Ge Yang, Ph.D.
Associate Professor of Biomedical Engineering and Computational Biology

Contact Information

Office Laboratory
Scott Hall 4N103 Laboratory for Computational and Engineering Cell Biology
Carnegie Mellon University Scott Hall 3113-3114
5000 Forbes Ave. Carnegie Mellon University
Pittsburgh, PA 15213 5000 Forbes Ave.
Phone: 412-268-3186 Pittsburgh, PA 15213
Fax: 412-268-1173 Phone: 412-268-3186

Research Interests

My research interests are in 1) computational and systems biology; and 2) biomedical image informatics. Current research topics include:

  • Computational analysis and modeling of spatiotemporal organization of intracellular organelle networks
  • Computational analysis and modeling of organelle transport in complex geometry of neurons
  • Deep learning based techniques for computational analysis of biological images 

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

  • Best Paper Award (with Hao-Chih Lee), IEEE International Symposium on Biomedical Imaging (ISBI), 2015
  • Best Paper Award (with Kuan-Chieh Chen), International Symposium on Computational Modeling of Image Objects (CompIMAGE'14), 2014
  • 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


Publications: Journal Papers, Reviews, & Book Chapters

  1. Li A., Chai X., Zhang Y. J.* and Yang G.* (2018) Isogeometric analysis based simulation and analysis of material transport in complex geometry of neurons, submitted .
  2. Ba Q., Yu Y., Lee H.-C., and Yang G. (2018) High-resolution imaging and quantitative analysis of mitochondrial dynamics in Drosophila larval segmental axons,  submitted.
  3. Chai X., Ba. Q., and Yang G. (2018) Characterizing robustness and sensitivity of convolutional neural networks for quantitative analysis of mitochondrial morphology, Quantitative Biology, in press
  4. Ba Q., Raghavan G., Kiselyov K., and Yang G. (2018) Whole-cell scale dynamic organization of lysosomes revealed by spatial statistical analysis, Cell Reports. vol. 23, pp. 3591-3606.
  5. Ming X., Chai X., Muthakana H., Liang X., Yang G., Zeev-Ben-Mordehai T. and Xing E. (2017) Deep learning based subdivision approach for large scale macromolecules structure recovery from electron cryo tomograms, Bioinformatics, vol. 33, pp. i13-i22. 
  6. Rastogi S. K., Raghavan G., Yang G.* and Cohen-Karni T.* (2017) Effect of graphene on nonneuronal and neuronal cell viability and stress, Nano Letters, vol. 17, pp. 3297-3301. 
  7. Ba Q., and Yang G. (2016) Intracellular organelle networks: Understanding their organization and communication through systems-level modeling and analysis, Frontiers in Biology, doi:10.1007/s11515-016-1436-9. (PDF)
  8. Yu Y., Lee H.-C., Chen K.-C., Suhan J., Qiu M., Ba Q. and Yang G. (2016) Inner membrane fusion mediates spatial distribution of axonal mitochondria, Scientific Reports, doi:10.1038/srep18981. (PDF)
  9. Lee H.-C., Liao T., Zhang Y. J., and Yang G. (2015) Shape component analysis: structure-preserving dimension reduction on biological shape spaces, Bioinformatics, doi: 10.1093/bioinformatics/btv648. (PDF)(MATLAB Code)
  10. Liao T., Lee H.-C., Yang G., Zhang Y. J. (2015) Shape correspondence analysis for biomolecules based on volumetric eigenfunctions, Mol. Based Math. Biol., vol. 3, pp. 112-127.
  11. Weaver L. N., Ems-McClung S. C., Chen S. H., Yang G., Shaw S. L., and Walczak C. E. (2015) The Ran-GTP gradient spatially regulates XCTK2 in the spindle, Current Biology, vol. 25, pp. 1509-1514.
  12. Yang G. and Lee H.-C. (2015) Computational image analysis for cell mechanobiology, in Integrative Mechanobiology: Micro and Nano Techniques in Cell Mechanobiology, Yu Sun, Craig Simmon, Deok-Ho Kim eds, Cambridge University Press, to appear.
  13. 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.
  14. 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.
  15. 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.
  16. 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.
  17. 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)
  18. 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.
  19. 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.
  20. 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.
  21. 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.
  22. 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.
  23. Cameron, L.A., Houghtaling, B.R., and Yang G. (2010) Fluorescent Speckle Microscopy, inOptical Imaging Techniques: a Laboratory Manual, Yuste R. eds., Cold Spring Harbor Laboratory Press, pp. 667-682.
  24. 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.
  25. 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.
  26. 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.
  27. Dorn J., Danuser G., and Yang G. (2007) Computational processing and analysis of dynamic fluorescence image data, inFluorescent Proteins, Methods in Cell Biology, vol. 85, pp. 497-538.
  28. 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)
  29. 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.
  30. Yang G. and Nelson, B.J. (2007) Fundamentals of microscopy and machine vision, inLife Science Automation: Fundamentals and Applications, Zhang M.J., Nelson B.J., and Felder R.A. eds., pp.125-149, Artech House.
  31. Cameron L.A., Yang G., Cimini D., Canman J.C., Kisurina-Evgenieva O., Khodjakov A., Danuser G., and Salmon E.D. (2006) Kinesin 5-independent poleward flux of kinetochore microtubules in PtK1 cells, Journal of Cell Biology, vol. 173, pp. 173-179. (Cover)
  32. Shah S., Yang G., Danuser G., and Goldstein L.S.B. (2006) Axonal transport: imaging and modeling of a neuronal process, inProc. Nobel Symposium 131: Controlled Nanoscale Motion in Biological and Artificial Systems. Lecture Notes in Physics, vol. 711, pp. 65-84, Springer-Verlag.
  33. 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.
  34. 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.
  35. Yang G. and Nelson B.J. (2003) Automated microassembly, in MEMS Packaging, T.-R. Hsu ed., pp. 109-140, IEE Press.
  36. 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. Chai X., Ba Q., and Yang G. (2018) Characterizing robustness and sensitivity of convolutional neural networks in segmentation of fluorescence microscopy images, 2018 IEEE International Conference on Image Processing (ICIP), accepted
  2. Chai X., Qian D., Ba Q., Li A., Zhang J., and Yang G. (2017) Image-based measurement of cargo traffic flow in complex neurite networks,Proc. 2017 IEEE International Conference on Image Processing (ICIP), pp. 3290-3294.
  3. Yang H., Wang J., Tang H., Ba Q., Yang G., and Tang X. (2017) Mitochondrial shape analysis using large deformation diffeomorphic metric curve matching, 2017 IEEE Engineering in Medicine and Biology Conference (EMBC), pp. 4062-4065.
  4. Chen K.C., Yu Y., Kovacevic J., and Yang G. (2015) A sliding-window data aggregation method for super-resolution imaging of live cells, Proc. 2015 IEEE International Symposium on Biomedical Imaging (ISBI), pp. 785-788. Selected for oral presentation.
  5. Lee H.-C. and Yang G. (2015) Image-based computational methods for characterizing whole-cell scale spatiotemporal dynamics of intracellular transport, Proc. 2015 IEEE International Symposium on Biomedical Imaging (ISBI), pp. 699-702, ISBI 2015 Best Paper Award.
  6. 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), pp. 867-871.
  7. 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), pp. 4260-4263.
  8. 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 (Computational Modeling of Image Objects), Lecture Notes in Computer Science, vol. 8641, pp. 292-303. CompIMAGE'14 Best Paper Award.
  9. 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), pp. 205-208.
  10. 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), pp. 254-257. Selected for oral presentation
  11. 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), pp. 991-994. Selected for oral presentation.
  12. 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.
  13. 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.
  14. 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.
  15. 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. Selected for oral presentation.
  16. 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.
  17. 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.
  18. 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.
  19. 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.
  20. 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.
  21. 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.
  22. 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

  • Angran Li (Fall 2016-), Ph.D. student, Mechanical Engineering (co-advised with Prof. Jessica Zhang)
  • Qinle Ba (Fall 2013-), Ph.D. student, Biomedical Engineering
  • Sahil Rastogi (Fall 2015-) Ph.D. student, Biomedical Engineering (co-advised with Prof. Tzahi Cohen-Karni)
  • Xiaoqi Chai (Fall 2015-) Ph.D. student, Biomedical Engineering
  • Siyu Chen (Fall 2017-) M.S. student, Biomedical Engineering

Alumni of Yang Research Group

External Research Funding

  • Samuel and Emma Winters Foundation
  • National Science Foundation

In Memory of Tony Pawson (1952-2013)

"Indeed, I think that new and unpredictable ideas flowing from fundamental research in the sciences and humanities will be essential for us to transcend the problems we face in combating disease, climate change and social upheaval. I personally envisage a world in which the diseases that afflict mankind are fully brought to bay, so that every child born into the world has the promise of a full and natural life span. At this challenging time in history, this may seem overly optimistic, but I believe that humankind has the genius, the altruism and the passion to make this a reality. As I said in my acceptance speech yesterday, we are a young and inventive species."

- Tony Pawson, Kyoto Prize Commemorative Lecture, 2008