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Brian Shy, MD, PhD

Title(s)Assistant Professor, Laboratory Medicine
SchoolSchool of Medicine
Address1855 Folsom Street, #269A
San Francisco CA 94103
PronounsHe/Him/His
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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. Development of a Fully Non-Viral 1XX-enhanced BCMA CAR-T Cell Therapy for Multiple Myeloma. bioRxiv. 2026 Apr 22. Talbot A, Li K, Lee JHJ, Lang S, Liu C, Kalter N, Li Z, Mortazavi Y, Almudhfar N, Muldoon JJ, Allain V, Nyberg W, Chung JJ, Wang C, Qi Z, Krishnappa N, Ha AS, Kong D, Houser D, Paruthiyil S, Ahmadi M, Ji Y, Rosenberg M, Acevedo LA, Liang B, Briseno K, Kwek SS, Giannikopoulos P, Rivière I, Sadelain M, Oh DY, Marson A, Hendel A, Martin T, Eyquem J, Shy BR. PMID: 42079140; PMCID: PMC13131766.
      View in: PubMed   Mentions:
    2. Ultra-large targeted DNA integrations in primary human cells. bioRxiv. 2026 Apr 09. Kernick C, Chow L, Alejandro M, Li K, Foisey MG, Yang X, Hilburger C, Lu J, Wu L, McClellan A, Takacsi-Nagy O, Brajenovic R, Theberath NE, Fuentes EC, Lin E, Hartman A, Truong T, Lee JHJ, Workley L, Ha AS, Ji Y, Putnam N, Andronikou N, Fatima N, Dotson M, Wong KA, Burns CH, Engelhard FAS, Stoyanova E, Vukovic M, Adie T, Lim WA, Roybal K, Santostefano K, Almeida R, Allen GM, Shy BR, Roth TL. PMID: 41993426; PMCID: PMC13081881.
      View in: PubMed   Mentions:
    3. Synthetic Hybrid Receptors for Safer and Programmable T Cell Therapy. bioRxiv. 2026 Jan 23. Foisey MG, Garcia J, Li X, Yang X, Hilburger C, Thienpont C, Chaves-Martinez A, Belkaya S, Truong T, Zhu I, Liu R, Hyrenius-Wittsten A, Almeida R, Shy BR, Allen GM, Wyman S, Roybal KT. PMID: 41648153; PMCID: PMC12871671.
      View in: PubMed   Mentions:
    4. Transfusion-induced HLA antibodies are short-lived and rarely recur post-heart transplantation: a single-center retrospective study with implications for virtual crossmatching. Front Immunol. 2026; 17:1729124. Rajalingam R, Maruthamuthu S, Shy BR, Cunniffe J, Lowe D, Aljohani OA, Wieselthaler G. PMID: 41646845; PMCID: PMC12867846.
      View in: PubMed   Mentions:    Fields:    Translation:Humans
    5. Gene-corrected regulatory T cell therapy for IL2RA deficiency. Mol Ther. 2026 Mar 04; 34(3):1367-1381. Ha AS, Kalter N, Rosenberg M, Acevedo LA, Liang B, Liu W, Paruthiyil S, Sinha M, Vu A, Nguyen V, Qi Z, Krishnappa N, Shu J, Yu J, Catanzaro J, Bluestone JA, Tang Q, Urnov FD, Marson A, Hendel A, Herold KC, Shy BR, Esensten JH. PMID: 41376159; PMCID: PMC12974163.
      View in: PubMed   Mentions:    Fields:    Translation:HumansCells
    6. Pharmacokinetics, lineage identity, and trafficking of ex vivo expanded polyclonal regulatory T cells in a prospective randomized clinical trial of kidney transplant recipients with allograft inflammation. Am J Transplant. 2026 Apr; 26(4):744-759. Chandran S, Leung JC, Vu A, Lee K, Fitch M, Esensten JH, Shy BR, Putnam AL, Lares A, Acevedo LA, Nguyen V, Liu W, Armstrong B, Laszik ZG, Mannon RB, Friedewald JJ, Naik A, Davis S, Sarwal M, Hellerstein M, Morsheimer M, Goldstein J, Tang Q, Vincenti FG. PMID: 41314617; PMCID: PMC12971219.
      View in: PubMed   Mentions:    Fields:    Translation:HumansCells
    7. Characterizing and controlling CRISPR repair outcomes in nondividing human cells. Nat Commun. 2025 Nov 17; 16(1):9883. Ramadoss GN, Namaganda SJ, Kumar MM, Hamilton JR, Sharma R, Chow KG, Workley LA, Macklin BL, Sun M, Ha AS, Liu JC, Fellmann C, Watry HL, Dierks PH, Bose RS, Jin J, Perez BS, Sandoval Espinoza CR, Matia MP, Lu SH, Judge LM, Shy BR, Nussenzweig A, Adamson B, Murthy N, Doudna JA, Kampmann M, Conklin BR. PMID: 41249169; PMCID: PMC12623481.
      View in: PubMed   Mentions: 2     Fields:    Translation:HumansCells
    8. Integrated epigenetic and genetic programming of primary human T cells. Nat Biotechnol. 2025 Oct 21. Goudy L, Ha A, Borah AA, Umhoefer JM, Chow L, Tran C, Winters A, Talbot A, Hernandez R, Li Z, Subramanya S, Arab A, Kale N, Lee JHJ, Muldoon JJ, Liu C, Schmidt R, Santangelo P, Carnevale J, Eyquem J, Shy BR, Marson A, Gilbert LA. PMID: 41120666.
      View in: PubMed   Mentions: 1     Fields:    
    9. Structure-guided engineering of CCL27 enhances natural ligand CAR T-cells against CCR10 for multiple myeloma. bioRxiv. 2025 Aug 23. Chilakapati N, Patiño-Escobar B, Chen EY, Dalal R, de Montagnac J, Johnson H, Kang AS, Akagi N, Ramos E, Phojanakong P, Salangsang F, Zeng Y, Chari A, Chung A, Kumar AD, Martin TG, Wolf JL, Shy BR, Steri V, Karlon WJ, Kortemme T, Barwick BG, Wiita AP. PMID: 40894691; PMCID: PMC12393364.
      View in: PubMed   Mentions:
    10. SEED-Selection enables high-efficiency enrichment of primary T cells edited at multiple loci. Nat Biotechnol. 2025 Dec; 43(12):2043-2053. Chang CR, Vykunta VS, Lee JHJ, Li K, Kochendoerfer C, Muldoon JJ, Wang CH, Mazumder T, Sun Y, Goodman DB, Nyberg WA, Liu C, Allain V, Rothrock A, Ye CJ, Marson A, Shy BR, Eyquem J. PMID: 39910194; PMCID: PMC12320447.
      View in: PubMed   Mentions: 3     Fields:    Translation:HumansCells
    11. Central control of dynamic gene circuits governs T cell rest and activation. Nature. 2025 01; 637(8047):930-939. Arce MM, Umhoefer JM, Arang N, Kasinathan S, Freimer JW, Steinhart Z, Shen H, Pham MTN, Ota M, Wadhera A, Dajani R, Dorovskyi D, Chen YY, Liu Q, Zhou Y, Swaney DL, Obernier K, Shy BR, Carnevale J, Satpathy AT, Krogan NJ, Pritchard JK, Marson A. PMID: 39663454; PMCID: PMC11754113.
      View in: PubMed   Mentions: 13     Fields:    Translation:HumansCells
    12. Antigen-Specific T Cell Receptor Discovery for Treating Progressive Multifocal Leukoencephalopathy. bioRxiv. 2024 Nov 04. Gupta S, Martinov T, Thelen A, Sunahara M, Mureli S, Vazquez A, Gerdts J, Dandekar R, Cortese I, Fouassier C, Schanzer E, Urnov FD, Marson A, Shy BR, Greenberg PD, Wilson MR. PMID: 39574748; PMCID: PMC11580961.
      View in: PubMed   Mentions:
    13. Bidirectional epigenetic editing reveals hierarchies in gene regulation. Nat Biotechnol. 2025 Mar; 43(3):355-368. Pacalin NM, Steinhart Z, Shi Q, Belk JA, Dorovskyi D, Kraft K, Parker KR, Shy BR, Marson A, Chang HY. PMID: 38760566; PMCID: PMC11569274.
      View in: PubMed   Mentions: 14     Fields:    Translation:HumansCells
    14. Engineering an Escherichia coli strain for production of long single-stranded DNA. Nucleic Acids Res. 2024 Apr 24; 52(7):4098-4107. Shen K, Flood JJ, Zhang Z, Ha A, Shy BR, Dueber JE, Douglas SM. PMID: 38499480; PMCID: PMC11040142.
      View in: PubMed   Mentions: 4     Fields:    Translation:Cells
    15. Engineering an Escherichia coli strain for production of long single-stranded DNA. bioRxiv. 2024 Mar 01. Shen K, Flood JJ, Zhang Z, Ha A, Shy BR, Dueber JE, Douglas SM. PMID: 38464036; PMCID: PMC10925301.
      View in: PubMed   Mentions:
    16. Ultra-high efficiency T cell reprogramming at multiple loci with SEED-Selection. bioRxiv. 2024 Feb 07. Chang CR, Vykunta VS, Goodman DB, Muldoon JJ, Nyberg WA, Liu C, Allain V, Rothrock A, Wang CH, Marson A, Shy BR, Eyquem J. PMID: 38370809; PMCID: PMC10871224.
      View in: PubMed   Mentions:
    17. Base-editing mutagenesis maps alleles to tune human T cell functions. Nature. 2024 01; 625(7996):805-812. Schmidt R, Ward CC, Dajani R, Armour-Garb Z, Ota M, Allain V, Hernandez R, Layeghi M, Xing G, Goudy L, Dorovskyi D, Wang C, Chen YY, Ye CJ, Shy BR, Gilbert LA, Eyquem J, Pritchard JK, Dodgson SE, Marson A. PMID: 38093011; PMCID: PMC11065414.
      View in: PubMed   Mentions: 55     Fields:    Translation:HumansCells
    18. Peptide-mediated delivery of CRISPR enzymes for the efficient editing of primary human lymphocytes. Nat Biomed Eng. 2023 05; 7(5):647-660. Foss DV, Muldoon JJ, Nguyen DN, Carr D, Sahu SU, Hunsinger JM, Wyman SK, Krishnappa N, Mendonsa R, Schanzer EV, Shy BR, Vykunta VS, Allain V, Li Z, Marson A, Eyquem J, Wilson RC. PMID: 37147433; PMCID: PMC10129304.
      View in: PubMed   Mentions: 67     Fields:    Translation:HumansAnimalsCells
    19. Dynamic phosphatase-recruitment controls B-cell selection and oncogenic signaling. bioRxiv. 2023 Mar 15. Lee J, Robinson ME, Sun R, Kume K, Ma N, Cosgun KN, Chan LN, Leveille E, Geng H, Vykunta VS, Shy BR, Marson A, Katz S, Chen J, Paietta E, Meffre E, Vaidehi N, Müschen M. PMID: 36993276; PMCID: PMC10054997.
      View in: PubMed   Mentions:
    20. Pooled screening of CAR T cells identifies diverse immune signaling domains for next-generation immunotherapies. Sci Transl Med. 2022 11 09; 14(670):eabm1463. Goodman DB, Azimi CS, Kearns K, Talbot A, Garakani K, Garcia J, Patel N, Hwang B, Lee D, Park E, Vykunta VS, Shy BR, Ye CJ, Eyquem J, Marson A, Bluestone JA, Roybal KT. PMID: 36350984; PMCID: PMC9939256.
      View in: PubMed   Mentions: 43     Fields:    Translation:HumansCells
    21. High-yield genome engineering in primary cells using a hybrid ssDNA repair template and small-molecule cocktails. Nat Biotechnol. 2023 04; 41(4):521-531. Shy BR, Vykunta VS, Ha A, Talbot A, Roth TL, Nguyen DN, Pfeifer WG, Chen YY, Blaeschke F, Shifrut E, Vedova S, Mamedov MR, Chung JJ, Li H, Yu R, Wu D, Wolf J, Martin TG, Castro CE, Ye L, Esensten JH, Eyquem J, Marson A. PMID: 36008610; PMCID: PMC10065198.
      View in: PubMed   Mentions: 108     Fields:    Translation:HumansCells
    22. Proceedings from the Blood and Marrow Transplant Clinical Trials Network Myeloma Intergroup Workshop on Immune and Cellular Therapy in Multiple Myeloma. Transplant Cell Ther. 2022 08; 28(8):446-454. Holstein SA, Asimakopoulos F, Azab AK, Bianchi G, Bhutani M, Crews LA, Cupedo T, Giles H, Gooding S, Hillengass J, John L, Kaiser S, Lee L, Maclachlan K, Pasquini MC, Pichiorri F, Shah N, Shokeen M, Shy BR, Smith EL, Verona R, Usmani SZ, McCarthy PL. PMID: 35605882; PMCID: PMC9357156.
      View in: PubMed   Mentions:    Fields:    Translation:Humans
    23. CRISPR-Cas9-mediated nuclear transport and genomic integration of nanostructured genes in human primary cells. Nucleic Acids Res. 2022 02 22; 50(3):1256-1268. Lin-Shiao E, Pfeifer WG, Shy BR, Saffari Doost M, Chen E, Vykunta VS, Hamilton JR, Stahl EC, Lopez DM, Sandoval Espinoza CR, Deyanov AE, Lew RJ, Poirer MG, Marson A, Castro CE, Doudna JA. PMID: 35104875; PMCID: PMC8860605.
      View in: PubMed   Mentions: 39     Fields:    Translation:Humans
    24. Polyclonal Regulatory T Cell Manufacturing Under cGMP: A Decade of Experience. Front Immunol. 2021; 12:744763. Balcerek J, Shy BR, Putnam AL, Masiello LM, Lares A, Dekovic F, Acevedo L, Lee MR, Nguyen V, Liu W, Paruthiyil S, Xu J, Leinbach AS, Bluestone JA, Tang Q, Esensten JH. PMID: 34867967; PMCID: PMC8636860.
      View in: PubMed   Mentions: 17     Fields:    Translation:HumansCellsPHPublic Health
    25. Targeted delivery of CRISPR-Cas9 and transgenes enables complex immune cell engineering. Cell Rep. 2021 06 01; 35(9):109207. Hamilton JR, Tsuchida CA, Nguyen DN, Shy BR, McGarrigle ER, Sandoval Espinoza CR, Carr D, Blaeschke F, Marson A, Doudna JA. PMID: 34077734; PMCID: PMC8236216.
      View in: PubMed   Mentions: 114     Fields:    Translation:HumansCells
    26. Hospital-Based Donor Recruitment and Predonation Serologic Testing for COVID-19 Convalescent Plasma. Am J Clin Pathol. 2021 Mar 15; 155(4):515-521. Balcerek J, Trejo E, Levine K, Couey P, Kornberg ZV, Rogine C, Young C, Li PJ, Shy BR, Taylor JE, Bakhtary S, Friedlander T, Lynch KL, Bern C, Esensten JH. PMID: 33399201; PMCID: PMC7929413.
      View in: PubMed   Mentions:    Fields:    Translation:Humans
    27. Magnitude and Kinetics of Anti-Severe Acute Respiratory Syndrome Coronavirus 2 Antibody Responses and Their Relationship to Disease Severity. Clin Infect Dis. 2021 01 27; 72(2):301-308. Lynch KL, Whitman JD, Lacanienta NP, Beckerdite EW, Kastner SA, Shy BR, Goldgof GM, Levine AG, Bapat SP, Stramer SL, Esensten JH, Hightower AW, Bern C, Wu AHB. PMID: 33501951; PMCID: PMC7454426.
      View in: PubMed   Mentions: 143     Fields:    Translation:HumansCells
    28. SARS-CoV-2 seroprevalence and neutralizing activity in donor and patient blood. Nat Commun. 2020 09 17; 11(1):4698. Ng DL, Goldgof GM, Shy BR, Levine AG, Balcerek J, Bapat SP, Prostko J, Rodgers M, Coller K, Pearce S, Franz S, Du L, Stone M, Pillai SK, Sotomayor-Gonzalez A, Servellita V, Martin CSS, Granados A, Glasner DR, Han LM, Truong K, Akagi N, Nguyen DN, Neumann NM, Qazi D, Hsu E, Gu W, Santos YA, Custer B, Green V, Williamson P, Hills NK, Lu CM, Whitman JD, Stramer SL, Wang C, Reyes K, Hakim JMC, Sujishi K, Alazzeh F, Pham L, Thornborrow E, Oon CY, Miller S, Kurtz T, Simmons G, Hackett J, Busch MP, Chiu CY. PMID: 32943630; PMCID: PMC7499171.
      View in: PubMed   Mentions: 130     Fields:    Translation:HumansCellsPHPublic Health
    29. Evaluation of SARS-CoV-2 serology assays reveals a range of test performance. Nat Biotechnol. 2020 10; 38(10):1174-1183. Whitman JD, Hiatt J, Mowery CT, Shy BR, Yu R, Yamamoto TN, Rathore U, Goldgof GM, Whitty C, Woo JM, Gallman AE, Miller TE, Levine AG, Nguyen DN, Bapat SP, Balcerek J, Bylsma SA, Lyons AM, Li S, Wong AW, Gillis-Buck EM, Steinhart ZB, Lee Y, Apathy R, Lipke MJ, Smith JA, Zheng T, Boothby IC, Isaza E, Chan J, Acenas DD, Lee J, Macrae TA, Kyaw TS, Wu D, Ng DL, Gu W, York VA, Eskandarian HA, Callaway PC, Warrier L, Moreno ME, Levan J, Torres L, Farrington LA, Loudermilk RP, Koshal K, Zorn KC, Garcia-Beltran WF, Yang D, Astudillo MG, Bernstein BE, Gelfand JA, Ryan ET, Charles RC, Iafrate AJ, Lennerz JK, Miller S, Chiu CY, Stramer SL, Wilson MR, Manglik A, Ye CJ, Krogan NJ, Anderson MS, Cyster JG, Ernst JD, Wu AHB, Lynch KL, Bern C, Hsu PD, Marson A. PMID: 32855547; PMCID: PMC7740072.
      View in: PubMed   Mentions: 157     Fields:    Translation:HumansCellsPHPublic Health
    30. Magnitude and kinetics of anti-SARS-CoV-2 antibody responses and their relationship to disease severity. Clin Infect Dis. 2020 Jul 14. Lynch KL, Whitman JD, Lacanienta NP, Beckerdite EW, Kastner SA, Shy BR, Goldgof GM, Levine AG, Bapat SP, Stramer SL, Esensten JH, Hightower AW, Bern C, Wu AHB. PMID: 32663256; PMCID: PMC7454426.
      View in: PubMed   Mentions:    Fields:    
    31. SARS-CoV-2 seroprevalence and neutralizing activity in donor and patient blood from the San Francisco Bay Area. medRxiv. 2020 May 25. Ng DL, Goldgof GM, Shy BR, Levine AG, Balcerek J, Bapat SP, Prostko J, Rodgers M, Coller K, Pearce S, Franz S, Du L, Stone M, Pillai SK, Sotomayor-Gonzalez A, Servellita V, Martin CSS, Granados A, Glasner DR, Han LM, Truong K, Akagi N, Nguyen DN, Neumann NM, Qazi D, Hsu E, Gu W, Santos YA, Custer B, Green V, Williamson P, Hills NK, Lu CM, Whitman JD, Stramer S, Wang C, Reyes K, Hakim JMC, Sujishi K, Alazzeh F, Pham L, Oon CY, Miller S, Kurtz T, Hackett J, Simmons G, Busch MP, Chiu CY. PMID: 32511477; PMCID: PMC7273245.
      View in: PubMed   Mentions:
    32. Test performance evaluation of SARS-CoV-2 serological assays. medRxiv. 2020 May 17. Whitman JD, Hiatt J, Mowery CT, Shy BR, Yu R, Yamamoto TN, Rathore U, Goldgof GM, Whitty C, Woo JM, Gallman AE, Miller TE, Levine AG, Nguyen DN, Bapat SP, Balcerek J, Bylsma SA, Lyons AM, Li S, Wong AW, Gillis-Buck EM, Steinhart ZB, Lee Y, Apathy R, Lipke MJ, Smith JA, Zheng T, Boothby IC, Isaza E, Chan J, Acenas DD, Lee J, Macrae TA, Kyaw TS, Wu D, Ng DL, Gu W, York VA, Eskandarian HA, Callaway PC, Warrier L, Moreno ME, Levan J, Torres L, Farrington LA, Loudermilk R, Koshal K, Zorn KC, Garcia-Beltran WF, Yang D, Astudillo MG, Bernstein BE, Gelfand JA, Ryan ET, Charles RC, Iafrate AJ, Lennerz JK, Miller S, Chiu CY, Stramer SL, Wilson MR, Manglik A, Ye CJ, Krogan NJ, Anderson MS, Cyster JG, Ernst JD, Wu AHB, Lynch KL, Bern C, Hsu PD, Marson A. PMID: 32511497; PMCID: PMC7273265.
      View in: PubMed   Mentions: 12  
    33. Co-incident insertion enables high efficiency genome engineering in mouse embryonic stem cells. Nucleic Acids Res. 2016 09 19; 44(16):7997-8010. Shy BR, MacDougall MS, Clarke R, Merrill BJ. PMID: 27484482; PMCID: PMC5027516.
      View in: PubMed   Mentions: 36     Fields:    Translation:AnimalsCells
    34. Regulation of Tcf7l1 DNA binding and protein stability as principal mechanisms of Wnt/β-catenin signaling. Cell Rep. 2013 Jul 11; 4(1):1-9. Shy BR, Wu CI, Khramtsova GF, Zhang JY, Olopade OI, Goss KH, Merrill BJ. PMID: 23810553; PMCID: PMC3759994.
      View in: PubMed   Mentions: 67     Fields:    Translation:HumansAnimalsCells
    35. MpzR98C arrests Schwann cell development in a mouse model of early-onset Charcot-Marie-Tooth disease type 1B. Brain. 2012 Jul; 135(Pt 7):2032-47. Saporta MA, Shy BR, Patzko A, Bai Y, Pennuto M, Ferri C, Tinelli E, Saveri P, Kirschner D, Crowther M, Southwood C, Wu X, Gow A, Feltri ML, Wrabetz L, Shy ME. PMID: 22689911; PMCID: PMC3381724.
      View in: PubMed   Mentions: 43     Fields:    Translation:AnimalsCells
    36. Function of Wnt/β-catenin in counteracting Tcf3 repression through the Tcf3-β-catenin interaction. Development. 2012 Jun; 139(12):2118-29. Wu CI, Hoffman JA, Shy BR, Ford EM, Fuchs E, Nguyen H, Merrill BJ. PMID: 22573616; PMCID: PMC3357906.
      View in: PubMed   Mentions: 66     Fields:    Translation:AnimalsCells
    37. Opposing effects of Tcf3 and Tcf1 control Wnt stimulation of embryonic stem cell self-renewal. Nat Cell Biol. 2011 Jun 19; 13(7):762-70. Yi F, Pereira L, Hoffman JA, Shy BR, Yuen CM, Liu DR, Merrill BJ. PMID: 21685894; PMCID: PMC3129424.
      View in: PubMed   Mentions: 180     Fields:    Translation:AnimalsCells
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