Jeffery F. Miller, Ph.D.


(310) 206-7926


Director, California NanoSystems Institute
Fred Kavli Chair, NanoSystems Sciences
M. Philip Davis Chair, Microbiology, Immunology & Molecular Genetics
Associate Director, Pacific Southwest Regional Center of Excellence in Biodefense and Emerging Infectious Diseases

Professor, Microbiology, Immunology & Molecular GeneticsMember, CTSI, California NanoSystems Institute, Gene Regulation GPB Home Area, Genetics & Genomics GPB Home Area, Immunity, Microbes & Molecular Pathogenesis GPB Home Area


Research Interests
Our laboratory studies molecular mechanisms of bacterial pathogenesis and the evolution of functional diversity in bacteria and bacteriophage. Multidisciplinary approaches are applied to a variety of interests including: i) biochemical and genetic studies of signal transduction networks that regulate the infectious cycles of Bordetella pertussis, which causes whooping cough, and Burkholderia pseudomallei, which causes life threatening systemic diseases, ii) alterations in host cell signaling pathways by Bordetella and Burkholderia, iv) biofilm formation and the hyper-colonization phenotype of Staphylococcus epidermiditis, and v) microevolutionary adaptation by diversity-generating retroelements, which function to introduce vast amounts of diversity in bacterial target proteins. Our research group includes graduate students, postdoctoral fellows and physician-scientists with expertise in computational biology and modeling, bacterial genomics, bacterial physiology, cell biology, neonatology, and infectious diseases. Numerous former trainees hold tenured or tenure-track academic positions at research universities. Since joining UCLA in 1990, we have received continuous funding from the NIH, as well as support from the American Cancer Society, the US Department of Agriculture, the Pew Foundation, and the Defense Threat Reduction Agency of the Department of Defense.

Jeff F. Miller, Ph.D., studies molecular mechanisms of bacterial pathogenesis and the evolution of functional diversity in bacteria and phage. He received his bachelor’s degree in Chemistry from Case Western Reserve University and his Ph.D. in Molecular Biology from Tufts Univ. School of Medicine. After postdoctoral training with Dr. Stanley Falkow at Stanford, he joined the faculty at UCLA in 1990. From 2002-2014 he held the M. Philip Davis Chair in Microbiology and Immunology and served as Chairman of the Department of Microbiology, Immunology and Molecular Genetics. In November, 2014, he was appointed as the Fred Kavli Endowed Chair in NanoSystems Sciences and Director of the California NanoSystems Institute at UCLA. In 2004, Dr. Miller co-founded AvidBiotics Corp., a biotherapeutics company in South San Francisco. In 2009 he was appointed by the Secretary of Health and Human Services to serve on the National Science Advisory Board for Biosecurity and he is a voting member of the Board. From 2008-2010 he was Chair of the General Meeting of the American Society for Microbiology (ASM), and from 2012-2014 he served as President of ASM, which represents 40,000 members in the US and abroad. Dr. Miller is a former Pew Scholar in the Biomedical Sciences, a member of the American Academy of Microbiology, a fellow of the American Association for the Advancement of Science, and in April, 2015 he was elected to membership in the National Academy of Sciences.

Arambula, D., Wong, W., Medhekar, B., Guo, H., Gingery, M., Czornyj, E., Liu M., Dey, S., Ghosh, P., Miller, J.F. Surface display of a massively variable lipoprotein by a Legionella diversity-generating retroelement. Proc. Natl. Acad. Sci. 2013; (110): 8212-8217.
Alayyoui, M., Guo, H., Dey, S., Golnazarian, T., Brooks, G., Rong, A., Miller, J.F., Ghosh, P. Structure of the essential diversit-generating retroelement protein Avd and its functional interaction with reverse transcriptase. Structure 2013; (21): 266-276.
Miller, J. F. Gaming the competition in microbial cell-cell interactions. The EMBO journal. 2013; 32(6): 778-80.
Fitz-Gibbon, S., Tomida, S., Chiu, B., Nguyen, L., Du, C., Liu, M., Elashoff, D., Erfe, M. C., Loncaric, A., Kim, J., Modlin, R., Miller, J.F., Sodergren, E., Craft, N., Weinstock G., Li H. Propionibacterium acnes Strain Populations in the Human Skin Microbiome Associated with Acne. The Journal of investigative dermatology. 2013; 53(2): .
Ahuja, U., Liu, M., Tomida, S., Park, J., Souda, P., Whitelegge, J., Li, H., Harvill, E.T., Parkhill, J., Miller, J.F. Phenotypic and genomic analysis of hypervirulent human-associated Bordetella bronchiseptica. BMC microbiology. 2012; 12(5): 167.
Weaver Westbrook M, Milisavljevic Vladana, Miller Jeff F, Di Carlo Dino Fluid flow induces biofilm formation in Staphylococcus epidermidis polysaccharide intracellular adhesin-positive clinical isolates. Applied and environmental microbiology. 2012; 78(16): 5890-6.
Marinelli, L.J., Fitz-Gibbon, S., Hayes, C., Bowman, C., Inkeles, M., Loncaric, A., Russell, D.A., Jacobs-Sera, D., Cokus, S., Pellegrini, M., Kim, J., Miller, J.F., Hatfull, G.F., Modlin, R.L. Propionibacterium acnes bacteriophages display limited genetic diversity and broad killing activity against bacterial skin isolates.mBio. 2012; 3(5): .
Guo Huatao, Tse Longping V, Nieh Angela W, Czornyj Elizabeth, Williams Steven, Oukil Sabrina, Liu Vincent B, Miller Jeff F Target site recognition by a diversity-generating retroelement. PLoS genetics. 2011; 7(12): e1002414.
French, C.T., Toesca, I.J., Wu, T., Teslaa, T., Beaty, S., Wong, W., Liu, M., Schroeder, I., Chiou, P., Teitell, M., Miller, J.F. Dissection of the Burkholderia intracellular life cycle using a photothermal nanoblade. Proc. Natl. Acad. Sci. 2011; 108(29): 12095-100.
Guo H., Tse, L.V., Nieh, A.W., Czornyj, E., Williams, S., Oukil, S., Liu, V.B. & Miller, J.F. Target site recognition by a diversity-generating retroelement. PLoS Genetics 2011; (7): e1002414.
Dai W, Hodes A, Hui WH, Gingery M, Miller JF, Zhou ZH. Three-dimensional structure of tropism-switching Bordetella bacteriophage. Proc Natl Acad Sci USA. 2010; 107(9): 4347-52.
Medhekar, B., Shrivastava, R., Mattoo, S., Gingery, M.A. & Miller, J.F. Bordetella Bsp22 forms a filamentous type III secretion system tip complex and is immunoprotective in vitro and in vivo. Molecular Microbiology. 2009; 71(2): 492-504.
French CT, Panina EM, Yeh SH, Griffith N, Arambula DG, Miller JF. The Bordetella type III secretion system effector BteA contains a conserved N-terminal motif that guides bacterial virulence factors to lipid rafts. Cell Microbiol. 2009; 11(12): 1735-49.
French Christopher T, Panina Ekaterina M, Yeh Sylvia H, Griffith Natasha, Arambula Diego G, Miller Jeff F The Bordetella type III secretion system effector BteA contains a conserved N-terminal motif that guides bacterial virulence factors to lipid rafts. Cellular microbiology. 2009; 11(12): 1735-49.
Liu Scot D, Tomassian Tamar, Bruhn Kevin W, Miller Jeff F, Poirier Françoise, Miceli M Carrie Galectin-1 tunes TCR binding and signal transduction to regulate CD8 burst size. Journal of immunology (Baltimore, Md. : 1950). 2009; 182(9): 5283-95.
Shrivastava Ruchi, Miller Jeff F Virulence factor secretion and translocation by Bordetella species. Current opinion in microbiology. 2009; 12(1): 88-93.
Medhekar Bob, Shrivastava Ruchi, Mattoo Seema, Gingery Mari, Miller Jeff F Bordetella Bsp22 forms a filamentous type III secretion system tip complex and is immunoprotective in vitro and in vivo. Molecular microbiology. 2009; 71(2): 492-504.
Ruchi Shrivastava1 and Jeff F Miller Virulence factor secretion and translocation by Bordetella species . Current Opinion in Microbiology. 2009; 12(1): 88-93 .
Guo Huatao, Tse Longping V, Barbalat Roman, Sivaamnuaiphorn Sameer, Xu Min, Doulatov Sergei, Miller Jeff F Diversity-generating retroelement homing regenerates target sequences for repeated rounds of codon rewriting and protein diversification. Molecular cell. 2008; 31(6): 813-23.
Guo, H., Tse, V., Barbalet, R., Sivaamnuaiphorn, S., Xu, M., Sergei Doulatov & Miller, J.F. Diversity-Generating Retroelement Homing Regenerates Target Sequences for Repeated Rounds of Codon Rewriting and Protein Diversification. Molecular Cell. 2008; 31(6): 813-823.
Miller J.L., Le Coq, J., Hodes, A., Barbalat, R., Miller, J.F. & P. Ghosh Selective ligand recognition by a diversity-generating retroelement variable protein. PLoS Biology. 2008; 6(6): 1195-1207.
Medhekar, B. and J.F. Miller Diversity-generating retroelements. Current Opinion in Microbiology. 2007; 10(4): 388-395.
Bruhn, K.W., Craft, N. & J.F. Miller Listeria monocytogenes as a vaccine vector. Microbes and Infection 2007; 9(10): 1226-35.
Cummings, C.A., Bootsma, H.J., Relman, D.A. & J.F. Miller. Species- and strain-specific control of a complex, flexible regulon by Bordetella BvgAS. J. Bacteriology . 2006; 188(5): 1775-1785.
Chang, C. and J.F. Miller Campylobacter jejuni Colonization of Mice with Limited Enteric Flora . Infection and Immunity. 2006; 74(9): 5261-5271.
Prins, R.M., Craft, N., Bruhn, K.W., Khan-Farooqi, H., Koya, R.C., Stripecke, R., Miller, J.F. & L.M. Liau. The TLR-7 agonist, imiquimod, enhances dendritic cell survival and promotes tumor antigen-specific T cell priming: relation to central nervous system antitumor immunity. J. Immunology. 2006; 176: 157-164.
McMahon, SA Miller, JL Lawton, JA Kerkow, DE Hodes, A Marti-Renom, MA Doulatov, S Narayanan, E Sali, A Miller, JF Ghosh, P The C-type lectin fold as an evolutionary solution for massive sequence variation. Nature structural & molecular biology. . 2005; 12(10): 886-92.
Panina, EM Mattoo, S Griffith, N Kozak, NA Yuk, MH Miller, JF A genome-wide screen identifies a Bordetella type III secretion effector and candidate effectors in other species. Molecular microbiology. . 2005; 58(1): 267-79.
Kozak, NA Mattoo, S Foreman-Wykert, AK Whitelegge, JP Miller, JF Interactions between partner switcher orthologs BtrW and BtrV regulate type III secretion in Bordetella. Journal of bacteriology. . 2005; 187(16): 5665-76.
Foreman-Wykert, A.K., & J.F. Miller A new animal model of Bordetella pertussis infection and immunity. Trends in Microbiology. 2005; 13(12): 559-560.
Craft, N Bruhn, KW Nguyen, BD Prins, R Lin, JW Liau, LM Miller, JF The TLR7 agonist imiquimod enhances the anti-melanoma effects of a recombinant Listeria monocytogenes vaccine. Journal of immunology (Baltimore, Md. : 1950) . 2005; 175(3): 1983-90.
Bruhn, K.W., Craft N., Nguyen B.D., Yip J. & Miller J.F. Characterization of anti-self CD8 T-cell responses stimulated by recombinant Listeria monocytogenes expressing the melanoma antigen TRP-2. Vaccine . 2005; 23(33): 4263-4272.
Doulatov, S., Hodes, A., Dai, L., Mandhana, N., Liu, M., Deora, R., Simons, R.W., Zimmerly, S. & J.F. Miller Tropism switching in Bordetella bacteriophage defines a family of diversity-generating retroelements. Nature. 2004; 431: 476-481.
Joseph SB, Bradley MN, Castrillo A, Bruhn KW, Mak PA, Pei L, Hogenesch J, O’connell RM, Cheng G, Saez E, Miller JF, Tontonoz P LXR-dependent gene expression is important for macrophage survival and the innate immune response. Cell. 2004; 119(2): 299-309.
MacKichan JK, Gaynor EC, Chang C, Cawthraw S, Newell DG, Miller JF and S Falkow The Campylobacter jejuni dccRS two-component system is required for optimal in vivo colonization but is dispensable for in vitro growth. Molecular Microbiology. 2004; 54(5): 1269-1286.
Starks, H., Bruhn, K.W., Shen, H., Barry, R.A., Dubensky, T., Hinrichs, D.J., Higgins, D.E., Miller, J.F., Giedlin, M., & H.G. Bouwer Listeria monocytogenes as a vaccine vector: virulence attenuation or existing antivector immunity does not diminish therapeutic efficacy. Journal of Immunology. 2004; 173(1): 420-427.
O’Connell, RM Saha, SK Vaidya, SA Bruhn, KW Miranda, GA Zarnegar, B Perry, AK Nguyen, BO Lane, TF Taniguchi, T Miller, JF Cheng, G Type I interferon production enhances susceptibility to Listeria monocytogenes infection. The Journal of experimental medicine. . 2004; 200(4): 437-45.
Mattoo, S Yuk, MH Huang, LL Miller, JF Regulation of type III secretion in Bordetella. Molecular microbiology. . 2004; 52(4): 1201-14.
Stockbauer, KE Foreman-Wykert, AK Miller, JF Bordetella type III secretion induces caspase 1-independent necrosis. Cellular microbiology. . 2003; 5(2): 123-32.
Miller, JF Bacteriophage and the evolution of epidemic cholera. Infection and immunity. . 2003; 71(6): 2981-2.
Foreman-Wykert, A.K. and J.F. Miller Hypervirulence and Pathogen Fitness. Trends in Microbiology. 2003; 11(3): 105-108.
Liu, M., Deora, R., Doulatov, S.R., Gingery, M., Eiserling, F.A., Preston, A., Simons, R.W., Cotter, P.A., Parkhill, J. & J.F. Miller Reverse Transcriptase-Mediated Tropism Switching in Bordetella Bacteriophage . Science. 2002; 295: 2091-2094.
Chin, AI Dempsey, PW Bruhn, K Miller, JF Xu, Y Cheng, G Involvement of receptor-interacting protein 2 in innate and adaptive immune responses. Nature. 2002; 416(6877): 190-4.