Insights into the strategy of micro-environmental adaptation: Transcriptomic analysis of two alvinocaridid shrimps at a hydrothermal vent

High rates of apoptosis visualized in the symbiont-bearing gills of deep-sea Bathymodiolus mussels

(2019) Bérénice Piquet et al.   PLoS One

The EMBL-EBI search and sequence analysis tools APIs in 2019

(2019) Fábio Madeira et al.   NUCLEIC ACIDS RESEARCH

Identification and characterization of a symbiotic agglutination-related C-type lectin from the hydrothermal vent shrimp Rimicaris exoculata

(2019) Xiao-Li Liu et al.   FISH & SHELLFISH IMMUNOLOGY

Adaptation to the deep-sea hydrothermal vents and cold seeps: Insights from the transcriptomes of Alvinocaris longirostris in both environments

(2018) Min Hui et al.   DEEP-SEA RESEARCH PART I-OCEANOGRAPHIC RESEARCH PAPERS

Invertebrate Trehalose-6-Phosphate Synthase Gene: Genetic Architecture, Biochemistry, Physiological Function, and Potential Applications

(2018) Bin Tang et al.   Frontiers in Physiology

The roles of mucus-forming mucins, peritrophins and peritrophins with mucin domains in the insect midgut

(2017) R. O. Dias et al.   INSECT MOLECULAR BIOLOGY

Ensembl Genomes 2018: an integrated omics infrastructure for non-vertebrate species

(2017) Paul Julian Kersey et al.   NUCLEIC ACIDS RESEARCH

Comparative transcriptome analysis of Rimicaris sp. reveals novel molecular features associated with survival in deep-sea hydrothermal vent

(2017) Jian Zhang et al.   Scientific Reports

Adaptation and evolution of deep-sea scale worms (Annelida: Polynoidae): insights from transcriptome comparison with a shallow-water species

(2017) Yanjie Zhang et al.   Scientific Reports

Different thermal preferences for brooding and larval dispersal of two neighboring shrimps in deep-sea hydrothermal vent fields

(2016) Hiromi Watanabe et al.   Marine Ecology-An Evolutionary Perspective

BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs

(2015) Felipe A. Simão et al.   BIOINFORMATICS

Is the deep-sea crab Chaceon affinis able to induce a thermal stress response?

(2015) Nélia C. Mestre et al.   COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY A-MOLECULAR & INTEGRATIVE PHYSIOLOGY

Water column imaging with multibeam echo-sounding in the mid-Okinawa Trough: Implications for distribution of deep-sea hydrothermal vent sites and the cause of acoustic water column anomaly

(2015) Kentaro Nakamura et al.   GEOCHEMICAL JOURNAL

Molecular Insights into the Role of Aqueous Trehalose Solution on Temperature-Induced Protein Denaturation

(2015) Subrata Paul et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Genetic population structure of four hydrothermal vent shrimp species (Alvinocarididae) in the Okinawa Trough, Northwest Pacific

(2015) T Yahagi et al.   MARINE ECOLOGY PROGRESS SERIES

Phylogeny and New Classification of Hydrothermal Vent and Seep Shrimps of the Family Alvinocarididae (Decapoda)

(2015) Alexander L. Vereshchaka et al.   PLoS One

Transcriptome sequencing of three Ranunculus species (Ranunculaceae) reveals candidate genes in adaptation from terrestrial to aquatic habitats

(2015) Ling-Yun Chen et al.   Scientific Reports

High-throughput transcriptome sequencing of the cold seep mussel Bathymodiolus platifrons

(2015) Yue Him Wong et al.   Scientific Reports

Genetic population structure of four hydrothermal vent shrimp species (Alvinocarididae) in the Okinawa Trough, Northwest Pacific

(2015) T Yahagi et al.   MARINE ECOLOGY PROGRESS SERIES

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

(2014) Lam-Tung Nguyen et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

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

Innate immune recognition of the microbiota promotes host-microbial symbiosis

(2013) Hiutung Chu et al.   NATURE IMMUNOLOGY

De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis

(2013) Brian J Haas et al.   Nature Protocols

Influence of Natural Thermal Gradients on Whole Animal Rates of Protein Synthesis in Marine Gammarid Amphipods

(2013) Samuel P. S. Rastrick et al.   PLoS One

ParaAT: A parallel tool for constructing multiple protein-coding DNA alignments

(2012) Zhang Zhang et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

Capacity for thermal acclimation differs between populations and phylogenetic lineages within a species

(2012) Frank Seebacher et al.   FUNCTIONAL ECOLOGY

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

(2011) Bo Li et al.   BMC BIOINFORMATICS

Hydrothermal faunal assemblages and habitat characterisation at the Eiffel Tower edifice (Lucky Strike, Mid-Atlantic Ridge)

(2011) Daphne Cuvelier et al.   Marine Ecology-An Evolutionary Perspective

Antimicrobial Peptides Keep Insect Endosymbionts Under Control

(2011) F. H. Login et al.   SCIENCE

Comparison of heat-shock responses between the hydrothermal vent shrimp Rimicaris exoculata and the related coastal shrimp Palaemonetes varians

(2010) Delphine Cottin et al.   JOURNAL OF EXPERIMENTAL MARINE BIOLOGY AND ECOLOGY

Identification of differentially expressed genes in the hydrothermal vent shrimp Rimicaris exoculata exposed to heat stress

(2010) Delphine Cottin et al.   Marine Genomics

Discovery of a black smoker vent field and vent fauna at the Arctic Mid-Ocean Ridge

(2010) Rolf B. Pedersen et al.   Nature Communications

KaKs_Calculator 2.0: A Toolkit Incorporating Gamma-Series Methods and Sliding Window Strategies

(2010) Dapeng Wang et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses

(2009) S. Capella-Gutierrez et al.   BIOINFORMATICS

Thermal biology of the deep-sea vent annelid Paralvinella grasslei: in vivo studies

(2008) D. Cottin et al.   JOURNAL OF EXPERIMENTAL BIOLOGY

Detoxification mechanisms in shrimp: Comparative approach between hydrothermal vent fields and estuarine environments

(2008) Maria Gonzalez-Rey et al.   MARINE ENVIRONMENTAL RESEARCH