Automated and Accurate Estimation of Gene Family Abundance from Shotgun Metagenomes

Average genome size estimation improves comparative metagenomics and sheds light on the functional ecology of the human microbiome

(2015) Stephen Nayfach et al.   GENOME BIOLOGY

Mucin glycan foraging in the human gut microbiome

(2015) Louise E. Tailford et al.   Frontiers in Genetics

Lambda: the local aligner for massive biological data

(2014) Hannes Hauswedell et al.   BIOINFORMATICS

The Treatment-Naive Microbiome in New-Onset Crohn’s Disease

(2014) Dirk Gevers et al.   Cell Host & Microbe

Characterization of Glycosaminoglycan (GAG) Sulfatases from the Human Gut SymbiontBacteroides thetaiotaomicronReveals the First GAG-specific Bacterial Endosulfatase

(2014) Jonathan E. Ulmer et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

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

(2014) H Bjørn Nielsen et al.   NATURE BIOTECHNOLOGY

Oxidative Stress: An Essential Factor in the Pathogenesis of Gastrointestinal Mucosal Diseases

(2014) Asima Bhattacharyya et al.   PHYSIOLOGICAL REVIEWS

Comparative Analysis of Functional Metagenomic Annotation and the Mappability of Short Reads

(2014) Rogan Carr et al.   PLoS One

An introduction to the analysis of shotgun metagenomic data

(2014) Thomas J. Sharpton   Frontiers in Plant Science

Temporal variability in soil microbial communities across land-use types

(2013) Christian L Lauber et al.   ISME Journal

Does active Crohn's disease have decreased intestinal antioxidant capacity?

(2013) Marco Antonio S. Pinto et al.   Journal of Crohns & Colitis

An Artificial Functional Family Filter in Homolog Searching in Next-generation Sequencing Metagenomics

(2013) Ruofei Du et al.   PLoS One

Reconstructing the Microbial Diversity and Function of Pre-Agricultural Tallgrass Prairie Soils in the United States

(2013) N. Fierer et al.   SCIENCE

Microbiota of De-Novo Pediatric IBD: Increased Faecalibacterium Prausnitzii and Reduced Bacterial Diversity in Crohn's But Not in Ulcerative Colitis

(2012) Richard Hansen et al.   AMERICAN JOURNAL OF GASTROENTEROLOGY

Gene and translation initiation site prediction in metagenomic sequences

(2012) Doug Hyatt et al.   BIOINFORMATICS

Short-read reading-frame predictors are not created equal: sequence error causes loss of signal

(2012) William L Trimble et al.   BMC BIOINFORMATICS

Sifting through genomes with iterative-sequence clustering produces a large, phylogenetically diverse protein-family resource

(2012) Thomas J Sharpton et al.   BMC BIOINFORMATICS

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

Stochastic and deterministic assembly processes in subsurface microbial communities

(2012) James C Stegen et al.   ISME Journal

A framework for human microbiome research

(2012)   NATURE

Structure, function and diversity of the healthy human microbiome

(2012)   NATURE

Genomic variation landscape of the human gut microbiome

(2012) Siegfried Schloissnig et al.   NATURE

Grinder: a versatile amplicon and shotgun sequence simulator

(2012) Florent E. Angly 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

Metabolic Reconstruction for Metagenomic Data and Its Application to the Human Microbiome

(2012) Sahar Abubucker et al.   PLoS Computational Biology

Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment

(2012) Xochitl C Morgan et al.   GENOME BIOLOGY

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

(2011) Y. Zhao et al.   BIOINFORMATICS

CloVR: A virtual machine for automated and portable sequence analysis from the desktop using cloud computing

(2011) Samuel V Angiuoli et al.   BMC BIOINFORMATICS

Accurate and fast estimation of taxonomic profiles from metagenomic shotgun sequences

(2011) Bo Liu et al.   BMC GENOMICS

Twin Study Indicates Loss of Interaction Between Microbiota and Mucosa of Patients With Ulcerative Colitis

(2011) Patricia Lepage et al.   GASTROENTEROLOGY

Illumina-based analysis of microbial community diversity

(2011) Patrick H Degnan et al.   ISME Journal

Sulfatases and a RadicalS-Adenosyl-l-methionine (AdoMet) Enzyme Are Key for Mucosal Foraging and Fitness of the Prominent Human Gut Symbiont,Bacteroides thetaiotaomicron

(2011) Alhosna Benjdia et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

IMG/M: the integrated metagenome data management and comparative analysis system

(2011) V. M. Markowitz et al.   NUCLEIC ACIDS RESEARCH

Accelerated Profile HMM Searches

(2011) Sean R. Eddy   PLoS Computational Biology

Mucolytic Bacteria With Increased Prevalence in IBD Mucosa Augment In Vitro Utilization of Mucin by Other Bacteria

(2010) Chin Wen Png et al.   AMERICAN JOURNAL OF GASTROENTEROLOGY

SmashCommunity: a metagenomic annotation and analysis tool: Fig. 1.

(2010) Manimozhiyan Arumugam et al.   BIOINFORMATICS

Serum vitamin B12 and folate status in patients with inflammatory bowel diseases

(2010) Mustafa Yakut et al.   European Journal of Internal Medicine

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 Taxonomic and Functional Diversity of Microbes at a Temperate Coastal Site: A ‘Multi-Omic’ Study of Seasonal and Diel Temporal Variation

(2010) Jack A. Gilbert et al.   PLoS One

ShotgunFunctionalizeR: an R-package for functional comparison of metagenomes

(2009) Erik Kristiansson et al.   BIOINFORMATICS

IMG ER: a system for microbial genome annotation expert review and curation

(2009) Victor M. Markowitz et al.   BIOINFORMATICS

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

(2009) Weizhong Li   BMC BIOINFORMATICS

Lipopolysaccharide exposure is linked to activation of the acute phase response and growth failure in pediatric Crohnʼs disease and murine colitis

(2009) Brad A. Pasternak et al.   INFLAMMATORY BOWEL DISEASES

MicrobesOnline: an integrated portal for comparative and functional genomics

(2009) P. S. Dehal et al.   NUCLEIC ACIDS RESEARCH

FIGfams: yet another set of protein families

(2009) Folker Meyer et al.   NUCLEIC ACIDS RESEARCH

Origin of an Alternative Genetic Code in the Extremely Small and GC–Rich Genome of a Bacterial Symbiont

(2009) John P. McCutcheon et al.   PLoS Genetics

Metagenomics: Read Length Matters

(2008) K. E. Wommack et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

The metagenomics RAST server – a public resource for the automatic phylogenetic and functional analysis of metagenomes

(2008) F Meyer et al.   BMC BIOINFORMATICS

Altered status of antioxidant vitamins and fatty acids in patients with inactive inflammatory bowel disease

(2008) Susanne Hengstermann et al.   CLINICAL NUTRITION

LPS/TLR4 signal transduction pathway

(2008) Yong-Chen Lu et al.   CYTOKINE

Hyperhomocysteinemia in Inflammatory Bowel Disease Patients Without Past Intestinal Resections

(2008) Yusuf Erzin et al.   JOURNAL OF CLINICAL GASTROENTEROLOGY