Publications
Papers
- 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, Accepted September 2007.
- 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.
- Limin Lin and James P. Brody, Analyzing DNA-Protein Interactions on a Chip. Chapter 10 in Integrated Biochips for DNA Analysis, Landes Biosciences, 2007.
- Alan I. Lee and James P. Brody, Diversity in the activity of individual enzymes., Current Pharmaceutical Biotechnology, 6, p 415--25, 2005.
- H. Garrett R. Thompson and James P. Brody. Rpn8, AfCS-Nature Molecule Pages, (doi:10.1038/mp.a003584.01) 2005.
- Alan I. Lee and James P. Brody, Single Molecule Enzymology of Chymotrypsin using Water-in-oil Emulsion, Biophysical Journal, 88, p 4303-4311, 2005.
- Hermann B. Frieboes and James P. Brody, Telomere loss limits the rate of human epithelial tumor formation Preprint arXiv:q-bio.TO/0502004.
- Alan Lee and James P. Brody, New assay for multiple single molecule enzyme kinetics. Proc. of the SPIE 5699,p 482-490, 2005.
- 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
- 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.
- 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.
- 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.
- 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.
- Lifeng Zheng, Peter J. Burke, and James P. Brody, "Electronic
manipulation of DNA and Proteins," Proc. of the SPIE 5331, 126, 2004.
- 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.
- 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).
- 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.
- 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.
- 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.
- 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.
- James P. Brody and Stephan R. Quake, “A
self-assembled
microlensing rotational probe.” Applied
Physics Letters, 74,
p 144 – 6, 1999.
- 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.
- 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.
- 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.
- 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.
- 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.).
- 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.
- 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.
- James P. Brody, Ted Cox, Thomas A. J. Duke,
and Wayne D. Volkmuth,
“Stretch Genes,” Physics
Today, p 32 – 36,
February 1997.
- 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.
- James P. Brody, Thor D. Osborne,
Fred K. Forster, and Paul Yager, “A
Planar Microfabricated Fluid Filter,” Sensors and
Actuators A: Physical, 54,
p 704 – 708, June 1996.
- 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.
- 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.
- 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.
- 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.
- Brody JP, Osborn TD, Forster FK, and Yager P.
“A planar microfabricated fluid
filter.” Transducers ’95, Stockholm, Sweden June
1995.
- 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.
- 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
- 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.
- Brody, James P. US Patent No. 5,726,404 Valveless
liquid microswitch, March 10, 1998.
- 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.
- 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.
- Yager; Paul; Brody; James P.;
US Patent No. 5,971,158 Absorption-enhanced differential extraction device,
October 26,
1999.
- 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.
- 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.
- Brody, James P.; and Osborn,
Thor D. US Patent No. 6,387,290 Tangential flow planar microfabricated fluid filter,
May 14, 2002.
- 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.
- Quake; Stephen R. and Brody,
James P. US Patent No. 6,614,598 Microlensing
particles and applications. September 2, 2003.
- Yager, Paul and Brody, James P. US Patent No. 6,695,147, Absorption Enhanced
Differential Extraction Device, February 24, 2004
- 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.
- Quake; Stephen R., Brody; James P.,US Patent No. 6,958,865, Microlicensing particles and applications, October 25, 2005.
-
Quake; Stephen R., Brody; James P., US Patent No. 7,248,413, Microlensing particles and applications July 24, 2007.
Abstracts/Posters
- 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.
- 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.
- 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.
- 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.
- 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.
- 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
- Lee
AI; Brody JP “New assay for multiple single molecule enzyme kinetics” 2004 BMES
Annual Fall Meeting.
- 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.
- L.
Zheng, S. Li, P. Burke, and J. Brody.
“Towards Single Molecule DNA Manipulation with Nanotube Electrodes,”
205th Meeting of The Electrochemical Society. 2004.
- 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.
- 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.
- 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.
- 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.
- Lee AI; Brody JP “Single enzyme
kinetics of chymotrypsin” Biophysical Journal
2002, 82, 1, 237, 2002.
- Brody, JP. “Statistics of DNA microarray data,” March
Meeting of the American Physical Society, W23.004. 2001.
- Brody, JP and Quake, SR “A
self-assembled
microlensing probe,” March Meeting of the
American Physical Society, BC32.08, 1998.
- 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.
- Brody, JP. Austin, RH and
Bitensky, M “Active
Cytoskeleton in Red Blood Cells,” March
Meeting of the American Physical Society, E13.10. 1994.
- Brody, J, Austin B, and
Bitensky M. “Red blood cell
flow through a microfabricated structure” Biophysical
Journal 66, A85, 1994.
- 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