The light-induced transcriptome of the zebrafish pineal gland reveals complex regulation of the circadian clockwork by light

Linking Oxygen to Time: The Bidirectional Interaction Between the Hypoxic Signaling Pathway and the Circadian Clock

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Casein Kinase 1δ Activity: A Key Element in the Zebrafish Circadian Timing System

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Extensive alternative polyadenylation during zebrafish development

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Systematic identification of edited microRNAs in the human brain

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MicroRNAs in the Pineal Gland

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Micro-Managing the Circadian Clock: The Role of microRNAs in Biological Timekeeping

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Regulation of per and cry Genes Reveals a Central Role for the D-Box Enhancer in Light-Dependent Gene Expression

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Systematic Identification of Rhythmic Genes Reveals camk1gb as a New Element in the Circadian Clockwork

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It's time to swim! Zebrafish and the circadian clock

(2011) Gad Vatine et al.   FEBS LETTERS

Barcoding bias in high-throughput multiplex sequencing of miRNA

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The Light Responsive Transcriptome of the Zebrafish: Function and Regulation

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A Blind Circadian Clock in Cavefish Reveals that Opsins Mediate Peripheral Clock Photoreception

(2011) Nicola Cavallari et al.   PLOS BIOLOGY

Characterizing Light-Regulated Retinal MicroRNAs Reveals Rapid Turnover as a Common Property of Neuronal MicroRNAs

(2010) Jacek Krol et al.   CELL

MULTIPLE PAR AND E4BP4 bZIP TRANSCRIPTION FACTORS IN ZEBRAFISH: DIVERSE SPATIAL AND TEMPORAL EXPRESSION PATTERNS

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Comprehensive comparative analysis of strand-specific RNA sequencing methods

(2010) Joshua Z Levin et al.   NATURE METHODS

miRBase: integrating microRNA annotation and deep-sequencing data

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Thyrotroph Embryonic Factor Regulates Light-Induced Transcription of Repair Genes in Zebrafish Embryonic Cells

(2010) Daria Gavriouchkina et al.   PLoS One

A scaling normalization method for differential expression analysis of RNA-seq data

(2010) Mark D Robinson et al.   GENOME BIOLOGY

Structural and Functional Evolution of the Pineal Melatonin System in Vertebrates

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TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

Transcriptome analysis of the zebrafish pineal gland

(2009) Reiko Toyama et al.   DEVELOPMENTAL DYNAMICS

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources

(2009) Da Wei Huang et al.   Nature Protocols

Post-translational modifications in circadian rhythms

(2009) Arun Mehra et al.   TRENDS IN BIOCHEMICAL SCIENCES

Light Directs Zebrafish period2 Expression via Conserved D and E Boxes

(2009) Gad Vatine et al.   PLOS BIOLOGY

Novel functions for Period 3 and Exo-rhodopsin in rhythmic transcription and melatonin biosynthesis within the zebrafish pineal organ

(2008) Lain X. Pierce et al.   BRAIN RESEARCH

Minireview: The Nuclear Hormone Receptor Family Round the Clock

(2008) Michèle Teboul et al.   MOLECULAR ENDOCRINOLOGY

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS

Disturbed Clockwork Resetting in Sharp-1 and Sharp-2 Single and Double Mutant Mice

(2008) Moritz J. Rossner et al.   PLoS One