A genome-phenome association study in native microbiomes identifies a mechanism for cytosine modification in DNA and RNA

Nondestructive enzymatic deamination enables single-molecule long-read amplicon sequencing for the determination of 5-methylcytosine and 5-hydroxymethylcytosine at single-base resolution

(2021) Zhiyi Sun et al.   GENOME RESEARCH

Metaepigenomic analysis reveals the unexplored diversity of DNA methylation in an environmental prokaryotic community

(2019) Satoshi Hiraoka et al.   Nature Communications

Clinical metagenomics

(2019) Charles Y. Chiu et al.   NATURE REVIEWS GENETICS

Scientists’ warning to humanity: microorganisms and climate change

(2019) Ricardo Cavicchioli et al.   NATURE REVIEWS MICROBIOLOGY

7-Deazaguanine modifications protect phage DNA from host restriction systems

(2019) Geoffrey Hutinet et al.   Nature Communications

Identification and biosynthesis of thymidine hypermodifications in the genomic DNA of widespread bacterial viruses

(2018) Yan-Jiun Lee et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A phylogenetic method to perform genome-wide association studies in microbes that accounts for population structure and recombination

(2018) Caitlin Collins et al.   PLoS Computational Biology

The Pfam protein families database in 2019

(2018) Sara El-Gebali et al.   NUCLEIC ACIDS RESEARCH

metaSPAdes: a new versatile metagenomic assembler

(2017) Sergey Nurk et al.   GENOME RESEARCH

Shotgun metagenomics, from sampling to analysis

(2017) Christopher Quince et al.   NATURE BIOTECHNOLOGY

A Review on the Applications of Next Generation Sequencing Technologies as Applied to Food-Related Microbiome Studies

(2017) Yu Cao et al.   Frontiers in Microbiology

Toward Accurate and Quantitative Comparative Metagenomics

(2016) Stephen Nayfach et al.   CELL

Biosynthesis and Function of Modified Bases in Bacteria and Their Viruses

(2016) Peter Weigele et al.   CHEMICAL REVIEWS

cooccur: Probabilistic Species Co-Occurrence Analysis inR

(2016) Daniel M. Griffith et al.   Journal of Statistical Software

Structure and function of the global ocean microbiome

(2015) S. Sunagawa et al.   SCIENCE

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

Specialized Metabolites from the Microbiome in Health and Disease

(2014) Gil Sharon et al.   Cell Metabolism

Large-Scale Metagenomic-Based Study of Antibiotic Resistance in the Environment

(2014) Joseph Nesme et al.   CURRENT BIOLOGY

Metagenomic small molecule discovery methods

(2014) Zachary Charlop-Powers et al.   CURRENT OPINION IN MICROBIOLOGY

Predicting the virulence of MRSA from its genome sequence

(2014) M. Laabei et al.   GENOME RESEARCH

Comprehensive Identification of Single Nucleotide Polymorphisms Associated with Beta-lactam Resistance within Pneumococcal Mosaic Genes

(2014) Claire Chewapreecha et al.   PLoS Genetics

An introduction to the analysis of shotgun metagenomic data

(2014) Thomas J. Sharpton   Frontiers in Plant Science

Computational identification of novel biochemical systems involved in oxidation, glycosylation and other complex modifications of bases in DNA

(2013) Lakshminarayan M. Iyer et al.   NUCLEIC ACIDS RESEARCH

Genome-wide association study identifies vitamin B5 biosynthesis as a host specificity factor in Campylobacter

(2013) S. K. Sheppard et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Metagenome-wide analysis of antibiotic resistance genes in a large cohort of human gut microbiota

(2013) Yongfei Hu et al.   Nature Communications

TheO-Carbamoyltransferase TobZ Catalyzes an Ancient Enzymatic Reaction

(2012) Christoph Parthier et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

CD-HIT: accelerated for clustering the next-generation sequencing data

(2012) Limin Fu et al.   BIOINFORMATICS

Methylcytosine and Normal Cytosine Deamination by the Foreign DNA Restriction Enzyme APOBEC3A

(2012) Michael A. Carpenter et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Efficient deamination of 5-methylcytosines in DNA by human APOBEC3A, but not by AID or APOBEC3G

(2012) Priyanga Wijesinghe et al.   NUCLEIC ACIDS RESEARCH

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

(2011) Guillaume Marçais et al.   BIOINFORMATICS

Metagenomic Discovery of Biomass-Degrading Genes and Genomes from Cow Rumen

(2011) M. Hess et al.   SCIENCE

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Methods for comparative metagenomics

(2009) Daniel H Huson et al.   BMC BIOINFORMATICS

Genetic Editing of HBV DNA by Monodomain Human APOBEC3 Cytidine Deaminases and the Recombinant Nature of APOBEC3G

(2009) Michel Henry et al.   PLoS One