Ma, M Zhao, et al. Spatiotemporal single-cell analysis of gene expression in the mouse suprachiasmatic nucleus. Nat Neurosci. 2020, in press, .
[36]
JJ Li, GR Grant, JB Hogenesch, et al. Considerations for RNA-seq analysis of circadian rhythms. Meth Enzymol. 2015, 551: 349-367.
[37]
A Pizarro, K Hayer, NF Lahens, et al. CircaDB: a database of mammalian circadian gene expression profiles. Nucleic Acids Res. 2012, 41(D1): D1009-D1013.
[38]
VR Patel, K Eckel-Mahan, P Sassone-Corsi, et al. CircadiOmics: integrating circadian genomics, transcriptomics, proteomics and metabolomics. Nat Methods. 2012, 9(8): 772-773.
[39]
SJ Li, K Shui, Y Zhang, et al. CGDB: a database of circadian genes in eukaryotes. Nucleic Acids Res. 2017, 45(D1): D397-D403.
[40]
XF Li, LS Shi, K Zhang, et al. CirGRDB: a database for the genome-wide deciphering circadian genes and regulators. Nucleic Acids Res. 2018, 46(D1): D64-D70.
[41]
MS Robles, J Cox, M Mann. In-vivo quantitative proteomics reveals a key contribution of post- transcriptional mechanisms to the circadian regulation of liver metabolism. PLoS Genet. 2014, 10(1): e1004047.
[42]
A Kauffmann, R Gentleman, W Huber. ArrayQualityMetrics—a bioconductor package for quality assessment of microarray data. Bioinformatics. 2009, 25(3): 415-416.
[43]
LG Wang, SQ Wang, W Li. RSeQC: quality control of RNA-seq experiments. Bioinformatics. 2012, 28(16): 2184-2185.
[44]
PY Hsu, SL Harmer. Global profiling of the circadian transcriptome using microarrays. In Methods in Molecular Biology. New York, NY: Springer New York, 2014.
[45]
A Dobin, CA Davis, F Schlesinger, et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics. 2013, 29(1): 15-21.
[46]
S Anders, PT Pyl, W Huber. HTSeq—a Python framework to work with high-throughput sequencing data. Bioinformatics. 2015, 31(2): 166-169.
[47]
B Li, CN Dewey. RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinform. 2011, 12: 323.
[48]
NL Bray, H Pimentel, P Melsted, et al. Near-optimal probabilistic RNA-seq quantification. Nat Biotechnol. 2016, 34(5): 525-527.
[49]
CJ Doherty, SA Kay. Circadian control of global gene expression patterns. Annu Rev Genet. 2010, 44: 419-444.
[50]
ME Hughes, JB Hogenesch, K Kornacker. JTK_ CYCLE: an efficient nonparametric algorithm for detecting rhythmic components in genome-scale data sets. J Biol Rhythms. 2010, 25(5): 372-380.
[51]
R Yang, Z Su. Analyzing circadian expression data by harmonic regression based on autoregressive spectral estimation. Bioinformatics. 2010, 26(12): i168-i174.
[52]
RD Yang, C Zhang, Z Su. LSPR: an integrated periodicity detection algorithm for unevenly sampled temporal microarray data. Bioinformatics. 2011, 27(7): 1023-1025.
[53]
PF Thaben, PO Westermark. Detecting rhythms in time series with RAIN. J Biol Rhythms. 2014, 29(6): 391-400.
[54]
JA Perea, A Deckard, SB Haase, et al. SW1PerS: Sliding windows and 1-persistence scoring; discovering periodicity in gene expression time series data. BMC Bioinformatics. 2015, 16: 257.
[55]
AL Hutchison, M Maienschein-Cline, AH Chiang, et al. Improved statistical methods enable greater sensitivity in rhythm detection for genome-wide data. PLoS Comput Biol. 2015, 11(3): e1004094.
[56]
AL Hutchison, R Allada, AR Dinner. Bootstrapping and empirical Bayes methods improve rhythm detection in sparsely sampled data. J Biol Rhythms. 2018, 33(4): 339-349.
[57]
Y Ren, CI Hong, S Lim, et al. Finding clocks in genes: a Bayesian approach to estimate periodicity. Biomed Res Int. 2016, 2016: 3017475.
[58]
F Agostinelli, N Ceglia, B Shahbaba, et al. What time is it? Deep learning approaches for circadian rhythms. Bioinformatics. 2016, 32(19): 3051.
[59]
JJ Hughey, T Hastie, AJ Butte. ZeitZeiger: supervised learning for high-dimensional data from an oscillatory system. Nucleic Acids Res. 2016, 44(8): e80.
[60]
G Wu, RC Anafi, ME Hughes, et al. MetaCycle: an integrated R package to evaluate periodicity in large scale data. Bioinformatics. 2016, 32(21): 3351-3353.
[61]
H De Los Santos, EJ Collins, C Mann, et al. ECHO: an application for detection and analysis of oscillators identifies metabolic regulation on genome-wide circadian output. Bioinformatics. 2020, 36(3): 773-781.
[62]
A Deckard, RC Anafi, JB Hogenesch, et al. Design and analysis of large-scale biological rhythm studies: a comparison of algorithms for detecting periodic signals in biological data. Bioinformatics. 2013, 29(24): 3174-3180.
[63]
G Wu, J Zhu, J Yu, et al. Evaluation of five methods for genome-wide circadian gene identification. J Biol Rhythms. 2014, 29(4): 231-242.
[64]
EF Glynn, J Chen, AR Mushegian. Detecting periodic patterns in unevenly spaced gene expression time series using Lomb-Scargle periodograms. Bioinformatics. 2006, 22(3): 310-316.
[65]
A Avizienis, L Chen. On the Implementation of N-version Programming for Software Fault Tolerance during Execution. In Proceedings of COMPSAC 77. 1977:149-155.
[66]
M Carlucci, A Kriščiūnas, HH Li, et al. DiscoRhythm: an easy-to-use web application and R package for discovering rhythmicity. Bioinformatics. 2019: btz834.
[67]
PF Thaben, PO Westermark. Differential rhythmicity: detecting altered rhythmicity in biological data. Bioinformatics. 2016, 32(18): 2800-2808.
[68]
R Parsons, R Parsons, N Garner, et al. CircaCompare: a method to estimate and statistically support differences in mesor, amplitude and phase, between circadian rhythms. Bioinformatics. 2020, 36(4): 1208-1212.
[69]
JM Singer, JJ Hughey. LimoRhyde: a flexible approach for differential analysis of rhythmic transcriptome data. J Biol Rhythms. 2019, 34(1): 5-18.
[70]
JM Singer, DY Fu, JJ Hughey. Simphony: simulating large-scale, rhythmic data. PeerJ. 2019, 7: e6985.
[71]
G Wu, J Zhu, FH He, et al. Gene and genome parameters of mammalian liver circadian genes (LCGs). PLoS One. 2012, 7(10): e46961.
[72]
Y Benjamini, Y Hochberg. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J Royal Stat Soc: Ser B Methodol. 1995, 57(1): 289-300.
[73]
A Subramanian, P Tamayo, VK Mootha, et al. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci USA. 2005, 102(43): 15545-15550.
[74]
DW Huang, BT Sherman, QN Tan, et al. DAVID Bioinformatics Resources: expanded annotation database and novel algorithms to better extract biology from large gene lists. Nucleic Acids Res. 2007, 35(suppl_2): W169-W175.
[75]
MV Kuleshov, MR Jones, AD Rouillard, et al. Enrichr: a comprehensive gene set enrichment analysis web server 2016 update. Nucleic Acids Res. 2016, 44(W1): W90-W97.
[76]
R Zhang, AA Podtelezhnikov, JB Hogenesch, et al. Discovering biology in periodic data through phase set enrichment analysis (PSEA). J Biol Rhythms. 2016, 31(3): 244-257.
[77]
MJ Deery, ES Maywood, JE Chesham, et al. Proteomic analysis reveals the role of synaptic vesicle cycling in sustaining the suprachiasmatic circadian clock. Curr Biol. 2009, 19(23): 2031-2036.
[78]
A Videnovic, PC Zee. Consequences of circadian disruption on neurologic health. Sleep Med Clin. 2015, 10(4): 469-480.
[79]
JZ Li, BG Bunney, F Meng, et al. Circadian patterns of gene expression in the human brain and disruption in major depressive disorder. Proc Natl Acad Sci USA. 2013, 110(24): 9950-9955.
[80]
CY Chen, RW Logan, TZ Ma, et al. Effects of aging on circadian patterns of gene expression in the human prefrontal cortex. Proc Natl Acad Sci USA. 2016, 113(1): 206-211.
[81]
ML Seney, K Cahill, JF 3rd Enwright, et al. Diurnal rhythms in gene expression in the prefrontal cortex in schizophrenia. Nat Commun. 2019, 10(1): 3355.
[82]
MD Ruben, JB Hogenesch, DF Smith. Sleep and circadian medicine: time of day in the neurologic clinic. Neurol Clin. 2019, 37(3): 615-629.
[83]
JJ Li, RY Yu, F Emran, et al. Achilles-mediated and sex-specific regulation of circadian mRNA rhythms in drosophila. J Biol Rhythms. 2019, 34(2): 131-143.