Circadian dynamics of the teleost skin immune-microbiome interface

The Light-Inducible Genes Per2, Cry1a, and Cry2a Regulate Oxidative Status in Zebrafish

(2021) Yikelamu Alifu et al.   BIOLOGICAL & PHARMACEUTICAL BULLETIN

Marine artificial light at night: An empirical and technical guide

(2021) Svenja Tidau et al.   Methods in Ecology and Evolution

Time to integrate biotechnological approaches into fish gut microbiome research

(2021) Gian Marco Luna et al.   CURRENT OPINION IN BIOTECHNOLOGY

Trait-Based Comparison of Coral and Sponge Microbiomes

(2020) Cara L. Fiore et al.   Scientific Reports

Specialization of mucosal immunoglobulins in pathogen control and microbiota homeostasis occurred early in vertebrate evolution

(2020) Zhen Xu et al.   Science Immunology

Bacterial Infection Disrupts Clock Gene Expression to Attenuate Immune Responses

(2020) María José de Leone et al.   CURRENT BIOLOGY

PICRUSt2 for prediction of metagenome functions

(2020) Gavin M. Douglas et al.   NATURE BIOTECHNOLOGY

The role of the gut microbiome in sustainable teleost aquaculture

(2020) William Bernard Perry et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Japanese flounder (Paralichthys olivaceus) Bmal1 is involved in the regulation of inflammatory response and bacterial infection

(2020) Peng Zhang et al.   AQUACULTURE

Prior exposure to long-day photoperiods alters immune responses and increases susceptibility to parasitic infection in stickleback

(2020) James R. Whiting et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Comparative Analysis of the Core Proteomes among the Pseudomonas Major Evolutionary Groups Reveals Species-Specific Adaptations for Pseudomonas aeruginosa and Pseudomonas chlororaphis

(2020) Marios Nikolaidis et al.   Diversity-Basel

Circadian clock components Bmal1 and Clock1 regulate tlr9 gene expression in the Japanese medaka (Oryzias latipes)

(2020) Genki Taira et al.   FISH & SHELLFISH IMMUNOLOGY

Comparative transcriptomics reveal conserved impacts of rearing density on immune response of two important aquaculture species

(2020) Amy R. Ellison et al.   FISH & SHELLFISH IMMUNOLOGY

Crosstalk between circadian rhythms and the microbiota

(2020) James Alexander Pearson et al.   IMMUNOLOGY

Circadian Host-Microbiome Interactions in Immunity

(2020) Thomas D. Butler et al.   Frontiers in Immunology

Innate cell-mediated cytotoxicity of CD8+ T cells against the protozoan parasite Ichthyophthirius multifiliis in the ginbuna crucian carp, Carassius auratus langsdorfii

(2020) Masaki Sukeda et al.   DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY

The evolutionary ecology of circadian rhythms in infection

(2019) Mary L. Westwood et al.   Nature Ecology & Evolution

Circadian oscillation of TNF-α gene expression regulated by clock gene, BMAL1 and CLOCK1, in the Japanese medaka (Oryzias latipes)

(2019) Teika Onoue et al.   INTERNATIONAL IMMUNOPHARMACOLOGY

The skin microbiome of vertebrates

(2019) Ashley A. Ross et al.   Microbiome

Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2

(2019) Evan Bolyen et al.   NATURE BIOTECHNOLOGY

MetaBAT 2: an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies

(2019) Dongwan D. Kang et al.   PeerJ

Diet–microbiome–disease: Investigating diet’s influence on infectious disease resistance through alteration of the gut microbiome

(2019) Erica V. Harris et al.   PLoS Pathogens

Identification of human circadian genes based on time course gene expression profiles by using a deep learning method

(2018) Peng Cui et al.   BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR BASIS OF DISEASE

Minimap2: pairwise alignment for nucleotide sequences

(2018) Heng Li   BIOINFORMATICS

Structural absorption by barbule microstructures of super black bird of paradise feathers

(2018) Dakota E. McCoy et al.   Nature Communications

Influence of artificially induced light pollution on the hormone system of two common fish species, perch and roach, in a rural habitat

(2018) Anika Brüning et al.   Conservation Physiology

Cannabidiol affects circadian clock core complex and its regulation in microglia cells

(2018) Geneviève Lafaye et al.   ADDICTION BIOLOGY

Transcriptomic response to parasite infection in Nile tilapia (Oreochromis niloticus) depends on rearing density

(2018) Amy R Ellison et al.   BMC GENOMICS

Critical Role for a Subset of Intestinal Macrophages in Shaping Gut Microbiota in Adult Zebrafish

(2018) Alison M. Earley et al.   Cell Reports

T-Cell Exhaustion in Chronic Infections: Reversing the State of Exhaustion and Reinvigorating Optimal Protective Immune Responses

(2018) Alireza Saeidi et al.   Frontiers in Immunology

Fish intestinal microbiome: diversity and symbiosis unravelled by metagenomics

(2017) A.M. Tarnecki et al.   JOURNAL OF APPLIED MICROBIOLOGY

The Life and Times of Parasites: Rhythms in Strategies for Within-host Survival and Between-host Transmission

(2017) Sarah E. Reece et al.   JOURNAL OF BIOLOGICAL RHYTHMS

Association between light at night, melatonin secretion, sleep deprivation, and the internal clock: Health impacts and mechanisms of circadian disruption

(2017) Yvan Touitou et al.   LIFE SCIENCES

MicrobiomeAnalyst: a web-based tool for comprehensive statistical, visual and meta-analysis of microbiome data

(2017) Achal Dhariwal et al.   NUCLEIC ACIDS RESEARCH

Systems Chronotherapeutics

(2017) Annabelle Ballesta et al.   PHARMACOLOGICAL REVIEWS

Metacoder: An R package for visualization and manipulation of community taxonomic diversity data

(2017) Zachary S. L. Foster et al.   PLoS Computational Biology

New Paradigms to Help Solve the Global Aquaculture Disease Crisis

(2017) Grant D. Stentiford et al.   PLoS Pathogens

Under Pressure: Interactions between Commensal Microbiota and the Teleost Immune System

(2017) Cecelia Kelly et al.   Frontiers in Immunology

The Dark Side of Light: A Transdisciplinary Research Agenda for Light Pollution Policy

(2017) Franz Hölker et al.   ECOLOGY AND SOCIETY

Innate immune defenses exhibit circadian rhythmicity and differential temporal sensitivity to a bacterial endotoxin in Nile tilapia (Oreochromis niloticus)

(2016) Carlo C. Lazado et al.   FISH & SHELLFISH IMMUNOLOGY

T Cell Immune Deficiency in zap70 Mutant Zebrafish

(2016) John C. Moore et al.   MOLECULAR AND CELLULAR BIOLOGY

The microbiome and innate immunity

(2016) Christoph A. Thaiss et al.   NATURE

DADA2: High-resolution sample inference from Illumina amplicon data

(2016) Benjamin J Callahan et al.   NATURE METHODS

The healthy human microbiome

(2016) Jason Lloyd-Price et al.   Genome Medicine

Evaluation of Lysis Methods for the Extraction of Bacterial DNA for Analysis of the Vaginal Microbiota

(2016) Christina Gill et al.   PLoS One

SeqKit: A Cross-Platform and Ultrafast Toolkit for FASTA/Q File Manipulation

(2016) Wei Shen et al.   PLoS One

Infectious Diseases Affect Marine Fisheries and Aquaculture Economics

(2015) Kevin D. Lafferty et al.   Annual Review of Marine Science

Phenotypic and molecular characterization and pathology of Flectobacillus roseus causing flectobacillosis in captive held carp Labeo rohita (Ham.) fingerlings

(2015) Harresh Adikesavalu et al.   AQUACULTURE

A new view of the fish gut microbiome: Advances from next-generation sequencing

(2015) Mahdi Ghanbari et al.   AQUACULTURE

MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph

(2015) Dinghua Li et al.   BIOINFORMATICS

Effects of Diurnal Variation of Gut Microbes and High-Fat Feeding on Host Circadian Clock Function and Metabolism

(2015) Vanessa Leone et al.   Cell Host & Microbe

Signatures of resistance to Lepeophtheirus salmonis include a TH2-type response at the louse-salmon interface

(2015) Laura M. Braden et al.   DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY

CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes

(2015) Donovan H. Parks et al.   GENOME RESEARCH

Rhythmicity of the intestinal microbiota is regulated by gender and the host circadian clock

(2015) Xue Liang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Improved Statistical Methods Enable Greater Sensitivity in Rhythm Detection for Genome-Wide Data

(2015) Alan L. Hutchison et al.   PLoS Computational Biology

Anvi’o: an advanced analysis and visualization platform for ‘omics data

(2015) A. Murat Eren et al.   PeerJ

Emerging flavobacterial infections in fish: A review

(2015) Thomas P. Loch et al.   Journal of Advanced Research

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Diet and Feeding Pattern Affect the Diurnal Dynamics of the Gut Microbiome

(2014) Amir Zarrinpar et al.   Cell Metabolism

Diet type dictates the gut microbiota and the immune response against Yersinia ruckeri in rainbow trout (Oncorhynchus mykiss)

(2014) Hans-Christian Ingerslev et al.   FISH & SHELLFISH IMMUNOLOGY

Circadian Clock Proteins and Immunity

(2014) Anne M. Curtis et al.   IMMUNITY

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

The rainbow trout genome provides novel insights into evolution after whole-genome duplication in vertebrates

(2014) Camille Berthelot et al.   Nature Communications

Teleost microbiomes: the state of the art in their characterization, manipulation and importance in aquaculture and fisheries

(2014) Martin S. Llewellyn et al.   Frontiers in Microbiology

Aquacultured Rainbow Trout (Oncorhynchus mykiss) Possess a Large Core Intestinal Microbiota That Is Resistant to Variation in Diet and Rearing Density

(2013) S. Wong et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

The microbiome and regulation of mucosal immunity

(2013) Andrew J. McDermott et al.   IMMUNOLOGY

Environmental Circadian Disruption Elevates the IL-6 Response to Lipopolysaccharide in Blood

(2013) Kandis L. Adams et al.   JOURNAL OF BIOLOGICAL RHYTHMS

phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data

(2013) Paul J. McMurdie et al.   PLoS One

Probiotics in aquaculture: a current assessment

(2013) Tania Pérez-Sánchez et al.   Reviews in Aquaculture

Phylogenomic analysis of bacterial and archaeal sequences with AMPHORA2

(2012) Martin Wu et al.   BIOINFORMATICS

Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms

(2012) J Gregory Caporaso et al.   ISME Journal

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

The expression of CD8α discriminates distinct T cell subsets in teleost fish

(2011) Fumio Takizawa et al.   DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY

Vector potential of the salmon louse Lepeophtheirus salmonis in the transmission of infectious haematopoietic necrosis virus (IHNV)

(2011) E Jakob et al.   DISEASES OF AQUATIC ORGANISMS

Diel variations in the selected serum immune parameters in Oreochromis mossambicus

(2011) C. Binuramesh et al.   FISH & SHELLFISH IMMUNOLOGY

Identification and characterization of lactic acid bacteria isolated from rainbow trout, Oncorhynchus mykiss (Walbaum), with inhibitory activity against Lactococcus garvieae

(2011) T Pérez-Sánchez et al.   JOURNAL OF FISH DISEASES

Timing of plant immune responses by a central circadian regulator

(2011) Wei Wang et al.   NATURE

Metagenomic systems biology of the human gut microbiome reveals topological shifts associated with obesity and inflammatory bowel disease

(2011) S. Greenblum et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Dysregulation of Inflammatory Responses by Chronic Circadian Disruption

(2010) O. Castanon-Cervantes et al.   JOURNAL OF IMMUNOLOGY

Injection of LPS Causes Transient Suppression of Biological Clock Genes in Rats

(2008) Kazuyuki Okada et al.   JOURNAL OF SURGICAL RESEARCH