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List of works by Charles Y. Chiu

2291. A Real-Time Sequencing Approach for Simultaneous Metagenomic and Transcriptomic-Based Diagnosis of Infectious Diseases

article by Benjamin Briggs et al published November 2018 in Open Forum Infectious Diseases

236. The Comparative Utility Of Metagenomic Next-Generation Sequencing and Universal PCR for Pathogen Detection on Cerebrospinal Fluid: A Retrospective Analysis From a Tertiary Care Center

scientific article published on 23 October 2019

2563. Clinical Metagenomic Next-Generation Sequencing for Diagnosis of Meningitis and Encephalitis

617. Characterization and Development of the Infant Gut Virome: A STORK Study

article

A Child With Intermittent Headaches and Eosinophilic Meningitis.

scientific article published on 9 February 2018

A Genomic Survey of SARS-CoV-2 Reveals Multiple Introductions into Northern California without a Predominant Lineage

scientific article published on 31 March 2020

A SARS-CoV-2 serological assay to determine the presence of blocking antibodies that compete for human ACE2 binding

scientific article published on 29 May 2020

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

scientific article

A metagenomic analysis of pandemic influenza A (2009 H1N1) infection in patients from North America

scientific article (publication date: 18 October 2010)

A mouse model of paralytic myelitis caused by enterovirus D68.

scientific article

A novel adenovirus species associated with an acute respiratory outbreak in a baboon colony and evidence of coincident human infection

scientific article published on 16 April 2013

A novel bocavirus in canine liver

scientific article published on 13 February 2013

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

scientific article published on 31 March 2015

A novel rhabdovirus associated with acute hemorrhagic fever in central Africa

scientific article published in September 2012

Actionable diagnosis of neuroleptospirosis by next-generation sequencing

scientific article

Acute Flaccid Myelitis of Unknown Etiology in California, 2012-2015.

scientific article published on December 2015

Acute Liver Failure of Indeterminate Etiology: A Comprehensive Systematic Approach by An Expert Committee to Establish Causality

scientific article published on 27 June 2018

Acute Zika virus infection in an asymptomatic blood donor at the onset of the Puerto Rico epidemic

scientific article published on 13 August 2019

An ensemble strategy that significantly improves de novo assembly of microbial genomes from metagenomic next-generation sequencing data

scientific article

Antibodies to the Novel Human Pegivirus 2 Are Associated with Active and Resolved Infections

scientific article

Association of COVID-19 Infections in San Francisco in Early March 2020 with Travel to New York and Europe

scientific article published on 07 April 2020

Associations of Early COVID-19 Cases in San Francisco with Domestic and International Travel

scientific article published on 21 May 2020

Author Correction: Efficacy of an inactivated Zika vaccine against virus infection during pregnancy in mice and marmosets

scientific article published in 2022

Author Correction: Metagenomic sequencing with spiked primer enrichment for viral diagnostics and genomic surveillance

scientific article published on 01 March 2020

Bacteriologic features of surgical site infections following breast surgery

scientific article published on October 2009

Bas-Congo Virus

article from 2014

Bas-Congo virus: another deadly virus?

scientific article published in February 2013

Beatrice Hill Virus Represents a Novel Species in the Genus Tibrovirus (Mononegavirales: Rhabdoviridae).

scientific article published on 26 January 2017

COVID-19 Variant Detection with a High-Fidelity CRISPR-Cas12 Enzyme

scientific article published in 2022

CRISPR-Cas12-based detection of SARS-CoV-2

scientific article published on 16 April 2020

Characterization of the Bas-Congo virus glycoprotein and its function in pseudotyped viruses

scientific article published on 19 June 2013

Clinical Metagenomic Next-Generation Sequencing for Pathogen Detection

Clinical Metagenomic Sequencing for Diagnosis of Meningitis and Encephalitis

scientific article published on 01 June 2019

Clinical Outcomes and Serologic Response in Solid Organ Transplant Recipients with COVID-19: A Case Series from the United States

scientific article published on 01 June 2020

Clinical Utility of Unbiased Metagenomic Next-Generation Sequencing in Diagnosis of Acute Infectious Diseases: A Prospective Case Series

scientific article published on 9 December 2015

Clinical features, diagnostics, and outcomes of patients presenting with acute respiratory illness: a comparison of patients with and without COVID-19

scientific article published on 06 May 2020

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

scientific article

Clinical metagenomics

scientific article published on 01 June 2019

Coinfections of Zika and Chikungunya Viruses in Bahia, Brazil, Identified by Metagenomic Next-Generation Sequencing

scientific article

Competitive SARS-CoV-2 Serology Reveals Most Antibodies Targeting the Spike Receptor-Binding Domain Compete for ACE2 Binding

scientific article published on 16 September 2020

Complete genome sequence of sequential Pandoraea apista isolates from the same cystic fibrosis patient supports a model of chronic colonization with in vivo strain evolution over time

scientific article published on 11 October 2016

Concerns over the origin of NIH-CQV, a novel virus discovered in Chinese patients with seronegative hepatitis

scientific article published on 26 February 2014

Correction: A Novel Rhabdovirus Associated with Acute Hemorrhagic Fever in Central Africa

scientific article published on 18 March 2016

Correction: Correction: A Novel Rhabdovirus Associated with Acute Hemorrhagic Fever in Central Africa

scientific article published on 7 September 2017

Correction: Cross-Species Transmission of a Novel Adenovirus Associated with a Fulminant Pneumonia Outbreak in a New World Monkey Colony

Correction: Cross-Species Transmission of a Novel Adenovirus Associated with a Fulminant Pneumonia Outbreak in a New World Monkey Colony.

scientific article

Cross-species transmission of a novel adenovirus associated with a fulminant pneumonia outbreak in a new world monkey colony

scientific article published in July 2011

Cryo-EM imaging of the catalytic subunit of the DNA-dependent protein kinase

scientific article published on December 1998

Cryo-EM visualization of an exposed RGD epitope on adenovirus that escapes antibody neutralization

scientific article published on March 1997

Cryptic transmission of SARS-CoV-2 in Washington State

scientific article published on 06 April 2020

Cryptic transmission of SARS-CoV-2 in Washington state

scientific article published on 10 September 2020

Cultivation and serological characterization of a human Theiler's-like cardiovirus associated with diarrheal disease

scientific article

Cutting-Edge Infectious Disease Diagnostics with CRISPR

scientific article published on 01 June 2018

DNA microarray for detection of gastrointestinal viruses.

scientific article

Diagnosis of Fatal Human Case of St. Louis Encephalitis Virus Infection by Metagenomic Sequencing, California, 2016.

scientific article published on October 2017

Diagnosis of a critical respiratory illness caused by human metapneumovirus by use of a pan-virus microarray

scientific article published on 9 May 2007

Diagnosis of neuroinvasive astrovirus infection in an immunocompromised adult with encephalitis by unbiased next-generation sequencing

scientific article

Differentiation enhances Zika virus infection of neuronal brain cells

scientific article published in Scientific Reports

Digitally collected cryo-electron micrographs for single particle reconstruction

scientific article published on May 2000

Direct Comparison of SARS-CoV-2 Analytical Limits of Detection across Seven Molecular Assays

scientific article published on 10 July 2020

Discovery of a Novel Human Pegivirus in Blood Associated with Hepatitis C Virus Co-Infection

scientific article published on 11 December 2015

Discovery of a novel polyomavirus in acute diarrheal samples from children

scientific article

Discovery of a persistent Zika virus lineage in Bahia, Brazil

article

Distinct Zika Virus Lineage in Salvador, Bahia, Brazil

scientific article

Draft Genome Sequence of Mycobacterium arupense Strain GUC1.

scientific article published on 11 June 2015

Draft Genome Sequence of Mycobacterium elephantis Strain Lipa

scientific article published on 25 June 2015

Draft Genome Sequence of Mycobacterium heckeshornense Strain RLE.

scientific article published on 27 August 2015

Draft Genome Sequence of Mycobacterium heraklionense Strain Davo

scientific article published on 23 July 2015

Draft Genome Sequence of Mycobacterium obuense Strain UC1, Isolated from Patient Sputum

scientific article published on 11 June 2015

E-Predict: a computational strategy for species identification based on observed DNA microarray hybridization patterns

scientific article

Epidemic establishment and cryptic transmission of Zika virus in Brazil and the Americas

scientific article

Epidemiological and genomic characterization of community-acquired Clostridium difficile infections

scientific article published on 31 August 2018

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

scientific article published on 11 January 2016

Establishment and characterization of an oral tongue squamous cell carcinoma cell line from a never-smoking patient

scientific article

Evaluation of SARS-CoV-2 serology assays reveals a range of test performance

scientific article published on 27 August 2020

Experimental Zika Virus Infection in a New World Monkey Model Reproduces Key Features of the Human Disease

scientific article

Experimental Zika Virus Infection in the Pregnant Common Marmoset Induces Spontaneous Fetal Loss and Neurodevelopmental Abnormalities

scholarly article published 4 February 2018

Experimental Zika Virus Infection in the Pregnant Common Marmoset Induces Spontaneous Fetal Loss and Neurodevelopmental Abnormalities.

scientific article published in May 2018

Experimental Zika Virus Inoculation in a New World Monkey Model Reproduces Key Features of the Human Infection

scientific article published on 7 December 2017

Experimental cross-species infection of common marmosets by titi monkey adenovirus

scientific article

Exploratory analysis of the potential for advanced diagnostic testing to reduce healthcare expenditures of patients hospitalized with meningitis or encephalitis

scientific article published on 15 January 2020

First Complete Genome Sequence of Corynebacterium riegelii.

scientific article published on 30 March 2017

First Draft Genome Sequences of Neisseria sp. Strain 83E34 and Neisseria sp. Strain 74A18, Previously Identified as CDC Eugonic Fermenter 4b Species.

scientific article published on 10 November 2016

Gastroenteritis, Hepatitis, Encephalopathy, and Human Herpesvirus 6 Detection in an Immunocompetent Child: Benefits and Risks of Syndromic Multiplex Molecular Panel Testing

scientific article published on 14 June 2019

Genome Sequence of Bivens Arm Virus, a Tibrovirus Belonging to the Species Tibrogargan virus (Mononegavirales: Rhabdoviridae)

scientific article

Genomic Assays for Identification of Chikungunya Virus in Blood Donors, Puerto Rico, 2014.

scientific article published in August 2015

Genomic Epidemiology Reconstructs the Introduction and Spread of Zika Virus in Central America and Mexico.

scientific article published on 24 May 2018

Genomic surveillance reveals multiple introductions of SARS-CoV-2 into Northern California ⬇️

scientific article published on 08 June 2020

Hepatitis E Virus-Associated Meningoencephalitis in a Lung Transplant Recipient Diagnosed by Clinical Metagenomic Sequencing

scientific article

Human Tibroviruses: Commensals or Lethal Pathogens?

scientific article published on 25 February 2020

Human, Nonhuman Primate, and Bat Cells Are Broadly Susceptible to Tibrovirus Particle Cell Entry

scientific article published on 26 April 2019

Identification of cardioviruses related to Theiler's murine encephalomyelitis virus in human infections.

scholarly article

Identification of high-risk human papillomavirus and Rb/E2F pathway genomic alterations in mutually exclusive subsets of colorectal neuroendocrine carcinoma

scientific article published on 20 September 2018

Idiopathic pneumonia syndrome after hematopoietic cell transplantation: evidence of occult infectious etiologies

scientific article published on 27 April 2015

In-depth investigation of archival and prospectively collected samples reveals no evidence for XMRV infection in prostate cancer

scientific article

Integrating host response and unbiased microbe detection for lower respiratory tract infection diagnosis in critically ill adults

article published in the Proceedings of the National Academy of Sciences of the United States of America

LB14. Cerebrospinal Fluid Profiling of the Human Host Response Reveals Species-Specific Enterovirus Biosignatures in Acute Flaccid Myelitis Cases

scientific article published on 23 October 2019

Laboratory validation of a clinical metagenomic sequencing assay for pathogen detection in cerebrospinal fluid

scientific article published on 16 April 2019

Laser electron accelerators for radiation medicine: a feasibility study.

scientific article published in July 2004

List of Contributors

Longitudinal Transcriptome Analysis Reveals a Sustained Differential Gene Expression Signature in Patients Treated for Acute Lyme Disease

scientific article published on 12 February 2016

Metagenomic Next-Generation Sequencing of the 2014 Ebola Virus Disease Outbreak in the Democratic Republic of the Congo

scientific article published on 26 August 2019

Metagenomic Sequencing Detects Respiratory Pathogens in Hematopoietic Cellular Transplant Patients

scientific article published on 7 July 2017

Metagenomic sequencing with spiked primer enrichment for viral diagnostics and genomic surveillance

scientific article published on 13 January 2020

Metagenomic-based Surveillance of Pacific Coast tick Dermacentor occidentalis Identifies Two Novel Bunyaviruses and an Emerging Human Ricksettsial Pathogen.

scientific article published on 25 September 2017

Metagenomics for the discovery of novel human viruses

scientific article

Microarray detection of human parainfluenzavirus 4 infection associated with respiratory failure in an immunocompetent adult

scientific article published in September 2006

Miscarriage and stillbirth following maternal Zika virus infection in nonhuman primates

scholarly article by Dawn M Dudley et al published August 2018 in Nature Medicine

Morbidity and mortality of short-bowel syndrome in infants with abdominal wall defects.

scientific article

NEW GENOMES FROM THE CONGO BASIN EXPAND HISTORY OF CRF01_AE ORIGIN AND DISSEMINATION

scientific article published on 12 April 2020

Nanopore DNA Sequencing and Genome Assembly on the International Space Station.

scientific article published on 21 December 2017

Neurobrucellosis: Unexpected Answer From Metagenomic Next-Generation Sequencing.

scientific article published on 6 January 2017

Neutralizing immunity in vaccine breakthrough infections from the SARS-CoV-2 Omicron and Delta variants

No viral association found in a set of differentiated vulvar intraepithelial neoplasia cases by human papillomavirus and pan-viral microarray testing

scientific article

Pan-viral serology implicates enteroviruses in acute flaccid myelitis

scientific article published on 21 October 2019

Pandemic (H1N1) 2009 infection in patients with hematologic malignancy

scientific article published in December 2010

Point-Counterpoint: Should We Be Performing Metagenomic Next-Generation Sequencing for Infectious Disease Diagnosis in the Clinical Laboratory?

scientific article published on 24 February 2020

Polyoma virus-associated carcinomas of the urologic tract: a clinicopathologic and molecular study

scientific article published on 15 May 2018

Publisher Correction: Experimental Zika Virus Infection in the Pregnant Common Marmoset Induces Spontaneous Fetal Loss and Neurodevelopmental Abnormalities

scientific article published in Scientific Reports

RNA-Seq Analysis of Gene Expression, Viral Pathogen, and B-Cell/T-Cell Receptor Signatures in Complex Chronic Disease

scientific article

Rapid Detection of 2019 Novel Coronavirus SARS-CoV-2 Using a CRISPR-based DETECTR Lateral Flow Assay

scientific article (preprint)

Rapid metagenomic identification of viral pathogens in clinical samples by real-time nanopore sequencing analysis

scientific article (publication date: 3 June 2015)

Rapid metagenomic identification of viral pathogens in clinical samples by real-time nanopore sequencing analysis.

scientific article

Rapid pathogen detection by metagenomic next-generation sequencing of infected body fluids

scientific article published on 09 November 2020

ReScan, a Multiplex Diagnostic Pipeline, Pans Human Sera for SARS-CoV-2 Antigens

scientific article published on 13 May 2020

Recovery of divergent avian bornaviruses from cases of proventricular dilatation disease: identification of a candidate etiologic agent

scientific article

Review: resolution issues in single-particle reconstruction

scientific article

Rosavirus: the prototype of a proposed new genus of the Picornaviridae family

scientific article

SARS-CoV-2 seroprevalence and neutralizing activity in donor and patient blood

scientific article published on 17 September 2020

SARS-CoV-2 seroprevalence and neutralizing activity in donor and patient blood from the San Francisco Bay Area

scientific article published on 25 May 2020

Severe Epididymo-Orchitis and Encephalitis Complicating Anti-PD-1 Therapy

scientific article published on 01 April 2019

Shotgun transcriptome, spatial omics, and isothermal profiling of SARS-CoV-2 infection reveals unique host responses, viral diversification, and drug interactions

scientific article published on 12 March 2021

Single-molecule sequencing detection of N6-methyladenine in microbial reference materials

scientific article published in Nature Communications

Streptococcus suis meningitis, United States

scientific article published in January 2008

Structural analysis of a fiber-pseudotyped adenovirus with ocular tropism suggests differential modes of cell receptor interactions

scientific article

Taxonomy of the order Mononegavirales: update 2018.

scientific article published on 11 April 2018

Test performance evaluation of SARS-CoV-2 serological assays

scientific article published on 29 April 2020

The B.1.427/1.429 (epsilon) SARS-CoV-2 variants are more virulent than ancestral B.1 (614G) in Syrian hamsters

scientific article published on 10 February 2022

The complete genome of klassevirus - a novel picornavirus in pediatric stool

scientific article published on 18 June 2009

The eukaryotic gut virome in hematopoietic stem cell transplantation: new clues in enteric graft-versus-host disease.

scientific article

The genome sequence of Lone Star virus, a highly divergent bunyavirus found in the Amblyomma americanum tick

scientific article

The hidden threat of unidentified agents of disease in human and veterinary biologicals ⬇️

scientific article published on April 23, 2013

The long march: a sample preparation technique that enhances contig length and coverage by high-throughput short-read sequencing

scientific article

The mitochondrial genome and a 60-kb nuclear DNA segment from Naegleria fowleri, the causative agent of primary amoebic meningoencephalitis.

scientific article published on 29 January 2013

The perils of pathogen discovery: origin of a novel parvovirus-like hybrid genome traced to nucleic acid extraction spin columns

scientific article

Thoracic CT findings of novel influenza A (H1N1) infection in immunocompromised patients

scientific article

Toward an understanding of changes in diversity associated with fecal microbiome transplantation based on 16S rRNA gene deep sequencing

scientific article

Two Rapidly Growing Mycobacterial Species Isolated from a Brain Abscess: First Whole-Genome Sequences of Mycobacterium immunogenum and Mycobacterium llatzerense

scientific article published on 29 April 2015

Two human immunodeficiency virus Type 2 cases in US blood donors including serologic, molecular, and genomic characterization of an epidemiologically unusual case

scientific article published on 15 April 2016

Two sides of a coin: a Zika virus mutation selected in pregnant rhesus macaques promotes fetal infection in mice but at a cost of reduced fitness in nonpregnant macaques and diminished transmissibility by vectors

scientific article published on 30 September 2020

Unlocking capacities of genomics for the COVID-19 response and future pandemics

scientific article published on 08 April 2022

Upregulation of HERV-K is Linked to Immunity and Inflammation in Pulmonary Arterial Hypertension

scientific article published on 21 September 2017

Using a pan-viral microarray assay (Virochip) to screen clinical samples for viral pathogens

scientific article

Utility of DNA microarrays for detection of viruses in acute respiratory tract infections in children

scientific article published on 07 March 2008

Utility of Metagenomic Next-Generation Sequencing for Characterization of HIV and Human Pegivirus Diversity

scientific article published on 23 November 2015

Validation of Metagenomic Next-Generation Sequencing Tests for Universal Pathogen Detection

scientific article

Viral Surveillance in Serum Samples From Patients With Acute Liver Failure By Metagenomic Next-Generation Sequencing

scientific article published on 19 July 2017

Viral infection in acute exacerbation of idiopathic pulmonary fibrosis

scientific article

Viral pathogen discovery ⬇️

scientific article published on May 29, 2013

Whole blood human transcriptome and virome analysis of ME/CFS patients experiencing post-exertional malaise following cardiopulmonary exercise testing

scientific article published on 21 March 2019

Whole-Genome Sequencing of Methicillin-Resistant Staphylococcus aureus Resistant to Fifth-Generation Cephalosporins Reveals Potential Non-mecA Mechanisms of Resistance

scientific article published on 18 February 2016

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