Necrotizing enterocolitis is preceded by increased gut bacterial replication, Klebsiella, and fimbriae-encoding bacteria

Metagenomic engineering of the mammalian gut microbiome in situ

(2019) Carlotta Ronda et al.   NATURE METHODS

Genome-resolved metagenomics of eukaryotic populations during early colonization of premature infants and in hospital rooms

(2019) Matthew R. Olm et al.   Microbiome

Identification of a Botulinum Neurotoxin-like Toxin in a Commensal Strain of Enterococcus faecium

(2018) Sicai Zhang et al.   Cell Host & Microbe

Recovery of genomes from metagenomes via a dereplication, aggregation and scoring strategy

(2018) Christian M. K. Sieber et al.   Nature Microbiology

Machine Learning Leveraging Genomes from Metagenomes Identifies Influential Antibiotic Resistance Genes in the Infant Gut Microbiome

(2018) Sumayah F. Rahman et al.   mSystems

The Pfam protein families database in 2019

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

dRep: a tool for fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication

(2017) Matthew R Olm et al.   ISME Journal

MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets

(2017) Martin Steinegger et al.   NATURE BIOTECHNOLOGY

Strain-resolved analysis of hospital rooms and infants reveals overlap between the human and room microbiome

(2017) Brandon Brooks et al.   Nature Communications

VirFinder: a novel k-mer based tool for identifying viral sequences from assembled metagenomic data

(2017) Jie Ren et al.   Microbiome

Intestinal dysbiosis in preterm infants preceding necrotizing enterocolitis: a systematic review and meta-analysis

(2017) Mohan Pammi et al.   Microbiome

ViromeScan: a new tool for metagenomic viral community profiling

(2016) Simone Rampelli et al.   BMC GENOMICS

Functional interactions of archaea, bacteria and viruses in a hypersaline endolithic community

(2016) Alexander Crits-Christoph et al.   ENVIRONMENTAL MICROBIOLOGY

Evidence for persistent and shared bacterial strains against a background of largely unique gut colonization in hospitalized premature infants

(2016) Tali Raveh-Sadka et al.   ISME Journal

Measurement of bacterial replication rates in microbial communities

(2016) Christopher T Brown et al.   NATURE BIOTECHNOLOGY

Antibiotics, birth mode, and diet shape microbiome maturation during early life

(2016) Nicholas A. Bokulich et al.   Science Translational Medicine

Metagenomic Sequencing with Strain-Level Resolution Implicates Uropathogenic E. coli in Necrotizing Enterocolitis and Mortality in Preterm Infants

(2016) Doyle V. Ward et al.   Cell Reports

MaxBin 2.0: an automated binning algorithm to recover genomes from multiple metagenomic datasets

(2015) Yu-Wei Wu et al.   BIOINFORMATICS

antiSMASH 3.0—a comprehensive resource for the genome mining of biosynthetic gene clusters

(2015) Tilmann Weber et al.   NUCLEIC ACIDS RESEARCH

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

(2015) T. Korem et al.   SCIENCE

The role of quorum sensing in Escherichia coli (ETEC) virulence factors

(2015) Régis Tuchtenhagen Sturbelle et al.   VETERINARY MICROBIOLOGY

Gut bacteria are rarely shared by co-hospitalized premature infants, regardless of necrotizing enterocolitis development

(2015) Tali Raveh-Sadka et al.   eLife

VirSorter: mining viral signal from microbial genomic data

(2015) Simon Roux et al.   PeerJ

IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

(2014) Lam-Tung Nguyen et al.   MOLECULAR BIOLOGY AND EVOLUTION

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

Binning metagenomic contigs by coverage and composition

(2014) Johannes Alneberg et al.   NATURE METHODS

Profile Hidden Markov Models for the Detection of Viruses within Metagenomic Sequence Data

(2014) Peter Skewes-Cox et al.   PLoS One

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Bacterial Quorum Sensing: Its Role in Virulence and Possibilities for Its Control

(2013) S. T. Rutherford et al.   Cold Spring Harbor Perspectives in Medicine

Early microbial and metabolomic signatures predict later onset of necrotizing enterocolitis in preterm infants

(2013) Ardythe L Morrow et al.   Microbiome

IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth

(2012) Y. Peng et al.   BIOINFORMATICS

Ribosomally synthesized and post-translationally modified peptide natural products: overview and recommendations for a universal nomenclature

(2012) Paul G. Arnison et al.   NATURAL PRODUCT REPORTS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Gamma-Butyrolactone Regulatory System of Streptomyces chattanoogensis Links Nutrient Utilization, Metabolism, and Development

(2011) Yi-Ling Du et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

BIGSdb: Scalable analysis of bacterial genome variation at the population level

(2011) Keith A Jolley et al.   BMC BIOINFORMATICS

Necrotizing Enterocolitis

(2011) Josef Neu et al.   NEW ENGLAND JOURNAL OF MEDICINE

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

New Insights Into the Pathogenesis and Treatment of Necrotizing Enterocolitis: Toll-Like Receptors and Beyond

(2010) Amin Afrazi et al.   PEDIATRIC RESEARCH

Redefining the Role of Intestinal Microbes in the Pathogenesis of Necrotizing Enterocolitis

(2010) M. J. Morowitz et al.   PEDIATRICS

Strain-resolved community genomic analysis of gut microbial colonization in a premature infant

(2010) M. J. Morowitz et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Isolation of a Variant of Subtilosin A with Hemolytic Activity

(2009) T. Huang et al.   JOURNAL OF BACTERIOLOGY

FastTree: Computing Large Minimum Evolution Trees with Profiles instead of a Distance Matrix

(2009) M. N. Price et al.   MOLECULAR BIOLOGY AND EVOLUTION

Necrotizing Enterocolitis – 150 Years of Fruitless Search for the Cause

(2009) Michael Obladen   Neonatology

Origins and virulence mechanisms of uropathogenic Escherichia coli

(2008) Travis J. Wiles et al.   EXPERIMENTAL AND MOLECULAR PATHOLOGY