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Navigating Clinical Utilization of Direct-from-Specimen Metagenomic Pathogen Detection: Clinical Applications, Limitations, and Testing Recommendations. Clin Chem. 2020 11 01; 66(11):1381-1395.
Filkins LM, Bryson AL, Miller SA, Mitchell SL. PMID: 33141913.
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HumansAnimalsCells
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Point-Counterpoint: Should We Be Performing Metagenomic Next-Generation Sequencing for Infectious Disease Diagnosis in the Clinical Laboratory? J Clin Microbiol. 2020 02 24; 58(3).
Miller S, Chiu C, Rodino KG, Miller MB. PMID: 31619533.
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11 Fields:
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Humans
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839. Effect of Clostridioides difficile (C. difficile) Toxin Test Reporting on Clinical Treatment and Outcomes of Toxin-Negative PCR-Positive Patients at Five California Hospitals. Open Forum Infectious Diseases. 2019 Oct 23; 6(Supplement_2):s10-s11.
Christopher R Polage, Jonathan Grein, Margie Morgan, Sarah B Doernberg, Steve Miller, Raymond Chinn, Cathy Woerle, Jennifer Yim, Cassiana Bittencourt, Sneha Krishna, Nicolle Anne Ocampo, Laurel Gibbs, Shannon C Mabalot, Kathleen A Quan, Usme Khusbu, Keith M Madey, Czarina Ganzon, Fatemeh Memar, Christian B Pascual, Stuart Cohen, Catherine Liu, Deborah S Yokoe, Susan S Huang. .
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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. Open Forum Infectious Diseases. 2019 Oct 23; 6(Suppl 2):s134-s135.
Andrew D Kerkhoff, Michelle Matzko, Charles Chiu, Steve Miller, Jennifer M Babik. .
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Clinical metagenomics. Nat Rev Genet. 2019 06; 20(6):341-355.
Chiu CY, Miller SA. PMID: 30918369.
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2563. Clinical Metagenomic Next-Generation Sequencing for Diagnosis of Meningitis and Encephalitis. Open Forum Infectious Diseases. 2018 Nov 26; 5(suppl_1):s72-s72.
Michael Wilson, Hannah Sample, Kelsey Zorn, Samia N Naccache, Steve Miller, Charles Y Chiu. .
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2291. A Real-Time Sequencing Approach for Simultaneous Metagenomic and Transcriptomic-Based Diagnosis of Infectious Diseases. Open Forum Infectious Diseases. 2018 Nov 26; 5(suppl_1):s679-s679.
Benjamin Briggs, Scot Federman, Xian Ding Deng, Wei Gu, Guixia Yu, Claudia Sanchez San Martin, Steve Miller, Charles Y Chiu. .
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Metagenomic Next-Generation Sequencing for Pathogen Detection and Identification. Advanced Techniques in Diagnostic Microbiology. 2018 Jan 1; 617-632.
Steve Miller, Charles Chiu. .
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Neurobrucellosis: Unexpected Answer From Metagenomic Next-Generation Sequencing. J Pediatric Infect Dis Soc. 2017 Nov 24; 6(4):393-398.
Mongkolrattanothai K, Naccache SN, Bender JM, Samayoa E, Pham E, Yu G, Dien Bard J, Miller S, Aldrovandi G, Chiu CY. PMID: 28062553.
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24 Fields:
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HumansCells
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First Draft Genome Sequences of Neisseria sp. Strain 83E34 and Neisseria sp. Strain 74A18, Previously Identified as CDC Eugonic Fermenter 4b Species. Genome Announc. 2016 Nov 10; 4(6).
Greninger AL, Streithorst J, Chiu CY, Miller S. PMID: 27834718.
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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. Diagn Microbiol Infect Dis. 2017 Jan; 87(1):1-6.
Greninger AL, Streithorst J, Golden JA, Chiu CY, Miller S. PMID: 28336132.
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4 Fields:
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HumansCells
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Monitoring for Viral Infections in Transplant Patients. Clinical Microbiology Newsletter. 2016 Aug 1; 38(16):129-134.
Steve Miller. .
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Clinical Experience Using Broad-Range Polymerase Chain Reaction-Based Sequencing for Pathogen Identification. Open Forum Infectious Diseases. 2015 Dec 9; 2(suppl_1):99.
Rachel Rutishauser, Steve Miller. .
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Draft Genome Sequence of Mycobacterium heckeshornense Strain RLE. Genome Announc. 2015 Aug 27; 3(4).
Greninger AL, Cunningham G, Chiu CY, Miller S. PMID: 26316632.
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Draft Genome Sequence of Mycobacterium heraklionense Strain Davo. Genome Announc. 2015 Jul 23; 3(4).
Greninger AL, Cunningham G, Chiu CY, Miller S. PMID: 26205863.
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Draft Genome Sequence of Mycobacterium elephantis Strain Lipa. Genome Announc. 2015 Jun 25; 3(3).
Greninger AL, Cunningham G, Yu JM, Hsu ED, Chiu CY, Miller S. PMID: 26112791.
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Draft Genome Sequence of Mycobacterium obuense Strain UC1, Isolated from Patient Sputum. Genome Announc. 2015 Jun 11; 3(3).
Greninger AL, Cunningham G, Hsu ED, Yu JM, Chiu CY, Miller S. PMID: 26067960.
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Draft Genome Sequence of Mycobacterium arupense Strain GUC1. Genome Announc. 2015 Jun 11; 3(3).
Greninger AL, Cunningham G, Yu JM, Hsu ED, Chiu CY, Miller S. PMID: 26067970.
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Two Rapidly Growing Mycobacterial Species Isolated from a Brain Abscess: First Whole-Genome Sequences of Mycobacterium immunogenum and Mycobacterium llatzerense. J Clin Microbiol. 2015 Jul; 53(7):2374-7.
Greninger AL, Langelier C, Cunningham G, Keh C, Melgar M, Chiu CY, Miller S. PMID: 25926490.
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17 Fields:
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HumansCells
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Diagnosis of neuroinvasive astrovirus infection in an immunocompromised adult with encephalitis by unbiased next-generation sequencing. Clin Infect Dis. 2015 Mar 15; 60(6):919-23.
Naccache SN, Peggs KS, Mattes FM, Phadke R, Garson JA, Grant P, Samayoa E, Federman S, Miller S, Lunn MP, Gant V, Chiu CY. PMID: 25572898.
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107 Fields:
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HumansCells
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Actionable diagnosis of neuroleptospirosis by next-generation sequencing. N Engl J Med. 2014 Jun 19; 370(25):2408-17.
Wilson MR, Naccache SN, Samayoa E, Biagtan M, Bashir H, Yu G, Salamat SM, Somasekar S, Federman S, Miller S, Sokolic R, Garabedian E, Candotti F, Buckley RH, Reed KD, Meyer TL, Seroogy CM, Galloway R, Henderson SL, Gern JE, DeRisi JL, Chiu CY. PMID: 24896819.
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230 Fields:
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HumansCells
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A cloud-compatible bioinformatics pipeline for ultrarapid pathogen identification from next-generation sequencing of clinical samples. Genome Res. 2014 Jul; 24(7):1180-92.
Naccache SN, Federman S, Veeraraghavan N, Zaharia M, Lee D, Samayoa E, Bouquet J, Greninger AL, Luk KC, Enge B, Wadford DA, Messenger SL, Genrich GL, Pellegrino K, Grard G, Leroy E, Schneider BS, Fair JN, Martínez MA, Isa P, Crump JA, DeRisi JL, Sittler T, Hackett J, Miller S, Chiu CY. PMID: 24899342.
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164 Fields:
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Humans
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First report of tenosynovitis in an immunocompetent person caused by Mycobacterium heraklionense. JMM Case Reports. 2014 Jun 1; 1(2).
Malak Abedalthagafi, Oren Rosenberg, Steve Miller. .
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Evaluation of Glutamate Dehydrogenase Immunoassay Screening with Toxin Confirmation for the Diagnosis of Clostridium difficile Infection. Lab Medicine. 2013 Aug 1; 44(3):e65-e71.
Steve Miller, Arun Wiita, Carolyn Wright, Helen Reyes, Catherine Liu. .
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Using a pan-viral microarray assay (Virochip) to screen clinical samples for viral pathogens. J Vis Exp. 2011 Apr 27; (50).
Chen EC, Miller SA, DeRisi JL, Chiu CY. PMID: 21559002.
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30 Fields:
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HumansCells
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Pandemic (H1N1) 2009 infection in patients with hematologic malignancy. Emerg Infect Dis. 2010 Dec; 16(12):1910-7.
Liu C, Schwartz BS, Vallabhaneni S, Nixon M, Chin-Hong PV, Miller SA, Chiu C, Damon L, Drew WL. PMID: 21122221.
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6 Fields:
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HumansCellsPHPublic Health
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Cytologic evaluation can predict microbial culture results for infectious causes of pulmonary nodules in patients undergoing fine needle aspiration biopsy. Diagn Microbiol Infect Dis. 2010 Nov; 68(3):330-3.
Miller SA, van Zante A, Schwartz BS. PMID: 20955918.
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1 Fields:
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Humans
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Detection of vancomycin-intermediate Staphylococcus aureus with the updated Trek-Sensititre System and the MicroScan System. Comparison with results from the conventional Etest and CLSI standardized MIC methods. Am J Clin Pathol. 2010 Jun; 133(6):844-8.
Nadarajah R, Post LR, Liu C, Miller SA, Sahm DF, Brooks GF. PMID: 20472841.
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12 Fields:
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HumansCells
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Thoracic CT findings of novel influenza A (H1N1) infection in immunocompromised patients. Emerg Radiol. 2010 Jul; 17(4):299-307.
Elicker BM, Schwartz BS, Liu C, Chen EC, Miller SA, Chiu CY, Webb WR. PMID: 20111882.
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15 Fields:
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HumansCells
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Clinical Comparison of 99th Percentile and 10% Coefficient of Variation Cutoff Values for Four Commercially Available Troponin I Assays. Lab Medicine. 2009 Aug 1; 40(8):470-473.
Michael Bonham, Steve Miller. .
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Evaluation of a new-generation line-probe assay that detects 5' untranslated and core regions to genotype and subtype hepatitis C virus. Am J Clin Pathol. 2007 Aug; 128(2):300-4.
Nadarajah R, Khan GY, Miller SA, Brooks GF. PMID: 17638666.
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5 Fields:
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HumansCells
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Gene expression patterns during adaptation of a helminth parasite to different environmental niches. Genome Biol. 2007; 8(4):R65.
Jolly ER, Chin CS, Miller S, Bahgat MM, Lim KC, DeRisi J, McKerrow JH. PMID: 17456242.
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48 Fields:
Translation:
Animals