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Chiu Laboratory / UCSF-Abbott Viral Diagnostics and Discovery Center (VDDC)

Viral pathogen discovery (Chiu, Current Opinion in Microbiology. What are microarrays and deep sequencing? Chiu and Miller, Microbe. Genomic assays for identification of chikungunya virus in blood donors, Puerto Rico, 2014. Emerging Infectious Diseases 2015. A novel outbreak enterovirus D68 strain associated with acute flaccid myelitis cases in the United States from 2012-2014. Clinical Infectious Diseases 2015. Actionable diagnosis of neuroleptospirosis by next-generation sequencing. J Euk Microbiol 2013.

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Chiu Laboratory / UCSF-Abbott Viral Diagnostics and Discovery Center (VDDC) | chiulab.ucsf.edu Reviews

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Viral pathogen discovery (Chiu, Current Opinion in Microbiology. What are microarrays and deep sequencing? Chiu and Miller, Microbe. Genomic assays for identification of chikungunya virus in blood donors, Puerto Rico, 2014. Emerging Infectious Diseases 2015. A novel outbreak enterovirus D68 strain associated with acute flaccid myelitis cases in the United States from 2012-2014. Clinical Infectious Diseases 2015. Actionable diagnosis of neuroleptospirosis by next-generation sequencing. J Euk Microbiol 2013.

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Chiu Laboratory / UCSF-Abbott Viral Diagnostics and Discovery Center (VDDC) | chiulab.ucsf.edu Reviews

https://chiulab.ucsf.edu

Viral pathogen discovery (Chiu, Current Opinion in Microbiology. What are microarrays and deep sequencing? Chiu and Miller, Microbe. Genomic assays for identification of chikungunya virus in blood donors, Puerto Rico, 2014. Emerging Infectious Diseases 2015. A novel outbreak enterovirus D68 strain associated with acute flaccid myelitis cases in the United States from 2012-2014. Clinical Infectious Diseases 2015. Actionable diagnosis of neuroleptospirosis by next-generation sequencing. J Euk Microbiol 2013.

INTERNAL PAGES

chiulab.ucsf.edu

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Press

http://chiulab.ucsf.edu/press.html

Click here to collapse newspaper press. Diagnosis of Neuroleptospirosis by Next-Generation Sequencing - the New York Times. In a First, Test of DNA Finds Root of Illness (June 5th, 2014). Quick DNA Tests Crack Medical Mysteries Otherwise Missed (June 5th, 2014). Study Confirms Erroneous Link Between Prostate Cancer and Retrovirus from Mice. Researchers trace back contamination of XMRV in cancer tissue sample (September 18th, 2012). The Final Chapter on XMRV and Prostate Cancer. Don't Use a Broom to Sweep...

2

UCSF Research Lab

http://chiulab.ucsf.edu/personnel.html

Charles Chiu, MD/PhD. Associate Professor, Laboratory Medicine. And Medicine / Infectious Diseases. Director of the UCSF Viral Diagnostics and Discovery Center. Assistant Director, UCSF Clinical Microbiology Laboratory. Steve Miller, MD/PhD. Associate Professor, Laboratory Medicine. Director, UCSF Clinical Microbiology Laboratory. Co-Director, UCSF Viral Diagnostics and Discovery Center. Samia Naccache, PhD. Deanna Lee, PhD. Guixia Yu, BS. Research Associate, Chiu Laboratory. Erik Samayoa, BS/CLS. Curren...

3

UCSF Research Lab

http://chiulab.ucsf.edu/lab.html

Research in the Chiu laboratory focuses on detection of known and novel viral agents. In acute diseases suspected to have an infectious etiology. We use the ViroChip microarray. A viral microarray with 60,000 probes designed to detect all viruses, both known and novel, on the basis of sequence homology. In parallel, we employ next-generation sequencing. The National Research Fund for Tick-Borne Diseases (NRFTD). The University of California Discovery Grant Program. And the Rogers Family Foundation.

4

UCSF Research Lab

http://chiulab.ucsf.edu/collab.html

We are unable to perform clinical diagnostic testing, and only recommend that patients see their personal physician to discuss available clinical test options. Our center, in conjunction with the UCSF Clinical Microbiology Laboratory, has developed and is in the process of validating new clinical diagnostic tests. One such test is a metagenomic next-generation sequencing (mNGS) test. This web site will be continually updated as new sample types and indications are available for clinical testing.

5

SURPI™

http://chiulab.ucsf.edu/surpi

Sequence-based Ultra-Rapid Pathogen Identification. SURPI™ is a computational pipeline for pathogen identification from complex metagenomic next-generation sequencing (NGS) data generated from clinical samples. Our manuscript describing SURPI™ has been published in Genome Research. SURPI™ is available under the 2-clause BSD license on github. A script to install SURPI™ locally is available. The script is designed to install SURPI™ and all software dependencies onto a machine running Ubunt...Link to an AM...

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Viral pathogen discovery (Chiu, Current Opinion in Microbiology. What are microarrays and deep sequencing? Chiu and Miller, Microbe. Genomic assays for identification of chikungunya virus in blood donors, Puerto Rico, 2014. Emerging Infectious Diseases 2015. A novel outbreak enterovirus D68 strain associated with acute flaccid myelitis cases in the United States from 2012-2014. Clinical Infectious Diseases 2015. Actionable diagnosis of neuroleptospirosis by next-generation sequencing. J Euk Microbiol 2013.

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