Hologenome analysis of two marine sponges with different microbiomes

The HMA-LMA Dichotomy Revisited: an Electron Microscopical Survey of 56 Sponge Species

(2016) Volker Gloeckner et al.   BIOLOGICAL BULLETIN

InterProScan 5: genome-scale protein function classification

(2014) P. Jones et al.   BIOINFORMATICS

Revealing microbial functional activities in the Red Sea spongeStylissa carteriby metatranscriptomics

(2014) Lucas Moitinho-Silva et al.   ENVIRONMENTAL MICROBIOLOGY

The Analysis of Eight Transcriptomes from All Poriferan Classes Reveals Surprising Genetic Complexity in Sponges

(2014) Ana Riesgo et al.   MOLECULAR BIOLOGY AND EVOLUTION

L_RNA_scaffolder: scaffolding genomes with transcripts

(2013) Wei Xue et al.   BMC GENOMICS

Optimizing de novo assembly of short-read RNA-seq data for phylogenomics

(2013) Ya Yang et al.   BMC GENOMICS

Development of an ecophysiological model for Diplosphaera colotermitum TAV2, a termite hindgut Verrucomicrobium

(2013) Jantiya Isanapong et al.   ISME Journal

The Characterization of Sponge NLRs Provides Insight into the Origin and Evolution of This Innate Immune Gene Family in Animals

(2013) Benedict Yuen 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

Specificity and transcriptional activity of microbiota associated with low and high microbial abundance sponges from the Red Sea

(2013) Lucas Moitinho-Silva et al.   MOLECULAR ECOLOGY

Sequencing of the sea lamprey (Petromyzon marinus) genome provides insights into vertebrate evolution

(2013) Jeramiah J Smith et al.   NATURE GENETICS

Animals in a bacterial world, a new imperative for the life sciences

(2013) Margaret McFall-Ngai et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Extensive Differences in Gene Expression Between Symbiotic and Aposymbiotic Cnidarians

(2013) Erik M. Lehnert et al.   G3-Genes Genomes Genetics

GFOLD: a generalized fold change for ranking differentially expressed genes from RNA-seq data

(2012) Jianxing Feng et al.   BIOINFORMATICS

CD-HIT: accelerated for clustering the next-generation sequencing data

(2012) Limin Fu et al.   BIOINFORMATICS

A beginner's guide to eukaryotic genome annotation

(2012) Mark Yandell et al.   NATURE REVIEWS GENETICS

Genomic insights into the marine sponge microbiome

(2012) Ute Hentschel et al.   NATURE REVIEWS MICROBIOLOGY

dcGO: database of domain-centric ontologies on functions, phenotypes, diseases and more

(2012) Hai Fang et al.   NUCLEIC ACIDS RESEARCH

Functional equivalence and evolutionary convergence in complex communities of microbial sponge symbionts

(2012) L. Fan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Identification and removal of ribosomal RNA sequences from metatranscriptomes

(2011) Robert Schmieder et al.   BIOINFORMATICS

MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects

(2011) Carson Holt et al.   BMC BIOINFORMATICS

Optimizing de novo transcriptome assembly from short-read RNA-Seq data: a comparative study

(2011) Qiong-Yi Zhao et al.   BMC BIOINFORMATICS

Assessing the complex sponge microbiota: core, variable and species-specific bacterial communities in marine sponges

(2011) Susanne Schmitt et al.   ISME Journal

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

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

InterPro in 2011: new developments in the family and domain prediction database

(2011) S. Hunter et al.   NUCLEIC ACIDS RESEARCH

The Conserved Scavenger Receptor Cysteine-Rich Superfamily in Therapy and Diagnosis

(2011) V. G. Martinez et al.   PHARMACOLOGICAL REVIEWS

New paradigms for the evolution of beneficial infections

(2011) Joel L. Sachs et al.   TRENDS IN ECOLOGY & EVOLUTION

Metaorganisms as the new frontier

(2011) Thomas C.G. Bosch et al.   ZOOLOGY

The alarmin functions of high-mobility group proteins

(2010) De Yang et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Pyrosequencing reveals highly diverse and species-specific microbial communities in sponges from the Red Sea

(2010) On On Lee et al.   ISME Journal

Functional genomic signatures of sponge bacteria reveal unique and shared features of symbiosis

(2010) Torsten Thomas et al.   ISME Journal

The Amphimedon queenslandica genome and the evolution of animal complexity

(2010) Mansi Srivastava et al.   NATURE

De novo assembly and analysis of RNA-seq data

(2010) Gordon Robertson et al.   NATURE METHODS

Evolutionary microbial genomics: insights into bacterial host adaptation

(2010) Christina Toft et al.   NATURE REVIEWS GENETICS

A complex journey: transmission of microbial symbionts

(2010) Monika Bright et al.   NATURE REVIEWS MICROBIOLOGY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

ABySS: A parallel assembler for short read sequence data

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

Symbiotic competence in Lotus japonicus is affected by plant nitrogen status: transcriptomic identification of genes affected by a new signalling pathway

(2009) Selim Omrane et al.   NEW PHYTOLOGIST

The Pfam protein families database

(2009) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

Microbial co-habitation and lateral gene transfer: what transposases can tell us

(2009) Sean D Hooper et al.   GENOME BIOLOGY

Compagen, a comparative genomics platform for early branching metazoan animals, reveals early origins of genes regulating stem-cell differentiation

(2008) Georg Hemmrich et al.   BIOESSAYS

Velvet: Algorithms for de novo short read assembly using de Bruijn graphs

(2008) D. R. Zerbino et al.   GENOME RESEARCH

High-mobility group box protein 1 (HMGB1): an alarmin mediating the pathogenesis of rheumatic disease

(2008) David S Pisetsky et al.   ARTHRITIS RESEARCH & THERAPY