GRASP: Guided Reference-based Assembly of Short Peptides

Environmental DNA for wildlife biology and biodiversity monitoring

(2014) Kristine Bohmann et al.   TRENDS IN ECOLOGY & EVOLUTION

The role of metagenomics in understanding the human microbiome in health and disease

(2014) Rebeca Martín et al.   Virulence

SPA: a short peptide assembler for metagenomic data

(2013) Youngik Yang et al.   NUCLEIC ACIDS RESEARCH

Pfam: the protein families database

(2013) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

Interactive effects of global climate change and pollution on marine microbes: the way ahead

(2013) Francisco J. R. C. Coelho et al.   Ecology and Evolution

Phylogenomic analysis of bacterial and archaeal sequences with AMPHORA2

(2012) Martin Wu et al.   BIOINFORMATICS

IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth

(2012) Y. Peng et al.   BIOINFORMATICS

Application of metagenomic techniques in mining enzymes from microbial communities for biofuel synthesis

(2012) Mei-Ning Xing et al.   BIOTECHNOLOGY ADVANCES

Next-generation sequencing technologies for environmental DNA research

(2012) SHADI SHOKRALLA et al.   MOLECULAR ECOLOGY

A framework for human microbiome research

(2012)   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

Meta-IDBA: a de Novo assembler for metagenomic data

(2011) Y. Peng et al.   BIOINFORMATICS

RAPSearch: a fast protein similarity search tool for short reads

(2011) Yuzhen Ye et al.   BMC BIOINFORMATICS

Integrative analysis of environmental sequences using MEGAN4

(2011) D. H. Huson et al.   GENOME RESEARCH

A human gut microbial gene catalogue established by metagenomic sequencing

(2010) Junjie Qin et al.   NATURE

FragGeneScan: predicting genes in short and error-prone reads

(2010) Mina Rho et al.   NUCLEIC ACIDS RESEARCH

The JCVI standard operating procedure for annotating prokaryotic metagenomic shotgun sequencing data

(2010) David M. Tanenbaum et al.   Standards in Genomic Sciences

Reduced amino acid alphabets exhibit an improved sensitivity and selectivity in fold assignment

(2009) Eric L. Peterson et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Bioprospecting metagenomes: glycosyl hydrolases for converting biomass

(2009) Luen-Luen Li et al.   Biotechnology for Biofuels

Analysis and comparison of very large metagenomes with fast clustering and functional annotation

(2009) Weizhong Li   BMC BIOINFORMATICS

Plant biomass degradation by gut microbiomes: more of the same or something new?

(2009) Mark Morrison et al.   CURRENT OPINION IN BIOTECHNOLOGY

The NIH Human Microbiome Project

(2009) et al.   GENOME RESEARCH

Next-Generation DNA Sequencing Methods

(2008) Elaine R. Mardis   Annual Review of Genomics and Human Genetics

MetaGeneAnnotator: Detecting Species-Specific Patterns of Ribosomal Binding Site for Precise Gene Prediction in Anonymous Prokaryotic and Phage Genomes

(2008) H. Noguchi et al.   DNA RESEARCH

A high-resolution, nucleosome position map of C. elegans reveals a lack of universal sequence-dictated positioning

(2008) A. Valouev et al.   GENOME RESEARCH