John B. Hogenesch, PhD - Publications

Affiliations: 
Pharmacology Cincinnati Children's Hospital and Medical Center, USA 
Area:
genomics, computational biology, drug discovery, circadian rhythms
Website:
hogeneschlab.org

170 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
2022 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. is a null mutation of Cryptochrome 1 in Syrian hamsters. Proceedings of the National Academy of Sciences of the United States of America. 119: e2123560119. PMID 35471909 DOI: 10.1073/pnas.2123560119  0.712
2022 Zhang T, Du X, Gu Y, Dong Y, Zhang W, Yuan Z, Huang X, Zou C, Zhou Y, Liu Z, Tao H, Yang L, Wu G, Hogenesch JB, Zhou CJ, et al. Analysis of Diurnal Variations in Heart Rate: Potential Applications for Chronobiology and Cardiovascular Medicine. Frontiers in Physiology. 13: 835198. PMID 35350693 DOI: 10.3389/fphys.2022.835198  0.323
2021 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. Plos Genetics. 17: e1009933. PMID 34807912 DOI: 10.1371/journal.pgen.1009933  0.817
2021 Wu G, Francey LJ, Ruben MD, Hogenesch JB. Normalized coefficient of variation (nCV): a method to evaluate circadian clock robustness in population scale data. Bioinformatics (Oxford, England). PMID 34726689 DOI: 10.1093/bioinformatics/btab731  0.766
2021 Rosselot AE, Park M, Kim M, Matsu-Ura T, Wu G, Flores DE, Subramanian KR, Lee S, Sundaram N, Broda TR, McCauley HA, Hawkins JA, Chetal K, Salomonis N, Shroyer NF, ... ... Hogenesch JB, et al. Ontogeny and function of the circadian clock in intestinal organoids. The Embo Journal. e106973. PMID 34704277 DOI: 10.15252/embj.2020106973  0.455
2021 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. 22: 692. PMID 34563123 DOI: 10.1186/s12864-021-07934-2  0.665
2021 Stokes K, Nunes M, Trombley C, Flôres DEFL, 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. Cellular and Molecular Gastroenterology and Hepatology. PMID 34534703 DOI: 10.1016/j.jcmgh.2021.08.001  0.49
2021 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. 10. PMID 33599610 DOI: 10.7554/eLife.63003  0.74
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  0.766
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  0.824
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  0.455
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  0.683
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  0.721
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  0.826
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  0.455
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  0.693
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  0.404
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  0.759
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  0.494
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  0.477
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  0.813
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  0.805
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  0.738
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  0.829
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  0.786
2018 Castellana S, Mazza T, Capocefalo D, Genov N, Biagini T, Fusilli C, Scholkmann F, Relógio A, Hogenesch JB, Mazzoccoli G. Systematic Analysis of Mouse Genome Reveals Distinct Evolutionary and Functional Properties Among Circadian and Ultradian Genes. Frontiers in Physiology. 9: 1178. PMID 30190679 DOI: 10.3389/Fphys.2018.01178  0.481
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  0.367
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  0.679
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  0.482
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  0.755
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  0.774
2017 Francey LJ, Hogenesch JB. It's not all in the brain. Elife. 6. PMID 28850329 DOI: 10.7554/Elife.30561  0.712
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  0.334
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  0.805
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  0.741
2017 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. PMID 28439010 DOI: 10.1073/Pnas.1619320114  0.82
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  0.803
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  0.752
2016 Love MI, Hogenesch JB, Irizarry RA. Modeling of RNA-seq fragment sequence bias reduces systematic errors in transcript abundance estimation. Nature Biotechnology. PMID 27669167 DOI: 10.1038/Nbt.3682  0.313
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  0.815
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  0.77
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  0.651
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  0.831
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  0.74
2016 Erion R, King AN, Wu G, Hogenesch JB, Sehgal A. Author response: Neural clocks and Neuropeptide F/Y regulate circadian gene expression in a peripheral metabolic tissue Elife. DOI: 10.7554/Elife.13552.023  0.62
2016 Vaquero-Garcia J, Barrera A, Gazzara MR, González-Vallinas J, Lahens NF, Hogenesch JB, Lynch KW, Barash Y. Author response: A new view of transcriptome complexity and regulation through the lens of local splicing variations Elife. DOI: 10.7554/Elife.11752.080  0.712
2016 Kim EJ, Lahens N, Ricciotti E, Manduchi E, Grosser T, Fitzgerald G, Hogenesch J, Grant G. Resampling-based read-level normalization of RNA-Seq for differential expression analysis F1000research. 5. DOI: 10.7490/F1000Research.1112772.1  0.741
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  0.726
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  0.382
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  0.823
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  0.807
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  0.709
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  0.808
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  0.817
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  0.728
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  0.345
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  0.768
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  0.668
2015 Lee Y, Jang AR, Francey LJ, Sehgal A, Hogenesch JB. Author response: KPNB1 mediates PER/CRY nuclear translocation and circadian clock function Elife. DOI: 10.7554/Elife.08647.020  0.802
2015 Anton L, Olarerin-George AO, Hogenesch JB, Elovitz MA. Clinical and demographic characteristics of Preeclampsia case-control study. Plos One. DOI: 10.1371/Journal.Pone.0122707.T001  0.72
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  0.754
2014 Toung JM, Lahens N, Hogenesch JB, Grant G. Detection theory in identification of RNA-DNA sequence differences using RNA-sequencing. Plos One. 9: e112040. PMID 25396741 DOI: 10.1371/Journal.Pone.0112040  0.699
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  0.835
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  0.791
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  0.785
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  0.834
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  0.784
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  0.485
2014 Altman BJ, Hsieh A, Gouw AM, Stine ZE, Venkataraman A, Bellovin DI, Diskin SJ, Lu W, Zhang S, Felsher DW, Maris JM, Lazar MA, Rabinowitz JD, Hogenesch JB, Dang CV. Abstract 2953: Rev-erbα modulates Myc-driven cancer cell growth and altered metabolism Cancer Research. 74: 2953-2953. DOI: 10.1158/1538-7445.Am2014-2953  0.795
2014 Hsieh AL, Altman BJ, Venkataraman A, Bellovin DI, Felsher DW, Hogenesch JB, Dang CV. Abstract 1419: Oncogenic Myc disrupts NAMPT circadian oscillation in mouse hepatocellular carcinoma cell line Cancer Research. 74: 1419-1419. DOI: 10.1158/1538-7445.Am2014-1419  0.8
2014 Hsieh A, Altman B, Stine Z, Gouw A, Venkataraman A, Li B, Goraksha-Hicks P, Diskin S, Bellovin D, Celeste Simon M, Rathmell J, Lazar M, Maris J, Felsher D, Hogenesch J, et al. TM-06 * MYC AND MYCN DISRUPTION OF THE MOLECULAR CLOCK IN CANCER CELLS Neuro-Oncology. 16: v214-v214. DOI: 10.1093/Neuonc/Nou278.6  0.79
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  0.825
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  0.764
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  0.768
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  0.733
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  0.453
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  0.551
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  0.762
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  0.737
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  0.745
2013 Shimomura K, Kumar V, Koike N, Kim T, Chong J, Buhr ED, Whiteley AR, Low SS, Omura C, Fenner D, Owens JR, Richards M, Yoo S, Hong H, Vitaterna MH, ... ... Hogenesch J, et al. Author response: Usf1, a suppressor of the circadian Clock mutant, reveals the nature of the DNA-binding of the CLOCK:BMAL1 complex in mice Elife. DOI: 10.7554/Elife.00426.021  0.55
2013 Altman BJ, Hsieh A, Gouw A, Venkataraman A, Li B, Bellovin D, Simon MC, Felsher D, Hogenesch J, Dang CV. Abstract 4616: Oncogenic c- and N-Myc disrupt circadian rhythm. Cancer Research. 73: 4616-4616. DOI: 10.1158/1538-7445.Am2013-4616  0.816
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  0.781
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  0.777
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  0.699
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  0.74
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  0.733
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  0.727
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  0.694
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  0.688
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  0.319
2011 Hogenesch JB, Herzog ED. Intracellular and intercellular processes determine robustness of the circadian clock. Febs Letters. 585: 1427-34. PMID 21536033 DOI: 10.1016/J.Febslet.2011.04.048  0.464
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  0.779
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  0.561
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  0.491
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  0.787
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  0.637
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  0.748
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  0.794
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  0.782
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  0.768
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  0.809
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  0.803
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  0.837
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  0.691
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  0.824
2009 Hogenesch JB. It's all in a day's work: Regulation of DNA excision repair by the circadian clock. Proceedings of the National Academy of Sciences of the United States of America. 106: 2481-2. PMID 19240220 DOI: 10.1073/Pnas.0813323106  0.408
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  0.423
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  0.769
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  0.78
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  0.385
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  0.768
2008 Miller MF, Cohen ED, Goss AM, Baggs J, Hogenesch J, Morrisey EE. Synergistic activation of canonical signaling by a subset of Wnt ligands Developmental Biology. 319: 606. DOI: 10.1016/J.Ydbio.2008.05.453  0.688
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  0.826
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  0.709
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  0.649
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  0.342
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  0.601
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  0.756
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  0.838
2006 Lee K A, Burgoon LD, Lamb L, Dere E, Zacharewski TR, Hogenesch JB, LaPres JJ. Identification and characterization of genes susceptible to transcriptional cross-talk between the hypoxia and dioxin signaling cascades. Chemical Research in Toxicology. 19: 1284-93. PMID 17040097 DOI: 10.1021/Tx060068D  0.418
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  0.829
2006 Lee K, Burgoon LD, Lamb L, Dere E, Zacharewski TR, Hogenesch JB, LaPres JJ. Identification and Characterization of Genes Susceptible to Transcriptional Cross-Talk between the Hypoxia and Dioxin Signaling Cascades Volume 19, Number 10, October, 2006, pp 1284−1293 Chemical Research in Toxicology. 19: 1702-1702. DOI: 10.1021/Tx600294R  0.33
2005 Gurkan C, Lapp H, Hogenesch JB, Balch WE. Exploring trafficking GTPase function by mRNA expression profiling: use of the SymAtlas web-application and the Membrome datasets. Methods in Enzymology. 403: 1-10. PMID 16473572 DOI: 10.1016/S0076-6879(05)03001-6  0.41
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  0.744
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  0.809
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  0.808
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  0.711
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  0.772
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  0.336
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  0.838
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  0.412
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  0.39
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  0.679
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  0.746
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  0.731
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  0.335
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  0.836
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  0.79
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  0.779
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  0.694
2004 Van Gelder RN, Hogenesch JB. Clean thoughts about dirty genes. Journal of Biological Rhythms. 19: 3-9. PMID 14964699 DOI: 10.1177/0748730403261123  0.396
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  0.761
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 DOI: 10.1002/0470090839.Ch13  0.849
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 DOI: 10.1002/0470090839.Ch6  0.782
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 DOI: 10.1016/J.Molcel.2003.08.013  0.368
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  0.79
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 DOI: 10.1523/Jneurosci.23-13-05607.2003  0.388
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  0.785
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  0.784
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  0.303
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 DOI: 10.1177/0748730403252245  0.802
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 DOI: 10.1016/S0962-8924(03)00006-0  0.78
2003 Ueda H, Hayashi S, Matsuyama S, Yomo T, Hashimoto S, Kay S, Hogenesch J, Iino M. Underlying Principles in Transcriptional Dynamics from E. coli to Man Seibutsu Butsuri. 43: S6. DOI: 10.2142/biophys.43.S6_1  0.605
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  0.809
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 DOI: 10.1523/Jneurosci.22-21-09305.2002  0.832
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  0.697
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  0.839
2002 Panda S, Hogenesch JB, Kay SA. Circadian rhythms from flies to human. Nature. 417: 329-35. PMID 12015613 DOI: 10.1038/417329A  0.788
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  0.822
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  0.792
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  0.829
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  0.838
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 DOI: 10.1523/Jneurosci.20-13-J0002.2000  0.78
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  0.703
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  0.664
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 DOI: 10.1073/Pnas.95.10.5474  0.732
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  0.679
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  0.688
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 DOI: 10.1093/Nar/22.15.3038  0.704
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