Charles Chiu, MD, PhD

Professor

Charles Chiu, M.D./Ph.D. is Professor of Laboratory Medicine and Medicine, Division of Infectious Diseases at University of California, San Francisco and Director of the UCSF Clinical Microbiology Laboratory. Chiu currently leads a translational research laboratory focused on the development and clinical validation of metagenomic next-generation sequencing (mNGS) and host response profiling assays for diagnosis of infections, outbreak investigation, and pathogen discovery. He is a principal developer of a CRISPR-Cas12a based assay for the diagnosis of COVID-19, for which FDA Emergency Use Authorization was obtained in July of 2020, and has achieved FDA breakthrough device designation for mNGS assays for pathogen identification from cerebrospinal and respiratory fluids. Chiu also leverages machine learning based approaches to develop host response classification models based on RNA gene expression for differential diagnosis of central nervous system infections, infection-associated chronic illnesses (Lyme disease, chronic fatigue syndrome, and long COVID), and hyperinflammatory syndromes such as sepsis and multi-systm inflammatory syndrome in children (MIS-C). Chiu’s work is supported by funding from the National Institutes of Health (NIH), US Center for Disease Control and Prevention (CDC), Biomedical Advanced Research and Development Authority (BARDA), Abbott Laboratories, Chan-Zuckerberg Biohub, the Steven and Alexandra Cohen Foundation, and the California Initiative to Advance Precision Medicine. Dr. Chiu has authored more than 200 peer-reviewed publications, holds over 15 patents and patent applications, is a co-founder of Delve Bio, and serves on the scientific advisory board of Delve Bio, Biomeme, Mammoth Biosciences, Flightpath Biosciences, Biomesense, and Poppy Health.
Education
11/2022 - Diversity, Equity, and Inclusion Champion Training, University of California
M.D., 2001 - School of Medicine, University of California Los Angeles
Websites
Publications

  1. Loy CJ, Servellita V, Sotomayor-Gonzalez A, Bliss A, Lenz JS, Belcher E, Suslovic W, Nguyen J, Williams ME, Oseguera M, Gardiner MA, P.E.M.K.D.R.G., C.H.A.R.M.S. the Study Group, Choi JH, Hsiao HM, Wang H, Kim J, Shimizu C, Tremoulet AH, Delaney M, DeBiasi RL, Rostad CA, Burns JC, Chiu CY, De Vlaminck I. Plasma cell-free RNA signatures of inflammatory syndromes in children. 2024. PMID: 39240972


  2. Li GX, Gopchandani K, Brazer N, Tippett A, Choi C, Hsiao HM, Oseguera M, Foresythe A, Bhattacharya S, Servellita V, Sotomayor Gonzalez A, Spinler JK, Gonzalez MD, Gulick D, Kraft C, Kasinathan V, Wang YFW, Dien Bard J, Chen PY, Flores-Vazquez J, Odom John AR, Planet PJ, Devaraj S, Annapragada AV, Luna RA, Chiu CY, Rostad CA. Clinical Features and Outcomes of Pediatric and Adult Patients Hospitalized for Coronavirus Disease 2019: A Comparison Across Age Strata. 2024. PMID: 39183814


  3. Griffin IS, Smith DJ, Annambhotla P, Gold JAW, Ostrosky-Zeichner L, Kauffman CA, Gade L, Litvintseva A, Friedman DZ, Nishio Lucar AG, Parpia TC, Lieberman J, Bujan J, Corkrean J, Divatia MK, Grimes K, Lin J, Mobley C, Schwartz MR, Hannawi B, Malilay A, O'Boye A, Lysne J, Subramani MV, Heckmann H, Servellita V, Chiu C, Basavaraju SV. Outcomes in solid organ transplant recipients receiving organs from a donor with Fusarium solani species complex meningitis. 2024. PMID: 39012471


  4. Su LD, Chiu CY, Gaston D, Hogan CA, Miller S, Simon DW, Thakur KT, Yang S, Piantadosi A. Clinical Metagenomic Next-Generation Sequencing for Diagnosis of Central Nervous System Infections: Advances and Challenges. 2024. PMID: 38992308


  5. Loy CJ, Servellita V, Sotomayor-Gonzalez A, Bliss A, Lenz J, Belcher E, Suslovic W, Nguyen J, Williams ME, Oseguera M, Gardiner MA, Pediatric Emergency Medicine Kawasaki Disease Research Group (PEMKDRG), CHARMS Study Group, Choi JH, Hsiao HM, Wang H, Kim J, Shimizu C, Tremoulet A, Delaney M, DeBiasi RL, Rostad CA, Burns JC, Chiu CY, Vlaminck I. Plasma Cell-free RNA Signatures of Inflammatory Syndromes in Children. 2024. PMID: 38496479


  6. Suryawanshi RK, Taha TY, McCavitt-Malvido M, Silva I, Khalid MM, Syed AM, Chen IP, Saldhi P, Sreekumar B, Montano M, Foresythe K, Tabata T, Kumar GR, Sotomayor-Gonzalez A, Servellita V, Gliwa A, Nguyen J, Kojima N, Arellanor T, Bussanich A, Hess V, Shacreaw M, Lopez L, Brobeck M, Turner F, Wang Y, Ghazarian S, Davis G, Rodriguez D, Doudna J, Spraggon L, Chiu CY, Ott M. Previous exposure to Spike-providing parental strains confers neutralizing immunity to XBB lineage and other SARS-CoV-2 recombinants in the context of vaccination. 2023. PMID: 37869789


  7. Thebault S, Gandelman S, Lane C, Kim EJ, Pileggi C, Zuroff L, Yamashita LD, Schindler MK, Chiu C, Wilson MR, Berger JR, Markowitz C, Bar-Or A, Fuller R, Brandstadter R, Pruitt AA, Jacobs DA. Severe Neuroinvasive West Nile Virus in Association With Anti-CD20 Monotherapy for Multiple Sclerosis. 2023. PMID: 37562975


  8. Gould CV, Free RJ, Bhatnagar J, Soto RA, Royer TL, Maley WR, Moss S, Berk MA, Craig-Shapiro R, Kodiyanplakkal RPL, Westblade LF, Muthukumar T, Puius YA, Raina A, Hadi A, Gyure KA, Trief D, Pereira M, Kuehnert MJ, Ballen V, Kessler DA, Dailey K, Omura C, Doan T, Miller S, Wilson MR, Lehman JA, Ritter JM, Lee E, Silva-Flannery L, Reagan-Steiner S, Velez JO, Laven JJ, Fitzpatrick KA, Panella A, Davis EH, Hughes HR, Brault AC, St George K, Dean AB, Ackelsberg J, Basavaraju SV, Chiu CY, Staples JE, Yellow Fever Vaccine Virus Transplant and Transfusion Investigation Team. Transmission of yellow fever vaccine virus through blood transfusion and organ transplantation in the USA in 2021: report of an investigation. 2023. PMID: 37544313


  9. Weisgerber DW, Langer K, Servellita V, Xu P, Chiu CY, Abate AR. Viral load quantitation at the point-of-care with shaken digital droplet RT-LAMP. 2023. PMID: 37431299


  10. Rolfes M, Harroud A, Zorn KC, Tubati A, Omura C, Kurtz K, Matloubian M, Berger A, Chiu CY, Wilson MR, Ramachandran PS. Complement Factor I Gene Variant as a Treatable Cause of Recurrent Aseptic Neutrophilic Meningitis: A Case Report. 2023. PMID: 37339889


  11. Deyoe JE, Kelly JD, Grijalva CG, Bonenfant G, Lu S, Anglin K, Garcia-Knight M, Pineda-Ramirez J, Briggs Hagen M, Saydah S, Abedi GR, Goldberg SA, Tassetto M, Zhang A, Donohue KC, Davidson MC, Diaz Sanchez R, Djomaleu M, Mathur S, Shak JR, Deeks SG, Peluso MJ, Chiu CY, Zhu Y, Halasa NB, Chappell JD, Mellis A, Reed C, Andino R, Martin JN, Zhou B, Talbot HK, Midgley CM, Rolfes MA. Association of culturable-virus detection and household transmission of SARS-CoV-2 - California and Tennessee, 2020-2022. 2023. PMID: 36705269


  12. Haddock NL, Barkal LJ, Ram-Mohan N, Kaber G, Chiu CY, Bhatt AS, Yang S, Bollyky PL. Phage diversity in cell-free DNA identifies bacterial pathogens in human sepsis cases. 2023. PMID: 37308590


  13. 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. Metagenomic Detection of Divergent Insect- and Bat-Associated Viruses in Plasma from Two African Individuals Enrolled in Blood-Borne Surveillance. 2023. PMID: 37113001


  14. 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, Gliwa A, Bhakta K, Perez MA, Hussaini L, Anderson EJ, Chahroudi A, Delaney M, Butte AJ, DeBiasi RL, Rostad CA, De Vlaminck I, Chiu CY. Nucleic acid biomarkers of immune response and cell and tissue damage in children with COVID-19 and MIS-C. 2023. PMID: 37279751


  15. Farrington M, Elenz J, Ginsberg M, Chiu CY, Miller S, Pangonis SF. Powassan Virus Infection Detected by Metagenomic Next-Generation Sequencing, Ohio, USA. 2023. PMID: 36958034


  16. Servellita V, Gonzalez AS, 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, Morales C, Oluniyi PE, Nguyen J, Tan J, Stryke D, Jaber R, Leslie MT, Lyons Z, Hedman HD, Parashar U, Sullivan M, Wroblewski K, Oberste MS, Tate JE, Baker JM, Sugerman D, Potts C, Lu X, Chhabra P, Pediatric Hepatitis of Unknown Etiology Working Group, Ingram LA, Shiau H, Britt W, Sanchez LHG, Ciric C, Rostad CA, Vinj? J, Kirking HL, Wadford DA, Raborn RT, St George K, Chiu CY. Adeno-associated virus type 2 in US children with acute severe hepatitis. 2023. PMID: 36996871


  17. 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. Purifying selection decreases the potential for Bangui orthobunyavirus outbreaks in humans. 2023. PMID: 37025159


  18. 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. Longitudinal comparison of the developing gut virome in infants and their mothers. 2023. PMID: 36758519


  19. 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 JA, Fitzpatrick K, Velez JO, Davis EH, Hughes HR, Panella A, Brault A, Erin Staples J, Gould CV, Tanna S. Transfusion-Transmitted Cache Valley Virus Infection in a Kidney Transplant Recipient with Meningoencephalitis. 2022. PMID: 35883256


  20. 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. Successful Treatment of Balamuthia mandrillaris Granulomatous Amebic Encephalitis with Nitroxoline. 2023. PMID: 36573629


  21. 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, Santos YA, Fox DM, Ortega V, N??r AM, Baric RS, Stanley SA, Aguilar HC, Esko JD, Chiu CY, Pak JE, Beatty PR, Harris E. SARS-CoV-2 Spike triggers barrier dysfunction and vascular leak via integrins and TGF-� signaling. 2022. PMID: 36494335


  22. 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, Wadford DA, Andino R, Kelly JD, Hanson C, Chiu CY. Neutralizing Immunity Induced Against the Omicron BA.1 and BA.2 Variants in Vaccine Breakthrough Infections. 2022. PMID: 36134603


  23. Daniel Kelly J, Lu S, Anglin K, Garcia-Knight M, Pineda-Ramirez J, Goldberg SA, Tassetto M, Zhang A, Donohue K, Davidson MC, Romero M, Sanchez RD, Djomaleu M, Mathur S, Chen JY, Forman CA, Servellita V, Montejano RD, Shak JR, Rutherford GW, Deeks SG, Abedi GR, Rolfes MA, Saydah S, Briggs-Hagen M, Peluso MJ, Chiu C, Midgley CM, Andino R, Martin JN. Magnitude and determinants of SARS-CoV-2 household transmission: a longitudinal cohort study. 2022. PMID: 35788827


  24. 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, Mathur S, Servellita V, McIlwain D, Gaudiliere B, Chen J, Martinez EO, Tavs JM, Bronstone G, Weiss J, Watson JT, Briggs-Hagen M, Abedi GR, Rutherford GW, Deeks SG, Chiu C, Saydah S, Peluso MJ, Midgley CM, Martin JN, Andino R, Kelly JD. Infectious viral shedding of SARS-CoV-2 Delta following vaccination: A longitudinal cohort study. 2022. PMID: 36095030


  25. Sachdev DD, Chew Ng R, Sankaran M, Ernst A, Hernandez KT, Servellita V, Sotomayor-Gonzalez A, Stoltey J, Cohen SE, Nguyen TQ, Chiu C, Philip S. Contact tracing outcomes among household contacts of fully vaccinated COVID-19 patients - San Francisco, California, January 29-July 2, 2021. 2021. PMID: 34928340


  26. 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, Dick EJ, Chuba C, Gonzalez O, Brasky KM, Dutton J, Rutherford JN, Coffey LL, Singapuri A, Martin CSS, Chiu CY, Thomas SJ, Modjarrad K, Patterson JL, Blackman MA. Author Correction: Efficacy of an inactivated Zika vaccine against virus infection during pregnancy in mice and marmosets. 2022. PMID: 35987764


  27. 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. COVID-19 in Vaccinated Versus Unvaccinated Hematologic Malignancy Patients. 2022. PMID: 35426225


  28. 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, Kauppinen S, Rouskin S, N??r AM. An intranasal ASO therapeutic targeting SARS-CoV-2. 2022. PMID: 35922434


  29. 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. A diagnostic classifier for gene expression-based identification of early Lyme disease. 2022. PMID: 35879995


  30. 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. Metagenomic prediction of antimicrobial resistance in critically ill patients with lower respiratory tract infections. 2022. PMID: 35818068


  31. 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, Chiu CY. COVID-19 Variant Detection with a High-Fidelity CRISPR-Cas12 Enzyme. 2022. PMID: 35766492


  32. 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, Servellita V, Gliwa A, Nguyen J, Silva I, Milbes B, Kojima N, Hess V, Shacreaw M, Lopez L, Brobeck M, Turner F, Soveg FW, George AF, Fang X, Maishan M, Matthay M, Morris MK, Wadford D, Hanson C, Greene WC, Andino R, Spraggon L, Roan NR, Chiu CY, Doudna JA, Ott M. Limited cross-variant immunity from SARS-CoV-2 Omicron without vaccination. 2022. PMID: 35584773


  33. 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, Pak VM, Nagaraj SH, Smith AL, Skums P, Pasaniuc B, Komissarov A, Mason CE, Bortz E, Lemey P, Kondrashov F, Beerenwinkel N, Lam TT, Wu NC, Zelikovsky A, Knight R, Crandall KA, Mangul S. Unlocking capacities of genomics for the COVID-19 response and future pandemics. 2022. PMID: 35396471


  34. 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, Hackett J, Andino R, Wadford DA, Hanson C, Doudna J, Ott M, Chiu CY. Neutralizing immunity in vaccine breakthrough infections from the SARS-CoV-2 Omicron and Delta variants. 2022. PMID: 35429436


  35. 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. Individualized Constellation of Killer Cell Immunoglobulin-Like Receptors and Cognate HLA Class I Ligands that Controls Natural Killer Cell Antiviral Immunity Predisposes COVID-19. 2022. PMID: 35273641


  36. 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, Stanley S, Miller CJ. The B.1.427/1.429 (epsilon) SARS-CoV-2 variants are more virulent than ancestral B.1 (614G) in Syrian hamsters. 2022. PMID: 35143587


  37. Suryawanshi RK, Chen IP, Ma T, Syed AM, Simoneau CR, Ciling A, Khalid MM, Sreekumar B, Chen PY, George AF, Kumar GR, Montano M, Garcia-Knight MA, Brazer N, Saldhi P, Sotomayor-Gonzalez A, Servellita V, Gliwa A, Nguyen J, Silva I, Milbes B, Kojima N, Hess V, Shacreaw M, Lopez L, Brobeck M, Turner F, Soveg FW, Fang X, Maishan M, Matthay M, Morris MK, Wadford D, Hanson C, Greene WC, Andino R, Spraggon L, Roan NR, Chiu CY, Doudna J, Ott M. Limited cross-variant immunity after infection with the SARS-CoV-2 Omicron variant without vaccination. 2022. PMID: 35075459


  38. 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, Dick EJ, Chuba C, Gonzalez O, Brasky KM, Dutton J, Rutherford JN, Coffey LL, Singapuri A, Martin CSS, Chiu CY, Thomas SJ, Modjarrad K, Patterson JL, Blackman MA. Efficacy of an inactivated Zika vaccine against virus infection during pregnancy in mice and marmosets. 2022. PMID: 35087081


  39. 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, Snell LB, Nebbia G, Douthwaite S, Tanuri A, Singh L, de Oliveira T, Ahouidi A, Mboup S, Cloherty GA. Detection of SARS-CoV-2 variants by Abbott molecular, antigen, and serological tests. 2022. PMID: 35086043


  40. 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, Frias E, Rodgers M, Cloherty G, Hackett J, Hanson C, Wadford D, Philip S, Topper S, Sachdev D, Chiu CY. Predominance of antibody-resistant SARS-CoV-2 variants in vaccine breakthrough cases from the San Francisco Bay Area, California. 2022. PMID: 35013591


  42. Davar K, Wilson MR, Miller S, Chiu CY, Vijayan T. A Rare Bird: Diagnosis of Psittacosis Meningitis by Clinical Metagenomic Next-Generation Sequencing. 2021. PMID: 34934772


  43. 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 SA, Gelfand JM, Miller S, Wang L, Tihan T, DeRisi JL, Chiu CY, Wilson MR. Detection of Neoplasms by Metagenomic Next-Generation Sequencing of Cerebrospinal Fluid. 2021. PMID: 34515766


  44. 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, Gelfand AA, Johnson-Kerner BL, Nash K, Krishnamoorthy KS, Chitnis T, Ding JZ, McMillan HJ, Chiu CY, Briggs B, Glaser CA, Yen C, Chu V, Wadford DA, Dominguez SR, Ng TFF, Marine RL, Lopez AS, Nix WA, Soldatos A, Gorman MP, Benson L, Messacar K, Konopka-Anstadt JL, Oberste MS, DeRisi JL, Wilson MR. Author Correction: Pan-viral serology implicates enteroviruses in acute flaccid myelitis. 2021. PMID: 34548659


  45. 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, Stanley S, Miller CJ. The B.1.427/1.429 (epsilon) SARS-CoV-2 variants are more virulent than ancestral B.1 (614G) in Syrian hamsters. 2021. PMID: 34462750


  46. Chamie G, Marquez C, Crawford E, Peng J, Petersen M, Schwab D, Schwab J, Martinez J, Es DJ, Black D, Gandhi M, Kerkhoff AD, Jain V, Sergi F, Jacobo J, Rojas S, Tulier-Laiwa V, Gallardo-Brown T, Appa A, Chiu C, Rodgers M, Hackett J, Kistler A, Hao S, Kamm J, Dynerman D, Batson J, Greenhouse B, DeRisi J, Havlir DV. SARS-CoV-2 Community Transmission disproportionately affects Latinx population during Shelter-in-Place in San Francisco. 2020. PMID: 32821935


  47. 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, Vallari A, Rodgers MA, Prostko J, Hackett J, Trinh L, Wrin T, Petropoulos CJ, Chiu CY, Norris PJ, DiGermanio C, Stone M, Busch MP, Elledge SK, Zhou XX, Wells JA, Shu A, Kurtz TW, Pak JE, Wu W, Burbelo PD, Cohen JI, Rutishauser RL, Martin JN, Deeks SG, Henrich TJ, Rodriguez-Barraquer I, Greenhouse B. SARS-CoV-2 antibody magnitude and detectability are driven by disease severity, timing, and assay. 2021. PMID: 34330709


  48. 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, Eliáš M, Slamovits CH, Weirauch MT, Fritz-Laylin L, Marciano-Cabral F, Puzon GJ, Walsh T, Chiu C, Dacks JB. Genomics and transcriptomics yields a system-level view of the biology of the pathogen Naegleria fowleri. 2021. PMID: 34294116


  49. 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. Use of Metagenomic Next-Generation Sequencing to Identify Pathogens in Pediatric Osteoarticular Infections. 2021. PMID: 34322569


  50. 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, Tong S, Batson J, Chiu CY. Introduction, Transmission Dynamics, and Fate of Early Severe Acute Respiratory Syndrome Coronavirus 2 Lineages in Santa Clara County, California. 2021. PMID: 33893501


  51. 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 WB, Shi PY, Davis-Gardner ME, Suthar MS, Knight MG, Andino R, Chiu CY, Ellebedy AH, Fremont DH, Whelan SPJ, Crowe JE, Purcell L, Corti D, Boon ACM, Diamond MS. In vivo monoclonal antibody efficacy against SARS-CoV-2 variant strains. 2021. PMID: 34153975


  52. Lagenaur LA, Hemmerling A, Chiu C, Miller S, Lee PP, Cohen CR, Parks TP. Connecting the dots: Translating the vaginal microbiome into a drug. 2020. PMID: 33330916


  53. 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, Prakash S, Simko J, Chiu CY. Detection of cryptogenic malignancies from metagenomic whole genome sequencing of body fluids. 2021. PMID: 34074327


  54. 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 W, Shi PY, Garcia-Knight M, Andino R, Chiu C, Ellebedy A, Fremont D, Whelan S, Crowe J, Purcell L, Corti D, Boon A. In vivo monoclonal antibody efficacy against SARS-CoV-2 variant strains. 2021. PMID: 34013259


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  56. Haddad AF, Hofmann JW, Oh T, Jacques L, Yu G, Chiu C, Nolan A, Strober J, Gupta N. Pathologic Findings Associated With a Case of Acute Flaccid Myelitis. 2021. PMID: 33870421


  57. 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 X, Wong D, Spencer E, Robles-Sikisaka R, Kurzban E, Hughes LD, Deng X, Wang C, Servellita V, Valentine H, De Hoff P, Seaver P, Sathe S, Gietzen K, Sickler B, Antico J, Hoon K, Liu J, Harding A, Bakhtar O, Basler T, Austin B, MacCannell D, Isaksson M, Febbo PG, Becker D, Laurent M, McDonald E, Yeo GW, Knight R, Laurent LC, de Feo E, Worobey M, Chiu CY, Suchard MA, Lu JT, Lee W, Andersen KG. Emergence and rapid transmission of SARS-CoV-2 B.1.1.7 in the United States. 2021. PMID: 33861950


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  65. Gu W, Deng X, Reyes K, Hsu E, Wang C, Sotomayor-Gonzalez A, Federman S, Bushnell B, Miller S, Chiu C. Associations of Early COVID-19 Cases in San Francisco with Domestic and International Travel. 2020. PMID: 32436571


  66. Karmarkar E, Blanco I, Amornkul P, DuBois A, Deng X, Moonan PK, Rubenstein BL, Miller DA, Kennedy I, Yu J, Dauterman J, Ongpin M, Hathaway W, Hoo L, Trammell S, Ememu E, Yu G, Khwaja Z, Lu W, Talai N, Jain S, Louie J, Philip S, Federman S, Masinde G, Wadford DA, Bobba N, Stoltey J, Smith A, Epson E, Chiu C, Bennett A, Vasquez AM, Williams T. Timely Intervention and Control of a Novel Coronavirus (COVID-19) Outbreak at a Large Skilled Nursing Facility - San Francisco, California, 2020. 2020. PMID: 33308357


  67. 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. Fatal Case of Chronic Jamestown Canyon Virus Encephalitis Diagnosed by Metagenomic Sequencing in Patient Receiving Rituximab. 2020. PMID: 33261720


  68. Lemos D, Stuart JB, Louie W, Singapuri A, Ramírez AL, Watanabe J, Usachenko J, Keesler RI, Martin CS, Li T, Martyn C, Oliveira G, Saraf S, Grubaugh ND, Andersen KG, Thissen J, Allen J, Borucki M, Tsetsarkin KA, Pletnev AG, Chiu CY, Van Rompay KKA, Coffey LL. 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. 2020. PMID: 32999034


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  70. 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, Havlir D, Greenhouse B. Universal Polymerase Chain Reaction and Antibody Testing Demonstrate Little to No Transmission of Severe Acute Respiratory Syndrome Coronavirus 2 in a Rural Community. 2020. PMID: 34109255


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  72. Chiu CY, Sarwal A, Mon AM, Tan YE, Shah V. Gastrointestinal: COVID-19 related ischemic bowel disease. 2020. PMID: 32985002


  73. 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, Nussenzweig MC, DeRisi JL, Wilson MR. ReScan, a Multiplex Diagnostic Pipeline, Pans Human Sera for SARS-CoV-2 Antigens. 2020. PMID: 32995758


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  75. 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, Glasner DR, Han LM, Truong K, Akagi N, Nguyen DN, Neumann NM, Qazi D, Hsu E, Gu W, Santos YA, Custer B, Green V, Williamson P, Hills NK, Lu CM, Whitman JD, Stramer SL, Wang C, Reyes K, Hakim JMC, Sujishi K, Alazzeh F, Pham L, Thornborrow E, Oon CY, Miller S, Kurtz T, Simmons G, Hackett J, Busch MP, Chiu CY. SARS-CoV-2 seroprevalence and neutralizing activity in donor and patient blood. 2020. PMID: 32943630


  76. Byrnes JR, Zhou XX, Lui I, Elledge SK, Glasgow JE, Lim SA, Loudermilk RP, Chiu CY, Wang TT, Wilson MR, Leung KK, Wells JA. Competitive SARS-CoV-2 Serology Reveals Most Antibodies Targeting the Spike Receptor-Binding Domain Compete for ACE2 Binding. 2020. PMID: 32938700


  77. Mohon AN, Oberding L, Hundt J, van Marle G, Pabbaraju K, Berenger B, Lisboa L, Griener T, Czub M, Doolan C, Servelitta V, Chiu C, Greninger A, Jerome K, Pillai DR. Optimization and clinical validation of dual-target RT-LAMP for SARS-CoV-2. 2020. PMID: 32941977


  78. 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 CD, Ilcisin M, Lacombe K, Lee J, Kiavand A, Richardson M, Sibley TR, Truong M, Wolf CR, Nickerson DA, Rieder MJ, Englund JA, Hadfield J, Hodcroft EB, Huddleston J, Moncla LH, Müller NF, Neher RA, Deng X, Gu W, Federman S, Chiu C, Duchin JS, Gautom R, Melly G, Hiatt B, Dykema P, Lindquist S, Queen K, Tao Y, Uehara A, Tong S, MacCannell D, Armstrong GL, Baird GS, Chu HY, Shendure J, Jerome KR. Cryptic transmission of SARS-CoV-2 in Washington state. 2020. PMID: 32913002


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  80. 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 AW, Gillis-Buck EM, Steinhart ZB, Lee Y, Apathy R, Lipke MJ, Smith JA, Zheng T, Boothby IC, Isaza E, Chan J, Acenas DD, Lee J, Macrae TA, Kyaw TS, Wu D, Ng DL, Gu W, York VA, Eskandarian HA, Callaway PC, Warrier L, Moreno ME, Levan J, Torres L, Farrington LA, Loudermilk RP, Koshal K, Zorn KC, Garcia-Beltran WF, Yang D, Astudillo MG, Bernstein BE, Gelfand JA, Ryan ET, Charles RC, Iafrate AJ, Lennerz JK, Miller S, Chiu CY, Stramer SL, Wilson MR, Manglik A, Ye CJ, Krogan NJ, Anderson MS, Cyster JG, Ernst JD, Wu AHB, Lynch KL, Bern C, Hsu PD, Marson A. Evaluation of SARS-CoV-2 serology assays reveals a range of test performance. 2020. PMID: 32855547


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  83. 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 CY, Havlir D, Greenhouse B. Universal PCR and antibody testing demonstrate little to no transmission of SARS-CoV-2 in a rural community. 2020. PMID: 32839781


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  89. Byrnes JR, Zhou XX, Lui I, Elledge SK, Glasgow JE, Lim SA, Loudermilk R, Chiu CY, Wilson MR, Leung KK, Wells JA. A SARS-CoV-2 serological assay to determine the presence of blocking antibodies that compete for human ACE2 binding. 2020. PMID: 32511506


  90. Ng D, Goldgof G, Shy B, Levine A, Balcerek J, Bapat SP, Prostko J, Rodgers M, Coller K, Pearce S, Franz S, Du L, Stone M, Pillai S, Sotomayor-Gonzalez A, Servellita V, Sanchez-San Martin C, Granados A, Glasner DR, Han LM, Truong K, Akagi N, Nguyen DN, Neumann N, Qazi D, Hsu E, Gu W, Santos YA, Custer B, Green V, Williamson P, Hills NK, Lu CM, Whitman JD, Stramer S, Wang C, Reyes K, Hakim J, Sujishi K, Alazzeh F, Pharm L, Oon CY, Miller S, Kurtz T, Hackett J, Simmons G, Busch MP, Chiu CY. SARS-CoV-2 seroprevalence and neutralizing activity in donor and patient blood from the San Francisco Bay Area. 2020. PMID: 32511477


  91. 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. New Genomes from the Congo Basin Expand History of CRF01_AE Origin and Dissemination. 2020. PMID: 32281388


  92. 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 AW, Gillis-Buck EM, Steinhart ZB, Lee Y, Apathy R, Lipke MJ, Smith JA, Zheng T, Boothby IC, Isaza E, Chan J, Acenas DD, Lee J, Macrae TA, Kyaw TS, Wu D, Ng DL, Gu W, York VA, Eskandarian HA, Callaway PC, Warrier L, Moreno ME, Levan J, Torres L, Farrington LA, Loudermilk R, Koshal K, Zorn KC, Garcia-Beltran WF, Yang D, Astudillo MG, Bernstein BE, Gelfand JA, Ryan ET, Charles RC, Iafrate AJ, Lennerz JK, Miller S, Chiu CY, Stramer SL, Wilson MR, Manglik A, Ye CJ, Krogan NJ, Anderson MS, Cyster JG, Ernst JD, Wu AHB, Lynch KL, Bern C, Hsu PD, Marson A. Test performance evaluation of SARS-CoV-2 serological assays. 2020. PMID: 32511497


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  97. 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 CD, Ilcisin M, Lacombe K, Lee J, Kiavand A, Richardson M, Sibley TR, Truong M, Wolf CR, Nickerson DA, Rieder MJ, Englund JA, Hadfield J, Hodcroft EB, Huddleston J, Moncla LH, Müller NF, Neher RA, Deng X, Gu W, Federman S, Chiu C, Duchin J, Gautom R, Melly G, Hiatt B, Dykema P, Lindquist S, Queen K, Tao Y, Uehara A, Tong S, MacCannell D, Armstrong GL, Baird GS, Chu HY, Shendure J, Jerome KR. Cryptic transmission of SARS-CoV-2 in Washington State. 2020. PMID: 32511596


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  101. Kuhn JH, Pan H, Chiu CY, Stremlau M. Human Tibroviruses: Commensals or Lethal Pathogens? 2020. PMID: 32106547


  104. 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, Kaptue L, McArthur C, Muñoz-Medina JE, Gonzalez-Bonilla CR, López S, Arias CF, Arevalo S, Miller S, Stone M, Busch M, Hsieh K, Messenger S, Wadford DA, Rodgers M, Cloherty G, Faria NR, Thézé J, Pybus OG, Neto Z, Morais J, Taveira N, R Hackett J, Chiu CY. Metagenomic sequencing with spiked primer enrichment for viral diagnostics and genomic surveillance. 2020. PMID: 31932713


  106. 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 GA, Sample HA, Zorn KC, Banerji D, Khan LM, Bove R, Hauser SL, Gelfand AA, Johnson-Kerner BL, Nash K, Krishnamoorthy KS, Chitnis T, Ding JZ, McMillan HJ, Chiu CY, Briggs B, Glaser CA, Yen C, Chu V, Wadford DA, Dominguez SR, Ng TFF, Marine RL, Lopez AS, Nix WA, Soldatos A, Gorman MP, Benson L, Messacar K, Konopka-Anstadt JL, Oberste MS, DeRisi JL, Wilson MR. Pan-viral serology implicates enteroviruses in acute flaccid myelitis. 2019. PMID: 31636453


  107. 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, Kapetshi J, Pybus OG, Muyembe-Tamfum JJ, Chiu C. Metagenomic Next-Generation Sequencing of the 2014 Ebola Virus Disease Outbreak in the Democratic Republic of the Congo. 2019. PMID: 31315955


  108. Saa P, Chiu C, Grimm K, Yu G, Benjamin RJ, Corash L, Stramer SL. Acute Zika virus infection in an asymptomatic blood donor at the onset of the Puerto Rico epidemic. 2019. PMID: 31407817


  110. 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, Bender J, Dien Bard J, Murkey J, Carlson M, Vespa PM, Vijayan T, Allyn PR, Campeau S, Humphries RM, Klausner JD, Ganzon CD, Memar F, Ocampo NA, Zimmermann LL, Cohen SH, Polage CR, DeBiasi RL, Haller B, Dallas R, Maron G, Hayden R, Messacar K, Dominguez SR, Miller S, Chiu CY. Clinical Metagenomic Sequencing for Diagnosis of Meningitis and Encephalitis. 2019. PMID: 31189036


  111. Chiu CY, Miller SA. Clinical metagenomics. 2019. PMID: 30918369


  112. 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. Human, Nonhuman Primate, and Bat Cells Are Broadly Susceptible to Tibrovirus Particle Cell Entry. 2019. PMID: 31105663


  113. 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. Laboratory validation of a clinical metagenomic sequencing assay for pathogen detection in cerebrospinal fluid. 2019. PMID: 30992304


  114. Quach HT, Robbins CJ, Balko JM, Chiu CY, Miller S, Wilson MR, Nelson GE, Johnson DB. Severe Epididymo-Orchitis and Encephalitis Complicating Anti-PD-1 Therapy. 2019. PMID: 30936376


  115. 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 DM, Chiu CY. Whole blood human transcriptome and virome analysis of ME/CFS patients experiencing post-exertional malaise following cardiopulmonary exercise testing. 2019. PMID: 30897114


  116. McIntyre ABR, Alexander N, Grigorev K, Bezdan D, Sichtig H, Chiu CY, Mason CE. Single-molecule sequencing detection of N6-methyladenine in microbial reference materials. 2019. PMID: 30718479


  117. Saporta-Keating SR, Simões EAF, Yu G, Federman S, Mirsky D, Dominguez SR, Chiu CY, Messacar K. A Child With Intermittent Headaches and Eosinophilic Meningitis. 2018. PMID: 29438532


  118. 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, Wilson J, Miller S, Matthay MA, Pollard KS, Christenson S, Calfee CS, DeRisi JL. Integrating host response and unbiased microbe detection for lower respiratory tract infection diagnosis in critically ill adults. 2018. PMID: 30482864


  119. Benjamin Briggs, Scot Federman, Xian Ding Deng, Wei Gu, Guixia Yu, Claudia Sanchez San Martin, Steve Miller, Charles Y Chiu. 2291. A Real-Time Sequencing Approach for Simultaneous Metagenomic and Transcriptomic-Based Diagnosis of Infectious Diseases. 2018. PMID:


  120. Michael Wilson, Hannah Sample, Kelsey Zorn, Samia N Naccache, Steve Miller, Charles Y Chiu. 2563. Clinical Metagenomic Next-Generation Sequencing for Diagnosis of Meningitis and Encephalitis. 2018. PMID:


  121. Andrea Granados, Susanna K Tan, Jerome Bouquet, Charles Y Chiu, Julie Parsonnet, Lauri Green. 617. Characterization and Development of the Infant Gut Virome: A STORK Study. 2018. PMID:


  122. 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, Patterson JL. Publisher Correction: Experimental Zika Virus Infection in the Pregnant Common Marmoset Induces Spontaneous Fetal Loss and Neurodevelopmental Abnormalities. 2018. PMID: 30367092


  123. Gu W, Miller S, Chiu CY. Clinical Metagenomic Next-Generation Sequencing for Pathogen Detection. 2018. PMID: 30355154


  124. Sánchez-San Martín C, Li T, Bouquet J, Streithorst J, Yu G, Paranjpe A, Chiu CY. Differentiation enhances Zika virus infection of neuronal brain cells. 2018. PMID: 30266962


  125. 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. Identification of high-risk human papillomavirus and Rb/E2F pathway genomic alterations in mutually exclusive subsets of colorectal neuroendocrine carcinoma. 2018. PMID: 30237525


  126. Thornton CS, Rubin JE, Greninger AL, Peirano G, Chiu CY, Pillai DR. Epidemiological and genomic characterization of community-acquired Clostridium difficile infections. 2018. PMID: 30170546


  127. 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, Tamhankar M, Seferovic M, Aagaard KM, Martín CS, Chiu CY, Panganiban AT, Veazey RS, Wang X, Maness NJ, Gilbert MH, Bohm RP, Adams Waldorf KM, Gale M, Rajagopal L, Hotchkiss CE, Mohr EL, Capuano SV, Simmons HA, Mejia A, Friedrich TC, Golos TG, O'Connor DH. Miscarriage and stillbirth following maternal Zika virus infection in nonhuman primates. 2018. PMID: 29967348


  128. 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 of Indeterminate Etiology: A Comprehensive Systematic Approach by An Expert Committee to Establish Causality. 2018. PMID: 29946176


  130. 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 EM, Busch M, Muñoz-Medina JE, González-Bonilla CR, Wolinsky S, López S, Arias CF, Bonsall D, Chiu CY, Pybus OG. Genomic Epidemiology Reconstructs the Introduction and Spread of Zika Virus in Central America and Mexico. 2018. PMID: 29805095


  131. 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, Luthringer DJ. Polyoma virus-associated carcinomas of the urologic tract: a clinicopathologic and molecular study. 2018. PMID: 29765141


  132. Seferovic M, Martín CS, 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, Patterson JL. Experimental Zika Virus Infection in the Pregnant Common Marmoset Induces Spontaneous Fetal Loss and Neurodevelopmental Abnormalities. 2018. PMID: 29717225


  133. 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, Collins PL, Dietzgen RG, Dolja VV, Dolnik O, Domier LL, Dürrwald R, Dye JM, Easton AJ, Ebihara H, Echevarría JE, Fooks AR, Formenty PBH, Fouchier RAM, Freuling CM, Ghedin E, Goldberg TL, Hewson R, Horie M, Hyndman TH, Jiang D, Kityo R, Kobinger GP, Kondo H, Koonin EV, Krupovic M, Kurath G, Lamb RA, Lee B, Leroy EM, Maes P, Maisner A, Marston DA, Mor SK, Müller T, Mühlberger E, Ramírez VMN, Netesov SV, Ng TFF, Nowotny N, Palacios G, Patterson JL, Paweska JT, Payne SL, Prieto K, Rima BK, Rota P, Rubbenstroth D, Schwemmle M, Siddell S, Smither SJ, Song Q, Song T, Stenglein MD, Stone DM, Takada A, Tesh RB, Thomazelli LM, Tomonaga K, Tordo N, Towner JS, Vasilakis N, Vázquez-Morón S, Verdugo C, Volchkov VE, Wahl V, Walker PJ, Wang D, Wang LF, Wellehan JFX, Wiley MR, Whitfield AE, Wolf YI, Yè G, Zhang YZ, Kuhn JH. Taxonomy of the order Mononegavirales: update 2018. 2018. PMID: 29637429


  134. 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 Sequencing Detects Respiratory Pathogens in Hematopoietic Cellular Transplant Patients. Volume 197 of Issue 4. 2018. PMID: 28686513


  136. 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, Alexander N, Yu G, Mason CE, Burton AS. Nanopore DNA Sequencing and Genome Assembly on the International Space Station. Volume 7 of Issue 1. 2017. PMID: 29269933


  137. 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. Experimental Zika Virus Inoculation in a New World Monkey Model Reproduces Key Features of the Human Infection. Volume 7 of Issue 1. 2017. PMID: 29215081


  138. 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. A composite of exhaled LTB4 , LXA4 , FeNO, and FEV1 as an "asthma classification ratio" characterizes childhood asthma. 2017. PMID: 28944471


  139. Mongkolrattanothai K, Naccache SN, Bender JM, Samayoa E, Pham E, Yu G, Dien Bard J, Miller S, Aldrovandi G, Chiu CY. Neurobrucellosis: Unexpected Answer From Metagenomic Next-Generation Sequencing. Volume 6 of Issue 4. 2017. PMID: 28062553


  140. Somasekar S, Lee D, Rule J, Naccache SN, Stone M, Busch MP, Sanders C, Lee WM, Chiu CY. Viral Surveillance in Serum Samples From Patients With Acute Liver Failure By Metagenomic Next-Generation Sequencing. Volume 65 of Issue 9. 2017. PMID: 29020199


  141. 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. Diagnosis of Fatal Human Case of St. Louis Encephalitis Virus Infection by Metagenomic Sequencing, California, 2016. 2017. PMID: 28930022


  143. 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, Montoya JG, Robinson WH, Fantl WJ, Nolan GP, Zamanian RT, Nicolls MR, Chiu CY, Ariza ME, Rabinovitch M. Upregulation of Human Endogenous Retrovirus-K Is Linked to Immunity and Inflammation in Pulmonary Arterial Hypertension. Volume 136 of Issue 20. 2017. PMID: 28935667


  144. 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 E, Wolfe ND, Chiu CY, Leroy EM. Correction: Correction: A Novel Rhabdovirus Associated with Acute Hemorrhagic Fever in Central Africa. Volume 13 of Issue 9. 2017. PMID: 28880960


  145. 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. The eukaryotic gut virome in hematopoietic stem cell transplantation: new clues in enteric graft-versus-host disease. Volume 23 of Issue 9. 2017. PMID: 28759053


  146. Murkey JA, Chew KW, Carlson M, Shannon CL, Sirohi D, Sample HA, Wilson MR, Vespa P, Humphries RM, Miller S, Klausner JD, Chiu CY. Hepatitis E Virus-Associated Meningoencephalitis in a Lung Transplant Recipient Diagnosed by Clinical Metagenomic Sequencing. Volume 4 of Issue 3. 2017. PMID: 28721353


  147. 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 WK, Carmo EH, Coelho GE, Santelli ACFS, Vinhal LC, Henriques CM, Simpson JT, Loose M, Andersen KG, Grubaugh ND, Somasekar S, Chiu CY, Muñoz-Medina JE, Gonzalez-Bonilla CR, Arias CF, Lewis-Ximenez LL, Baylis SA, Chieppe AO, Aguiar SF, Fernandes CA, Lemos PS, Nascimento BLS, Monteiro HAO, Siqueira IC, de Queiroz MG, de Souza TR, Bezerra JF, Lemos MR, Pereira GF, Loudal D, Moura LC, Dhalia R, França RF, Magalhães T, Marques ET, Jaenisch T, Wallau GL, de Lima MC, Nascimento V, de Cerqueira EM, de Lima MM, Mascarenhas DL, Neto JPM, Levin AS, Tozetto-Mendoza TR, Fonseca SN, Mendes-Correa MC, Milagres FP, Segurado A, Holmes EC, Rambaut A, Bedford T, Nunes MRT, Sabino EC, Alcantara LCJ, Loman NJ, Pybus OG. Establishment and cryptic transmission of Zika virus in Brazil and the Americas. 2017. PMID: 28538727


  148. 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. Establishment and characterization of an oral tongue squamous cell carcinoma cell line from a never-smoking patient. Volume 69. 2017. PMID: 28559012


  149. Greninger AL, Streithorst J, Chiu CY, Miller S. First Complete Genome Sequence of Corynebacterium riegelii. Volume 5 of Issue 13. 2017. PMID: 28360160


  151. Hixon AM, Yu G, Leser JS, Yagi S, Clarke P, Chiu CY, Tyler KL. A mouse model of paralytic myelitis caused by enterovirus D68. Volume 13 of Issue 2. 2017. PMID: 28231269


  152. 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, Patrick DM. RNA-Seq Analysis of Gene Expression, Viral Pathogen, and B-Cell/T-Cell Receptor Signatures in Complex Chronic Disease. Volume 64 of Issue 4. 2017. PMID: 28172519


  153. Schlaberg R, Chiu CY, Miller S, Procop GW, Weinstock G. Validation of Metagenomic Next-Generation Sequencing Tests for Universal Pathogen Detection. Volume 141 of Issue 6. 2017. PMID: 28169558


  154. Wiley MR, Prieto K, Blasdell KR, Caì Y, Campos Lawson C, Walker PJ, Chiu CY, Palacios G, Kuhn JH. Beatrice Hill Virus Represents a Novel Species in the Genus Tibrovirus (Mononegavirales: Rhabdoviridae). Volume 5 of Issue 4. 2017. PMID: 28126935


  156. 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. Longitudinal investigation of nasopharyngeal methicillin-resistant Staphylococcus aureus colonization in early infancy: The PATCH birth cohort study. 2016. PMID: 27793735


  157. Naccache SN, Thézé J, Sardi SI, Somasekar S, Greninger AL, Bandeira AC, Campos GS, Tauro LB, Faria NR, Pybus OG, Chiu CY. Distinct Zika Virus Lineage in Salvador, Bahia, Brazil. 2016. PMID: 27448188


  159. Sardi SI, Somasekar S, Naccache SN, Bandeira AC, Tauro LB, Campos GS, Chiu CY. Coinfections of Zika and Chikungunya Viruses in Bahia, Brazil, Identified by Metagenomic Next-Generation Sequencing. Volume 54 of Issue 9. 2016. PMID: 27413190


  160. Coller KE, Berg MG, Frankel M, Forberg K, Surani R, Chiu CY, Hackett J, Dawson GJ. Antibodies to the Novel Human Pegivirus 2 Are Associated with Active and Resolved Infections. Volume 54 of Issue 8. 2016. PMID: 27225404


  161. 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. Two human immunodeficiency virus Type 2 cases in US blood donors including serologic, molecular, and genomic characterization of an epidemiologically unusual case. Volume 56 of Issue 6 Pt 2. 2016. PMID: 27079968


  162. 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 E, Wolfe ND, Chiu CY, Leroy EM. Correction: A Novel Rhabdovirus Associated with Acute Hemorrhagic Fever in Central Africa. Volume 12 of Issue 3. 2016. PMID: 26991269


  163. Greninger AL, Chatterjee SS, Chan LC, Hamilton SM, Chambers HF, Chiu CY. Whole-Genome Sequencing of Methicillin-Resistant Staphylococcus aureus Resistant to Fifth-Generation Cephalosporins Reveals Potential Non-mecA Mechanisms of Resistance. Volume 11 of Issue 2. 2016. PMID: 26890675


  164. Bouquet J, Soloski MJ, Swei A, Cheadle C, Federman S, Billaud JN, Rebman AW, Kabre B, Halpert R, Boorgula M, Aucott JN, Chiu CY. Longitudinal Transcriptome Analysis Reveals a Sustained Differential Gene Expression Signature in Patients Treated for Acute Lyme Disease. Volume 7 of Issue 1. 2016. PMID: 26873097


  165. 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. Erratum to: Clinical metagenomic identification of Balamuthia mandrillaris encephalitis and assembly of the draft genome: the continuing case for reference genome sequencing. Volume 8 of Issue 1. 2016. PMID: 26750923


  166. 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. Discovery of a Novel Human Pegivirus in Blood Associated with Hepatitis C Virus Co-Infection. Volume 11 of Issue 12. 2015. PMID: 26658760


  167. 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. Chiu. Balamuthia Mandrillaris Encephalitis Detected by Next Generation Sequencing of Cerebrospinal Fluid. 2015. PMID:


  168. 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. Acute Flaccid Myelitis of Unknown Etiology in California, 2012-2015. Volume 314 of Issue 24. 2015. PMID: 26720027


  169. 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, Chiu CY. Clinical metagenomic identification of Balamuthia mandrillaris encephalitis and assembly of the draft genome: the continuing case for reference genome sequencing. Volume 7. 2015. PMID: 26620704


  170. Luk KC, Berg MG, Naccache SN, Kabre B, Federman S, Mbanya D, Kaptué L, Chiu CY, Brennan CA, Hackett J. Utility of Metagenomic Next-Generation Sequencing for Characterization of HIV and Human Pegivirus Diversity. Volume 10 of Issue 11. 2015. PMID: 26599538


  171. 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. Rapid metagenomic identification of viral pathogens in clinical samples by real-time nanopore sequencing analysis. Volume 7. 2015. PMID: 26416663


  172. Greninger AL, Cunningham G, Chiu CY, Miller S. Draft Genome Sequence of Mycobacterium heckeshornense Strain RLE. Volume 3 of Issue 4. 2015. PMID: 26316632


  173. Chiu CY, Bres V, Yu G, Krysztof D, Naccache SN, Lee D, Pfeil J, Linnen JM, Stramer SL. Genomic Assays for Identification of Chikungunya Virus in Blood Donors, Puerto Rico, 2014. Volume 21 of Issue 8. 2015. PMID: 26196378


  174. Greninger AL, Cunningham G, Chiu CY, Miller S. Draft Genome Sequence of Mycobacterium heraklionense Strain Davo. Volume 3 of Issue 4. 2015. PMID: 26205863


  175. Greninger AL, Cunningham G, Yu JM, Hsu ED, Chiu CY, Miller S. Draft Genome Sequence of Mycobacterium elephantis Strain Lipa. Volume 3 of Issue 3. 2015. PMID: 26112791


  176. Greninger AL, Cunningham G, Yu JM, Hsu ED, Chiu CY, Miller S. Draft Genome Sequence of Mycobacterium arupense Strain GUC1. Volume 3 of Issue 3. 2015. PMID: 26067970


  177. Greninger AL, Cunningham G, Hsu ED, Yu JM, Chiu CY, Miller S. Draft Genome Sequence of Mycobacterium obuense Strain UC1, Isolated from Patient Sputum. Volume 3 of Issue 3. 2015. PMID: 26067960


  178. Greninger AL, Langelier C, Cunningham G, Keh C, Melgar M, Chiu CY, Miller S. Two Rapidly Growing Mycobacterial Species Isolated from a Brain Abscess: First Whole-Genome Sequences of Mycobacterium immunogenum and Mycobacterium llatzerense. Volume 53 of Issue 7. 2015. PMID: 25926490


  179. 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. Idiopathic pneumonia syndrome after hematopoietic cell transplantation: evidence of occult infectious etiologies. Volume 125 of Issue 24. 2015. PMID: 25918347


  180. Saglam O, Samayoa E, Somasekar S, Naccache S, Iwasaki A, Chiu CY. No viral association found in a set of differentiated vulvar intraepithelial neoplasia cases by human papillomavirus and pan-viral microarray testing. Volume 10 of Issue 4. 2015. PMID: 25894343


  181. S. L. Stramer, R. Y. Dodd, C. Y. Chiu. Advances in testing technology to ensure transfusion safety – NAT and beyond. 2015. PMID:


  182. 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, Chiu CY. A novel outbreak enterovirus D68 strain associated with acute flaccid myelitis cases in the USA (2012-14): a retrospective cohort study. Volume 15 of Issue 6. 2015. PMID: 25837569


  183. Lauck M, Yú SQ, Caì Y, Hensley LE, Chiu CY, O'Connor DH, Kuhn JH. Genome Sequence of Bivens Arm Virus, a Tibrovirus Belonging to the Species Tibrogargan virus (Mononegavirales: Rhabdoviridae). Volume 3 of Issue 2. 2015. PMID: 25792044


  184. Deng X, Naccache SN, Ng T, Federman S, Li L, Chiu CY, Delwart EL. An ensemble strategy that significantly improves de novo assembly of microbial genomes from metagenomic next-generation sequencing data. Volume 43 of Issue 7. 2015. PMID: 25586223


  185. Naccache SN, Peggs KS, Mattes FM, Phadke R, Garson JA, Grant P, Samayoa E, Federman S, Miller S, Lunn MP, Gant V, Chiu CY. Diagnosis of neuroinvasive astrovirus infection in an immunocompromised adult with encephalitis by unbiased next-generation sequencing. Volume 60 of Issue 6. 2015. PMID: 25572898


  186. Martínez MA, Soto-Del Río Mde L, Gutiérrez RM, Chiu CY, Greninger AL, Contreras JF, López S, Arias CF, Isa P. DNA microarray for detection of gastrointestinal viruses. Volume 53 of Issue 1. 2014. PMID: 25355758


  187. 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. A cloud-compatible bioinformatics pipeline for ultrarapid pathogen identification from next-generation sequencing of clinical samples. Volume 24 of Issue 7. 2014. PMID: 24899342


  188. 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. Actionable diagnosis of neuroleptospirosis by next-generation sequencing. Volume 370 of Issue 25. 2014. PMID: 24896819


  189. Michael Wilson, Erik Samayoa, Samia Naccache, Sneha Somasekar, Guixia Yu, Joseph DeRisi, Charles Chiu. Next-Generation Sequencing for Pathogen Discovery in Meningoencephalitis (P2.306). 2014. PMID:


  190. Yao TC, Tsai HJ, Tu YL, Chang SW, Hua MC, Liao SL, Tsai MH, Chiu CY, Lai SH, Yeh KW, Huang JL. Multiplexed immunoglobulin E sensitization in relation to exhaled nitric oxide in a population sample of children. 2014. PMID: 24576320


  191. Naccache SN, Hackett J, Delwart EL, Chiu CY. Concerns over the origin of NIH-CQV, a novel virus discovered in Chinese patients with seronegative hepatitis. Volume 111 of Issue 11. 2014. PMID: 24572576


  192. Gilda Grard, Joseph Fair, Charles Chiu, Eric Leroy. Chapter 2 Bas-Congo Virus A Novel Rhabdovirus Associated with Acute Hemorrhagic Fever. 2014. PMID:


  193. Naccache SN, Greninger AL, Lee D, Coffey LL, Phan T, Rein-Weston A, Aronsohn A, Hackett J, Delwart EL, Chiu CY. The perils of pathogen discovery: origin of a novel parvovirus-like hybrid genome traced to nucleic acid extraction spin columns. Volume 87 of Issue 22. 2013. PMID: 24027301


  194. Charles Y Chiu, Dylan R Pillai. The microbiome and Clostridium difficile infection. 2013. PMID:


  195. Phan TG, Vo NP, Simmonds P, Samayoa E, Naccache S, Chiu CY, Delwart E. Rosavirus: the prototype of a proposed new genus of the Picornaviridae family. Volume 47 of Issue 3. 2013. PMID: 23943414


  196. 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. Experimental cross-species infection of common marmosets by titi monkey adenovirus. Volume 8 of Issue 7. 2013. PMID: 23894316


  197. Steffen I, Liss NM, Schneider BS, Fair JN, Chiu CY, Simmons G. Characterization of the Bas-Congo virus glycoprotein and its function in pseudotyped viruses. Volume 87 of Issue 17. 2013. PMID: 23785218


  198. Chiu CY. Viral pathogen discovery. Volume 16 of Issue 4. 2013. PMID: 23725672


  199. Swei A, Russell BJ, Naccache SN, Kabre B, Veeraraghavan N, Pilgard MA, Johnson BJ, Chiu CY. The genome sequence of Lone Star virus, a highly divergent bunyavirus found in the Amblyomma americanum tick. Volume 8 of Issue 4. 2013. PMID: 23637969


  201. Chiu CY, Yagi S, Lu X, Yu G, Chen EC, Liu M, Dick EJ, Carey KD, Erdman DD, Leland MM, Patterson JL. A novel adenovirus species associated with an acute respiratory outbreak in a baboon colony and evidence of coincident human infection. Volume 4 of Issue 2. 2013. PMID: 23592261


  202. Li L, Pesavento PA, Leutenegger CM, Estrada M, Coffey LL, Naccache SN, Samayoa E, Chiu C, Qiu J, Wang C, Deng X, Delwart E. A novel bocavirus in canine liver. Volume 10. 2013. PMID: 23402347


  203. Chiu C, Fair J, Leroy EM. Bas-Congo virus: another deadly virus? Volume 8 of Issue 2. 2013. PMID: 23374120


  204. Herman EK, Greninger AL, Visvesvara GS, Marciano-Cabral F, Dacks JB, Chiu CY. The mitochondrial genome and a 60-kb nuclear DNA segment from Naegleria fowleri, the causative agent of primary amoebic meningoencephalitis. Volume 60 of Issue 2. 2013. PMID: 23360210


  205. 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. Discovery of a novel polyomavirus in acute diarrheal samples from children. Volume 7 of Issue 11. 2012. PMID: 23166671


  206. Shahinas D, Silverman M, Sittler T, Chiu C, Kim P, Allen-Vercoe E, Weese S, Wong A, Low DE, Pillai DR. Toward an understanding of changes in diversity associated with fecal microbiome transplantation based on 16S rRNA gene deep sequencing. Volume 3 of Issue 5. 2012. PMID: 23093385


  207. 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 E, Wolfe ND, Chiu CY, Leroy EM. A novel rhabdovirus associated with acute hemorrhagic fever in central Africa. Volume 8 of Issue 9. 2012. PMID: 23028323


  208. 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. In-depth investigation of archival and prospectively collected samples reveals no evidence for XMRV infection in prostate cancer. Volume 7 of Issue 9. 2012. PMID: 23028701


  209. 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. Cross-species transmission of a novel adenovirus associated with a fulminant pneumonia outbreak in a new world monkey colony. Volume 7 of Issue 7. 2011. PMID: 21779173


  210. Chen EC, Miller SA, DeRisi JL, Chiu CY. Using a pan-viral microarray assay (Virochip) to screen clinical samples for viral pathogens. of Issue 50. 2011. PMID: 21559002


  211. 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. Viral infection in acute exacerbation of idiopathic pulmonary fibrosis. 2011. PMID: 21471095


  212. Liu C, Schwartz BS, Vallabhaneni S, Nixon M, Chin-Hong PV, Miller SA, Chiu C, Damon L, Drew WL. Pandemic (H1N1) 2009 infection in patients with hematologic malignancy. Volume 16 of Issue 12. 2010. PMID: 21122221


  213. 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. A metagenomic analysis of pandemic influenza A (2009 H1N1) infection in patients from North America. Volume 5 of Issue 10. 2010. PMID: 20976137


  215. Baum KT, Byars AW, deGrauw TJ, Dunn DW, Bates JE, Howe SR, Chiu CY, Austin JK. The effect of temperament and neuropsychological functioning on behavior problems in children with new-onset seizures. 2010. PMID: 20171932


  216. Chiu CY, Greninger AL, Chen EC, Haggerty TD, Parsonnet J, Delwart E, Derisi JL, Ganem D. Cultivation and serological characterization of a human Theiler's-like cardiovirus associated with diarrheal disease. Volume 84 of Issue 9. 2010. PMID: 20164225


  217. Tang P, Chiu C. Metagenomics for the discovery of novel human viruses. Volume 5 of Issue 2. 2010. PMID: 20143943


  218. Elicker BM, Schwartz BS, Liu C, Chen EC, Miller SA, Chiu CY, Webb WR. Thoracic CT findings of novel influenza A (H1N1) infection in immunocompromised patients. Volume 17 of Issue 4. 2010. PMID: 20111882


  220. Mukhtar RA, Throckmorton AD, Alvarado MD, Ewing CA, Esserman LJ, Chiu C, Hwang ES. Bacteriologic features of surgical site infections following breast surgery. Volume 198 of Issue 4. 2009. PMID: 19800462


  221. Greninger AL, Runckel C, Chiu CY, Haggerty T, Parsonnet J, Ganem D, DeRisi JL. The complete genome of klassevirus - a novel picornavirus in pediatric stool. Volume 6. 2009. PMID: 19538752


  222. Sorber K, Chiu C, Webster D, Dimon M, Ruby JG, Hekele A, DeRisi JL. The long march: a sample preparation technique that enhances contig length and coverage by high-throughput short-read sequencing. Volume 3 of Issue 10. 2008. PMID: 18941527


  223. 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. Identification of cardioviruses related to Theiler's murine encephalomyelitis virus in human infections. Volume 105 of Issue 37. 2008. PMID: 18768820


  224. 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. Recovery of divergent avian bornaviruses from cases of proventricular dilatation disease: identification of a candidate etiologic agent. Volume 5. 2008. PMID: 18671869


  225. Chiu CY, Urisman A, Greenhow TL, Rouskin S, Yagi S, Schnurr D, Wright C, Drew WL, Wang D, Weintrub PS, Derisi JL, Ganem D. Utility of DNA microarrays for detection of viruses in acute respiratory tract infections in children. Volume 153 of Issue 1. 2008. PMID: 18571541


  226. Lee GT, Chiu CY, Haller BL, Denn PM, Hall CS, Gerberding JL. Streptococcus suis meningitis, United States. Volume 14 of Issue 1. 2008. PMID: 18258107


  228. Chiu CY, Alizadeh AA, Rouskin S, Merker JD, Yeh E, Yagi S, Schnurr D, Patterson BK, Ganem D, DeRisi JL. Diagnosis of a critical respiratory illness caused by human metapneumovirus by use of a pan-virus microarray. Volume 45 of Issue 7. 2007. PMID: 17494722


  229. 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. Microarray detection of human parainfluenzavirus 4 infection associated with respiratory failure in an immunocompetent adult. Volume 43 of Issue 8. 2006. PMID: 16983602


  230. Urisman A, Fischer KF, Chiu CY, Kistler AL, Beck S, Wang D, DeRisi JL. E-Predict: a computational strategy for species identification based on observed DNA microarray hybridization patterns. Volume 6 of Issue 9. 2005. PMID: 16168085


  231. Thakur A, Chiu C, Quiros-Tejeira RE, Reyen L, Ament M, Atkinson JB, Fonkalsrud EW. Morbidity and mortality of short-bowel syndrome in infants with abdominal wall defects. 2002. PMID: 12467323


  232. Zangwill KM, Droge J, Mendelman P, Marcy SM, Partridge S, Chiu CY, Jing J, Chang SJ, Cho I, Ward JI. Prospective, randomized, placebo-controlled evaluation of the safety and immunogenicity of three lots of intranasal trivalent influenza vaccine among young children. 2001. PMID: 11734734


  233. Chiu CY, Wu E, Brown SL, Von Seggern DJ, Nemerow GR, Stewart PL. Structural analysis of a fiber-pseudotyped adenovirus with ocular tropism suggests differential modes of cell receptor interactions. 2001. PMID: 11333920


  234. Chiu CY, Wong WK, Mak HL, Chan CS, Kwok CH, Chan CH, Chan MK. Uterine artery embolisation for treatment of fibroids: experience in Chinese women. 2001. PMID: 11465313


  235. P.L. Stewart, C.Y. Chiu, D. Von Seggern, G.R. Nemerow. Cryo-Em Imaging of a Pseudotyped Adenovhtus with Ocular Cell Tropism. 2000. PMID:


  236. Stewart PL, Cary RB, Peterson SR, Chiu CY. Digitally collected cryo-electron micrographs for single particle reconstruction. 2000. PMID: 10816264


  237. Stewart PL, Chiu CY, Haley DA, Kong LB, Schlessman JL. Review: resolution issues in single-particle reconstruction. 1999. PMID: 10600559


  238. Chiu CY, Mathias P, Nemerow GR, Stewart PL. Structure of adenovirus complexed with its internalization receptor, alphavbeta5 integrin. 1999. PMID: 10400774


  239. Von Seggern DJ, Chiu CY, Fleck SK, Stewart PL, Nemerow GR. A helper-independent adenovirus vector with E1, E3, and fiber deleted: structure and infectivity of fiberless particles. 1999. PMID: 9882366


  240. Chiu CY, Cary RB, Chen DJ, Peterson SR, Stewart PL. Cryo-EM imaging of the catalytic subunit of the DNA-dependent protein kinase. 1998. PMID: 9837727


  241. Mullenbach GT, Chiu CY, Gyenes A, Blaney J, Rosenberg S, Marlowe CK, Brown S, Stratton-Thomas J, Montelione GT, George-Nascimento C, Stauber G. Modification of a receptor-binding surface of epidermal growth factor (EGF): analogs with enhanced receptor affinity at low pH or at neutrality. 1998. PMID: 9725626


  242. Stewart PL, Chiu CY, Huang S, Muir T, Zhao Y, Chait B, Mathias P, Nemerow GR. Cryo-EM visualization of an exposed RGD epitope on adenovirus that escapes antibody neutralization. 1997. PMID: 9135136


  243. Gryaznov S, Skorski T, Cucco C, Nieborowska-Skorska M, Chiu CY, Lloyd D, Chen JK, Koziolkiewicz M, Calabretta B. Oligonucleotide N3'-->P5' phosphoramidates as antisense agents. 1996. PMID: 8628685


  244. Greenberg DP, Lieberman JM, Marcy SM, Wong VK, Partridge S, Chang SJ, Chiu CY, Ward JI. Enhanced antibody responses in infants given different sequences of heterogeneous Haemophilus influenzae type b conjugate vaccines. 1995. PMID: 7844666