May 1, 2020: UCI BME research seminar: “Predicting Future Cancer Diagnoses with DNA Tests“.


  1. Chris Toh and James P. Brody, “Machine Learning in Healthcare,”  IntechOpen, accepted 2020.
  2. Buyung Zhang and James P Brody, “Artificial Intelligence,” Chapter 14 in Engineering-Medicine: Principles and Applications of Engineering in Medicine, CRC Press, 2019.
  3. Chris Toh and James P. Brody, “Analysis of copy number variation from germline DNA can predict individual cancer risk,” doi:, 2018.
  4. Trevor Sughrue, Michael A. Swiernik, Yang Huang and James P. Brody, “Laboratory tests as short-term correlates of stroke,” BMC Neurology (2016) 16:112.
  5. Trevor Sughrue and James P. Brody, “Breast tumor laterality in the United States depends upon the country of birth, but not race,” PLoS One 9 (8) 2014.
  6. James P. Brody, “The age-specific incidence anomaly suggests that cancers originate during development.” Biophysical Review and Letters, 1-12, 2014.
  7. Luis Soto-Ortiz and James P. Brody, “Similarities in the Age-Specific Incidence of Colon and Testicular Cancers” PLoS One. 2013 Jun 26; 8(6) ee66694
  8. Luis Soto-Ortiz and James P. Brody, “A theory of the cancer  age-specific incidence data based on extreme value distributions,” AIPAdvances 2, 011205, 2012.
  9. James P. Brody.  “RPN8,” Encyclopedia of Signaling Molecules, p 1691. (2012).
  10. James P. Brody, “Age-specific incidence data indicate four mutations are required for human testicular cancers.“, PLoS One. 2011;6(10):e25978. Epub 2011 Oct 6
  11. Grace Mao and James P. Brody, “Reverse engineering the yeast RNR1 transcriptional control system.“, PLoS One. 2010 Nov 16;5(11):e13895.
  12. James P. Brody,  “Parallel Routes of Human Carcinoma Development: Implications of the Age-Specific Incidence Data“, PLoS ONE, 4(9): e7053, doi:10.1371/journal.pone.0007053, 2009.
  13. Angela Y Chen, Ashish S. Jani, Lifeng Zheng, Peter J. Burke, and James P. Brody, “Microfabricated Arrays of Cylindrical Wells Facilitate Single-Molecule Enzymology of  alpha Chymotrypsin“, Biotechnology Progress, 2009, 25: 929–937.
  14. Bobak Mosadegh, Carlos Huang, Jeong Park, Hwas Sung Shin, Bong Geun Chung, Kun-Hong Lee; Sun-Kyu Hwang, Hyung Joon Kim, James Brody, Noo Li Jeon, “Generation of Stable Complex Gradients Across 2D Surfaces and 3D Gels”, Langmuir, 2007, 23(22) 10910-10912.
  15. Grace Mao and James P. Brody, Dynamic SPR monitoring of yeast nuclear protein binding to a cis-regulatory element. Biochemical and Biophysical Research Communications 363 p153–158, 2007.
  16. Limin Lin and James P. Brody, Analyzing DNA-Protein Interactions on a Chip. Chapter 10 in Integrated Biochips for DNA Analysis, Landes Biosciences, 2007.
  17. Alan I. Lee and James P. Brody, Diversity in the activity of individual enzymes., Current Pharmaceutical Biotechnology, 6, p 415–25, 2005.
  18. H. Garrett R. Thompson and James P. Brody. Rpn8AfCS-Nature Molecule Pages, (doi:10.1038/mp.a003584.01) 2005.
  19. Alan I. Lee and James P. Brody, Single Molecule Enzymology of Chymotrypsin using Water-in-oil EmulsionBiophysical Journal, 88, p 4303-4311, 2005.
  20. Alan Lee and James P. Brody, New assay for multiple single molecule enzyme kinetics. Proc. of the SPIE 5699,p 482-490, 2005.
  21. Limin Lin; Joseph W. Harris; H. Garrett R. Thompson; and James P. Brody, “Surface plasmon resonance sensors to identify cis-regulatory elements ; Analytical Chemistry, 76, 6555-6559. 2004
  22. Lifeng Zheng, James P. Brody, and Peter J. Burke, “Electronic manipulation of DNA, proteins, and nanoparticles for potential circuit
    ,” Biosensors and Bioelectronics, 20, 606-619, 2004.
  23. Lifeng Zheng, Shengdong Li, James P. Brody and Peter J. Burke, “Manipulating Nanoparticles in Solution with Electrically Contacted Nanotubes Using Dielectrophoresis,” Langmuir 20, 8612-8619,  2004.
  24. H. Garrett R. Thompson; Joseph W. Harris; and James P. Brody, “Post-translationally modified S12, Absent in Transformed Breast Epithelial Cells, is Not Associated with the 26S proteasome and is induced by Proteasome Inhibitor,” International Journal of Cancer, 111, 338-347. 2004.
  25. H. Garrett R. Thompson; Joseph W. Harris; Limin Lin and James P. Brody, “Identification of the protein ZIBRA, its genomic organization, regulation and expression in breast cancer cells,” Experimental Cell Research, 295(2) 448-459. 2004.
  26. Lifeng Zheng, Peter J. Burke, and James P. Brody, “Electronic manipulation of DNA and Proteins,” Proc. of  the SPIE 5331,
    126,  2004.
  27. Alan Lee, Peter J. Burke, and James P. Brody, “Electrochemiluminescene as a tool for microscopy at the nanoscale“, Proc. of  the SPIE 5331, 13,  2004.
  28. Lifeng Zheng, Shengdong Li, Peter J. Burke, and James P. Brody, “Towards Single Molecule Manipulation with Dielectrophoresis using Nanoelectrodes,”Proceedings of the Third IEEE Conference on Nanotechnology, 1, 437-440 (2003).
  29. H. Garrett Thompson, Joseph W. Harris, Barbara J. Wold, Fritz Lin, and
    James P. Brody, “P62 over-expression in breast tumors and its regulation by Prostate-Derived Ets Factor (PDEF) in breast cancer cells in vitro,” Oncogene.  Apr  17;22(15):2322-33, 2003.
  30. H. Garrett R. Thompson, Joseph W. Harris, Barbara J. Wold, Stephen R. Quake, and James P. Brody, “Identification and confirmation of a module of co-expressed genes.” Genome Research, 12 (10) 1517 – 1522, 2002.
  31. James P. Brody, Brian A. Williams, Barbara Wold, and Stephen Quake, “Significance and statistical errors in the analysis of DNA microarray data.” Proc. Natl. Acad. Sciences, 99 (20) 12975 – 12978, 2002.
  32. Peter H. Tran, Daniel A. Peiffer, Yongchol Shin, Lauren M. Meek, James .
    Brody, and Ken W. Y. Cho. “Microarray Optimizations: Increasing spot accuracy and automated identifications of true microarray signals.”  Nucleic Acids Research30 (12): e54, 2002.
  33. James P. Brody and Stephan R. Quake, “A self-assembled microlensing rotational probe.” Applied Physics Letters, 74, p 144 – 6, 1999.
  34. James B. Knight, Ashvin Vishwanath, James P. Brody, and Robert H. Austin, “Hydrodynamic Focusing on a Silicon Chip: Mixing Nanoliters in Microseconds.” Physical Review Letters, 80, p 3863 – 7, 1998.
  35. Olgica B. Bakajin, James P. Brody, Jeff Chou, Shirley S. Chan, Thomas Duke, James Knight, Lydia Sohn, Ashvin Vishwanath, Robert H. Austin, and Edward C. Cox “Polymer dynamics and fluid flow in
    microfabricated devices
    ,” Proc. SPIE Int. Soc. Opt. Eng 3258 p 100 – 13, 1998.
  36. Darrel J. Bell, James P. Brody, and Paul Yager, “Using poly
    (ethylene glycol) silane to prevent protein adsorption in microfabricated silicon channels
    ,” Proc. SPIE Int. Soc. Opt. Eng. 3258, 134 (1998) 3258, p 134 – 40, March 1998.
  37. Robert H. Carlson, Christopher V.Gabel, Shirley S. Chan, Robert H. Austin, James P. Brody, and James W. Winkelman, “Self Sorting of White Blood Cells in a Lattice,” Physical Review Letters, 78:11, p 2149 – 2152, 15 September 1997.
  38. James P. Brody and Paul Yager, “Diffusion based Extraction in a Microfabricated Structure.Sensors and Actuators A: Physical 58,
    p 13 – 16, March 1997 (or here.).
  39. Robert H. Carlson, Christopher V.Gabel, Shirley S. Chan, Robert H. Austin, James P. Brody, and James W. Winkelman, “Hydrodynamic
    activation and sorting of white blood cells in a microfabricated lattice
    Proc. SPIE Int. Soc. Opt. Eng. 2978, p 206 – 15, March 1997.
  40. James P. Brody, Andrew Evan Kamholz, and Paul Yager, “Prominent Microscopic Effects in Micro-fluidic Chemical Analysis Systems,” Proc.
    SPIE Int. Soc. Opt. Eng
    . 2978, p 103 – 110, March 1997.
  41. James P. Brody, Ted Cox, Thomas A. J. Duke, and Wayne D. Volkmuth, “Stretch Genes,” Physics Today, p 32 – 36, February 1997.
  42. James P. Brody, Paul Yager, Raymond Goldstein, and Robert H. Austin, “Biotechnology at Low Reynolds Numbers,” Biophysical Journal, 71:6,
    p 3430 – 3441, December 1996.
  43. James P. Brody, Thor D. Osborn, Fred K. Forster, and Paul Yager, “A Planar Microfabricated Fluid Filter,” Sensors and Actuators A: Physical, 54, p 704 – 708, June 1996.
  44. James P. Brody and Paul Yager, “Low Reynolds Number Micro-fluidic Devices,Hilton Head 1996 Solid-State Sensor and Actuator Workshop, p 105 – 108, June 1996.
  45. Mark R. Holl, Paul Galambos, Fred K. Forster, James P Brody, Martin Afromowitz, and Paul Yager, “Optimal Design of a Microfabricated Diffusion-based Extraction Device,” 1996 American
    Society of Mechanical Engineering Symposium on Micro
    Electromechanical Systems
    , p 183 – 189, November 1996.
  46. Bernhard H. Weigl, Mark R. Holl, David Schutte, James P. Brody, and Paul Yager, “Diffusion-based optical chemical detection in silicon flow structures,Analytical Methods and Instruments, special issue uTAS 96, p 174 – 184.
  47. James P. Brody, Yuqi Han, Mark R. Bitensky, and Robert H. Austin, “Deformation and Flow of Red Blood Cells in a Synthetic Lattice: Evidence for an Active Cytoskeleton,” Biophysical Journal68:6, p 2224 – 32, June 1995.
  48. Brody JP, Osborn TD, Forster FK, and Yager P.  “A planar microfabricated fluid filter.Transducers ’95, Stockholm, Sweden June 1995.
  49. Hewitt, J.N, Turner, E.L., Lawrence, C.R., Schneider, D.P. and Brody, J.P.
    A gravitational lens candidate with an unusually red optical counterpart.” Astronomical Journal, 104(3) 968- 979, 1992.
  50. Hewitt, J. N.; Burke, B. F.; Turner, E. L.; Schneider, D. P.; Lawrence, C. R.; Langston, G. I.; Brody, J. P, “Results of The VLA Gravitational Lens Survey,” Lecture Notes in Physics, 330, p.147, 1989.