Repeated evolution of circadian clock dysregulation in cavefish populations

CHOPCHOP v3: expanding the CRISPR web toolbox beyond genome editing

(2019) Kornel Labun et al.   NUCLEIC ACIDS RESEARCH

An adaptable chromosome preparation methodology for use in invertebrate research organisms

(2018) Longhua Guo et al.   BMC BIOLOGY

CRISPR mutagenesis confirms the role of oca2 in melanin pigmentation in Astyanax mexicanus

(2018) Hannah Klaassen et al.   DEVELOPMENTAL BIOLOGY

Early adipogenesis contributes to excess fat accumulation in cave populations of Astyanax mexicanus

(2018) Shaolei Xiong et al.   DEVELOPMENTAL BIOLOGY

Development of the Astyanax mexicanus circadian clock and non-visual light responses

(2018) Inga A. Frøland Steindal et al.   DEVELOPMENTAL BIOLOGY

Comprehensive phylogeny of ray-finned fishes (Actinopterygii) based on transcriptomic and genomic data

(2018) Lily C. Hughes et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Mutations in blind cavefish target the light-regulated circadian clock gene, period 2

(2018) Rosa Maria Ceinos et al.   Scientific Reports

Hypocretin underlies the evolution of sleep loss in the Mexican cavefish

(2018) James B Jaggard et al.   eLife

Genetic analysis reveals candidate genes for activity QTL in the blind Mexican tetra, Astyanax mexicanus

(2018) Brian M. Carlson et al.   PeerJ

The role of gene flow in rapid and repeated evolution of cave related traits in Mexican tetra, Astyanax mexicanus

(2018) Adam Herman et al.   MOLECULAR ECOLOGY

Insulin resistance in cavefish as an adaptation to a nutrient-limited environment

(2018) Misty R. Riddle et al.   NATURE

Modulation of DNA Repair Systems in Blind Cavefish during Evolution in Constant Darkness

(2018) Haiyu Zhao et al.   CURRENT BIOLOGY

The lateral line confers evolutionarily derived sleep loss in the Mexican cavefish

(2017) James Jaggard et al.   JOURNAL OF EXPERIMENTAL BIOLOGY

Circadian deep sequencing reveals stress-response genes that adopt robust rhythmic expression during aging

(2017) Rachael C. Kuintzle et al.   Nature Communications

Comparative Analysis of Vertebrate Diurnal/Circadian Transcriptomes

(2017) Greg Boyle et al.   PLoS One

Life in a dark biosphere: a review of circadian physiology in “arrhythmic” environments

(2016) Andrew David Beale et al.   JOURNAL OF COMPARATIVE PHYSIOLOGY B-BIOCHEMICAL SYSTEMIC AND ENVIRONMENTAL PHYSIOLOGY

Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown

(2016) Mihaela Pertea et al.   Nature Protocols

Transcriptional architecture of the mammalian circadian clock

(2016) Joseph S. Takahashi   NATURE REVIEWS GENETICS

Cavefish and the basis for eye loss

(2016) Jaya Krishnan et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Distinct genetic architecture underlies the emergence of sleep loss and prey-seeking behavior in the Mexican cavefish

(2015) Masato Yoshizawa et al.   BMC BIOLOGY

Alterations in Mc1r gene expression are associated with regressive pigmentation in Astyanax cavefish

(2015) Bethany A. Stahl et al.   DEVELOPMENT GENES AND EVOLUTION

High-throughput gene targeting and phenotyping in zebrafish using CRISPR/Cas9

(2015) Gaurav K. Varshney et al.   GENOME RESEARCH

Melatonin Is Required for the Circadian Regulation of Sleep

(2015) Avni V. Gandhi et al.   NEURON

GUIDANCE2: accurate detection of unreliable alignment regions accounting for the uncertainty of multiple parameters

(2015) Itamar Sela et al.   NUCLEIC ACIDS RESEARCH

The MEME Suite

(2015) Timothy L. Bailey et al.   NUCLEIC ACIDS RESEARCH

Melanocortin 4 receptor mutations contribute to the adaptation of cavefish to nutrient-poor conditions

(2015) Ariel C. Aspiras et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Impact of Sleep and Circadian Disruption on Energy Balance and Diabetes: A Summary of Workshop Discussions

(2015) Deanna M. Arble et al.   SLEEP

Impact of Sleep and Circadian Disruption on Energy Balance and Diabetes: A Summary of Workshop Discussions

(2015) Deanna M. Arble et al.   SLEEP

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

RELAX: Detecting Relaxed Selection in a Phylogenetic Framework

(2014) Joel O. Wertheim et al.   MOLECULAR BIOLOGY AND EVOLUTION

Circadian Rhythmicity and Light Sensitivity of the Zebrafish Brain

(2014) Helen A. Moore et al.   PLoS One

Eyeless Mexican Cavefish Save Energy by Eliminating the Circadian Rhythm in Metabolism

(2014) Damian Moran et al.   PLoS One

A mutation in the enzyme monoamine oxidase explains part of the Astyanax cavefish behavioural syndrome

(2014) Yannick Elipot et al.   Nature Communications

On the Adaptive Significance of Circadian Clocks for Their Owners

(2013) Koustubh M. Vaze et al.   CHRONOBIOLOGY INTERNATIONAL

Loss of Schooling Behavior in Cavefish through Sight-Dependent and Sight-Independent Mechanisms

(2013) Johanna E. Kowalko et al.   CURRENT BIOLOGY

Biological Clocks and Visual Systems in Cave-Adapted Animals at the Dawn of Speleogenomics

(2013) M. Friedrich   INTEGRATIVE AND COMPARATIVE BIOLOGY

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Efficient multiplex biallelic zebrafish genome editing using a CRISPR nuclease system

(2013) Li-En Jao et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Convergence in feeding posture occurs through different genetic loci in independently evolved cave populations of Astyanax mexicanus

(2013) J. E. Kowalko et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Animal activity around the clock with no overt circadian rhythms: patterns, mechanisms and adaptive value

(2013) G. Bloch et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Circadian rhythms in Mexican blind cavefish Astyanax mexicanus in the lab and in the field

(2013) Andrew Beale et al.   Nature Communications

Differences in chemosensory response between eyed and eyeless Astyanax mexicanus of the Rio Subterráneo cave

(2013) Jonathan Bibliowicz et al.   EvoDevo

Analysis of a Gene Regulatory Cascade Mediating Circadian Rhythm in Zebrafish

(2013) Ying Li et al.   PLoS Computational Biology

Deviation of innate circadian period from 24 h reduces longevity in mice

(2012) Sergiy Libert et al.   AGING CELL

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Evolutionary Shift from Fighting to Foraging in Blind Cavefish through Changes in the Serotonin Network

(2012) Yannick Elipot et al.   CURRENT BIOLOGY

The Circadian Protein Period 1 Contributes to Blood Pressure Control and Coordinately Regulates Renal Sodium Transport Genes

(2012) Lisa R. Stow et al.   HYPERTENSION

Fiji: an open-source platform for biological-image analysis

(2012) Johannes Schindelin et al.   NATURE METHODS

RORγ directly regulates the circadian expression of clock genes and downstream targets in vivo

(2012) Yukimasa Takeda et al.   NUCLEIC ACIDS RESEARCH

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

(2012) Philipp Mracek et al.   PLoS One

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

(2012) Adi Tovin et al.   PLoS Genetics

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

Evolutionary Convergence on Sleep Loss in Cavefish Populations

(2011) Erik R. Duboué et al.   CURRENT BIOLOGY

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

(2011) Gad Vatine et al.   FEBS LETTERS

RNAscope

(2011) Fay Wang et al.   JOURNAL OF MOLECULAR DIAGNOSTICS

Genome-Wide and Phase-Specific DNA-Binding Rhythms of BMAL1 Control Circadian Output Functions in Mouse Liver

(2011) Guillaume Rey et al.   PLOS BIOLOGY

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

(2011) Nicola Cavallari et al.   PLOS BIOLOGY

Circadian Control of Global Gene Expression Patterns

(2010) Colleen J. Doherty et al.   Annual Review of Genetics

Evolution of a Behavioral Shift Mediated by Superficial Neuromasts Helps Cavefish Find Food in Darkness

(2010) Masato Yoshizawa et al.   CURRENT BIOLOGY

Circadian Clock Gene Bmal1 Is Not Essential; Functional Replacement with its Paralog, Bmal2

(2010) Shuqun Shi et al.   CURRENT BIOLOGY

JTK_CYCLE: An Efficient Nonparametric Algorithm for Detecting Rhythmic Components in Genome-Scale Data Sets

(2010) Michael E. Hughes et al.   JOURNAL OF BIOLOGICAL RHYTHMS

Circadian and Homeostatic Regulation of Structural Synaptic Plasticity in Hypocretin Neurons

(2010) Lior Appelbaum et al.   NEURON

Circadian Integration of Metabolism and Energetics

(2010) J. Bass et al.   SCIENCE

Globally optimal stitching of tiled 3D microscopic image acquisitions

(2009) S. Preibisch et al.   BIOINFORMATICS

Pleiotropic functions of embryonic sonic hedgehog expression link jaw and taste bud amplification with eye loss during cavefish evolution

(2009) Yoshiyuki Yamamoto et al.   DEVELOPMENTAL BIOLOGY

Evidence for the adaptive significance of circadian rhythms

(2009) Shai Yerushalmi et al.   ECOLOGY LETTERS

Genetic and Molecular Analysis of Wild-Derived Arrhythmic Mice

(2009) Tsuyoshi Watanabe et al.   PLoS One

Adverse metabolic and cardiovascular consequences of circadian misalignment

(2009) F. A. J. L. Scheer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Light Directs Zebrafish period2 Expression via Conserved D and E Boxes

(2009) Gad Vatine et al.   PLOS BIOLOGY

A Novel Role for Mc1r in the Parallel Evolution of Depigmentation in Independent Populations of the Cavefish Astyanax mexicanus

(2009) Joshua B. Gross et al.   PLoS Genetics

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