Ge Yang, Ph.D.

Associate Professor, Department of Biomedical Engineering

Associate Professor, Lane Center for Computational Biology

Associate Professor, Department of Biological Sciences (courtesy appointment)

Contact Information

Office Laboratory
Mellon Institute 403 Computational Cell Dynamics Laboratory
Carnegie Mellon University Mellon Institute 280
4400 Fifth Ave. Carnegie Mellon University
Pittsburgh, PA 15213 4400 Fifth Ave.
Phone: 412-268-3186 Pittsburgh, PA 15213
Fax: 412-268-1173 Phone: 412-268-3281
Email: geyang@andrew.cmu.edu  

Research Interests

My research interests are in computational cell biology, bioimage informatics, molecular cell mechanics, and fluorescence imaging. Current research topics include:
  • Experimental and computational analysis of spatiotemporal regulatory mechanisms of axonal cargo transport
  • Active control of intracellular transport for targeted intracellular delivery
  • Imaging-based experimental and computational analysis of spatial-temporal dynamics of cell signaling and the cytoskeleton
  • Molecular cell mechanics of the cytoskeleton
  • Advanced experimental and computational fluorescence live imaging

Open Positions

  • We welcome undergraduate students with excellent academic records to participate in our research projects. Please contact Prof. Yang for potential opportunities.

Academic Affiliations

Academic Background

Honors & Awards

  • National Science Foundation Faculty Early Career Award, 2012
  • Invited participant, IEEE EMBS Forum on Grand Challenges in Biomedical Imaging, 2012
  • Invited participant, NSF Ideas Lab on Innovations in Biological Imaging and Visualization, 2010
  • Wimmer Faculty Fellow, Wimmer Foundation and Eberly Center for Teaching Excellence, Carnegie Mellon University, 2009
  • Nomination for Burroughs-Wellcome Interfaces in Science Award, Scripps Research Institute, 2007
  • Burroughs-Wellcome LJIS Interdisciplinary Fellowship, Burroughs-Wellcome Fund, 2006-2007
  • Excellent Student Award, Institute of Automation, Chinese Academy of Sciences, 1997
  • Elite Fellowship, Chinese Academy of Sciences, 1996
  • Guanghua Fellowship, Tsinghua University, 1989

Professional Services

Teaching

Publications: Journal Papers, Reviews, & Book Chapters

  1. Yang G. (2014) Image-based computational tracking and analysis of spindle protein dynamics, in Mitosis: Methods and Protocols, Methods in Molecular Biology, D. Sharp ed., vol. 1136, DOI 10.1007/978-1-4939-0329-0_5, Springer.
  2. Gunawardena S., Yang G., and Goldstein L. S. B. (2013) Presenilin controls kinesin-1 and dynein function during AP vesicle transport in vivo, Human Molecular Genetics, vol. 22, pp. 3838-3843.
  3. Yang G. (2013) Bioimage informatics for understanding spatiotemporal dynamics of cellular processes (invited review), Wiley Interdisciplinary Reviews Systems Biology and Medicine, vol. 5, pp. 367-380.
  4. Booth-Gauthier E. A., Alcoser T. A., Yang G., and Dahl K. N. (2012) Force-induced changes in subnuclear movement and rheology, Biophysical Journal, vol. 103, pp. 2423-2431.
  5. Reis R. F.*, Yang G.*, Szpankowski L., Weaver C., Shah S. B., Robinson J. T., Hays T. S., Danuser G., and Goldstein L. S. B. (2012) Molecular motor function in axonal transport in vivo probed by genetic and computational analysis in Drosophila, Molecular Biology of the Cell, vol. 23, pp. 1700-1714. (*: equal contribution)
  6. Gable A., Qiu M., Titus J., Balchand S., Ferenz N. F., Ma N., Fagerstrom C., Ross R. L., Yang G., and Wadsworth P. (2012), Dynamic reorganization of Eg5 in the mammalian spindle throughout mitosis requires dynein and TPX2, Molecular Biology of the Cell, vol. 23, pp. 1254-1266.
  7. Roy S., Yang G., Tang Y., and Scott D. (2012) A simple photoactivation and image analysis module for visualizing and analyzing axonal transport with high temporal resolution, Nature Protocols, vol. 7, pp. 62-68, 2012.
  8. Matov A., Edvall M.M., Yang G., and Gaudenz Danuser (2011), Optimal‐flow minimum-cost correspondence assignment in particle flow tracking, Computer Vision and Image Understanding, vol. 115, pp. 531-540.
  9. Weinger J., Qiu M., Yang G., and Kapoor T. (2011) A nonmotor microtubule binding site in kinesin-5 is required for filament crosslinking and sliding, Current Biology, vol. 21, pp. 1-7.
  10. Goodman B., Channels W., Qiu M., Iglesias P., Yang G.*, Zheng Y.* (2010) Lamin B counteracts the kinesin Eg5 to restrain spindle pole separation during spindle assembly, Journal of Biological Chemistry, vol. 285, pp. 35238-35244.
  11. Cameron, L.A., Houghtaling, B.R., and Yang G. (2010) Fluorescent Speckle Microscopy, in Optical Imaging Techniques: a Laboratory Manual, Yuste R. eds., Cold Spring Harbor Laboratory Press, pp. 667-682.
  12. Applegate, K., Yang G., Danuser, G. (2009) High-content analysis of cytoskeleton functions by fluorescent speckle microscopy, Nanotechnology, vol. 5, Nanomedicine, Vogel V. et al. eds., pp. 167-206, Wiley-VCH.
  13. Houghtaling B.R., Yang G.*, Matov A.*, Danuser G., and Kapoor T. (2009) Op18 reveals the contribution of non-kinetochore microtubules to the dynamic organization of the vertebrate meiotic spindle, Proceedings of the National Academy of Sciences, vol. 106, pp. 15338-15343.
  14. Yang G.*, Cameron L.A.*, Danuser G., and Salmon E.D. (2008) Regional variation of microtubule flux reveals microtubule organization in Xenopus extract meiotic spindles, Journal of Cell Biology, vol. 182, pp. 631-639.
  15. Dorn J., Danuser G., and Yang G. (2007) Computational processing and analysis of dynamic fluorescence image data, in Fluorescent Proteins, Methods in Cell Biology, vol. 85, pp. 497-538.
  16. Yang G.*, Houghtaling B.R.*, Gaetz J., Liu J.Z., Danuser G., and Kapoor T.M. (2007), Architectural dynamics of the meiotic spindle revealed by single-fluorophore imaging, Nature Cell Biology, vol. 9, pp. 1233-1242. (*equal contribution)
  17. Haghnia M., Cavalli V., Shah S.B., Schimmelpfeng K., Brusch R., Yang G., Herrera C., Pilling A., and Goldstein, L.S.B. (2007), Dynactin is required for coordinated bidirectional motility, but not for dynein membrane attachment, Molecular Biology of the Cell, vol. 18, pp. 2081-2089.
  18. Yang G. and Nelson, B.J. (2007) Fundamentals of microscopy and machine vision, in Life Science Automation: Fundamentals and Applications, Zhang M.J., Nelson B.J., and Felder R.A. eds., pp.125-149, Artech House.
  19. Cameron L.A., Yang G., Cimini D., Canman J.C., Kisurina-Evgenieva O., Khodjakov A., Danuser G., and Salmon E.D. (2006) A pulling-in mechanism produces the majority of kinetochore microtubule poleward flux in PtK1 cells, Journal of Cell Biology, vol. 173, pp. 173-179. (Cover)
  20. Shah S., Yang G., Danuser G., and Goldstein L.S.B. (2006) Axonal transport: imaging and modeling of a neuronal process, in Proc. Nobel Symposium 131: Controlled Nanoscale Motion in Biological and Artificial Systems. Lecture Notes in Physics, vol. 711, pp. 65-84, Springer-Verlag.
  21. Yang G. and Nelson B.J. (2005) Optomechatronic design of microassembly systems for manufacturing hybrid microsystems, IEEE Transactions on Industrial Electronics, vol. 52, pp. 1013-1023. 1989
  22. Yang G., Gaines J.A., and Nelson B.J. (2003) A supervisory wafer-level microassembly system for hybrid MEMS fabrication, Journal of Intelligent and Robotic Systems, vol. 37, pp. 43-68.
  23. Yang G. and Nelson B.J. (2003) Automated microassembly, in MEMS Packaging, T.-R. Hsu ed., pp. 109-140, IEE Press.
  24. Vikramaditya B., Nelson B.J., Yang G., and Enikov E.T. (2001) Microassembly of hybrid magnetic MEMS, Journal of Micromechatronics, vol. 1, pp. 99-116.

Publications: Peer Reviewed Conference Papers

  1. Chen K.C., Yang G., and Kovacevic J. (2014) Spatial density estimation based segmentation of super-resolution localization microscopy images, Proc. 2014 IEEE International Conference on Image Processing (ICIP), to appear.
  2. Xu J.Q., Yu Y., Lee H.-C., Fan Q., Winter J., and Yang G. (2014) Cell penetrating peptide mediated quantum dot delivery and release in live mammalian cells, Proc. 36th Annual International Conference of IEEE Engineering in Medicine and Biology Society (EMBC2014), to appear.
  3. Chen K.C., Qiu M., Kovacevic J., and Yang G. (2014) Computational image modeling for characterization and analysis of intracellular cargo transport, Proc. of CompIMAGE'14, to appear.
  4. Lee H.-C. and Yang G. (2014) Computational removal of background fluorescence for biological fluorescence microscopy, Proc. 2014 IEEE International Symposium on Biomedical Imaging (ISBI), to appear.
  5. Lee H.-C. and Yang G. (2014) Integrating dimension reduction with mean-shift clustering for biological shape classification, Proc. 2014 IEEE International Symposium on Biomedical Imaging (ISBI), to appear.
  6. Chen K.-C. Kovacevic J., and Yang G. (2014) Structure-based determination of imaging length for super-resolution localization microscopy, Proc. 2014 IEEE International Symposium on Biomedical Imaging (ISBI), to appear.
  7. Yang G. and Olivo-Marin J.-C. (2013) Image-based representation and modeling of spatiotemporal cell dynamics, Proc. 2013 IEEE International Symposium on Biomedical Imaging (ISBI), pp. 1198-1201.
  8. Qiu M. and Yang G. (2013), Drift correction for fluorescence live cell imaging through correlated motion detection, Proc. 2013 IEEE International Symposium on Biomedical Imaging (ISBI), pp. 452-455.
  9. Chen K.-C., Yu Y., Li R., Lee H.-C., Yang G., and Kovacevic J. (2012), Adaptive active-mask image segmentation for quantitative characterization of mitochondrial morphology, Proc. 2012 IEEE International Conference on Image Processing (ICIP), pp. 2033-2036.
  10. Qiu M., Lee H.-C., and Yang G. (2012), Nanometer resolution tracking and modeling of bidirectional axonal cargo transport, Proc. 2012 IEEE International Symposium on Biomedical Imaging (ISBI), pp. 992-995.
  11. Yang G. (2011) Nanometer resolution imaging and tracking of axonal cargo transport in normal and degenerative neurons (invited paper), Proc. 45th Annual Asilomar Conference on Signals, Systems, and Computers, pp. 431-435.
  12. Yang G., Matov A., and Danuser G. (2005) Reliable tracking of large-scale dense particle motion for fluorescent live cell imaging. Proc. Workshop on Computer Vision Methods for Bioinformatics, IEEE Int. Conf. Computer Vision and Pattern Recognition. pp. 9-17.
  13. Yang G. and Nelson B.J. (2003) Wavelet-based autofocusing and unsupervised segmentation of microscopic images. Proc. IEEE/RSJ Int. Conf. Intelligent Robots and Systems, vol. 3, pp. 2143-2148.
  14. Yang G. and Nelson B.J. (2003) Micromanipulation contact transition control by selective focusing and microforce control. Proc. IEEE Int. Conf. Robotics and Automation, vol. 3, pp. 3200-3206.
  15. Yang G. and Nelson B.J. (2002) Integration of microscopic vision and microforce feedback for microassembly. Proc. 3rd Int. Workshop on Microfactories, pp. 145-148.
  16. Greminger M., Yang G., and Nelson B.J. (2002) Sensing nanonewton level forces by visually tracking structural deformations. Proc. IEEE Int. Conf. Robotics and Automation, vol. 2, pp. 1943-1948.
  17. Yang G., Gaines J.A., and Nelson B.J. (2001) A flexible experimental workcell for efficient and reliable wafer-level 3D microassembly. Proc. IEEE Int. Conf. on Robotics and Automation, vol. 1, pp. 133-138.

Current Postdoc & Graduate Students

  • Qinle Ba (Fall 2013-), Ph.D. student, Biomedical Engineering
  • Hao-Chih Lee (Fall 2011-), Ph.D. student, Biomedical Engineering
  • Jackie Kuan-Chieh Chen (Fall 2011-), Ph.D. student, Biomedical Engineering, co-advised with Prof. Jelena Kovacevic.
  • Yiyi Yu (Fall 2010-), Ph.D. student, Biomedical Engineering
  • Harsh Saxena (Spring 2014 -) M.S. student, Biomedical Engineering
  • Sahil Rastogi (Fall 2013-) M.S. student, Biomedical Engineering

Alumni of Yang Research Group

External Research Funding

  • Samuel and Emma Winters Foundation
  • National Science Foundation