Brody Publications List

Publications

Papers

  1. Luis Soto-Ortiz and James P. Brody, "A theory of the cancer age-specific incidence data based on extreme value distributions," AIP Advances 2, 011205 2012.
  2. 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
  3. Grace Mao and James P. Brody, "Reverse engineering the yeast RNR1 transcriptional control system.", PLoS One. 2010 Nov 16;5(11):e13895.
  4. 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.
  5. 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.
  6. 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. 
  7. 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.
  8. Limin Lin and James P. Brody, Analyzing DNA-Protein Interactions on a Chip. Chapter 10 in Integrated Biochips for DNA Analysis, Landes Biosciences, 2007.
  9. Alan I. Lee and James P. Brody, Diversity in the activity of individual enzymes., Current Pharmaceutical Biotechnology, 6, p 415--25, 2005.
  10. H. Garrett R. Thompson and James P. Brody. Rpn8, AfCS-Nature Molecule Pages, (doi:10.1038/mp.a003584.01) 2005.
  11. Alan I. Lee and James P. Brody, Single Molecule Enzymology of Chymotrypsin using Water-in-oil Emulsion, Biophysical Journal, 88, p 4303-4311, 2005.
  12. Alan Lee and James P. Brody, New assay for multiple single molecule enzyme kinetics. Proc. of the SPIE 5699,p 482-490, 2005.
  13. 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
  14. Lifeng Zheng, James P. Brody, and Peter J. Burke, "Electronic manipulation of DNA, proteins, and nanoparticles for potential circuit assembly," Biosensors and Bioelectronics, 20, 606-619, 2004.
  15. 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.
  16. 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.
  17. 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.
  18. Lifeng Zheng, Peter J. Burke, and James P. Brody, "Electronic manipulation of DNA and Proteins," Proc. of  the SPIE 5331, 126,  2004.
  19. 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.
  20. 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).
  21. 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.
  22. 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.
  23. 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.
  24. Peter H. Tran, Daniel A. Peiffer, Yongchol Shin, Lauren M. Meek, James P. Brody, and Ken W. Y. Cho. “Microarray Optimizations: Increasing spot accuracy and automated identifications of true microarray signals.” Nucleic Acids Research, 30 (12): e54, 2002.
  25. James P. Brody and Stephan R. Quake, “A self-assembled microlensing rotational probe.” Applied Physics Letters, 74, p 144 – 6, 1999.
  26. 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.
  27. 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.
  28. 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.
  29. 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.
  30. 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.).
  31. 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.
  32. 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.
  33. James P. Brody, Ted Cox, Thomas A. J. Duke, and Wayne D. Volkmuth, “Stretch Genes,” Physics Today, p 32 – 36, February 1997.
  34. 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.
  35. 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.
  36. 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.
  37. 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.
  38. 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.
  39. 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 Journal, 68:6, p 2224 – 32, June 1995.
  40. Brody JP, Osborn TD, Forster FK, and Yager P.  “A planar microfabricated fluid filter.” Transducers ’95, Stockholm, Sweden June 1995.
  41. 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.
  42. 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.

Patents

  1. Yager; Paul; Weigl; Bernhard H.; Brody; James P.; Holl; Mark R. US Patent No. 5,716,852 Microfabricated diffusion based chemical sensor, February 10, 1998.
  2. Brody, James P. US Patent No. 5,726,404 Valveless liquid microswitch, March 10, 1998.
  3. Brody, James P.; and Osborn, Thor D. US Patent No. 5,922,210 Tangential flow planar microfabricated fluid filter and method of using thereof, July 13, 1999.
  4. Yager; Paul; Brody; James P.; Holl; Mark R.; Forster; Fred K.; Galambos; Paul C.; US Patent No. 5,932,100, Microfabricated differential extraction device and method, August 3, 1999.
  5. Yager; Paul; Brody; James P.; US Patent No. 5,971,158 Absorption-enhanced differential extraction device, October 26, 1999.
  6. Weigl; Bernhard H.; Yager; Paul; Brody; James P.; Holl; Mark R.; Kenny; Margaret; Schutte; David; Hixson; Gregory; Zebert; Diane; Kamholz; Andrew; Wu; Caicai, Altendorf, Eric. US Patent No. 5,972,710, Microfabricated diffusion based chemical sensor, October 26, 1999.
  7. Weigl; Bernhard H.; Yager; Paul; Brody; James P. US Patent No. 6,159,739 Device and method for 3-dimensional alignment of particles in microfabricated flow channels, December 12, 2000.
  8. Brody, James P.; and Osborn, Thor D. US Patent No. 6,387,290 Tangential flow planar microfabricated fluid filter, May 14, 2002.
  9. Weigl; Bernhard H.; Yager; Paul; Brody; James P.; Holl; Mark R.; Forster; Fred K. ; Altendorf; Eric; Galambos; Paul C.; Kenny; Margaret; Schutte; David; Hixson; Gregory; Zebert; Diane; Kamholz; Andrew; Wu; Caicai US Patent No. 6,454,945 Microfabricated Devices and Methods, September 24, 2002.
  10. Quake; Stephen R. and Brody, James P. US Patent No. 6,614,598 Microlensing particles and applications. September 2, 2003.
  11. Yager, Paul and Brody, James P. US Patent No. 6,695,147, Absorption Enhanced Differential Extraction Device, February 24, 2004
  12. Quake; Stephen R.,  van Dam; R. Michael, Brody; James P., Shafee; Rebecca US Patent No. 6,947,846, Non-metric tool for predicting gene relationships from expression data, September 20, 2005.
  13. Quake; Stephen R., Brody; James P.,US Patent No. 6,958,865, Microlicensing particles and applications, October 25, 2005.
  14. Quake; Stephen R., Brody; James P., US Patent No. 7,248,413, Microlensing particles and applications July 24, 2007.

Abstracts/Posters

  1. Angela Y Chen, Ashish S Jani, Lifeng Zheng, Peter J Burke, and James P. Brody, "Single Molecule Characterization of alpha-Chymotrypsin using microfabricated cylindrical chambers." 8th Annual UC Wide Bioengineering Symposium, June 2007. 
  2.  Grace Mao and James P. Brody, “Interactions of Nuclear Proteins to MBF Binding Site Monitored by Surface Plasmon Resonance”, 8th Annual UC Wide Bioengineering Symposium, June 2007.
  3. James P. Brody, “The age-specific incidence of human carcinomas is described by a normal distribution.” American Association of Cancer Research 2007 Annual Meeting,  Los Angeles. April 2007. 
  4. Lifeng Zheng, Shengdong Li, J. Brody, Peter Burke. “Self-Assembled Gold Nanowires from Nanoparticles,” Bulletin of the American Physical Society, P21.00004, APS March Meeting, 2005. 
  5.  Alan I. Lee and James P. Brody. “Water-in-oil Emulsion Based Assay for Single Molecule Enzymology on Chymotrypsin,” Biophysical Society 49th Annual Meeting, 2005.
  6.  Limin Lin, Joseph W. Harris, H. Garrett Thompson, James P. Brody. “Identifying transcriptional regulatory elements by using an SPR_based sensor,” Biophysical Society 49th Annual Meeting, 2005  
  7.  Lee AI; Brody JP “New assay for multiple single molecule enzyme kinetics” 2004 BMES Annual Fall Meeting. 
  8.  L. Lin, J. W. Harris, H. G. R. Thompson and J. P. Brody, “Surface Plasmon Resonance-based sensors can identify cis regulatory elements,” 2004 BMES Annual Fall Meeting. 
  9.  L. Zheng, S. Li, P. Burke, and J. Brody.  “Towards Single Molecule DNA Manipulation with Nanotube Electrodes,” 205th Meeting of The Electrochemical Society. 2004.
  10. James P. Brody, H. Garrett R. Thompson, Joseph W. Harris, Limin Lin, “Co-expression of a module of genes in cancer and normal tissue,”Experimental Biology 2003, 366.4, April 2003.
  11. Limin Lin, H. Garrett R Thompson, Joseph W. Harris, James P. Brody. “Regulation of FLJ10111 expression, a candidate breast cancer marker,” Experimental Biology 2003, 626.9, April 2003.
  12. H.G.R. Thompson, J.W. Harris, J.P. Brody. “Expression of Proteasome Subunit S12 in Normal and Transformed Breast Epithelial Cells.” 42nd Meeting of the American Society for Cell Biology, December 2002.
  13. Thompson HGR; Harris JW; Khosho AR; Martinez JE; Brody JP. “Computational analysis of publicly available data identifies co-expressed genes in breast cancer cells,” Biophysical Journal, 82, 2306, 2002.
  14. Lee AI; Brody JP “Single enzyme kinetics of chymotrypsin” Biophysical Journal 2002, 82, 1, 237, 2002.
  15. Brody, JP. “Statistics of DNA microarray data,” March Meeting of the American Physical Society, W23.004. 2001.
  16. Brody, JP and Quake, SR “A self-assembled microlensing probe,” March Meeting of the American Physical Society, BC32.08, 1998.
  17. Carlson R; Gabel CV; Chan SS; Austin RH; Brody JP; Winkleman J “Self-Sorting of white blood cells in a lattice,” Molecular Biology of the Cell 8, 2407, 1997.
  18. Brody, JP. Austin, RH and Bitensky, M “Active Cytoskeleton in Red Blood Cells,” March Meeting of the American Physical Society, E13.10. 1994.
  19. Brody, J, Austin B, and Bitensky M. “Red blood cell flow through a microfabricated structure” Biophysical Journal 66, A85, 1994.
  20. Ultra-fast Mixing Experiments; Poster presented at the 1997 Bioanalytical Sensors Gordon Conference

Presentations

Proposals

Miscellaneous

Tech Note on diffusion & sedimentation
Tech Note on max throughput in an H-filter