Charles Chiu, MD, PhD
Professor
Laboratory Medicine
School of Medicine

is a Professor of Laboratory Medicine and Medicine, Division of Infectious Diseases at University of California, San Francisco, Director of the UCSF-Abbott Viral Diagnostics and Discovery Center (VDDC), and Associate Director of the UCSF Clinical Microbiology Laboratory, He is a board-certified consulting infectious diseases physician at UCSF, and practices in both infectious diseases and clinical microbiology. Dr. Chiu obtained an MD and PhD in biophysics from UCLA and subsequently completed an internal medicine residency, infectious diseases fellowship, and postdoctoral research at UCSF. He heads a translational research laboratory engaged in clinical next-generation sequencing assay development for diagnosis of infectious diseases, pathogen discovery, bioinformatics software development, nanopore sequencing, and characterization of emerging infections (Lyme disease, enterovirus D68, and Zika virus). His work is supported by research grants from the NIH, Abbott Laboratories, Bay Area Lyme Disease Foundation, Global Lyme Alliance, USAID PREDICT program, UC Center for Accelerated Innovation, Sandler / Bowes Foundation, and California Initiative to Advance Precision Medicine. Dr. Chiu has authored more than 50 peer-reviewed publications, holds over 15 patents and patent applications, and serves on the scientific advisory board for Therabio, Karius, and Rubicon Genomics.

• Complement Factor I Gene Variant as a Treatable Cause of Recurrent Aseptic Neutrophilic Meningitis: A Case Report.
  Neurology(R) neuroimmunology & neuroinflammation 2023 Rolfes M, Harroud A, Zorn KC, Tubati A, Omura C, Kurtz K, Matloubian M, Berger A, Chiu CY, Wilson MR, Ramachandran PS
• Association of Culturable-Virus Detection and Household Transmission of SARS-CoV-2, California and Tennessee, 2020-2022.
  The Journal of infectious diseases 2023 Deyoe JE, Kelly JD, Grijalva CG, Bonenfant G, Lu S, Anglin K, Garcia-Knight M, Pineda-Ramirez J, Hagen MB, Saydah S, Abedi GR, Goldberg SA, Tassetto M, Zhang A, Donohue KC, Davidson MC, Sanchez RD, …
• Phage diversity in cell-free DNA identifies bacterial pathogens in human sepsis cases.
  Nature microbiology 2023 Haddock NL, Barkal LJ, Ram-Mohan N, Kaber G, Chiu CY, Bhatt AS, Yang S, Bollyky PL
• Metagenomic Detection of Divergent Insect- and Bat-Associated Viruses in Plasma from Two African Individuals Enrolled in Blood-Borne Surveillance.
  Viruses 2023 Orf GS, Olivo A, Harris B, Weiss SL, Achari A, Yu G, Federman S, Mbanya D, James L, Mampunza S, Chiu CY, Rodgers MA, Cloherty GA, Berg MG
• Nucleic acid biomarkers of immune response and cell and tissue damage in children with COVID-19 and MIS-C.
  Cell reports. Medicine 2023 Loy CJ, Sotomayor-Gonzalez A, Servellita V, Nguyen J, Lenz J, Bhattacharya S, Williams ME, Cheng AP, Bliss A, Saldhi P, Brazer N, Streithorst J, Suslovic W, Hsieh CJ, Bahar B, Wood N, Foresythe A, …
• Powassan Virus Infection Detected by Metagenomic Next-Generation Sequencing, Ohio, USA.
  Emerging infectious diseases 2023 Farrington M, Elenz J, Ginsberg M, Chiu CY, Miller S, Pangonis SF
• Adeno-associated virus type 2 in US children with acute severe hepatitis.
  Nature 2023 Servellita V, Sotomayor Gonzalez A, Lamson DM, Foresythe A, Huh HJ, Bazinet AL, Bergman NH, Bull RL, Garcia KY, Goodrich JS, Lovett SP, Parker K, Radune D, Hatada A, Pan CY, Rizzo K, Bertumen JB, …
• Purifying selection decreases the potential for Bangui orthobunyavirus outbreaks in humans.
  Virus evolution 2023 Orf GS, Perez LJ, Meyer TV, Luk KC, Forberg K, Rodgers MA, Hadji A, James L, Mampunza S, Achari A, Yu G, Federman S, Chiu CY, McArthur CA, Cloherty GA, Berg MG
• Longitudinal comparison of the developing gut virome in infants and their mothers.
  Cell host & microbe 2023 Walters WA, Granados AC, Ley C, Federman S, Stryke D, Santos Y, Haggerty T, Sotomayor-Gonzalez A, Servellita V, Ley RE, Parsonnet J, Chiu CY
• Transfusion-Transmitted Cache Valley Virus Infection in a Kidney Transplant Recipient With Meningoencephalitis.
  Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2023 Al-Heeti O, Wu EL, Ison MG, Saluja RK, Ramsey G, Matkovic E, Ha K, Hall S, Banach B, Wilson MR, Miller S, Chiu CY, McCabe M, Bari C, Zimler RA, Babiker H, Freeman D, Popovitch J, Annambhotla P, Lehman…
• Successful Treatment of Balamuthia mandrillaris Granulomatous Amebic Encephalitis with Nitroxoline.
  Emerging infectious diseases 2023 Spottiswoode N, Pet D, Kim A, Gruenberg K, Shah M, Ramachandran A, Laurie MT, Zia M, Fouassier C, Boutros CL, Lu R, Zhang Y, Servellita V, Bollen A, Chiu CY, Wilson MR, Valdivia L, DeRisi JL
• SARS-CoV-2 Spike triggers barrier dysfunction and vascular leak via integrins and TGF-β signaling.
  Nature communications 2022 Biering SB, Gomes de Sousa FT, Tjang LV, Pahmeier F, Zhu C, Ruan R, Blanc SF, Patel TS, Worthington CM, Glasner DR, Castillo-Rojas B, Servellita V, Lo NTN, Wong MP, Warnes CM, Sandoval DR, Clausen TM,…
• Neutralizing Immunity Induced Against the Omicron BA.1 and BA.2 Variants in Vaccine Breakthrough Infections.
  The Journal of infectious diseases 2022 Brazer N, Morris MK, Servellita V, Anglin K, Saldhi P, Garcia-Knight M, Bethancourt S, Sotomayor-Gonzalez A, Wang B, Foresythe A, Nguyen J, Gliwa AS, Pineda-Ramirez J, Sanchez RD, Zhang Y, Ott M, …
• Magnitude and Determinants of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Household Transmission: A Longitudinal Cohort Study.
  Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2022 Kelly JD, Lu S, Anglin K, Garcia-Knight M, Pineda-Ramirez J, Goldberg SA, Tassetto M, Zhang A, Donohue K, Davidson MC, Romero M, Diaz Sanchez R, Djomaleu M, Mathur S, Chen JY, Forman CA, Servellita V,…
• Infectious viral shedding of SARS-CoV-2 Delta following vaccination: A longitudinal cohort study.
  PLoS pathogens 2022 Garcia-Knight M, Anglin K, Tassetto M, Lu S, Zhang A, Goldberg SA, Catching A, Davidson MC, Shak JR, Romero M, Pineda-Ramirez J, Diaz-Sanchez R, Rugart P, Donohue K, Massachi J, Sans HM, Djomaleu M, …
• Contact-Tracing Outcomes Among Household Contacts of Fully Vaccinated Coronavirus Disease 2019 (COVID-19) Patients: San Francisco, California, 29 January-2 July 2021.
  Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2022 Sachdev DD, Chew Ng R, Sankaran M, Ernst A, Hernandez KT, Servellita V, Sotomayor-Gonzalez A, Stoltey J, Cohen SE, Nguyen TQ, Chiu CY, Philip S
• Author Correction: Efficacy of an inactivated Zika vaccine against virus infection during pregnancy in mice and marmosets.
  NPJ vaccines 2022 Kim IJ, Lanthier PA, Clark MJ, De La Barrera RA, Tighe MP, Szaba FM, Travis KL, Low-Beer TC, Cookenham TS, Lanzer KG, Bernacki DT, Johnson LL, Schneck AA, Ross CN, Tardif SD, Layne-Colon D, Mdaki SD, …
• An intranasal ASO therapeutic targeting SARS-CoV-2.
  Nature communications 2022 Zhu C, Lee JY, Woo JZ, Xu L, Nguyenla X, Yamashiro LH, Ji F, Biering SB, Van Dis E, Gonzalez F, Fox D, Wehri E, Rustagi A, Pinsky BA, Schaletzky J, Blish CA, Chiu C, Harris E, Sadreyev RI, Stanley S, …
• A diagnostic classifier for gene expression-based identification of early Lyme disease.
  Communications medicine 2022 Servellita V, Bouquet J, Rebman A, Yang T, Samayoa E, Miller S, Stone M, Lanteri M, Busch M, Tang P, Morshed M, Soloski MJ, Aucott J, Chiu CY
• Metagenomic prediction of antimicrobial resistance in critically ill patients with lower respiratory tract infections.
  Genome medicine 2022 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 …
• COVID-19 Variant Detection with a High-Fidelity CRISPR-Cas12 Enzyme.
  Journal of clinical microbiology 2022 Fasching CL, Servellita V, McKay B, Nagesh V, Broughton JP, Sotomayor-Gonzalez A, Wang B, Brazer N, Reyes K, Streithorst J, Deraney RN, Stanfield E, Hendriks CG, Fung B, Miller S, Ching J, Chen JS, …
• Limited cross-variant immunity from SARS-CoV-2 Omicron without vaccination.
  Nature 2022 Suryawanshi RK, Chen IP, Ma T, Syed AM, Brazer N, Saldhi P, Simoneau CR, Ciling A, Khalid MM, Sreekumar B, Chen PY, Kumar GR, Montano M, Gascon R, Tsou CL, Garcia-Knight MA, Sotomayor-Gonzalez A, …
• COVID-19 in vaccinated versus unvaccinated hematologic malignancy patients.
  Transplant infectious disease : an official journal of the Transplantation Society 2022 DeVoe C, Pandey S, Shariff D, Arora S, Henrich TJ, Yokoe DS, Langelier CR, Servellita V, Chiu C, Miller S, Babik JM, Chin-Hong P, Fung M
• Unlocking capacities of genomics for the COVID-19 response and future pandemics.
  Nature methods 2022 Knyazev S, Chhugani K, Sarwal V, Ayyala R, Singh H, Karthikeyan S, Deshpande D, Baykal PI, Comarova Z, Lu A, Porozov Y, Vasylyeva TI, Wertheim JO, Tierney BT, Chiu CY, Sun R, Wu A, Abedalthagafi MS, …
• Neutralizing immunity in vaccine breakthrough infections from the SARS-CoV-2 Omicron and Delta variants.
  Cell 2022 Servellita V, Syed AM, Morris MK, Brazer N, Saldhi P, Garcia-Knight M, Sreekumar B, Khalid MM, Ciling A, Chen PY, Kumar GR, Gliwa AS, Nguyen J, Sotomayor-Gonzalez A, Zhang Y, Frias E, Prostko J, …
• Individualized Constellation of Killer Cell Immunoglobulin-Like Receptors and Cognate HLA Class I Ligands that Controls Natural Killer Cell Antiviral Immunity Predisposes COVID-19.
  Frontiers in genetics 2022 Maruthamuthu S, Rajalingam K, Kaur N, Morvan MG, Soto J, Lee N, Kong D, Hu Z, Reyes K, Ng D, Butte AJ, Chiu C, Rajalingam R
• The B.1.427/1.429 (epsilon) SARS-CoV-2 variants are more virulent than ancestral B.1 (614G) in Syrian hamsters.
  PLoS pathogens 2022 Carroll T, Fox D, van Doremalen N, Ball E, Morris MK, Sotomayor-Gonzalez A, Servellita V, Rustagi A, Yinda CK, Fritts L, Port JR, Ma ZM, Holbrook MG, Schulz J, Blish CA, Hanson C, Chiu CY, Munster V, …
• Limited Cross-Variant Immunity after Infection with the SARS-CoV-2 Omicron Variant Without Vaccination.
  medRxiv : the preprint server for health sciences 2022 Suryawanshi RK, Chen IP, Ma T, Syed AM, Brazer N, Saldhi P, Simoneau CR, Ciling A, Khalid MM, Sreekumar B, Chen PY, Kumar GR, Montano M, Garcia-Knight MA, Sotomayor-Gonzalez A, Servellita V, Gliwa A, …
• Efficacy of an inactivated Zika vaccine against virus infection during pregnancy in mice and marmosets.
  NPJ vaccines 2022 Kim IJ, Lanthier PA, Clark MJ, De La Barrera RA, Tighe MP, Szaba FM, Travis KL, Low-Beer TC, Cookenham TS, Lanzer KG, Bernacki DT, Johnson LL, Schneck AA, Ross CN, Tardif SD, Layne-Colon D, Mdaki SD, …
• Detection of SARS-CoV-2 variants by Abbott molecular, antigen, and serological tests.
  Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology 2022 Rodgers MA, Olivo A, Harris BJ, Lark C, Luo X, Berg MG, Meyer TV, Mohaimani A, Orf GS, Goldstein Y, Fox AS, Hirschhorn J, Glen WB, Nolte F, Landay A, Jennings C, Moy J, Servellita V, Chiu C, Batra R, …
• Predominance of antibody-resistant SARS-CoV-2 variants in vaccine breakthrough cases from the San Francisco Bay Area, California.
  Nature microbiology 2022 Servellita V, Morris MK, Sotomayor-Gonzalez A, Gliwa AS, Torres E, Brazer N, Zhou A, Hernandez KT, Sankaran M, Wang B, Wong D, Wang C, Zhang Y, Reyes KR, Glasner D, Deng X, Streithorst J, Miller S, …
• The Role of Metagenomics and Next-Generation Sequencing in Infectious Disease Diagnosis.
  Clinical chemistry 2021 Miller S, Chiu C
• A Rare Bird: Diagnosis of Psittacosis Meningitis by Clinical Metagenomic Next-Generation Sequencing.
  Open forum infectious diseases 2021 Davar K, Wilson MR, Miller S, Chiu CY, Vijayan T
• Detection of Neoplasms by Metagenomic Next-Generation Sequencing of Cerebrospinal Fluid.
  JAMA neurology 2021 Gu W, Rauschecker AM, Hsu E, Zorn KC, Sucu Y, Federman S, Gopez A, Arevalo S, Sample HA, Talevich E, Nguyen ED, Gottschall M, Nourbakhsh B, Gold CA, Cree BAC, Douglas VC, Richie MB, Shah MP, Josephson…
• Author Correction: Pan-viral serology implicates enteroviruses in acute flaccid myelitis.
  Nature medicine 2021 Schubert RD, Hawes IA, Ramachandran PS, Ramesh A, Crawford ED, Pak JE, Wu W, Cheung CK, O'Donovan BD, Tato CM, Lyden A, Tan M, Sit R, Sowa GM, Sample HA, Zorn KC, Banerji D, Khan LM, Bove R, Hauser SL…
• The B.1.427/1.429 (epsilon) SARS-CoV-2 variants are more virulent than ancestral B.1 (614G) in Syrian hamsters.
  bioRxiv : the preprint server for biology 2021 Carroll T, Fox D, van Doremalen N, Ball E, Morris MK, Sotomayor-Gonzalez A, Servellita V, Rustagi A, Yinda CK, Fritts L, Port JR, Ma ZM, Holbrook M, Schulz J, Blish CA, Hanson C, Chiu CY, Munster V, …
• Community Transmission of Severe Acute Respiratory Syndrome Coronavirus 2 Disproportionately Affects the Latinx Population During Shelter-in-Place in San Francisco.
  Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2021 Chamie G, Marquez C, Crawford E, Peng J, Petersen M, Schwab D, Schwab J, Martinez J, Jones D, Black D, Gandhi M, Kerkhoff AD, Jain V, Sergi F, Jacobo J, Rojas S, Tulier-Laiwa V, Gallardo-Brown T, Appa…
• SARS-CoV-2 antibody magnitude and detectability are driven by disease severity, timing, and assay.
  Science advances 2021 Peluso MJ, Takahashi S, Hakim J, Kelly JD, Torres L, Iyer NS, Turcios K, Janson O, Munter SE, Thanh C, Donatelli J, Nixon CC, Hoh R, Tai V, Fehrman EA, Hernandez Y, Spinelli MA, Gandhi M, Palafox MA, …
• Genomics and transcriptomics yields a system-level view of the biology of the pathogen Naegleria fowleri.
  BMC biology 2021 Herman EK, Greninger A, van der Giezen M, Ginger ML, Ramirez-Macias I, Miller HC, Morgan MJ, Tsaousis AD, Velle K, Vargová R, Záhonová K, Najle SR, MacIntyre G, Muller N, Wittwer M, Zysset-Burri DC, …
• Use of Metagenomic Next-Generation Sequencing to Identify Pathogens in Pediatric Osteoarticular Infections.
  Open forum infectious diseases 2021 Ramchandar N, Burns J, Coufal NG, Pennock A, Briggs B, Stinnett R, Bradley J, Arnold J, Liu GY, Pring M, Upasani VV, Rickert K, Dimmock D, Chiu C, Farnaes L, Cannavino C
• Introduction, Transmission Dynamics, and Fate of Early Severe Acute Respiratory Syndrome Coronavirus 2 Lineages in Santa Clara County, California.
  The Journal of infectious diseases 2021 Villarino E, Deng X, Kemper CA, Jorden MA, Bonin B, Rudman SL, Han GS, Yu G, Wang C, Federman S, Bushnell B, CZB COVIDTracker Consortium, Wadford DA, Lin W, Tao Y, Paden CR, Bhatnagar J, MacCannell T,…
• In vivo monoclonal antibody efficacy against SARS-CoV-2 variant strains.
  Nature 2021 Chen RE, Winkler ES, Case JB, Aziati ID, Bricker TL, Joshi A, Darling TL, Ying B, Errico JM, Shrihari S, VanBlargan LA, Xie X, Gilchuk P, Zost SJ, Droit L, Liu Z, Stumpf S, Wang D, Handley SA, Stine …
• Connecting the Dots: Translating the Vaginal Microbiome Into a Drug.
  The Journal of infectious diseases 2021 Lagenaur LA, Hemmerling A, Chiu C, Miller S, Lee PP, Cohen CR, Parks TP
• Detection of cryptogenic malignancies from metagenomic whole genome sequencing of body fluids.
  Genome medicine 2021 Gu W, Talevich E, Hsu E, Qi Z, Urisman A, Federman S, Gopez A, Arevalo S, Gottschall M, Liao L, Tung J, Chen L, Lim H, Ho C, Kasowski M, Oak J, Holmes BJ, Yeh I, Yu J, Wang L, Miller S, DeRisi JL, …
• In vivo monoclonal antibody efficacy against SARS-CoV-2 variant strains.
  Research square 2021 Diamond M, Chen R, Winkler E, Case J, Aziati I, Bricker T, Joshi A, Darling T, Ying B, Errico J, Shrihari S, VanBlargan L, Xie X, Gilchuk P, Zost S, Droit L, Liu Z, Stumpf S, Wang D, Handley S, Stine …
• Transmission, infectivity, and neutralization of a spike L452R SARS-CoV-2 variant.
  Cell 2021 Deng X, Garcia-Knight MA, Khalid MM, Servellita V, Wang C, Morris MK, Sotomayor-González A, Glasner DR, Reyes KR, Gliwa AS, Reddy NP, Sanchez San Martin C, Federman S, Cheng J, Balcerek J, Taylor J, …
• Pathologic Findings Associated With a Case of Acute Flaccid Myelitis.
  Journal of neuropathology and experimental neurology 2021 Haddad AF, Hofmann JW, Oh T, Jacques L, Yu G, Chiu C, Nolan A, Strober J, Gupta N
• Emergence and rapid transmission of SARS-CoV-2 B.1.1.7 in the United States.
  Cell 2021 Washington NL, Gangavarapu K, Zeller M, Bolze A, Cirulli ET, Schiabor Barrett KM, Larsen BB, Anderson C, White S, Cassens T, Jacobs S, Levan G, Nguyen J, Ramirez JM, Rivera-Garcia C, Sandoval E, Wang …
• Shotgun transcriptome, spatial omics, and isothermal profiling of SARS-CoV-2 infection reveals unique host responses, viral diversification, and drug interactions.
  Nature communications 2021 Butler D, Mozsary C, Meydan C, Foox J, Rosiene J, Shaiber A, Danko D, Afshinnekoo E, MacKay M, Sedlazeck FJ, Ivanov NA, Sierra M, Pohle D, Zietz M, Gisladottir U, Ramlall V, Sholle ET, Schenck EJ, …
• Transmission, infectivity, and antibody neutralization of an emerging SARS-CoV-2 variant in California carrying a L452R spike protein mutation.
  medRxiv : the preprint server for health sciences 2021 Deng X, Garcia-Knight MA, Khalid MM, Servellita V, Wang C, Morris MK, Sotomayor-González A, Glasner DR, Reyes KR, Gliwa AS, Reddy NP, Martin CSS, Federman S, Cheng J, Balcerek J, Taylor J, Streithorst…
• SARS-CoV-2 antibody magnitude and detectability are driven by disease severity, timing, and assay.
  medRxiv : the preprint server for health sciences 2021 Peluso MJ, Takahashi S, Hakim J, Kelly JD, Torres L, Iyer NS, Turcios K, Janson O, Munter SE, Thanh C, Nixon CC, Hoh R, Tai V, Fehrman EA, Hernandez Y, Spinelli MA, Gandhi M, Palafox MA, Vallari A, …
• Genomic epidemiology identifies emergence and rapid transmission of SARS-CoV-2 B.1.1.7 in the United States.
  medRxiv : the preprint server for health sciences 2021 Washington NL, Gangavarapu K, Zeller M, Bolze A, Cirulli ET, Barrett KMS, Larsen BB, Anderson C, White S, Cassens T, Jacobs S, Levan G, Nguyen J, Ramirez JM, Rivera-Garcia C, Sandoval E, Wang X, Wong …
• A diagnostic host response biosignature for COVID-19 from RNA profiling of nasal swabs and blood.
  Science advances 2021 Ng DL, Granados AC, Santos YA, Servellita V, Goldgof GM, Meydan C, Sotomayor-Gonzalez A, Levine AG, Balcerek J, Han LM, Akagi N, Truong K, Neumann NM, Nguyen DN, Bapat SP, Cheng J, Martin CS, Federman…
• Cell-free DNA tissues of origin by methylation profiling reveals significant cell, tissue, and organ-specific injury related to COVID-19 severity.
  Med (New York, N.Y.) 2021 Cheng AP, Cheng MP, Gu W, Sesing Lenz J, Hsu E, Schurr E, Bourque G, Bourgey M, Ritz J, Marty FM, Chiu CY, Vinh DC, De Vlaminck I
• Digital droplet PCR accurately quantifies SARS-CoV-2 viral load from crude lysate without nucleic acid purification.
  Scientific reports 2021 Vasudevan HN, Xu P, Servellita V, Miller S, Liu L, Gopez A, Chiu CY, Abate AR
• Associations of Early COVID-19 Cases in San Francisco With Domestic and International Travel.
  Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2020 Gu W, Deng X, Reyes K, Hsu E, Wang C, Sotomayor-Gonzalez A, Federman S, Bushnell B, Miller S, Chiu CY
• Timely intervention and control of a novel coronavirus (COVID-19) outbreak at a large skilled nursing facility-San Francisco, California, 2020.
  Infection control and hospital epidemiology 2020 Karmarkar EN, Blanco I, Amornkul PN, DuBois A, Deng X, Moonan PK, Rubenstein BL, Miller DA, Kennedy I, Yu J, Dauterman JP, Ongpin M, Hathaway W, Hoo L, Trammell S, Dosunmu EF, Yu G, Khwaja Z, Lu W, …
• Fatal Case of Chronic Jamestown Canyon Virus Encephalitis Diagnosed by Metagenomic Sequencing in Patient Receiving Rituximab.
  Emerging infectious diseases 2020 Solomon IH, Ganesh VS, Yu G, Deng XD, Wilson MR, Miller S, Milligan TA, Mukerji SS, Mathewson A, Linxweiler J, Morse D, Ritter JM, Staples JE, Hughes H, Gould CV, Sabeti PC, Chiu CY, Piantadosi A
• 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.
  Journal of virology 2020 Lemos D, Stuart JB, Louie W, Singapuri A, Ramírez AL, Watanabe J, Usachenko J, Keesler RI, Sanchez-San Martin C, Li T, Martyn C, Oliveira G, Saraf S, Grubaugh ND, Andersen KG, Thissen J, Allen J, …
• Rapid pathogen detection by metagenomic next-generation sequencing of infected body fluids.
  Nature medicine 2020 Gu W, Deng X, Lee M, Sucu YD, Arevalo S, Stryke D, Federman S, Gopez A, Reyes K, Zorn K, Sample H, Yu G, Ishpuniani G, Briggs B, Chow ED, Berger A, Wilson MR, Wang C, Hsu E, Miller S, DeRisi JL, Chiu …
• Universal Polymerase Chain Reaction and Antibody Testing Demonstrate Little to No Transmission of Severe Acute Respiratory Syndrome Coronavirus 2 in a Rural Community.
  Open forum infectious diseases 2020 Appa A, Takahashi S, Rodriguez-Barraquer I, Chamie G, Sawyer A, Duarte E, Hakim J, Turcios K, Vinden J, Janson O, Manglik A, Peluso MJ, Deeks SG, Henrich TJ, Torres L, Rodgers M, Hackett J, Chiu C, …
• Rapid deployment of SARS-CoV-2 testing: The CLIAHUB.
  PLoS pathogens 2020 Crawford ED, Acosta I, Ahyong V, Anderson EC, Arevalo S, Asarnow D, Axelrod S, Ayscue P, Azimi CS, Azumaya CM, Bachl S, Bachmutsky I, Bhaduri A, Brown JB, Batson J, Behnert A, Boileau RM, Bollam SR, …
• Gastrointestinal: COVID-19 related ischemic bowel disease.
  Journal of gastroenterology and hepatology 2020 Chiu CY, Sarwal A, Mon AM, Tan YE, Shah V
• ReScan, a Multiplex Diagnostic Pipeline, Pans Human Sera for SARS-CoV-2 Antigens.
  Cell reports. Medicine 2020 Zamecnik CR, Rajan JV, Yamauchi KA, Mann SA, Loudermilk RP, Sowa GM, Zorn KC, Alvarenga BD, Gaebler C, Caskey M, Stone M, Norris PJ, Gu W, Chiu CY, Ng D, Byrnes JR, Zhou XX, Wells JA, Robbiani DF, …
• Metagenomic sequencing of stool samples in Bangladeshi infants: virome association with poliovirus shedding after oral poliovirus vaccination.
  Scientific reports 2020 Tan SK, Granados AC, Bouquet J, Hoy-Schulz YE, Green L, Federman S, Stryke D, Haggerty TD, Ley C, Yeh MT, Jannat K, Maldonado YA, Andino R, Parsonnet J, Chiu CY
• SARS-CoV-2 seroprevalence and neutralizing activity in donor and patient blood.
  Nature communications 2020 Ng DL, Goldgof GM, Shy BR, Levine AG, Balcerek J, Bapat SP, Prostko J, Rodgers M, Coller K, Pearce S, Franz S, Du L, Stone M, Pillai SK, Sotomayor-Gonzalez A, Servellita V, Martin CSS, Granados A, …
• Competitive SARS-CoV-2 Serology Reveals Most Antibodies Targeting the Spike Receptor-Binding Domain Compete for ACE2 Binding.
  mSphere 2020 Byrnes JR, Zhou XX, Lui I, Elledge SK, Glasgow JE, Lim SA, Loudermilk RP, Chiu CY, Wang TT, Wilson MR, Leung KK, Wells JA
• Optimization and clinical validation of dual-target RT-LAMP for SARS-CoV-2.
  Journal of virological methods 2020 Mohon AN, Oberding L, Hundt J, van Marle G, Pabbaraju K, Berenger BM, Lisboa L, Griener T, Czub M, Doolan C, Servellita V, Chiu CY, Greninger AL, Jerome KR, Pillai DR
• Cryptic transmission of SARS-CoV-2 in Washington state.
  Science (New York, N.Y.) 2020 Bedford T, Greninger AL, Roychoudhury P, Starita LM, Famulare M, Huang ML, Nalla A, Pepper G, Reinhardt A, Xie H, Shrestha L, Nguyen TN, Adler A, Brandstetter E, Cho S, Giroux D, Han PD, Fay K, Frazar…
• Digital droplet PCR accurately quantifies SARS-CoV-2 viral load from crude lysate without nucleic acid purification.
  medRxiv : the preprint server for health sciences 2020 Vasudevan H, Xu P, Servellita V, Miller S, Liu L, Gopez A, Chiu CY, Abate AR
• Evaluation of SARS-CoV-2 serology assays reveals a range of test performance.
  Nature biotechnology 2020 Whitman JD, Hiatt J, Mowery CT, Shy BR, Yu R, Yamamoto TN, Rathore U, Goldgof GM, Whitty C, Woo JM, Gallman AE, Miller TE, Levine AG, Nguyen DN, Bapat SP, Balcerek J, Bylsma SA, Lyons AM, Li S, Wong …
• Clinical features, diagnostics, and outcomes of patients presenting with acute respiratory illness: A retrospective cohort study of patients with and without COVID-19.
  EClinicalMedicine 2020 Shah SJ, Barish PN, Prasad PA, Kistler A, Neff N, Kamm J, Li LM, Chiu CY, Babik JM, Fang MC, Abe-Jones Y, Alipanah N, Alvarez FN, Botvinnik OB, Castaneda G, CZB CLIAhub Consortium, Dadasovich RM, …
• Direct Comparison of SARS-CoV-2 Analytical Limits of Detection across Seven Molecular Assays.
  Journal of clinical microbiology 2020 Fung B, Gopez A, Servellita V, Arevalo S, Ho C, Deucher A, Thornborrow E, Chiu C, Miller S
• Universal PCR and antibody testing demonstrate little to no transmission of SARS-CoV-2 in a rural community.
  medRxiv : the preprint server for health sciences 2020 Appa A, Takahashi S, Rodriguez-Barraquer I, Chamie G, Sawyer A, Consortium C, Duarte E, Hakim J, Turcios K, Vinden J, Janson O, Manglik A, Peluso MJ, Deeks SG, Henrich TJ, Torres L, Rodgers M, Hackett…
• STROBE-metagenomics: a STROBE extension statement to guide the reporting of metagenomics studies.
  The Lancet. Infectious diseases 2020 Bharucha T, Oeser C, Balloux F, Brown JR, Carbo EC, Charlett A, Chiu CY, Claas ECJ, de Goffau MC, de Vries JJC, Eloit M, Hopkins S, Huggett JF, MacCannell D, Morfopoulou S, Nath A, O'Sullivan DM, …
• Cell-Free DNA in Blood Reveals Significant Cell, Tissue and Organ Specific injury and Predicts COVID-19 Severity.
  medRxiv : the preprint server for health sciences 2020 Cheng AP, Cheng MP, Gu W, Lenz JS, Hsu E, Schurr E, Bourque G, Bourgey M, Ritz J, Marty F, Chiu CY, Vinh DC, Vlaminck I
• Clinical outcomes and serologic response in solid organ transplant recipients with COVID-19: A case series from the United States.
  American journal of transplantation : official journal of the American Society of Transplantation and the American Society of Transplant Surgeons 2020 Fung M, Chiu CY, DeVoe C, Doernberg SB, Schwartz BS, Langelier C, Henrich TJ, Yokoe D, Davis J, Hays SR, Chandran S, Kukreja J, Ng D, Prostko J, Taylor R, Reyes K, Bainbridge E, Bond A, Chin-Hong P, …
• SARS-CoV-2 Community Transmission During Shelter-in-Place in San Francisco.
  medRxiv 2020 Gabriel Chamie, Carina Marquez, Emily Crawford, James Peng, Maya Petersen, Daniel Schwab, Joshua Schwab, Jackie Martinez, Diane Jones, Douglas Black, Monica Gandhi, Andrew D. Kerkhoff, Vivek Jain, …
• Genomic surveillance reveals multiple introductions of SARS-CoV-2 into Northern California.
  Science (New York, N.Y.) 2020 Deng X, Gu W, Federman S, du Plessis L, Pybus OG, Faria NR, Wang C, Yu G, Bushnell B, Pan CY, Guevara H, Sotomayor-Gonzalez A, Zorn K, Gopez A, Servellita V, Hsu E, Miller S, Bedford T, Greninger AL, …
• A SARS-CoV-2 serological assay to determine the presence of blocking antibodies that compete for human ACE2 binding.
  medRxiv : the preprint server for health sciences 2020 Byrnes JR, Zhou XX, Lui I, Elledge SK, Glasgow JE, Lim SA, Loudermilk R, Chiu CY, Wilson MR, Leung KK, Wells JA
• SARS-CoV-2 seroprevalence and neutralizing activity in donor and patient blood from the San Francisco Bay Area.
  medRxiv : the preprint server for health sciences 2020 Ng DL, Goldgof GM, Shy BR, Levine AG, Balcerek J, Bapat SP, Prostko J, Rodgers M, Coller K, Pearce S, Franz S, Du L, Stone M, Pillai SK, Sotomayor-Gonzalez A, Servellita V, Martin CSS, Granados A, …
• New Genomes from the Congo Basin Expand History of CRF01_AE Origin and Dissemination.
  AIDS research and human retroviruses 2020 Junqueira DM, Wilkinson E, Vallari A, Deng X, Achari A, Yu G, McArthur C, Kaptue L, Mbanya D, Chiu C, Cloherty GA, de Oliveira T, Rodgers MA
• Test performance evaluation of SARS-CoV-2 serological assays.
  medRxiv : the preprint server for health sciences 2020 Whitman JD, Hiatt J, Mowery CT, Shy BR, Yu R, Yamamoto TN, Rathore U, Goldgof GM, Whitty C, Woo JM, Gallman AE, Miller TE, Levine AG, Nguyen DN, Bapat SP, Balcerek J, Bylsma SA, Lyons AM, Li S, Wong …
• ReScan, a Multiplex Diagnostic Pipeline, Pans Human Sera for SARS-CoV-2 Antigens.
  medRxiv 2020 Colin R. Zamecnik, Jayant V. Rajan, Kevin A. Yamauchi, Sabrina A. Mann, Gavin M. Sowa, Kelsey C. Zorn, Bonny D. Alvarenga, Mars Stone, Philip J. Norris, Wei Gu, Charles Y Chiu, Joseph L. DeRisi, …
• Clinical features, diagnostics, and outcomes of patients presenting with acute respiratory illness: a comparison of patients with and without COVID-19.
  medRxiv : the preprint server for health sciences 2020 Shah SJ, Barish PN, Prasad PA, Kistler AL, Neff N, Kamm J, Li LM, Chiu CY, Babick JM, Fang MC, Abe-Jones Y, Alipanah N, Alvarez FN, Botvinnik OB, Davis JM, Castenada GD, Consortium C, Dadasovich RM, …
• CRISPR-Cas12-based detection of SARS-CoV-2.
  Nature biotechnology 2020 Broughton JP, Deng X, Yu G, Fasching CL, Servellita V, Singh J, Miao X, Streithorst JA, Granados A, Sotomayor-Gonzalez A, Zorn K, Gopez A, Hsu E, Gu W, Miller S, Pan CY, Guevara H, Wadford DA, Chen JS…
• Association of COVID-19 Infections in San Francisco in Early March 2020 with Travel to New York and Europe.
  medRxiv : the preprint server for health sciences 2020 Gu W, Reyes K, Hsu E, Miller S, Chiu C
• Cryptic transmission of SARS-CoV-2 in Washington State.
  medRxiv : the preprint server for health sciences 2020 Bedford T, Greninger AL, Roychoudhury P, Starita LM, Famulare M, Huang ML, Nalla A, Pepper G, Reinhardt A, Xie H, Shrestha L, Nguyen TN, Adler A, Brandstetter E, Cho S, Giroux D, Han PD, Fay K, Frazar…
• A Genomic Survey of SARS-CoV-2 Reveals Multiple Introductions into Northern California without a Predominant Lineage.
  medRxiv : the preprint server for health sciences 2020 Deng X, Gu W, Federman S, du Plessis L, Pybus OG, Faria N, Wang C, Yu G, Pan CY, Guevara H, Sotomayor-Gonzalez A, Zorn K, Gopez A, Servellita V, Hsu E, Miller S, Bedford T, Greninger AL, Roychoudhury …
• Rapid Detection of 2019 Novel Coronavirus SARS-CoV-2 Using a CRISPR-based DETECTR Lateral Flow Assay.
  medRxiv : the preprint server for health sciences 2020 Broughton JP, Deng X, Yu G, Fasching CL, Singh J, Streithorst J, Granados A, Sotomayor-Gonzalez A, Zorn K, Gopez A, Hsu E, Gu W, Miller S, Pan CY, Guevara H, Wadford DA, Chen JS, Chiu CY
• Author Correction: Metagenomic sequencing with spiked primer enrichment for viral diagnostics and genomic surveillance.
  Nature microbiology 2020 Deng X, Achari A, Federman S, Yu G, Somasekar S, Bártolo I, Yagi S, Mbala-Kingebeni P, Kapetshi J, Ahuka-Mundeke S, Muyembe-Tamfum JJ, Ahmed AA, Ganesh V, Tamhankar M, Patterson JL, Ndembi N, Mbanya D…
• Human Tibroviruses: Commensals or Lethal Pathogens?
  Viruses 2020 Kuhn JH, Pan H, Chiu CY, Stremlau M
• Point-Counterpoint: Should We Be Performing Metagenomic Next-Generation Sequencing for Infectious Disease Diagnosis in the Clinical Laboratory?
  Journal of clinical microbiology 2020 Miller S, Chiu C, Rodino KG, Miller MB
• Exploratory analysis of the potential for advanced diagnostic testing to reduce healthcare expenditures of patients hospitalized with meningitis or encephalitis.
  PloS one 2020 Fulton BD, Proudman DG, Sample HA, Gelfand JM, Chiu CY, DeRisi JL, Wilson MR
• Metagenomic sequencing with spiked primer enrichment for viral diagnostics and genomic surveillance.
  Nature microbiology 2020 Deng X, Achari A, Federman S, Yu G, Somasekar S, Bártolo I, Yagi S, Mbala-Kingebeni P, Kapetshi J, Ahuka-Mundeke S, Muyembe-Tamfum JJ, Ahmed AA, Ganesh V, Tamhankar M, Patterson JL, Ndembi N, Mbanya D…
• 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 Andrew D Kerkhoff, Michelle Matzko, Charles Chiu, Steve Miller, Jennifer M Babik
• Pan-viral serology implicates enteroviruses in acute flaccid myelitis.
  Nature medicine 2019 Schubert RD, Hawes IA, Ramachandran PS, Ramesh A, Crawford ED, Pak JE, Wu W, Cheung CK, O'Donovan BD, Tato CM, Lyden A, Tan M, Sit R, Sowa GM, Sample HA, Zorn KC, Banerji D, Khan LM, Bove R, Hauser SL…
• Metagenomic Next-Generation Sequencing of the 2014 Ebola Virus Disease Outbreak in the Democratic Republic of the Congo.
  Journal of clinical microbiology 2019 Li T, Mbala-Kingebeni P, Naccache SN, Thézé J, Bouquet J, Federman S, Somasekar S, Yu G, Sanchez-San Martin C, Achari A, Schneider BS, Rimoin AW, Rambaut A, Nsio J, Mulembakani P, Ahuka-Mundeke S, …
• Acute Zika virus infection in an asymptomatic blood donor at the onset of the Puerto Rico epidemic.
  Transfusion 2019 Saa P, Chiu C, Grimm K, Yu G, Benjamin RJ, Corash L, Stramer SL
• Gastroenteritis, Hepatitis, Encephalopathy, and Human Herpesvirus 6 Detection in an Immunocompetent Child: Benefits and Risks of Syndromic Multiplex Molecular Panel Testing.
  The Journal of pediatrics 2019 Olson CA, Dominguez SR, Miller S, Chiu CY, Messacar K
• Clinical Metagenomic Sequencing for Diagnosis of Meningitis and Encephalitis.
  The New England journal of medicine 2019 Wilson MR, Sample HA, Zorn KC, Arevalo S, Yu G, Neuhaus J, Federman S, Stryke D, Briggs B, Langelier C, Berger A, Douglas V, Josephson SA, Chow FC, Fulton BD, DeRisi JL, Gelfand JM, Naccache SN, …
• Clinical metagenomics.
  Nature reviews. Genetics 2019 Chiu CY, Miller SA
• Human, Nonhuman Primate, and Bat Cells Are Broadly Susceptible to Tibrovirus Particle Cell Entry.
  Frontiers in microbiology 2019 Caì Y, Yú S, Jangra RK, Postnikova EN, Wada J, Tesh RB, Whelan SPJ, Lauck M, Wiley MR, Finch CL, Radoshitzky SR, O'Connor DH, Palacios G, Chandran K, Chiu CY, Kuhn JH
• Laboratory validation of a clinical metagenomic sequencing assay for pathogen detection in cerebrospinal fluid.
  Genome research 2019 Miller S, Naccache SN, Samayoa E, Messacar K, Arevalo S, Federman S, Stryke D, Pham E, Fung B, Bolosky WJ, Ingebrigtsen D, Lorizio W, Paff SM, Leake JA, Pesano R, DeBiasi R, Dominguez S, Chiu CY
• Severe Epididymo-Orchitis and Encephalitis Complicating Anti-PD-1 Therapy.
  The oncologist 2019 Quach HT, Robbins CJ, Balko JM, Chiu CY, Miller S, Wilson MR, Nelson GE, Johnson DB
• Whole blood human transcriptome and virome analysis of ME/CFS patients experiencing post-exertional malaise following cardiopulmonary exercise testing.
  PloS one 2019 Bouquet J, Li T, Gardy JL, Kang X, Stevens S, Stevens J, VanNess M, Snell C, Potts J, Miller RR, Morshed M, McCabe M, Parker S, Uyaguari M, Tang P, Steiner T, Chan WS, De Souza AM, Mattman A, Patrick …
• Single-molecule sequencing detection of N6-methyladenine in microbial reference materials.
  Nature communications 2019 McIntyre ABR, Alexander N, Grigorev K, Bezdan D, Sichtig H, Chiu CY, Mason CE
• A Child With Intermittent Headaches and Eosinophilic Meningitis.
  Journal of the Pediatric Infectious Diseases Society 2018 Saporta-Keating SR, Simões EAF, Yu G, Federman S, Mirsky D, Dominguez SR, Chiu CY, Messacar K
• Integrating host response and unbiased microbe detection for lower respiratory tract infection diagnosis in critically ill adults.
  Proceedings of the National Academy of Sciences of the United States of America 2018 Langelier C, Kalantar KL, Moazed F, Wilson MR, Crawford ED, Deiss T, Belzer A, Bolourchi S, Caldera S, Fung M, Jauregui A, Malcolm K, Lyden A, Khan L, Vessel K, Quan J, Zinter M, Chiu CY, Chow ED, …
• 2291. A Real-Time Sequencing Approach for Simultaneous Metagenomic and Transcriptomic-Based Diagnosis of Infectious Diseases.
  Open Forum Infectious Diseases 2018 Benjamin Briggs, Scot Federman, Xian Ding Deng, Wei Gu, Guixia Yu, Claudia Sanchez San Martin, Steve Miller, Charles Y Chiu
• 2563. Clinical Metagenomic Next-Generation Sequencing for Diagnosis of Meningitis and Encephalitis.
  Open Forum Infectious Diseases 2018 Michael Wilson, Hannah Sample, Kelsey Zorn, Samia N Naccache, Steve Miller, Charles Y Chiu
• 617. Characterization and Development of the Infant Gut Virome: A STORK Study.
  Open Forum Infectious Diseases 2018 Andrea Granados, Susanna K Tan, Jerome Bouquet, Charles Y Chiu, Julie Parsonnet, Lauri Green
• Publisher Correction: Experimental Zika Virus Infection in the Pregnant Common Marmoset Induces Spontaneous Fetal Loss and Neurodevelopmental Abnormalities.
  Scientific reports 2018 Seferovic M, Sánchez-San Martín C, Tardif SD, Rutherford J, Castro ECC, Li T, Hodara VL, Parodi LM, Giavedoni L, Layne-Colon D, Tamhankar M, Yagi S, Martyn C, Reyes K, Suter MA, Aagaard KM, Chiu CY, …
• Clinical Metagenomic Next-Generation Sequencing for Pathogen Detection.
  Annual review of pathology 2018 Gu W, Miller S, Chiu CY
• Differentiation enhances Zika virus infection of neuronal brain cells.
  Scientific reports 2018 Sánchez-San Martín C, Li T, Bouquet J, Streithorst J, Yu G, Paranjpe A, Chiu CY
• Identification of high-risk human papillomavirus and Rb/E2F pathway genomic alterations in mutually exclusive subsets of colorectal neuroendocrine carcinoma.
  Modern pathology : an official journal of the United States and Canadian Academy of Pathology, Inc 2018 Shamir ER, Devine WP, Pekmezci M, Umetsu SE, Krings G, Federman S, Cho SJ, Saunders TA, Jen KY, Bergsland E, Jones K, Kim GE, Kakar S, Chiu CY, Joseph NM
• Epidemiological and genomic characterization of community-acquired Clostridium difficile infections.
  BMC infectious diseases 2018 Thornton CS, Rubin JE, Greninger AL, Peirano G, Chiu CY, Pillai DR
• Miscarriage and stillbirth following maternal Zika virus infection in nonhuman primates.
  Nature medicine 2018 Dudley DM, Van Rompay KK, Coffey LL, Ardeshir A, Keesler RI, Bliss-Moreau E, Grigsby PL, Steinbach RJ, Hirsch AJ, MacAllister RP, Pecoraro HL, Colgin LM, Hodge T, Streblow DN, Tardif S, Patterson JL, …
• Acute Liver Failure of Indeterminate Etiology: A Comprehensive Systematic Approach by An Expert Committee to Establish Causality.
  The American journal of gastroenterology 2018 Ganger DR, Rule J, Rakela J, Bass N, Reuben A, Stravitz RT, Sussman N, Larson AM, James L, Chiu C, Lee WM, Acute Liver Failure Study Group
• Cutting-Edge Infectious Disease Diagnostics with CRISPR.
  Cell host & microbe 2018 Chiu C
• Genomic Epidemiology Reconstructs the Introduction and Spread of Zika Virus in Central America and Mexico.
  Cell host & microbe 2018 Thézé J, Li T, du Plessis L, Bouquet J, Kraemer MUG, Somasekar S, Yu G, de Cesare M, Balmaseda A, Kuan G, Harris E, Wu CH, Ansari MA, Bowden R, Faria NR, Yagi S, Messenger S, Brooks T, Stone M, Bloch …
• Polyoma virus-associated carcinomas of the urologic tract: a clinicopathologic and molecular study.
  Modern pathology : an official journal of the United States and Canadian Academy of Pathology, Inc 2018 Sirohi D, Vaske C, Sanborn Z, Smith SC, Don MD, Lindsey KG, Federman S, Vankalakunti M, Koo J, Bose S, Peralta-Venturina M, Ziffle JV, Grenert JP, Miller S, Chiu C, Amin MB, Simko JP, Stohr BA, …
• Experimental Zika Virus Infection in the Pregnant Common Marmoset Induces Spontaneous Fetal Loss and Neurodevelopmental Abnormalities.
  Scientific reports 2018 Seferovic M, Sánchez-San Martín C, Tardif SD, Rutherford J, Castro ECC, Li T, Hodara VL, Parodi LM, Giavedoni L, Layne-Colon D, Tamhankar M, Yagi S, Martyn C, Reyes K, Suter MA, Aagaard KM, Chiu CY, …
• Taxonomy of the order Mononegavirales: update 2018.
  Archives of virology 2018 Amarasinghe GK, Aréchiga Ceballos NG, Banyard AC, Basler CF, Bavari S, Bennett AJ, Blasdell KR, Briese T, Bukreyev A, Caì Y, Calisher CH, Campos Lawson C, Chandran K, Chapman CA, Chiu CY, Choi KS, …
• Metagenomic Sequencing Detects Respiratory Pathogens in Hematopoietic Cellular Transplant Patients.
  American journal of respiratory and critical care medicine 2018 Langelier C, Zinter MS, Kalantar K, Yanik GA, Christenson S, O'Donovan B, White C, Wilson M, Sapru A, Dvorak CC, Miller S, Chiu CY, DeRisi JL
• Metagenomic Next-Generation Sequencing for Pathogen Detection and Identification.
  Advanced Techniques in Diagnostic Microbiology 2018 Steve Miller, Charles Chiu
• Nanopore DNA Sequencing and Genome Assembly on the International Space Station.
  Scientific reports 2017 Castro-Wallace SL, Chiu CY, John KK, Stahl SE, Rubins KH, McIntyre ABR, Dworkin JP, Lupisella ML, Smith DJ, Botkin DJ, Stephenson TA, Juul S, Turner DJ, Izquierdo F, Federman S, Stryke D, Somasekar S,…
• Experimental Zika Virus Inoculation in a New World Monkey Model Reproduces Key Features of the Human Infection.
  Scientific reports 2017 Chiu CY, Sánchez-San Martín C, Bouquet J, Li T, Yagi S, Tamhankar M, Hodara VL, Parodi LM, Somasekar S, Yu G, Giavedoni LD, Tardif S, Patterson J
• A composite of exhaled LTB4 , LXA4 , FeNO, and FEV1 as an "asthma classification ratio" characterizes childhood asthma.
  Allergy 2017 Chen LC, Tseng HM, Kuo ML, Chiu CY, Liao SL, Su KW, Tsai MH, Hua MC, Lai SH, Yao TC, Yeh KW, Wu AH, Huang JL, Huang SK
• Neurobrucellosis: Unexpected Answer From Metagenomic Next-Generation Sequencing.
  Journal of the Pediatric Infectious Diseases Society 2017 Mongkolrattanothai K, Naccache SN, Bender JM, Samayoa E, Pham E, Yu G, Dien Bard J, Miller S, Aldrovandi G, Chiu CY
• Viral Surveillance in Serum Samples From Patients With Acute Liver Failure By Metagenomic Next-Generation Sequencing.
  Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2017 Somasekar S, Lee D, Rule J, Naccache SN, Stone M, Busch MP, Sanders C, Lee WM, Chiu CY
• Diagnosis of Fatal Human Case of St. Louis Encephalitis Virus Infection by Metagenomic Sequencing, California, 2016.
  Emerging infectious diseases 2017 Chiu CY, Coffey LL, Murkey J, Symmes K, Sample HA, Wilson MR, Naccache SN, Arevalo S, Somasekar S, Federman S, Stryke D, Vespa P, Schiller G, Messenger S, Humphries R, Miller S, Klausner JD
• Metagenomic-based Surveillance of Pacific Coast tick Dermacentor occidentalis Identifies Two Novel Bunyaviruses and an Emerging Human Ricksettsial Pathogen.
  Scientific reports 2017 Bouquet J, Melgar M, Swei A, Delwart E, Lane RS, Chiu CY
• Upregulation of Human Endogenous Retrovirus-K Is Linked to Immunity and Inflammation in Pulmonary Arterial Hypertension.
  Circulation 2017 Saito T, Miyagawa K, Chen SY, Tamosiuniene R, Wang L, Sharpe O, Samayoa E, Harada D, Moonen JAJ, Cao A, Chen PI, Hennigs JK, Gu M, Li CG, Leib RD, Li D, Adams CM, Del Rosario PA, Bill M, Haddad F, …
• Correction: Correction: A Novel Rhabdovirus Associated with Acute Hemorrhagic Fever in Central Africa.
  PLoS pathogens 2017 Grard G, Fair JN, Lee D, Slikas E, Steffen I, Muyembe JJ, Sittler T, Veeraraghavan N, Ruby JG, Wang C, Makuwa M, Mulembakani P, Tesh RB, Mazet J, Rimoin AW, Taylor T, Schneider BS, Simmons G, Delwart …
• The eukaryotic gut virome in hematopoietic stem cell transplantation: new clues in enteric graft-versus-host disease.
  Nature medicine 2017 Legoff J, Resche-Rigon M, Bouquet J, Robin M, Naccache SN, Mercier-Delarue S, Federman S, Samayoa E, Rousseau C, Piron P, Kapel N, Simon F, Socié G, Chiu CY
• Hepatitis E Virus-Associated Meningoencephalitis in a Lung Transplant Recipient Diagnosed by Clinical Metagenomic Sequencing.
  Open forum infectious diseases 2017 Murkey JA, Chew KW, Carlson M, Shannon CL, Sirohi D, Sample HA, Wilson MR, Vespa P, Humphries RM, Miller S, Klausner JD, Chiu CY
• Establishment and cryptic transmission of Zika virus in Brazil and the Americas.
  Nature 2017 Faria NR, Quick J, Claro IM, Thézé J, de Jesus JG, Giovanetti M, Kraemer MUG, Hill SC, Black A, da Costa AC, Franco LC, Silva SP, Wu CH, Raghwani J, Cauchemez S, du Plessis L, Verotti MP, de Oliveira …
• Establishment and characterization of an oral tongue squamous cell carcinoma cell line from a never-smoking patient.
  Oral oncology 2017 Wang SJ, Asthana S, van Zante A, Heaton CM, Phuchareon J, Stein L, Higuchi S, Kishimoto T, Chiu CY, Olshen AB, McCormick F, Tetsu O
• First Complete Genome Sequence of Corynebacterium riegelii.
  Genome announcements 2017 Greninger AL, Streithorst J, Chiu CY, Miller S
• A hospital-wide screening programme to control an outbreak of vancomycin-resistant enterococci in a large tertiary hospital in Hong Kong.
  Hong Kong medical journal = Xianggang yi xue za zhi 2017 Lai CK, Wong SY, Lee SS, Siu HK, Chiu CY, Tsang DN, Ip MP, Hung CT
• A mouse model of paralytic myelitis caused by enterovirus D68.
  PLoS pathogens 2017 Hixon AM, Yu G, Leser JS, Yagi S, Clarke P, Chiu CY, Tyler KL
• RNA-Seq Analysis of Gene Expression, Viral Pathogen, and B-Cell/T-Cell Receptor Signatures in Complex Chronic Disease.
  Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2017 Bouquet J, Gardy JL, Brown S, Pfeil J, Miller RR, Morshed M, Avina-Zubieta A, Shojania K, McCabe M, Parker S, Uyaguari M, Federman S, Tang P, Steiner T, Otterstater M, Holt R, Moore R, Chiu CY, …
• Validation of Metagenomic Next-Generation Sequencing Tests for Universal Pathogen Detection.
  Archives of pathology & laboratory medicine 2017 Schlaberg R, Chiu CY, Miller S, Procop GW, Weinstock G, Professional Practice Committee and Committee on Laboratory Practices of the American Society for Mi, Microbiology Resource Committee of the …
• Beatrice Hill Virus Represents a Novel Species in the Genus Tibrovirus (Mononegavirales: Rhabdoviridae).
  Genome announcements 2017 Wiley MR, Prieto K, Blasdell KR, Caì Y, Campos Lawson C, Walker PJ, Chiu CY, Palacios G, Kuhn JH
• First Draft Genome Sequences of Neisseria sp. Strain 83E34 and Neisseria sp. Strain 74A18, Previously Identified as CDC Eugonic Fermenter 4b Species.
  Genome announcements 2016 Greninger AL, Streithorst J, Chiu CY, Miller S
• Longitudinal investigation of nasopharyngeal methicillin-resistant Staphylococcus aureus colonization in early infancy: The PATCH birth cohort study.
  Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases 2016 Tsai MH, Chiu CY, Shih HJ, Liao SL, Hua MC, Huang SH, Yao TC, Lai SH, Huang TS, Yeh KW, Chen LC, Su KW, Lim WH, Chang YJ, Chiang CH, Huang SY, Huang JL
• Distinct Zika Virus Lineage in Salvador, Bahia, Brazil.
  Emerging infectious diseases 2016 Naccache SN, Thézé J, Sardi SI, Somasekar S, Greninger AL, Bandeira AC, Campos GS, Tauro LB, Faria NR, Pybus OG, Chiu CY
• 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.
  Diagnostic microbiology and infectious disease 2016 Greninger AL, Streithorst J, Golden JA, Chiu CY, Miller S
• Coinfections of Zika and Chikungunya Viruses in Bahia, Brazil, Identified by Metagenomic Next-Generation Sequencing.
  Journal of clinical microbiology 2016 Sardi SI, Somasekar S, Naccache SN, Bandeira AC, Tauro LB, Campos GS, Chiu CY
• Antibodies to the Novel Human Pegivirus 2 Are Associated with Active and Resolved Infections.
  Journal of clinical microbiology 2016 Coller KE, Berg MG, Frankel M, Forberg K, Surani R, Chiu CY, Hackett J, Dawson GJ
• Two human immunodeficiency virus Type 2 cases in US blood donors including serologic, molecular, and genomic characterization of an epidemiologically unusual case.
  Transfusion 2016 Stramer SL, Yu G, Herron R, Espinoza N, Foster GA, Naccache SN, Brodsky JP, Ong E, Linnen JM, Dyer N, Styer LM, Parker MM, Chiu CY
• Correction: A Novel Rhabdovirus Associated with Acute Hemorrhagic Fever in Central Africa.
  PLoS pathogens 2016 Grard G, Fair JN, Lee D, Slikas E, Steffen I, Muyembe JJ, Sittler T, Veeraraghavan N, Ruby JG, Wang C, Makuwa M, Mulembakani P, Tesh RB, Mazet J, Rimoin AW, Taylor T, Schneider BS, Simmons G, Delwart …
• Whole-Genome Sequencing of Methicillin-Resistant Staphylococcus aureus Resistant to Fifth-Generation Cephalosporins Reveals Potential Non-mecA Mechanisms of Resistance.
  PloS one 2016 Greninger AL, Chatterjee SS, Chan LC, Hamilton SM, Chambers HF, Chiu CY
• Longitudinal Transcriptome Analysis Reveals a Sustained Differential Gene Expression Signature in Patients Treated for Acute Lyme Disease.
  mBio 2016 Bouquet J, Soloski MJ, Swei A, Cheadle C, Federman S, Billaud JN, Rebman AW, Kabre B, Halpert R, Boorgula M, Aucott JN, Chiu CY
• Erratum to: Clinical metagenomic identification of Balamuthia mandrillaris encephalitis and assembly of the draft genome: the continuing case for reference genome sequencing.
  Genome medicine 2016 Greninger AL, Messacar K, Dunnebacke T, Naccache SN, Federman S, Bouquet J, Mirsky D, Nomura Y, Yagi S, Glaser C, Vollmer M, Press CA, Kleinschmidt-DeMasters BK, Dominguez SR, Chiu CY
• Discovery of a Novel Human Pegivirus in Blood Associated with Hepatitis C Virus Co-Infection.
  PLoS pathogens 2015 Berg MG, Lee D, Coller K, Frankel M, Aronsohn A, Cheng K, Forberg K, Marcinkus M, Naccache SN, Dawson G, Brennan C, Jensen DM, Hackett J, Chiu CY
• Balamuthia Mandrillaris Encephalitis Detected by Next Generation Sequencing of Cerebrospinal Fluid.
  Open Forum Infectious Diseases 2015 Yosuke Nomura, Alex Greninger, Kevin Messacar, Thelma Dunnebacke, Samia N. Naccache, Jerome Bouquet, David Mirsky, Craig Press, B. K. Kleinschmidt-Demasters, Sarah Parker, Samuel Dominguez, Charles Y.…
• Acute Flaccid Myelitis of Unknown Etiology in California, 2012-2015.
  JAMA 2015 Van Haren K, Ayscue P, Waubant E, Clayton A, Sheriff H, Yagi S, Glenn-Finer R, Padilla T, Strober JB, Aldrovandi G, Wadford DA, Chiu CY, Xia D, Harriman K, Watt JP, Glaser CA
• Clinical metagenomic identification of Balamuthia mandrillaris encephalitis and assembly of the draft genome: the continuing case for reference genome sequencing.
  Genome medicine 2015 Greninger AL, Messacar K, Dunnebacke T, Naccache SN, Federman S, Bouquet J, Mirsky D, Nomura Y, Yagi S, Glaser C, Vollmer M, Press CA, Kleinschmidt-DeMasters BK, Klenschmidt-DeMasters BK, Dominguez SR…
• Utility of Metagenomic Next-Generation Sequencing for Characterization of HIV and Human Pegivirus Diversity.
  PloS one 2015 Luk KC, Berg MG, Naccache SN, Kabre B, Federman S, Mbanya D, Kaptué L, Chiu CY, Brennan CA, Hackett J
• Rapid metagenomic identification of viral pathogens in clinical samples by real-time nanopore sequencing analysis.
  Genome medicine 2015 Greninger AL, Naccache SN, Federman S, Yu G, Mbala P, Bres V, Stryke D, Bouquet J, Somasekar S, Linnen JM, Dodd R, Mulembakani P, Schneider BS, Muyembe-Tamfum JJ, Stramer SL, Chiu CY
• Draft Genome Sequence of Mycobacterium heckeshornense Strain RLE.
  Genome announcements 2015 Greninger AL, Cunningham G, Chiu CY, Miller S
• Genomic Assays for Identification of Chikungunya Virus in Blood Donors, Puerto Rico, 2014.
  Emerging infectious diseases 2015 Chiu CY, Bres V, Yu G, Krysztof D, Naccache SN, Lee D, Pfeil J, Linnen JM, Stramer SL
• Draft Genome Sequence of Mycobacterium heraklionense Strain Davo.
  Genome announcements 2015 Greninger AL, Cunningham G, Chiu CY, Miller S
• Draft Genome Sequence of Mycobacterium elephantis Strain Lipa.
  Genome announcements 2015 Greninger AL, Cunningham G, Yu JM, Hsu ED, Chiu CY, Miller S
• Draft Genome Sequence of Mycobacterium arupense Strain GUC1.
  Genome announcements 2015 Greninger AL, Cunningham G, Yu JM, Hsu ED, Chiu CY, Miller S
• Draft Genome Sequence of Mycobacterium obuense Strain UC1, Isolated from Patient Sputum.
  Genome announcements 2015 Greninger AL, Cunningham G, Hsu ED, Yu JM, Chiu CY, Miller S
• Two Rapidly Growing Mycobacterial Species Isolated from a Brain Abscess: First Whole-Genome Sequences of Mycobacterium immunogenum and Mycobacterium llatzerense.
  Journal of clinical microbiology 2015 Greninger AL, Langelier C, Cunningham G, Keh C, Melgar M, Chiu CY, Miller S
• Idiopathic pneumonia syndrome after hematopoietic cell transplantation: evidence of occult infectious etiologies.
  Blood 2015 Seo S, Renaud C, Kuypers JM, Chiu CY, Huang ML, Samayoa E, Xie H, Yu G, Fisher CE, Gooley TA, Miller S, Hackman RC, Myerson D, Sedlak RH, Kim YJ, Fukuda T, Fredricks DN, Madtes DK, Jerome KR, Boeckh M
• No viral association found in a set of differentiated vulvar intraepithelial neoplasia cases by human papillomavirus and pan-viral microarray testing.
  PloS one 2015 Saglam O, Samayoa E, Somasekar S, Naccache S, Iwasaki A, Chiu CY
• Advances in testing technology to ensure transfusion safety – NAT and beyond.
  ISBT Science Series 2015 S. L. Stramer, R. Y. Dodd, C. Y. Chiu
• A novel outbreak enterovirus D68 strain associated with acute flaccid myelitis cases in the USA (2012-14): a retrospective cohort study.
  The Lancet. Infectious diseases 2015 Greninger AL, Naccache SN, Messacar K, Clayton A, Yu G, Somasekar S, Federman S, Stryke D, Anderson C, Yagi S, Messenger S, Wadford D, Xia D, Watt JP, Van Haren K, Dominguez SR, Glaser C, Aldrovandi G…
• Genome Sequence of Bivens Arm Virus, a Tibrovirus Belonging to the Species Tibrogargan virus (Mononegavirales: Rhabdoviridae).
  Genome announcements 2015 Lauck M, Yú SQ, Caì Y, Hensley LE, Chiu CY, O'Connor DH, Kuhn JH
• An ensemble strategy that significantly improves de novo assembly of microbial genomes from metagenomic next-generation sequencing data.
  Nucleic acids research 2015 Deng X, Naccache SN, Ng T, Federman S, Li L, Chiu CY, Delwart EL
• Diagnosis of neuroinvasive astrovirus infection in an immunocompromised adult with encephalitis by unbiased next-generation sequencing.
  Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2015 Naccache SN, Peggs KS, Mattes FM, Phadke R, Garson JA, Grant P, Samayoa E, Federman S, Miller S, Lunn MP, Gant V, Chiu CY
• DNA microarray for detection of gastrointestinal viruses.
  Journal of clinical microbiology 2014 Martínez MA, Soto-Del Río Mde L, Gutiérrez RM, Chiu CY, Greninger AL, Contreras JF, López S, Arias CF, Isa P
• A cloud-compatible bioinformatics pipeline for ultrarapid pathogen identification from next-generation sequencing of clinical samples.
  Genome research 2014 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…
• Actionable diagnosis of neuroleptospirosis by next-generation sequencing.
  The New England journal of medicine 2014 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,…
• Next-Generation Sequencing for Pathogen Discovery in Meningoencephalitis (P2.306).
  Neurology 2014 Michael Wilson, Erik Samayoa, Samia Naccache, Sneha Somasekar, Guixia Yu, Joseph DeRisi, Charles Chiu
• Multiplexed immunoglobulin E sensitization in relation to exhaled nitric oxide in a population sample of children.
  Allergy 2014 Yao TC, Tsai HJ, Tu YL, Chang SW, Hua MC, Liao SL, Tsai MH, Chiu CY, Lai SH, Yeh KW, Huang JL, PATCH study group
• Concerns over the origin of NIH-CQV, a novel virus discovered in Chinese patients with seronegative hepatitis.
  Proceedings of the National Academy of Sciences of the United States of America 2014 Naccache SN, Hackett J, Delwart EL, Chiu CY
• Chapter 2 Bas-Congo Virus A Novel Rhabdovirus Associated with Acute Hemorrhagic Fever.
  Emerging Infectious Diseases 2014 Gilda Grard, Joseph Fair, Charles Chiu, Eric Leroy
• The perils of pathogen discovery: origin of a novel parvovirus-like hybrid genome traced to nucleic acid extraction spin columns.
  Journal of virology 2013 Naccache SN, Greninger AL, Lee D, Coffey LL, Phan T, Rein-Weston A, Aronsohn A, Hackett J, Delwart EL, Chiu CY
• The microbiome and Clostridium difficile infection.
  2013 Charles Y Chiu, Dylan R Pillai
• Rosavirus: the prototype of a proposed new genus of the Picornaviridae family.
  Virus genes 2013 Phan TG, Vo NP, Simmonds P, Samayoa E, Naccache S, Chiu CY, Delwart E
• Experimental cross-species infection of common marmosets by titi monkey adenovirus.
  PloS one 2013 Yu G, Yagi S, Carrion R, Chen EC, Liu M, Brasky KM, Lanford RE, Kelly KR, Bales KL, Schnurr DP, Canfield DR, Patterson JL, Chiu CY
• Characterization of the Bas-Congo virus glycoprotein and its function in pseudotyped viruses.
  Journal of virology 2013 Steffen I, Liss NM, Schneider BS, Fair JN, Chiu CY, Simmons G
• Viral pathogen discovery.
  Current opinion in microbiology 2013 Chiu CY
• The genome sequence of Lone Star virus, a highly divergent bunyavirus found in the Amblyomma americanum tick.
  PloS one 2013 Swei A, Russell BJ, Naccache SN, Kabre B, Veeraraghavan N, Pilgard MA, Johnson BJ, Chiu CY
• The hidden threat of unidentified agents of disease in human and veterinary biologicals.
  Biologicals : journal of the International Association of Biological Standardization 2013 Chiu C
• A novel adenovirus species associated with an acute respiratory outbreak in a baboon colony and evidence of coincident human infection.
  mBio 2013 Chiu CY, Yagi S, Lu X, Yu G, Chen EC, Liu M, Dick EJ, Carey KD, Erdman DD, Leland MM, Patterson JL
• A novel bocavirus in canine liver.
  Virology journal 2013 Li L, Pesavento PA, Leutenegger CM, Estrada M, Coffey LL, Naccache SN, Samayoa E, Chiu C, Qiu J, Wang C, Deng X, Delwart E
• Bas-Congo virus: another deadly virus?
  Future microbiology 2013 Chiu C, Fair J, Leroy EM
• The mitochondrial genome and a 60-kb nuclear DNA segment from Naegleria fowleri, the causative agent of primary amoebic meningoencephalitis.
  The Journal of eukaryotic microbiology 2013 Herman EK, Greninger AL, Visvesvara GS, Marciano-Cabral F, Dacks JB, Chiu CY
• Discovery of a novel polyomavirus in acute diarrheal samples from children.
  PloS one 2012 Yu G, Greninger AL, Isa P, Phan TG, Martínez MA, de la Luz Sanchez M, Contreras JF, Santos-Preciado JI, Parsonnet J, Miller S, DeRisi JL, Delwart E, Arias CF, Chiu CY
• Toward an understanding of changes in diversity associated with fecal microbiome transplantation based on 16S rRNA gene deep sequencing.
  mBio 2012 Shahinas D, Silverman M, Sittler T, Chiu C, Kim P, Allen-Vercoe E, Weese S, Wong A, Low DE, Pillai DR
• A novel rhabdovirus associated with acute hemorrhagic fever in central Africa.
  PLoS pathogens 2012 Grard G, Fair JN, Lee D, Slikas E, Steffen I, Muyembe JJ, Sittler T, Veeraraghavan N, Ruby JG, Wang C, Makuwa M, Mulembakani P, Tesh RB, Mazet J, Rimoin AW, Taylor T, Schneider BS, Simmons G, Delwart …
• In-depth investigation of archival and prospectively collected samples reveals no evidence for XMRV infection in prostate cancer.
  PloS one 2012 Lee D, Das Gupta J, Gaughan C, Steffen I, Tang N, Luk KC, Qiu X, Urisman A, Fischer N, Molinaro R, Broz M, Schochetman G, Klein EA, Ganem D, Derisi JL, Simmons G, Hackett J, Silverman RH, Chiu CY
• Cross-species transmission of a novel adenovirus associated with a fulminant pneumonia outbreak in a new world monkey colony.
  PLoS pathogens 2011 Chen EC, Yagi S, Kelly KR, Mendoza SP, Tarara RP, Canfield DR, Maninger N, Rosenthal A, Spinner A, Bales KL, Schnurr DP, Lerche NW, Chiu CY
• Using a pan-viral microarray assay (Virochip) to screen clinical samples for viral pathogens.
  Journal of visualized experiments : JoVE 2011 Chen EC, Miller SA, DeRisi JL, Chiu CY
• Viral infection in acute exacerbation of idiopathic pulmonary fibrosis.
  American journal of respiratory and critical care medicine 2011 Wootton SC, Kim DS, Kondoh Y, Chen E, Lee JS, Song JW, Huh JW, Taniguchi H, Chiu C, Boushey H, Lancaster LH, Wolters PJ, DeRisi J, Ganem D, Collard HR
• Pandemic (H1N1) 2009 infection in patients with hematologic malignancy.
  Emerging infectious diseases 2010 Liu C, Schwartz BS, Vallabhaneni S, Nixon M, Chin-Hong PV, Miller SA, Chiu C, Damon L, Drew WL
• A metagenomic analysis of pandemic influenza A (2009 H1N1) infection in patients from North America.
  PloS one 2010 Greninger AL, Chen EC, Sittler T, Scheinerman A, Roubinian N, Yu G, Kim E, Pillai DR, Guyard C, Mazzulli T, Isa P, Arias CF, Hackett J, Schochetman G, Miller S, Tang P, Chiu CY
• Identification of two novel missense mutations in the KAL1 gene in Han Chinese subjects with Kallmann Syndrome.
  Journal of endocrinological investigation 2010 Jap TS, Chiu CY, Lirng JF, Won GS
• The effect of temperament and neuropsychological functioning on behavior problems in children with new-onset seizures.
  Epilepsy & behavior : E&B 2010 Baum KT, Byars AW, deGrauw TJ, Dunn DW, Bates JE, Howe SR, Chiu CY, Austin JK
• Cultivation and serological characterization of a human Theiler's-like cardiovirus associated with diarrheal disease.
  Journal of virology 2010 Chiu CY, Greninger AL, Chen EC, Haggerty TD, Parsonnet J, Delwart E, Derisi JL, Ganem D
• Metagenomics for the discovery of novel human viruses.
  Future microbiology 2010 Tang P, Chiu C
• Thoracic CT findings of novel influenza A (H1N1) infection in immunocompromised patients.
  Emergency radiology 2010 Elicker BM, Schwartz BS, Liu C, Chen EC, Miller SA, Chiu CY, Webb WR
• Differential bacterial dynamics promote emergent community robustness to lake mixing: an epilimnion to hypolimnion transplant experiment.
  Environmental microbiology 2009 Shade A, Chiu CY, McMahon KD
• Bacteriologic features of surgical site infections following breast surgery.
  American journal of surgery 2009 Mukhtar RA, Throckmorton AD, Alvarado MD, Ewing CA, Esserman LJ, Chiu C, Hwang ES
• The complete genome of klassevirus - a novel picornavirus in pediatric stool.
  Virology journal 2009 Greninger AL, Runckel C, Chiu CY, Haggerty T, Parsonnet J, Ganem D, DeRisi JL
• The long march: a sample preparation technique that enhances contig length and coverage by high-throughput short-read sequencing.
  PloS one 2008 Sorber K, Chiu C, Webster D, Dimon M, Ruby JG, Hekele A, DeRisi JL
• Identification of cardioviruses related to Theiler's murine encephalomyelitis virus in human infections.
  Proceedings of the National Academy of Sciences of the United States of America 2008 Chiu CY, Greninger AL, Kanada K, Kwok T, Fischer KF, Runckel C, Louie JK, Glaser CA, Yagi S, Schnurr DP, Haggerty TD, Parsonnet J, Ganem D, DeRisi JL
• Recovery of divergent avian bornaviruses from cases of proventricular dilatation disease: identification of a candidate etiologic agent.
  Virology journal 2008 Kistler AL, Gancz A, Clubb S, Skewes-Cox P, Fischer K, Sorber K, Chiu CY, Lublin A, Mechani S, Farnoushi Y, Greninger A, Wen CC, Karlene SB, Ganem D, DeRisi JL
• Utility of DNA microarrays for detection of viruses in acute respiratory tract infections in children.
  The Journal of pediatrics 2008 Chiu CY, Urisman A, Greenhow TL, Rouskin S, Yagi S, Schnurr D, Wright C, Drew WL, Wang D, Weintrub PS, Derisi JL, Ganem D
• Streptococcus suis meningitis, United States.
  Emerging infectious diseases 2008 Lee GT, Chiu CY, Haller BL, Denn PM, Hall CS, Gerberding JL
• Availability and immobilization of 137Cs in subtropical high mountain forest and grassland soils.
  Journal of environmental radioactivity 2007 Chiu CY, Wang CJ, Huang CC
• Diagnosis of a critical respiratory illness caused by human metapneumovirus by use of a pan-virus microarray.
  Journal of clinical microbiology 2007 Chiu CY, Alizadeh AA, Rouskin S, Merker JD, Yeh E, Yagi S, Schnurr D, Patterson BK, Ganem D, DeRisi JL
• Microarray detection of human parainfluenzavirus 4 infection associated with respiratory failure in an immunocompetent adult.
  Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2006 Chiu CY, Rouskin S, Koshy A, Urisman A, Fischer K, Yagi S, Schnurr D, Eckburg PB, Tompkins LS, Blackburn BG, Merker JD, Patterson BK, Ganem D, DeRisi JL
• E-Predict: a computational strategy for species identification based on observed DNA microarray hybridization patterns.
  Genome biology 2005 Urisman A, Fischer KF, Chiu CY, Kistler AL, Beck S, Wang D, DeRisi JL
• Morbidity and mortality of short-bowel syndrome in infants with abdominal wall defects.
  The American surgeon 2002 Thakur A, Chiu C, Quiros-Tejeira RE, Reyen L, Ament M, Atkinson JB, Fonkalsrud EW
• Prospective, randomized, placebo-controlled evaluation of the safety and immunogenicity of three lots of intranasal trivalent influenza vaccine among young children.
  The Pediatric infectious disease journal 2001 Zangwill KM, Droge J, Mendelman P, Marcy SM, Partridge S, Chiu CY, Jing J, Chang SJ, Cho I, Ward JI
• Structural analysis of a fiber-pseudotyped adenovirus with ocular tropism suggests differential modes of cell receptor interactions.
  Journal of virology 2001 Chiu CY, Wu E, Brown SL, Von Seggern DJ, Nemerow GR, Stewart PL
• Uterine artery embolisation for treatment of fibroids: experience in Chinese women.
  Singapore medical journal 2001 Chiu CY, Wong WK, Mak HL, Chan CS, Kwok CH, Chan CH, Chan MK
• Cryo-Em Imaging of a Pseudotyped Adenovhtus with Ocular Cell Tropism.
  Microscopy and Microanalysis 2000 P.L. Stewart, C.Y. Chiu, D. Von Seggern, G.R. Nemerow
• Digitally collected cryo-electron micrographs for single particle reconstruction.
  Microscopy research and technique 2000 Stewart PL, Cary RB, Peterson SR, Chiu CY
• Review: resolution issues in single-particle reconstruction.
  Journal of structural biology 1999 Stewart PL, Chiu CY, Haley DA, Kong LB, Schlessman JL
• Structure of adenovirus complexed with its internalization receptor, alphavbeta5 integrin.
  Journal of virology 1999 Chiu CY, Mathias P, Nemerow GR, Stewart PL
• A helper-independent adenovirus vector with E1, E3, and fiber deleted: structure and infectivity of fiberless particles.
  Journal of virology 1999 Von Seggern DJ, Chiu CY, Fleck SK, Stewart PL, Nemerow GR
• Cryo-EM imaging of the catalytic subunit of the DNA-dependent protein kinase.
  Journal of molecular biology 1998 Chiu CY, Cary RB, Chen DJ, Peterson SR, Stewart PL
• Modification of a receptor-binding surface of epidermal growth factor (EGF): analogs with enhanced receptor affinity at low pH or at neutrality.
  Protein engineering 1998 Mullenbach GT, Chiu CY, Gyenes A, Blaney J, Rosenberg S, Marlowe CK, Brown S, Stratton-Thomas J, Montelione GT, George-Nascimento C, Stauber G
• Cryo-EM visualization of an exposed RGD epitope on adenovirus that escapes antibody neutralization.
  The EMBO journal 1997 Stewart PL, Chiu CY, Huang S, Muir T, Zhao Y, Chait B, Mathias P, Nemerow GR
• Oligonucleotide N3'-->P5' phosphoramidates as antisense agents.
  Nucleic acids research 1996 Gryaznov S, Skorski T, Cucco C, Nieborowska-Skorska M, Chiu CY, Lloyd D, Chen JK, Koziolkiewicz M, Calabretta B
• Enhanced antibody responses in infants given different sequences of heterogeneous Haemophilus influenzae type b conjugate vaccines.
  The Journal of pediatrics 1995 Greenberg DP, Lieberman JM, Marcy SM, Wong VK, Partridge S, Chang SJ, Chiu CY, Ward JI
• Immunogenicity of Haemophilus influenzae type b tetanus toxoid conjugate vaccine in young infants. The Kaiser-UCLA Vaccine Study Group.
  The Journal of infectious diseases 1994 Greenberg DP, Vadheim CM, Partridge S, Chang SJ, Chiu CY, Ward JI
• Comparison of naturally acquired and vaccine-induced antibodies to Haemophilus influenzae type b capsular polysaccharide.
  Infection and immunity 1993 Jelonek MT, Chang SJ, Chiu CY, Park MK, Nahm MH, Ward JI
• Effects of age, breast feeding, and household structure on Haemophilus influenzae type b disease risk and antibody acquisition in Alaskan Eskimos.
  American journal of epidemiology 1991 Petersen GM, Silimperi DR, Chiu CY, Ward JI
• Haemophilus influenzae type b anticapsular antibody responses to PRP-pertussis and PRP-D vaccines in Alaska native infants.
  The Journal of infectious diseases 1988 Ward JI, Brenneman G, Lepow M, Lum M, Burkhart K, Chiu CY
• Developmental and metabolic regulation of the Drosophila melanogaster 3-hydroxy-3-methylglutaryl coenzyme A reductase.
  Molecular and cellular biology 1988 Gertler FB, Chiu CY, Richter-Mann L, Chin DJ