Genomic and transcriptomic analyses illuminate the molecular basis of the unique lifestyle of a tubeworm, Lamellibrachia satsuma

DAVID: a web server for functional enrichment analysis and functional annotation of gene lists (2021 update)

(2022) Brad T Sherman et al.   NUCLEIC ACIDS RESEARCH

Efficient assembly of nanopore reads via highly accurate and intact error correction

(2021) Ying Chen et al.   Nature Communications

Genomic Signatures Supporting the Symbiosis and Formation of Chitinous Tube in the Deep-Sea Tubeworm Paraescarpia echinospica

(2021) Yanan Sun et al.   MOLECULAR BIOLOGY AND EVOLUTION

BUSCO Update: Novel and Streamlined Workflows along with Broader and Deeper Phylogenetic Coverage for Scoring of Eukaryotic, Prokaryotic, and Viral Genomes

(2021) Mosè Manni et al.   MOLECULAR BIOLOGY AND EVOLUTION

Novel Insights on Obligate Symbiont Lifestyle and Adaptation to Chemosynthetic Environment as Revealed by the Giant Tubeworm Genome

(2021) André Luiz de Oliveira et al.   MOLECULAR BIOLOGY AND EVOLUTION

UniProt: the universal protein knowledgebase in 2021

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Cell Biology of Coral Symbiosis: Foundational Study Can Inform Solutions to the Coral Reef Crisis

(2019) Virginia M Weis   INTEGRATIVE AND COMPARATIVE BIOLOGY

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

Genomic adaptations to chemosymbiosis in the deep-sea seep-dwelling tubeworm Lamellibrachia luymesi

(2019) Yuanning Li et al.   BMC BIOLOGY

Distinct functions of TMC channels: a comparative overview

(2019) Xiaomin Yue et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

Genomic, transcriptomic, and proteomic insights into the symbiosis of deep-sea tubeworm holobionts

(2019) Yi Yang et al.   ISME Journal

Host-Microbe Interactions in the Chemosynthetic Riftia pachyptila Symbiosis

(2019) Tjorven Hinzke et al.   mBio

The mitochondrial genome of the deep-sea tubeworm Paraescarpia echinospica (Siboglinidae, Annelida) and its phylogenetic implications

(2018) Yanan Sun et al.   Mitochondrial DNA Part B-Resources

Purge Haplotigs: allelic contig reassignment for third-gen diploid genome assemblies

(2018) Michael J. Roach et al.   BMC BIOINFORMATICS

Salmon provides fast and bias-aware quantification of transcript expression

(2017) Rob Patro et al.   NATURE METHODS

Complex heatmaps reveal patterns and correlations in multidimensional genomic data

(2016) Zuguang Gu et al.   BIOINFORMATICS

Evolution of Sulfur Binding by Hemoglobin in Siboglinidae (Annelida) with Special Reference to Bone-Eating Worms, Osedax

(2016) Damien S. Waits et al.   JOURNAL OF MOLECULAR EVOLUTION

The complete mitochondrial genome sequence of the tubeworm Lamellibrachia satsuma and structural conservation in the mitochondrial genome control regions of Order Sabellida

(2016) Ajit Kumar Patra et al.   Marine Genomics

Phylogenetic relationship between symbionts of tubeworm Lamellibrachia satsuma and the sediment microbial community in Kagoshima Bay

(2016) Ajit Kumar Patra et al.   Ocean Science Journal

Current advances in the novel functions of hypoxia-inducible factor and prolyl hydroxylase in invertebrates

(2015) L. Wang et al.   INSECT MOLECULAR BIOLOGY

StringTie enables improved reconstruction of a transcriptome from RNA-seq reads

(2015) Mihaela Pertea et al.   NATURE BIOTECHNOLOGY

HISAT: a fast spliced aligner with low memory requirements

(2015) Daehwan Kim et al.   NATURE METHODS

LINKS: Scalable, alignment-free scaffolding of draft genomes with long reads

(2015) René L. Warren et al.   GigaScience

InterProScan 5: genome-scale protein function classification

(2014) P. Jones et al.   BIOINFORMATICS

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

HoxandParaHoxgenes: A review on molluscs

(2014) Maria Assunta Biscotti et al.   GENESIS

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

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

The genomes of four tapeworm species reveal adaptations to parasitism

(2013) Isheng J. Tsai et al.   NATURE

The lysosome: from waste bag to potential therapeutic target

(2013) Hanna Appelqvist et al.   Journal of Molecular Cell Biology

Four invertebrate-type lysozyme genes from triangle-shell pearl mussel (Hyriopsis cumingii)

(2012) Qian Ren et al.   FISH & SHELLFISH IMMUNOLOGY

Insights into bilaterian evolution from three spiralian genomes

(2012) Oleg Simakov et al.   NATURE

Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation

(2012) Davis J. McCarthy et al.   NUCLEIC ACIDS RESEARCH

Pathogen Recognition by the Innate Immune System

(2011) Himanshu Kumar et al.   INTERNATIONAL REVIEWS OF IMMUNOLOGY

New Perspectives on the Ecology and Evolution of Siboglinid Tubeworms

(2011) Ana Hilário et al.   PLoS One

The role of pattern-recognition receptors in innate immunity: update on Toll-like receptors

(2010) Taro Kawai et al.   NATURE IMMUNOLOGY

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

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

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

Insect chitinase and chitinase-like proteins

(2009) Yasuyuki Arakane et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

Serine proteases

(2009) Enrico Di Cera   IUBMB LIFE

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

(2009) Da Wei Huang et al.   Nature Protocols

Regulation of Oxygen Homeostasis by Hypoxia-Inducible Factor 1

(2009) Gregg L. Semenza   PHYSIOLOGY

Domain organization and phylogenetic analysis of proteins from the chitin deacetylase gene family of Tribolium castaneum and three other species of insects

(2008) Radhika Dixit et al.   INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY

Turning a hobby into a job: How duplicated genes find new functions

(2008) Gavin C. Conant et al.   NATURE REVIEWS GENETICS

Symbiotic diversity in marine animals: the art of harnessing chemosynthesis

(2008) Nicole Dubilier et al.   NATURE REVIEWS MICROBIOLOGY