GUTSS: An Alignment-Free Sequence Comparison Method for Use in Human Intestinal Microbiome and Fecal Microbiota Transplantation Analysis

Alignment-free methods for metagenomic profiling

(2015) Shanshan Gao et al.   BMC BIOINFORMATICS

Dynamics and Stabilization of the Human Gut Microbiome during the First Year of Life

(2015) Fredrik Bäckhed et al.   Cell Host & Microbe

Fecal Microbiota Transplantation Induces Remission in Patients With Active Ulcerative Colitis in a Randomized Controlled Trial

(2015) Paul Moayyedi et al.   GASTROENTEROLOGY

Fecal Microbial Transplant Effect on Clinical Outcomes and Fecal Microbiome in Active Crohnʼs Disease

(2015) David L. Suskind et al.   INFLAMMATORY BOWEL DISEASES

Accurate read-based metagenome characterization using a hierarchical suite of unique signatures

(2015) Tracey Allen K. Freitas et al.   NUCLEIC ACIDS RESEARCH

Variable alterations of the microbiota, without metabolic or immunological change, following faecal microbiota transplantation in patients with chronic pouchitis

(2015) J. Landy et al.   Scientific Reports

Dynamic changes in short- and long-term bacterial composition following fecal microbiota transplantation for recurrent Clostridium difficile infection

(2015) Alexa Weingarden et al.   Microbiome

Accurate genome relative abundance estimation for closely related species in a metagenomic sample

(2014) Michael B Sohn et al.   BMC BIOINFORMATICS

Fecal Microbiota Transplant for Relapsing Clostridium difficile Infection Using a Frozen Inoculum From Unrelated Donors: A Randomized, Open-Label, Controlled Pilot Study

(2014) Ilan Youngster et al.   CLINICAL INFECTIOUS DISEASES

Recovery of the Gut Microbiome following Fecal Microbiota Transplantation

(2014) A. M. Seekatz et al.   mBio

Temporal Bacterial Community Dynamics Vary Among Ulcerative Colitis Patients After Fecal Microbiota Transplantation

(2013) Sieglinde Angelberger et al.   AMERICAN JOURNAL OF GASTROENTEROLOGY

Compression-based distance (CBD): a simple, rapid, and accurate method for microbiota composition comparison

(2013) Fang Yang et al.   BMC BIOINFORMATICS

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

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

Escherichia coli Dysbiosis Correlates With Gastrointestinal Dysfunction in Children With Cystic Fibrosis

(2013) Lucas R. Hoffman et al.   CLINICAL INFECTIOUS DISEASES

Meta-analyses of studies of the human microbiota

(2013) C. A. Lozupone et al.   GENOME RESEARCH

Alteration of Intestinal Dysbiosis by Fecal Microbiota Transplantation Does not Induce Remission in Patients with Chronic Active Ulcerative Colitis

(2013) Patrizia K. Kump et al.   INFLAMMATORY BOWEL DISEASES

High throughput sequencing methods and analysis for microbiome research

(2013) Julia M. Di Bella et al.   JOURNAL OF MICROBIOLOGICAL METHODS

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

(2013) Mads Albertsen et al.   NATURE BIOTECHNOLOGY

Microbiota Dynamics in Patients Treated with Fecal Microbiota Transplantation for Recurrent Clostridium difficile Infection

(2013) Yang Song et al.   PLoS One

Reconstructing the Genomic Content of Microbiome Taxa through Shotgun Metagenomic Deconvolution

(2013) Rogan Carr et al.   PLoS Computational Biology

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

(2013) Todd J Treangen et al.   GENOME BIOLOGY

Stool substitute transplant therapy for the eradication of Clostridium difficile infection: ‘RePOOPulating’ the gut

(2013) Elaine O Petrof et al.   Microbiome

The Microbiome and Inflammatory Bowel Disease: Is There a Therapeutic Role for Fecal Microbiota Transplantation?

(2012) Christopher J Damman et al.   AMERICAN JOURNAL OF GASTROENTEROLOGY

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

Compareads: comparing huge metagenomic experiments

(2012) Nicolas Maillet et al.   BMC BIOINFORMATICS

Time series community genomics analysis reveals rapid shifts in bacterial species, strains, and phage during infant gut colonization

(2012) I. Sharon et al.   GENOME RESEARCH

MetaCluster 4.0: A Novel Binning Algorithm for NGS Reads and Huge Number of Species

(2012) Yi Wang et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

A framework for human microbiome research

(2012)   NATURE

Genomic variation landscape of the human gut microbiome

(2012) Siegfried Schloissnig et al.   NATURE

Metagenomic microbial community profiling using unique clade-specific marker genes

(2012) Nicola Segata et al.   NATURE METHODS

Metagenomic abundance estimation and diagnostic testing on species level

(2012) Martin S. Lindner et al.   NUCLEIC ACIDS RESEARCH

Optimizing Read Mapping to Reference Genomes to Determine Composition and Species Prevalence in Microbial Communities

(2012) John Martin et al.   PLoS One

A Statistical Framework for Accurate Taxonomic Assignment of Metagenomic Sequencing Reads

(2012) Hongmei Jiang et al.   PLoS One

Joint Analysis of Multiple Metagenomic Samples

(2012) Yael Baran et al.   PLoS Computational Biology

Chapter 12: Human Microbiome Analysis

(2012) Xochitl C. Morgan et al.   PLoS Computational Biology

Targeted Restoration of the Intestinal Microbiota with a Simple, Defined Bacteriotherapy Resolves Relapsing Clostridium difficile Disease in Mice

(2012) Trevor D. Lawley et al.   PLoS Pathogens

A fast, lock-free approach for efficient parallel counting of occurrences of k-mers

(2011) Guillaume Marçais et al.   BIOINFORMATICS

Accurate and fast estimation of taxonomic profiles from metagenomic shotgun sequences

(2011) Bo Liu et al.   BMC GENOMICS

Integrative analysis of environmental sequences using MEGAN4

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

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

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

A non-negative matrix factorization framework for identifying modular patterns in metagenomic profile data

(2011) Xingpeng Jiang et al.   JOURNAL OF MATHEMATICAL BIOLOGY

Fecal microbiota transplantation and emerging applications

(2011) Thomas J. Borody et al.   Nature Reviews Gastroenterology & Hepatology

MTR: taxonomic annotation of short metagenomic reads using clustering at multiple taxonomic ranks

(2010) Fabio Gori et al.   BIOINFORMATICS

A Pyrosequencing Study in Twins Shows That Gastrointestinal Microbial Profiles Vary With Inflammatory Bowel Disease Phenotypes

(2010) Ben P. Willing et al.   GASTROENTEROLOGY

Alignment-Free Sequence Comparison (II): Theoretical Power of Comparison Statistics

(2010) Lin Wan et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

A human gut microbial gene catalogue established by metagenomic sequencing

(2010) Junjie Qin et al.   NATURE

Misidentification of the Bray-Curtis similarity index

(2008) PM Yoshioka   MARINE ECOLOGY PROGRESS SERIES

A core gut microbiome in obese and lean twins

(2008) Peter J. Turnbaugh et al.   NATURE