Jeff F. Miller, Ph.D.

Work Titles
California NanoSystems Institute Director, California NanoSystems Institute Fred Kavli Chair, NanoSystems Sciences Member, California NanoSystems Institute
UCI Associate Director, Pacific Southwest Regional Center of Excellence in Biodefense and Emerging Infectious Diseases
UCLA M. Philip Davis Chair, Professor, Microbiology, Immunology & Molecular Genetics Member, Gene Regulation GPB Home Area Member, Immunity, Microbes & Molecular Pathogenesis GPB Home Area
Ph.D., Tufts University School of Medicine, 1986
B.A., Case Western Reserve University, 1980
2003 Fellow, American Academy of Microbiology
1986 - 1990 Stanford University School of Medicine, Postdoctoral Fellow

Contact Information:

Work Email Address:

Fax Number:

(310) 206-5668

Lab Number:

(310) 206-9053

Office Phone Number:

(310) 206-7926

Work Phone Number:

(310) 206-0240

Office Address:

615 Charles E. Young Drive South
Mail Code: 174718
Los Angeles, CA 90095

Research Interest:

Molecular Mechanisms of Bacterial Virulence

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.

Detailed Biography:

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.


A selected list of publications:

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.
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.
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): .
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): .
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.
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.
Ting-Hsiang Wu, Tara Teslaa, Sheraz Kalim, Christopher T. French, Shahriar Moghadam, Randolph Wall, Jeffery F. Miller, Owen N. Witte, Michael A. Teitell, and Pei-Yu Chiou   Photothermal Nanoblade for Large Cargo Delivery into Mammalian Cells Anal. Chem, 2011; 83(4): 1321-7.
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.
Ruchi Shrivastava1 and Jeff F Miller   Virulence factor secretion and translocation by Bordetella species Current Opinion in Microbiology, 2009; 12(1): 88-93 .
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.
Bruhn, K.W., Craft, N. & J.F. Miller   Listeria monocytogenes as a vaccine vector, Microbes and Infection, 2007; 9(10): 1226-35.
Medhekar, B. and J.F. Miller   Diversity-generating retroelements Current Opinion in Microbiology, 2007; 10(4): 388-395.
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., Bruhn, K.W., Craft, N., Lin, J.W., Kim, C.H., Odesa, S.K., Miller, J.F. & L.M. Liau.   Central nervous system tumor immunity generated by a recombinant listeria monocytogenes vaccine targeting tyrosinase related protein-2 and real-time imaging of intracranial tumor burden Neurosurgery , 2006; 58(1): 169-178.
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.
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.
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.
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.
Vergara-Irigaray, N., Chavarri-Martinez, A., Rodriguez-Cuesta, J., Miller, J.F., Cotter, P.A. & G. Martinez de Tejada   Evaluation of the role of the Bvg intermediate phase in Bordetella pertussis during experimental respiratory infection Infect Immun, 2005; 73: 748-60.
Liu, M., Gingery, M., Doulatov, S.R., Liu, Y., Hodes, A., Baker, S., Davis, P., Simmonds, M., Churcher, C., Mungall, K., Quail, M.A., Preston, A., Harvill, E.T., Maskell, D.J., Eiserling, F.A., Parkhill, J., & J.F. Miller   Genomic and genetic analysis of Bordetella bacteriophages encoding reverse transcriptase-mediated tropism-switching cassettes J. Bacteriology, 2004; 186(5): 1503-1517.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
Miller, JF   Bacteriophage and the evolution of epidemic cholera Infection and immunity. , 2003; 71(6): 2981-2.
Stockbauer, KE Foreman-Wykert, AK Miller, JF   Bordetella type III secretion induces caspase 1-independent necrosis Cellular microbiology. , 2003; 5(2): 123-32.
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.

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