E
Erik Samayoa
Researcher at University of California, San Francisco
Publications - 13
Citations - 1439
Erik Samayoa is an academic researcher from University of California, San Francisco. The author has contributed to research in topics: Assay sensitivity & Transplantation. The author has an hindex of 9, co-authored 12 publications receiving 1034 citations.
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Journal ArticleDOI
A cloud-compatible bioinformatics pipeline for ultrarapid pathogen identification from next-generation sequencing of clinical samples
Samia N. Naccache,Scot Federman,Narayanan Veeraraghavan,Matei Zaharia,Deanna Lee,Erik Samayoa,Jerome Bouquet,Alexander L. Greninger,Ka Cheung Luk,Barryett Enge,Debra A. Wadford,Sharon Messenger,Gillian Genrich,Kristen Pellegrino,Gilda Grard,Eric M. Leroy,Bradley S. Schneider,Joseph N. Fair,Miguel Ángel Martínez,Pavel Isa,John A. Crump,Joseph L. DeRisi,Taylor Sittler,John Hackett,Steve Miller,Charles Y. Chiu +25 more
TL;DR: SURPI is described, a computational pipeline for pathogen identification from complex metagenomic NGS data generated from clinical samples, and use of the pipeline is demonstrated in the analysis of 237 clinical samples comprising more than 1.1 billion sequences.
Journal ArticleDOI
Laboratory validation of a clinical metagenomic sequencing assay for pathogen detection in cerebrospinal fluid
Steve Miller,Samia N. Naccache,Samia N. Naccache,Erik Samayoa,Kevin Messacar,Shaun Arevalo,Scot Federman,Doug Stryke,Elizabeth Pham,Becky Fung,William J. Bolosky,Danielle Ingebrigtsen,Walter Lorizio,Sandra M. Paff,John A. Leake,Rick L. Pesano,Roberta L. DeBiasi,Samuel R. Dominguez,Charles Y. Chiu +18 more
TL;DR: The analytic performance of a laboratory-validated mNGS assay for pan-pathogen detection, to be used clinically for diagnosis of neurological infections from CSF, is demonstrated.
Journal ArticleDOI
Diagnosis of neuroinvasive astrovirus infection in an immunocompromised adult with encephalitis by unbiased next-generation sequencing
Samia N. Naccache,Karl S. Peggs,Frank M. Mattes,Rahul Phadke,Jeremy A. Garson,Paul Grant,Erik Samayoa,Scot Federman,Steve Miller,Michael P. Lunn,Vanya Gant,Charles Y. Chiu +11 more
TL;DR: The sequencing and confirmatory studies revealed neuroinvasive infection of the brain by an astrovirus belonging to a recently discovered VA/HMO clade.
Posted ContentDOI
Laboratory Validation of a Clinical Metagenomic Sequencing Assay for Pathogen Detection in Cerebrospinal Fluid
Steve Miller,Samia N. Naccache,Erik Samayoa,Kevin Messacar,Shaun Arevalo,Scot Federman,Doug Stryke,Elizabeth Pham,Becky Fung,William J. Bolosky,Danielle Ingebrigtsen,Walter Lorizio,Sandra M. Paff,John A. Leake,Rick L. Pesano,Roberta L. DeBiasi,Samuel R. Dominguez,Charles Y. Chiu +17 more
TL;DR: The results demonstrate the analytic performance of a laboratory-validated mNGS assay for pan-pathogen detection, to be used clinically for diagnosis of neurological infections from CSF, and quality metrics, threshold values, and limits of detection were established.
Journal ArticleDOI
Idiopathic pneumonia syndrome after hematopoietic cell transplantation: evidence of occult infectious etiologies
Sachiko Seo,Christian Renaud,Jane Kuypers,Jane Kuypers,Charles Y. Chiu,Meei Li Huang,Meei Li Huang,Erik Samayoa,Hu Xie,Guixia Yu,Cynthia E. Fisher,Ted Gooley,Steven P. Miller,Robert C. Hackman,Robert C. Hackman,David Myerson,David Myerson,Ruth Hall Sedlak,Yae Jean Kim,Takahiro Fukuda,David N. Fredricks,David K. Madtes,Keith R. Jerome,Keith R. Jerome,Michael Boeckh +24 more
TL;DR: It was demonstrated that approximately half of patients with IPS had pathogens detected in BAL, and pathogen detection was associated with increased mortality, indicating that an expanded infection detection panel can significantly increase the diagnostic precision for idiopathic pneumonia.