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John B. Hogenesch, PhD - Publications

Pharmacology Cincinnati Children's Hospital and Medical Center, USA 
genomics, computational biology, drug discovery, circadian rhythms

148 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2020 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. 12: 73. PMID 32825850 DOI: 10.1186/s13073-020-00768-9  1
2020 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 & Behavior. 113132. PMID 32791179 DOI: 10.1016/j.physbeh.2020.113132  0.32
2020 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 Febs Journal. PMID 32383312 DOI: 10.1111/febs.15360  1
2020 Nayak G, Zhang KX, Vemaraju S, Odaka Y, Buhr ED, Holt-Jones A, Kernodle S, Smith AN, Upton BA, D'Souza S, Zhan JJ, Diaz N, Nguyen MT, Mukherjee R, Gordon SA, ... ... Hogenesch JB, et al. Adaptive Thermogenesis in Mice Is Enhanced by Opsin 3-Dependent Adipocyte Light Sensing. Cell Reports. 30: 672-686.e8. PMID 31968245 DOI: 10.1016/j.celrep.2019.12.043  1
2019 Smith DF, Ruben MD, Francey LJ, Walch OJ, Hogenesch JB. When Should You Take Your Medicines? Journal of Biological Rhythms. 748730419892099. PMID 31813349 DOI: 10.1177/0748730419892099  1
2019 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 the United States of America. PMID 31575744 DOI: 10.1073/pnas.1909557116  1
2019 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. 9: 11883. PMID 31417156 DOI: 10.1038/s41598-019-48341-8  1
2019 Ruben MD, Smith DF, FitzGerald GA, Hogenesch JB. Dosing time matters. Science (New York, N.Y.). 365: 547-549. PMID 31395773 DOI: 10.1126/science.aax7621  1
2019 Cederroth CR, Albrecht U, Bass J, Brown SA, Dyhrfjeld-Johnsen J, Gachon F, Green CB, Hastings MH, Helfrich-Förster C, Hogenesch JB, Lévi F, Loudon A, Lundkvist GB, Meijer JH, Rosbash M, et al. Medicine in the Fourth Dimension. Cell Metabolism. 30: 238-250. PMID 31390550 DOI: 10.1016/j.cmet.2019.06.019  0.92
2019 Ruben MD, Hogenesch JB, Smith DF. Sleep and Circadian Medicine: Time of Day in the Neurologic Clinic. Neurologic Clinics. 37: 615-629. PMID 31256793 DOI: 10.1016/j.ncl.2019.03.004  0.92
2019 Foteinou PT, Venkataraman A, Francey LJ, Anafi RC, Hogenesch JB, Doyle FJ. Reply to Furlan et al.: The role of SIRT1 in cell autonomous clock function. Proceedings of the National Academy of Sciences of the United States of America. PMID 31239349 DOI: 10.1073/pnas.1907923116  1
2019 Zhang Z, Hunter L, Wu G, Maidstone R, Mizoro Y, Vonslow R, Fife M, Hopwood T, Begley N, Saer B, Wang P, Cunningham P, Baxter M, Durrington H, Blaikley JF, ... ... Hogenesch JB, et al. Genome-wide effect of pulmonary airway epithelial cell-specific Bmal1 deletion. Faseb Journal : Official Publication of the Federation of American Societies For Experimental Biology. fj201801682R. PMID 30794439 DOI: 10.1096/fj.201801682R  1
2019 Resuehr D, Wu G, Johnson RL, Young ME, Hogenesch JB, Gamble KL. Shift Work Disrupts Circadian Regulation of the Transcriptome in Hospital Nurses. Journal of Biological Rhythms. 748730419826694. PMID 30712475 DOI: 10.1177/0748730419826694  1
2018 Wu G, Ruben MD, Schmidt RE, Francey LJ, Smith DF, Anafi RC, Hughey JJ, Tasseff R, Sherrill JD, Oblong JE, Mills KJ, Hogenesch JB. Population-level rhythms in human skin with implications for circadian medicine. Proceedings of the National Academy of Sciences of the United States of America. PMID 30377266 DOI: 10.1073/pnas.1809442115  1
2018 Foteinou PT, Venkataraman A, Francey LJ, Anafi RC, Hogenesch JB, Doyle FJ. Computational and experimental insights into the circadian effects of SIRT1. Proceedings of the National Academy of Sciences of the United States of America. PMID 30348778 DOI: 10.1073/pnas.1803410115  1
2018 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 co-activator taz. Human Molecular Genetics. PMID 30215740 DOI: 10.1093/hmg/ddy322  1
2018 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. 10. PMID 30209245 DOI: 10.1126/scitranslmed.aat8806  1
2018 von Allmen DC, Francey LJ, Rogers GM, Ruben MD, Cohen AP, Wu G, Schmidt RE, Ishman SL, Amin RS, Hogenesch JB, Smith DF. Circadian Dysregulation: The Next Frontier in Obstructive Sleep Apnea Research. Otolaryngology--Head and Neck Surgery : Official Journal of American Academy of Otolaryngology-Head and Neck Surgery. 194599818797311. PMID 30200807 DOI: 10.1177/0194599818797311  1
2018 Zhang X, Xue C, Lin J, Ferguson JF, Weiner A, Liu W, Han Y, Hinkle C, Li W, Jiang H, Gosai S, Hachet M, Garcia BA, Gregory BD, Soccio RE, ... Hogenesch JB, et al. Interrogation of nonconserved human adipose lincRNAs identifies a regulatory role of in adipocyte metabolism. Science Translational Medicine. 10. PMID 29925637 DOI: 10.1126/scitranslmed.aar5987  0.32
2018 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. 14: e1007369. PMID 29750810 DOI: 10.1371/journal.pgen.1007369  0.8
2018 Yang Y, Adebali O, Wu G, Selby CP, Chiou YY, 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 the United States of America. PMID 29735688 DOI: 10.1073/pnas.1804493115  1
2018 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. PMID 29475951 DOI: 10.1074/jbc.RA117.000874  1
2017 Hughes ME, Abruzzi KC, Allada R, Anafi R, Arpat AB, Asher G, Baldi P, de Bekker C, Bell-Pedersen D, Blau J, Brown S, Ceriani MF, Chen Z, Chiu JC, Cox J, ... ... Hogenesch JB, et al. Guidelines for Genome-Scale Analysis of Biological Rhythms. Journal of Biological Rhythms. 748730417728663. PMID 29098954 DOI: 10.1177/0748730417728663  1
2017 Francey LJ, Hogenesch JB. It's not all in the brain. Elife. 6. PMID 28850329 DOI: 10.7554/eLife.30561  1
2017 Ruben MD, Hogenesch JB. Circadian Rhythms: Move Over Neurons - Astrocytes Mediate SCN Clock Function. Current Biology : Cb. 27: R350-R352. PMID 28486120 DOI: 10.1016/j.cub.2017.03.055  0.92
2017 Krishnaiah SY, Wu G, Altman BJ, Growe J, Rhoades SD, Coldren F, Venkataraman A, Olarerin-George AO, Francey LJ, Mukherjee S, Girish S, Selby CP, Cal S, Er U, Sianati B, ... ... Hogenesch JB, et al. Clock Regulation of Metabolites Reveals Coupling between Transcription and Metabolism. Cell Metabolism. 25: 1206. PMID 28467936 DOI: 10.1016/j.cmet.2017.04.023  1
2017 Babb PL, Lahens NF, Correa-Garhwal SM, Nicholson DN, Kim EJ, Hogenesch JB, Kuntner M, Higgins L, Hayashi CY, Agnarsson I, Voight BF. The Nephila clavipes genome highlights the diversity of spider silk genes and their complex expression. Nature Genetics. PMID 28459453 DOI: 10.1038/ng.3852  1
2017 Krishnaiah SY, Wu G, Altman BJ, Growe J, Rhoades SD, Coldren F, Venkataraman A, Olarerin-George AO, Francey LJ, Mukherjee S, Girish S, Selby CP, Cal S, Er U, Sianati B, ... ... Hogenesch JB, et al. Clock Regulation of Metabolites Reveals Coupling between Transcription and Metabolism. Cell Metabolism. 25: 961-974.e4. PMID 28380384 DOI: 10.1016/j.cmet.2017.03.019  1
2016 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. 17: 214. PMID 27760556 DOI: 10.1186/s13059-016-1076-z  1
2016 Sengupta A, Krishnaiah SY, Rhoades S, Growe J, Slaff B, Venkataraman A, Olarerin-George AO, Van Dang C, Hogenesch JB, Weljie AM. Deciphering the Duality of Clock and Growth Metabolism in a Cell Autonomous System Using NMR Profiling of the Secretome. Metabolites. 6. PMID 27472375 DOI: 10.3390/metabo6030023  1
2016 Wu G, Anafi RC, Hughes ME, Kornacker K, Hogenesch JB. MetaCycle: an integrated R package to evaluate periodicity in large scale data. Bioinformatics (Oxford, England). PMID 27378304 DOI: 10.1093/bioinformatics/btw405  1
2016 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. 5. PMID 27077948 DOI: 10.7554/eLife.13552  1
2016 Zhang R, Podtelezhnikov AA, Hogenesch JB, Anafi RC. Discovering Biology in Periodic Data through Phase Set Enrichment Analysis (PSEA). Journal of Biological Rhythms. 31: 244-57. PMID 26955841 DOI: 10.1177/0748730416631895  0.88
2016 Vaquero-Garcia J, Barrera A, Gazzara MR, González-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. 5. PMID 26829591 DOI: 10.7554/eLife.11752  1
2015 Manderfield LJ, Engleka KA, Aghajanian H, Gupta M, Yang S, Li L, Baggs JE, Hogenesch JB, Olson EN, Epstein JA. Pax3 and Hippo Signaling Coordinate Melanocyte Gene Expression in Neural Crest. Cell Reports. 10: 841. PMID 30849859 DOI: 10.1016/j.celrep.2015.01.041  1
2015 Ma D, Liu T, Chang L, Rui C, Xiao Y, Li S, Hogenesch JB, Chen YE, Lin JD. The Liver Clock Controls Cholesterol Homeostasis through Trib1 Protein-mediated Regulation of PCSK9/Low Density Lipoprotein Receptor (LDLR) Axis. The Journal of Biological Chemistry. 290: 31003-12. PMID 26547624 DOI: 10.1074/jbc.M115.685982  1
2015 DeBruyne JP, Baggs JE, Sato TK, Hogenesch JB. Ubiquitin ligase Siah2 regulates RevErbα degradation and the mammalian circadian clock. Proceedings of the National Academy of Sciences of the United States of America. 112: 12420-5. PMID 26392558 DOI: 10.1073/pnas.1501204112  1
2015 Altman BJ, Hsieh AL, Sengupta A, Krishnanaiah SY, Stine ZE, Walton ZE, Gouw AM, Venkataraman A, Li B, Goraksha-Hicks P, Diskin SJ, Bellovin DI, Simon MC, Rathmell JC, Lazar MA, ... ... Hogenesch JB, et al. MYC Disrupts the Circadian Clock and Metabolism in Cancer Cells. Cell Metabolism. 22: 1009-19. PMID 26387865 DOI: 10.1016/j.cmet.2015.09.003  1
2015 Hayer KE, Pizarro A, Lahens NF, Hogenesch JB, Grant GR. Benchmark analysis of algorithms for determining and quantifying full-length mRNA splice forms from RNA-seq data. Bioinformatics (Oxford, England). 31: 3938-45. PMID 26338770 DOI: 10.1093/bioinformatics/btv488  1
2015 Jang C, Lahens NF, Hogenesch JB, Sehgal A. Ribosome profiling reveals an important role for translational control in circadian gene expression. Genome Research. 25: 1836-47. PMID 26338483 DOI: 10.1101/gr.191296.115  1
2015 Lee Y, Jang AR, Francey LJ, Sehgal A, Hogenesch JB. KPNB1 mediates PER/CRY nuclear translocation and circadian clock function. Elife. 4. PMID 26319354 DOI: 10.7554/eLife.08647  1
2015 Anton L, Olarerin-George AO, Hogenesch JB, Elovitz MA. Placental expression of miR-517a/b and miR-517c contributes to trophoblast dysfunction and preeclampsia. Plos One. 10: e0122707. PMID 25799546 DOI: 10.1371/journal.pone.0122707  1
2015 Wolman MA, Jain RA, Marsden KC, Bell H, Skinner J, Hayer KE, Hogenesch JB, Granato M. A genome-wide screen identifies PAPP-AA-mediated IGFR signaling as a novel regulator of habituation learning. Neuron. 85: 1200-11. PMID 25754827 DOI: 10.1016/j.neuron.2015.02.025  1
2015 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. 43: 2535-42. PMID 25712092 DOI: 10.1093/nar/gkv136  1
2015 Banerjee S, Hayer K, Hogenesch JB, Granato M. Zebrafish foxc1a drives appendage-specific neural circuit development. Development (Cambridge, England). 142: 753-62. PMID 25670796 DOI: 10.1242/dev.115816  0.36
2015 Li J, Grant GR, Hogenesch JB, Hughes ME. Considerations for RNA-seq analysis of circadian rhythms. Methods in Enzymology. 551: 349-67. PMID 25662464 DOI: 10.1016/bs.mie.2014.10.020  1
2015 Wolman MA, Jain RA, Marsden KC, Bell H, Skinner J, Hayer KE, Hogenesch JB, Granato M. Errata to A Genome-wide Screen Identifies PAPP-AA-Mediated IGFR Signaling as a Novel Regulator of Habituation Learning [Neuron, 85, (2015), 1200-1211] Neuron. 87: 906-907. DOI: 10.1016/j.neuron.2015.08.009  1
2014 Manderfield LJ, Engleka KA, Aghajanian H, Gupta M, Yang S, Li L, Baggs JE, Hogenesch JB, Olson EN, Epstein JA. Pax3 and hippo signaling coordinate melanocyte gene expression in neural crest. Cell Reports. 9: 1885-95. PMID 25466249 DOI: 10.1016/j.celrep.2014.10.061  1
2014 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. 111: 16219-24. PMID 25349387 DOI: 10.1073/pnas.1408886111  1
2014 Perez-Santángelo S, Mancini E, Francey LJ, Schlaen RG, Chernomoretz A, Hogenesch JB, Yanovsky MJ. Role for LSM genes in the regulation of circadian rhythms. Proceedings of the National Academy of Sciences of the United States of America. 111: 15166-71. PMID 25288739 DOI: 10.1073/pnas.1409791111  1
2014 Pellegrino R, Kavakli IH, Goel N, Cardinale CJ, Dinges DF, Kuna ST, Maislin G, Van Dongen HP, Tufik S, Hogenesch JB, Hakonarson H, Pack AI. A novel BHLHE41 variant is associated with short sleep and resistance to sleep deprivation in humans. Sleep. 37: 1327-36. PMID 25083013 DOI: 10.5665/sleep.3924  1
2014 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. 15: R86. PMID 24981968 DOI: 10.1186/gb-2014-15-6-r86  1
2014 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. Plos Biology. 12: e1001840. PMID 24737000 DOI: 10.1371/journal.pbio.1001840  1
2014 Ramanathan C, Xu H, Khan SK, Shen Y, Gitis PJ, Welsh DK, Hogenesch JB, Liu AC. Cell type-specific functions of period genes revealed by novel adipocyte and hepatocyte circadian clock models. Plos Genetics. 10: e1004244. PMID 24699442 DOI: 10.1371/journal.pgen.1004244  1
2014 Hughes ME, Peeler J, Hogenesch JB, Trojanowski JQ. The growth and impact of Alzheimer disease centers as measured by social network analysis. Jama Neurology. 71: 412-20. PMID 24514750 DOI: 10.1001/jamaneurol.2013.6225  1
2013 Musiek ES, Lim MM, Yang G, Bauer AQ, Qi L, Lee Y, Roh JH, Ortiz-Gonzalez X, Dearborn JT, Culver JP, Herzog ED, Hogenesch JB, Wozniak DF, Dikranian K, Giasson BI, et al. Circadian clock proteins regulate neuronal redox homeostasis and neurodegeneration. The Journal of Clinical Investigation. 123: 5389-400. PMID 24270424 DOI: 10.1172/JCI70317  1
2013 Kasowski M, Kyriazopoulou-Panagiotopoulou S, Grubert F, Zaugg JB, Kundaje A, Liu Y, Boyle AP, Zhang QC, Zakharia F, Spacek DV, Li J, Xie D, Olarerin-George A, Steinmetz LM, Hogenesch JB, et al. Extensive variation in chromatin states across humans. Science (New York, N.Y.). 342: 750-2. PMID 24136358 DOI: 10.1126/science.1242510  0.8
2013 Deckard A, Anafi RC, Hogenesch JB, Haase SB, Harer J. Design and analysis of large-scale biological rhythm studies: a comparison of algorithms for detecting periodic signals in biological data. Bioinformatics (Oxford, England). 29: 3174-80. PMID 24058056 DOI: 10.1093/bioinformatics/btt541  1
2013 Anton L, Olarerin-George AO, Schwartz N, Srinivas S, Bastek J, Hogenesch JB, Elovitz MA. miR-210 inhibits trophoblast invasion and is a serum biomarker for preeclampsia. The American Journal of Pathology. 183: 1437-45. PMID 24035613 DOI: 10.1016/j.ajpath.2013.07.021  1
2013 Karpowicz P, Zhang Y, Hogenesch JB, Emery P, Perrimon N. The circadian clock gates the intestinal stem cell regenerative state. Cell Reports. 3: 996-1004. PMID 23583176 DOI: 10.1016/j.celrep.2013.03.016  0.32
2013 Shimomura K, Kumar V, Koike N, Kim TK, Chong J, Buhr ED, Whiteley AR, Low SS, Omura C, Fenner D, Owens JR, Richards M, Yoo SH, Hong HK, Vitaterna MH, ... ... Hogenesch J, et al. Usf1, a suppressor of the circadian Clock mutant, reveals the nature of the DNA-binding of the CLOCK:BMAL1 complex in mice. Elife. 2: e00426. PMID 23580255 DOI: 10.7554/eLife.00426  1
2013 Olarerin-George AO, Anton L, Hwang YC, Elovitz MA, Hogenesch JB. A functional genomics screen for microRNA regulators of NF-kappaB signaling. Bmc Biology. 11: 19. PMID 23448136 DOI: 10.1186/1741-7007-11-19  1
2013 Miller MF, Cohen ED, Baggs JE, Hogenesch JB, Morrisey EE. High throughput genomic screen identifies multiple factors that promote cooperative Wnt signaling. Plos One. 8: e55782. PMID 23383281 DOI: 10.1371/journal.pone.0055782  1
2013 Pizarro A, Hayer K, Lahens NF, Hogenesch JB. CircaDB: a database of mammalian circadian gene expression profiles. Nucleic Acids Research. 41: D1009-13. PMID 23180795 DOI: 10.1093/nar/gks1161  1
2013 Venkataraman A, Ballance H, Hogenesch JB. The Role of the Circadian System in Homeostasis Handbook of Systems Biology. 407-426. DOI: 10.1016/B978-0-12-385944-0.00021-6  1
2012 Wozniak MA, Cheng CQ, Shen CJ, Gao L, Olarerin-George AO, Won KJ, Hogenesch JB, Chen CS. Adhesion regulates MAP kinase/ternary complex factor exchange to control a proliferative transcriptional switch. Current Biology : Cb. 22: 2017-26. PMID 23063436 DOI: 10.1016/j.cub.2012.08.050  1
2012 Miller MF, Cohen ED, Baggs JE, Lu MM, Hogenesch JB, Morrisey EE. Wnt ligands signal in a cooperative manner to promote foregut organogenesis. Proceedings of the National Academy of Sciences of the United States of America. 109: 15348-53. PMID 22949635 DOI: 10.1073/pnas.1201583109  1
2012 Hughes ME, Hong HK, Chong JL, Indacochea AA, Lee SS, Han M, Takahashi JS, Hogenesch JB. Brain-specific rescue of Clock reveals system-driven transcriptional rhythms in peripheral tissue. Plos Genetics. 8: e1002835. PMID 22844252 DOI: 10.1371/journal.pgen.1002835  1
2012 Yusuf D, Butland SL, Swanson MI, Bolotin E, Ticoll A, Cheung WA, Zhang XY, Dickman CT, Fulton DL, Lim JS, Schnabl JM, Ramos OH, Vasseur-Cognet M, de Leeuw CN, Simpson EM, ... ... Hogenesch JB, et al. The transcription factor encyclopedia. Genome Biology. 13: R24. PMID 22458515 DOI: 10.1186/gb-2012-13-3-r24  1
2012 Merrick D, Chapin H, Baggs JE, Yu Z, Somlo S, Sun Z, Hogenesch JB, Caplan MJ. The γ-secretase cleavage product of polycystin-1 regulates TCF and CHOP-mediated transcriptional activation through a p300-dependent mechanism. Developmental Cell. 22: 197-210. PMID 22178500 DOI: 10.1016/j.devcel.2011.10.028  1
2011 Grant GR, Farkas MH, Pizarro AD, Lahens NF, Schug J, Brunk BP, Stoeckert CJ, Hogenesch JB, Pierce EA. Comparative analysis of RNA-Seq alignment algorithms and the RNA-Seq unified mapper (RUM). Bioinformatics (Oxford, England). 27: 2518-28. PMID 21775302 DOI: 10.1093/bioinformatics/btr427  1
2011 Xu K, DiAngelo JR, Hughes ME, Hogenesch JB, Sehgal A. The circadian clock interacts with metabolic physiology to influence reproductive fitness. Cell Metabolism. 13: 639-54. PMID 21641546 DOI: 10.1016/j.cmet.2011.05.001  1
2011 Hogenesch JB, Ueda HR. Understanding systems-level properties: timely stories from the study of clocks. Nature Reviews. Genetics. 12: 407-16. PMID 21556016 DOI: 10.1038/nrg2972  0.48
2011 DeBruyne JP, Hogenesch JB. A CRY in the Night. Developmental Cell. 20: 144-5. PMID 21316582 DOI: 10.1016/j.devcel.2011.01.014  1
2010 Andrews JL, Zhang X, McCarthy JJ, McDearmon EL, Hornberger TA, Russell B, Campbell KS, Arbogast S, Reid MB, Walker JR, Hogenesch JB, Takahashi JS, Esser KA. CLOCK and BMAL1 regulate MyoD and are necessary for maintenance of skeletal muscle phenotype and function. Proceedings of the National Academy of Sciences of the United States of America. 107: 19090-5. PMID 20956306 DOI: 10.1073/pnas.1014523107  1
2010 Hughes ME, Peeler J, Hogenesch JB. Network dynamics to evaluate performance of an academic institution. Science Translational Medicine. 2: 53ps49. PMID 20944088 DOI: 10.1126/scitranslmed.3001580  1
2010 Baggs JE, Hogenesch JB. Genomics and systems approaches in the mammalian circadian clock. Current Opinion in Genetics & Development. 20: 581-7. PMID 20926286 DOI: 10.1016/j.gde.2010.08.009  1
2010 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. 25: 372-80. PMID 20876817 DOI: 10.1177/0748730410379711  1
2010 Baggs JE, Hughes ME, Hogenesch JB. The network as the target. Wiley Interdisciplinary Reviews. Systems Biology and Medicine. 2: 127-33. PMID 20836017 DOI: 10.1002/wsbm.57  1
2010 McIntosh BE, Hogenesch JB, Bradfield CA. Mammalian Per-Arnt-Sim proteins in environmental adaptation. Annual Review of Physiology. 72: 625-45. PMID 20148691 DOI: 10.1146/annurev-physiol-021909-135922  0.92
2010 Paschos GK, Baggs JE, Hogenesch JB, FitzGerald GA. The role of clock genes in pharmacology. Annual Review of Pharmacology and Toxicology. 50: 187-214. PMID 20055702 DOI: 10.1146/annurev.pharmtox.010909.105621  1
2010 Huss JW, 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. 38: D633-9. PMID 19755503 DOI: 10.1093/nar/gkp760  1
2009 Zhang EE, Liu AC, Hirota T, Miraglia LJ, Welch G, Pongsawakul PY, Liu X, Atwood A, Huss JW, Janes J, Su AI, Hogenesch JB, Kay SA. A genome-wide RNAi screen for modifiers of the circadian clock in human cells. Cell. 139: 199-210. PMID 19765810 DOI: 10.1016/j.cell.2009.08.031  1
2009 McCarthy EV, Baggs JE, Geskes JM, Hogenesch JB, Green CB. Generation of a novel allelic series of cryptochrome mutants via mutagenesis reveals residues involved in protein-protein interaction and CRY2-specific repression. Molecular and Cellular Biology. 29: 5465-76. PMID 19687303 DOI: 10.1128/MCB.00641-09  1
2009 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. 5: e1000442. PMID 19343201 DOI: 10.1371/journal.pgen.1000442  1
2009 Warzecha CC, Sato TK, Nabet B, Hogenesch JB, Carstens RP. ESRP1 and ESRP2 are epithelial cell-type-specific regulators of FGFR2 splicing. Molecular Cell. 33: 591-601. PMID 19285943 DOI: 10.1016/j.molcel.2009.01.025  1
2009 Baggs JE, Price TS, DiTacchio L, Panda S, Fitzgerald GA, Hogenesch JB. Network features of the mammalian circadian clock. Plos Biology. 7: e52. PMID 19278294 DOI: 10.1371/journal.pbio.1000052  1
2009 Bailey MJ, Coon SL, Carter DA, Humphries A, Kim JS, Shi Q, Gaildrat P, Morin F, Ganguly S, Hogenesch JB, Weller JL, Rath MF, Møller M, Baler R, Sugden D, et al. Night/day changes in pineal expression of >600 genes: central role of adrenergic/cAMP signaling. The Journal of Biological Chemistry. 284: 7606-22. PMID 19103603 DOI: 10.1074/jbc.M808394200  1
2008 Price TS, Baggs JE, Curtis AM, Fitzgerald GA, Hogenesch JB. WAVECLOCK: wavelet analysis of circadian oscillation. Bioinformatics (Oxford, England). 24: 2794-5. PMID 18931366 DOI: 10.1093/bioinformatics/btn521  1
2008 Hogenesch JB, Su AI. Clock gene wikis available: join the "long tail". Journal of Biological Rhythms. 23: 456-7. PMID 18838611 DOI: 10.1177/0748730408322866  0.92
2008 Kumaki Y, Ukai-Tadenuma M, Uno KD, Nishio J, Masumoto KH, Nagano M, Komori T, Shigeyoshi Y, Hogenesch JB, Ueda HR. Analysis and synthesis of high-amplitude Cis-elements in the mammalian circadian clock. Proceedings of the National Academy of Sciences of the United States of America. 105: 14946-51. PMID 18815372 DOI: 10.1073/pnas.0802636105  0.48
2008 Gumireddy K, Young DD, Xiong X, Hogenesch JB, Huang Q, Deiters A. Small-molecule inhibitors of microrna miR-21 function. Angewandte Chemie (International Ed. in English). 47: 7482-4. PMID 18712719 DOI: 10.1002/anie.200801555  1
2008 Yang L, Walker JR, Hogenesch JB, Thomas RS. NetAtlas: a Cytoscape plugin to examine signaling networks based on tissue gene expression. In Silico Biology. 8: 47-52. PMID 18430989  0.64
2007 Hughes M, Deharo L, Pulivarthy SR, Gu J, Hayes K, Panda S, Hogenesch JB. High-resolution time course analysis of gene expression from pituitary. Cold Spring Harbor Symposia On Quantitative Biology. 72: 381-6. PMID 18419295 DOI: 10.1101/sqb.2007.72.011  1
2007 Amelio AL, Miraglia LJ, Conkright JJ, Mercer BA, Batalov S, Cavett V, Orth AP, Busby J, Hogenesch JB, Conkright MD. A coactivator trap identifies NONO (p54nrb) as a component of the cAMP-signaling pathway. Proceedings of the National Academy of Sciences of the United States of America. 104: 20314-9. PMID 18077367 DOI: 10.1073/pnas.0707999105  1
2007 Kozlov SV, Bogenpohl JW, Howell MP, Wevrick R, Panda S, Hogenesch JB, Muglia LJ, Van Gelder RN, Herzog ED, Stewart CL. The imprinted gene Magel2 regulates normal circadian output. Nature Genetics. 39: 1266-72. PMID 17893678 DOI: 10.1038/ng2114  1
2007 Halsey TA, Yang L, Walker JR, Hogenesch JB, Thomas RS. A functional map of NFkappaB signaling identifies novel modulators and multiple system controls. Genome Biology. 8: R104. PMID 17553156 DOI: 10.1186/gb-2007-8-6-r104  0.64
2007 McCarthy JJ, Andrews JL, McDearmon EL, Campbell KS, Barber BK, Miller BH, Walker JR, Hogenesch JB, Takahashi JS, Esser KA. Identification of the circadian transcriptome in adult mouse skeletal muscle. Physiological Genomics. 31: 86-95. PMID 17550994 DOI: 10.1152/physiolgenomics.00066.2007  0.92
2007 Su AI, Hogenesch JB. Power-law-like distributions in biomedical publications and research funding. Genome Biology. 8: 404. PMID 17472739 DOI: 10.1186/gb-2007-8-4-404  0.92
2007 Miller BH, McDearmon EL, Panda S, Hayes KR, Zhang J, Andrews JL, Antoch MP, Walker JR, Esser KA, Hogenesch JB, Takahashi JS. Circadian and CLOCK-controlled regulation of the mouse transcriptome and cell proliferation. Proceedings of the National Academy of Sciences of the United States of America. 104: 3342-7. PMID 17360649 DOI: 10.1073/pnas.0611724104  1
2006 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. 38: 312-9. PMID 16474406 DOI: 10.1038/ng1745  1
2005 Rudic RD, McNamara P, Reilly D, Grosser T, Curtis AM, Price TS, Panda S, Hogenesch JB, FitzGerald GA. Bioinformatic analysis of circadian gene oscillation in mouse aorta. Circulation. 112: 2716-24. PMID 16230482 DOI: 10.1161/CIRCULATIONAHA.105.568626  1
2005 Baggs JE, Hayes KR, Hogenesch JB. Comparative genomics as a tool in the understanding of eukaryotic transcriptional regulation. Current Opinion in Genetics & Development. 15: 634-9. PMID 16226457 DOI: 10.1016/j.gde.2005.09.012  1
2005 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 (New York, N.Y.). 309: 1570-3. PMID 16141075 DOI: 10.1126/science.1115901  0.92
2005 Harada JN, Bower KE, Orth AP, Callaway S, Nelson CG, Laris C, Hogenesch JB, Vogt PK, Chanda SK. Identification of novel mammalian growth regulatory factors by genome-scale quantitative image analysis. Genome Research. 15: 1136-44. PMID 16024821 DOI: 10.1101/gr.3889305  1
2005 Gurkan C, Lapp H, Alory C, Su AI, Hogenesch JB, Balch WE. Large-scale profiling of Rab GTPase trafficking networks: the membrome. Molecular Biology of the Cell. 16: 3847-64. PMID 15944222 DOI: 10.1091/mbc.e05-01-0062  0.92
2005 Vengellur A, Phillips JM, Hogenesch JB, LaPres JJ. Gene expression profiling of hypoxia signaling in human hepatocellular carcinoma cells. Physiological Genomics. 22: 308-18. PMID 15942021 DOI: 10.1152/physiolgenomics.00045.2004  1
2005 Hayes KR, Baggs JE, Hogenesch JB. Circadian clocks are seeing the systems biology light. Genome Biology. 6: 219. PMID 15892879 DOI: 10.1186/gb-2005-6-5-219  1
2005 Walker JR, Hogenesch JB. RNA profiling in circadian biology. Methods in Enzymology. 393: 366-76. PMID 15817299 DOI: 10.1016/S0076-6879(05)93016-4  1
2005 Zhang X, Odom DT, Koo SH, Conkright MD, Canettieri G, Best J, Chen H, Jenner R, Herbolsheimer E, Jacobsen E, Kadam S, Ecker JR, Emerson B, Hogenesch JB, Unterman T, et al. Genome-wide analysis of cAMP-response element binding protein occupancy, phosphorylation, and target gene activation in human tissues. Proceedings of the National Academy of Sciences of the United States of America. 102: 4459-64. PMID 15753290 DOI: 10.1073/pnas.0501076102  0.44
2005 Sandberg ML, Sutton SE, Pletcher MT, Wiltshire T, Tarantino LM, Hogenesch JB, Cooke MP. c-Myb and p300 regulate hematopoietic stem cell proliferation and differentiation. Developmental Cell. 8: 153-66. PMID 15691758 DOI: 10.1016/j.devcel.2004.12.015  1
2005 Panda S, Nayak SK, Campo B, Walker JR, Hogenesch JB, Jegla T. Illumination of the melanopsin signaling pathway. Science (New York, N.Y.). 307: 600-4. PMID 15681390 DOI: 10.1126/science.1105121  1
2004 Panda S, Hogenesch JB. It's all in the timing: many clocks, many outputs. Journal of Biological Rhythms. 19: 374-87. PMID 15534318 DOI: 10.1177/0748730404269008  1
2004 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. 2: e377. PMID 15523558 DOI: 10.1371/journal.pbio.0020377  1
2004 Joseph SB, Bradley MN, Castrillo A, Bruhn KW, Mak PA, Pei L, Hogenesch J, O'connell RM, Cheng G, Saez E, Miller JF, Tontonoz P. LXR-dependent gene expression is important for macrophage survival and the innate immune response. Cell. 119: 299-309. PMID 15479645 DOI: 10.1016/j.cell.2004.09.032  1
2004 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. 43: 527-37. PMID 15312651 DOI: 10.1016/j.neuron.2004.07.018  1
2004 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 the United States of America. 101: 6062-7. PMID 15075390 DOI: 10.1073/pnas.0400782101  0.92
2004 Walker JR, Su AI, Self DW, Hogenesch JB, Lapp H, Maier R, Hoyer D, Bilbe G. Applications of a rat multiple tissue gene expression data set. Genome Research. 14: 742-9. PMID 15060018 DOI: 10.1101/gr.2161804  0.92
2004 Ueda HR, Hayashi S, Matsuyama S, Yomo T, Hashimoto S, Kay SA, Hogenesch JB, Iino M. Universality and flexibility in gene expression from bacteria to human. Proceedings of the National Academy of Sciences of the United States of America. 101: 3765-9. PMID 14999098 DOI: 10.1073/pnas.0306244101  1
2004 Grechez-Cassiau A, Panda S, Lacoche S, Teboul M, Azmi S, Laudet V, Hogenesch JB, Taneja R, Delaunay F. The transcriptional repressor STRA13 regulates a subset of peripheral circadian outputs. The Journal of Biological Chemistry. 279: 1141-50. PMID 14581485 DOI: 10.1074/jbc.M305369200  1
2003 Hogenesch JB, Panda S, Kay S, Takahashi JS. Circadian transcriptional output in the SCN and liver of the mouse. Novartis Foundation Symposium. 253: 171-80; discussion 5. PMID 14712921  1
2003 Panda S, Hogenesch JB, Kay SA. Circadian light input in plants, flies and mammals. Novartis Foundation Symposium. 253: 73-82; discussion 82. PMID 14712915  1
2003 Conkright MD, Canettieri G, Screaton R, Guzman E, Miraglia L, Hogenesch JB, Montminy M. TORCs: transducers of regulated CREB activity. Molecular Cell. 12: 413-23. PMID 14536081  0.44
2003 Chanda SK, White S, Orth AP, Reisdorph R, Miraglia L, Thomas RS, DeJesus P, Mason DE, Huang Q, Vega R, Yu DH, Nelson CG, Smith BM, Terry R, Linford AS, ... ... Hogenesch JB, et al. Genome-scale functional profiling of the mammalian AP-1 signaling pathway. Proceedings of the National Academy of Sciences of the United States of America. 100: 12153-8. PMID 14514886 DOI: 10.1073/pnas.1934839100  0.92
2003 Reyes TM, Walker JR, DeCino C, Hogenesch JB, Sawchenko PE. Categorically distinct acute stressors elicit dissimilar transcriptional profiles in the paraventricular nucleus of the hypothalamus. The Journal of Neuroscience : the Official Journal of the Society For Neuroscience. 23: 5607-16. PMID 12843263  0.64
2003 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 (New York, N.Y.). 301: 525-7. PMID 12829787 DOI: 10.1126/science.1086179  1
2003 Conkright MD, Guzmán E, Flechner L, Su AI, Hogenesch JB, Montminy M. Genome-wide analysis of CREB target genes reveals a core promoter requirement for cAMP responsiveness. Molecular Cell. 11: 1101-8. PMID 12718894 DOI: 10.1016/s1097-2765(03)00134-5  0.92
2003 Downes M, Verdecia MA, Roecker AJ, Hughes R, Hogenesch JB, Kast-Woelbern HR, Bowman ME, Ferrer JL, Anisfeld AM, Edwards PA, Rosenfeld JM, Alvarez JG, Noel JP, Nicolaou KC, Evans RM. A chemical, genetic, and structural analysis of the nuclear bile acid receptor FXR. Molecular Cell. 11: 1079-92. PMID 12718892 DOI: 10.1016/S1097-2765(03)00104-7  1
2003 Sato TK, Panda S, Kay SA, Hogenesch JB. DNA arrays: applications and implications for circadian biology. Journal of Biological Rhythms. 18: 96-105. PMID 12693865  1
2003 Panda S, Sato TK, Hampton GM, Hogenesch JB. An array of insights: application of DNA chip technology in the study of cell biology. Trends in Cell Biology. 13: 151-6. PMID 12628348  1
2002 Panda S, Sato TK, Castrucci AM, Rollag MD, DeGrip WJ, Hogenesch JB, Provencio I, Kay SA. Melanopsin (Opn4) requirement for normal light-induced circadian phase shifting. Science (New York, N.Y.). 298: 2213-6. PMID 12481141 DOI: 10.1126/science.1076848  1
2002 Ceriani MF, Hogenesch JB, Yanovsky M, Panda S, Straume M, Kay SA. Genome-wide expression analysis in Drosophila reveals genes controlling circadian behavior. The Journal of Neuroscience : the Official Journal of the Society For Neuroscience. 22: 9305-19. PMID 12417656  1
2002 Li S, Liao J, Cutler G, Hoey T, Hogenesch JB, Cooke MP, Schultz PG, Ling XB. Comparative analysis of human genome assemblies reveals genome-level differences. Genomics. 80: 138-9. PMID 12160725 DOI: 10.1006/geno.2002.6824  1
2002 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 (New York, N.Y.). 296: 2046-9. PMID 12016205 DOI: 10.1126/science.1073140  1
2002 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. 109: 307-20. PMID 12015981 DOI: 10.1016/s0092-8674(02)00722-5  1
2002 Panda S, Hogenesch JB, Kay SA. Circadian rhythms from flies to human. Nature. 417: 329-35. PMID 12015613 DOI: 10.1038/417329a  1
2002 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 the United States of America. 99: 4465-70. PMID 11904358 DOI: 10.1073/pnas.012025199  0.92
2001 Hogenesch JB, Ching KA, Batalov S, Su AI, Walker JR, Zhou Y, Kay SA, Schultz PG, Cooke MP. A comparison of the Celera and Ensembl predicted gene sets reveals little overlap in novel genes. Cell. 106: 413-5. PMID 11534548 DOI: 10.1016/S0092-8674(01)00467-6  1
2001 Reyes TM, Lewis K, Perrin MH, Kunitake KS, Vaughan J, Arias CA, Hogenesch JB, Gulyas J, Rivier J, Vale WW, Sawchenko PE. Urocortin II: a member of the corticotropin-releasing factor (CRF) neuropeptide family that is selectively bound by type 2 CRF receptors. Proceedings of the National Academy of Sciences of the United States of America. 98: 2843-8. PMID 11226328 DOI: 10.1073/pnas.051626398  1
2000 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. 103: 1009-17. PMID 11163178 DOI: 10.1016/S0092-8674(00)00205-1  1
2000 Harmer SL, Hogenesch JB, Straume M, Chang HS, Han B, Zhu T, Wang X, Kreps JA, Kay SA. Orchestrated transcription of key pathways in Arabidopsis by the circadian clock. Science (New York, N.Y.). 290: 2110-3. PMID 11118138 DOI: 10.1126/science.290.5499.2110  1
2000 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. 20: RC83. PMID 10864977  1
2000 Gu YZ, Hogenesch JB, Bradfield CA. The PAS superfamily: sensors of environmental and developmental signals. Annual Review of Pharmacology and Toxicology. 40: 519-61. PMID 10836146 DOI: 10.1146/annurev.pharmtox.40.1.519  0.92
1998 Gu YZ, Moran SM, Hogenesch JB, Wartman L, Bradfield CA. Molecular characterization and chromosomal localization of a third alpha-class hypoxia inducible factor subunit, HIF3alpha. Gene Expression. 7: 205-13. PMID 9840812  1
1998 Hogenesch JB, Gu YZ, Jain S, Bradfield CA. The basic-helix-loop-helix-PAS orphan MOP3 forms transcriptionally active complexes with circadian and hypoxia factors. Proceedings of the National Academy of Sciences of the United States of America. 95: 5474-9. PMID 9576906  0.92
1997 Luo G, Gu YZ, Jain S, Chan WK, Carr KM, Hogenesch JB, Bradfield CA. Molecular characterization of the murine Hif-1 alpha locus. Gene Expression. 6: 287-99. PMID 9368100  1
1997 Hogenesch JB, Chan WK, Jackiw VH, Brown RC, Gu YZ, Pray-Grant 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. 272: 8581-93. PMID 9079689 DOI: 10.1074/jbc.272.13.8581  1
1994 Carver LA, Hogenesch JB, Bradfield CA. Tissue specific expression of the rat Ah-receptor and ARNT mRNAs. Nucleic Acids Research. 22: 3038-44. PMID 8065918  0.92
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