Clinical metagenomic identification of Balamuthia mandrillaris encephalitis and assembly of the draft genome: the continuing case for reference genome sequencing

DiagnosingBalamuthia mandrillarisEncephalitis With Metagenomic Deep Sequencing

(2015) Michael R. Wilson et al.   ANNALS OF NEUROLOGY

NxTrim: optimized trimming of Illumina mate pair reads: Table 1.

(2015) Jared O’Connell et al.   BIOINFORMATICS

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

A tale of two approaches

(2015) Ryan D. Schubert et al.   CURRENT OPINION IN NEUROLOGY

Novel culture medium for the axenic growth of Balamuthia mandrillaris

(2015) Luis Fernando Lares-Jiménez et al.   DIAGNOSTIC MICROBIOLOGY AND INFECTIOUS DISEASE

A novel outbreak enterovirus D68 strain associated with acute flaccid myelitis cases in the USA (2012–14): a retrospective cohort study

(2015) Alexander L Greninger et al.   LANCET INFECTIOUS DISEASES

Accurate read-based metagenome characterization using a hierarchical suite of unique signatures

(2015) Tracey Allen K. Freitas et al.   NUCLEIC ACIDS RESEARCH

Genome-wide identification of pathogenicity factors of the free-living amoeba Naegleria fowleri

(2014) Denise C Zysset-Burri et al.   BMC GENOMICS

Efficient de novo assembly of highly heterozygous genomes from whole-genome shotgun short reads

(2014) Rei Kajitani et al.   GENOME RESEARCH

A cloud-compatible bioinformatics pipeline for ultrarapid pathogen identification from next-generation sequencing of clinical samples

(2014) S. N. Naccache et al.   GENOME RESEARCH

Successful Treatment of Granulomatous Amoebic Encephalitis with Combination Antimicrobial Therapy

(2014) Hideki Kato et al.   INTERNAL MEDICINE

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

Actionable Diagnosis of Neuroleptospirosis by Next-Generation Sequencing

(2014) Michael R. Wilson et al.   NEW ENGLAND JOURNAL OF MEDICINE

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

The In Vitro Efficacy of Antimicrobial Agents Against the Pathogenic Free-Living AmoebaBalamuthia mandrillaris

(2013) Arine F. Ahmad et al.   JOURNAL OF EUKARYOTIC MICROBIOLOGY

The Mitochondrial Genome and a 60-kb Nuclear DNA Segment fromNaegleria fowleri, the Causative Agent of Primary Amoebic Meningoencephalitis

(2013) Emily K. Herman et al.   JOURNAL OF EUKARYOTIC MICROBIOLOGY

The Perils of Pathogen Discovery: Origin of a Novel Parvovirus-Like Hybrid Genome Traced to Nucleic Acid Extraction Spin Columns

(2013) S. N. Naccache et al.   JOURNAL OF VIROLOGY

Bacterial genome sequencing in the clinic: bioinformatic challenges and solutions

(2013) W. Florian Fricke et al.   NATURE REVIEWS GENETICS

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

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

Cordyceps militaris (Hypocreales: Cordycipitaceae): transcriptional analysis and molecular characterization of cox1 and group I intron with putative LAGLIDADG endonuclease

(2011) Zhuangli Zheng et al.   WORLD JOURNAL OF MICROBIOLOGY & BIOTECHNOLOGY

Successful Treatment ofBalamuthia mandrillarisAmoebic Infection with Extensive Neurological and Cutaneous Involvement

(2010) Dalila Y. Martínez et al.   CLINICAL INFECTIOUS DISEASES

Genetic Detection and Characterization of Lujo Virus, a New Hemorrhagic Fever–Associated Arenavirus from Southern Africa

(2009) Thomas Briese et al.   PLoS Pathogens

Detection of Balamuthia mandrillaris DNA by real-time PCR targeting the RNase P gene

(2008) Albrecht F Kiderlen et al.   BMC MICROBIOLOGY

Increasing Importance of Balamuthia mandrillaris

(2008) A. Matin et al.   CLINICAL MICROBIOLOGY REVIEWS