Associate Professor Dr.-Ing. Kuangyu Shi

Associate Professor Dr.-ing Kuangyu Shi
Senior Scientist	Head of Lab for Artificial Intelligence & Translational Theranostics
Email:k.shi@tum.de	Email:kuangyu.shi@dbmr.unibe.ch
Address:	Address:
Chair for Computer Aided Medical Procedures & Augmented Reality Fakultät für Informatik Technische Universität München Boltzmannstr. 3 85748 Garching b. München	Lab for Artificial Intelligence & Translational Theranostics Dept. Nuclear Medicine Inselspital University of Bern 3010 Bern

Research Focus

• Translational molecular imaging computing
• Deep learning for computer-aided diagnosis
• Computational modeling of molecular imaging and tumor microenvironment

Short CV

• 04/2018 – present
  Lab for Artificial Intelligence & Translational Theranostics Dept. Nuclear Medicine, Inselspital, University of Bern, Switzerland
  • Head of Lab for Artificial Intelligence & Translational Theranostics
  

• 04/2018 – present
  Chair for Computer-aided Medical Procedures, Dept. Informatics, Technical University of Munich, Germany
  • Senior scientist
  

• 05/2018
  Dept. Informatics, Technical University of Munich, Germany
  • Habilitation
  

• 12/2011 – 03/2018
  Dept. Nuclear Medicine, Technical University of Munich, Germany
  • Head of subgroup for translational molecular imaging computing supported by Prof. Sibylle Ziegler and Prof. Markus Schwaiger
  

• 12/2008 – 11/2011
  Dept. Radiation Oncology & Dept. Nuclear Medicine, Technical University of Munich, Germany
  • Postdoctoral researcher
  

• 02/2005 – 11/2008
  Max-Planck Institute for Computer Science, Saarbrücken, Germany
  • Ph.D in Computer Science, supervised by Prof. Holger Theisel and Prof. Hans-Peter Seidel
  

• 10/2003 – 01/2005
  International Max-Planck Research School, Saarbrücken, Germany
  • Master in Computer Science
  

• 09/1999 – 07/2003
  Nanjing University, China
  • Bachelor in Computer Science & Bachelor in Physics
  

Teaching

Open Positions

My lab in Bern is opening several PhD and Postdoc positions:

Candidates in computer science, bio-medical engineering, medicine, biology or related fields with interest in participating in an interdisciplinary team of international scientists and motivation in develop-ing/establishing cutting-edge technologies and methods for molecular imaging and radionuclide therapy are encouraged to apply. The salaries of these positions are according to the standard of University of Bern.

Candidates are expected to have
• Strong communication and collaboration skills
• A good command of English
• Strong motivation in clinically translational research

and in-depth knowledge in at least one of the following fields:
• Machine learning, deep learning and programming with python
• Image processing, computer vision and programming with related language
• Semiconductor detector, nuclear physics and Monte-Carlo simulation
• Computational simulation, finite-element method and programming with related language
• Neuroimaging, clinical neuroscience and data analysis
• Tumor imaging, clinical oncology and data analysis
• Molecular biology, organoid and preclinical experiments

Applicants are requested to send a motivation letter, CV and the names and two recommendation letters to PD Dr. Kuangyu Shi and Prof. Dr. Axel Rominger, email: kuangyu.shi@dbmr.unibe.ch and axel.rominger@insel.ch before 15.12.2019.

Publications

• T Grimmer†∗, K Shi†∗, J Diehl-Schmid, B Natale, A Drzezga, S Frster, H Frstl, M Schwaiger, I Yakushev, HJ Wester, A Kurz, BH Yousefi. 18F-FIBT may expand PET for -amyloid imaging in neurodegenerative diseases. Mol Psychiatry 2018 Aug 17 († Equal contribution)

• L. Xu, G. Tetteh, J. Lipkova, Y. Zhao, H. Li, P. Christ, M. Piraud, A. Buck, K. Shi†∗ and B. H. Menze†. Automated Whole-Body Bone Lesion Detection for Multiple Myeloma on 68GaPentixafor PET/CT Imaging Using Deep Learning Methods. Contrast Media Mol Imaging, Epub online Jan. 2018 († Equal contribution, * Corresponding author)

• L Xu, P Vaupel, BH Menze, K Shi. Impact of Temporal Heterogeneity of Acute Hypoxia on the Radiation Response of Experimental Tumors. Adv Exp Med Biol 2018;1072:189-194

• L. Xu, P. Vaupel, S. Bai, B. H. Menze, K. Shi. Computational Simulation of Tumor Hypoxia Based on in vivo Microvasculature Assessed in a Dorsal Skin Window Chamber. Adv Exp Med Biol 2017;977:109-117

• K. Shi, C. Bayer, F. Gaertner, S. T. Astner, J.J. Wilkens, F. Nuesslin, P. Vaupel, S. I. Ziegler. Matching the reaction-diffusion simulation to dynamic [18F]FMISO PET measurements in tumors: extension to a flow-limited oxygen-dependent model. Physiol Meas 2017; 38 (2): 188-204

• K. Shi, S. Fu¨rst, L. Sun, M. Lukas, N. Navab, S. F¨orster, S. I. Ziegler. Individual refinement of attenuation correction maps for hybrid PET/MR based on multi-resolution regional learning. Comput Med Imaging Graph 2017; in press

• H. Zhang, P. Wu, S. I. Ziegler, Y. Guan, Y. Wang, J. Ge, M. Schwaiger, S. C. Huang, C. Zuo, S. F¨orster, K Shi. Data-driven Identification of Intensity Normalization Region based on Longitudinal Coherency of 18F-FDG Metabolism in the Healthy Brain. NeuroImage^? 2017; 146:589-599

• Z. Liu, Z. Jian, Q. Wang, T. Cheng, B. Feuerecker, M. Schwaiger, S.-C. Huang, S. I. Ziegler, K. Shi. A Continuously Infused Microfluidic Radioassay System for the Characterization of Cellular Pharmacokinetics. J Nucl Med 2016; 57(10):1548-1555

• K. Shi, C. Bayer, S. T. Astner, F. C. Gaertner, P. Vaupel, M. Schwaiger, S. C. Huang, S. I. Ziegler. Quantitative Analysis of [18F]FMISO PET for Tumor Hypoxia: Correlation of Modeling Results with Immunohistochemistry. Mol Imaging Biol 2017; 19(1):120-129

• K. Shi, S. I. Ziegler, P Vaupel. Molecular imaging of tumor hypoxia: Existing problems and their potential model-based solutions. Adv Exp Med Biol 2016; 923:87-93

• Q. Wang, Z. Liu, S. I. Ziegler, K. Shi. Enhancing spatial resolution of 18F positron imaging with the timepix detector by classification of primary fired pixels using support vector machine. Phys Med Biol 2015; 60(13):5261-5278

• X. Cheng, Z. Li, Z. Liu, N. Navab, S. C. Huang, U. Keller, S. I. Ziegler, K. Shi. Direct Parametric Image Reconstruction in Reduced Parameter Space for Rapid Multi-Tracer PET Imaging. IEEE Trans Med Imaging 2015; 34(7):1498-1512

• Q. Wang, P. Vaupel, S. I. Ziegler, K. Shi. Exploring the quantitative relationship between metabolism and enzymatic phenotype by physiological modeling of glucose metabolism and lactate oxidation in solid tumors. Phys Med Biol 2015; 60(6): 2547-2571

• X. Cheng, C. Bayer, C. A. Maftei, S. T. Astner, P. Vaupel, S. I. Ziegler, K. Shi. Preclinical evaluation of parametric image reconstruction of [18F]FMISO PET: correlation with ex vivo immunohistochemistry. Phys Med Biol 2014;59(2):347-62

• Q. Wang, J. Tous, Z. Liu, S. I. Ziegler, K. Shi. Evaluation of Timepix Silicon Detector for the Detection of 18F Positrons. J Inst 2014

• K. Shi, M. Souvatzoglou, S.T. Astner, P. Vaupel, F. Nu¨sslin, J. J. Wilkens, S. I. Ziegler. Quantitative assessment of hypoxia kinetic models by a cross-study of dynamic 18F-FAZA and 15OH2O in patients with head and neck tumors. J Nucl Med, 51(9) 2010

• K. Shi, H. Theisel, T. Weinkauf, H. C. Hege and H. P. Seidel. Visualizing Transport Structures of Time-dependent Flow Fields. IEEE Computer Graphics and Applications, 28(5), 2008

• K. Shi, H. Theisel, T. Weinkauf, H. Hauser, H. C. Hege and H.-P. Seidel. Extracting Separation Surfaces of Path-line Oriented Topology in Periodic 2D Time-Dependent Vector Fields. Journal of WSCG, 2007