Scot Federman

Title(s)Head of Computation, Biochemistry and Biophysics
SchoolSchool of Medicine
Address499 Illinois, #352
San Francisco CA 94158
PronounsHe/Him/His
ORCID ORCID Icon0000-0001-8712-3131 Additional info
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    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help. to make corrections and additions.
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    Altmetrics Details PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. Variants in tubule epithelial regulatory elements mediate most heritable differences in human kidney function. bioRxiv. 2024 Jun 22. Loeb GB, Kathail P, Shuai R, Chung R, Grona RJ, Peddada S, Sevim V, Federman S, Mader K, Chu A, Davitte J, Du J, Gupta AR, Ye CJ, Shafer S, Przybyla L, Rapiteanu R, Ioannidis N, Reiter JF. PMID: 38948875; PMCID: PMC11212968.
      View in: PubMed   Mentions:
    2. Compact CRISPR genetic screens enabled by improved guide RNA library cloning. Genome Biol. 2024 01 19; 25(1):25. Heo SJ, Enriquez LD, Federman S, Chang AY, Mace R, Shevade K, Nguyen P, Litterman AJ, Shafer S, Przybyla L, Chow ED. PMID: 38243310; PMCID: PMC10797759.
      View in: PubMed   Mentions: 1     Fields:    Translation:HumansCells
    3. Metagenomic Detection of Divergent Insect- and Bat-Associated Viruses in Plasma from Two African Individuals Enrolled in Blood-Borne Surveillance. Viruses. 2023 04 21; 15(4). Orf GS, Olivo A, Harris B, Weiss SL, Achari A, Yu G, Federman S, Mbanya D, James L, Mampunza S, Chiu CY, Rodgers MA, Cloherty GA, Berg MG. PMID: 37113001; PMCID: PMC10145552.
      View in: PubMed   Mentions: 5     Fields:    Translation:AnimalsCells
    4. Longitudinal comparison of the developing gut virome in infants and their mothers. Cell Host Microbe. 2023 02 08; 31(2):187-198.e3. Walters WA, Granados AC, Ley C, Federman S, Stryke D, Santos Y, Haggerty T, Sotomayor-Gonzalez A, Servellita V, Ley RE, Parsonnet J, Chiu CY. PMID: 36758519; PMCID: PMC9950819.
      View in: PubMed   Mentions: 12     Fields:    Translation:HumansCells
    5. Detection of Neoplasms by Metagenomic Next-Generation Sequencing of Cerebrospinal Fluid. JAMA Neurol. 2021 11 01; 78(11):1355-1366. Gu W, Rauschecker AM, Hsu E, Zorn KC, Sucu Y, Federman S, Gopez A, Arevalo S, Sample HA, Talevich E, Nguyen ED, Gottschall M, Nourbakhsh B, Gold CA, Cree BAC, Douglas VC, Richie MB, Shah MP, Josephson SA, Gelfand JM, Miller S, Wang L, Tihan T, DeRisi JL, Chiu CY, Wilson MR. PMID: 34515766; PMCID: PMC8438621.
      View in: PubMed   Mentions: 7     Fields:    Translation:Humans
    6. Introduction, Transmission Dynamics, and Fate of Early Severe Acute Respiratory Syndrome Coronavirus 2 Lineages in Santa Clara County, California. J Infect Dis. 2021 07 15; 224(2):207-217. Villarino E, Deng X, Kemper CA, Jorden MA, Bonin B, Rudman SL, Han GS, Yu G, Wang C, Federman S, Bushnell B, CZB COVIDTracker Consortium, Wadford DA, Lin W, Tao Y, Paden CR, Bhatnagar J, MacCannell T, Tong S, Batson J, Chiu CY. PMID: 33893501; PMCID: PMC8135363.
      View in: PubMed   Mentions: 1     Fields:    Translation:HumansCellsPHPublic Health
    7. Detection of cryptogenic malignancies from metagenomic whole genome sequencing of body fluids. Genome Med. 2021 06 01; 13(1):98. Gu W, Talevich E, Hsu E, Qi Z, Urisman A, Federman S, Gopez A, Arevalo S, Gottschall M, Liao L, Tung J, Chen L, Lim H, Ho C, Kasowski M, Oak J, Holmes BJ, Yeh I, Yu J, Wang L, Miller S, DeRisi JL, Prakash S, Simko J, Chiu CY. PMID: 34074327; PMCID: PMC8167833.
      View in: PubMed   Mentions: 11     Fields:    Translation:Humans
    8. Transmission, infectivity, and neutralization of a spike L452R SARS-CoV-2 variant. Cell. 2021 06 24; 184(13):3426-3437.e8. Deng X, Garcia-Knight MA, Khalid MM, Servellita V, Wang C, Morris MK, Sotomayor-González A, Glasner DR, Reyes KR, Gliwa AS, Reddy NP, Sanchez San Martin C, Federman S, Cheng J, Balcerek J, Taylor J, Streithorst JA, Miller S, Sreekumar B, Chen PY, Schulze-Gahmen U, Taha TY, Hayashi JM, Simoneau CR, Kumar GR, McMahon S, Lidsky PV, Xiao Y, Hemarajata P, Green NM, Espinosa A, Kath C, Haw M, Bell J, Hacker JK, Hanson C, Wadford DA, Anaya C, Ferguson D, Frankino PA, Shivram H, Lareau LF, Wyman SK, Ott M, Andino R, Chiu CY. PMID: 33991487; PMCID: PMC8057738.
      View in: PubMed   Mentions: 298     Fields:    Translation:HumansCells
    9. Shotgun transcriptome, spatial omics, and isothermal profiling of SARS-CoV-2 infection reveals unique host responses, viral diversification, and drug interactions. Nat Commun. 2021 03 12; 12(1):1660. Butler D, Mozsary C, Meydan C, Foox J, Rosiene J, Shaiber A, Danko D, Afshinnekoo E, MacKay M, Sedlazeck FJ, Ivanov NA, Sierra M, Pohle D, Zietz M, Gisladottir U, Ramlall V, Sholle ET, Schenck EJ, Westover CD, Hassan C, Ryon K, Young B, Bhattacharya C, Ng DL, Granados AC, Santos YA, Servellita V, Federman S, Ruggiero P, Fungtammasan A, Chin CS, Pearson NM, Langhorst BW, Tanner NA, Kim Y, Reeves JW, Hether TD, Warren SE, Bailey M, Gawrys J, Meleshko D, Xu D, Couto-Rodriguez M, Nagy-Szakal D, Barrows J, Wells H, O'Hara NB, Rosenfeld JA, Chen Y, Steel PAD, Shemesh AJ, Xiang J, Thierry-Mieg J, Thierry-Mieg D, Iftner A, Bezdan D, Sanchez E, Campion TR, Sipley J, Cong L, Craney A, Velu P, Melnick AM, Shapira S, Hajirasouliha I, Borczuk A, Iftner T, Salvatore M, Loda M, Westblade LF, Cushing M, Wu S, Levy S, Chiu C, Schwartz RE, Tatonetti N, Rennert H, Imielinski M, Mason CE. PMID: 33712587; PMCID: PMC7954844.
      View in: PubMed   Mentions: 117     Fields:    Translation:HumansCellsPHPublic Health
    10. Transmission, infectivity, and antibody neutralization of an emerging SARS-CoV-2 variant in California carrying a L452R spike protein mutation. medRxiv. 2021 Mar 09. Deng X, Garcia-Knight MA, Khalid MM, Servellita V, Wang C, Morris MK, Sotomayor-González A, Glasner DR, Reyes KR, Gliwa AS, Reddy NP, Martin CSS, Federman S, Cheng J, Balcerek J, Taylor J, Streithorst JA, Miller S, Kumar GR, Sreekumar B, Chen PY, Schulze-Gahmen U, Taha TY, Hayashi J, Simoneau CR, McMahon S, Lidsky PV, Xiao Y, Hemarajata P, Green NM, Espinosa A, Kath C, Haw M, Bell J, Hacker JK, Hanson C, Wadford DA, Anaya C, Ferguson D, Lareau LF, Frankino PA, Shivram H, Wyman SK, Ott M, Andino R, Chiu CY. PMID: 33758899; PMCID: PMC7987058.
      View in: PubMed   Mentions: 6  
    11. A diagnostic host response biosignature for COVID-19 from RNA profiling of nasal swabs and blood. Sci Adv. 2021 02; 7(6). Ng DL, Granados AC, Santos YA, Servellita V, Goldgof GM, Meydan C, Sotomayor-Gonzalez A, Levine AG, Balcerek J, Han LM, Akagi N, Truong K, Neumann NM, Nguyen DN, Bapat SP, Cheng J, Martin CS, Federman S, Foox J, Gopez A, Li T, Chan R, Chu CS, Wabl CA, Gliwa AS, Reyes K, Pan CY, Guevara H, Wadford D, Miller S, Mason CE, Chiu CY. PMID: 33536218; PMCID: PMC7857687.
      View in: PubMed   Mentions: 48     Fields:    Translation:HumansCells
    12. Associations of Early COVID-19 Cases in San Francisco With Domestic and International Travel. Clin Infect Dis. 2020 12 31; 71(11):2976-2980. Gu W, Deng X, Reyes K, Hsu E, Wang C, Sotomayor-Gonzalez A, Federman S, Bushnell B, Miller S, Chiu CY. PMID: 32436571; PMCID: PMC7314204.
      View in: PubMed   Mentions: 4     Fields:    Translation:HumansCells
    13. Timely intervention and control of a novel coronavirus (COVID-19) outbreak at a large skilled nursing facility-San Francisco, California, 2020. Infect Control Hosp Epidemiol. 2021 10; 42(10):1173-1180. Karmarkar EN, Blanco I, Amornkul PN, DuBois A, Deng X, Moonan PK, Rubenstein BL, Miller DA, Kennedy I, Yu J, Dauterman JP, Ongpin M, Hathaway W, Hoo L, Trammell S, Dosunmu EF, Yu G, Khwaja Z, Lu W, Talai NZ, Jain S, Louie JK, Philip SS, Federman S, Masinde G, Wadford DA, Bobba N, Stoltey J, Smith A, Epson E, Chiu CY, Bennett AS, Vasquez AM, Williams T. PMID: 33308357; PMCID: PMC8144818.
      View in: PubMed   Mentions: 12     Fields:    Translation:HumansCellsPHPublic Health
    14. Rapid pathogen detection by metagenomic next-generation sequencing of infected body fluids. Nat Med. 2021 01; 27(1):115-124. 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. PMID: 33169017; PMCID: PMC9020267.
      View in: PubMed   Mentions: 226     Fields:    Translation:HumansAnimalsCells
    15. Metagenomic sequencing of stool samples in Bangladeshi infants: virome association with poliovirus shedding after oral poliovirus vaccination. Sci Rep. 2020 09 21; 10(1):15392. 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. PMID: 32958861; PMCID: PMC7506025.
      View in: PubMed   Mentions: 4     Fields:    Translation:HumansCellsPHPublic Health
    16. Cryptic transmission of SARS-CoV-2 in Washington state. Science. 2020 10 30; 370(6516):571-575. 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, Seattle Flu Study Investigators, 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. PMID: 32913002; PMCID: PMC7810035.
      View in: PubMed   Mentions: 172     Fields:    Translation:HumansCellsPHPublic Health
    17. Clinical features, diagnostics, and outcomes of patients presenting with acute respiratory illness: A retrospective cohort study of patients with and without COVID-19. EClinicalMedicine. 2020 Oct; 27:100518. 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. PMID: 32864588; PMCID: PMC7447618.
      View in: PubMed   Mentions: 43  
    18. Genomic surveillance reveals multiple introductions of SARS-CoV-2 into Northern California. Science. 2020 07 31; 369(6503):582-587. Deng X, Gu W, Federman S, du Plessis L, Pybus OG, Faria NR, 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. PMID: 32513865; PMCID: PMC7286545.
      View in: PubMed   Mentions: 162     Fields:    Translation:HumansCellsPHPublic Health
    19. Clinical features, diagnostics, and outcomes of patients presenting with acute respiratory illness: a comparison of patients with and without COVID-19. medRxiv. 2020 May 06. 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. PMID: 32511488; PMCID: PMC7273256.
      View in: PubMed   Mentions: 2  
    20. Cryptic transmission of SARS-CoV-2 in Washington State. medRxiv. 2020 Apr 06. 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, Seattle Flu Study Investigators, 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. PMID: 32511596; PMCID: PMC7276023.
      View in: PubMed   Mentions:
    21. A Genomic Survey of SARS-CoV-2 Reveals Multiple Introductions into Northern California without a Predominant Lineage. medRxiv. 2020 Mar 30. Deng X, Gu W, Federman S, du Plessis L, Pybus OG, 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 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, Chan C, Yu AT, Chai SJ, Villarino E, Bonin B, Wadford DA, Chiu CY. PMID: 32511579; PMCID: PMC7276006.
      View in: PubMed   Mentions: 2  
    22. Author Correction: Metagenomic sequencing with spiked primer enrichment for viral diagnostics and genomic surveillance. Nat Microbiol. 2020 Mar; 5(3):525. 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. PMID: 31965087; PMCID: PMC7608365.
      View in: PubMed   Mentions: 2     Fields:    
    23. Metagenomic sequencing with spiked primer enrichment for viral diagnostics and genomic surveillance. Nat Microbiol. 2020 03; 5(3):443-454. 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. PMID: 31932713; PMCID: PMC7047537.
      View in: PubMed   Mentions: 76     Fields:    Translation:HumansCells
    24. Metagenomic Next-Generation Sequencing of the 2014 Ebola Virus Disease Outbreak in the Democratic Republic of the Congo. J Clin Microbiol. 2019 09; 57(9). 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. PMID: 31315955; PMCID: PMC6711896.
      View in: PubMed   Mentions: 11     Fields:    Translation:HumansCellsPHPublic Health
    25. Clinical Metagenomic Sequencing for Diagnosis of Meningitis and Encephalitis. N Engl J Med. 2019 06 13; 380(24):2327-2340. 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. PMID: 31189036; PMCID: PMC6764751.
      View in: PubMed   Mentions: 374     Fields:    Translation:HumansCTClinical Trials
    26. Laboratory validation of a clinical metagenomic sequencing assay for pathogen detection in cerebrospinal fluid. Genome Res. 2019 05; 29(5):831-842. 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. PMID: 30992304; PMCID: PMC6499319.
      View in: PubMed   Mentions: 245     Fields:    Translation:HumansCells
    27. A Child With Intermittent Headaches and Eosinophilic Meningitis. J Pediatric Infect Dis Soc. 2018 Dec 03; 7(4):355-357. Saporta-Keating SR, Simões EAF, Yu G, Federman S, Mirsky D, Dominguez SR, Chiu CY, Messacar K. PMID: 29438532; PMCID: PMC6276032.
      View in: PubMed   Mentions: 2     Fields:    Translation:HumansAnimals
    28. Identification of high-risk human papillomavirus and Rb/E2F pathway genomic alterations in mutually exclusive subsets of colorectal neuroendocrine carcinoma. Mod Pathol. 2019 02; 32(2):290-305. 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. PMID: 30237525.
      View in: PubMed   Mentions: 24     Fields:    Translation:Humans
    29. Polyoma virus-associated carcinomas of the urologic tract: a clinicopathologic and molecular study. Mod Pathol. 2018 09; 31(9):1429-1441. 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. PMID: 29765141.
      View in: PubMed   Mentions: 9     Fields:    Translation:HumansCells
    30. Nanopore DNA Sequencing and Genome Assembly on the International Space Station. Sci Rep. 2017 12 21; 7(1):18022. 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. PMID: 29269933; PMCID: PMC5740133.
      View in: PubMed   Mentions: 138     Fields:    Translation:AnimalsCells
    31. Diagnosis of Fatal Human Case of St. Louis Encephalitis Virus Infection by Metagenomic Sequencing, California, 2016. Emerg Infect Dis. 2017 10; 23(10):1964-1968. 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. PMID: 28930022; PMCID: PMC5621550.
      View in: PubMed   Mentions: 44     Fields:    Translation:HumansCells
    32. The eukaryotic gut virome in hematopoietic stem cell transplantation: new clues in enteric graft-versus-host disease. Nat Med. 2017 Sep; 23(9):1080-1085. 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. PMID: 28759053.
      View in: PubMed   Mentions: 74     Fields:    Translation:HumansCells
    33. RNA-Seq Analysis of Gene Expression, Viral Pathogen, and B-Cell/T-Cell Receptor Signatures in Complex Chronic Disease. Clin Infect Dis. 2017 02 15; 64(4):476-481. 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, Complex Chronic Disease Study Group. PMID: 28172519; PMCID: PMC5850034.
      View in: PubMed   Mentions: 12     Fields:    Translation:HumansCells
    34. Longitudinal Transcriptome Analysis Reveals a Sustained Differential Gene Expression Signature in Patients Treated for Acute Lyme Disease. mBio. 2016 Feb 12; 7(1):e00100-16. Bouquet J, Soloski MJ, Swei A, Cheadle C, Federman S, Billaud JN, Rebman AW, Kabre B, Halpert R, Boorgula M, Aucott JN, Chiu CY. PMID: 26873097; PMCID: PMC4791844.
      View in: PubMed   Mentions: 51     Fields:    Translation:HumansAnimalsCells
    35. Erratum to: Clinical metagenomic identification of Balamuthia mandrillaris encephalitis and assembly of the draft genome: the continuing case for reference genome sequencing. Genome Med. 2016 Jan 11; 8(1):1. 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. PMID: 26750923; PMCID: PMC4707724.
      View in: PubMed   Mentions:    Fields:    
    36. Clinical metagenomic identification of Balamuthia mandrillaris encephalitis and assembly of the draft genome: the continuing case for reference genome sequencing. Genome Med. 2015 Dec 01; 7:113. 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. PMID: 26620704; PMCID: PMC4665321.
      View in: PubMed   Mentions: 64     Fields:    Translation:HumansAnimals
    37. Utility of Metagenomic Next-Generation Sequencing for Characterization of HIV and Human Pegivirus Diversity. PLoS One. 2015; 10(11):e0141723. Luk KC, Berg MG, Naccache SN, Kabre B, Federman S, Mbanya D, Kaptué L, Chiu CY, Brennan CA, Hackett J. PMID: 26599538; PMCID: PMC4658132.
      View in: PubMed   Mentions: 20     Fields:    Translation:HumansCells
    38. Rapid metagenomic identification of viral pathogens in clinical samples by real-time nanopore sequencing analysis. Genome Med. 2015 Sep 29; 7:99. 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. PMID: 26416663; PMCID: PMC4587849.
      View in: PubMed   Mentions: 244     Fields:    Translation:HumansCells
    39. A novel outbreak enterovirus D68 strain associated with acute flaccid myelitis cases in the USA (2012-14): a retrospective cohort study. Lancet Infect Dis. 2015 Jun; 15(6):671-82. 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. PMID: 25837569; PMCID: PMC6027625.
      View in: PubMed   Mentions: 177     Fields:    Translation:HumansCellsPHPublic Health
    40. An ensemble strategy that significantly improves de novo assembly of microbial genomes from metagenomic next-generation sequencing data. Nucleic Acids Res. 2015 Apr 20; 43(7):e46. Deng X, Naccache SN, Ng T, Federman S, Li L, Chiu CY, Delwart EL. PMID: 25586223; PMCID: PMC4402509.
      View in: PubMed   Mentions: 152     Fields:    Translation:HumansCells
    41. Diagnosis of neuroinvasive astrovirus infection in an immunocompromised adult with encephalitis by unbiased next-generation sequencing. Clin Infect Dis. 2015 Mar 15; 60(6):919-23. Naccache SN, Peggs KS, Mattes FM, Phadke R, Garson JA, Grant P, Samayoa E, Federman S, Miller S, Lunn MP, Gant V, Chiu CY. PMID: 25572898; PMCID: PMC4345816.
      View in: PubMed   Mentions: 156     Fields:    Translation:HumansCells
    42. Actionable diagnosis of neuroleptospirosis by next-generation sequencing. N Engl J Med. 2014 Jun 19; 370(25):2408-17. 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. PMID: 24896819; PMCID: PMC4134948.
      View in: PubMed   Mentions: 429     Fields:    Translation:HumansCells
    43. A cloud-compatible bioinformatics pipeline for ultrarapid pathogen identification from next-generation sequencing of clinical samples. Genome Res. 2014 Jul; 24(7):1180-92. 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. PMID: 24899342; PMCID: PMC4079973.
      View in: PubMed   Mentions: 231     Fields:    Translation:Humans
    44. Pleckstrin homology domain-interacting protein (PHIP) as a marker and mediator of melanoma metastasis. Proc Natl Acad Sci U S A. 2012 May 01; 109(18):7067-72. De Semir D, Nosrati M, Bezrookove V, Dar AA, Federman S, Bienvenu G, Venna S, Rangel J, Climent J, Meyer Tamgüney TM, Thummala S, Tong S, Leong SP, Haqq C, Billings P, Miller JR, Sagebiel RW, Debs R, Kashani-Sabet M. PMID: 22511720; PMCID: PMC3344978.
      View in: PubMed   Mentions: 30     Fields:    Translation:HumansAnimalsCells
    45. Gene expression and biological pathways in tissue of men with prostate cancer in a randomized clinical trial of lycopene and fish oil supplementation. PLoS One. 2011; 6(9):e24004. Magbanua MJ, Roy R, Sosa EV, Weinberg V, Federman S, Mattie MD, Hughes-Fulford M, Simko J, Shinohara K, Haqq CM, Carroll PR, Chan JM. PMID: 21912659; PMCID: PMC3164676.
      View in: PubMed   Mentions: 24     Fields:    Translation:Humans
    46. Nutritional supplements, COX-2 and IGF-1 expression in men on active surveillance for prostate cancer. Cancer Causes Control. 2011 Jan; 22(1):141-50. Chan JM, Weinberg V, Magbanua MJ, Sosa E, Simko J, Shinohara K, Federman S, Mattie M, Hughes-Fulford M, Haqq C, Carroll PR. PMID: 21103921; PMCID: PMC3002170.
      View in: PubMed   Mentions: 23     Fields:    Translation:Humans
    47. Functional modulation of IGF-binding protein-3 expression in melanoma. J Invest Dermatol. 2010 Aug; 130(8):2071-9. Dar AA, Majid S, Nosrati M, de Semir D, Federman S, Kashani-Sabet M. PMID: 20357812; PMCID: PMC3023991.
      View in: PubMed   Mentions: 19     Fields:    Translation:HumansCells
    48. Metabolic, pathologic, and genetic analysis of prostate tissues: quantitative evaluation of histopathologic and mRNA integrity after HR-MAS spectroscopy. NMR Biomed. 2010 May; 23(4):391-8. Santos CF, Kurhanewicz J, Tabatabai ZL, Simko JP, Keshari KR, Gbegnon A, Santos RD, Federman S, Shinohara K, Carroll PR, Haqq CM, Swanson MG. PMID: 20033906; PMCID: PMC2891902.
      View in: PubMed   Mentions: 19     Fields:    Translation:HumansCells
    49. A comparison of RNA amplification techniques at sub-nanogram input concentration. BMC Genomics. 2009 Jul 20; 10:326. Lang JE, Magbanua MJ, Scott JH, Makrigiorgos GM, Wang G, Federman S, Esserman LJ, Park JW, Haqq CM. PMID: 19619282; PMCID: PMC2724417.
      View in: PubMed   Mentions: 15     Fields:    Translation:HumansCells
    50. Ribozyme-mediated targeting of IkappaBgamma inhibits melanoma invasion and metastasis. Am J Pathol. 2009 Mar; 174(3):1009-16. Torabian SZ, de Semir D, Nosrati M, Bagheri S, Dar AA, Fong S, Liu Y, Federman S, Simko J, Haqq C, Debs RJ, Kashani-Sabet M. PMID: 19179607; PMCID: PMC2665760.
      View in: PubMed   Mentions: 6     Fields:    Translation:AnimalsCells
    51. Genes and pathways downstream of telomerase in melanoma metastasis. Proc Natl Acad Sci U S A. 2006 Jul 25; 103(30):11306-11. Bagheri S, Nosrati M, Li S, Fong S, Torabian S, Rangel J, Moore DH, Federman S, Laposa RR, Baehner FL, Sagebiel RW, Cleaver JE, Haqq C, Debs RJ, Blackburn EH, Kashani-Sabet M. PMID: 16847266; PMCID: PMC1544082.
      View in: PubMed   Mentions: 55     Fields:    Translation:Animals
    52. The gene expression signatures of melanoma progression. Proc Natl Acad Sci U S A. 2005 Apr 26; 102(17):6092-7. Haqq C, Nosrati M, Sudilovsky D, Crothers J, Khodabakhsh D, Pulliam BL, Federman S, Miller JR, Allen RE, Singer MI, Leong SP, Ljung BM, Sagebiel RW, Kashani-Sabet M. PMID: 15833814; PMCID: PMC1087936.
      View in: PubMed   Mentions: 174     Fields:    Translation:Humans
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