Hogenesch Lab

Publications

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:e08647.

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.

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. Editor, Schibler U. PLoS biology. 2014; 12: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.

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.

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. Editor, Barsh GS. PLoS Genetics. 2009; 5: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. Editor, Schibler U. PLoS biology. 2009; 7:e52.

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.

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. Editor, Steve O'Rahilly. PLoS biology. 2004; 2: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.

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.

Schwartz, PB; Nukaya, M; Berres, ME; Rubinstein, CD; Wu, G; Hogenesch, JB; Bradfield, CA; Ronnekleiv-Kelly, SM. The circadian clock is disrupted in pancreatic cancer. Editor, Dallmann R. PLoS Genetics. 2023; 19:e1010770.

Koritala, BS C; Lee, YY; Gaspar, LS; Bhadri, SS; Su, W; Wu, G; Francey, LJ; Ruben, MD; Gong, MC; Hogenesch, JB; et al. Obstructive sleep apnea in a mouse model is associated with tissue-specific transcriptomic changes in circadian rhythmicity and mean 24-hour gene expression. Editor, Hattar S. PLoS biology. 2023; 21:e3002139.

Cal-Kayitmazbatir, S; Francey, LJ; Lee, Y; Liu, AC; Hogenesch, JB. PSMD11 modulates circadian clock function through PER and CRY nuclear translocation. Editor, Foulkes NS. PloS one. 2023; 18:e0283463.

Gumz, ML; Shimbo, D; Abdalla, M; Balijepalli, RC; Benedict, C; Chen, Y; Earnest, DJ; Gamble, KL; Garrison, SR; Gong, MC; et al. Toward Precision Medicine: Circadian Rhythm of Blood Pressure and Chronotherapy for Hypertension - 2021 NHLBI Workshop Report. Hypertension. 2023; 80:503-522.

Wang, YM; Dandoy, CE; Smith, DF; Hogenesch, JB. Go to bed!: Sleep as a risk factor for adolescent hypertension. Progress in Pediatric Cardiology. 2023; 68:101613.

Wang, YZ M; Taggart, CB; Huber, JF; Davies, SM; Smith, DF; Hogenesch, JB; Dandoy, CE. Daytime-restricted parenteral feeding is associated with earlier oral intake in children following stem cell transplant. The Journal of Clinical Investigation. 2023; 133:e167275.

Lee, YY; Endale, M; Wu, G; Ruben, MD; Francey, LJ; Morris, AR; Choo, NY; Anafi, RC; Smith, DF; Liu, AC; et al. Integration of genome-scale data identifies candidate sleep regulators. Sleep. 2023; 46:zsac279.

Wang, YM; Taggart, CB; Huber, J; Davies, SM; Smith, DF; Hogenesch, JB; Dandoy, DC E. 167 Earlier Oral Intake in Pediatric Stem Cell Transplant Patients Receiving Time-Restricted Feeding: A Prospective, Randomized Trial. Transplantation and cellular therapy. 2023; 29:s135.

Rosselot, AE; Park, M; Kim, M; Matsu-Ura, T; Wu, G; Flores, DE; Subramanian, KR; Lee, S; Sundaram, N; Broda, TR; et al. Ontogeny and function of the circadian clock in intestinal organoids. The EMBO Journal. 2022; 41:e106973.

Wu, G; Ruben, MD; Francey, LJ; Lee, YY; Anafi, RC; Hogenesch, JB. An in silico genome-wide screen for circadian clock strength in human samples. Editor, Mathelier A. Bioinformatics. 2022; 38:5375-5382.

Riley, JM; Hamparian, CN; Sestito, AP; Duggins, AL; Owens, TL; Witt, RM; Simmons, D; Byars, K; Hogenesch, JB; Dye, TJ; et al. Outcomes of Pre-treatment and Post-treatment measures after therapy for pediatric circadian disorders. Sleep Medicine. 2022; 100:s51-s52.

Witt, RM; Riley, JM; Hamparian, CN; Owens, TL; Simmons, D; Byars, KC; Hogenesch, JB; Smith, DF; Dye, TJ. Safe and Effective Use of Suvorexant in Children with Neurodevelopmental Disorders: A Single-Center, Retrospective Study of Clinical Practice. Sleep Medicine. 2022; 100:s172-s173.

Riley, JM; Hamparian, CN; Sestito, AP; Duggins, AL; Owens, TL; Witt, RM; Simmons, D; Byars, K; Hogenesch, JB; Dye, TJ; et al. Developing a Multidisciplinary Pediatric Circadian Medicine Clinic: The Circadian and Complex Sleep Disorders Clinic. Sleep Medicine. 2022; 100:s46-s47.

Witt, RM; Riley, JM; Hamparian, CN; Owens, TL; Simmons, D; Byars, KC; Hogenesch, JB; Smith, DF; Dye, TJ. Suvorexant Is Safe and Effective in a Pediatric Population: A Single-Center, Retrospective Study. Sleep Medicine. 2022; 100:s208.

Petito, GT; Housekeeper, J; Buroker, J; Scholle, C; Ervin, B; Frink, C; Greiner, HM; Skoch, J; Mangano, FT; Dye, TJ; et al. Diurnal rhythms of spontaneous intracranial high-frequency oscillations. Seizure-European Journal of Epilepsy. 2022; 102:105-112.

Lee, YY; Cal-Kayitmazbatir, S; Francey, LJ; Bahiru, MS; Hayer, KE; Wu, G; Zeller, MJ; Roberts, R; Speers, J; Koshalek, J; et al. duper is a null mutation of Cryptochrome 1 in Syrian hamsters. Proceedings of the National Academy of Sciences of USA. 2022; 119:e2123560119.

Zhang, T; Du, X; Gu, Y; Dong, Y; Zhang, W; Yuan, Z; Huang, X; Zou, C; Zhou, Y; Liu, Z; et al. Analysis of Diurnal Variations in Heart Rate: Potential Applications for Chronobiology and Cardiovascular Medicine. Frontiers in Physiology. 2022; 13:835198.

Wu, G; Francey, LJ; Ruben, MD; Hogenesch, JB. Normalized coefficient of variation (nCV): a method to evaluate circadian clock robustness in population scale data. Editor, Alkan C. Bioinformatics. 2021; 37:4581-4583.

Lahens, NF; Brooks, TG; Sarantopoulou, D; Nayak, S; Lawrence, C; Mrcela, A; Srinivasan, A; Schug, J; Hogenesch, JB; Barash, Y; et al. CAMPAREE: a robust and configurable RNA expression simulator. BMC Genomics. 2021; 22:692.

Shen, Y; Endale, M; Wang, W; Morris, AR; Francey, LJ; Harold, RL; Hammers, DW; Huo, Z; Partch, CL; Hogenesch, JB; et al. NF-κB modifies the mammalian circadian clock through interaction with the core clock protein BMAL1. Editor, Kramer A. PLoS Genetics. 2021; 17:e1009933.

Turgeon, RD; Althouse, AD; Cohen, JB; Enache, B; Hogenesch, JB; Johansen, ME; Mehta, R; Meyerowitz-Katz, G; Ziaeian, B; Hiremath, S. Lowering Nighttime Blood Pressure With Bedtime Dosing of Antihypertensive Medications: Controversies in Hypertension - Con Side of the Argument. Hypertension. 2021; 78:871-878.

Turgeon, R; Althouse, A; Cohen, JB; Enache, B; Hogenesch, JB; Johansen, M; Mehta, R; Meyerowitz-Katz, G; Ziaeian, B; Hiremath, S. Response to Lowering Nighttime Blood Pressure with Bedtime Dosing of Antihypertensive Medications: Controversies in Hypertension - Pro Side of the Argument. Hypertension. 2021; 78:893.

Wu, G; Lee, YY; Gulla, EM; Potter, A; Kitzmiller, J; Ruben, MD; Salomonis, N; Whitsett, JA; Francey, LJ; Hogenesch, JB; et al. Short-term exposure to intermittent hypoxia leads to changes in gene expression seen in chronic pulmonary disease. eLife. 2021; 10:e63003.

Cal-Kayitmazbatir, S; Kulkoyluoglu-Cotul, E; Growe, J; Selby, CP; Rhoades, SD; Malik, D; Oner, H; Asimgil, H; Francey, LJ; Sancar, A; et al. CRY1-CBS binding regulates circadian clock function and metabolism. FEBS Journal. 2021; 288:614-639.

Stokes, K; Nunes, M; Trombley, C; Flôres, DE F L; Wu, G; Taleb, Z; Alkhateeb, A; Banskota, S; Harris, C; Love, OP; et al. The Circadian Clock Gene, Bmal1, Regulates Intestinal Stem Cell Signaling and Represses Tumor Initiation. CMGH Cellular and Molecular Gastroenterology and Hepatology. 2021; 12:1847-1872.e0.

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.

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; 12:73.

Wu, G; Ruben, MD; Lee, Y; Li, J; Hughes, ME; Hogenesch, JB. Genome-wide studies of time of day in the brain: Design and analysis. Brain Science Advances. 2020; 6:92-105.

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; 9:11883.

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.

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.