Publications

• Ang Jocelyn, Song Lisa Yun, D'Souza Sara, Hong Irene L, Luhar Rohan, Yung Madeline, Miller Jeffrey H.   Mutagen Synergy: Hypermutability Generated by Specific Pairs of Base Analogs Journal of bacteriology, 2016; 198(20): 2776-83. 
• Song Lisa Yun, Goff Marisa, Davidian Christina, Mao Zhiyuan, London Marisa, Lam Karen, Yung Madeline, Miller Jeffrey H.  Mutational Consequences of Ciprofloxacin in Escherichia coli Antimicrobial agents and chemotherapy, 2016; 60(10): 6165-72. 
• Song LY, D’Souza S, Lam K, Kang TM, Yeh P, Miller JH. Exploring Synergy between Classic Mutagens and Antibiotics To Examine Mechanisms of Synergy and Antibiotic Action. Antimicrobial Agents and Chemotherapy. 2016;60(3):1515-1520. doi:10.1128/AAC.02485-15.
• Zhou A, Kang TM, Yuan J, et al. Synergistic Interactions of Vancomycin with Different Antibiotics against Escherichia coli: Trimethoprim and Nitrofurantoin Display Strong Synergies with Vancomycin against Wild-Type E. coli. Antimicrobial Agents and Chemotherapy. 2015;59(1):276-281. doi:10.1128/AAC.03502-14.
• Kang TM, Yuan J, Zhou A, Beppler C, Miller JH. Deoxycytidine Deaminase-Deficient Escherichia coli Strains Display Acute Sensitivity to Cytidine, Adenosine, and Guanosine and Increased Sensitivity to a Range of Antibiotics, Including Vancomycin. Journal of Bacteriology. 2014;196(11):1950-1957. doi:10.1128/JB.01383-13.
• Becket E, Tse L, Yung M, Cosico A, Miller JH. Polynucleotide Phosphorylase Plays an Important Role in the Generation of Spontaneous Mutations in Escherichia coli. Journal of Bacteriology. 2012;194(20):5613-5620. doi:10.1128/JB.00962-12.
• Kang TM, Yuan J, Nguyen A, Becket E, Yang H, Miller JH. The Aminoglycoside Antibiotic Kanamycin Damages DNA Bases in Escherichia coli: Caffeine Potentiates the DNA-Damaging Effects of Kanamycin while Suppressing Cell Killing by Ciprofloxacin in Escherichia coli and Bacillus anthracis. Antimicrobial Agents and Chemotherapy. 2012;56(6):3216-3223. doi:10.1128/AAC.00066-12.
• Liu A, Fong A, Becket E, et al. Selective Advantage of Resistant Strains at Trace Levels of Antibiotics: a Simple and Ultrasensitive Color Test for Detection of Antibiotics and Genotoxic Agents. Antimicrobial Agents and Chemotherapy. 2011;55(3):1204-1210. doi:10.1128/AAC.01182-10.
• Tran L, van Baarsel JA, Washburn RS, Gottesman ME, Miller JH. Single-Gene Deletion Mutants of Escherichia coli with Altered Sensitivity to Bicyclomycin, an Inhibitor of Transcription Termination Factor Rho. Journal of Bacteriology. 2011;193(9):2229-2235. doi:10.1128/JB.01463-10.
• Becket E, Chen F, Tamae C, Miller JH. Determination of Hypersensitivity to Genotoxic Agents Among Escherichia coli Single Gene Knockout Mutants. DNA repair. 2010;9(9):949-957. doi:10.1016/j.dnarep.2010.06.008.
• Liu A, Tran L, Becket E, et al. Antibiotic Sensitivity Profiles Determined with an Escherichia coli Gene Knockout Collection: Generating an Antibiotic Bar Code. Antimicrobial Agents and Chemotherapy. 2010;54(4):1393-1403. doi:10.1128/AAC.00906-09.
• Tamae C, Liu A, Kim K, et al. Determination of Antibiotic Hypersensitivity among 4,000 Single-Gene-Knockout Mutants of Escherichia coli . Journal of Bacteriology. 2008;190(17):5981-5988. doi:10.1128/JB.01982-07.
• Yang H, Miller JH. Deletion of dnaN1 generates a mutator phenotype in Bacillus anthracis. DNA repair. 2008;7(3):507-514. doi:10.1016/j.dnarep.2007.10.003.
• Zeibell K, Aguila S, Yan Shi V, Chan A, Yang H, Miller JH. Mutagenesis and Repair in Bacillus anthracis: the Effect of Mutators. Journal of Bacteriology. 2007;189(6):2331-2338. doi:10.1128/JB.01656-06.
• Gabrovsky, V., Yamamoto, L., and Miller, J. H.  2005.  Mutator effects in Escherichia coli caused by the expresison of specific foreign genes.  J. Bacteriol. 187:5044-5048.
• Hong ES, Yeung A, Funchain P, Slupska MM, Miller JH. Mutants with Temperature-Sensitive Defects in the Escherichia coli Mismatch Repair System: Sensitivity to Mispairs Generated In Vivo. Journal of Bacteriology. 2005;187(3):840-846. doi:10.1128/JB.187.3.840-846.2005.
• Miller, J. H. Perspective on mutagenesis and repair:  The standard model and alternate modes of mutagenesis.  Critical Rev. Biochem. and Molec. Biol.  (2005)40, 155-179.
• Kim, M., Wolff, E., Huang, T., Garibyan, L., Earl, A. M., Battista, J. R., and Miller, J. H. Developing a genetic system in Deinococcus radiodurans for analyzing mutations. Genetics (2004) 166, 661-668.
• Xie, Y., Yang, H., Cunanan, C., Okamoto, K., Shibata, D., Pan, J., Barnes, D. E., Lindahl, T., McIlhatton, M., Fishel, R., and Miller, J. H. Deficiencies in mouse Myh and Ogg1 result in tumor predisposition and G to T mutations in codon 12 of the K-ras oncogene in lung tumors. Cancer Res. (2004) 64, 3096-3102.
• Yang, H., Wolff, E., Kim, M., Diep, A., and Miller, J. H. Identification of mutator genes and mutation pathways in Escherichia coli using a multicopy cloning approach. Molec. Microbiol. (2004) 53, 283-295.
• Garibyan, L., Huang, T., Kim, M., Wolff, E., Nguyen, A., Nguyen, T., Diep, A., Hu, K., Iverson, A., Yang, H., and Miller, J.H. Use of the rpoB Gene to Determine the Specificity of Base Substitution Mutations on the Escherichia coli Chromosome.  DNA Repair (2003) 2, 593-608.
• Kim M, Huang T, Miller JH. Competition between MutY and Mismatch Repair at A · C Mispairs In Vivo. Journal of Bacteriology. 2003;185(15):4626-4629. doi:10.1128/JB.185.15.4626-4629.2003.
• Fitz-Gibbon, S., Ladner, H., Kim, U.J., Stetter, K.O., Simon, M.I., and Miller, J.H. Genome sequence of the hyperthermophilic crenarchaeon Pyrobaculum aerophilum.  Proc. Natl. Acad. Sci. U.S.A. (2002) 99, 984-989.
• Funchain P, Yeung A, Stewart J, Clendenin WM, Miller JH. Amplification of Mutator Cells in a Population as a  Result of Horizontal Transfer. Journal of Bacteriology. 2001;183(12):3737-3741. doi:10.1128/JB.183.12.3737-3741.2001.
• Yang H, Phan IT, Fitz-Gibbon S, et al. A thermostable endonuclease III  homolog from the archaeon Pyrobaculum aerophilum. Nucleic Acids Research. 2001;29(3):604-613.
• Miller, J.H., Yeung, A., Funchain, P., Mao, E., Stewart, J., Luther, W., and Slupska, M.M. Temporary and permanent mutators lacking the mismatch repair system: the enhancement of mutators in cell populations.  Cold Spring Harbor Symp. Quant. Biol. (2000) 65, 241-252.
• Yang H, Fitz-Gibbon S, Marcotte EM, Tai JH, Hyman EC, Miller JH. Characterization of a Thermostable DNA Glycosylase Specific for U/G and T/G Mismatches from the Hyperthermophilic Archaeon Pyrobaculum aerophilum. Journal of Bacteriology. 2000;182(5):1272-1279.
• Slupska MM, Luther WM, Chiang J-H, Yang H, Miller JH. Functional Expression of hMYH, a Human Homolog of the Escherichia coli MutY Protein. Journal of Bacteriology. 1999;181(19):6210-6213.
• Miller, J. H.  The relevance of bacterial mutators to understanding human cancer.  In Cancer Profiles (J. Tooze, editor).  Cold Spring Harbor Laboratory Press (1996) 28, 41-153.
• Slupska, M. M., Baikalov, C., Lloyd, R., and Miller, J. H.  Mutator tRNAs are encoded by the Escherichia coli mutator genes mutA and mutC:  A novel pathway for mutagenesis.  Proc. Acad. Nat. Sci. USA.(1996) 93, 4380-4385.
• Michaels, M. L., Cruz, C., Grollman, A. P. and Miller, J. H. Evidence that MutY and MutM combine to prevent mutations by an oxidatively damaged form of guanine in DNA.  Proc. Nat. Acad. Sci. U.S.A.  (1992) 89, 7022-7025.
• Nghiem, Y., Cabrera, M., Cupples, C. G., and Miller, J. H. The mutY gene:  A mutator locus in Escherichia coli that generates GC-TA transversions.  Proc. Nat. Acad.Sci. U.S.A. (1988) 85, 2709-2713.
• Slupska MM, King AG, Lu LI, et al. Examination of the Role of DNA Polymerase Proofreading in the Mutator Effect of Miscoding tRNAs. Journal of Bacteriology. 1998;180(21):5712-5717.

Books Edited

• Brenner, S. and Miller, J. H. (2001).  Encyclopedia of Genetics.  Vol. 1-4.  Academic Press, London, 2800pp.

• Mao, E.F., Lane, L., Lee, J., and Miller, J.H.  The proliferation of mutators in a cell population.  J. Bacteriol. (1997) 35, 417-422.Books

• Miller, J.H. (1972). Experiments in Molecular Genetics.  Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, 466 pp.

• Miller, J.H. (1992).  A Short Course in Bacterial Genetics:  A Laboratory Manual for Escherichia coli and Related Bacteria. Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, 456 pp.

• Miller, J.H. (1992).  A Short Course in Bacterial Genetics:  A Handbook for Escherichia coli and Related Baceria.  Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York, 437 pp.

• Miller J.H. (1996).  Discovering Molecular Genetics:  A Case Study Course with Problems and Scenarios. Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, 700 pp.

• Griffiths, A. J. F., Wessler, S. R., Lewontin, R. C., and Gelbart, W. M., Suzuki, D. T., and Miller, J. H. (2004). An Introduction to Genetic Analysis, 8th edition.  W.H. Freeman, New York, 782 pp.