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
5722014
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
4622005
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
3902015
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
3832014
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
3272015
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
2542019
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
2282015
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
2232017
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
1782015
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
1572006
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
1542020
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
1382020
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
1162019
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
862015
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
722017
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
672021
Diagnosis of fatal human case of St. Louis encephalitis virus infection by metagenomic sequencing, California, 2016
CY Chiu, LL Coffey, J Murkey, K Symmes, HA Sample, MR Wilson, ...
Emerging infectious diseases 23 (10), 1964, 2017
622017
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
622016
Gene expression and biological pathways in tissue of men with prostate cancer in a randomized clinical trial of lycopene and fish oil supplementation
MJM Magbanua, R Roy, EV Sosa, V Weinberg, S Federman, MD Mattie, ...
PloS one 6 (9), e24004, 2011
572011
Nutritional supplements, COX-2 and IGF-1 expression in men on active surveillance for prostate cancer
JM Chan, V Weinberg, MJ Magbanua, E Sosa, J Simko, K Shinohara, ...
Cancer Causes & Control 22 (1), 141-150, 2011
552011
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Articles 1–20