1. Wroblewska A*, Dhainaut M*, Ben-Zvi B, Rose SA, Park ES, Amir ED, Bektesevic A, Baccarini A, Merad M, Rahman AH, Brown BD. Protein barcodes enable high-dimensional single-cell CRISPR screens. Cell. In Press.

  2. Agudo J, Park ES, Rose SA, Alibo E, Sweeney R, Dhainaut M, Kobayashi KS, Sachidanandam R, Baccarini A, Merad M, Brown BD. Quiescent tissue stem cells evade immune surveillance. Immunity. 2018 Feb 20; 48(2): 271-285.e5

  3. Jeong D, Yoo J, Lee P, Kepreotis S, Lee A, Whalquist C, Brown B, Kho C, Mercola M, Hajjar R. miR-25 Tough Decoy enhances cardiac function in heart failure. Molecular Therapy. 2017 Nov 26. pii:S1525-0016(17)30573- 7.

  4. Jobson J, Brown BD. Micromanaging tolerance in hemophilia A gene therapy. Molecular Therapy. 2017 Jun 15. pii: S1525-0016(17)30261- 7.

  5. Chia G, Agudo J, Treff N, Sauer MV, Billing D, Brown BD, Baer R, Egli D. Genomic instability during reprogramming by nuclear transfer is DNA replication dependent. Nature Cell Biology. 2017 Apr;19(4):282-291

  6. Chung CY, Sun Z, Mullokandov G, Bosch A, Qadeer ZA, Cihan E, Rapp Z, Parson, R, Aguirre-Ghiso JA, Farias EF, Brown BD, Gaspar-Maia A, Bernstein E. Cbx8 Acts Non-canonically with Wdr5 to Promote Mammary Tumorigenesis. Cell Reports. 2016 Jul 12;16(2):472-86.

  7. Dwyer DF, Barrett NA, Austen KF; Immunological Genome Project Consortium. Expression profiling of constitutive mast cells reveals a unique identity within the immune system. Nature Immunology. 2016 Jul;17(7):878-87.

  8. Salmon H, Idoyaga J, Rahman A, Leboeuf M, Remark R, Jordan S, Casanova-Acebes M, Khudoynazarova M, Agudo J, Tung N, Chakarov S, Rivera C, Hogstad B, Bosenberg M, Hashimoto D, Gnjatic S, Bhardwaj N, Palucka AK, Brown BD, Brody J, Ginhoux F, Merad M. Expansion and Activation of CD103+ Dendritic Cell Progenitors at the Tumor Site Enhances Tumor Responses to Therapeutic PD-L1 and BRAF Inhibition. Immunity. 2016 Apr 19;44(4):924-938.

  9. Agudo J, Brown BD. Silence of the ROS. Immunity. 2016 Mar 15;44(3):520-2.

  10. Kidd BA*, Wroblewska A*, Boland MR, Agudo J, Merad M, Tatonetti NP, Brown BD^, Dudley JT. Mapping the effects of drugs on the immune system. Nature Biotechnology. 2016 Jan;34(1):47-54. ^Co-corresponding author.

  11. Brown BD, Merad M. Archives and citation miss equal authors. Nature. 2015 Dec. 16;528(7582):333.

  12. Agudo JA, Ruzo A, Park E, Sweeney R, Kana V, Wu M, Zhao Y, Egli D, Merad M, Brown BD. GFP- specific T cells enable targeted cell depletion and visualization of T-cell interactions. Nature Biotechnology. 2015 Dec;33(12):1287-1292. 

  13. Andikyan V, Mullokandov G, Agudo J, Sachidanandam R, Fishman D, Bacccarini A, Brown BD. MicroRNA activity profile in the ovarian cancer cell line OVCAR3 identifies a proapoptotic effect of miR-23a. Advances in Genomics and Genetics. 2015:5 355-364.

  14. Mulero-Navarro S, Sevilla A, Roman AC, Lee DF, D’Souza S, Pardo S, Riess I, Su J, Cohen N, Schaniel C, Rodriguez NA, Baccarini A, Brown BD, Cavé H, Caye A, Strullu M, Park CY, Yalcin A, Dhandapany PS, Yongchao G, Edelmann L, Bahieg S, Raynal P, Flex E, Tartaglia M, Moore KA, Lemischka IR, Gelb BD. Myeloid dysregulation in a human induced pluripotent stem cell model of PTPN11-associated juvenile myelomonocytic leukemia. Cell Reports. 2015 Oct 20;13(3):504-15.

  15. Upadhyay R, Hammerich L, Peng P, Brown B, Merad M, Brody JD. Lymphoma: Immune Evasion Strategies. Cancers. 2015 Apr 30;7(2):736-62.

  16. Brown BD. A shot in the bone corrects genetic disease. Molecular Therapy. 2015 Apr;23(4):614-5.

  17. Robinette ML, Fuchs A, Cortez VS, Lee JS, Wang Y, Durum SK, Gilfillan S, Colonna M; the Immunological Genome Consortium. Transcriptional programs define molecular characteristics of innate lymphoid cell classes and subsets. Nature Immunology. 2015 Mar;16(3):306-17.

  18. Hanniford D, Segura M, Jirau-Serrano X, Darvishian F, Berman R, Shapiro R, Pavlick A, Brown BD, Osman I, and Hernando E. Identification of metastasis-suppressive microRNAs in primary melanoma. The Journal of the National Cancer Institute. 2015 Feb 12;107(3).

  19. Israelow B*, Mullokandov G*, Agudo J, Sourisseau M, Bashir A, Brown BD^ and Evans MJ^. Hepatitis C virus genetics affects miR-122 requirements and response to miR-122 inhibitors. Nature Communications. 2014 Nov 18;5:5408. ^Co-corresponding.

  20. Mostafavi S, Ortiz-Lopez A, Bogue MA, Hattori K, Pop C, Koller D, Mathis D, Benoist C; Immunological Genome Consortium. Variation and genetic control of gene expression in primary immunocytes across inbred mouse strains. J Immunol. 2014 Nov 1;193(9):4485-96.

  21. Nair-Gupta P, Baccarini A, Tung N, Fabian F, Florey O, Huang Y, Banerjee M, Overholtzer M, Tampé R, Brown BD, Whiteheart SW, and Blander JM. TLRs Control Phagosomal MHC-I Delivery from Endosomal Recycling Compartments to Aid Crosspresentation in Dendritic Cells. Cell. Jul 31;158(3):506-21

  22. Chong RA, Wu K, Spratt DE, Yang Y, Lee C, Nayak J, Xu M, Elkholi R, Tappin I, Li J, Hurwitz J, Brown BD, Chipuk JE, Xhen ZJ, Sanchez R, Shaw GS, Huang L, Pan ZQ. A Pivotal Role for the Ubiquitin Y59-E51 Loop in Lysine-48 Polyubiquitination. Proc Natl Acad Sci U S A. 2014 Jun 10;111(23):8434-9.

  23. Agudo JA, Ruzo A, Tung N, Salmon H, Leboeuf M, Hashimoto D, Becker C, Garrett-Sinha LA, Baccarini A, Merad M, Brown BD. The microRNA-126/VEGFR2 axis controls the innate response to pathogen-associated nucleic acids. Nature Immunology. 2014 Jan;15(1):54-62.

  24. Parikh A, Lee C, Joseph P, Marchini S, Baccarini A, Kolev V, Romualdi C, Fruscio R, Shah H, Wang FQ, Mullokandov G, Fishman D, D'Incalci M, Rahaman J, Kalir T, Redline R, Brown BD, Narla G, and DiFeo A. microRNA-181a plays a critical role in ovarian cancer progression through the regulation of epithelial-mesenchymal transition. Nature Communications. 2014 Jan 7;5:2977.

  25. Ergun A, Doran G, Costello JC, Paik HH, Collins JJ, Mathis D, Benoist C; ImmGen Consortium. Differential splicing across immune system lineages. Proc Natl Acad Sci U S A. 2013 Aug 27;110(35):14324-9.

  26. Mingueneau M, Kreslavsky T, Gray D, Heng T, Cruse R, Ericson J, Bendall S, Spitzer MH, Nolan GP, Kobayashi K, von Boehmer H, Mathis D, Benoist C; Immunological Genome Consortium. The transcriptional landscape of ab T cell differentiation. Nature Immunology. 2013 Jun;14(6):619-32.

  27. Jojic V, Shay T, Sylvia K, Zuk O, Sun X, Kang J, Regev A, Koller D; Immunological Genome Project Consortium. Identification of transcriptional regulators in the mouse immune system. Nature Immunology. 2013 Jun;14(6):633-43.

  28. Malhotra N, Narayan K, Cho OH, Sylvia KE, Yin C, Melichar H, Rashighi M, Lefebvre V, Harris JE, Berg LJ, Kang J; Immunological Genome Project Consortium. A network of high-mobility group box transcription factors programs innate interleukin-17 production. Immunity. 2013 Apr 18;38(4):681-93.

  29. Best JA, Blair DA, Knell J, Yang E, Mayya V, Doedens A, Dustin ML, Goldrath AW; Immunological Genome Project Consortium. Transcriptional insights into the CD8(+) T cell response to infection and memory T cell formation. Nature Immunology. 2013 Apr;14(4):404-12.

  30. Brown BD. Stealth gene therapy. Blood. 2013 Mar 21;121(12):2168-9.

  31. Cohen NR, Brennan PJ, Shay T, Watts GF, Brigl M, Kang J, Brenner MB; ImmGen Project Consortium. Shared and distinct transcriptional programs underlie the hybrid nature of iNKT cells. Nature Immunology. 2013 Jan;14(1):90-9.

  32. Shay T, Jojic V, Zuk O, Rothamel K, Puyraimond-Zemmour D, Feng T, Wakamatsu E, Benoist C, Koller D, Regev A; the ImmGen Consortium. Conservation and divergence in the transcriptional programs of the human and mouse immune systems. Proc Natl Acad Sci U S A. 2013 Feb 19;110(8):2946-51.

  33. Agudo JA, Ruzo A, Kitur K, Sachidanandam R, Blander JM, Brown BD. A TLR and non-TLR mediated innate response to lentiviruses restricts hepatocyte entry and can be ameliorated by pharmacological blockade. Molecular Therapy. 2012 Dec;20(12):2257-67.

  34. Helft J, Manicassamy B, Guermonprez P, Hashimoto D, Silvin A, Agudo J, Brown BD, Schmolke M, Miller J, Murphy KM, García-Sastre A, Merad M. Lung CD103+ dendritic cells are resistant to influenza virus infection in vivo and promote cytotoxic T cell immunity through the crossrepresentation of virally infected cells. Journal of Clinical Investigation. 2012 Nov 1;122(11):4037-47.

  35. Gautier EL, Shay T, Miller J, Greter M, Jakubzick C, Ivanov S, Helft J, Chow A, Elpek KG, Gordonov S, Mazloom AR, Ma'ayan A, Chua WJ, Hansen TH, Turley SJ, Merad M, Randolph GJ; The Immunological Genome Project Consortium. Gene-expression profiles and transcriptional regulatory pathways that underlie the identity and diversity of mouse tissue macrophages. Nature Immunology. 2012 Nov;13(11):1118-28.

  36. Bezman NA, Kim CC, Sun JC, Min-Oo G, Hendricks DW, Kamimura Y, Best JA, Goldrath AW, Lanier LL; The Immunological Genome Project Consortium. Molecular definition of the identity and activation of natural killer cells. Nature Immunology.  2012 Oct;13(10):1000-9.

  37. Mullokandov G*, Baccarini A*, Ruzo A*, Jayaprakash AD, Tung N, Israelow B, Evans MJ, Sachidanandam R, Brown BD. High-throughput assessment of microRNA activity and function using microRNA sensor and decoy libraries. Nature Methods. 2012 Jul 1;9(8):840-6. *equal contribution.  

  38. Miller JC, Brown BD*, Shay T, Gautier EL, Jojic V, Cohain A, Pandey G, Leboeuf M, Elpek KG, Helft J, Hashimoto D, Chow A, Price J, Greter M, Bogunovic M, Bellemare-Pelletier A, Frenette PS, Randolph GJ, Turley SJ, Merad M. Deciphering the transcriptional network of the DC lineage. Nature Immunology. 2012 Sep;13(9):888-99.

  39. Greter M, Helft J, Chow A, Hashimoto D, Mortha A, Agudo-Cantero JA, Bogunovic M, Gautier EL, Miller J, Leboeuf M, Lu G, Aloman C, Brown BD, Pollard JW, Xiong H, Randolph GJ, Chipuk JE, Frenette P, Merad M. GM-CSF controls non-lymphoid tissue dendritic cell homeostasis but is dispensable for the differentiation of inflammatory dendritic cells. Immunity. 2012 Jun 29;36(6):1031-46.

  40. Narayan K, Sylvia KE, Malhotra N, Yin CC, Martens G, Vallerskog T, Kornfeld H, Xiong N, Cohen NR, Brenner MB, Berg LJ, Kang J.; The Immunological Genome Project Consortium. Intrathymic programming of effector fates in three molecularly distinct T cell subtypes.Nature Immunology. 2012 Apr 1;13(5):511-8.

  41. Malhotra D, Fletcher AL, Astarita J, Lukacs-Kornek V, Tayalia P, Gonzalez SF, Elpek KG, Chang SK, Knoblich K, Hemler ME, Brenner MB, Carroll MC, Mooney DJ, Turley SJ.; The Immunological Genome Project Consortium. Transcriptional profiling of stroma from inflamed and resting lymph nodes defines immunological hallmarks. Nature Immunology.  2012 Apr 1;13(5):499-510.

  42. Chow A, Brown BD, Merad M. Dissecting the Mononuclear Phagocytic System in the Molecular Age. Nature Reviews Immunology. 2011 Oct 25;11(11):788-98.

  43. Jayaprakash A, Jabado O, Brown BD, Sachidanandam R. Identification and remediation of biases in the activity of RNA-ligases in deep sequencing of small RNAs. Nucleic Acids Research. 2011 Nov 1;39(21):e141.

  44. Baccarini A, Chauhan H, Gardner TJ, Jayaprakash AD, Sachidanandam R, Brown BD. Kinetic analysis reveals the fate of a microRNA following target regulation in mammalian cells. Current Biology. 2011 Mar 8;21(5):369-76.

  45. Matsui H, Hegadorn C, Ozelo M, Burnett E, Tuttle A, Labelle A, McCray PB Jr, Naldini L, Brown B, Hough C, Lillicrap D. A microRNA-regulated and GP64-pseudotyped lentiviral vector mediates stable expression of FVIII in a murine model of Hemophilia A. Molecular Therapy. 2011 Apr;19(4):723-30.

  46. Rossetti M, Gregori S, Hauben E, Sergi Sergi L, Brown BD, Naldini L, Roncarolo MG. HIV-1-derived lentiviral vectors directly activate plasmacytoid dendritic cells, which in turn induce the maturation of myeloid dendritic cells. Human Gene Therapy. 2011 Feb;22(2):177-88.

  47. Baccarini A, Brown BD. Monitoring MicroRNA Activity and Validating MicroRNA Targets by Reporter-Based Approaches. Methods in Molecular Biology. 2010;667:215-33.

  48. Annoni A*, Brown BD*, Cantore A, Sergi Sergi L, Naldini L, Roncarolo MG. In vivo delivery of a microRNA regulated transgene induces antigen-specific regulatory T cells and promotes immunological tolerance. Blood 2009 Dec 10;114(25):5152-61 *equal contribution.

  49. Salerno E, Scaglione BJ, Coffman FD, Brown BD, Baccarini A, Fernandes H, Marti G, Raveche ES. Correcting miR-15a/16 genetic defect in New Zealand Black mouse model of CLL enhances drug sensitivity. Molecular Cancer Therapeutics. 2009 Sep;8(9):2684-92.

  50. Brown BD, Naldini L. Exploiting and antagonizing microRNA regulation for therapeutic and experimental applications. Nature Reviews Genetics 2009 Aug;10(8):578-85.

  51. Matsui H, Shibata M, Brown B, Labelle A, Hegadorn C, Andrews C, Chuah M, VandenDriessche T, Miao CH, Hough C, Lillicrap D. A murine model for induction of long-term immunologic tolerance to factor VIII does not require persistent detectable levels of plasma factor VIII and involves contributions from Foxp3+ T regulatory cells. Blood. 2009 Jul 16;114(3):677-85.

  52. Gentner B, Schira G, Giustacchini A, Amendola M, Brown BD, Ponzoni M, Naldini L. Stable knockdown of microRNA in vivo by lentiviral vectors. Nature Methods. 2009 Jan;6(1):63-6.

  53. Brown BD, Gentner B, Cantore A, Colleoni S, Amendola M, Zingale A, Baccarini A, Lazzari G, Galli C, Naldini L. Endogenous microRNAs Can Be Broadly Exploited to Regulate Transgene Expression According to Tissue, Lineage, and Differentiation State. Nature Biotechnology.2007 Dec;25(12):1457-1467.

  54. Brown BD, Cantore A, Annoni A, Sergi Sergi L, Lombardo A, Della Valle P, D’Angelo A, Naldini L. A microRNA-regulated Lentiviral Vector Mediates Stable Correction of Hemophilia B Mice. Blood. 2007 Dec 15;110(13):4144-52.

  55. Matsui H, Shibata M, Brown B, Labelle A, Hegadorn C, Andrews C, Hebbel RP, Galipeau J, Hough C, Lillicrap D. Ex Vivo Gene Therapy for Hemophilia A That Enhances Safe Delivery and Sustained In Vivo FVIII Expression From Lentivirally-engineered Endothelial Progenitors.Stem Cells. 2007 Oct;25(10):2660-9.

  56. Brown BD, Sitia G, Annoni A, Hauben E, Sergi Sergi L, Zingale A, Roncarolo MG, Guidotti L, Naldini L. In vivo administration of lentiviral vectors triggers a type I interferon response that restricts hepatocyte gene transfer and promotes vector clearance. Blood. 2007 April; 109(7): 2797-2805.

  57. Brown BD, Venneri MA, Zingale A, Sergi Sergi L, Naldini L. Endogenous microRNA regulation suppresses transgene expression in hematopoietic lineages and enables stable gene transfer. Nature Medicine 2006 May;12(5):585-91.

  58. Rawle FE, Shi CX, Brown B, McKinven A, Tinlin S, Graham FL, Hough C, Lillicrap D. Heterogeneity of the immune response to adenovirus-mediated factor VIII gene therapy in different inbred hemophilic mouse strains. Journal of Gene Medicine 2004 Dec;6(12):1358-68.

  59. Brown BD, Shi CX, Webster S, Graham FL, Lillicrap DP. Helper-dependent adenoviral vectors provide Factor VIII expression in the absence of inhibitor development in a canine model of hemophilia A. Blood. 2004 Feb 1;103(3):804-10.

  60. Brown BD, Grant F, Shi CX, McKinven A, Tinlin S, Graham FL, Lillicrap DP. Factors influencing therapeutic efficacy and the host immune response to helper-dependent adenoviral gene therapy in hemophilia A mice. Journal of Thrombosis and Haemostasis. 2004 Jan;2(1):111-8.

  61. Kinkley SM, Brown BD, Lyng AT, Schep GN, Lillicrap DP, Taylor SAM. Absence of overt iron overload in two individuals compound heterozygous for a 22 base pair deletion of exon 2 and the C282Y missense mutation of the Hfe gene. Clinical Genetics. 2003 Feb;63(2):163-5.

  62. Chuah MK, Schiedner G, Thorrez L, Brown B, Johnston M, Gillijns V, Hertel S, Van Rooijen N, Lillicrap D, Collen D, VandenDriessche T, Kochanek S. Therapeutic factor VIII levels and negligible toxicity in mouse and dog models of hemophilia A following gene therapy with high-capacity adenoviral vectors. Blood. 2003 Mar 1;101(5):1734-43.

  63. Brown BD and Lillicrap D. Dangerous liaisons: the role of "danger" signals in the immune response to gene therapy. Blood. 2002 Aug 15;100(4):1133-40.