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Scot Federman
Scot Federman
Bioinformatics Programmer
Verified email at ucsf.edu
Title
Cited by
Cited by
Year
Actionable diagnosis of neuroleptospirosis by next-generation sequencing
MR Wilson, SN Naccache, E Samayoa, M Biagtan, H Bashir, G Yu, ...
New England Journal of Medicine 370 (25), 2408-2417, 2014
7272014
The gene expression signatures of melanoma progression
C Haqq, M Nosrati, D Sudilovsky, J Crothers, D Khodabakhsh, BL Pulliam, ...
Proceedings of the National Academy of Sciences 102 (17), 6092-6097, 2005
5052005
Rapid metagenomic identification of viral pathogens in clinical samples by real-time nanopore sequencing analysis
AL Greninger, SN Naccache, S Federman, G Yu, P Mbala, V Bres, ...
Genome medicine 7 (1), 1-13, 2015
4862015
Clinical metagenomic sequencing for diagnosis of meningitis and encephalitis
MR Wilson, HA Sample, KC Zorn, S Arevalo, G Yu, J Neuhaus, ...
New England Journal of Medicine 380 (24), 2327-2340, 2019
4822019
A cloud-compatible bioinformatics pipeline for ultrarapid pathogen identification from next-generation sequencing of clinical samples
SN Naccache, S Federman, N Veeraraghavan, M Zaharia, D Lee, ...
Genome research 24 (7), 1180-1192, 2014
4462014
A novel outbreak enterovirus D68 strain associated with acute flaccid myelitis cases in the USA (2012–14): a retrospective cohort study
AL Greninger, SN Naccache, K Messacar, A Clayton, G Yu, S Somasekar, ...
The Lancet Infectious Diseases 15 (6), 671-682, 2015
3632015
Transmission, infectivity, and neutralization of a spike L452R SARS-CoV-2 variant
X Deng, MA Garcia-Knight, MM Khalid, V Servellita, C Wang, MK Morris, ...
Cell 184 (13), 3426-3437. e8, 2021
3502021
Nanopore DNA sequencing and genome assembly on the International Space Station
SL Castro-Wallace, CY Chiu, KK John, SE Stahl, KH Rubins, ...
Scientific reports 7 (1), 1-12, 2017
3062017
Diagnosis of neuroinvasive astrovirus infection in an immunocompromised adult with encephalitis by unbiased next-generation sequencing
SN Naccache, KS Peggs, FM Mattes, R Phadke, JA Garson, P Grant, ...
Clinical Infectious Diseases 60 (6), 919-923, 2015
2672015
Laboratory validation of a clinical metagenomic sequencing assay for pathogen detection in cerebrospinal fluid
S Miller, SN Naccache, E Samayoa, K Messacar, S Arevalo, S Federman, ...
Genome research 29 (5), 831-842, 2019
2492019
Cryptic transmission of SARS-CoV-2 in Washington state
T Bedford, AL Greninger, P Roychoudhury, LM Starita, M Famulare, ...
Science 370 (6516), 571-575, 2020
2412020
Transmission, infectivity, and antibody neutralization of an emerging SARS-CoV-2 variant in California carrying a L452R spike protein mutation
X Deng, MA Garcia-Knight, MM Khalid, V Servellita, C Wang, MK Morris, ...
MedRxiv, 2021
2352021
Genomic surveillance reveals multiple introductions of SARS-CoV-2 into Northern California
X Deng, W Gu, S Federman, L Du Plessis, OG Pybus, NR Faria, C Wang, ...
Science 369 (6503), 582-587, 2020
2282020
An ensemble strategy that significantly improves de novo assembly of microbial genomes from metagenomic next-generation sequencing data
X Deng, SN Naccache, T Ng, S Federman, L Li, CY Chiu, EL Delwart
Nucleic acids research 43 (7), e46-e46, 2015
2162015
Rapid pathogen detection by metagenomic next-generation sequencing of infected body fluids
W Gu, X Deng, M Lee, YD Sucu, S Arevalo, D Stryke, S Federman, ...
Nature Medicine 27 (1), 115-124, 2021
1792021
Genes and pathways downstream of telomerase in melanoma metastasis
S Bagheri, M Nosrati, S Li, S Fong, S Torabian, J Rangel, DH Moore, ...
Proceedings of the National Academy of Sciences 103 (30), 11306-11311, 2006
1622006
The eukaryotic gut virome in hematopoietic stem cell transplantation: new clues in enteric graft-versus-host disease
J Legoff, M Resche-Rigon, J Bouquet, M Robin, SN Naccache, ...
Nature medicine 23 (9), 1080-1085, 2017
1052017
Clinical metagenomic identification of Balamuthia mandrillaris encephalitis and assembly of the draft genome: the continuing case for reference genome sequencing
AL Greninger, K Messacar, T Dunnebacke, SN Naccache, S Federman, ...
Genome medicine 7 (1), 1-14, 2015
1012015
Metagenomic sequencing with spiked primer enrichment for viral diagnostics and genomic surveillance
X Deng, A Achari, S Federman, G Yu, S Somasekar, I Bártolo, S Yagi, ...
Nature microbiology 5 (3), 443-454, 2020
962020
Longitudinal transcriptome analysis reveals a sustained differential gene expression signature in patients treated for acute Lyme disease
J Bouquet, MJ Soloski, A Swei, C Cheadle, S Federman, JN Billaud, ...
MBio 7 (1), e00100-16, 2016
872016
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