Precision identification of diverse bloodstream pathogens in the gut microbiome

Microbial strain-level population structure and genetic diversity from metagenomes

(2017) Duy Tin Truong et al.   GENOME RESEARCH

metaSPAdes: a new versatile metagenomic assembler

(2017) Sergey Nurk et al.   GENOME RESEARCH

Integrated meta-omic analyses of the gastrointestinal tract microbiome in patients undergoing allogeneic hematopoietic stem cell transplantation

(2017) Anne Kaysen et al.   Translational Research

metaSNV: A tool for metagenomic strain level analysis

(2017) Paul Igor Costea et al.   PLoS One

An integrated metagenomics pipeline for strain profiling reveals novel patterns of bacterial transmission and biogeography

(2016) Stephen Nayfach et al.   GENOME RESEARCH

Measurement of bacterial replication rates in microbial communities

(2016) Christopher T Brown et al.   NATURE BIOTECHNOLOGY

ggtree: anrpackage for visualization and annotation of phylogenetic trees with their covariates and other associated data

(2016) Guangchuang Yu et al.   Methods in Ecology and Evolution

CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes

(2015) Donovan H. Parks et al.   GENOME RESEARCH

A Year of Infection in the Intensive Care Unit: Prospective Whole Genome Sequencing of Bacterial Clinical Isolates Reveals Cryptic Transmissions and Novel Microbiota

(2015) David J. Roach et al.   PLoS Genetics

Etiology, clinical features and outcomes of pre-engraftment and post-engraftment bloodstream infection in hematopoietic SCT recipients

(2014) C Gudiol et al.   BONE MARROW TRANSPLANTATION

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

(2014) Molly K Gibson et al.   ISME Journal

Fecal colonization and infection withPseudomonas aeruginosain recipients of allogeneic hematopoietic stem cell transplantation

(2014) L. Nesher et al.   Transplant Infectious Disease

SRST2: Rapid genomic surveillance for public health and hospital microbiology labs

(2014) Michael Inouye et al.   Genome Medicine

Overall burden of bloodstream infection and nosocomial bloodstream infection in North America and Europe

(2013) M. Goto et al.   CLINICAL MICROBIOLOGY AND INFECTION

Leukemia and risk of recurrent Escherichia coli bacteremia: genotyping implicates E. coli translocation from the colon to the bloodstream

(2013) A. Samet et al.   EUROPEAN JOURNAL OF CLINICAL MICROBIOLOGY & INFECTIOUS DISEASES

Genetic variation of a bacterial pathogen within individuals with cystic fibrosis provides a record of selective pressures

(2013) Tami D Lieberman et al.   NATURE GENETICS

Incidence, risk factors, and outcome of bloodstream infections during the pre-engraftment phase in 521 allogeneic hematopoietic stem cell transplantations

(2013) O. Blennow et al.   Transplant Infectious Disease

Snakemake--a scalable bioinformatics workflow engine

(2012) J. Koster et al.   BIOINFORMATICS

Intestinal Domination and the Risk of Bacteremia in Patients Undergoing Allogeneic Hematopoietic Stem Cell Transplantation

(2012) Ying Taur et al.   CLINICAL INFECTIOUS DISEASES

Distribution of Pathogens in Central Line–Associated Bloodstream Infections among Patients with and without Neutropenia following Chemotherapy Evidence for a Proposed Modification to the Current Surveillance Definition

(2012) James P. Steinberg et al.   INFECTION CONTROL AND HOSPITAL EPIDEMIOLOGY

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

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

Emergence of carbapenem-resistant Enterobacteriaceae as causes of bloodstream infections in patients with hematologic malignancies

(2012) Michael J. Satlin et al.   LEUKEMIA & LYMPHOMA

Tracking a Hospital Outbreak of Carbapenem-Resistant Klebsiella pneumoniae with Whole-Genome Sequencing

(2012) E. S. Snitkin et al.   Science Translational Medicine

BamTools: a C++ API and toolkit for analyzing and managing BAM files

(2011) D. W. Barnett et al.   BIOINFORMATICS

Genome-wide recombination drives diversification of epidemic strains of Acinetobacter baumannii

(2011) E. S. Snitkin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

phangorn: phylogenetic analysis in R

(2010) Klaus Peter Schliep   BIOINFORMATICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

Vancomycin-resistant Enterococcus domination of intestinal microbiota is enabled by antibiotic treatment in mice and precedes bloodstream invasion in humans

(2010) Carles Ubeda et al.   JOURNAL OF CLINICAL INVESTIGATION

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

(2010) Morgan N. Price et al.   PLoS One

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Blood Stream Infections in Allogeneic Hematopoietic Stem Cell Transplant Recipients: Reemergence of Gram-Negative Rods and Increasing Antibiotic Resistance

(2009) Malgorzata Mikulska et al.   BIOLOGY OF BLOOD AND MARROW TRANSPLANTATION

Clinical Practice Guidelines for the Diagnosis and Management of Intravascular Catheter‐Related Infection: 2009 Update by the Infectious Diseases Society of America

(2009) Leonard A. Mermel et al.   CLINICAL INFECTIOUS DISEASES

Organised Genome Dynamics in the Escherichia coli Species Results in Highly Diverse Adaptive Paths

(2009) Marie Touchon et al.   PLoS Genetics