Survey of (Meta)genomic Approaches for Understanding Microbial Community Dynamics

Genome Reconstruction from Metagenomic Data Sets Reveals Novel Microbes in the Brackish Waters of the Caspian Sea

(2016) Maliheh Mehrshad et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Genome-wide selective sweeps and gene-specific sweeps in natural bacterial populations

(2016) Matthew L Bendall et al.   ISME Journal

(Meta)genomic insights into the pathogenome of Cellulosimicrobium cellulans

(2016) Anukriti Sharma et al.   Scientific Reports

Metataxonomic and Metagenomic Approaches vs. Culture-Based Techniques for Clinical Pathology

(2016) Sarah K. Hilton et al.   Frontiers in Microbiology

Metagenomics Reveals Pervasive Bacterial Populations and Reduced Community Diversity across the Alaska Tundra Ecosystem

(2016) Eric R. Johnston et al.   Frontiers in Microbiology

Recovering complete and draft population genomes from metagenome datasets

(2016) Naseer Sangwan et al.   Microbiome

Differential Functional Constraints Cause Strain-Level Endemism in Polynucleobacter Populations

(2016) Naseer Sangwan et al.   mSystems

Pan-genome dynamics of Pseudomonas gene complements enriched across hexachlorocyclohexane dumpsite

(2015) Anukriti Sharma et al.   BMC GENOMICS

Antimicrobial stewardship - can we afford to do without it?

(2015) Anna Aryee et al.   BRITISH JOURNAL OF CLINICAL PHARMACOLOGY

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

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

Dual Transcriptomic Profiling of Host and Microbiota during Health and Disease in Pediatric Asthma

(2015) Marcos Pérez-Losada et al.   PLoS One

Growth dynamics of gut microbiota in health and disease inferred from single metagenomic samples

(2015) T. Korem et al.   SCIENCE

Application of metagenomics in the human gut microbiome

(2015) Wei-Lin Wang et al.   WORLD JOURNAL OF GASTROENTEROLOGY

Arsenic rich Himalayan hot spring metagenomics reveal genetically novel predator-prey genotypes

(2015) Naseer Sangwan et al.   Environmental Microbiology Reports

Genomes of Planktonic Acidimicrobiales : Widening Horizons for Marine Actinobacteria by Metagenomics

(2015) Carolina Megumi Mizuno et al.   mBio

Reconstructing rare soil microbial genomes using in situ enrichments and metagenomics

(2015) Tom O. Delmont et al.   Frontiers in Microbiology

Challenges and opportunities in understanding microbial communities with metagenome assembly (accompanied by IPython Notebook tutorial)

(2015) Adina Howe et al.   Frontiers in Microbiology

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

Faster sequence homology searches by clustering subsequences

(2014) Shuji Suzuki et al.   BIOINFORMATICS

Comparison of different assembly and annotation tools on analysis of simulated viral metagenomic communities in the gut

(2014) Jorge F Vázquez-Castellanos et al.   BMC GENOMICS

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

(2014) H Bjørn Nielsen et al.   NATURE BIOTECHNOLOGY

Binning metagenomic contigs by coverage and composition

(2014) Johannes Alneberg et al.   NATURE METHODS

Explaining microbial genomic diversity in light of evolutionary ecology

(2014) Otto X. Cordero et al.   NATURE REVIEWS MICROBIOLOGY

GHOSTX: An Improved Sequence Homology Search Algorithm Using a Query Suffix Array and a Database Suffix Array

(2014) Shuji Suzuki et al.   PLoS One

Coupling Between Protein Level Selection and Codon Usage Optimization in the Evolution of Bacteria and Archaea

(2014) W. Ran et al.   mBio

Comparative Analyses of Nonpathogenic, Opportunistic, and Totally Pathogenic Mycobacteria Reveal Genomic and Biochemical Variabilities and Highlight the Survival Attributes of Mycobacterium tuberculosis

(2014) Syed Asad Rahman et al.   mBio

Microbial communities evolve faster in extreme environments

(2014) Sheng-Jin Li et al.   Scientific Reports

Kraken: ultrafast metagenomic sequence classification using exact alignments

(2014) Derrick E Wood et al.   GENOME BIOLOGY

Reconstructing an ancestral genotype of two hexachlorocyclohexane-degrading Sphingobium species using metagenomic sequence data

(2013) Naseer Sangwan et al.   ISME Journal

Devosia lucknowensis sp. nov., a bacterium isolated from hexachlorocyclohexane (HCH) contaminated pond soil

(2013) Ankita Dua et al.   JOURNAL OF MICROBIOLOGY

Environmental shaping of codon usage and functional adaptation across microbial communities

(2013) Maša Roller et al.   NUCLEIC ACIDS RESEARCH

Pfam: the protein families database

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

Rapid 16S rRNA Next-Generation Sequencing of Polymicrobial Clinical Samples for Diagnosis of Complex Bacterial Infections

(2013) Stephen J. Salipante et al.   PLoS One

Systematic Identification of Gene Families for Use as “Markers” for Phylogenetic and Phylogeny-Driven Ecological Studies of Bacteria and Archaea and Their Major Subgroups

(2013) Dongying Wu et al.   PLoS One

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

(2013) Todd J Treangen et al.   GENOME BIOLOGY

REAPR: a universal tool for genome assembly evaluation

(2013) Martin Hunt et al.   GENOME BIOLOGY

Should We Standardize the 1,700-Year-Old Fecal Microbiota Transplantation?

(2012) Faming Zhang et al.   AMERICAN JOURNAL OF GASTROENTEROLOGY

Phylogenomic analysis of bacterial and archaeal sequences with AMPHORA2

(2012) Martin Wu et al.   BIOINFORMATICS

Draft Genome Sequence of Thermus sp. Strain RL, Isolated from a Hot Water Spring Located atop the Himalayan Ranges at Manikaran, India

(2012) V. Dwivedi et al.   JOURNAL OF BACTERIOLOGY

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

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

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

Metagenomic microbial community profiling using unique clade-specific marker genes

(2012) Nicola Segata et al.   NATURE METHODS

Transforming clinical microbiology with bacterial genome sequencing

(2012) Xavier Didelot et al.   NATURE REVIEWS GENETICS

Rapid Whole-Genome Sequencing for Investigation of a Neonatal MRSA Outbreak

(2012) Claudio U. Köser et al.   NEW ENGLAND JOURNAL OF MEDICINE

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

(2012) Toshiaki Namiki et al.   NUCLEIC ACIDS RESEARCH

DoriC 5.0: an updated database of oriC regions in both bacterial and archaeal genomes

(2012) Feng Gao et al.   NUCLEIC ACIDS RESEARCH

Assessment of Metagenomic Assembly Using Simulated Next Generation Sequencing Data

(2012) Daniel R. Mende et al.   PLoS One

Comparative Metagenomic Analysis of Soil Microbial Communities across Three Hexachlorocyclohexane Contamination Levels

(2012) Naseer Sangwan et al.   PLoS One

In Situ Evolutionary Rate Measurements Show Ecological Success of Recently Emerged Bacterial Hybrids

(2012) V. J. Denef et al.   SCIENCE

Population Genomics of Early Events in the Ecological Differentiation of Bacteria

(2012) B. J. Shapiro et al.   SCIENCE

The Black Queen Hypothesis: Evolution of Dependencies through Adaptive Gene Loss

(2012) J. J. Morris et al.   mBio

Metagenomes of Mediterranean Coastal Lagoons

(2012) Rohit Ghai et al.   Scientific Reports

Genome-wide identification and characterization of replication origins by deep sequencing

(2012) Jia Xu et al.   GENOME BIOLOGY

Ray Meta: scalable de novo metagenome assembly and profiling

(2012) Sébastien Boisvert et al.   GENOME BIOLOGY

Meta-IDBA: a de Novo assembler for metagenomic data

(2011) Y. Peng et al.   BIOINFORMATICS

FR-HIT, a very fast program to recruit metagenomic reads to homologous reference genomes

(2011) Beifang Niu et al.   BIOINFORMATICS

Pathogen comparative genomics in the next-generation sequencing era: genome alignments, pangenomics and metagenomics

(2011) B. Hu et al.   Briefings in Functional Genomics

Genome-wide detection of chromosomal rearrangements, indels, and mutations in circular chromosomes by short read sequencing

(2011) Ole Skovgaard et al.   GENOME RESEARCH

PhymmBL expanded: confidence scores, custom databases, parallelization and more

(2011) Arthur Brady et al.   NATURE METHODS

Experimental and analytical tools for studying the human microbiome

(2011) Justin Kuczynski et al.   NATURE REVIEWS GENETICS

Origins of theE. coliStrain Causing an Outbreak of Hemolytic–Uremic Syndrome in Germany

(2011) David A. Rasko et al.   NEW ENGLAND JOURNAL OF MEDICINE

Whole-Genome Sequencing and Social-Network Analysis of a Tuberculosis Outbreak

(2011) Jennifer L. Gardy et al.   NEW ENGLAND JOURNAL OF MEDICINE

HMMER web server: interactive sequence similarity searching

(2011) R. D. Finn et al.   NUCLEIC ACIDS RESEARCH

Mining Virulence Genes Using Metagenomics

(2011) Pedro Belda-Ferre et al.   PLoS One

The Human Gut Microbiome: Ecology and Recent Evolutionary Changes

(2010) Jens Walter et al.   Annual Review of Microbiology

NBC: the Naive Bayes Classification tool webserver for taxonomic classification of metagenomic reads

(2010) G. L. Rosen et al.   BIOINFORMATICS

GASSST: global alignment short sequence search tool

(2010) Guillaume Rizk et al.   BIOINFORMATICS

De novo assembly of short sequence reads

(2010) K. Paszkiewicz et al.   BRIEFINGS IN BIOINFORMATICS

Average genome size: a potential source of bias in comparative metagenomics

(2010) Bánk Beszteri et al.   ISME Journal

Metagenomics: Facts and Artifacts, and Computational Challenges

(2010) John C. Wooley et al.   JOURNAL OF COMPUTER SCIENCE AND TECHNOLOGY

Microbial phylogeny and diversity: Small subunit ribosomal RNA sequence analysis and beyond

(2010) J. Rajendhran et al.   MICROBIOLOGICAL RESEARCH

The Origin of the Haitian Cholera Outbreak Strain

(2010) Chen-Shan Chin et al.   NEW ENGLAND JOURNAL OF MEDICINE

The Systemic Imprint of Growth and Its Uses in Ecological (Meta)Genomics

(2010) Sara Vieira-Silva et al.   PLoS Genetics

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

BOAT: Basic Oligonucleotide Alignment Tool

(2009) Shu-Qi Zhao et al.   BMC GENOMICS

Metagenomic islands of hyperhalophiles: the case of Salinibacter ruber

(2009) Lejla Pašić et al.   BMC GENOMICS

Personalized copy number and segmental duplication maps using next-generation sequencing

(2009) Can Alkan et al.   NATURE GENETICS

Do symbiotic bacteria subvert host immunity?

(2009) Lora V. Hooper   NATURE REVIEWS MICROBIOLOGY

Functional Characterization of the Antibiotic Resistance Reservoir in the Human Microflora

(2009) M. O. A. Sommer et al.   SCIENCE

The GAAS Metagenomic Tool and Its Estimations of Viral and Microbial Average Genome Size in Four Major Biomes

(2009) Florent E. Angly et al.   PLoS Computational Biology

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

SOAP: short oligonucleotide alignment program

(2008) R. Li et al.   BIOINFORMATICS

Using quality scores and longer reads improves accuracy of Solexa read mapping

(2008) Andrew D Smith et al.   BMC BIOINFORMATICS

Mapping short DNA sequencing reads and calling variants using mapping quality scores

(2008) H. Li et al.   GENOME RESEARCH

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

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