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Items: 1 to 50 of 138

1.

Polycystin-1 regulates bone development through an interaction with the transcriptional co-activator taz.

Merrick D, Mistry K, Wu J, Gresko N, Baggs JE, Hogenesch JB, Sun Z, Caplan MJ.

Hum Mol Genet. 2018 Sep 12. doi: 10.1093/hmg/ddy322. [Epub ahead of print]

PMID:
30215740
2.

A database of tissue-specific rhythmically expressed human genes has potential applications in circadian medicine.

Ruben MD, Wu G, Smith DF, Schmidt RE, Francey LJ, Lee YY, Anafi RC, Hogenesch JB.

Sci Transl Med. 2018 Sep 12;10(458). pii: eaat8806. doi: 10.1126/scitranslmed.aat8806.

PMID:
30209245
3.

Circadian Dysregulation: The Next Frontier in Obstructive Sleep Apnea Research.

von Allmen DC, Francey LJ, Rogers GM, Ruben MD, Cohen AP, Wu G, Schmidt RE, Ishman SL, Amin RS, Hogenesch JB, Smith DF.

Otolaryngol Head Neck Surg. 2018 Sep 11:194599818797311. doi: 10.1177/0194599818797311. [Epub ahead of print]

PMID:
30200807
4.

Systematic Analysis of Mouse Genome Reveals Distinct Evolutionary and Functional Properties Among Circadian and Ultradian Genes.

Castellana S, Mazza T, Capocefalo D, Genov N, Biagini T, Fusilli C, Scholkmann F, Relógio A, Hogenesch JB, Mazzoccoli G.

Front Physiol. 2018 Aug 23;9:1178. doi: 10.3389/fphys.2018.01178. eCollection 2018.

5.

Interrogation of nonconserved human adipose lincRNAs identifies a regulatory role of linc-ADAL in adipocyte metabolism.

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, Seale P, Li M, Reilly MP.

Sci Transl Med. 2018 Jun 20;10(446). pii: eaar5987. doi: 10.1126/scitranslmed.aar5987.

PMID:
29925637
6.

mTOR signaling regulates central and peripheral circadian clock function.

Ramanathan C, Kathale ND, Liu D, Lee C, Freeman DA, Hogenesch JB, Cao R, Liu AC.

PLoS Genet. 2018 May 11;14(5):e1007369. doi: 10.1371/journal.pgen.1007369. eCollection 2018 May.

7.

Cisplatin-DNA adduct repair of transcribed genes is controlled by two circadian programs in mouse tissues.

Yang Y, Adebali O, Wu G, Selby CP, Chiou YY, Rashid N, Hu J, Hogenesch JB, Sancar A.

Proc Natl Acad Sci U S A. 2018 May 22;115(21):E4777-E4785. doi: 10.1073/pnas.1804493115. Epub 2018 May 7.

PMID:
29735688
8.

Soluble syntaxin 3 functions as a transcriptional regulator.

Giovannone AJ, Winterstein C, Bhattaram P, Reales E, Low SH, Baggs JE, Xu M, Lalli MA, Hogenesch JB, Weimbs T.

J Biol Chem. 2018 Apr 13;293(15):5478-5491. doi: 10.1074/jbc.RA117.000874. Epub 2018 Feb 23.

PMID:
29475951
9.

Guidelines for Genome-Scale Analysis of Biological Rhythms.

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, Crowell AM, DeBruyne JP, Dijk DJ, DiTacchio L, Doyle FJ, Duffield GE, Dunlap JC, Eckel-Mahan K, Esser KA, FitzGerald GA, Forger DB, Francey LJ, Fu YH, Gachon F, Gatfield D, de Goede P, Golden SS, Green C, Harer J, Harmer S, Haspel J, Hastings MH, Herzel H, Herzog ED, Hoffmann C, Hong C, Hughey JJ, Hurley JM, de la Iglesia HO, Johnson C, Kay SA, Koike N, Kornacker K, Kramer A, Lamia K, Leise T, Lewis SA, Li J, Li X, Liu AC, Loros JJ, Martino TA, Menet JS, Merrow M, Millar AJ, Mockler T, Naef F, Nagoshi E, Nitabach MN, Olmedo M, Nusinow DA, Ptáček LJ, Rand D, Reddy AB, Robles MS, Roenneberg T, Rosbash M, Ruben MD, Rund SSC, Sancar A, Sassone-Corsi P, Sehgal A, Sherrill-Mix S, Skene DJ, Storch KF, Takahashi JS, Ueda HR, Wang H, Weitz C, Westermark PO, Wijnen H, Xu Y, Wu G, Yoo SH, Young M, Zhang EE, Zielinski T, Hogenesch JB.

J Biol Rhythms. 2017 Oct;32(5):380-393. doi: 10.1177/0748730417728663. Epub 2017 Nov 3.

10.

Experimental and statistical reevaluation provides no evidence for Drosophila courtship song rhythms.

Stern DL, Clemens J, Coen P, Calhoun AJ, Hogenesch JB, Arthur BJ, Murthy M.

Proc Natl Acad Sci U S A. 2017 Sep 12;114(37):9978-9983. doi: 10.1073/pnas.1707471114. Epub 2017 Aug 29.

11.

It's not all in the brain.

Francey LJ, Hogenesch JB.

Elife. 2017 Aug 29;6. pii: e30561. doi: 10.7554/eLife.30561.

12.

Circadian Rhythms: Move Over Neurons - Astrocytes Mediate SCN Clock Function.

Ruben MD, Hogenesch JB.

Curr Biol. 2017 May 8;27(9):R350-R352. doi: 10.1016/j.cub.2017.03.055.

13.

Clock Regulation of Metabolites Reveals Coupling between Transcription and Metabolism.

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, Sengupta A, Anafi RC, Kavakli IH, Sancar A, Baur JA, Dang CV, Hogenesch JB, Weljie AM.

Cell Metab. 2017 May 2;25(5):1206. doi: 10.1016/j.cmet.2017.04.023. No abstract available.

14.

The Nephila clavipes genome highlights the diversity of spider silk genes and their complex expression.

Babb PL, Lahens NF, Correa-Garhwal SM, Nicholson DN, Kim EJ, Hogenesch JB, Kuntner M, Higgins L, Hayashi CY, Agnarsson I, Voight BF.

Nat Genet. 2017 Jun;49(6):895-903. doi: 10.1038/ng.3852. Epub 2017 May 1.

PMID:
28459453
15.

CYCLOPS reveals human transcriptional rhythms in health and disease.

Anafi RC, Francey LJ, Hogenesch JB, Kim J.

Proc Natl Acad Sci U S A. 2017 May 16;114(20):5312-5317. doi: 10.1073/pnas.1619320114. Epub 2017 Apr 24.

16.

Clock Regulation of Metabolites Reveals Coupling between Transcription and Metabolism.

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, Sengupta A, Anafi RC, Kavakli IH, Sancar A, Baur JA, Dang CV, Hogenesch JB, Weljie AM.

Cell Metab. 2017 Apr 4;25(4):961-974.e4. doi: 10.1016/j.cmet.2017.03.019. Erratum in: Cell Metab. 2017 May 2;25(5):1206.

17.

Modeling of RNA-seq fragment sequence bias reduces systematic errors in transcript abundance estimation.

Love MI, Hogenesch JB, Irizarry RA.

Nat Biotechnol. 2016 Dec;34(12):1287-1291. doi: 10.1038/nbt.3682. Epub 2016 Sep 26.

18.

MetaCycle: an integrated R package to evaluate periodicity in large scale data.

Wu G, Anafi RC, Hughes ME, Kornacker K, Hogenesch JB.

Bioinformatics. 2016 Nov 1;32(21):3351-3353. Epub 2016 Jul 4.

19.

The Local Edge Machine: inference of dynamic models of gene regulation.

McGoff KA, Guo X, Deckard A, Kelliher CM, Leman AR, Francey LJ, Hogenesch JB, Haase SB, Harer JL.

Genome Biol. 2016 Oct 19;17(1):214.

20.

Deciphering the Duality of Clock and Growth Metabolism in a Cell Autonomous System Using NMR Profiling of the Secretome.

Sengupta A, Krishnaiah SY, Rhoades S, Growe J, Slaff B, Venkataraman A, Olarerin-George AO, Van Dang C, Hogenesch JB, Weljie AM.

Metabolites. 2016 Jul 27;6(3). pii: E23. doi: 10.3390/metabo6030023.

21.

Neural clocks and Neuropeptide F/Y regulate circadian gene expression in a peripheral metabolic tissue.

Erion R, King AN, Wu G, Hogenesch JB, Sehgal A.

Elife. 2016 Apr 14;5. pii: e13552. doi: 10.7554/eLife.13552.

22.

Discovering Biology in Periodic Data through Phase Set Enrichment Analysis (PSEA).

Zhang R, Podtelezhnikov AA, Hogenesch JB, Anafi RC.

J Biol Rhythms. 2016 Jun;31(3):244-57. doi: 10.1177/0748730416631895. Epub 2016 Mar 8.

PMID:
26955841
23.

A new view of transcriptome complexity and regulation through the lens of local splicing variations.

Vaquero-Garcia J, Barrera A, Gazzara MR, González-Vallinas J, Lahens NF, Hogenesch JB, Lynch KW, Barash Y.

Elife. 2016 Feb 1;5:e11752. doi: 10.7554/eLife.11752.

24.

The Liver Clock Controls Cholesterol Homeostasis through Trib1 Protein-mediated Regulation of PCSK9/Low Density Lipoprotein Receptor (LDLR) Axis.

Ma D, Liu T, Chang L, Rui C, Xiao Y, Li S, Hogenesch JB, Chen YE, Lin JD.

J Biol Chem. 2015 Dec 25;290(52):31003-12. doi: 10.1074/jbc.M115.685982. Epub 2015 Nov 7.

25.

Ubiquitin ligase Siah2 regulates RevErbα degradation and the mammalian circadian clock.

DeBruyne JP, Baggs JE, Sato TK, Hogenesch JB.

Proc Natl Acad Sci U S A. 2015 Oct 6;112(40):12420-5. doi: 10.1073/pnas.1501204112. Epub 2015 Sep 21.

26.

MYC Disrupts the Circadian Clock and Metabolism in Cancer Cells.

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, Maris JM, Felsher DW, Hogenesch JB, Weljie AM, Dang CV.

Cell Metab. 2015 Dec 1;22(6):1009-19. doi: 10.1016/j.cmet.2015.09.003. Epub 2015 Sep 17.

27.

Benchmark analysis of algorithms for determining and quantifying full-length mRNA splice forms from RNA-seq data.

Hayer KE, Pizarro A, Lahens NF, Hogenesch JB, Grant GR.

Bioinformatics. 2015 Dec 15;31(24):3938-45. doi: 10.1093/bioinformatics/btv488. Epub 2015 Sep 3.

28.

Ribosome profiling reveals an important role for translational control in circadian gene expression.

Jang C, Lahens NF, Hogenesch JB, Sehgal A.

Genome Res. 2015 Dec;25(12):1836-47. doi: 10.1101/gr.191296.115. Epub 2015 Sep 3.

29.

KPNB1 mediates PER/CRY nuclear translocation and circadian clock function.

Lee Y, Jang AR, Francey LJ, Sehgal A, Hogenesch JB.

Elife. 2015 Aug 29;4. doi: 10.7554/eLife.08647.

30.

Placental expression of miR-517a/b and miR-517c contributes to trophoblast dysfunction and preeclampsia.

Anton L, Olarerin-George AO, Hogenesch JB, Elovitz MA.

PLoS One. 2015 Mar 23;10(3):e0122707. doi: 10.1371/journal.pone.0122707. eCollection 2015.

31.

A genome-wide screen identifies PAPP-AA-mediated IGFR signaling as a novel regulator of habituation learning.

Wolman MA, Jain RA, Marsden KC, Bell H, Skinner J, Hayer KE, Hogenesch JB, Granato M.

Neuron. 2015 Mar 18;85(6):1200-11. doi: 10.1016/j.neuron.2015.02.025. Epub 2015 Mar 5. Erratum in: Neuron. 2015 Aug 19;87(4):906-7.

32.

Assessing the prevalence of mycoplasma contamination in cell culture via a survey of NCBI's RNA-seq archive.

Olarerin-George AO, Hogenesch JB.

Nucleic Acids Res. 2015 Mar 11;43(5):2535-42. doi: 10.1093/nar/gkv136. Epub 2015 Feb 24.

33.

Zebrafish foxc1a drives appendage-specific neural circuit development.

Banerjee S, Hayer K, Hogenesch JB, Granato M.

Development. 2015 Feb 15;142(4):753-62. doi: 10.1242/dev.115816.

34.

Considerations for RNA-seq analysis of circadian rhythms.

Li J, Grant GR, Hogenesch JB, Hughes ME.

Methods Enzymol. 2015;551:349-67. doi: 10.1016/bs.mie.2014.10.020. Epub 2014 Dec 26.

PMID:
25662464
35.

Pax3 and hippo signaling coordinate melanocyte gene expression in neural crest.

Manderfield LJ, Engleka KA, Aghajanian H, Gupta M, Yang S, Li L, Baggs JE, Hogenesch JB, Olson EN, Epstein JA.

Cell Rep. 2014 Dec 11;9(5):1885-1895. doi: 10.1016/j.celrep.2014.10.061. Epub 2014 Nov 26.

36.

Detection theory in identification of RNA-DNA sequence differences using RNA-sequencing.

Toung JM, Lahens N, Hogenesch JB, Grant G.

PLoS One. 2014 Nov 14;9(11):e112040. doi: 10.1371/journal.pone.0112040. eCollection 2014.

37.

A circadian gene expression atlas in mammals: implications for biology and medicine.

Zhang R, Lahens NF, Ballance HI, Hughes ME, Hogenesch JB.

Proc Natl Acad Sci U S A. 2014 Nov 11;111(45):16219-24. doi: 10.1073/pnas.1408886111. Epub 2014 Oct 27.

38.

Role for LSM genes in the regulation of circadian rhythms.

Perez-Santángelo S, Mancini E, Francey LJ, Schlaen RG, Chernomoretz A, Hogenesch JB, Yanovsky MJ.

Proc Natl Acad Sci U S A. 2014 Oct 21;111(42):15166-71. doi: 10.1073/pnas.1409791111. Epub 2014 Oct 6.

39.

A novel BHLHE41 variant is associated with short sleep and resistance to sleep deprivation in humans.

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.

Sleep. 2014 Aug 1;37(8):1327-36. doi: 10.5665/sleep.3924. Erratum in: Sleep. 2015 Nov;38(11):1827.

40.

IVT-seq reveals extreme bias in RNA sequencing.

Lahens NF, Kavakli IH, Zhang R, Hayer K, Black MB, Dueck H, Pizarro A, Kim J, Irizarry R, Thomas RS, Grant GR, Hogenesch JB.

Genome Biol. 2014 Jun 30;15(6):R86. doi: 10.1186/gb-2014-15-6-r86.

41.

Machine learning helps identify CHRONO as a circadian clock component.

Anafi RC, Lee Y, Sato TK, Venkataraman A, Ramanathan C, Kavakli IH, Hughes ME, Baggs JE, Growe J, Liu AC, Kim J, Hogenesch JB.

PLoS Biol. 2014 Apr 15;12(4):e1001840. doi: 10.1371/journal.pbio.1001840. eCollection 2014 Apr.

42.

Cell type-specific functions of period genes revealed by novel adipocyte and hepatocyte circadian clock models.

Ramanathan C, Xu H, Khan SK, Shen Y, Gitis PJ, Welsh DK, Hogenesch JB, Liu AC.

PLoS Genet. 2014 Apr 3;10(4):e1004244. doi: 10.1371/journal.pgen.1004244. eCollection 2014 Apr.

43.

The growth and impact of Alzheimer disease centers as measured by social network analysis.

Hughes ME, Peeler J, Hogenesch JB, Trojanowski JQ.

JAMA Neurol. 2014 Apr;71(4):412-20. doi: 10.1001/jamaneurol.2013.6225.

44.

Circadian clock proteins regulate neuronal redox homeostasis and neurodegeneration.

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, Weaver DR, Holtzman DM, Fitzgerald GA.

J Clin Invest. 2013 Dec;123(12):5389-400. doi: 10.1172/JCI70317. Epub 2013 Nov 25.

45.

Extensive variation in chromatin states across humans.

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, Kellis M, Batzoglou S, Snyder M.

Science. 2013 Nov 8;342(6159):750-2. doi: 10.1126/science.1242510. Epub 2013 Oct 17.

46.

Design and analysis of large-scale biological rhythm studies: a comparison of algorithms for detecting periodic signals in biological data.

Deckard A, Anafi RC, Hogenesch JB, Haase SB, Harer J.

Bioinformatics. 2013 Dec 15;29(24):3174-80. doi: 10.1093/bioinformatics/btt541. Epub 2013 Sep 20.

47.

miR-210 inhibits trophoblast invasion and is a serum biomarker for preeclampsia.

Anton L, Olarerin-George AO, Schwartz N, Srinivas S, Bastek J, Hogenesch JB, Elovitz MA.

Am J Pathol. 2013 Nov;183(5):1437-1445. doi: 10.1016/j.ajpath.2013.07.021. Epub 2013 Sep 10.

48.

The circadian clock gates the intestinal stem cell regenerative state.

Karpowicz P, Zhang Y, Hogenesch JB, Emery P, Perrimon N.

Cell Rep. 2013 Apr 25;3(4):996-1004. doi: 10.1016/j.celrep.2013.03.016. Epub 2013 Apr 11.

49.

A functional genomics screen for microRNA regulators of NF-kappaB signaling.

Olarerin-George AO, Anton L, Hwang YC, Elovitz MA, Hogenesch JB.

BMC Biol. 2013 Feb 28;11:19. doi: 10.1186/1741-7007-11-19.

50.

High throughput genomic screen identifies multiple factors that promote cooperative Wnt signaling.

Miller MF, Cohen ED, Baggs JE, Hogenesch JB, Morrisey EE.

PLoS One. 2013;8(1):e55782. doi: 10.1371/journal.pone.0055782. Epub 2013 Jan 31.

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