Charles Chiu, MD, PhD

ASSISTANT PROF IN RES-HCOMP
Laboratory Medicine
+1 415 514-8219

Charles Chiu, M.D./Ph.D. 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.

Publications: 

Connecting the dots: Translating the vaginal microbiome into a drug.

The Journal of infectious diseases

Lagenaur LA, Hemmerling A, Chiu C, Miller S, Lee PP, Cohen CR, Parks TP

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

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

Fatal Case of Chronic Jamestown Canyon Virus Encephalitis Diagnosed by Metagenomic Sequencing in Patient Receiving Rituximab.

Emerging infectious diseases

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

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

Rapid pathogen detection by metagenomic next-generation sequencing of infected body fluids.

Nature medicine

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 CY

Universal PCR and antibody testing demonstrate little to no transmission of SARS-CoV-2 in a rural community.

Open forum infectious diseases

Ayesha Appa, Saki Takahashi, Isabel Rodriguez-Barraquer, Gabriel Chamie, Aenor Sawyer, Elias Duarte, Jill Hakim, Keirstinne Turcios, Joanna Vinden, Owen Janson, Aashish Manglik, Michael J Peluso, Steven G Deeks, Timothy J Henrich, Leonel Torres, Mary Rodgers, John Hackett, Charles Chiu, Diane Havlir, Bryan Greenhouse

Rapid deployment of SARS-CoV-2 testing: The CLIAHUB.

PLoS pathogens

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, Bonny AR, Booth D, Borja MJB, Brown D, Buie B, Burnett CE, Byrnes LE, Cabral KA, Cabrera JP, Caldera S, Canales G, Castañeda GR, Chan AP, Chang CR, Charles-Orszag A, Cheung C, Chio U, Chow ED, Citron YR, Cohen A, Cohn LB, Chiu C, Cole MA, Conrad DN, Constantino A, Cote A, Crayton-Hall T, Darmanis S, Detweiler AM, Dial RL, Dong S, Duarte EM, Dynerman D, Egger R, Fanton A, Frumm SM, Fu BXH, Garcia VE, Garcia J, Gladkova C, Goldman M, Gomez-Sjoberg R, Gordon MG, Grove JCR, Gupta S, Haddjeri-Hopkins A, Hadley P, Haliburton J, Hao SL, Hartoularos G, Herrera N, Hilberg M, Ho KYE, Hoppe N, Hosseinzadeh S, Howard CJ, Hussmann JA, Hwang E, Ingebrigtsen D, Jackson JR, Jowhar ZM, Kain D, Kim JYS, Kistler A, Kreutzfeld O, Kulsuptrakul J, Kung AF, Langelier C, Laurie MT, Lee L, Leng K, Leon KE, Leonetti MD, Levan SR, Li S, Li AW, Liu J, Lubin HS, Lyden A, Mann J, Mann S, Margulis G, Marquez DM, Marsh BP, Martyn C, McCarthy EE, McGeever A, Merriman AF, Meyer LK, Miller S, Moore MK, Mowery CT, Mukhtar T, Mwakibete LL, Narez N, Neff NF, Osso LA, Oviedo D, Peng S, Phelps M, Phong K, Picard P, Pieper LM, Pincha N, Pisco AO, Pogson A, Pourmal S, Puccinelli RR, Puschnik AS, Rackaityte E, Raghavan P, Raghavan M, Reese J, Replogle JM, Retallack H, Reyes H, Rose D, Rosenberg MF, Sanchez-Guerrero E, Sattler SM, Savy L, See SK, Sellers KK, Serpa PH, Sheehy M, Sheu J, Silas S, Streithorst JA, Strickland J, Stryke D, Sunshine S, Suslow P, Sutanto R, Tamura S, Tan M, Tan J, Tang A, Tato CM, Taylor JC, Tenvooren I, Thompson EM, Thornborrow EC, Tse E, Tung T, Turner ML, Turner VS, Turnham RE, Turocy MJ, Vaidyanathan TV, Vainchtein ID, Vanaerschot M, Vazquez SE, Wandler AM, Wapniarski A, Webber JT, Weinberg ZY, Westbrook A, Wong AW, Wong E, Worthington G, Xie F, Xu A, Yamamoto T, Yang Y, Yarza F, Zaltsman Y, Zheng T, DeRisi JL

ReScan, a Multiplex Diagnostic Pipeline, Pans Human Sera for SARS-CoV-2 Antigens.

Cell reports. Medicine

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

Metagenomic sequencing of stool samples in Bangladeshi infants: virome association with poliovirus shedding after oral poliovirus vaccination.

Scientific reports

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

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

Competitive SARS-CoV-2 Serology Reveals Most Antibodies Targeting the Spike Receptor-Binding Domain Compete for ACE2 Binding.

mSphere

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

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

Cryptic transmission of SARS-CoV-2 in Washington state.

Science (New York, N.Y.)

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

Digital droplet PCR accurately quantifies SARS-CoV-2 viral load from crude lysate without nucleic acid purification.

medRxiv : the preprint server for health sciences

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

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

Clinical features, diagnostics, and outcomes of patients presenting with acute respiratory illness: A retrospective cohort study of patients with and without COVID-19.

EClinicalMedicine

Shah SJ, Barish PN, Prasad PA, Kistler A, Neff N, Kamm J, Li LM, Chiu CY, Babik JM, Fang MC, Kangelaris KN, Langelier C, Abe-Jones Y, Alipanah N, Alvarez FN, Botvinnik OB, Castaneda G

Direct Comparison of SARS-CoV-2 Analytical Limits of Detection across Seven Molecular Assays.

Journal of clinical microbiology

Fung B, Gopez A, Servellita V, Arevalo S, Ho C, Deucher A, Thornborrow E, Chiu C, Miller S

SARS-CoV-2 Community Transmission disproportionately affects Latinx population during Shelter-in-Place in San Francisco.

Clinical infectious diseases : an official publication of the Infectious Diseases Society of America

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

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

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

STROBE-metagenomics: a STROBE extension statement to guide the reporting of metagenomics studies.

The Lancet. Infectious diseases

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, Reoma LB, Shaw LP, Sidorov I, Simner PJ, Van Tan L, Thomson EC, van Dorp L, Wilson MR, Breuer J, Field N

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

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

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, Babik JM

SARS-CoV-2 Community Transmission During Shelter-in-Place in San Francisco.

medRxiv

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, Francesco Sergi, Jon Jacobo, Susana Rojas, Valerie Tulier-Laiwa, Tracy Gallardo-Brown, Ayesha Appa, Charles Y Chiu, Mary Rodgers, John Hackett, Amy Kistler, Samantha Hao, Jack Kamm, David Dynerman, Joshua Batson, Bryan Greenhouse, Joe DeRisi, Diane V. Havlir

Genomic surveillance reveals multiple introductions of SARS-CoV-2 into Northern California.

Science (New York, N.Y.)

Deng X, Gu W, Federman S, du Plessis L, Pybus OG, Faria N, 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, Roychoudhury P, Starita LM, Famulare M, Chu HY, Shendure J, Jerome KR, Anderson C, Gangavarapu K, Zeller M, Spencer E, Andersen KG, MacCannell D, Paden CR, Li Y, Zhang J, Tong S, Armstrong G, Morrow S, Willis M, Matyas BT, Mase S, Kasirye O, Park M, Masinde G, Chan C, Yu AT, Chai SJ, Villarino E, Bonin B, Wadford DA, Chiu CY

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

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

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

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

Gu W, Deng X, Reyes K, Hsu E, Wang C, Sotomayor-Gonzalez A, Federman S, Bushnell B, Miller S, Chiu C

Test performance evaluation of SARS-CoV-2 serological assays.

medRxiv : the preprint server for health sciences

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

ReScan, a Multiplex Diagnostic Pipeline, Pans Human Sera for SARS-CoV-2 Antigens.

medRxiv

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, Michael R Wilson

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

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, Deng X, DeRisi JL, Detweiler AM, Federman S, Haliburton JR, Hao SL, Kerkhoff AD, Kumar R, Malcolm K, Mann SA, Martinez SP, Marya R, Mick E, Mwakibete LL, Najafi N, Peluso MJ, Phelps MS, Pisco AO, Ratnasiri K, Rubio LA, Sellas AB, Sherwood KD, Sheu J, Spottiswoode N, Tan M, Yu G, Kangelaris KN, Langelier C

CRISPR-Cas12-based detection of SARS-CoV-2.

Nature biotechnology

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, Chiu CY

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

Gu W, Reyes K, Hsu E, Miller S, Chiu CY

Cryptic transmission of SARS-CoV-2 in Washington State.

medRxiv : the preprint server for health sciences

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

A Genomic Survey of SARS-CoV-2 Reveals Multiple Introductions into Northern California without a Predominant Lineage.

medRxiv : the preprint server for health sciences

Deng X, Gu W, Federman S, Du Plessis L, Pybus O, 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 A, Roychoudhury P, Famulare M, Chu HY, Shendure J, Starita L, Anderson C, Gangavarapu K, Zeller M, Spencer E, Andersen K, MacCannell D, Tong S, Armstrong G, Paden C, Li Y, Zhang Y, Morrow S, Willis M, Matyas B, Mase S, Kasirye O, Park M, Chan C, Yu A, Chai S, Villarino E, Bonin B, Wadford D, Chiu CY

Rapid Detection of 2019 Novel Coronavirus SARS-CoV-2 Using a CRISPR-based DETECTR Lateral Flow Assay.

medRxiv : the preprint server for health sciences

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

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, Hackett JR, Chiu CY

Human Tibroviruses: Commensals or Lethal Pathogens?

Viruses

Kuhn JH, Pan H, Chiu CY, Stremlau M

Metagenomic sequencing with spiked primer enrichment for viral diagnostics and genomic surveillance.

Nature microbiology

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

Pan-viral serology implicates enteroviruses in acute flaccid myelitis.

Nature medicine

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

Metagenomic Next-Generation Sequencing of the 2014 Ebola Virus Disease Outbreak in the Democratic Republic of the Congo.

Journal of clinical microbiology

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 CY

Acute Zika virus infection in an asymptomatic blood donor at the onset of the Puerto Rico epidemic.

Transfusion

Saa P, Chiu C, Grimm K, Yu G, Benjamin RJ, Corash L, Stramer SL

Clinical Metagenomic Sequencing for Diagnosis of Meningitis and Encephalitis.

The New England journal of medicine

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 metagenomics.

Nature reviews. Genetics

Chiu CY, Miller SA

Human, Nonhuman Primate, and Bat Cells Are Broadly Susceptible to Tibrovirus Particle Cell Entry.

Frontiers in microbiology

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

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

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

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

Single-molecule sequencing detection of N6-methyladenine in microbial reference materials.

Nature communications

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

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

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

2291. A Real-Time Sequencing Approach for Simultaneous Metagenomic and Transcriptomic-Based Diagnosis of Infectious Diseases.

Open forum infectious diseases

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

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

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

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

Clinical Metagenomic Next-Generation Sequencing for Pathogen Detection.

Annual review of pathology

Gu W, Miller S, Chiu CY

Differentiation enhances Zika virus infection of neuronal brain cells.

Scientific reports

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

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

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

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

Acute Liver Failure of Indeterminate Etiology: A Comprehensive Systematic Approach by An Expert Committee to Establish Causality.

The American journal of gastroenterology

Ganger DR, Rule J, Rakela J, Bass N, Reuben A, Stravitz RT, Sussman N, Larson AM, James L, Chiu C, Lee WM

Genomic Epidemiology Reconstructs the Introduction and Spread of Zika Virus in Central America and Mexico.

Cell host & microbe

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

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

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

Experimental Zika Virus Infection in the Pregnant Common Marmoset Induces Spontaneous Fetal Loss and Neurodevelopmental Abnormalities.

Scientific reports

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

Taxonomy of the order Mononegavirales: update 2018.

Archives of virology

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

Metagenomic Sequencing Detects Respiratory Pathogens in Hematopoietic Cellular Transplant Patients.

American journal of respiratory and critical care medicine

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

Steve Miller, Charles Chiu

Nanopore DNA Sequencing and Genome Assembly on the International Space Station.

Scientific reports

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

Experimental Zika Virus Inoculation in a New World Monkey Model Reproduces Key Features of the Human Infection.

Scientific reports

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

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

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

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

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

Upregulation of Human Endogenous Retrovirus-K Is Linked to Immunity and Inflammation in Pulmonary Arterial Hypertension.

Circulation

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

Correction: Correction: A Novel Rhabdovirus Associated with Acute Hemorrhagic Fever in Central Africa.

PLoS pathogens

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

The eukaryotic gut virome in hematopoietic stem cell transplantation: new clues in enteric graft-versus-host disease.

Nature medicine

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

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

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 characterization of an oral tongue squamous cell carcinoma cell line from a never-smoking patient.

Oral oncology

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

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

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

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

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

Validation of Metagenomic Next-Generation Sequencing Tests for Universal Pathogen Detection.

Archives of pathology & laboratory medicine

Schlaberg R, Chiu CY, Miller S, Procop GW, Weinstock G

Beatrice Hill Virus Represents a Novel Species in the Genus Tibrovirus (Mononegavirales: Rhabdoviridae).

Genome announcements

Wiley MR, Prieto K, Blasdell KR, Caì Y, Campos Lawson C, Walker PJ, Chiu CY, Palacios G, Kuhn JH

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

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

Naccache SN, Thézé J, Sardi SI, Somasekar S, Greninger AL, Bandeira AC, Campos GS, Tauro LB, Faria NR, Pybus OG, Chiu CY

Coinfections of Zika and Chikungunya Viruses in Bahia, Brazil, Identified by Metagenomic Next-Generation Sequencing.

Journal of clinical microbiology

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

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

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

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

Longitudinal Transcriptome Analysis Reveals a Sustained Differential Gene Expression Signature in Patients Treated for Acute Lyme Disease.

mBio

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

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

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

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

Acute Flaccid Myelitis of Unknown Etiology in California, 2012-2015.

JAMA

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

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

Utility of Metagenomic Next-Generation Sequencing for Characterization of HIV and Human Pegivirus Diversity.

PloS one

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

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

Greninger AL, Cunningham G, Chiu CY, Miller S

Genomic Assays for Identification of Chikungunya Virus in Blood Donors, Puerto Rico, 2014.

Emerging infectious diseases

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

Greninger AL, Cunningham G, Chiu CY, Miller S

Draft Genome Sequence of Mycobacterium elephantis Strain Lipa.

Genome announcements

Greninger AL, Cunningham G, Yu JM, Hsu ED, Chiu CY, Miller S

Draft Genome Sequence of Mycobacterium arupense Strain GUC1.

Genome announcements

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

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

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

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

Advances in testing technology to ensure transfusion safety – NAT and beyond.

ISBT Science Series

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

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

Genome Sequence of Bivens Arm Virus, a Tibrovirus Belonging to the Species Tibrogargan virus (Mononegavirales: Rhabdoviridae).

Genome announcements

Lauck M, Yú SQ, Caì Y, Hensley LE, Chiu CY, O'Connor DH, Kuhn JH

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

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

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

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

Actionable diagnosis of neuroleptospirosis by next-generation sequencing.

The New England journal of medicine

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

Multiplexed immunoglobulin E sensitization in relation to exhaled nitric oxide in a population sample of children.

Allergy

Yao TC, Tsai HJ, Tu YL, Chang SW, Hua MC, Liao SL, Tsai MH, Chiu CY, Lai SH, Yeh KW, Huang JL

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

Naccache SN, Hackett J, Delwart EL, Chiu CY

Chapter 2 Bas-Congo Virus A Novel Rhabdovirus Associated with Acute Hemorrhagic Fever.

Emerging infectious diseases

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

Naccache SN, Greninger AL, Lee D, Coffey LL, Phan T, Rein-Weston A, Aronsohn A, Hackett J, Delwart EL, Chiu CY

Rosavirus: the prototype of a proposed new genus of the Picornaviridae family.

Virus genes

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

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

Steffen I, Liss NM, Schneider BS, Fair JN, Chiu CY, Simmons G

Viral pathogen discovery.

Current opinion in microbiology

Chiu CY

The genome sequence of Lone Star virus, a highly divergent bunyavirus found in the Amblyomma americanum tick.

PloS one

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

Chiu C

A novel adenovirus species associated with an acute respiratory outbreak in a baboon colony and evidence of coincident human infection.

mBio

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

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

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

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

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

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

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

In-depth investigation of archival and prospectively collected samples reveals no evidence for XMRV infection in prostate cancer.

PloS one

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

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

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

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

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

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

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

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

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

Tang P, Chiu C

Thoracic CT findings of novel influenza A (H1N1) infection in immunocompromised patients.

Emergency radiology

Elicker BM, Schwartz BS, Liu C, Chen EC, Miller SA, Chiu CY, Webb WR

Bacteriologic features of surgical site infections following breast surgery.

American journal of surgery

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

Greninger AL, Runckel C, Chiu CY, Haggerty T, Parsonnet J, Ganem D, 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

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

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

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

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

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

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

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

Urisman A, Fischer KF, Chiu CY, Kistler AL, Beck S, Wang D, DeRisi JL

Uterine artery embolisation for treatment of fibroids: experience in Chinese women.

Singapore medical journal

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

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

Stewart PL, Cary RB, Peterson SR, Chiu CY

Review: resolution issues in single-particle reconstruction.

Journal of structural biology

Stewart PL, Chiu CY, Haley DA, Kong LB, Schlessman JL

Structure of adenovirus complexed with its internalization receptor, alphavbeta5 integrin.

Journal of virology

Chiu CY, Mathias P, Nemerow GR, Stewart PL

Cryo-EM imaging of the catalytic subunit of the DNA-dependent protein kinase.

Journal of molecular biology

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

Mullenbach GT, Chiu CY, Gyenes A, Blaney J, Rosenberg S, Marlowe CK, Brown S, Stratton-Thomas J, Montelione GT, George-Nascimento C, Stauber G

Oligonucleotide N3'-->P5' phosphoramidates as antisense agents.

Nucleic acids research

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

Greenberg DP, Lieberman JM, Marcy SM, Wong VK, 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

Jelonek MT, Chang SJ, Chiu CY, Park MK, Nahm MH, Ward JI

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