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

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

Symbiont population control by host-symbiont metabolic interaction in Symbiodiniaceae-cnidarian associations

(2020) Tingting Xiang et al.   Nature Communications

Widespread patterns of gene loss in the evolution of the animal kingdom

(2020) Cristina Guijarro-Clarke et al.   Nature Ecology & Evolution

Gene gain and loss across the metazoan tree of life

(2020) Rosa Fernández et al.   Nature Ecology & Evolution

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

Newly discovered occurrences and gene tree of the extracellular globins and linker chains from the giant hexagonal bilayer hemoglobin in metazoans

(2019) Flávia A Belato et al.   Genome Biology and Evolution

SignalP 5.0 improves signal peptide predictions using deep neural networks

(2019) José Juan Almagro Armenteros et al.   NATURE BIOTECHNOLOGY

Assembly of long, error-prone reads using repeat graphs

(2019) Mikhail Kolmogorov et al.   NATURE BIOTECHNOLOGY

The quagga mussel genome and the evolution of freshwater tolerance

(2019) Andrew D Calcino et al.   DNA RESEARCH

Genomics of Urea Transport and Catabolism in Cyanobacteria: Biotechnological Implications

(2019) Théo Veaudor et al.   Frontiers in Microbiology

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

Pathogenic mutations of the human mitochondrial citrate carrier SLC25A1 lead to impaired citrate export required for lipid, dolichol, ubiquinone and sterol synthesis

(2018) Homa Majd et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS

Minimap2: pairwise alignment for nucleotide sequences

(2018) Heng Li   BIOINFORMATICS

The stoichiometry of coral-dinoflagellate symbiosis: carbon and nitrogen cycles are balanced in the recycling and double translocation system

(2018) Yasuaki Tanaka et al.   ISME Journal

Evolution of the bilaterian mouth and anus

(2018) Claus Nielsen et al.   Nature Ecology & Evolution

Canu: scalable and accurate long-read assembly via adaptivek-mer weighting and repeat separation

(2017) Sergey Koren et al.   GENOME RESEARCH

UFBoot2: Improving the Ultrafast Bootstrap Approximation

(2017) Diep Thi Hoang et al.   MOLECULAR BIOLOGY AND EVOLUTION

ModelFinder: fast model selection for accurate phylogenetic estimates

(2017) Subha Kalyaanamoorthy et al.   NATURE METHODS

GeSeq – versatile and accurate annotation of organelle genomes

(2017) Michael Tillich et al.   NUCLEIC ACIDS RESEARCH

The Notch pathway in the annelidPlatynereis: insights into chaetogenesis and neurogenesis processes

(2017) Eve Gazave et al.   Open Biology

The Role of Hemocytes in the Hawaiian Bobtail Squid, Euprymna scolopes: A Model Organism for Studying Beneficial Host–Microbe Interactions

(2017) Sarah J. McAnulty et al.   Frontiers in Microbiology

Nemertean and phoronid genomes reveal lophotrochozoan evolution and the origin of bilaterian heads

(2017) Yi-Jyun Luo et al.   Nature Ecology & Evolution

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

The Biochemistry and Physiology of Mitochondrial Fatty Acid β-Oxidation and Its Genetic Disorders

(2016) Sander M. Houten et al.   Annual Review of Physiology

Haematopoiesis in molluscs: A review of haemocyte development and function in gastropods, cephalopods and bivalves

(2016) E.A. Pila et al.   DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY

Near-optimal probabilistic RNA-seq quantification

(2016) Nicolas L Bray et al.   NATURE BIOTECHNOLOGY

Mechanisms of transcription factor evolution in Metazoa

(2016) Jonathan F. Schmitz et al.   NUCLEIC ACIDS RESEARCH

PANTHER version 11: expanded annotation data from Gene Ontology and Reactome pathways, and data analysis tool enhancements

(2016) Huaiyu Mi et al.   NUCLEIC ACIDS RESEARCH

tRNAscan-SE On-line: integrating search and context for analysis of transfer RNA genes

(2016) Todd M. Lowe et al.   NUCLEIC ACIDS RESEARCH

IBS: an illustrator for the presentation and visualization of biological sequences: Fig. 1.

(2015) Wenzhong Liu et al.   BIOINFORMATICS

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

(2015) Felipe A. Simão et al.   BIOINFORMATICS

The genome of the Pacific oyster Crassostrea gigas brings new insights on the massive expansion of the C1q gene family in Bivalvia

(2015) Marco Gerdol et al.   DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY

Mitogenomics reveals phylogeny and repeated motifs in control regions of the deep-sea family Siboglinidae (Annelida)

(2015) Yuanning Li et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Hemichordate genomes and deuterostome origins

(2015) Oleg Simakov et al.   NATURE

Major evolutionary transitions in individuality

(2015) Stuart A. West et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Endosymbionts escape dead hydrothermal vent tubeworms to enrich the free-living population

(2015) Julia Klose et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Evolving new organisms via symbiosis

(2015) E. T. Kiers et al.   SCIENCE

Getting to the bottom of anal evolution

(2015) Andreas Hejnol et al.   ZOOLOGISCHER ANZEIGER

Antioxidant responses and cellular adjustments to oxidative stress

(2015) Cristina Espinosa-Diez et al.   Redox Biology

InterProScan 5: genome-scale protein function classification

(2014) P. Jones 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

Maintenance of essential amino acid synthesis pathways in the Blattabacterium cuenoti symbiont of a wood-feeding cockroach

(2013) G. Tokuda et al.   Biology Letters

Hematopoiesis and hematopoietic organs in arthropods

(2013) Melina Grigorian et al.   DEVELOPMENT GENES AND EVOLUTION

Estimating Gene Gain and Loss Rates in the Presence of Error in Genome Assembly and Annotation Using CAFE 3

(2013) Mira V. Han et al.   MOLECULAR BIOLOGY AND EVOLUTION

The genomes of four tapeworm species reveal adaptations to parasitism

(2013) Isheng J. Tsai et al.   NATURE

Challenges in homology search: HMMER3 and convergent evolution of coiled-coil regions

(2013) Jaina Mistry et al.   NUCLEIC ACIDS RESEARCH

PhyloBayes MPI: Phylogenetic Reconstruction with Infinite Mixtures of Profiles in a Parallel Environment

(2013) Nicolas Lartillot et al.   SYSTEMATIC BIOLOGY

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

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

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Ecological interactions drive evolutionary loss of traits

(2012) Jacintha Ellers et al.   ECOLOGY LETTERS

MITOS: Improved de novo metazoan mitochondrial genome annotation

(2012) Matthias Bernt et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

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

The complex world of WNT receptor signalling

(2012) Christof Niehrs   NATURE REVIEWS MOLECULAR CELL BIOLOGY

TGFβ signalling in context

(2012) Joan Massagué   NATURE REVIEWS MOLECULAR CELL BIOLOGY

The metatrochophore of a deep-sea hydrothermal vent vestimentiferan (Polychaeta: Siboglinidae)

(2012) Monika Bright et al.   ORGANISMS DIVERSITY & EVOLUTION

Expression and Putative Function of Innate Immunity Genes under in situ Conditions in the Symbiotic Hydrothermal Vent Tubeworm Ridgeia piscesae

(2012) Spencer V. Nyholm et al.   PLoS One

The Evolution of the Wnt Pathway

(2012) T. W. Holstein   Cold Spring Harbor Perspectives in Biology

Physiological homogeneity among the endosymbionts of Riftia pachyptila and Tevnia jerichonana revealed by proteogenomics

(2011) Antje Gardebrecht et al.   ISME Journal

The mitochondrial carnitine/acylcarnitine carrier: Function, structure and physiopathology

(2011) Cesare Indiveri et al.   MOLECULAR ASPECTS OF MEDICINE

Mechanisms and functions of Hedgehog signalling across the metazoa

(2011) Philip W. Ingham et al.   NATURE REVIEWS GENETICS

New Perspectives on the Ecology and Evolution of Siboglinid Tubeworms

(2011) Ana Hilário et al.   PLoS One

The metabolic demands of endosymbiotic chemoautotrophic metabolism on host physiological capacities

(2010) J. J. Childress et al.   JOURNAL OF EXPERIMENTAL BIOLOGY

Evolutionary Dynamics of the wnt Gene Family: A Lophotrochozoan Perspective

(2010) S.-J. Cho et al.   MOLECULAR BIOLOGY AND EVOLUTION

De novo assembly and analysis of RNA-seq data

(2010) Gordon Robertson et al.   NATURE METHODS

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

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

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Dynamics of cell proliferation and apoptosis reflect different life strategies in hydrothermal vent and cold seep vestimentiferan tubeworms

(2009) Bettina Pflugfelder et al.   CELL AND TISSUE RESEARCH

The regulation of TGF  signal transduction

(2009) A. Moustakas et al.   DEVELOPMENT

Survey of genome size in 28 hydrothermal vent species covering 10 families

(2009) Eric Bonnivard et al.   GENOME

A Novel Member of Solute Carrier Family 25 (SLC25A42) Is a Transporter of Coenzyme A and Adenosine 3′,5′-Diphosphate in Human Mitochondria

(2009) Giuseppe Fiermonte et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Direct Evidence That Extracellular Giant Hemoglobin is Produced in Chloragogen Tissues in a Beard Worm, Oligobrachia mashikoi (Frenulata, Siboglinidae, Annelida)

(2009) Shigeyuki Nakahama et al.   ZOOLOGICAL SCIENCE

Progress in systematics: from Siboglinidae to Pogonophora and Vestimentifera and back to Siboglinidae

(2008) Fredrik Pleijel et al.   COMPTES RENDUS BIOLOGIES

Metabolic versatility of the Riftia pachyptila endosymbiont revealed through metagenomics

(2008) Julie C. Robidart et al.   ENVIRONMENTAL MICROBIOLOGY