Is the trophosome of Ridgeia piscesae monoclonal?

Insights into Symbiont Population Structure among Three Vestimentiferan Tubeworm Host Species at Eastern Pacific Spreading Centers

(2016) Maëva Perez et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Pollux: platform independent error correction of single and mixed genomes

(2015) Eric Marinier et al.   BMC BIOINFORMATICS

Evaluation of variant detection software for pooled next-generation sequence data

(2015) Howard W. Huang et al.   BMC BIOINFORMATICS

Review of alignment and SNP calling algorithms for next-generation sequencing data

(2015) M. Mielczarek et al.   JOURNAL OF APPLIED GENETICS

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

Population Genomic Analysis of 962 Whole Genome Sequences of Humans Reveals Natural Selection in Non-Coding Regions

(2015) Fuli Yu et al.   PLoS One

Assessing single nucleotide variant detection and genotype calling on whole-genome sequenced individuals

(2014) Anthony Youzhi Cheng et al.   BIOINFORMATICS

Dual symbiosis with co-occurring sulfur-oxidizing symbionts in vestimentiferan tubeworms from a Mediterranean hydrothermal vent

(2014) Judith Zimmermann et al.   ENVIRONMENTAL MICROBIOLOGY

Molecular study of bacterial diversity within the trophosome of the vestimentiferan tubewormRidgeia piscesae

(2014) Nathalie L. Forget et al.   Marine Ecology-An Evolutionary Perspective

Diversification of CRISPR within coexisting genotypes in a natural population of the bloom-forming cyanobacterium Microcystis aeruginosa

(2014)   MICROBIOLOGY-SGM

Performance comparison of SNP detection tools with illumina exome sequencing data—an assessment using both family pedigree information and sample-matched SNP array data

(2014) Ming Yi et al.   NUCLEIC ACIDS RESEARCH

Comparing a few SNP calling algorithms using low-coverage sequencing data

(2013) Xiaoqing Yu et al.   BMC BIOINFORMATICS

A survey of tools for variant analysis of next-generation genome sequencing data

(2013) S. Pabinger et al.   BRIEFINGS IN BIOINFORMATICS

Crass: identification and reconstruction of CRISPR from unassembled metagenomic data

(2013) Connor T. Skennerton et al.   NUCLEIC ACIDS RESEARCH

A tale of three next generation sequencing platforms: comparison of Ion torrent, pacific biosciences and illumina MiSeq sequencers

(2012) Michael Quail et al.   BMC GENOMICS

A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff

(2012) Pablo Cingolani et al.   FLY

The highly dynamic CRISPR1 system ofStreptococcus agalactiaecontrols the diversity of its mobilome

(2012) Maria-José Lopez-Sanchez et al.   MOLECULAR MICROBIOLOGY

Performance comparison of benchtop high-throughput sequencing platforms

(2012) Nicholas J Loman et al.   NATURE BIOTECHNOLOGY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Metaproteomics of a gutless marine worm and its symbiotic microbial community reveal unusual pathways for carbon and energy use

(2012) M. Kleiner et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Persisting Viral Sequences Shape Microbial CRISPR-based Immunity

(2012) Ariel D. Weinberger et al.   PLoS Computational Biology

BamTools: a C++ API and toolkit for analyzing and managing BAM files

(2011) D. W. Barnett et al.   BIOINFORMATICS

Quality control and preprocessing of metagenomic datasets

(2011) R. Schmieder et al.   BIOINFORMATICS

Identification and correction of systematic error in high-throughput sequence data

(2011) Frazer Meacham et al.   BMC BIOINFORMATICS

Fast Identification and Removal of Sequence Contamination from Genomic and Metagenomic Datasets

(2011) Robert Schmieder et al.   PLoS One

Mutation Rate Inferred From Synonymous Substitutions in a Long-Term Evolution Experiment With Escherichia coli

(2011) Sébastien Wielgoss et al.   G3-Genes Genomes Genetics

Fast and accurate long-read alignment with Burrows–Wheeler transform

(2010) Heng Li et al.   BIOINFORMATICS

A survey of sequence alignment algorithms for next-generation sequencing

(2010) H. Li et al.   BRIEFINGS IN BIOINFORMATICS

A map of human genome variation from population-scale sequencing

(2010) Richard M. Durbin et al.   NATURE

CRISPR Associated Diversity within a Population of Sulfolobus islandicus

(2010) Nicole L. Held et al.   PLoS One

Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities

(2009) P. D. Schloss et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

VarScan: variant detection in massively parallel sequencing of individual and pooled samples

(2009) Daniel C. Koboldt et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Molecular characterization of bacteria associated with the trophosome and the tube of Lamellibrachia sp., a siboglinid annelid from cold seeps in the eastern Mediterranean

(2009) Sébastien Duperron et al.   FEMS MICROBIOLOGY ECOLOGY

Evidence for Homologous Recombination in Intracellular Chemosynthetic Clam Symbionts

(2009) F. J. Stewart et al.   MOLECULAR BIOLOGY AND EVOLUTION

Metabolic versatility of the Riftia pachyptila endosymbiont revealed through metagenomics

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

Unexpected co-occurrence of six bacterial symbionts in the gills of the cold seep mussel Idas sp. (Bivalvia: Mytilidae)

(2008) Sébastien Duperron et al.   ENVIRONMENTAL MICROBIOLOGY

Directional dispersal between mid-ocean ridges: deep-ocean circulation and gene flow inRidgeia piscesae

(2008) C. R. YOUNG et al.   MOLECULAR ECOLOGY

Substantial biases in ultra-short read data sets from high-throughput DNA sequencing

(2008) J. C. Dohm et al.   NUCLEIC ACIDS RESEARCH

Insight into Microevolution of Yersinia pestis by Clustered Regularly Interspaced Short Palindromic Repeats

(2008) Yujun Cui et al.   PLoS One

Metagenome analysis of an extreme microbial symbiosis reveals eurythermal adaptation and metabolic flexibility

(2008) J. J. Grzymski et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA