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

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

Identification of a d-Arabinose-5-Phosphate Isomerase in the Gram-Positive Clostridium tetani

(2017) David L. Cech et al.   JOURNAL OF BACTERIOLOGY

Maturation of the infant microbiome community structure and function across multiple body sites and in relation to mode of delivery

(2017) Derrick M Chu et al.   NATURE MEDICINE

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

(2017) Brandon Brooks et al.   Nature Communications

Cesarean or Vaginal Birth Does Not Impact the Longitudinal Development of the Gut Microbiome in a Cohort of Exclusively Preterm Infants

(2017) Christopher J. Stewart et al.   Frontiers in Microbiology

Colonization and Succession within the Human Gut Microbiome by Archaea, Bacteria, and Microeukaryotes during the First Year of Life

(2017) Linda Wampach et al.   Frontiers in 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

Natural history of the infant gut microbiome and impact of antibiotic treatment on bacterial strain diversity and stability

(2016) Moran Yassour et al.   Science Translational Medicine

The effects of antibiotics on the microbiome throughout development and alternative approaches for therapeutic modulation

(2016) Amy Langdon et al.   Genome Medicine

Developmental dynamics of the preterm infant gut microbiota and antibiotic resistome

(2016) Molly K. Gibson et al.   Nature Microbiology

Gut Microbiome Developmental Patterns in Early Life of Preterm Infants: Impacts of Feeding and Gender

(2016) Xiaomei Cong et al.   PLoS One

Outcomes for Extremely Premature Infants

(2015) Hannah C. Glass et al.   ANESTHESIA AND ANALGESIA

Intestinal Microbiota Development in Preterm Neonates and Effect of Perinatal Antibiotics

(2015) Silvia Arboleya et al.   JOURNAL OF PEDIATRICS

Temporal and spatial variation of the human microbiota during pregnancy

(2015) Daniel B. DiGiulio et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2015) Tali Raveh-Sadka et al.   eLife

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

Stress responses as determinants of antimicrobial resistance in Pseudomonas aeruginosa: multidrug efflux and more

(2014) Keith Poole   CANADIAN JOURNAL OF MICROBIOLOGY

Improved annotation of antibiotic resistance determinants reveals microbial resistomes cluster by ecology

(2014) Molly K Gibson et al.   ISME Journal

Antibiotics and the gut microbiota

(2014) Sheetal R. Modi et al.   JOURNAL OF CLINICAL INVESTIGATION

Early Empiric Antibiotic Use in Preterm Infants Is Associated with Lower Bacterial Diversity and Higher Relative Abundance of Enterobacter

(2014) Corryn Greenwood et al.   JOURNAL OF PEDIATRICS

Binning metagenomic contigs by coverage and composition

(2014) Johannes Alneberg et al.   NATURE METHODS

Maternal intrapartum antibiotics and decreased vertical transmission ofLactobacillusto neonates during birth

(2013) Leea Keski-Nisula et al.   ACTA PAEDIATRICA

PERMANOVA, ANOSIM, and the Mantel test in the face of heterogeneous dispersions: What null hypothesis are you testing?

(2013) Marti J. Anderson et al.   ECOLOGICAL MONOGRAPHS

The Long-Term Stability of the Human Gut Microbiota

(2013) J. J. Faith et al.   SCIENCE

Multi-class AdaBoost

(2013) Trevor Hastie et al.   Statistics and Its Interface

The human microbiome as a reservoir of antimicrobial resistance

(2013) John Penders et al.   Frontiers in Microbiology

High-Throughput Sequencing Reveals the Incomplete, Short-Term Recovery of Infant Gut Microbiota following Parenteral Antibiotic Treatment with Ampicillin and Gentamicin

(2012) Fiona Fouhy et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

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

(2012) Y. Peng et al.   BIOINFORMATICS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

The Application of Ecological Theory Toward an Understanding of the Human Microbiome

(2012) E. K. Costello et al.   SCIENCE

Comparative Genomics of Klebsiella pneumoniae Strains with Different Antibiotic Resistance Profiles

(2011) Vinod Kumar et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

HMMER web server: interactive sequence similarity searching

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

The Class D β-lactamase family: residues governing the maintenance and diversity of function

(2011) Agnieszka Szarecka et al.   PROTEIN ENGINEERING DESIGN & SELECTION

Pan-genome sequence analysis using Panseq: an online tool for the rapid analysis of core and accessory genomic regions

(2010) Chad Laing et al.   BMC BIOINFORMATICS

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

VanA-Type Vancomycin-Resistant Staphylococcus aureus

(2009) B. Perichon et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Efflux-Mediated Drug Resistance in Bacteria

(2009) Xian-Zhi Li et al.   DRUGS

Influence of antibiotic exposure in the early postnatal period on the development of intestinal microbiota

(2009) Shigemitsu Tanaka et al.   FEMS IMMUNOLOGY AND MEDICAL MICROBIOLOGY

Intestinal Microbial Ecology in Premature Infants Assessed with Non–Culture-Based Techniques

(2009) Maka Mshvildadze et al.   JOURNAL OF PEDIATRICS

Lipopolysaccharide: Biosynthetic pathway and structure modification

(2009) Xiaoyuan Wang et al.   PROGRESS IN LIPID RESEARCH

The Epidemic of Antibiotic-Resistant Infections: A Call to Action for the Medical Community from the Infectious Diseases Society of America

(2007) B. Spellberg et al.   CLINICAL INFECTIOUS DISEASES