Separating the signal from the noise in metagenomic cell-free DNA sequencing

Analytical and clinical validation of a microbial cell-free DNA sequencing test for infectious disease

(2019) Timothy A. Blauwkamp et al.   Nature Microbiology

Does the human placenta delivered at term have a microbiota? Results of cultivation, quantitative real-time PCR, 16S rRNA gene sequencing, and metagenomics

(2019) Kevin R. Theis et al.   AMERICAN JOURNAL OF OBSTETRICS AND GYNECOLOGY

A cell-free DNA metagenomic sequencing assay that integrates the host injury response to infection

(2019) Alexandre Pellan Cheng et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The immunophenotype of amniotic fluid leukocytes in normal and complicated pregnancies

(2018) Nardhy Gomez-Lopez et al.   AMERICAN JOURNAL OF REPRODUCTIVE IMMUNOLOGY

Urinary cell-free DNA is a versatile analyte for monitoring infections of the urinary tract

(2018) Philip Burnham et al.   Nature Communications

Improving saliva shotgun metagenomics by chemical host DNA depletion

(2018) Clarisse A. Marotz et al.   Microbiome

Recognizing the reagent microbiome

(2018) Marcus C. de Goffau et al.   Nature Microbiology

Simple statistical identification and removal of contaminant sequences in marker-gene and metagenomics data

(2018) Nicole M. Davis et al.   Microbiome

Lack of detection of a human placenta microbiome in samples from preterm and term deliveries

(2018) Jacob S. Leiby et al.   Microbiome

Contamination in Low Microbial Biomass Microbiome Studies: Issues and Recommendations

(2018) Raphael Eisenhofer et al.   TRENDS IN MICROBIOLOGY

Clinical chorioamnionitis at term IX: in vivo evidence of intra-amniotic inflammasome activation

(2018) Nardhy Gomez-Lopez et al.   JOURNAL OF PERINATAL MEDICINE

Cell-free DNA Comprises an In Vivo Nucleosome Footprint that Informs Its Tissues-Of-Origin

(2016) Matthew W. Snyder et al.   CELL

Single-stranded DNA library preparation uncovers the origin and diversity of ultrashort cell-free DNA in plasma

(2016) Philip Burnham et al.   Scientific Reports

Clinical chorioamnionitis at term II: the intra-amniotic inflammatory response

(2015) Roberto Romero et al.   JOURNAL OF PERINATAL MEDICINE

Clinical chorioamnionitis at term I: microbiology of the amniotic cavity using cultivation and molecular techniques

(2015) Roberto Romero et al.   JOURNAL OF PERINATAL MEDICINE

Noninvasive monitoring of infection and rejection after lung transplantation

(2015) Iwijn De Vlaminck et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Novel Molecular Microbiologic Technique for the Rapid Diagnosis of Microbial Invasion of the Amniotic Cavity and Intra-Amniotic Infection in Preterm Labor with Intact Membranes

(2014) Roberto Romero et al.   AMERICAN JOURNAL OF REPRODUCTIVE IMMUNOLOGY

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Chorioamnionitis: epidemiology of newborn management and outcome United States 2008

(2014) M H Malloy   Journal of Perinatology

Characterization of the vaginal microbiota of healthy Canadian women through the menstrual cycle

(2014) Bonnie Chaban et al.   Microbiome

Pulling out the 1%: Whole-Genome Capture for the Targeted Enrichment of Ancient DNA Sequencing Libraries

(2013) Meredith L. Carpenter et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Temporal Response of the Human Virome to Immunosuppression and Antiviral Therapy

(2013) Iwijn De Vlaminck et al.   CELL

Integrative analysis of genome-wide loss of heterozygosity and monoallelic expression at nucleotide resolution reveals disrupted pathways in triple-negative breast cancer

(2012) G. Ha et al.   GENOME RESEARCH

Metagenomic microbial community profiling using unique clade-specific marker genes

(2012) Nicola Segata et al.   NATURE METHODS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Accurate Genome Relative Abundance Estimation Based on Shotgun Metagenomic Reads

(2011) Li C. Xia et al.   PLoS One

Analysis of the Size Distributions of Fetal and Maternal Cell-Free DNA by Paired-End Sequencing

(2010) H. C. Fan et al.   CLINICAL CHEMISTRY

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Noninvasive diagnosis of fetal aneuploidy by shotgun sequencing DNA from maternal blood

(2008) H. C. Fan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA