MetaFast: fast reference-free graph-based comparison of shotgun metagenomic data

Weakly supervised learning of biomedical information extraction from curated data

(2016) Suvir Jain et al.   BMC BIOINFORMATICS

MaxBin 2.0: an automated binning algorithm to recover genomes from multiple metagenomic datasets

(2015) Yu-Wei Wu et al.   BIOINFORMATICS

Uncovering the novel characteristics of Asian honey bee, Apis cerana, by whole genome sequencing

(2015) Doori Park et al.   BMC GENOMICS

Gut Microbiome Diversity among Cheyenne and Arapaho Individuals from Western Oklahoma

(2015) Krithivasan Sankaranarayanan et al.   CURRENT BIOLOGY

Metagenome Sequencing of the Hadza Hunter-Gatherer Gut Microbiota

(2015) Simone Rampelli et al.   CURRENT BIOLOGY

MetaPhlAn2 for enhanced metagenomic taxonomic profiling

(2015) Duy Tin Truong et al.   NATURE METHODS

The MG-RAST metagenomics database and portal in 2015

(2015) Andreas Wilke et al.   NUCLEIC ACIDS RESEARCH

EBI metagenomics in 2016 - an expanding and evolving resource for the analysis and archiving of metagenomic data

(2015) Alex Mitchell et al.   NUCLEIC ACIDS RESEARCH

Bacterial rose garden for metagenomic SNP-based phylogeny visualization

(2015) Dmitry Alexeev et al.   BioData Mining

Spatial and temporal dynamics of virus occurrence in two freshwater lakes captured through metagenomic analysis

(2015) Mohammad Mohiuddin et al.   Frontiers in Microbiology

Geospatial Resolution of Human and Bacterial Diversity with City-Scale Metagenomics

(2015) Ebrahim Afshinnekoo et al.   Cell Systems

Biodiversity and distribution of polar freshwater DNA viruses

(2015) D. Aguirre de Carcer et al.   Science Advances

Census-based rapid and accurate metagenome taxonomic profiling

(2014) Amirhossein Shamsaddini et al.   BMC GENOMICS

Metagenomes from two microbial consortia associated with Santa Barbara seep oil

(2014) Erik R. Hawley et al.   Marine Genomics

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

(2014) H Bjørn Nielsen et al.   NATURE BIOTECHNOLOGY

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

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

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

Kraken: ultrafast metagenomic sequence classification using exact alignments

(2014) Derrick E Wood et al.   GENOME BIOLOGY

FOCUS: an alignment-free model to identify organisms in metagenomes using non-negative least squares

(2014) Genivaldo Gueiros Z. Silva et al.   PeerJ

New Approaches Indicate Constant Viral Diversity despite Shifts in Assemblage Structure in an Australian Hypersaline Lake

(2013) Joanne B. Emerson et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

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

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

New developments of alignment-free sequence comparison: measures, statistics and next-generation sequencing

(2013) K. Song et al.   BRIEFINGS IN BIOINFORMATICS

A metagenomic snapshot of taxonomic and functional diversity in an alpine glacier cryoconite ecosystem

(2013) Arwyn Edwards et al.   Environmental Research Letters

Human gut microbiota community structures in urban and rural populations in Russia

(2013) Alexander V. Tyakht et al.   Nature Communications

MetAMOS: a modular and open source metagenomic assembly and analysis pipeline

(2013) Todd J Treangen et al.   GENOME BIOLOGY

MetaCluster 5.0: a two-round binning approach for metagenomic data for low-abundance species in a noisy sample

(2012) Y. Wang et al.   BIOINFORMATICS

Reference-independent comparative metagenomics using cross-assembly: crAss

(2012) Bas E. Dutilh et al.   BIOINFORMATICS

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

(2012) Anton Bankevich et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

A metagenome-wide association study of gut microbiota in type 2 diabetes

(2012) Junjie Qin et al.   NATURE

Structure, function and diversity of the healthy human microbiome

(2012)   NATURE

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

(2012) Toshiaki Namiki et al.   NUCLEIC ACIDS RESEARCH

Metagenomics and future perspectives in virus discovery

(2012) John L Mokili et al.   Current Opinion in Virology

Ray Meta: scalable de novo metagenome assembly and profiling

(2012) Sébastien Boisvert et al.   GENOME BIOLOGY

METAGENOMIC TAXONOMIC CLASSIFICATION USING EXTREME LEARNING MACHINES

(2012) ZEEHASHAM RASHEED et al.   Journal of Bioinformatics and Computational Biology

Meta-IDBA: a de Novo assembler for metagenomic data

(2011) Y. Peng et al.   BIOINFORMATICS

A Novel Abundance-Based Algorithm for Binning Metagenomic Sequences Using l-tuples

(2011) Yu-Wei Wu et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

A human gut microbial gene catalogue established by metagenomic sequencing

(2010) Junjie Qin et al.   NATURE

Effect of read-mapping biases on detecting allele-specific expression from RNA-sequencing data

(2009) Jacob F. Degner et al.   BIOINFORMATICS

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

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

MetaSim—A Sequencing Simulator for Genomics and Metagenomics

(2008) Daniel C. Richter et al.   PLoS One