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; Baur, JA; Dang, CV; Hogenesch, JB; Weljie, AM. 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 (NAR). 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; Grant, GR; Hogenesch, JB. 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; Kim, J; Hogenesch, JB. 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 (NAR). 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 (NAR). 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; Su, AI; Hogenesch, JB; Kay, SA. 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; Cooke, MP; Walker, JR; Hogenesch, JB. 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; Kay, SA; Van Gelder, RN; Hogenesch, JB. 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; Bevan, S; Patapoutian, A. 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; Patapoutian, A; Hampton, GM; Schultz, PG; Hogenesch, JB. 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.

Liu, AC; Shen, Y; Serbinski, CR; He, H; Roman, D; Endale, M; Aschbacher-Smith, L; King, KA; Granadillo, JL; López, I; Krueger, DA; Dye, TJ; Smith, DF; Hogenesch, JB; Prada, CE. Clinical and functional studies of MTOR variants in Smith-Kingsmore syndrome reveal deficits of circadian rhythm and sleep-wake behavior. Human Genetics and Genomics Advances. 2024; 5:100333.

Schrader, LA; Ronnekleiv-Kelly, SM; Hogenesch, JB; Bradfield, CA; Malecki, KM C. Circadian disruption, clock genes, and metabolic health. The Journal of Clinical Investigation. 2024; 134:e170998.

Wang, YZ M; Huber, JF; Flesch, L; Demmel, K; Lane, A; Beebe, DW; Crosby, LE; Hogenesch, JB; Smith, DF; Davies, SM; Dandoy, CE. Trajectory of Sleep, Depression, and Quality of Life in Pediatric HSCT Recipients. Transplantation and Cellular Therapy. 2024; 30:632.e1-632.e5.

Yang, Y; Wu, G; Sancar, A; Hogenesch, JB. Mutations of the circadian clock genes Cry, Per, or Bmal1 have different effects on the transcribed and nontranscribed strands of cycling genes. Proceedings of the National Academy of Sciences of USA. 2024; 121:e2316731121.

Li, SY; Hammarlund, JA; Wu, G; Lian, JW; Howell, SJ; Clarke, RB; Adamson, AD; Gonçalves, CF; Hogenesch, JB; Anafi, RC; Meng, QJ. Tumor circadian clock strength influences metastatic potential and predicts patient prognosis in luminal A breast cancer. Proceedings of the National Academy of Sciences of USA. 2024; 121:e2311854121.

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; Smith, DF. 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; St-Onge, MP; Wang, X; Wright, J; Oh, YS. 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; Hogenesch, JB. 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.

Swanson, GR; Biglin, M; Raff, H; Chouhan, V; Jochum, S; Shaikh, M; Francey, L; Bishehsari, F; Hogenesch, J; Keshavarzian, A. Impact of Chronotherapy on 6-Mercaptopurine Metabolites in Inflammatory Bowel Disease: A Pilot Crossover Trial. Clinical and Translational Gastroenterology. 2023; 14:e00549.

Rosselot, AE; Park, M; Kim, M; Matsu-Ura, T; Wu, G; Flores, DE; Subramanian, KR; Lee, S; Sundaram, N; Broda, TR; Wells, JM; Hogenesch, JB; Moore, SR; Hong, CI. 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; Smith, DF. 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; Smith, DF. 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; Hogenesch, JB; Glauser, TA; Holland, KD; Arya, R. 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; Berres, ME; Bittman, EL; Hogenesch, JB. 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; Hogenesch, JB; Zhou, CJ; Zhou, F; Xu, Y. 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; Mrčela, A; Srinivasan, A; Schug, J; Hogenesch, JB; Barash, Y; Grant, GR. 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; Wu, ZH; Liu, AC. 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; Smith, DF. 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; Kruger, WD; Hogenesch, JB; Weljie, A; Anafi, RC; Kavakli, IH. CRY1-CBS binding regulates circadian clock function and metabolism. The Federation of European Biochemical Societies (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; Khan, WI; Rueda, L; Hogenesch, JB; Karpowicz, P. 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.