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

IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era

(2020) Bui Quang Minh et al.   MOLECULAR BIOLOGY AND EVOLUTION

The Scaly-foot Snail genome and implications for the origins of biomineralised armour

(2020) Jin Sun et al.   Nature Communications

Ecological characterization of cold-seep epifauna in the south China sea

(2020) Yu Zhao et al.   DEEP-SEA RESEARCH PART I-OCEANOGRAPHIC RESEARCH PAPERS

Host-Endosymbiont Genome Integration in a Deep-Sea Chemosymbiotic Clam

(2020) Jack Chi-Ho Ip et al.   MOLECULAR BIOLOGY AND EVOLUTION

Conservative route to genome compaction in a miniature annelid

(2020) José M. Martín-Durán et al.   Nature Ecology & Evolution

RAxML-NG: a fast, scalable and user-friendly tool for maximum likelihood phylogenetic inference

(2019) Alexey M Kozlov et al.   BIOINFORMATICS

Characterization of a thaumarchaeal symbiont that drives incomplete nitrification in the tropical sponge Ianthella basta

(2019) Florian U. Moeller et al.   ENVIRONMENTAL MICROBIOLOGY

Comparative transcriptomic analysis illuminates the host-symbiont interactions in the deep-sea mussel Bathymodiolus platifrons

(2019) Hao Wang et al.   DEEP-SEA RESEARCH PART I-OCEANOGRAPHIC RESEARCH PAPERS

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

(2019) Yuanning Li et al.   BMC BIOLOGY

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

Endosymbiont genomes yield clues of tubeworm success

(2018) Yuanning Li et al.   ISME Journal

Novel Genes, Ancient Genes, and Gene Co-Option Contributed to the Genetic Basis of the Radula, a Molluscan Innovation

(2018) Leon Hilgers et al.   MOLECULAR BIOLOGY AND EVOLUTION

Involvement of a host Cathepsin L in symbiont-induced cell death

(2018) Suzanne M. Peyer et al.   MicrobiologyOpen

Transcriptional changes in the Japanese scallop (Mizuhopecten yessoensis) shellinfested by Polydora provide insights into the molecular mechanism of shell formation and immunomodulation

(2018) Junxia Mao et al.   Scientific Reports

ModelFinder: fast model selection for accurate phylogenetic estimates

(2017) Subha Kalyaanamoorthy et al.   NATURE METHODS

Functional horizontal gene transfer from bacteria to eukaryotes

(2017) Filip Husnik et al.   NATURE REVIEWS MICROBIOLOGY

Massive horizontal transfer of transposable elements in insects

(2017) Jean Peccoud et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds

(2017) Olga Dudchenko et al.   SCIENCE

Adaptation to deep-sea chemosynthetic environments as revealed by mussel genomes

(2017) Jin Sun et al.   Nature Ecology & Evolution

Scallop genome provides insights into evolution of bilaterian karyotype and development

(2017) Shi Wang et al.   Nature Ecology & Evolution

Transcriptomic and proteomic insights into innate immunity and adaptations to a symbiotic lifestyle in the gutless marine worm Olavius algarvensis

(2016) Juliane Wippler et al.   BMC GENOMICS

Immunological properties of oxygen-transport proteins: hemoglobin, hemocyanin and hemerythrin

(2016) Christopher J. Coates et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

Insights from the Shell Proteome: Biomineralization to Adaptation

(2016) Jaison Arivalagan et al.   MOLECULAR BIOLOGY AND EVOLUTION

Redundans: an assembly pipeline for highly heterozygous genomes

(2016) Leszek P. Pryszcz et al.   NUCLEIC ACIDS RESEARCH

Phylogenomics of tubeworms (Siboglinidae, Annelida) and comparative performance of different reconstruction methods

(2016) Yuanning Li et al.   ZOOLOGICA SCRIPTA

Juicer Provides a One-Click System for Analyzing Loop-Resolution Hi-C Experiments

(2016) Neva C. Durand et al.   Cell Systems

Detection of Prokaryotic Genes in the Amphimedon queenslandica Genome

(2016) Cecilia Conaco et al.   PLoS One

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

(2015) Felipe A. Simão et al.   BIOINFORMATICS

Uncertainty in the Timing of Origin of Animals and the Limits of Precision in Molecular Timescales

(2015) Mario dos Reis et al.   CURRENT BIOLOGY

Infiltration of chitin by protein coacervates defines the squid beak mechanical gradient

(2015) YerPeng Tan et al.   Nature Chemical Biology

HISAT: a fast spliced aligner with low memory requirements

(2015) Daehwan Kim et al.   NATURE METHODS

The role of lysosome in cell death regulation

(2015) Feifei Yu et al.   TUMOR BIOLOGY

The Lingula genome provides insights into brachiopod evolution and the origin of phosphate biomineralization

(2015) Yi-Jyun Luo et al.   Nature Communications

Repbase Update, a database of repetitive elements in eukaryotic genomes

(2015) Weidong Bao et al.   Mobile DNA

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement

(2014) Bruce J. Walker et al.   PLoS One

The MaSuRCA genome assembler

(2013) Aleksey V. Zimin et al.   BIOINFORMATICS

Lysosomal cell death at a glance

(2013) S. Aits et al.   JOURNAL OF CELL SCIENCE

The Skeletal Proteome of the Coral Acropora millepora: The Evolution of Calcification by Co-Option and Domain Shuffling

(2013) Paula Ramos-Silva 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

Hox gene expression during postlarval development of the polychaete Alitta virens

(2013) Nadezhda I Bakalenko et al.   EvoDevo

Expression of Hox genes during regeneration of nereid polychaete Alitta (Nereis) virens (Annelida, Lophotrochozoa)

(2013) Elena L Novikova et al.   EvoDevo

On the instability and evolutionary age of deep-sea chemosynthetic communities

(2012) Robert C. Vrijenhoek   DEEP-SEA RESEARCH PART II-TOPICAL STUDIES IN OCEANOGRAPHY

The oyster genome reveals stress adaptation and complexity of shell formation

(2012) Guofan Zhang et al.   NATURE

Insights into bilaterian evolution from three spiralian genomes

(2012) Oleg Simakov et al.   NATURE

Knowing your friends: invertebrate innate immunity fosters beneficial bacterial symbioses

(2012) Spencer V. Nyholm et al.   NATURE REVIEWS MICROBIOLOGY

clusterProfiler: an R Package for Comparing Biological Themes Among Gene Clusters

(2012) Guangchuang Yu et al.   OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY

In-depth proteomic analysis of a mollusc shell: acid-soluble and acid-insoluble matrix of the limpet Lottia gigantea

(2012) Karlheinz Mann et al.   Proteome Science

A fast, lock-free approach for efficient parallel counting of occurrences of k-mers

(2011) Guillaume Marçais et al.   BIOINFORMATICS

Myosin-5, kinesin-1 and myosin-17 cooperate in secretion of fungal chitin synthase

(2011) Martin Schuster et al.   EMBO JOURNAL

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

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

New Perspectives on the Ecology and Evolution of Siboglinid Tubeworms

(2011) Ana Hilário et al.   PLoS One

REVIGO Summarizes and Visualizes Long Lists of Gene Ontology Terms

(2011) Fran Supek et al.   PLoS One

Genes encoding proteins with peritrophin A-type chitin-binding domains in Tribolium castaneum are grouped into three distinct families based on phylogeny, expression and function

(2010) Sinu Jasrapuria et al.   INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY

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

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

Myosin Motor-Like Domain of the Class VI Chitin Synthase CsmB Is Essential to Its Functions inAspergillus nidulans

(2009) Makusu TSUIZAKI et al.   BIOSCIENCE BIOTECHNOLOGY AND BIOCHEMISTRY

Comparative genomic analyses of the human fungal pathogens Coccidioides and their relatives

(2009) T. J. Sharpton et al.   GENOME RESEARCH

Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome

(2009) E. Lieberman-Aiden et al.   SCIENCE

The role of the immune system in the initiation and persistence of the Euprymna scolopes–Vibrio fischeri symbiosis

(2009) Margaret McFall-Ngai et al.   SEMINARS IN IMMUNOLOGY

Cathepsins: Key modulators of cell death and inflammatory responses

(2008) Sébastien Conus et al.   BIOCHEMICAL PHARMACOLOGY

The amphioxus genome and the evolution of the chordate karyotype

(2008) Nicholas H. Putnam et al.   NATURE

Symbiotic diversity in marine animals: the art of harnessing chemosynthesis

(2008) Nicole Dubilier et al.   NATURE REVIEWS MICROBIOLOGY