John B Hogenesch

John B Hogenesch

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John B Hogenesch

Publications by authors named "John B Hogenesch"

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A large-scale study reveals 24-h operational rhythms in hospital treatment.

Proc Natl Acad Sci U S A 2019 Oct 1;116(42):20953-20958. Epub 2019 Oct 1.

Divisions of Pediatric Otolaryngology and Pulmonary and Sleep Medicine, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229;

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http://dx.doi.org/10.1073/pnas.1909557116DOI Listing
October 2019

Sleep and Circadian Medicine: Time of Day in the Neurologic Clinic.

Neurol Clin 2019 Aug 11;37(3):615-629. Epub 2019 May 11.

Division of Pediatric Otolaryngology, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH 45229, USA; Division of Pulmonary and Sleep Medicine, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH 45229, USA; Department of Otolaryngology-Head and Neck Surgery, University of Cincinnati School of Medicine, 231 Albert Sabin Way, Cincinnati, OH 45267, USA. Electronic address:

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http://dx.doi.org/10.1016/j.ncl.2019.03.004DOI Listing
August 2019

Dosing time matters.

Science 2019 08;365(6453):547-549

Divisions of Human Genetics and Immunobiology, Center for Chronobiology, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, 240 Albert Sabin Way, Cincinnati, OH 45229, USA.

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http://dx.doi.org/10.1126/science.aax7621DOI Listing
August 2019

The NRON complex controls circadian clock function through regulated PER and CRY nuclear translocation.

Sci Rep 2019 Aug 15;9(1):11883. Epub 2019 Aug 15.

Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA.

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http://dx.doi.org/10.1038/s41598-019-48341-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6695496PMC
August 2019

Reply to Furlan et al.: The role of SIRT1 in cell autonomous clock function.

Proc Natl Acad Sci U S A 2019 Jul 25;116(27):13173. Epub 2019 Jun 25.

Department of Chemical Engineering, University of California, Santa Barbara, CA 93106;

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http://dx.doi.org/10.1073/pnas.1907923116DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6613096PMC
July 2019

Shift Work Disrupts Circadian Regulation of the Transcriptome in Hospital Nurses.

J Biol Rhythms 2019 Apr 4;34(2):167-177. Epub 2019 Feb 4.

Department of Psychiatry and Behavioral Neurobiology.

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http://dx.doi.org/10.1177/0748730419826694DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6542471PMC
April 2019

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

Otolaryngol Head Neck Surg 2018 12 11;159(6):948-955. Epub 2018 Sep 11.

1 Department of Otolaryngology-Head and Neck Surgery, College of Medicine, University of Cincinnati, Cincinnati, Ohio, USA.

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http://dx.doi.org/10.1177/0194599818797311DOI Listing
December 2018

Computational and experimental insights into the circadian effects of SIRT1.

Proc Natl Acad Sci U S A 2018 11 22;115(45):11643-11648. Epub 2018 Oct 22.

Department of Chemical Engineering, University of California, Santa Barbara, CA 93106;

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http://dx.doi.org/10.1073/pnas.1803410115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6233098PMC
November 2018

Population-level rhythms in human skin with implications for circadian medicine.

Proc Natl Acad Sci U S A 2018 11 30;115(48):12313-12318. Epub 2018 Oct 30.

Division of Human Genetics and Immunobiology, Center for Chronobiology, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229;

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http://dx.doi.org/10.1073/pnas.1809442115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6275491PMC
November 2018

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

Sci Transl Med 2018 09;10(458)

Divisions of Human Genetics and Immunobiology, Center for Chronobiology, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, 240 Albert Sabin Way, Cincinnati, OH 45229, USA.

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http://stm.sciencemag.org/lookup/doi/10.1126/scitranslmed.aa
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http://dx.doi.org/10.1126/scitranslmed.aat8806DOI Listing
September 2018

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

Proc Natl Acad Sci U S A 2018 05 7;115(21):E4777-E4785. Epub 2018 May 7.

Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599;

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http://dx.doi.org/10.1073/pnas.1804493115DOI Listing
May 2018

mTOR signaling regulates central and peripheral circadian clock function.

PLoS Genet 2018 05 11;14(5):e1007369. Epub 2018 May 11.

Department of Biological Sciences, University of Memphis, Memphis, Tennessee, United States of America.

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http://dx.doi.org/10.1371/journal.pgen.1007369DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5965903PMC
May 2018

Soluble syntaxin 3 functions as a transcriptional regulator.

J Biol Chem 2018 04 23;293(15):5478-5491. Epub 2018 Feb 23.

From the Department of Molecular, Cellular, and Developmental Biology and Neuroscience Research Institute, University of California, Santa Barbara, California 93106-9625,

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http://www.jbc.org/lookup/doi/10.1074/jbc.RA117.000874
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http://dx.doi.org/10.1074/jbc.RA117.000874DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5900775PMC
April 2018

Guidelines for Genome-Scale Analysis of Biological Rhythms.

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

27 Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA.

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http://dx.doi.org/10.1177/0748730417728663DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5692188PMC
October 2017

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

Proc Natl Acad Sci U S A 2017 Sep 29;114(37):9978-9983. Epub 2017 Aug 29.

Princeton Neuroscience Institute, Princeton University, Princeton, NJ 08544.

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http://dx.doi.org/10.1073/pnas.1707471114DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5604024PMC
September 2017

It's not all in the brain.

Elife 2017 08 29;6. Epub 2017 Aug 29.

Divisions of Human Genetics and Immunobiology, Cincinnati Children's Hospital Medical Cente, Cincinnati, United States.

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http://dx.doi.org/10.7554/eLife.30561DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5576482PMC
August 2017

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

Nat Genet 2017 Jun 1;49(6):895-903. Epub 2017 May 1.

Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA.

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http://dx.doi.org/10.1038/ng.3852DOI Listing
June 2017

CYCLOPS reveals human transcriptional rhythms in health and disease.

Proc Natl Acad Sci U S A 2017 05 24;114(20):5312-5317. Epub 2017 Apr 24.

Department of Biology, University of Pennsylvania, Philadelphia, PA 19104.

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http://dx.doi.org/10.1073/pnas.1619320114DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5441789PMC
May 2017

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

Curr Biol 2017 05;27(9):R350-R352

Divisions of Perinatal Biology and Immunobiology, Perinatal Institute, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, 240 Albert Sabin Way, Cincinnati, OH 45229, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cub.2017.03.055DOI Listing
May 2017

Clock Regulation of Metabolites Reveals Coupling between Transcription and Metabolism.

Cell Metab 2017 Apr;25(4):961-974.e4

Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Institute of Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA. Electronic address:

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http://www.cell.com/cell-metabolism/pdf/S1550-4131(17)30171-
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http://linkinghub.elsevier.com/retrieve/pii/S155041311730171
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http://dx.doi.org/10.1016/j.cmet.2017.03.019DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5479132PMC
April 2017

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

Nat Biotechnol 2016 Dec 26;34(12):1287-1291. Epub 2016 Sep 26.

Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA.

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http://dx.doi.org/10.1038/nbt.3682DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5143225PMC
December 2016

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

Bioinformatics 2016 11 4;32(21):3351-3353. Epub 2016 Jul 4.

Department of Systems Pharmacology and Translational Therapeutics, Institute for Translational Medicine and Therapeutics.

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http://dx.doi.org/10.1093/bioinformatics/btw405DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5079475PMC
November 2016

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

Metabolites 2016 Jul 27;6(3). Epub 2016 Jul 27.

Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5041122PMC
http://dx.doi.org/10.3390/metabo6030023DOI Listing
July 2016

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

J Biol Rhythms 2016 06 8;31(3):244-57. Epub 2016 Mar 8.

Department of Medicine and Center for Sleep and Circadian Neurobiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania

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http://dx.doi.org/10.1177/0748730416631895DOI Listing
June 2016

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

Elife 2016 04 14;5. Epub 2016 Apr 14.

Howard Hughes Medical Institute, University of Pennsylvania, Philadelphia, United States.

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http://dx.doi.org/10.7554/eLife.13552DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4862751PMC
April 2016

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

PLoS One 2015 23;10(3):e0122707. Epub 2015 Mar 23.

Maternal and Child Health Research Program, Department of Obstetrics and Gynecology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0122707PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4370750PMC
February 2016

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

Elife 2016 Feb 1;5:e11752. Epub 2016 Feb 1.

Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States.

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http://dx.doi.org/10.7554/eLife.11752DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4801060PMC
February 2016

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

Genome Res 2015 Dec 3;25(12):1836-47. Epub 2015 Sep 3.

Department of Neuroscience, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania 19104, USA; Howard Hughes Medical Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania 19104, USA.

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http://dx.doi.org/10.1101/gr.191296.115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4665005PMC
December 2015

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

Bioinformatics 2015 Dec 3;31(24):3938-45. Epub 2015 Sep 3.

University of Pennsylvania, Institute for Translational Medicine and Therapeutics, Philadelphia, PA 19104, Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104, USA.

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http://dx.doi.org/10.1093/bioinformatics/btv488DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4673975PMC
December 2015

MYC Disrupts the Circadian Clock and Metabolism in Cancer Cells.

Cell Metab 2015 Dec 17;22(6):1009-19. Epub 2015 Sep 17.

Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Division of Hematology-Oncology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cmet.2015.09.003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4818967PMC
December 2015

Considerations for RNA-seq analysis of circadian rhythms.

Methods Enzymol 2015 26;551:349-67. Epub 2014 Dec 26.

Department of Biology, University of Missouri-St. Louis, St. Louis, Missouri, USA. Electronic address:

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http://dx.doi.org/10.1016/bs.mie.2014.10.020DOI Listing
October 2015

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

Proc Natl Acad Sci U S A 2015 Oct 21;112(40):12420-5. Epub 2015 Sep 21.

Department of Pharmacology, Penn Genome Frontiers Institute, Institute for Translational Medicine and Therapeutics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia PA, 19104

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http://dx.doi.org/10.1073/pnas.1501204112DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4603519PMC
October 2015

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

Elife 2015 Aug 29;4. Epub 2015 Aug 29.

Department of Systems Pharmacology and Translational Therapeutics, Institute for Translational Medicine and Therapeutics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, United States.

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https://elifesciences.org/content/4/e08647v1.pdf
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https://elifesciences.org/content/4/e08647-download.pdf
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http://elifesciences.org/lookup/doi/10.7554/eLife.08647
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http://dx.doi.org/10.7554/eLife.08647DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4597257PMC
August 2015

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

PLoS One 2014 14;9(11):e112040. Epub 2014 Nov 14.

Institute for Biomedical Informatics, University of Pennsylvania School of Medicine, Philadelphia, PA, United States of America; Institute for Translational Medicine and Therapeutics, University of Pennsylvania School of Medicine, Philadelphia, PA, United States of America; Department of Genetics, University of Pennsylvania School of Medicine, Philadelphia, PA, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0112040PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4232354PMC
July 2015

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

Nucleic Acids Res 2015 Mar 24;43(5):2535-42. Epub 2015 Feb 24.

Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA

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http://dx.doi.org/10.1093/nar/gkv136DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4357728PMC
March 2015

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

Neuron 2015 Mar 5;85(6):1200-11. Epub 2015 Mar 5.

Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, 1157 BRB II/III, 421 Curie Boulevard, Philadelphia, PA 19104, USA. Electronic address:

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http://dx.doi.org/10.1016/j.neuron.2015.02.025DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4368495PMC
March 2015

Zebrafish foxc1a drives appendage-specific neural circuit development.

Development 2015 Feb;142(4):753-62

Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA

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http://dx.doi.org/10.1242/dev.115816DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4325381PMC
February 2015

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

Cell Rep 2014 Dec 26;9(5):1885-1895. Epub 2014 Nov 26.

Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA 19104, USA; Penn Cardiovascular Institute, University of Pennsylvania, Philadelphia, PA 19104, USA. Electronic address:

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http://www.cell.com/cell-reports/pdf/S2211-1247(14)00930-9.p
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http://www.cell.com/cell-reports/pdf/S2211-1247(15)00066-2.p
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http://linkinghub.elsevier.com/retrieve/pii/S221112471400930
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http://dx.doi.org/10.1016/j.celrep.2014.10.061DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4267159PMC
December 2014

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

Proc Natl Acad Sci U S A 2014 Nov 27;111(45):16219-24. Epub 2014 Oct 27.

Department of Pharmacology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104; and

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http://dx.doi.org/10.1073/pnas.1408886111DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4234565PMC
November 2014

Role for LSM genes in the regulation of circadian rhythms.

Proc Natl Acad Sci U S A 2014 Oct 6;111(42):15166-71. Epub 2014 Oct 6.

Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos Aires-Consejo Nacional de Investigaciones Científicas y Técnicas, C1405BWE, Buenos Aires, Argentina; and

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http://dx.doi.org/10.1073/pnas.1409791111DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4210300PMC
October 2014

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

Sleep 2014 Aug 1;37(8):1327-36. Epub 2014 Aug 1.

Center for Sleep and Circadian Neurobiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA ; Division of Sleep Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA.

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http://dx.doi.org/10.5665/sleep.3924DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4096202PMC
August 2014

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

JAMA Neurol 2014 Apr;71(4):412-20

Center for Neurodegenerative Disease Research, Philadelphia, Pennsylvania5Department of Pathology and Laboratory Medicine, Institute on Aging, University of Pennsylvania School of Medicine, Philadelphia.

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http://dx.doi.org/10.1001/jamaneurol.2013.6225DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4096555PMC
April 2014

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

PLoS Genet 2014 Apr 3;10(4):e1004244. Epub 2014 Apr 3.

Department of Biological Sciences, University of Memphis, Memphis, Tennessee, United States of America; Feinstone Genome Research Center, University of Memphis, Memphis, Tennessee, United States of America.

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http://dx.doi.org/10.1371/journal.pgen.1004244DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3974647PMC
April 2014

Machine learning helps identify CHRONO as a circadian clock component.

PLoS Biol 2014 Apr 15;12(4):e1001840. Epub 2014 Apr 15.

Center for Sleep and Circadian Neurobiology, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America; Department of Pharmacology and the Institute for Translational Medicine and Therapeutics, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America.

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http://dx.doi.org/10.1371/journal.pbio.1001840DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3988006PMC
April 2014

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

Bioinformatics 2013 Dec 20;29(24):3174-80. Epub 2013 Sep 20.

Program in Computational Biology and Bioinformatics, Department of Mathematics, Duke University, Durham, NC 27708, USA, Department of Medicine, Department of Pharmacology, Institute for Translational Medicine and Therapeutics, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA and Department of Biology, Duke University, Durham, NC 27708, USA.

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http://dx.doi.org/10.1093/bioinformatics/btt541DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4471443PMC
December 2013

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

Am J Pathol 2013 Nov 10;183(5):1437-1445. Epub 2013 Sep 10.

Maternal and Child Health Research Program, Department of Obstetrics and Gynecology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania. Electronic address:

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http://dx.doi.org/10.1016/j.ajpath.2013.07.021DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3814521PMC
November 2013

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

PLoS One 2013 31;8(1):e55782. Epub 2013 Jan 31.

Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0055782PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3561354PMC
July 2013

The circadian clock gates the intestinal stem cell regenerative state.

Cell Rep 2013 Apr 11;3(4):996-1004. Epub 2013 Apr 11.

Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.

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http://dx.doi.org/10.1016/j.celrep.2013.03.016DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3982394PMC
April 2013

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

BMC Biol 2013 Feb 28;11:19. Epub 2013 Feb 28.

Genomics and Computational Biology Graduate Group, 1420 Blockley Hall, 423 Guardian Drive, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA.

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http://dx.doi.org/10.1186/1741-7007-11-19DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3621838PMC
February 2013

Brain-specific rescue of Clock reveals system-driven transcriptional rhythms in peripheral tissue.

PLoS Genet 2012 26;8(7):e1002835. Epub 2012 Jul 26.

Department of Cellular and Molecular Physiology, Yale School of Medicine, New Haven, CT, USA.

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http://dx.doi.org/10.1371/journal.pgen.1002835DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3405989PMC
January 2013

CircaDB: a database of mammalian circadian gene expression profiles.

Nucleic Acids Res 2013 Jan 24;41(Database issue):D1009-13. Epub 2012 Nov 24.

The Institute for Translational Medicine and Therapeutics, University of Pennsylvania, 3400 Civic Center Boulevard, Building 421, Philadelphia, PA 19104, USA.

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http://dx.doi.org/10.1093/nar/gks1161DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3531170PMC
January 2013

The transcription factor encyclopedia.

Authors:
Dimas Yusuf Stefanie L Butland Magdalena I Swanson Eugene Bolotin Amy Ticoll Warren A Cheung Xiao Yu Cindy Zhang Christopher T D Dickman Debra L Fulton Jonathan S Lim Jake M Schnabl Oscar H P Ramos Mireille Vasseur-Cognet Charles N de Leeuw Elizabeth M Simpson Gerhart U Ryffel Eric W-F Lam Ralf Kist Miranda S C Wilson Raquel Marco-Ferreres Jan J Brosens Leonardo L Beccari Paola Bovolenta Bérénice A Benayoun Lara J Monteiro Helma D C Schwenen Lars Grontved Elizabeth Wederell Susanne Mandrup Reiner A Veitia Harini Chakravarthy Pamela A Hoodless M Michela Mancarelli Bruce E Torbett Alison H Banham Sekhar P Reddy Rebecca L Cullum Michaela Liedtke Mario P Tschan Michelle Vaz Angie Rizzino Mariastella Zannini Seth Frietze Peggy J Farnham Astrid Eijkelenboom Philip J Brown David Laperrière Dominique Leprince Tiziana de Cristofaro Kelly L Prince Marrit Putker Luis del Peso Gieri Camenisch Roland H Wenger Michal Mikula Marieke Rozendaal Sylvie Mader Jerzy Ostrowski Simon J Rhodes Capucine Van Rechem Gaylor Boulay Sam W Z Olechnowicz Mary B Breslin Michael S Lan Kyster K Nanan Michael Wegner Juan Hou Rachel D Mullen Stephanie C Colvin Peter John Noy Carol F Webb Matthew E Witek Scott Ferrell Juliet M Daniel Jason Park Scott A Waldman Daniel J Peet Michael Taggart Padma-Sheela Jayaraman Julien J Karrich Bianca Blom Farhad Vesuna Henriette O'Geen Yunfu Sun Richard M Gronostajski Mark W Woodcroft Margaret R Hough Edwin Chen G Nicholas Europe-Finner Magdalena Karolczak-Bayatti Jarrod Bailey Oliver Hankinson Venu Raman David P LeBrun Shyam Biswal Christopher J Harvey Jason P DeBruyne John B Hogenesch Robert F Hevner Christophe Héligon Xin M Luo Marissa Cathleen Blank Kathleen Joyce Millen David S Sharlin Douglas Forrest Karin Dahlman-Wright Chunyan Zhao Yuriko Mishima Satrajit Sinha Rumela Chakrabarti Elodie Portales-Casamar Frances M Sladek Philip H Bradley Wyeth W Wasserman

Genome Biol 2012 ;13(3):R24

Department of Medical Genetics, Faculty of Medicine, Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, University of British Columbia, Vancouver, Canada.

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http://genomebiology.com/2012/13/3/R24
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http://dx.doi.org/10.1186/gb-2012-13-3-r24DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3439975PMC
September 2012

Wnt ligands signal in a cooperative manner to promote foregut organogenesis.

Proc Natl Acad Sci U S A 2012 Sep 4;109(38):15348-53. Epub 2012 Sep 4.

Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA 19104, USA.

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http://dx.doi.org/10.1073/pnas.1201583109DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3458331PMC
September 2012

The γ-secretase cleavage product of polycystin-1 regulates TCF and CHOP-mediated transcriptional activation through a p300-dependent mechanism.

Dev Cell 2012 Jan 15;22(1):197-210. Epub 2011 Dec 15.

Department of Cellular and Molecular Physiology, Yale University School of Medicine, New Haven, CT 06510, USA.

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http://dx.doi.org/10.1016/j.devcel.2011.10.028DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3264829PMC
January 2012

Understanding systems-level properties: timely stories from the study of clocks.

Nat Rev Genet 2011 Jun 10;12(6):407-16. Epub 2011 May 10.

Department of Pharmacology, Penn Center for Bioinformatics, Penn Genome Frontiers Institute, Institute for Translational Medicine and Therapeutics, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA.

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http://dx.doi.org/10.1038/nrg2972DOI Listing
June 2011

The circadian clock interacts with metabolic physiology to influence reproductive fitness.

Cell Metab 2011 Jun;13(6):639-54

Department of Neuroscience, Howard Hughes Medical Institute, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA.

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http://dx.doi.org/10.1016/j.cmet.2011.05.001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3152999PMC
June 2011

Intracellular and intercellular processes determine robustness of the circadian clock.

FEBS Lett 2011 May 28;585(10):1427-34. Epub 2011 Apr 28.

Department of Pharmacology, Institute for Translational Medicine and Therapeutics, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA.

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http://dx.doi.org/10.1016/j.febslet.2011.04.048DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3117285PMC
May 2011

The network as the target.

Wiley Interdiscip Rev Syst Biol Med 2010 Mar-Apr;2(2):127-133

Institution for Translational Medicine and Therapeutics, School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.

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http://dx.doi.org/10.1002/wsbm.57DOI Listing
February 2011

A CRY in the Night.

Dev Cell 2011 Feb;20(2):144-5

Department of Pharmacology, Institute for Translational Medicine and Therapeutics, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA.

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http://dx.doi.org/10.1016/j.devcel.2011.01.014DOI Listing
February 2011

Genomics and systems approaches in the mammalian circadian clock.

Curr Opin Genet Dev 2010 Dec;20(6):581-7

Department of Pharmacology, Institute for Translational Medicine and Therapeutics, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, United States.

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http://dx.doi.org/10.1016/j.gde.2010.08.009DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2982940PMC
December 2010

JTK_CYCLE: an efficient nonparametric algorithm for detecting rhythmic components in genome-scale data sets.

J Biol Rhythms 2010 Oct;25(5):372-80

Department of Cellular and Molecular Physiology, Yale School of Medicine, New Haven, CT, USA.

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http://dx.doi.org/10.1177/0748730410379711DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3119870PMC
October 2010

Network dynamics to evaluate performance of an academic institution.

Sci Transl Med 2010 Oct;2(53):53ps49

Department of Cellular and Molecular Physiology, Yale School of Medicine, New Haven, CT 06520, USA.

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http://dx.doi.org/10.1126/scitranslmed.3001580DOI Listing
October 2010

Mammalian Per-Arnt-Sim proteins in environmental adaptation.

Annu Rev Physiol 2010 ;72:625-45

McArdle Laboratory for Cancer Research, School of Medicine and Public Health, University of Wisconsin, Madison, WI 53706, USA.

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http://dx.doi.org/10.1146/annurev-physiol-021909-135922DOI Listing
May 2010

The role of clock genes in pharmacology.

Annu Rev Pharmacol Toxicol 2010 ;50:187-214

Department of Pharmacology, Institute for Translational Medicine and Therapeutics, University of Pennsylvania School of Medicine, Philadelphia, 19104, USA.

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http://dx.doi.org/10.1146/annurev.pharmtox.010909.105621DOI Listing
March 2010

The Gene Wiki: community intelligence applied to human gene annotation.

Nucleic Acids Res 2010 Jan 15;38(Database issue):D633-9. Epub 2009 Sep 15.

Genomics Institute of the Novartis Research Foundation, San Diego, CA 92121, USA.

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http://dx.doi.org/10.1093/nar/gkp760DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2808918PMC
January 2010

Generation of a novel allelic series of cryptochrome mutants via mutagenesis reveals residues involved in protein-protein interaction and CRY2-specific repression.

Mol Cell Biol 2009 Oct 17;29(20):5465-76. Epub 2009 Aug 17.

Department of Neuroscience, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., NB4.204G, Dallas, TX 75390-7433, USA.

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http://mcb.asm.org/cgi/doi/10.1128/MCB.00641-09
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http://dx.doi.org/10.1128/MCB.00641-09DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2756885PMC
October 2009

Harmonics of circadian gene transcription in mammals.

PLoS Genet 2009 Apr 3;5(4):e1000442. Epub 2009 Apr 3.

Department of Pharmacology, Institute for Translational Medicine and Therapeutics, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America.

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http://dx.doi.org/10.1371/journal.pgen.1000442DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2654964PMC
April 2009

Network features of the mammalian circadian clock.

PLoS Biol 2009 Mar;7(3):e52

Department of Pharmacology and the Institute for Translational Medicine and Therapeutics, University of Pennsylvania School of Medicine, Philadelphia, PA, USA.

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http://dx.doi.org/10.1371/journal.pbio.1000052DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2653556PMC
March 2009

ESRP1 and ESRP2 are epithelial cell-type-specific regulators of FGFR2 splicing.

Mol Cell 2009 Mar;33(5):591-601

Department of Medicine, Renal Division, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA.

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http://dx.doi.org/10.1016/j.molcel.2009.01.025DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2702247PMC
March 2009

It's all in a day's work: Regulation of DNA excision repair by the circadian clock.

Authors:
John B Hogenesch

Proc Natl Acad Sci U S A 2009 Feb;106(8):2481-2

Department of Pharmacology, Institute for Translational Medicine and Therapeutics, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA.

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http://dx.doi.org/10.1073/pnas.0813323106DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2650288PMC
February 2009

WAVECLOCK: wavelet analysis of circadian oscillation.

Bioinformatics 2008 Dec 17;24(23):2794-5. Epub 2008 Oct 17.

Institute of Psychiatry, Kings College London.

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http://dx.doi.org/10.1093/bioinformatics/btn521DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2639275PMC
December 2008

Small-molecule inhibitors of microrna miR-21 function.

Angew Chem Int Ed Engl 2008 ;47(39):7482-4

The Wistar Institute, 3601 Spruce Street, Philadelphia, PA 19104, USA.

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http://dx.doi.org/10.1002/anie.200801555DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3428715PMC
November 2008

Clock gene wikis available: join the "long tail".

J Biol Rhythms 2008 Oct;23(5):456-7

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http://dx.doi.org/10.1177/0748730408322866DOI Listing
October 2008

Analysis and synthesis of high-amplitude Cis-elements in the mammalian circadian clock.

Proc Natl Acad Sci U S A 2008 Sep 24;105(39):14946-51. Epub 2008 Sep 24.

Laboratory for Systems Biology, Center for Developmental Biology, RIKEN, 2-2-3 Minatojima-Minamimachi, Chuo-ku, Kobe 650-0047, Japan.

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http://dx.doi.org/10.1073/pnas.0802636105DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2553039PMC
September 2008

NetAtlas: a Cytoscape plugin to examine signaling networks based on tissue gene expression.

In Silico Biol 2008 ;8(1):47-52

The Hamner Institutes for Health Sciences, 6 Davis Drive, Research Triangle Park, NC 27709-2137, USA.

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July 2008

A functional map of NFkappaB signaling identifies novel modulators and multiple system controls.

Genome Biol 2007 ;8(6):R104

The Hamner Institutes for Health Sciences, 6 Davis Drive, PO Box 12137, Research Triangle Park, NC 27709-2137, USA.

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http://dx.doi.org/10.1186/gb-2007-8-6-r104DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2394752PMC
February 2008

A coactivator trap identifies NONO (p54nrb) as a component of the cAMP-signaling pathway.

Proc Natl Acad Sci U S A 2007 Dec 11;104(51):20314-9. Epub 2007 Dec 11.

Departments of Cancer Biology and Molecular Therapeutics and Translational Research Institute, The Scripps Research Institute, 5353 Parkside Drive, Jupiter, FL 33458, USA.

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http://dx.doi.org/10.1073/pnas.0707999105DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2154428PMC
December 2007

The imprinted gene Magel2 regulates normal circadian output.

Nat Genet 2007 Oct 23;39(10):1266-72. Epub 2007 Sep 23.

Cancer and Developmental Biology Laboratory, National Cancer Institute, Frederick, Maryland 21702, USA.

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http://dx.doi.org/10.1038/ng2114DOI Listing
October 2007

Circadian and CLOCK-controlled regulation of the mouse transcriptome and cell proliferation.

Proc Natl Acad Sci U S A 2007 Feb 20;104(9):3342-7. Epub 2007 Feb 20.

Department of Neurobiology and Physiology, and Howard Hughes Medical Institute, Northwestern University, Evanston, IL 60208, USA.

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http://dx.doi.org/10.1073/pnas.0611724104DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1802006PMC
February 2007

Identification and characterization of genes susceptible to transcriptional cross-talk between the hypoxia and dioxin signaling cascades.

Chem Res Toxicol 2006 Oct;19(10):1284-93

Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824, USA.

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http://dx.doi.org/10.1021/tx060068dDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3152583PMC
October 2006

Feedback repression is required for mammalian circadian clock function.

Nat Genet 2006 Mar 12;38(3):312-9. Epub 2006 Feb 12.

Genomics Institute of the Novartis Research Foundation, 10675 John J. Hopkins Dr., San Diego, California 92121, USA.

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http://dx.doi.org/10.1038/ng1745DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1994933PMC
March 2006