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IDseq-An open source cloud-based pipeline and analysis service for metagenomic pathogen detection and monitoring.
Kalantar KL, Carvalho T, de Bourcy CFA, Dimitrov B, Dingle G, Egger R, Han J, Holmes OB, Juan YF, King R, Kislyuk A, Lin MF, Mariano M, Morse T, Reynoso LV, Cruz DR, Sheu J, Tang J, Wang J, Zhang MA, Zhong E, Ahyong V, Lay S, Chea S, Bohl JA, Manning JE, Tato CM, DeRisi JL. Kalantar KL, et al. Among authors: sheu j. Gigascience. 2020 Oct 15;9(10):giaa111. doi: 10.1093/gigascience/giaa111. Gigascience. 2020. PMID: 33057676 Free PMC article.
Discovering disease-causing pathogens in resource-scarce Southeast Asia using a global metagenomic pathogen monitoring system.
Bohl JA, Lay S, Chea S, Ahyong V, Parker DM, Gallagher S, Fintzi J, Man S, Ponce A, Sreng S, Kong D, Oliveira F, Kalantar K, Tan M, Fahsbender L, Sheu J, Neff N, Detweiler AM, Yek C, Ly S, Sath R, Huch C, Kry H, Leang R, Huy R, Lon C, Tato CM, DeRisi JL, Manning JE. Bohl JA, et al. Among authors: sheu j. Proc Natl Acad Sci U S A. 2022 Mar 15;119(11):e2115285119. doi: 10.1073/pnas.2115285119. Epub 2022 Mar 1. Proc Natl Acad Sci U S A. 2022. PMID: 35238677 Free PMC article.
Metagenomic next-generation sequencing of samples from pediatric febrile illness in Tororo, Uganda.
Ramesh A, Nakielny S, Hsu J, Kyohere M, Byaruhanga O, de Bourcy C, Egger R, Dimitrov B, Juan YF, Sheu J, Wang J, Kalantar K, Langelier C, Ruel T, Mpimbaza A, Wilson MR, Rosenthal PJ, DeRisi JL. Ramesh A, et al. Among authors: sheu j. PLoS One. 2019 Jun 20;14(6):e0218318. doi: 10.1371/journal.pone.0218318. eCollection 2019. PLoS One. 2019. PMID: 31220115 Free PMC article.
Unbiased Metagenomic Sequencing for Pediatric Meningitis in Bangladesh Reveals Neuroinvasive Chikungunya Virus Outbreak and Other Unrealized Pathogens.
Saha S, Ramesh A, Kalantar K, Malaker R, Hasanuzzaman M, Khan LM, Mayday MY, Sajib MSI, Li LM, Langelier C, Rahman H, Crawford ED, Tato CM, Islam M, Juan YF, de Bourcy C, Dimitrov B, Wang J, Tang J, Sheu J, Egger R, De Carvalho TR, Wilson MR, Saha SK, DeRisi JL. Saha S, et al. Among authors: sheu j. mBio. 2019 Dec 17;10(6):e02877-19. doi: 10.1128/mBio.02877-19. mBio. 2019. PMID: 31848287 Free PMC article.
Rapid metagenomic characterization of a case of imported COVID-19 in Cambodia.
Manning JE, Bohl JA, Lay S, Chea S, Sovann L, Sengdoeurn Y, Heng S, Vuthy C, Kalantar K, Ahyong V, Tan M, Sheu J, Tato CM, DeRisi JL, Baril L, Duong V, Dussart P, Karlsson EA. Manning JE, et al. Among authors: sheu j. bioRxiv [Preprint]. 2020 Mar 5:2020.03.02.968818. doi: 10.1101/2020.03.02.968818. bioRxiv. 2020. PMID: 32511296 Free PMC article. Preprint.
Rapid deployment of SARS-CoV-2 testing: The CLIAHUB.
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, Mukhta… See abstract for full author list ➔ Crawford ED, et al. Among authors: sheu j. PLoS Pathog. 2020 Oct 28;16(10):e1008966. doi: 10.1371/journal.ppat.1008966. eCollection 2020 Oct. PLoS Pathog. 2020. PMID: 33112933 Free PMC article. No abstract available.
Genomic Epidemiology and Transmission Dynamics of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) in Congregate Healthcare Facilities in Santa Clara County, California.
MacCannell T, Batson J, Bonin B, Astha KC, Quenelle R, Strong B, Lin W, Rudman SL, Dynerman D, Ayscue P, Han G, Kistler A, Villarino ME; Chan Zuckerberg Biohub COVIDTracker Consortium and the Santa Clara County Public Health Department’s Special Investgations Group. MacCannell T, et al. Clin Infect Dis. 2022 Mar 9;74(5):829-835. doi: 10.1093/cid/ciab553. Clin Infect Dis. 2022. PMID: 34328176 Free PMC article.
Clinical features, diagnostics, and outcomes of patients presenting with acute respiratory illness: A retrospective cohort study of patients with and without COVID-19.
Shah SJ, Barish PN, Prasad PA, Kistler A, Neff N, Kamm J, Li LM, Chiu CY, Babik JM, Fang MC, Abe-Jones Y, Alipanah N, Alvarez FN, Botvinnik OB, Castaneda G; CZB CLIAhub Consortium; Dadasovich RM, Davis J, Deng X, DeRisi JL, Detweiler AM, Federman S, Haliburton J, Hao S, Kerkhoff AD, Kumar GR, Malcolm KB, Mann SA, Martinez S, Mary RK, Mick E, Mwakibete L, Najafi N, Peluso MJ, Phelps M, Pisco AO, Ratnasiri K, Rubio LA, Sellas A, Sherwood KD, Sheu J, Spottiswoode N, Tan M, Yu G, Kangelaris KN, Langelier C. Shah SJ, et al. Among authors: sheu j. EClinicalMedicine. 2020 Oct;27:100518. doi: 10.1016/j.eclinm.2020.100518. Epub 2020 Aug 26. EClinicalMedicine. 2020. PMID: 32864588 Free PMC article.
Clinical features, diagnostics, and outcomes of patients presenting with acute respiratory illness: a comparison of patients with and without COVID-19.
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. Shah SJ, et al. Among authors: sheu j. medRxiv [Preprint]. 2020 May 6:2020.05.02.20082461. doi: 10.1101/2020.05.02.20082461. medRxiv. 2020. PMID: 32511488 Free PMC article. Preprint.
Identification of RNF213 as a potential suppressor of local invasion in intrahepatic cholangiocarcinoma.
Chiablaem K, Jinawath A, Nuanpirom J, Arora JK, Nasaree S, Thanomchard T, Singhto N, Chittavanich P, Suktitipat B, Charoensawan V, Chairoungdua A, Sheu JJ, Kiyotani K, Svasti J, Nakamura Y, Jinawath N. Chiablaem K, et al. Among authors: sheu jj. Lab Invest. 2024 May 7:102074. doi: 10.1016/j.labinv.2024.102074. Online ahead of print. Lab Invest. 2024. PMID: 38723854
1,378 results