Assessment of k-mer spectrum applicability for metagenomic dissimilarity analysis

Quality control of microbiota metagenomics by k-mer analysis

(2015) Florian Plaza Onate et al.   BMC GENOMICS

Extensive Strain-Level Copy-Number Variation across Human Gut Microbiome Species

(2015) Sharon Greenblum et al.   CELL

Structure and function of the global ocean microbiome

(2015) S. Sunagawa et al.   SCIENCE

Insights into the pan-microbiome: skin microbial communities of Chinese individuals differ from other racial groups

(2015) Marcus H. Y. Leung et al.   Scientific Reports

Inter-individual differences in the gene content of human gut bacterial species

(2015) Ana Zhu et al.   GENOME BIOLOGY

KAnalyze: a fast versatile pipelined K-mer toolkit

(2014) Peter Audano et al.   BIOINFORMATICS

Exploration and retrieval of whole-metagenome sequencing samples

(2014) Sohan Seth et al.   BIOINFORMATICS

AKE - the Accelerated k-mer Exploration web-tool for rapid taxonomic classification and visualization

(2014) Daniel Langenkämper et al.   BMC BIOINFORMATICS

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

(2014) H Bjørn Nielsen et al.   NATURE BIOTECHNOLOGY

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

Comparison of Metatranscriptomic Samples Based on k-Tuple Frequencies

(2014) Ying Wang et al.   PLoS One

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

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

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

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

Scalable metagenomic taxonomy classification using a reference genome database

(2013) Sasha K. Ames et al.   BIOINFORMATICS

Alignment-free supervised classification of metagenomes by recursive SVM

(2013) Hongfei Cui et al.   BMC GENOMICS

A New Unsupervised Binning Approach for Metagenomic Sequences Based on N-grams and Automatic Feature Weighting

(2013) Ruiqi Liao et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Antibiotic treatment expands the resistance reservoir and ecological network of the phage metagenome

(2013) Sheetal R. Modi et al.   NATURE

Resolving Prokaryotic Taxonomy without rRNA: Longer Oligonucleotide Word Lengths Improve Genome and Metagenome Taxonomic Classification

(2013) Eric B. Alsop et al.   PLoS One

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

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

Comparison of metagenomic samples using sequence signatures

(2012) Bai Jiang et al.   BMC GENOMICS

Current opportunities and challenges in microbial metagenome analysis--a bioinformatic perspective

(2012) H. Teeling et al.   BRIEFINGS IN BIOINFORMATICS

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

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

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Biodiversity and functional genomics in the human microbiome

(2012) Xochitl C. Morgan et al.   TRENDS IN GENETICS

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

(2011) Guillaume Marçais et al.   BIOINFORMATICS

Next generation sequencing and bioinformatic bottlenecks: the current state of metagenomic data analysis

(2011) Matthew B. Scholz et al.   CURRENT OPINION IN BIOTECHNOLOGY

The human gut virome: Inter-individual variation and dynamic response to diet

(2011) S. Minot 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

Metagenomic Analysis of the Viral Communities in Fermented Foods

(2010) Eun-Jin Park et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

UniFrac: an effective distance metric for microbial community comparison

(2010) Catherine Lozupone et al.   ISME Journal

Viruses in the faecal microbiota of monozygotic twins and their mothers

(2010) Alejandro Reyes et al.   NATURE

A human gut microbial gene catalogue established by metagenomic sequencing

(2010) Junjie Qin et al.   NATURE

Genomic DNA k-mer spectra: models and modalities

(2009) Benny Chor et al.   GENOME BIOLOGY

Community-wide analysis of microbial genome sequence signatures

(2009) Gregory J Dick et al.   GENOME BIOLOGY

Metagenomics in animal gastrointestinal ecosystem: Potential biotechnological prospects

(2008) Birbal Singh et al.   ANAEROBE

Barcodes for genomes and applications

(2008) Fengfeng Zhou et al.   BMC BIOINFORMATICS

MetaSim—A Sequencing Simulator for Genomics and Metagenomics

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