Biomedical and Agricultural Informatics

The PI of the group received his doctoral training in biomedical informatics. Since the late 1990s, he has been conducting research on biomedical imaging and informatics. At Penn State, he has been collaborating with faculty members in plant biology, agricultural sciences, pathology, and nutritional sciences on developing data science and artificial intelligence methods for solving highly-challenging real-world biomedical and agricultural problems of high societal impact.

The following is an archive of our publications in this area. They are in reverse chronical order.

  1. Xinye Zheng, Jianbo Ye, James Z. Wang and Jia Li, ``SCOTT: Shape-Location Combined Tracking with Optimal Transport,'' SIAM Journal on Mathematics of Data Science, vol. 2, no., pp. -, 24 pages, 2020. (download) (g-scholar)
  2. Alison D. Gernand, Jeffery A. Goldstein, W. Tony Parks, Yukun Chen, Zhuomin Zhang, Dolzodmaa Davaasuren, Chenyan Wu, Celeste Beck, Leigh Taylor and James Z. Wang, ``AI-based Rapid Placental Assessment Tool,'' Placenta, vol. 83, pp. e84-e85, 2019. [Presented at the International Federation of Placenta Associations Meeting, Buenos Aires, Argentina, September 2019] (download) (g-scholar)
  3. Hojae Yi, Yingtong Chen, James Z. Wang, Virendra M. Puri and Charles T. Anderson, ``The Stomatal Flexoskeleton: How the Biomechanics of Guard Cell Walls Animate an Elastic Pressure Vessel,'' Journal of Experimental Botany, Special Issue on Plant Biomechanics in the 21st Century, vol. 70, no. 14, pp. 3561-3572, 2019. (download) (g-scholar)
  4. Yukun Chen, Chenyan Wu, Zhuomin Zhang, Jeffery A. Goldstein, Alison D. Gernand and James Z. Wang, ``PlacentaNet: Automatic Morphological Characterization of Placenta Photos with Deep Learning,'' Proceedings of the International Conference on Medical Image Computing and Computer Assisted Interventions, pp. 487-495, Shenzhen, China, October 2019. (download) (g-scholar)
  5. Hojae Yi, Yue Rui, Baris Kandemir, James Z. Wang, Charles T. Anderson and Virendra M. Puri, ``Mechanical Effects of Cellulose, Xyloglucan, and Pectins on Stomatal Guard Cells of Arabidopsis thaliana,'' Frontiers in Plant Science, vol. 9, article 1566, pp. 1-18, 2018. (download) (g-scholar)
  6. Yue Rui, Yintong Chen, Baris Kandemir, Hojae Yi, James Z. Wang, Virendra M. Puri and Charles T. Anderson, ``Balancing Strength and Flexibility: How the Synthesis, Organization, and Modification of Guard Cell Walls Govern Stomatal Development and Dynamics,'' Frontiers in Plant Science, vol. 9, article 1202, pp. 1-11, 2018. (download) (g-scholar)
  7. Yue Rui, Chaowen Xiao, Hojae Yi, Baris Kandemir, James Z. Wang, Virendra M. Puri and Charles T. Anderson, ``POLYGALACTURONASE INVOLVED IN EXPANSION3 Functions in Seedling Development, Rosette Growth, and Stomatal Dynamics in Arabidopsis thaliana,'' The Plant Cell, vol. 29, no. 10, pp. 2413-2432, American Society of Plant Biologists, 2017. (download) (g-scholar)
  8. Yue Rui, Hojae Yi, Baris Kandemir, James Z. Wang, Virendra M. Puri and Charles T. Anderson, ``Integrating Cell Biology, Image Analysis, and Computational Mechanical Modeling to Analyze the Contributions of Cellulose and Xyloglucan to Stomatal Function,'' Plant Signaling & Behavior, vol. 11, no. 6, e1183086:1-4, 2016. (download) (g-scholar)
  9. Yue Rui, Chaowen Xiao, Hojae Yi, Baris Kandemir, James Z. Wang, Virendra M. Puri and Charles T. Anderson, ``GUARD CELL POLYGALACTURONASE1 Regulates Cell Expansion and Stomatal Dynamics in Arabidopsis Thaliana,'' Plant Cell Dynamics Meeting, June 2016. (download) (g-scholar)
  10. Brian A. Canada, Georgia Thomas, Keith Cheng and James Z. Wang, ``SHIRAZ: An Automated Histology Image Annotation System for Zebrafish Phenomics,'' Multimedia Tools and Applications, Special Issue on Hot Research Topics in Multimedia, vol. 51, no. 2, pp. 401-440, Springer, 2011. [invited] (download) (g-scholar)
  11. Brian A. Canada, Georgia K. Thomas, Keith C. Cheng, James Z. Wang and Yanxi Liu, ``Automatic Lattice Detection in Near-Regular Histology Array Images,'' Proceedings of the IEEE International Conference on Image Processing (ICIP), pp. 1452-1455, San Diego, California, IEEE, October 2008. (download) (g-scholar)
  12. Brian A. Canada, Georgia K. Thomas, Keith C. Cheng, James Z. Wang and Yanxi Liu, ``Towards Efficient Automated Characterization of Irregular Histology Images via Transformation to Frieze-Like Patterns,'' Proceedings of the ACM International Conference on Image and Video Retrieval, pp. 581-590, Niagara Falls, Canada, July 2008. (download) (g-scholar)
  13. Brian A. Canada, Georgia K. Thomas, Keith C. Cheng and James Z. Wang, ``Automated Segmentation and Classification of Zebrafish Histology Images for High-Throughput Phenotyping,'' Proceedings of the Third IEEE-NIH Life Science Systems and Applications Workshop, pp. 245-248, Bethesda, MD, November 2007. (download) (g-scholar)
  14. Dhiraj Joshi, Jia Li and James Z. Wang, ``A Computationally Efficient Approach to the Estimation of Two- and Three-dimensional Hidden Markov Models,'' IEEE Transactions on Image Processing, vol. 15, no. 7, pp. 1871-1886, 2006. [Abstracts were published in Proc. ICIP, 2004, 2005] (download) (g-scholar)
  15. Brian A. Canada, Keith C. Cheng and James Z. Wang, ``QCHARM: A Novel Computational and Scientific Visualization Framework for Facilitating Discovery and Improving Diagnostic Reliability in Medicine,'' Proceedings of the American Medical Informatics Association Annual Symposium, pp. 870, Washington, D.C., November 2006. (download) (g-scholar)
  16. Dhiraj Joshi, Jia Li and James Z. Wang, ``A Stochastic Modeling Approach to 3-D Image Modeling,'' Proceedings of the IEEE/NLM Life Science Systems and Application Workshop, pp. 120-121, IEEE, Bethesda, MD, July 2006. (download) (g-scholar)
  17. Dhiraj Joshi, Jia Li and James Z. Wang, ``Parameter Estimation of Multi-Dimensional Hidden Markov Models - A Scalable Approach,'' Proceedings of the IEEE International Conference on Image Processing (ICIP), Genova, Italy, vol. 3, pp. 149-152, IEEE, September 2005. (download) (g-scholar)
  18. Jia Li, Dhiraj Joshi and James Z. Wang, ``Stochastic Modeling of Volume Images with a 3-D Hidden Markov Model,'' Proceedings of the IEEE International Conference on Image Processing (ICIP), pp. 2359-2362, IEEE, Singapore, October 2004. (download) (g-scholar)
  19. Ya Zhang, Hongyuan Zha, James Z. Wang and Chao-Hsien Chu, ``Gene Co-regulation vs. Co-expression,'' Poster Proceedings of the International Conference on Research in Computational Molecular Biology (RECOMB), pp. 232-233, San Diego, CA, March 2004. (download) (g-scholar)
  20. Ya Zhang, Hongyuan Zha, James Z. Wang and Chao-Hsien Chu, ``Clustering of Time-Course Gene Expression Data,'' Poster Proceedings of the International Conference on Research in Computational Molecular Biology (RECOMB), pp. 240-241, San Diego, CA, March 2004. (download) (g-scholar)
  21. Eldar Giladi, Michael G. Walker, James Z. Wang and Wayne Volkmuth, ``SST: An Algorithm for Finding Near-Exact Sequence Matches in Time Proportional to the Logarithm of the Database Size,'' Bioinformatics, vol. 18, no. 6, pp. 873-879, 2002. [An abstract was published in RECOMB 2000] (download) (g-scholar)
  22. Ya Zhang and James Z. Wang, ``Progressive Display of Very High Resolution Images Using Wavelets,'' Journal of the American Medical Informatics Association, Proceedings of the AMIA Annual Symposium, vol. 2002 symposium suppl., pp. 944-948, San Antonio, TX, November 2002. [Selected to present at the plenary session at the AMIA Annual Symposium and nominated for the Best Paper Award] (download) (g-scholar)
  23. James Z. Wang, ``Wavelets and Imaging Informatics,'' Journal of Biomedical Informatics, (formerly Computers and Biomedical Research), vol. 34, no. 2, pp. 129-141, 2001. (download) (g-scholar)
  24. James Z. Wang, ``Pathfinder: Multiresolution Region-Based Searching of Pathology Images Using IRM,'' Journal of the American Medical Informatics Association, Proceedings of the AMIA Annual Symposium, vol. 2000 symposium suppl., pp. 883-887, Los Angeles, CA, November 2000. [Nominated for the Best Paper Award at the AMIA Annual Symposium] (download) (g-scholar)
  25. James Z. Wang, ``Region-Based Retrieval of Biomedical Images,'' Proceedings of the ACM Multimedia Conference, pp. 511-512, Los Angeles, CA, ACM, October 2000. (download) (g-scholar)
  26. Eldar Giladi, Michael G. Walker, James Z. Wang and Wayne Volkmuth, ``SST: An Algorithm for Searching Sequence Databases in Time Proportional to the Logarithm of the Database Size,'' Currents in Computational Molecular Biology, Poster Proceedings of the International Conference on Research in Computational Molecular Biology (RECOMB), Frontiers Science Series no. 30, S. Miyano, R. Shamir, T. Takagi (eds.), Universal Academy Press, Inc., Tokyo, Japan, April 2000. (download) (g-scholar)
  27. James Z. Wang, John Nguyen, Kin-Koi Lo, Christine Law and Donald Regula, ``Multiresolution Browsing of Pathology Images Using Wavelets,'' Journal of the American Medical Informatics Association, Proceedings of the AMIA Annual Symposium, vol. 1999 symposium suppl., pp. 340-344, Washington, D.C., November 1999. (download) (g-scholar)

In the midst of difficulty lies opportunity. - Albert Einstein

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