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

InterProScan 5: genome-scale protein function classification

(2014) P. Jones et al.   BIOINFORMATICS

De novo transcriptome analysis of Perna viridis highlights tissue-specific patterns for environmental studies

(2014) Priscilla TY Leung et al.   BMC GENOMICS

Genomic Sequence and Experimental Tractability of a New Decapod Shrimp Model, Neocaridina denticulata

(2014) Nathan Kenny et al.   Marine Drugs

MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0

(2013) Koichiro Tamura et al.   MOLECULAR BIOLOGY AND EVOLUTION

The oyster genome reveals stress adaptation and complexity of shell formation

(2012) Guofan Zhang et al.   NATURE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

NGS QC Toolkit: A Toolkit for Quality Control of Next Generation Sequencing Data

(2012) Ravi K. Patel et al.   PLoS One

Integrative analysis of environmental sequences using MEGAN4

(2011) D. H. Huson et al.   GENOME RESEARCH

Full-length transcriptome assembly from RNA-Seq data without a reference genome

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

Computational methods for transcriptome annotation and quantification using RNA-seq

(2011) Manuel Garber et al.   NATURE METHODS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

High-throughput sequencing and analysis of the gill tissue transcriptome from the deep-sea hydrothermal vent mussel Bathymodiolus azoricus

(2010) Raul Bettencourt et al.   BMC GENOMICS

Effect of long-term exposure to sulfides on taurine transporter gene expression in the gill of the deep-sea mussel Bathymodiolus platifrons, which harbors a methanotrophic symbiont

(2010) Tomoko Koito et al.   FISHERIES SCIENCE

Diverse and Novel nifH and nifH-Like Gene Sequences in the Deep-Sea Methane Seep Sediments of the Okhotsk Sea

(2009) H. Dang et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Exploring the human genome with functional maps

(2009) C. Huttenhower et al.   GENOME RESEARCH

Efficient algorithms for accurate hierarchical clustering of huge datasets: tackling the entire protein space

(2008) Y. Loewenstein et al.   BIOINFORMATICS

Possible role of a taurine transporter in the deep-sea musselBathymodiolus septemdierumin adaptation to hydrothermal vents

(2008) Koji Inoue et al.   FEBS LETTERS

Spatial variation of metal bioaccumulation in the hydrothermal vent mussel Bathymodiolus azoricus

(2008) Richard P. Cosson et al.   MARINE ENVIRONMENTAL RESEARCH

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi et al.   NATURE METHODS

An insect symbiosis is influenced by bacterium-specific polymorphisms in outer-membrane protein A

(2008) B. L. Weiss et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA