Assembly of viral genomes from metagenomes

The complete genome sequence for putative H2- and S-oxidizerCandidatusSulfuricurvum sp., assembledde novofrom an aquifer-derived metagenome

(2014) Kim M. Handley et al.   ENVIRONMENTAL MICROBIOLOGY

MetaCAA: A clustering-aided methodology for efficient assembly of metagenomic datasets

(2014) Rachamalla Maheedhar Reddy et al.   GENOMICS

Exploring the Potential of Next-Generation Sequencing in Detection of Respiratory Viruses

(2014) S. Prachayangprecha et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Novel divergent nidovirus in a python with pneumonia

(2014) R. Bodewes et al.   JOURNAL OF GENERAL VIROLOGY

Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes

(2014) H Bjørn Nielsen et al.   NATURE BIOTECHNOLOGY

Metagenomic Survey for Viruses in Western Arctic Caribou, Alaska, through Iterative Assembly of Taxonomic Units

(2014) Anita C. Schürch et al.   PLoS One

Tackling soil diversity with the assembly of large, complex metagenomes

(2014) Adina Chuang Howe et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Viral metagenomic analysis of feces of wild small carnivores

(2014) Rogier Bodewes et al.   Virology Journal

A highly abundant bacteriophage discovered in the unknown sequences of human faecal metagenomes

(2014) Bas E. Dutilh et al.   Nature Communications

An introduction to the analysis of shotgun metagenomic data

(2014) Thomas J. Sharpton   Frontiers in Plant Science

Evaluation of rapid and simple techniques for the enrichment of viruses prior to metagenomic virus discovery

(2013) Richard J. Hall et al.   JOURNAL OF VIROLOGICAL METHODS

Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes

(2013) Mads Albertsen et al.   NATURE BIOTECHNOLOGY

The Origin of Biased Sequence Depth in Sequence-Independent Nucleic Acid Amplification and Optimization for Efficient Massive Parallel Sequencing

(2013) Toon Rosseel et al.   PLoS One

A New Method for Extracting Skin Microbes Allows Metagenomic Analysis of Whole-Deep Skin

(2013) Marc Garcia-Garcerà et al.   PLoS One

Pandoraviruses: Amoeba Viruses with Genomes Up to 2.5 Mb Reaching That of Parasitic Eukaryotes

(2013) N. Philippe et al.   SCIENCE

Identification and characterization of a novel adenovirus in the cloacal bursa of gulls

(2013) R. Bodewes et al.   VIROLOGY

Empirical validation of viral quasispecies assembly algorithms: state-of-the-art and challenges

(2013) Mattia C. F. Prosperi et al.   Scientific Reports

Virus discovery: one step beyond

(2013) Saskia L Smits et al.   Current Opinion in Virology

A de novo metagenomic assembly program for shotgun DNA reads

(2012) Binbin Lai et al.   BIOINFORMATICS

Diarrhea Etiology in a Pediatric Emergency Department: A Case Control Study

(2012) Donna M. Denno et al.   CLINICAL INFECTIOUS DISEASES

MetaVelvet: an extension of Velvet assembler to de novo metagenome assembly from short sequence reads

(2012) Toshiaki Namiki et al.   NUCLEIC ACIDS RESEARCH

Assessment of Metagenomic Assembly Using Simulated Next Generation Sequencing Data

(2012) Daniel R. Mende et al.   PLoS One

Novel Bacterial Taxa in the Human Microbiome

(2012) Kristine M. Wylie et al.   PLoS One

Untangling Genomes from Metagenomes: Revealing an Uncultured Class of Marine Euryarchaeota

(2012) V. Iverson et al.   SCIENCE

Performance of VIDISCA-454 in Feces-Suspensions and Serum

(2012) Michel de Vries et al.   Viruses-Basel

A Novel Rhabdovirus Associated with Acute Hemorrhagic Fever in Central Africa

(2012) Gilda Grard et al.   PLoS Pathogens

Meta-IDBA: a de Novo assembler for metagenomic data

(2011) Y. Peng et al.   BIOINFORMATICS

Next generation sequencing and bioinformatic bottlenecks: the current state of metagenomic data analysis

(2011) Matthew B. Scholz et al.   CURRENT OPINION IN BIOTECHNOLOGY

Insights into antibiotic resistance through metagenomic approaches

(2011) Robert Schmieder et al.   Future Microbiology

Genomic analysis identifies association of Fusobacterium with colorectal carcinoma

(2011) A. D. Kostic et al.   GENOME RESEARCH

Genovo: De Novo Assembly for Metagenomes

(2011) Jonathan Laserson et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Metagenomic Analysis of the Viral Flora of Pine Marten and European Badger Feces

(2011) J. M. A. van den Brand et al.   JOURNAL OF VIROLOGY

The Pfam protein families database

(2011) M. Punta et al.   NUCLEIC ACIDS RESEARCH

Evaluating the Fidelity of De Novo Short Read Metagenomic Assembly Using Simulated Data

(2011) Miguel Pignatelli et al.   PLoS One

Human Picobirnaviruses Identified by Molecular Screening of Diarrhea Samples

(2010) M. van Leeuwen et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Microbe Hunting

(2010) W. I. Lipkin   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Suppression subtractive hybridisation allows selective sampling of metagenomic subsets of interest

(2009) Yi Vee Chew et al.   JOURNAL OF MICROBIOLOGICAL METHODS

MEME SUITE: tools for motif discovery and searching

(2009) T. L. Bailey et al.   NUCLEIC ACIDS RESEARCH

Viral genome sequencing by random priming methods

(2008) Appolinaire Djikeng et al.   BMC GENOMICS