- Home
- Publications
- Publication Search
- Publication Details
Title
Clinical metagenomics
Authors
Keywords
-
Journal
NATURE REVIEWS GENETICS
Volume -, Issue -, Pages -
Publisher
Springer Nature
Online
2019-03-28
DOI
10.1038/s41576-019-0113-7
References
Ask authors/readers for more resources
Related references
Note: Only part of the references are listed.- Analytical and clinical validation of a microbial cell-free DNA sequencing test for infectious disease
- (2019) Timothy A. Blauwkamp et al. Nature Microbiology
- Capturing sequence diversity in metagenomes with comprehensive and scalable probe design
- (2019) Hayden C. Metsky et al. NATURE BIOTECHNOLOGY
- Metagenomic Sequencing Detects Respiratory Pathogens in Hematopoietic Cellular Transplant Patients
- (2018) Charles Langelier et al. AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE
- Whole genome sequencing analysis for cancer genomics and precision medicine
- (2018) Hidewaki Nakagawa et al. CANCER SCIENCE
- Genomic Epidemiology Reconstructs the Introduction and Spread of Zika Virus in Central America and Mexico
- (2018) Julien Thézé et al. Cell Host & Microbe
- Liquid biopsy for infectious diseases: sequencing of cell-free plasma to detect pathogen DNA in patients with invasive fungal disease
- (2018) David K. Hong et al. DIAGNOSTIC MICROBIOLOGY AND INFECTIOUS DISEASE
- The role of gut microbiota in Clostridium difficile infection
- (2018) Michael Samarkos et al. European Journal of Internal Medicine
- The challenge of diagnostic metagenomics
- (2018) Alexander L. Greninger EXPERT REVIEW OF MOLECULAR DIAGNOSTICS
- Direct Detection and Identification of Prosthetic Joint Infection Pathogens in Synovial Fluid by Metagenomic Shotgun Sequencing
- (2018) Morgan I. Ivy et al. JOURNAL OF CLINICAL MICROBIOLOGY
- Tearing down the walls: FDA approves next generation sequencing (NGS) assays for actionable cancer genomic aberrations
- (2018) Matteo Allegretti et al. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH
- Standards and Guidelines for Validating Next-Generation Sequencing Bioinformatics Pipelines
- (2018) Somak Roy et al. JOURNAL OF MOLECULAR DIAGNOSTICS
- Recent insights into the tick microbiome gained through next-generation sequencing
- (2018) Telleasha L. Greay et al. Parasites & Vectors
- Integrated pathogen load and dual transcriptome analysis of systemic host-pathogen interactions in severe malaria
- (2018) Hyun Jae Lee et al. Science Translational Medicine
- A modular transcriptional signature identifies phenotypic heterogeneity of human tuberculosis infection
- (2018) Akul Singhania et al. Nature Communications
- Molecular detection of fungal pathogens in clinical specimens by 18S rDNA high-throughput screening in comparison to ITS PCR and culture
- (2018) K. Wagner et al. Scientific Reports
- Advances in liquid biopsy approaches for early detection and monitoring of cancer
- (2018) Anna Babayan et al. Genome Medicine
- The mosquito holobiont: fresh insight into mosquito-microbiota interactions
- (2018) Morgane Guégan et al. Microbiome
- A Reference Viral Database (RVDB) To Enhance Bioinformatics Analysis of High-Throughput Sequencing for Novel Virus Detection
- (2018) Norman Goodacre et al. mSphere
- American Gut: an Open Platform for Citizen Science Microbiome Research
- (2018) Daniel McDonald et al. mSystems
- Pulmonary Metagenomic Sequencing Suggests Missed Infections in Immunocompromised Children
- (2018) M S Zinter et al. CLINICAL INFECTIOUS DISEASES
- Right data for right patient—a precisionFDA NCI–CPTAC Multi-omics Mislabeling Challenge
- (2018) Emily Boja et al. NATURE MEDICINE
- Evaluation of Oxford Nanopore’s MinION Sequencing Device for Microbial Whole Genome Sequencing Applications
- (2018) Andrea D. Tyler et al. Scientific Reports
- A Systematic Review of the Efficacy and Safety of Fecal Microbiota Transplant for Clostridium difficile Infection in Immunocompromised Patients
- (2018) Oluwaseun Shogbesan et al. Canadian Journal of Gastroenterology and Hepatology
- ‘How to do it’—molecular investigation of a hospital outbreak
- (2018) A. Nutman et al. CLINICAL MICROBIOLOGY AND INFECTION
- Integrating host response and unbiased microbe detection for lower respiratory tract infection diagnosis in critically ill adults
- (2018) Charles Langelier et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Risk of Hepatocellular Cancer in HCV Patients Treated With Direct-Acting Antiviral Agents
- (2017) Fasiha Kanwal et al. GASTROENTEROLOGY
- Genome-wide host RNA signatures of infectious diseases: discovery and clinical translation
- (2017) Harriet D. Gliddon et al. IMMUNOLOGY
- Application of next generation sequencing in clinical microbiology and infection prevention
- (2017) Ruud H. Deurenberg et al. JOURNAL OF BIOTECHNOLOGY
- Molecular Diagnosis of Orthopedic-Device-Related Infection Directly from Sonication Fluid by Metagenomic Sequencing
- (2017) Teresa L. Street et al. JOURNAL OF CLINICAL MICROBIOLOGY
- Viral Pathogen Detection by Metagenomics and Pan-Viral Group Polymerase Chain Reaction in Children With Pneumonia Lacking Identifiable Etiology
- (2017) Robert Schlaberg et al. JOURNAL OF INFECTIOUS DISEASES
- Establishment and cryptic transmission of Zika virus in Brazil and the Americas
- (2017) N. R. Faria et al. NATURE
- Genomic epidemiology reveals multiple introductions of Zika virus into the United States
- (2017) Nathan D. Grubaugh et al. NATURE
- Shotgun metagenomics, from sampling to analysis
- (2017) Christopher Quince et al. NATURE BIOTECHNOLOGY
- Multiplex PCR method for MinION and Illumina sequencing of Zika and other virus genomes directly from clinical samples
- (2017) Joshua Quick et al. Nature Protocols
- Towards a genomics-informed, real-time, global pathogen surveillance system
- (2017) Jennifer L. Gardy et al. NATURE REVIEWS GENETICS
- Tumour virology in the era of high-throughput genomics
- (2017) Ka-Wei Tang et al. PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
- RNA-Seq analysis of peripheral blood mononuclear cells reveals unique transcriptional signatures associated with disease progression in dengue patients
- (2017) Arup Banerjee et al. Translational Research
- Comparison of DNA-, PMA-, and RNA-based 16S rRNA Illumina sequencing for detection of live bacteria in water
- (2017) Ru Li et al. Scientific Reports
- The role of the microbiome in human health and disease: an introduction for clinicians
- (2017) Vincent B Young BMJ-British Medical Journal
- Development and preliminary evaluation of a multiplexed amplification and next generation sequencing method for viral hemorrhagic fever diagnostics
- (2017) Annika Brinkmann et al. PLoS Neglected Tropical Diseases
- The blood DNA virome in 8,000 humans
- (2017) Ahmed Moustafa et al. PLoS Pathogens
- The role of the microbiome in human health and disease: an introduction for clinicians
- (2017) Vincent B Young BMJ-British Medical Journal
- Profiling bacterial communities by MinION sequencing of ribosomal operons
- (2017) Lee J. Kerkhof et al. Microbiome
- Schrödinger’s microbes: Tools for distinguishing the living from the dead in microbial ecosystems
- (2017) Joanne B. Emerson et al. Microbiome
- The human microbiome: an emerging tool in forensics
- (2017) Jarrad T. Hampton-Marcell et al. Microbial Biotechnology
- Clinical Utility of Universal PCR and its Real-world Impact on Patient Management
- (2017) Tinzar Basein et al. Open Forum Infectious Diseases
- A portable system for rapid bacterial composition analysis using a nanopore-based sequencer and laptop computer
- (2017) Satomi Mitsuhashi et al. Scientific Reports
- Nanopore DNA Sequencing and Genome Assembly on the International Space Station
- (2017) Sarah L. Castro-Wallace et al. Scientific Reports
- Advancements in Next-Generation Sequencing
- (2016) Shawn E. Levy et al. Annual Review of Genomics and Human Genetics
- Metagenomics and the Human Virome in Asymptomatic Individuals
- (2016) Nicolás Rascovan et al. Annual Review of Microbiology
- Evaluation of the External RNA Controls Consortium (ERCC) reference material using a modified Latin square design
- (2016) P. Scott Pine et al. BMC BIOTECHNOLOGY
- Globalizing and crowdsourcing biomedical research
- (2016) Ebrahim Afshinnekoo et al. BRITISH MEDICAL BULLETIN
- Assay optimization for molecular detection of Zika virus
- (2016) Victor M Corman et al. BULLETIN OF THE WORLD HEALTH ORGANIZATION
- Centrifuge: rapid and sensitive classification of metagenomic sequences
- (2016) Daehwan Kim et al. GENOME RESEARCH
- Depletion of Human DNA in Spiked Clinical Specimens for Improvement of Sensitivity of Pathogen Detection by Next-Generation Sequencing
- (2016) Mohammad R. Hasan et al. JOURNAL OF CLINICAL MICROBIOLOGY
- Clinical Evaluation of the Luminex NxTAG Respiratory Pathogen Panel
- (2016) Yi-Wei Tang et al. JOURNAL OF CLINICAL MICROBIOLOGY
- Assuring the Quality of Next-Generation Sequencing in Clinical Microbiology and Public Health Laboratories
- (2016) Amy S. Gargis et al. JOURNAL OF CLINICAL MICROBIOLOGY
- Multicenter Evaluation of BioFire FilmArray Meningitis/Encephalitis Panel for Detection of Bacteria, Viruses, and Yeast in Cerebrospinal Fluid Specimens
- (2016) Amy L. Leber et al. JOURNAL OF CLINICAL MICROBIOLOGY
- Comparison of microbial DNA enrichment tools for metagenomic whole genome sequencing
- (2016) Matthew Thoendel et al. JOURNAL OF MICROBIOLOGICAL METHODS
- A blood RNA signature for tuberculosis disease risk: a prospective cohort study
- (2016) Daniel E Zak et al. LANCET
- Real-time, portable genome sequencing for Ebola surveillance
- (2016) Joshua Quick et al. NATURE
- Real-time selective sequencing using nanopore technology
- (2016) Matthew Loose et al. NATURE METHODS
- A highly multiplexed and sensitive RNA-seq protocol for simultaneous analysis of host and pathogen transcriptomes
- (2016) Roi Avraham et al. Nature Protocols
- Automated sample preparation
- (2016) M. May SCIENCE
- Robust classification of bacterial and viral infections via integrated host gene expression diagnostics
- (2016) Timothy E. Sweeney et al. Science Translational Medicine
- Longitudinal Transcriptome Analysis Reveals a Sustained Differential Gene Expression Signature in Patients Treated for Acute Lyme Disease
- (2016) Jerome Bouquet et al. mBio
- Assessment of the latest NGS enrichment capture methods in clinical context
- (2016) Gema García-García et al. Scientific Reports
- Targeted next-generation sequencing for the detection of ciprofloxacin resistance markers using molecular inversion probes
- (2016) Christopher P. Stefan et al. Scientific Reports
- The healthy human microbiome
- (2016) Jason Lloyd-Price et al. Genome Medicine
- Impact of the gut microbiota on inflammation, obesity, and metabolic disease
- (2016) Claire L. Boulangé et al. Genome Medicine
- Characterization of the Gut Microbiome Using 16S or Shotgun Metagenomics
- (2016) Juan Jovel et al. Frontiers in Microbiology
- A genomic signature of influenza infection shows potential for presymptomatic detection, guiding early therapy, and monitoring clinical responses
- (2016) Micah T. McClain et al. Open Forum Infectious Diseases
- Gut microbiota composition and Clostridium difficile infection in hospitalized elderly individuals: a metagenomic study
- (2016) Christian Milani et al. Scientific Reports
- Benchmarking of the Oxford Nanopore MinION sequencing for quantitative and qualitative assessment of cDNA populations
- (2016) Spyros Oikonomopoulos et al. Scientific Reports
- Metagenomics for the discovery of pollutant degrading enzymes
- (2015) Lisa Ufarté et al. BIOTECHNOLOGY ADVANCES
- The truth about metagenomics: quantifying and counteracting bias in 16S rRNA studies
- (2015) J Paul Brooks et al. BMC MICROBIOLOGY
- Diagnosis of Neuroinvasive Astrovirus Infection in an Immunocompromised Adult With Encephalitis by Unbiased Next-Generation Sequencing
- (2015) Samia N. Naccache et al. CLINICAL INFECTIOUS DISEASES
- Enhanced virome sequencing using targeted sequence capture
- (2015) Todd N. Wylie et al. GENOME RESEARCH
- Laboratory Diagnosis of Lyme Disease
- (2015) Adriana R. Marques INFECTIOUS DISEASE CLINICS OF NORTH AMERICA
- Metagenomic Approach for Identification of the Pathogens Associated with Diarrhea in Stool Specimens
- (2015) Yanjiao Zhou et al. JOURNAL OF CLINICAL MICROBIOLOGY
- Next-Generation Sequencing for Infectious Disease Diagnosis and Management
- (2015) Martina I. Lefterova et al. JOURNAL OF MOLECULAR DIAGNOSTICS
- Cell-free DNA Analysis for Noninvasive Examination of Trisomy
- (2015) Mary E. Norton et al. NEW ENGLAND JOURNAL OF MEDICINE
- Virome Capture Sequencing Enables Sensitive Viral Diagnosis and Comprehensive Virome Analysis
- (2015) Thomas Briese et al. mBio
- Making the Leap from Research Laboratory to Clinic: Challenges and Opportunities for Next-Generation Sequencing in Infectious Disease Diagnostics
- (2015) Brittany Goldberg et al. mBio
- Rapid metagenomic identification of viral pathogens in clinical samples by real-time nanopore sequencing analysis
- (2015) Alexander L. Greninger et al. Genome Medicine
- The Value and Significance of Metagenomics of Marine Environments
- (2015) Fangqing Zhao et al. GENOMICS PROTEOMICS & BIOINFORMATICS
- Reagent and laboratory contamination can critically impact sequence-based microbiome analyses
- (2014) Susannah J Salter et al. BMC BIOLOGY
- A cloud-compatible bioinformatics pipeline for ultrarapid pathogen identification from next-generation sequencing of clinical samples
- (2014) S. N. Naccache et al. GENOME RESEARCH
- Comparative Evaluation of Two Commercial Multiplex Panels for Detection of Gastrointestinal Pathogens by Use of Clinical Stool Specimens
- (2014) R. Khare et al. JOURNAL OF CLINICAL MICROBIOLOGY
- Diagnosis of Childhood Tuberculosis and Host RNA Expression in Africa
- (2014) Suzanne T. Anderson et al. NEW ENGLAND JOURNAL OF MEDICINE
- Actionable Diagnosis of Neuroleptospirosis by Next-Generation Sequencing
- (2014) Michael R. Wilson et al. NEW ENGLAND JOURNAL OF MEDICINE
- Diagnostic metagenomics: potential applications to bacterial, viral and parasitic infections
- (2014) M. J. PALLEN PARASITOLOGY
- Microbial Contamination in Next Generation Sequencing: Implications for Sequence-Based Analysis of Clinical Samples
- (2014) Michael J. Strong et al. PLoS Pathogens
- Kraken: ultrafast metagenomic sequence classification using exact alignments
- (2014) Derrick E Wood et al. GENOME BIOLOGY
- Viral pathogen discovery
- (2013) Charles Y Chiu CURRENT OPINION IN MICROBIOLOGY
- A Culture-Independent Sequence-Based Metagenomics Approach to the Investigation of an Outbreak of Shiga-Toxigenic Escherichia coli O104:H4
- (2013) Nicholas J. Loman et al. JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION
- Evaluation of the BioFire FilmArray Respiratory Panel and the GenMark eSensor Respiratory Viral Panel on Lower Respiratory Tract Specimens
- (2013) P. Ruggiero et al. JOURNAL OF CLINICAL MICROBIOLOGY
- Metagenomic Analysis of Tuberculosis in a Mummy
- (2013) Jacqueline Z.-M. Chan et al. NEW ENGLAND JOURNAL OF MEDICINE
- Duodenal Infusion of Donor Feces for Recurrent Clostridium difficile
- (2013) Els van Nood et al. NEW ENGLAND JOURNAL OF MEDICINE
- A Host Transcriptional Signature for Presymptomatic Detection of Infection in Humans Exposed to Influenza H1N1 or H3N2
- (2013) Christopher W. Woods et al. PLoS One
- Gene Expression-Based Classifiers Identify Staphylococcus aureus Infection in Mice and Humans
- (2013) Sun Hee Ahn et al. PLoS One
- Rapid 16S rRNA Next-Generation Sequencing of Polymicrobial Clinical Samples for Diagnosis of Complex Bacterial Infections
- (2013) Stephen J. Salipante et al. PLoS One
- A Method for Selectively Enriching Microbial DNA from Contaminating Vertebrate Host DNA
- (2013) George R. Feehery et al. PLoS One
- Tracking a Hospital Outbreak of Carbapenem-Resistant Klebsiella pneumoniae with Whole-Genome Sequencing
- (2012) E. S. Snitkin et al. Science Translational Medicine
- Tumor viruses and cancer biology: Modulating signaling pathways for therapeutic intervention
- (2011) Abhik Saha et al. CANCER BIOLOGY & THERAPY
- Broad-Range 16S rRNA Gene Polymerase Chain Reaction for Diagnosis of Culture-Negative Bacterial Infections
- (2011) Silvana K. Rampini et al. CLINICAL INFECTIOUS DISEASES
- Validation of Laboratory-Developed Molecular Assays for Infectious Diseases
- (2010) E. M. Burd CLINICAL MICROBIOLOGY REVIEWS
- Blood Gene Expression Signatures Predict Invasive Candidiasis
- (2010) A. K. Zaas et al. Science Translational Medicine
- Gene Expression Signatures Diagnose Influenza and Other Symptomatic Respiratory Viral Infections in Humans
- (2009) Aimee K. Zaas et al. Cell Host & Microbe
- Next-Generation Sequencing: From Basic Research to Diagnostics
- (2009) K. V. Voelkerding et al. CLINICAL CHEMISTRY
- Basic Concepts of Microarrays and Potential Applications in Clinical Microbiology
- (2009) M. B. Miller et al. CLINICAL MICROBIOLOGY REVIEWS
- Gene-Expression Signatures in Breast Cancer
- (2009) Christos Sotiriou et al. NEW ENGLAND JOURNAL OF MEDICINE
- RNA-Seq: a revolutionary tool for transcriptomics
- (2008) Zhong Wang et al. NATURE REVIEWS GENETICS
- Clonal Integration of a Polyomavirus in Human Merkel Cell Carcinoma
- (2008) H. Feng et al. SCIENCE
Find Funding. Review Successful Grants.
Explore over 25,000 new funding opportunities and over 6,000,000 successful grants.
ExploreAdd your recorded webinar
Do you already have a recorded webinar? Grow your audience and get more views by easily listing your recording on Peeref.
Upload Now