Performance of Nanopore and Illumina Metagenomic Sequencing for Pathogen Detection and Transcriptome Analysis in Infantile Central Nervous System Infections

Next-Generation Sequencing to Detect Pathogens in Pediatric Febrile Neutropenia: A Single-Center Retrospective Study of 112 Cases

(2021) Kazuhiro Horiba et al.   Open Forum Infectious Diseases

Pediatric sepsis cases diagnosed with group B streptococcal meningitis using next-generation sequencing: a report of two cases

(2021) Kazuhiro Horiba et al.   BMC INFECTIOUS DISEASES

Meningitis Caused by the Live Varicella Vaccine Virus: Metagenomic Next Generation Sequencing, Immunology Exome Sequencing and Cytokine Multiplex Profiling

(2021) Prashanth S. Ramachandran et al.   Viruses-Basel

Performance of Metagenomic Next-Generation Sequencing for the Diagnosis of Viral Meningoencephalitis in a Resource-Limited Setting

(2020) Nguyen Thi Thu Hong et al.   Open Forum Infectious Diseases

Infectious and Autoimmune Causes of Encephalitis in Children

(2020) Timothy A. Erickson et al.   PEDIATRICS

Viruses Causing Aseptic Meningitis: A Tertiary Medical Center Experience With a Multiplex PCR Assay

(2020) Mohammed A. Aldriweesh et al.   Frontiers in Neurology

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

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

Plasmid DNA contaminant in molecular reagents

(2019) N. Wally et al.   Scientific Reports

Clinical metagenomics

(2019) Charles Y. Chiu et al.   NATURE REVIEWS GENETICS

Index hopping on the Illumina HiseqX platform and its consequences for ancient DNA studies

(2019) Tom van der Valk et al.   Molecular Ecology Resources

The causes and clinical features of childhood encephalitis: a multicentre, prospective, cohort study

(2019) P N Britton et al.   CLINICAL INFECTIOUS DISEASES

Nanopore metagenomics enables rapid clinical diagnosis of bacterial lower respiratory infection

(2019) Themoula Charalampous et al.   NATURE BIOTECHNOLOGY

Clinical Metagenomic Sequencing for Diagnosis of Meningitis and Encephalitis

(2019) Michael R. Wilson et al.   NEW ENGLAND JOURNAL OF MEDICINE

Metascape provides a biologist-oriented resource for the analysis of systems-level datasets

(2019) Yingyao Zhou et al.   Nature Communications

Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype

(2019) Daehwan Kim et al.   NATURE BIOTECHNOLOGY

Metagenomic analysis using next-generation sequencing of pathogens in bronchoalveolar lavage fluid from pediatric patients with respiratory failure

(2019) Suguru Takeuchi et al.   Scientific Reports

Minimap2: pairwise alignment for nucleotide sequences

(2018) Heng Li   BIOINFORMATICS

NanoPack: visualizing and processing long-read sequencing data

(2018) Wouter De Coster et al.   BIOINFORMATICS

A Guide to Utilization of the Microbiology Laboratory for Diagnosis of Infectious Diseases: 2018 Update by the Infectious Diseases Society of America and the American Society for Microbiologya

(2018) J Michael Miller et al.   CLINICAL INFECTIOUS DISEASES

ISG15 in antiviral immunity and beyond

(2018) Yi-Chieh Perng et al.   NATURE REVIEWS MICROBIOLOGY

Comprehensive detection of pathogens in immunocompromised children with bloodstream infections by next-generation sequencing

(2018) Kazuhiro Horiba et al.   Scientific Reports

Detection of Viral Pathogens With Multiplex Nanopore MinION Sequencing: Be Careful With Cross-Talk

(2018) Yifei Xu et al.   Frontiers in Microbiology

metaSPAdes: a new versatile metagenomic assembler

(2017) Sergey Nurk et al.   GENOME RESEARCH

Comprehensive detection of viruses in pediatric patients with acute liver failure using next-generation sequencing

(2017) Takako Suzuki et al.   JOURNAL OF CLINICAL VIROLOGY

A portable system for rapid bacterial composition analysis using a nanopore-based sequencer and laptop computer

(2017) Satomi Mitsuhashi et al.   Scientific Reports

Hospital admissions for viral meningitis in children in England over five decades: a population-based observational study

(2016) Natalie G Martin et al.   LANCET INFECTIOUS DISEASES

Coming of age: ten years of next-generation sequencing technologies

(2016) Sara Goodwin et al.   NATURE REVIEWS GENETICS

The Epidemiology of Hand, Foot and Mouth Disease in Asia

(2016) Wee Ming Koh et al.   PEDIATRIC INFECTIOUS DISEASE JOURNAL

Identification of Viruses in Cases of Pediatric Acute Encephalitis and Encephalopathy Using Next-Generation Sequencing

(2016) Jun-ichi Kawada et al.   Scientific Reports

Mx GTPases: dynamin-like antiviral machines of innate immunity

(2015) Otto Haller et al.   TRENDS IN MICROBIOLOGY

Trends in bacterial, mycobacterial, and fungal meningitis in England and Wales 2004–11: an observational study

(2014) Ifeanichukwu O Okike et al.   LANCET INFECTIOUS DISEASES

Neurological aspects of human parvovirus B19 infection: a systematic review

(2014) Faraj Barah et al.   REVIEWS IN MEDICAL VIROLOGY

Kraken: ultrafast metagenomic sequence classification using exact alignments

(2014) Derrick E Wood et al.   GENOME BIOLOGY

TCC: an R package for comparing tag count data with robust normalization strategies

(2013) Jianqiang Sun et al.   BMC BIOINFORMATICS

Human Parechovirus Central Nervous System Infections in Southern California Children

(2013) Susanna Felsenstein et al.   PEDIATRIC INFECTIOUS DISEASE JOURNAL

Inhibition of enterovirus 71 entry by transcription factor XBP1

(2012) Jia-Rong Jheng et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

Database resources of the National Center for Biotechnology Information

(2012)   NUCLEIC ACIDS RESEARCH

pROC: an open-source package for R and S+ to analyze and compare ROC curves

(2011) Xavier Robin et al.   BMC BIOINFORMATICS

Causes of encephalitis and differences in their clinical presentations in England: a multicentre, population-based prospective study

(2010) Julia Granerod et al.   LANCET INFECTIOUS DISEASES

Database indexing for production MegaBLAST searches

(2008) Aleksandr Morgulis et al.   BIOINFORMATICS

Epidemiology and Clinical Associations of Human Parechovirus Respiratory Infections

(2008) H. Harvala et al.   JOURNAL OF CLINICAL MICROBIOLOGY