Publications

Recent Virtual Talks

  1. May 2020: UCI BME Research Seminar: “Predicting Future Cancer Diagnoses with DNA Tests“.  This was a one hour research seminar, mostly for UCI BME students and faculty.
  2. December 2020: AACR Special Conference on Artificial Intelligence, Diagnosis, and Imaging “Genetic Risk scores for breast cancer based on machine learning analysis of chromosomal-scale length variation.”  This is a short seven minute talk providing an overview of our work on predictive cancer tests.  Afterwards, Warren Froelich, a science writer for Oncology Times interviewed me and produced this article covering my talk: “Genetic Risk Scores for Breast Cancer Based on Machine Learning.”
  3. May 2021: Physical Biology of the Cell: “A different approach to cancer.”  Steve Quake puts on an exclusive annual conference for lab students and alumni every year, usually in Hawaii.  This is the first one I “attended”.  I gave this 15 minute talk describing my research over the past 20 years.
  4. September 2023,  Genotype to Phenotype with Big Data / NIH All of Us.  A short research talk on my research interests for a faculty audience.
  5. September 2023, BME 3 Treating Diabetes.  A short talk on a General Education class I teach targeted to colleagues on in the  BME Department.

Recent Student Theses Supervised

  1. Yasaman Fatapour, “Application of Machine Learning for Risk Determination in Cancer Occurrence and Recurrence,” PhD Thesis, 2023.
  2. Kamran Ali, “Combination Therapeutic Discovery for Hematologic Malignancies,” PhD Thesis, 2023.
  3. Charmeine Ko, “Cancer Risk Determination through Chromosomal Scale Length Variations of Germline DNA,” PhD Thesis, 2022.
  4. Christopher Toh, “Chromosomal scale length variations as a genetic risk score for predicting complex human diseases in large scale genomic datasets,” PhD Thesis, 2021.
  5. Aditya Vyas, “Data Augmentation Policies for Cancer Classification,” Masters Thesis, 2020.
  6. Buyun Zhang, “Colorectal cancer predictive test using germ-line DNA data and multiple machine learning methods,” PhD Thesis 2019.
  7. Yige Lu, “A gradient boosting machine algorithm to predict age of glioblastoma incidence with copy number variation data,” Masters Thesis 2019.
  8. Winnie Fan, “Genomics and Epidemiological Analysis of Melanoma Laterality,” Masters Thesis, 2018.
  9. Liyu Cao, “Support Vector Machines for Kidney Cancer Classification,” Masters Thesis, 2018.
  10. Xinhan Tong, “Breast Cancer Prediction from Genome Segments with Machine Learning,” Masters Thesis, 2018.
  11. Trevor Sughrue, “Breast Tumor Laterality in the United States Depends Upon The Country of Birth, But Not Race,” Masters Thesis, 2015.
  12. Luis Soto-Ortiz, “An Investigation of the Developmental Origins of Cancer through an Analysis of Cancer Registry Data,” PhD Thesis, 2014.

Papers

  1. Yasaman Fatapour and James P Brody, “Polygenic Risk Scores for Breast Cancer with Cross-Racial Analysis,” Preprint, 2024.
  2. Yasaman Fatapour and James P Brody, “A compact encoding of the genome suitable for machine learning prediction of traits and genetic risk scores,” Bioarxiv, 2024, https://doi.org/10.1101/2024.04.03.587989.
  3. Kamran A. Ali, Reecha D. Shah, Anukriti Dhar, Nina M. Myers, Cameron Nguyen, Arisa Paul, Jordan E. Mancuso, A. Scott Patterson, James P. Brody, and Diane Heiser,  “Ex Vivo Discovery of Synergistic Drug Combinations for Hematologic Malignancies,” SLAS Discovery, 29:2, 2024.
  4. Kalan Leaks, Trina Norden-Krichmar, and James P. Brody, “Predicting Moderate Drinking Behaviors in NHANES Participants using Biochemical and Demographical Factors with Automated Machine Learning,”  Alcohol, 113:1, 2023.
  5. Charmeine Ko and James P Brody, “A Genetic Risk Score Using Human Chromosomal-Scale Length Variation Can Predict Breast Cancer,” Human Genomics 17. (53) 2023.
  6. Yasaman Fatapour, Arash Abiri, Edward Kuan, James P Brody, “Development of a supervised machine learning model to predict locoregional reappearance of oral tongue squamous cell carcinoma,” Cancers 2023 15(10), 2769.
  7. Yasaman Fatapour and James P. Brody. “Genetic Risk Scores and Missing Heritability in Ovarian Cancer,” Genes 2023, 14(3), 762; https://doi.org/10.3390/genes14030762
  8. Christopher Toh and James P. Brody, “A genetic risk score using human chromosomal-scale length variation can predict schizophrenia“. Sci Rep 11, 18866 (2021).
  9. James P. Brody, “Insulin was discovered 100 years ago – but it took a lot more than one scientific breakthrough to get a diabetes treatment to patients,” ASBMB Today August 2021.  Originally written for The Conversation, then syndicated through AP news.  The article also appeared on many other sites including: Yahoo News,  and Sina Technology (translated to Mandarin)
  10. James P. Brody, “Comment on ‘comparative analysis of triple-negative breast cancer transcriptomics of Kenyan, African American and Caucasian women’ by Saleh et al.,”  Translational Oncology, 2021 Sep; 14(0):101164 (2021).
  11. Charmeine Ko and James P. Brody, “A genetic risk score for glioblastoma multiforme based on copy number variations,” Cancer Treat Res Commun., 27:100352 (2021).
  12. Christopher Toh and James P. Brody, “Genetic risk score for ovarian cancer based on chromosomal-scale length variation,” BioData Min. Mar 9; 14(1):18 (2021).
  13. Christopher Toh and James P. Brody, “Evaluation of a genetic risk score for severity of COVID-19 using human chromosomal-scale length variation,”  Human Genomics 14:36 (2020).
  14. Chris Toh and James P. Brody, “Applications of Machine Learning in Healthcare”  Chapter 4 in Smart Manufacturing – When Artificial Intelligence Meets the Internet of Things,  IntechOpen, 2020.
  15. Buyung Zhang and James P Brody, “Artificial Intelligence,” Chapter 14 in Engineering-Medicine: Principles and Applications of Engineering in Medicine, CRC Press, 2019. https://doi.org/10.1201/9781351012270
  16. Chris Toh and James P. Brody, “Analysis of copy number variation from germline DNA can predict individual cancer risk,” doi: https://doi.org/10.1101/303339, 2018.
  17. Trevor Sughrue, Michael A. Swiernik, Yang Huang and James P. Brody, “Laboratory tests as short-term correlates of stroke,” BMC Neurology (2016) 16:112.
  18. 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.
  19. James P. Brody, “The age-specific incidence anomaly suggests that cancers originate during development.” Biophysical Review and Letters, 1-12, 2014.
  20. 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
  21. 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.
  22. James P. Brody.  “RPN8,” Encyclopedia of Signaling Molecules, p 1691. (2012).
  23. 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
  24. Grace Mao and James P. Brody, “Reverse engineering the yeast RNR1 transcriptional control system.“, PLoS One. 2010 Nov 16;5(11):e13895.
  25. 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.
  26. 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.
  27. 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.
  28. 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.
  29. Limin Lin and James P. Brody, Analyzing DNA-Protein Interactions on a Chip. Chapter 10 in Integrated Biochips for DNA Analysis, Landes Biosciences, 2007.
  30. Alan I. Lee and James P. Brody, Diversity in the activity of individual enzymes., Current Pharmaceutical Biotechnology, 6, p 415–25, 2005.
  31. H. Garrett R. Thompson and James P. Brody. Rpn8, AfCS-Nature Molecule Pages, (doi:10.1038/mp.a003584.01) 2005.
  32. Alan I. Lee and James P. Brody, Single Molecule Enzymology of Chymotrypsin using Water-in-oil Emulsion, Biophysical Journal, 88, p 4303-4311, 2005.
  33. Alan Lee and James P. Brody, New assay for multiple single molecule enzyme kinetics. Proc. of the SPIE 5699,p 482-490, 2005.
  34. 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
  35. 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.
  36. 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.
  37. 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.
  38. 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.
  39. Lifeng Zheng, Peter J. Burke, and James P. Brody, “Electronic manipulation of DNA and Proteins,” Proc. of  the SPIE 5331,
    126,  2004.
  40. 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.
  41. 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).
  42. 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.
  43. 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.
  44. 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.
  45. 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 Research, 30 (12): e54, 2002.
  46. James P. Brody and Stephan R. Quake, “A self-assembled microlensing rotational probe.” Applied Physics Letters, 74, p 144 – 6, 1999.
  47. 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.
  48. 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.
  49. 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.
  50. 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.
  51. 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.).
  52. 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.
  53. 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.
  54. James P. Brody, Ted Cox, Thomas A. J. Duke, and Wayne D. Volkmuth, “Stretch Genes,” Physics Today, p 32 – 36, February 1997.
  55. 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.
  56. 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.
  57. 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.
  58. 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.
  59. 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.
  60. 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.
  61. Brody JP, Osborn TD, Forster FK, and Yager P.  “A planar microfabricated fluid filter.” Transducers ’95, Stockholm, Sweden June 1995.
  62. 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.
  63. 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.