VAPiD: a lightweight cross-platform viral annotation pipeline and identification tool to facilitate virus genome submissions to NCBI GenBank

A decade of RNA virus metagenomics is (not) enough

(2018) Alexander L. Greninger   VIRUS RESEARCH

Validation and Implementation of Clinical Laboratory Improvements Act-Compliant Whole-Genome Sequencing in the Public Health Microbiology Laboratory

(2017) Varvara K. Kozyreva et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Myeloablation-associated deletion of ORF4 in a human coronavirus 229E infection

(2017) Alexander L. Greninger et al.   npj Genomic Medicine

Rapid Metagenomic Next-Generation Sequencing during an Investigation of Hospital-Acquired Human Parainfluenza Virus 3 Infections

(2016) Alexander L. Greninger et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Practical Value of Food Pathogen Traceability through Building a Whole-Genome Sequencing Network and Database

(2016) Marc W. Allard et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Real-time, portable genome sequencing for Ebola surveillance

(2016) Joshua Quick et al.   NATURE

NCBI prokaryotic genome annotation pipeline

(2016) Tatiana Tatusova et al.   NUCLEIC ACIDS RESEARCH

Recent Outbreaks of Shigellosis in California Caused by Two Distinct Populations of Shigella sonnei with either Increased Virulence or Fluoroquinolone Resistance

(2016) Varvara K. Kozyreva et al.   mSphere

Data sharing: Make outbreak research open access

(2015) Nathan L. Yozwiak et al.   NATURE

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

(2015) Alexander L. Greninger et al.   Genome Medicine

Prokka: rapid prokaryotic genome annotation

(2014) T. Seemann   BIOINFORMATICS

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

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

Kraken: ultrafast metagenomic sequence classification using exact alignments

(2014) Derrick E Wood et al.   GENOME BIOLOGY

ACBD3 Interaction with TBC1 Domain 22 Protein Is Differentially Affected by Enteroviral and Kobuviral 3A Protein Binding

(2013) A. L. Greninger et al.   mBio