A Graph-Centric Approach for Metagenome-Guided Peptide and Protein Identification in Metaproteomics

An assessment of US microbiome research

(2016) Elizabeth Stulberg et al.   Nature Microbiology

Utilizing de Bruijn graph of metagenome assembly for metatranscriptome analysis

(2015) Yuzhen Ye et al.   BIOINFORMATICS

MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph

(2015) Dinghua Li et al.   BIOINFORMATICS

PathVisio 3: An Extendable Pathway Analysis Toolbox

(2015) Martina Kutmon et al.   PLoS Computational Biology

SOAPdenovo-Trans: de novo transcriptome assembly with short RNA-Seq reads

(2014) Y. Xie et al.   BIOINFORMATICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Metatranscriptomics of the Human Oral Microbiome during Health and Disease

(2014) P. Jorth et al.   mBio

Community-integrated omics links dominance of a microbial generalist to fine-tuned resource usage

(2014) Emilie E. L. Muller et al.   Nature Communications

MS-GF+ makes progress towards a universal database search tool for proteomics

(2014) Sangtae Kim et al.   Nature Communications

Omics approaches to study host–microbiota interactions

(2013) Peter van Baarlen et al.   CURRENT OPINION IN MICROBIOLOGY

Metaproteomics of cellulose methanisation under thermophilic conditions reveals a surprisingly high proteolytic activity

(2013) Fan Lü et al.   ISME Journal

Computational meta'omics for microbial community studies

(2013) N. Segata et al.   Molecular Systems Biology

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

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

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

(2012) Toshiaki Namiki et al.   NUCLEIC ACIDS RESEARCH

Integrated Metagenomics/Metaproteomics Reveals Human Host-Microbiota Signatures of Crohn's Disease

(2012) Alison R. Erickson et al.   PLoS One

Cross-biome metagenomic analyses of soil microbial communities and their functional attributes

(2012) N. Fierer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Efficient and robust RNA-seq process for cultured bacteria and complex community transcriptomes

(2012) Georgia Giannoukos et al.   GENOME BIOLOGY

SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler

(2012) Ruibang Luo et al.   GigaScience

Meta-IDBA: a de Novo assembler for metagenomic data

(2011) Y. Peng et al.   BIOINFORMATICS

RAPSearch2: a fast and memory-efficient protein similarity search tool for next-generation sequencing data

(2011) Y. Zhao et al.   BIOINFORMATICS

Omics for understanding microbial functional dynamics

(2011) Janet K. Jansson et al.   ENVIRONMENTAL MICROBIOLOGY

Microbial metatranscriptomics in a permanent marine oxygen minimum zone

(2011) Frank J. Stewart et al.   ENVIRONMENTAL MICROBIOLOGY

Comparative metagenomic, phylogenetic and physiological analyses of soil microbial communities across nitrogen gradients

(2011) Noah Fierer et al.   ISME Journal

How to apply de Bruijn graphs to genome assembly

(2011) Phillip E C Compeau et al.   NATURE BIOTECHNOLOGY

eggNOG v3.0: orthologous groups covering 1133 organisms at 41 different taxonomic ranges

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

Metagenomics of the intestinal microbiota: potential applications

(2010) S. Dusko Ehrlich   GASTROENTEROLOGIE CLINIQUE ET BIOLOGIQUE

Comparative metaproteomics reveals ocean-scale shifts in microbial nutrient utilization and energy transduction

(2010) Robert M Morris et al.   ISME Journal

A human gut microbial gene catalogue established by metagenomic sequencing

(2010) Junjie Qin et al.   NATURE

Ab initio gene identification in metagenomic sequences

(2010) Wenhan Zhu et al.   NUCLEIC ACIDS RESEARCH

FragGeneScan: predicting genes in short and error-prone reads

(2010) Mina Rho et al.   NUCLEIC ACIDS RESEARCH

The NIH Human Microbiome Project

(2009) et al.   GENOME RESEARCH

Metatranscriptomics reveals unique microbial small RNAs in the ocean’s water column

(2009) Yanmei Shi et al.   NATURE

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

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

Shotgun metaproteomics of the human distal gut microbiota

(2008) Nathan C Verberkmoes et al.   ISME Journal

Abundance and diversity of microbial life in ocean crust

(2008) Cara M. Santelli et al.   NATURE

Metaproteomics Provides Functional Insight into Activated Sludge Wastewater Treatment

(2008) Paul Wilmes et al.   PLoS One