Scot Federman
Head of Computation
Biochemistry and Biophysics
School of Medicine

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• Laboratory for Genomics Research (lgr.bio)

Publications (56)

Top publication keywords:
Lyme DiseaseEbolavirusVirus DiseasesCerebrospinal FluidMetagenomicsGenome, ViralEncephalitisMyelitisCRISPR-Cas SystemsBody FluidsMetagenomeGenome, MicrobialVirusesHigh-Throughput Nucleotide SequencingCoinfection

• Simultaneous capture of single cell RNA-seq, ATAC-seq, and CRISPR perturbation enables multiomic screens to identify gene regulatory relationships.
  Cell reports methods 2025 Shevade K, Yang YA, Feng K, Mader K, Sevim V, Parsons J, Arora G, Elfawy H, Mace R, Federman S, Esanov R, Shafer S, Chow ED, Przybyla L
• SAMHD1 knockout hiPSC model enables high lentiviral transduction efficiency in myeloid cell types.
  Frontiers in genetics 2025 Li H, Afroze M, Arora G, Federman S, Shevade K, Yang YA, Nguyen P, Esanov R, Przybyla L, Litterman A, Shafer S
• Comparison of Plasma Metagenomic Next-generation Sequencing and PCR Methods for Epstein-Barr Virus Viral Load Monitoring in Nasopharyngeal Carcinoma.
  Anticancer research 2024 Vasudevan HN, Lazar AA, Reyes K, Rong DA, Arevalo S, Federman S, Chan JW, Chiu CY, Miller S, Yom SS
• Variants in tubule epithelial regulatory elements mediate most heritable differences in human kidney function.
  Nature genetics 2024 Loeb GB, Kathail P, Shuai RW, Chung R, Grona RJ, Peddada S, Sevim V, Federman S, Mader K, Chu AY, Davitte J, Du J, Gupta AR, Ye CJ, Shafer S, Przybyla L, Rapiteanu R, Ioannidis NM, Reiter JF
• Variants in tubule epithelial regulatory elements mediate most heritable differences in human kidney function.
  bioRxiv : the preprint server for biology 2024 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

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• Compact CRISPR genetic screens enabled by improved guide RNA library cloning.
  Genome biology 2024 Heo SJ, Enriquez LD, Federman S, Chang AY, Mace R, Shevade K, Nguyen P, Litterman AJ, Shafer S, Przybyla L, Chow ED
• Metagenomic Detection of Divergent Insect- and Bat-Associated Viruses in Plasma from Two African Individuals Enrolled in Blood-Borne Surveillance.
  Viruses 2023 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
• Longitudinal comparison of the developing gut virome in infants and their mothers.
  Cell host & microbe 2023 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
• Detection of Neoplasms by Metagenomic Next-Generation Sequencing of Cerebrospinal Fluid.
  JAMA neurology 2021 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…
• Introduction, Transmission Dynamics, and Fate of Early Severe Acute Respiratory Syndrome Coronavirus 2 Lineages in Santa Clara County, California.
  The Journal of infectious diseases 2021 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,…
• Detection of cryptogenic malignancies from metagenomic whole genome sequencing of body fluids.
  Genome medicine 2021 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, …
• Transmission, infectivity, and neutralization of a spike L452R SARS-CoV-2 variant.
  Cell 2021 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, …
• Shotgun transcriptome, spatial omics, and isothermal profiling of SARS-CoV-2 infection reveals unique host responses, viral diversification, and drug interactions.
  Nature communications 2021 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, …
• Transmission, infectivity, and antibody neutralization of an emerging SARS-CoV-2 variant in California carrying a L452R spike protein mutation.
  medRxiv : the preprint server for health sciences 2021 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…
• A diagnostic host response biosignature for COVID-19 from RNA profiling of nasal swabs and blood.
  Science advances 2021 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…
• Associations of Early COVID-19 Cases in San Francisco With Domestic and International Travel.
  Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2020 Gu W, Deng X, Reyes K, Hsu E, Wang C, Sotomayor-Gonzalez A, Federman S, Bushnell B, Miller S, Chiu CY
• Timely intervention and control of a novel coronavirus (COVID-19) outbreak at a large skilled nursing facility-San Francisco, California, 2020.
  Infection control and hospital epidemiology 2020 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, …
• Rapid pathogen detection by metagenomic next-generation sequencing of infected body fluids.
  Nature medicine 2020 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 …
• Metagenomic sequencing of stool samples in Bangladeshi infants: virome association with poliovirus shedding after oral poliovirus vaccination.
  Scientific reports 2020 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
• Cryptic transmission of SARS-CoV-2 in Washington state.
  Science (New York, N.Y.) 2020 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…
• 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 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, …
• Genomic surveillance reveals multiple introductions of SARS-CoV-2 into Northern California.
  Science (New York, N.Y.) 2020 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, …
• Clinical features, diagnostics, and outcomes of patients presenting with acute respiratory illness: a comparison of patients with and without COVID-19.
  medRxiv : the preprint server for health sciences 2020 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, …
• Cryptic transmission of SARS-CoV-2 in Washington State.
  medRxiv : the preprint server for health sciences 2020 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…
• A Genomic Survey of SARS-CoV-2 Reveals Multiple Introductions into Northern California without a Predominant Lineage.
  medRxiv : the preprint server for health sciences 2020 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 …
• Author Correction: Metagenomic sequencing with spiked primer enrichment for viral diagnostics and genomic surveillance.
  Nature microbiology 2020 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…
• Metagenomic sequencing with spiked primer enrichment for viral diagnostics and genomic surveillance.
  Nature microbiology 2020 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…
• Metagenomic Next-Generation Sequencing of the 2014 Ebola Virus Disease Outbreak in the Democratic Republic of the Congo.
  Journal of clinical microbiology 2019 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, …
• Clinical Metagenomic Sequencing for Diagnosis of Meningitis and Encephalitis.
  The New England journal of medicine 2019 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, …
• Laboratory validation of a clinical metagenomic sequencing assay for pathogen detection in cerebrospinal fluid.
  Genome research 2019 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
• A Child With Intermittent Headaches and Eosinophilic Meningitis.
  Journal of the Pediatric Infectious Diseases Society 2018 Saporta-Keating SR, Simões EAF, Yu G, Federman S, Mirsky D, Dominguez SR, Chiu CY, Messacar K
• Identification of high-risk human papillomavirus and Rb/E2F pathway genomic alterations in mutually exclusive subsets of colorectal neuroendocrine carcinoma.
  Modern pathology : an official journal of the United States and Canadian Academy of Pathology, Inc 2018 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
• Polyoma virus-associated carcinomas of the urologic tract: a clinicopathologic and molecular study.
  Modern pathology : an official journal of the United States and Canadian Academy of Pathology, Inc 2018 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, …
• Nanopore DNA Sequencing and Genome Assembly on the International Space Station.
  Scientific reports 2017 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,…
• Diagnosis of Fatal Human Case of St. Louis Encephalitis Virus Infection by Metagenomic Sequencing, California, 2016.
  Emerging infectious diseases 2017 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
• The eukaryotic gut virome in hematopoietic stem cell transplantation: new clues in enteric graft-versus-host disease.
  Nature medicine 2017 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
• RNA-Seq Analysis of Gene Expression, Viral Pathogen, and B-Cell/T-Cell Receptor Signatures in Complex Chronic Disease.
  Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2017 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, …
• Longitudinal Transcriptome Analysis Reveals a Sustained Differential Gene Expression Signature in Patients Treated for Acute Lyme Disease.
  mBio 2016 Bouquet J, Soloski MJ, Swei A, Cheadle C, Federman S, Billaud JN, Rebman AW, Kabre B, Halpert R, Boorgula M, Aucott JN, Chiu CY
• Erratum to: Clinical metagenomic identification of Balamuthia mandrillaris encephalitis and assembly of the draft genome: the continuing case for reference genome sequencing.
  Genome medicine 2016 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
• Clinical metagenomic identification of Balamuthia mandrillaris encephalitis and assembly of the draft genome: the continuing case for reference genome sequencing.
  Genome medicine 2015 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…
• Utility of Metagenomic Next-Generation Sequencing for Characterization of HIV and Human Pegivirus Diversity.
  PloS one 2015 Luk KC, Berg MG, Naccache SN, Kabre B, Federman S, Mbanya D, Kaptué L, Chiu CY, Brennan CA, Hackett J
• Rapid metagenomic identification of viral pathogens in clinical samples by real-time nanopore sequencing analysis.
  Genome medicine 2015 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
• A novel outbreak enterovirus D68 strain associated with acute flaccid myelitis cases in the USA (2012-14): a retrospective cohort study.
  The Lancet. Infectious diseases 2015 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…
• An ensemble strategy that significantly improves de novo assembly of microbial genomes from metagenomic next-generation sequencing data.
  Nucleic acids research 2015 Deng X, Naccache SN, Ng T, Federman S, Li L, Chiu CY, Delwart EL
• Diagnosis of neuroinvasive astrovirus infection in an immunocompromised adult with encephalitis by unbiased next-generation sequencing.
  Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2015 Naccache SN, Peggs KS, Mattes FM, Phadke R, Garson JA, Grant P, Samayoa E, Federman S, Miller S, Lunn MP, Gant V, Chiu CY
• A cloud-compatible bioinformatics pipeline for ultrarapid pathogen identification from next-generation sequencing of clinical samples.
  Genome research 2014 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…
• Actionable diagnosis of neuroleptospirosis by next-generation sequencing.
  The New England journal of medicine 2014 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,…
• Pleckstrin homology domain-interacting protein (PHIP) as a marker and mediator of melanoma metastasis.
  Proceedings of the National Academy of Sciences of the United States of America 2012 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, …
• 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 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
• Nutritional supplements, COX-2 and IGF-1 expression in men on active surveillance for prostate cancer.
  Cancer causes & control : CCC 2010 Chan JM, Weinberg V, Magbanua MJ, Sosa E, Simko J, Shinohara K, Federman S, Mattie M, Hughes-Fulford M, Haqq C, Carroll PR
• Functional modulation of IGF-binding protein-3 expression in melanoma.
  The Journal of investigative dermatology 2010 Dar AA, Majid S, Nosrati M, de Semir D, Federman S, Kashani-Sabet M
• Metabolic, pathologic, and genetic analysis of prostate tissues: quantitative evaluation of histopathologic and mRNA integrity after HR-MAS spectroscopy.
  NMR in biomedicine 2009 Santos CF, Kurhanewicz J, Tabatabai ZL, Simko JP, Keshari KR, Gbegnon A, Santos RD, Federman S, Shinohara K, Carroll PR, Haqq CM, Swanson MG
• A comparison of RNA amplification techniques at sub-nanogram input concentration.
  BMC genomics 2009 Lang JE, Magbanua MJ, Scott JH, Makrigiorgos GM, Wang G, Federman S, Esserman LJ, Park JW, Haqq CM
• Ribozyme-mediated targeting of IkappaBgamma inhibits melanoma invasion and metastasis.
  The American journal of pathology 2009 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
• Genes and pathways downstream of telomerase in melanoma metastasis.
  Proceedings of the National Academy of Sciences of the United States of America 2006 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
• The gene expression signatures of melanoma progression.
  Proceedings of the National Academy of Sciences of the United States of America 2005 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