Steve Miller, MD

Title(s)Volunteer Clinical Professor, Laboratory Medicine
SchoolSchool of Medicine
Address185 Berry Street Bldg B, #1235
San Francisco CA 94158
Phone415-353-9630
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    Altmetrics Details PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. Broad, Agnostic Pathogen Detection through Metagenomic Next Generation Sequencing (mNGS) of Cerebrospinal Fluid (CSF) to Diagnose CNS Infections (P7-10.007). Neurology. 2025 Apr 8; 104(7_Supplement_1). Crawford CE, Wang WF, Uehara UA, O’Donovan OB, Gimbrone GN, Gydush GG, Thippabhotla TS, Blicharz BT, Trefry TP, Lennon LN, DeSmet DT, DaSilva DM, Brodeur BW, McDaid ME, Paul PL, Dugan DC, DePina DR, Harold HJ, Conroy CO, Kantak-List KA, Gandbhir GO, Connell CC, Condron CC, Milbury MC, Miller MS. .
      View in: Publisher Site   Mentions:
    2. Clinical impact of metagenomic next-generation sequencing testing on cerebrospinal fluid in a pediatric cohort with suspected central nervous system infections. Journal of the Pediatric Infectious Diseases Society. 2024 Dec 31; 13(Supplement_3):s15-s15. de Lorenzi-Tognon dM, Benoit BP, Brazer BN, Servellita SV, Oseguera OM, Streithorst SJ, Hillberg HM, Ingebrigtsen ID, Zorn ZK, Wilson WM, Blicharz BT, Wong WA, O’Donovan OB, Murray MB, Miller MS, Chiu CC. .
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    3. Pathogen Detection and Associated Patient Characteristics from Clinical Metagenomic Nextgeneration Sequencing Testing for Neurological Infections (S25.002). Neurology. 2024 Apr 9; 102(17_supplement_1). Wong WA, O’Donovan OB, Brazer BN, Nguyen NJ, Oseguera OM, Tang TJ, Omura OC, Servellita SV, Benoit BP, Kelly KE, Miller MS, Chiu CC. .
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    4. In host evolution of beta lactam resistance during active treatment for Pseudomonas aeruginosa bacteremia. Front Cell Infect Microbiol. 2023; 13:1241608. Spottiswoode N, Hao S, Sanchez-Guerrero E, Detweiler AM, Mekonen H, Neff N, Macmillan H, Schwartz BS, Engel J, DeRisi JL, Miller SA, Langelier CR. PMID: 37712060; PMCID: PMC10499174.
      View in: PubMed   Mentions: 2     Fields:    Translation:HumansCells
    5. Metagenomic prediction of antimicrobial resistance in critically ill patients with lower respiratory tract infections. Genome Med. 2022 07 12; 14(1):74. Serpa PH, Deng X, Abdelghany M, Crawford E, Malcolm K, Caldera S, Fung M, McGeever A, Kalantar KL, Lyden A, Ghale R, Deiss T, Neff N, Miller SA, Doernberg SB, Chiu CY, DeRisi JL, Calfee CS, Langelier CR. PMID: 35818068; PMCID: PMC9275031.
      View in: PubMed   Mentions: 26     Fields:    Translation:Humans
    6. Detection of Neoplasms by Metagenomic Next-Generation Sequencing of Cerebrospinal Fluid (S27.004). Neurology. 2022 May 3; 98(18_supplement). Gu GW, Rauschecker RA, Hsu HE, Zorn ZK, Sucu SY, Federman FS, Arevalo AS, Sample SH, Nguyen NE, Talevich TE, Nourbakhsh NB, Gold GC, Cree CB, Douglas DV, Richie RM, Shah SM, Josephson JS, Gelfand GJ, Miller MS, Wang WL, Tihan TT, Wilson WM. .
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    7. Prolonged silent carriage, genomic virulence potential and transmission between staff and patients characterize a neonatal intensive care unit (NICU) outbreak of methicillin-resistant Staphylococcus aureus (MRSA). Infect Control Hosp Epidemiol. 2023 01; 44(1):40-46. Madera S, McNeil N, Serpa PH, Kamm J, Pak C, Caughell C, Nichols A, Dynerman D, Li LM, Sanchez-Guerrero E, Phelps MS, Detweiler AM, Neff N, Reyes H, Miller SA, Yokoe DS, DeRisi JL, Ramirez-Avila L, Langelier CR. PMID: 35311638.
      View in: PubMed   Mentions: 7     Fields:    Translation:HumansCellsPHPublic Health
    8. 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.
      View in: PubMed   Mentions: 29     Fields:    Translation:HumansAnimalsCells
    9. Randomized Trial of Lactin-V to Prevent Recurrence of Bacterial Vaginosis. Obstetrical & Gynecological Survey. 2020 Oct 1; 75(10):601-602. Cohen CC, Wierzbicki WM, French FA, Morris MS, Newmann NS, Reno RH, Green GL, Miller MS, Powell PJ, Parks PT, Hemmerling HA. .
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    10. 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; PMCID: PMC7041574.
      View in: PubMed   Mentions: 39     Fields:    Translation:Humans
    11. 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. Polage PC, Grein GJ, Morgan MM, Doernberg DS, Miller MS, Chinn CR, Woerle WC, Yim YJ, Bittencourt BC, Krishna KS, Ocampo ON, Gibbs GL, Mabalot MS, Quan QK, Khusbu KU, Madey MK, Ganzon GC, Memar MF, Pascual PC, Cohen CS, Liu LC, Yokoe YD, Huang HS. .
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    12. 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. Kerkhoff KA, Matzko MM, Chiu CC, Miller MS, Babik BJ. .
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    13. Clinical metagenomics. Nat Rev Genet. 2019 06; 20(6):341-355. Chiu CY, Miller SA. PMID: 30918369; PMCID: PMC6858796.
      View in: PubMed   Mentions: 656     Fields:    Translation:HumansAnimalsCellsPHPublic Health
    14. 2563. Clinical Metagenomic Next-Generation Sequencing for Diagnosis of Meningitis and Encephalitis. Open Forum Infectious Diseases. 2018 Nov 26; 5(suppl_1):s72-s72. Wilson WM, Sample SH, Zorn ZK, Naccache NS, Miller MS, Chiu CC. .
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    15. 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. Briggs BB, Federman FS, Deng DX, Gu GW, Yu YG, San Martin SC, Miller MS, Chiu CC. .
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    16. Metagenomic Next-Generation Sequencing for Pathogen Detection and Identification. Advanced Techniques in Diagnostic Microbiology. 2018 Jan 1; 617-632. Miller MS, Chiu CC. .
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    17. 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; PMCID: PMC6251619.
      View in: PubMed   Mentions: 54     Fields:    Translation:HumansCells
    18. 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; PMCID: PMC5105111.
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    19. 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.
      View in: PubMed   Mentions: 7     Fields:    Translation:HumansCells
    20. Monitoring for Viral Infections in Transplant Patients. Clinical Microbiology Newsletter. 2016 Aug 1; 38(16):129-134. Miller MS. .
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    21. Clinical Experience Using Broad-Range Polymerase Chain Reaction-Based Sequencing for Pathogen Identification. Open Forum Infectious Diseases. 2015 Dec 9; 2(suppl_1):99. Rutishauser RR, Miller MS. .
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    22. 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; PMCID: PMC4551876.
      View in: PubMed   Mentions: 1  
    23. 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; PMCID: PMC4513157.
      View in: PubMed   Mentions: 3  
    24. 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; PMCID: PMC4481289.
      View in: PubMed   Mentions: 1  
    25. 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; PMCID: PMC4463524.
      View in: PubMed   Mentions: 5  
    26. 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; PMCID: PMC4463534.
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    27. Chapter 11 Solid and Suspension Microarrays for Microbial Diagnostics. . 2015 May 14; 42:395-431. Miller MS, Karaoz KU, Brodie BE, Dunbar DS. .
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    28. 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; PMCID: PMC4473206.
      View in: PubMed   Mentions: 31     Fields:    Translation:HumansCells
    29. 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; PMCID: PMC4345816.
      View in: PubMed   Mentions: 168     Fields:    Translation:HumansCells
    30. 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; PMCID: PMC4134948.
      View in: PubMed   Mentions: 461     Fields:    Translation:HumansCells
    31. 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; PMCID: PMC4079973.
      View in: PubMed   Mentions: 241     Fields:    Translation:Humans
    32. First report of tenosynovitis in an immunocompetent person caused by Mycobacterium heraklionense. JMM Case Reports. 2014 Jun 1; 1(2). Abedalthagafi AM, Rosenberg RO, Miller MS. .
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    33. 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. Miller MS, Wiita WA, Wright WC, Reyes RH, Liu LC. .
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    34. 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; PMCID: PMC3169278.
      View in: PubMed   Mentions: 38     Fields:    Translation:HumansCells
    35. 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; PMCID: PMC3294592.
      View in: PubMed   Mentions: 6     Fields:    Translation:HumansCellsPHPublic Health
    36. 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.
      View in: PubMed   Mentions: 2     Fields:    Translation:Humans
    37. 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.
      View in: PubMed   Mentions: 12     Fields:    Translation:HumansCells
    38. 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; PMCID: PMC2880241.
      View in: PubMed   Mentions: 18     Fields:    Translation:HumansCells
    39. 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. Bonham BM, Miller MS. .
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    40. 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.
      View in: PubMed   Mentions: 4     Fields:    Translation:HumansCells
    41. 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; PMCID: PMC1896014.
      View in: PubMed   Mentions: 50     Fields:    Translation:Animals
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