Hogenesch Lab

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 USA. 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. Bioinformatics. 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 USA. 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: biology for the post-genomic era. 2014; 15:R86-R86.

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:e1001840-e1001840.

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; 11:19-19.

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; 2:53ps49-53ps49.

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:e1000442-e1000442.

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:e52-e1000052.

Price, TS; Baggs, JE; Curtis, AM; FitzGerald, GA; Hogenesch, JB. WAVECLOCK: wavelet analysis of circadian oscillation. Bioinformatics. 2008; 24:2794-2795.

Su, AI; Hogenesch, JB. Power-law-like distributions in biomedical publications and research funding. Genome Biology: biology for the post-genomic era. 2007; 8:404-404.

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:e377-e377.

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 USA. 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 USA. 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. The Journal of neuroscience : the official journal of the Society for Neuroscience. 2000; 20:RC83-RC83.

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. The Journal of biological chemistry. 1997; 272:8581-8593.

Sorrell, J; Yates, E; Rivir, M; Woods, SC; Hogenesch, JB; Perez-Tilve, D. The central melanocortin system mediates the benefits of time-restricted feeding on energy balance. Physiology and Behavior. 2020; 227:113132-113132.

Wu, G; Ruben, MD; Francey, LJ; Smith, DF; Sherrill, JD; Oblong, JE; Mills, KJ; Hogenesch, JB. A population-based gene expression signature of molecular clock phase from a single epidermal sample. Genome Medicine: medicine in the post-genomic era. 2020; 12.

Nayak, G; Zhang, KX; Vemaraju, S; Odaka, Y; Buhr, ED; Holt-Jones, A; Kernodle, S; Smith, AN; Upton, BA; D'Souza, S; et al. Adaptive Thermogenesis in Mice Is Enhanced by Opsin 3-Dependent Adipocyte Light Sensing. Cell Reports. 2020; 30:672-686.e8.

Smith, DF; Rubent, MD; Francey, LJ; Walch, OJ; Hogenesch, JB. When Should You Take Your Medicines?. Journal of Biological Rhythms. 2019; 34:582-583.

Lee, Y; Shen, Y; Francey, LJ; Ramanathan, C; Sehgal, A; Liu, AC; Hogenesch, JB. The NRON complex controls circadian clock function through regulated PER and CRY nuclear translocation. Scientific Reports. 2019; 9.

Ruben, MD; Francey, LJ; Guo, Y; Wu, G; Cooper, EB; Shah, AS; Hogenesch, JB; Smith, DF. A large-scale study reveals 24-h operational rhythms in hospital treatment. Proceedings of the National Academy of Sciences of USA. 2019; 116:20953-20958.

Ruben, MD; Smith, DF; FitzGerald, GA; Hogenesch, JB. Dosing time matters. Science. 2019; 365:547-549.

Cederroth, CR; Albrecht, U; Bass, J; Brown, SA; Dyhrfjeld-Johnsen, J; Gachon, F; Green, CB; Hastings, MH; Helfrich-Forster, C; Hogenesch, JB; et al. Medicine in the Fourth Dimension. Cell Metabolism. 2019; 30:238-250.

Ruben, MD; Hogenesch, JB; Smith, DF. Sleep and Circadian Medicine Time of Day in the Neurologic Clinic. Neurologic Clinics. 2019; 37:615-629.

Foteinou, PT; Venkataraman, A; Francey, LJ; Anafi, RC; Hogenesch, JB; III, DF J. REPLY TO FURLAN ET AL.: The role of SIRT1 in cell autonomous clock function. Proceedings of the National Academy of Sciences of USA. 2019; 116:13173-13173.

Zhang, Z; Hunter, L; Wu, G; Maidstone, R; Mizoro, Y; Vonslow, R; Fife, M; Hopwood, T; Begley, N; Saer, B; et al. Genome-wide effect of pulmonary airway epithelial cell-specific Bmal1 deletion. The FASEB journal : official publication of the Federation of American Societies for Experimental Biology. 2019; 33:6226-6238.

Resuehr, D; Wu, G; Jr, JR L; Young, ME; Hogenesch, JB; Gamble, KL. Shift Work Disrupts Circadian Regulation of the Transcriptome in Hospital Nurses. Journal of Biological Rhythms. 2019; 34:167-177.

Merrick, D; Mistry, K; Wu, J; Gresko, N; Baggs, JE; Hogenesch, JB; Sun, Z; Caplan, MJ. Polycystin-1 regulates bone development through an interaction with the transcriptional coactivator TAZ. Human Molecular Genetics. 2019; 28:16-30.

von Allmen, DC; Francey, LJ; Rogers, GM; Ruben, MD; Cohen, AP; Wu, G; Schmidt, RE; Ishman, SL; Amin, RS; Hogenesch, JB; et al. Circadian Dysregulation: The Next Frontier in Obstructive Sleep Apnea Research. Otolaryngology - Head and Neck Surgery. 2018; 159:948-955.

Wu, G; Ruben, MD; Schmidt, RE; Francey, LJ; Smith, DF; Anafi, RC; Hughey, JJ; Tasseff, R; Sherrill, JD; Oblong, JE; et al. Population-level rhythms in human skin with implications for circadian medicine. Proceedings of the National Academy of Sciences of USA. 2018; 115:12313-12318.

Foteinou, PT; Venkataraman, A; Francey, LJ; Anafi, RC; Hogenesch, JB; III, DF J. Computational and experimental insights into the circadian effects of SIRT1. Proceedings of the National Academy of Sciences of USA. 2018; 115:11643-11648.

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. Science Translational Medicine. 2018; 10:eaat8806-eaat8806.

Castellana, S; Mazza, T; Capocefalo, D; Genov, N; Biagini, T; Fusilli, C; Scholkmann, F; Relogio, A; Hogenesch, JB; Mazzoccoli, G. Systematic Analysis of Mouse Genome Reveals Distinct Evolutionary and Functional Properties Among Circadian and Ultradian Genes. Frontiers in Physiology. 2018; 9.

Zhang, X; Xue, C; Lin, J; Ferguson, JF; Weiner, A; Liu, W; Han, Y; Hinkle, C; Li, W; Jiang, H; et al. Interrogation of nonconserved human adipose lincRNAs identifies a regulatory role of linc-ADAL in adipocyte metabolism. Science Translational Medicine. 2018; 10:eaar5987-eaar5987.

Yang, Y; Adebali, O; Wu, G; Selby, CP; Chiou, Y; Rashid, N; Hu, J; Hogenesch, JB; Sancar, A. Cisplatin-DNA adduct repair of transcribed genes is controlled by two circadian programs in mouse tissues. Proceedings of the National Academy of Sciences of USA. 2018; 115:E4777-E4785.

Ramanathan, C; Kathale, ND; Liu, D; Lee, C; Freeman, DA; Hogenesch, JB; Cao, R; Liu, AC. mTOR signaling regulates central and peripheral circadian clock function. PLoS Genetics. 2018; 14:e1007369-e1007369.

Giovannone, AJ; Winterstein, C; Bhattaram, P; Reales, E; Low, SH; Baggs, JE; Xu, M; Lalli, MA; Hogenesch, JB; Weimbs, T. Soluble syntaxin 3 functions as a transcriptional regulator. The Journal of biological chemistry. 2018; 293:5478-5491.

Hughes, ME; Abruzzi, KC; Allada, R; Anafi, R; Arpat, AB; Asher, G; Baldi, P; de Bekker, C; Bell-Pedersen, D; Blau, J; et al. Guidelines for Genome-Scale Analysis of Biological Rhythms. Journal of Biological Rhythms. 2017; 32:380-393.

Stern, DL; Clemens, J; Coen, P; Calhoun, AJ; Hogenesch, JB; Arthur, BJ; Murthy, M. Experimental and statistical reevaluation provides no evidence for Drosophila courtship song rhythms. Proceedings of the National Academy of Sciences of USA. 2017; 114:9978-9983.

Francey, LY; Hogenesch, JB. It's not all in the brain. eLife. 2017; 6.

Babb, PL; Lahens, NF; Correa-Garhwal, SM; Nicholson, DN; Kim, EJ; Hogenesch, JB; Kuntner, M; Higgins, L; Hayashi, CY; Agnarsson, I; et al. The Nephila clavipes genome highlights the diversity of spider silk genes and their complex expression. Nature Genetics. 2017; 49:895-903.

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 USA. 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.

Love, MI; Hogenesch, JB; Irizarry, RA. Modeling of RNA-seq fragment sequence bias reduces systematic errors in transcript abundance estimation. Nature Biotechnology. 2016; 34:1287-1291.

McGoff, KA; Guo, X; Deckard, A; Kelliher, CM; Leman, AR; Francey, LJ; Hogenesch, JB; Haase, SB; Harer, JL. The Local Edge Machine: inference of dynamic models of gene regulation. Genome Biology: biology for the post-genomic era. 2016; 17.

Wu, G; Anafi, RC; Hughes, ME; Kornacker, K; Hogenesch, JB. MetaCycle: an integrated R package to evaluate periodicity in large scale data. Bioinformatics. 2016; 32:3351-3353.

Sengupta, A; Krishnaiah, SY; Rhoades, S; Growe, J; Slaff, B; Venkataraman, A; Olarerin-George, AO; Dang, CV; Hogenesch, JB; Weljie, AM. Deciphering the Duality of Clock and Growth Metabolism in a Cell Autonomous System Using NMR Profiling of the Secretome. Metabolites. 2016; 6:23-23.

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.

Erion, R; King, AN; Wu, G; Hogenesch, JB; Sehgal, A. Neural clocks and Neuropeptide F/Y regulate circadian gene expression in a peripheral metabolic tissue. eLife. 2016; 5.

Vaquero-Garcia, J; Barrera, A; Gazzara, MR; Gonzalez-Vallinas, J; Lahens, NF; Hogenesch, JB; Lynch, KW; Barash, Y. A new view of transcriptome complexity and regulation through the lens of local splicing variations. eLife. 2016; 5.