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.
2017;
114:5312-5317.
Ruben, MD; Hogenesch, JB.
Circadian Rhythms: Move Over Neurons - Astrocytes Mediate SCN Clock Function.
Current Biology.
2017;
27:R350-R352.
Krishnaiah, SY; Wu, G; Altman, BJ; Growe, J; Rhoades, SD; Coldren, F; Venkataraman, A; Olarerin-George, AO; Francey, LJ; Mukherjee, S; et al.
Clock Regulation of Metabolites Reveals Coupling between Transcription and Metabolism.
Cell Metabolism.
2017;
25:961-974.e4.
Wu, G; Anafi, RC; Hughes, ME; Kornacker, K; Hogenesch, JB.
MetaCycle: an integrated R package to evaluate periodicity in large scale data.
Computer Applications in the Biosciences.
2016;
32:3351-3353.
Zhang, R; Podtelezhnikov, AA; Hogenesch, JB; Anafi, RC.
Discovering Biology in Periodic Data through Phase Set Enrichment Analysis (PSEA).
Journal of Biological Rhythms.
2016;
31:244-257.
Lee, Y; Jang, AR; Francey, LJ; Sehgal, A; Hogenesch, JB.
KPNB1 mediates PER/CRY nuclear translocation and circadian clock function.
eLife.
2015;
4.
Olarerin-George, AO; Hogenesch, JB.
Assessing the prevalence of mycoplasma contamination in cell culture via a survey of NCBI's RNA-seq archive.
Nucleic Acids Research.
2015;
43:2535-2542.
Zhang, R; Lahens, NF; Ballance, HI; Hughes, ME; Hogenesch, JB.
A circadian gene expression atlas in mammals: implications for biology and medicine.
Proceedings of the National Academy of Sciences of the United States of America.
2014;
111:16219-16224.
Lahens, NF; Kavakli, IH; Zhang, R; Hayer, K; Black, MB; Dueck, H; Pizarro, A; Kim, J; Irizarry, R; Thomas, RS; et al.
IVT-seq reveals extreme bias in RNA sequencing.
Genome Biology.
2014;
15.
Anafi, RC; Lee, Y; Sato, TK; Venkataraman, A; Ramanathan, C; Kavakli, IH; Hughes, ME; Baggs, JE; Growe, J; Liu, AC; et al.
Machine learning helps identify CHRONO as a circadian clock component.
PLoS Biology.
2014;
12.
Olarerin-George, AO; Anton, L; Hwang, Y; Elovitz, MA; Hogenesch, JB.
A functional genomics screen for microRNA regulators of NF-kappaB signaling.
BMC Biology.
2013;
11.
Pizarro, A; Hayer, K; Lahens, NF; Hogenesch, JB.
CircaDB: a database of mammalian circadian gene expression profiles.
Nucleic Acids Research.
2013;
41:D1009-D1013.
Hughes, ME; Peeler, J; Hogenesch, JB.
Network dynamics to evaluate performance of an academic institution.
Science Translational Medicine.
2010;
2.
Hughes, ME; Hogenesch, JB; Kornacker, K.
JTK_CYCLE: an efficient nonparametric algorithm for detecting rhythmic components in genome-scale data sets.
Journal of Biological Rhythms.
2010;
25:372-380.
III, HJ W; 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 Research.
2010;
38:D633-D639.
Zhang, EE; Liu, AC; Hirota, T; Miraglia, LJ; Welch, G; Pongsawakul, PY; Liu, X; Atwood, A; III, HJ W; Janes, J; et al.
A genome-wide RNAi screen for modifiers of the circadian clock in human cells.
Cell.
2009;
139:199-210.
Hughes, ME; DiTacchio, L; Hayes, KR; Vollmers, C; Pulivarthy, S; Baggs, JE; Panda, S; Hogenesch, JB.
Harmonics of circadian gene transcription in mammals.
PLoS Genetics.
2009;
5.
Warzecha, CC; Sato, TK; Nabet, B; Hogenesch, JB; Carstens, RP.
ESRP1 and ESRP2 are epithelial cell-type-specific regulators of FGFR2 splicing.
Molecular Cell.
2009;
33:591-601.
Baggs, JE; Price, TS; DiTacchio, L; Panda, S; FitzGerald, GA; Hogenesch, JB.
Network features of the mammalian circadian clock.
PLoS Biology.
2009;
7.
Price, TS; Baggs, JE; Curtis, AM; FitzGerald, GA; Hogenesch, JB.
WAVECLOCK: wavelet analysis of circadian oscillation.
Computer Applications in the Biosciences.
2008;
24:2794-2795.
Su, AI; Hogenesch, JB.
Power-law-like distributions in biomedical publications and research funding.
Genome Biology.
2007;
8.
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.
Nature Genetics.
2006;
38:312-319.
Willingham, AT; Orth, AP; Batalov, S; Peters, EC; Wen, BG; Aza-Blanc, P; Hogenesch, JB; Schultz, PG.
A strategy for probing the function of noncoding RNAs finds a repressor of NFAT.
Science.
2005;
309:1570-1573.
Rudic, RD; McNamara, P; Curtis, AM; Boston, RC; Panda, S; Hogenesch, JB; FitzGerald, GA.
BMAL1 and CLOCK, two essential components of the circadian clock, are involved in glucose homeostasis.
PLoS Biology.
2004;
2.
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;
43:527-537.
Su, AI; Wiltshire, T; Batalov, S; Lapp, H; Ching, KA; Block, D; Zhang, J; Soden, R; Hayakawa, M; Kreiman, G; et al.
A gene atlas of the mouse and human protein-encoding transcriptomes.
Proceedings of the National Academy of Sciences of the United States of America.
2004;
101:6062-6067.
Conkright, MD; Canettieri, G; Screaton, R; Guzman, E; Miraglia, L; Hogenesch, JB; Montminy, M.
TORCs: transducers of regulated CREB activity.
Molecular Cell.
2003;
12:413-423.
Panda, S; Provencio, I; Tu, DC; Pires, SS; Rollag, MD; Castrucci, AM; Pletcher, MT; Sato, TK; Wiltshire, T; Andahazy, M; et al.
Melanopsin is required for non-image-forming photic responses in blind mice.
Science.
2003;
301:525-527.
Peier, AM; Reeve, AJ; Andersson, DA; Moqrich, A; Earley, TJ; Hergarden, AC; Story, GM; Colley, S; Hogenesch, JB; McIntyre, P; et al.
A heat-sensitive TRP channel expressed in keratinocytes.
Science.
2002;
296:2046-2049.
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;
109:307-320.
Su, AI; Cooke, MP; Ching, KA; Hakak, Y; Walker, JR; Wiltshire, T; Orth, AP; Vega, RG; Sapinoso, LM; Moqrich, A; et al.
Large-scale analysis of the human and mouse transcriptomes.
Proceedings of the National Academy of Sciences of the United States of America.
2002;
99:4465-4470.
Hogenesch, JB; Ching, KA; Batalov, S; Su, AI; Walker, JR; Zhou, YY; Kay, SA; Schultz, PG; Cooke, MP.
A comparison of the Celera and Ensembl predicted gene sets reveals little overlap in novel genes.
Cell.
2001;
106:413-415.
Bunger, MK; Wilsbacher, LD; Moran, SM; Clendenin, C; Radcliffe, LA; Hogenesch, JB; Simon, MC; Takahashi, JS; Bradfield, CA.
Mop3 is an essential component of the master circadian pacemaker in mammals.
Cell.
2000;
103:1009-1017.
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.
Journal of Neuroscience.
2000;
20.
Hogenesch, JB; Chan, WK; Jackiw, VH; Brown, RC; Gu, YZ; PrayGrant, 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.
Journal of Biological Chemistry.
1997;
272:8581-8593.