Assistant Professor

University of Kentucky | Biomedical Informatics | Computer Science

PI Mailing Address:
Lin Yang
Division of Biomedical Informatics,
Department of Biostatistics,
Department of Computer Science,
230D Multidisciplinary Science Building,
725 Rose Street,
University of Kentucky,
Lexington, KY, 40536-0082, U. S. A.
Phone: 859-218-2248
Fax: 859-257-9019

BICI2 Lab Mailing Address:
230A, B, C Multidisciplinary Science Building,
725 Rose Street,
Lexington, KY, 40536-0082, U. S. A.
Fax: 859-257-9019

Education

Ph. D., M. S.: Rutgers University | Electrical Computer Engineering
M. S., B. S.: Xian Jiaotong University | Information and Signal Processing

Publication

Selected Peer Reviewed Journals:

  1. Hongyuan Wang, Fuyong Xing, Hai Su, Arnold Stromberg, Lin Yang, “Novel image markers for non-small cell lung cancer classification and survival prediction”, Accepted to BMC Bioinformatics, 2014
  2. Xin Qi, Daihou Wang, Ivan Rodero, Javier Diaz-Montes, Rebekah H Gensure, Fuyong Xing, Hua Zhong, Lauri Goodell, Manish Parashar, David J Foran, Lin Yang, “Content-based histopathology image retrieval using CometCloud”, Accepted to BMC Bioinformatics, 2014
  3. Fujun Liu, Christopher S. Fry, Jyothi Mula, Janna R. Jackson, Jonah D. Lee, Charlotte A. Peterson, Lin Yang, “Automated fiber-type-specific cross-sectional area assessment and myonuclei counting in skeletal muscle”, Journal of Applied Physiology (JAP), Vol. 115, No. 11, pp. 1714-1724, 2013
  4. Fuyong Xing, Hai Su, Janna Neltner, Lin Yang, “Automatic Ki-67 counting using robust cell detection and online dictionary learning”, IEEE Transaction on Biomedical Engineering (TBME), Vol. 61, No. 3, pp. 859-870, 2013
  5. Fujun Liu, Abigail L. Mackey, Ratchakrit Srikuea, Karyn Esser, Lin Yang, “Automated image segmentation of haemotoxylin and eosin stained skeletal muscle cross-sections”, Journal of Microscopy (JM), Vol. 252, No. 3, pp. 275-285, 2013
  6. Lin Yang, Xin Qi, Fuyong Xing, Tahsin Kurc, Joel Saltz, David J. Foran, “Parallel content based sub-image retrieval using hierarchical searching”, Bioinformatics, Vol. 30, No. 7, pp. 996-1002, 2013
  7. Hai Su, Fuyong Xing, Jonah Lee, Charlotte Peterson, Lin Yang, “Automatic myonuclear detection in isolated single muscle fiber using robust ellipse fitting and sparse optimization”, Accepted to IEEE/ACM Transaction on Computational Biology and Bioinformatics (TCBB), 2013
  8. Baiyang Liu, Junzhou Huang, Casimir Kulikowski, Lin Yang, "Robust visual tracking using local sparse apperance model and K-Selection",IEEE Transaction on Pattern Analysis and Machine Intelligence (TPAMI), Vol. 35, No. 12, pp. 2968-2981, 2013
  9. Xin Qi, Fuyong Xing, David J. Foran and Lin Yang, "Robust segmentation of overlapping cells in histopathology specimens using parallel seed detection and repulsive level set ", IEEE Transaction on Biomedical Engineering (TBME), Vol. 59, No. 3, pp. 754-765, 2012
  10. Xin Qi, Fuyong Xing, David J. Foran, Lin Yang, "A fast, automatic segmentation algorithm for locating and delineating touching cell boundaries in Imaged histopathology ", Journal of Methods in Medical Informatics (JMMI), Vol. 51, No. 3, pp. 91- 102, 2012
  11. Rebekah H. Gensure, David J. Foran, Vincent M. Lee, Vyacheslav Gendel, Salma K. Jabbour, Darren R. Carpizo, John L. Nosher, Lin Yang, "Evaluation of hepatic tumor response to Yttrium-90 radioembolization therapy using texture signatures generated from contrast-enhanced CT images", Academic Radiology, Vol. 19, No. 10, pp. 1201-1207, 2012
  12. Xin Qi, Hyunjoo Kim, Fuyong Xing, Manish Parashar, David J. Foran, Lin Yang, “The analysis of image feature robustness using CometCloud”, Journal of Pathology Informatics (JPI), Vol. 3, No. 33, pp. 1-13, 2012
  13. David J. Foran , Lin Yang, Wenjin Chen, Jun Hu, Lauri A. Goodell, Michael Reiss, Fusheng Wang, Tahsin Kurc, Tony Pan, Ashish Sharma, and Joel Saltz. "Image miner: A software system for comparative analysis of tissue microarrays using content-based image retrieval, high-performance computing, and Grid technology", Journal of American Medical Information Association (JAMIA), Vol. 18, No. 4, pp. 403-415, 2011
  14. Lin Yang, Bogdan Georgescu, Yefeng Zheng, Wang Yang, Peter Meer and Dorin Comaniciu, "Prediction based collaborative trackers (PCT): A robust and accurate approach toward 3D medical object tracking", IEEE Transaction on Medical Imaging (TMI), Vol. 30, No. 11, pp. 1921-1932, 2011
  15. Jianqin Qu, Leiguang Gong and Lin Yang, "A 3D point matching algorithm for affine registration", International Journal of Computer Assisted Radiology and Surgery (IJCARS), Vol. 6, No. 2, pp. 229-237, 2010.
  16. Lin Yang, Oncel Tuzel, Wenjin Chen, Peter Meer, Gratian Salaru, Lauri A. Goodell and David J. Foran, "PathMiner: A web-based tool for computer assisted diagnostics in pathology", IEEE Transaction on Information Technology in Biomedicine (TITB), Vol. 13, No. 3, pp. 291-299, 2009
  17. Lin Yang, Wenjin Chen, Peter Meer, Gratian Salaru, Viktors Berstis and David J. Foran, "Virtual microscopy and grid-enabled decision support for large scale analysis of imaged pathology specimens", IEEE Transaction on Information Technology in Biomedicine (TITB), Vol. 13, No. 4, pp. 636-644, 2009
  18. Oncel Tuzel, Lin Yang, Peter Meer and David J. Foran, "Classification of hematologic malignancies using texton signatures", Pattern Analysis and Applications (PAA), Vol. 10, No. 4, pp. 277-290, 2007.
  19. Lin Yang, Peter Meer and David J. Foran, "Unsupervised segmentation based on robust estimation and color active contour models", IEEE Transaction on Information Technology in Biomedicine (TITB) , Vol. 9, No. 3, pp. 475-486, 2005.

Other Peer Reviewed Journals:

  1. Christopher S. Fry, Jonah D. Lee, Jyothi Mula, Tyler J. Kirby, Janna R. Jackson, Fujun Liu, Lin Yang, Esther E. Dupont-Versteegden, John J. McCarthy, Charlotte A. Peterson, "No causal relationship between loss of muscle satellite cells and sarcopenia", Accepted to Nature Medicine, 2014
  2. Sandra Donkervoort, Ying Hu, Tanya Stojkovic, Nicol Voermans, A. Reghan Foley, Meganne E Leach, Jahannaz Dastgir, Veronique Bolduc, Thomas Cullup, Alix de Becdelievre, Lin Yang, Hai Su, Katherine Meilleur, Alice Schindler, Erik-Jan Kamsteeg, Pascale Richard, Russell Butterfield, Thomas L. Winder, Thomas Crawford, Robert B. Weiss, Francesco Muntoni, Valerie Allamand, Carsten G. Bonnemann, "Mosaicism for dominant COLVI mutations as a cause for intra-familial phenotypic variability", Accepted to Human Mutation, 2014
  3. Michael Spencer, Lin Yang, Akosua Adu, Brian S. Finlin, Beibei Zhu, Lindsey R. Shipp, Neda Rasouli, Charlotte A. Peterson, Philip Kern, "Pioglitazone treatment reduces adipose tissue inflammation through reduction of mast cell and macrophage number and by improving vascularity", Accepted to PLOS ONE, 2014
  4. Nicolas Wein, Adeline Vulin, Maria Sofia Falzarano, Christina Al-Khalili Szigyarto, Baijayanta Maiti, Andrew Findlay, Kristin H. Heller, Mathias Uhlen, Baskar Bakthavachalu, Sonia Messina, Giuseppe Vita, Chiara Passarelli, Francesca Gualandi, Steve D. Wilton, Louise Rodino-Klapec, Lin Yang, Diane M. Dunn, Daniel Schoenberg, Robert B. Weiss, Michael T. Howard, Alessandra Ferlini, Kevin M. Flanigan, "A novel DMD IRES results in a functional N-truncated dystrophin, providing a potential route to therapy for patients with 5’ mutations", Accepted to Nature Medicine, 2014
  5. Michael W. Lawlor, Marissa G. Viola, Hui Meng, Rachel V. Edelstein,  Fujun Liu, Ke Yan, Elizabeth J. Luna, Alexandra Lerch-Gaggl, Ray Hoffmann, Christopher R. Pierson, Anna Buj-Bello, Jennifer L. Lachey, Scott Pearsall, Lin Yang, Cecilia Hillard, Alan H. Beggs, "Differential muscle hypertrophy is associated with satellite cell numbers and Akt pathway activation following activin type IIB receptor inhibition in Mtm1 p.R69C mice", Accepted to American Journal of Pathology (AJP), 2014

  6. Hui Meng, Paul M. L. Janssen, Robert W. Grange, Lin Yang, Alan H. Beggs, Lindsay C. Swanson, Stacy A. Cossette, Alison Frase, Martin K. Childers, Henk Granzier, Emanuela Gussoni, Michael W. Lawlor, "Tissue triage and freezing for models of skeletal muscle disease", Accepted to Journal of Visualized Experiments (JOVE), 2013
  7. Jyoti Mula, Jonah Lee, Fujun Liu, Lin Yang, Charlotte Peterson, "Automatic image analysis of skeletal muscle fibre cross-sectional area", Journal of Applied Physiology (JAP), Vol. 114, No. 1, pp. 148-155, 2013
  8. David J. Foran, Wenjin Chen and Lin Yang, "Automated image interpretation computer-assisted diagnosis", Analytical Cellular Pathology (ACP), Vol. 34, No. 6, pp. 279-300, 2011

Peer Reviewed Conferences:

  1. Xiaofan Zhang, Lin Yang, Wei Liu, Hai Su, Shaoting Zhang, "Mining histopathology images via compsite hashing and online learning", Accpeted to the 17th International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI), 2014
  2. Fujun Liu, Fuyong Xing, Lin Yang, “Robust muscle cell segmentation using region selection with dynamic programming”,2014 International Symposium on Biomedical Imaging (ISBI), 2013
  3. Fujun Liu, Fuyong Xing, Hai Su, Lin Yang, “Touching adipocyte cells decomposition using combinatorial optimization”,2014 International Symposium on Biomedical Imaging (ISBI), 2013
  4. Daihou Wang, Xin Qi, Manish Parashar, David J. Foran, Lin Yang, “High throughput content-based image retrieval using GPGPU”, The Six High Performance Computing Workshop Associated with The 16th International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI), Vol. 1, pp. 1-8, 2013
  5. Xin Qi, Daihou Wang, Javier Diaz-Montes, Ivan Rodero, Tony Pan, Abulimit Aji, Lee Cooper, Fuyong Xing, Manish Parashar, David J. Foran, Lin Yang, “Exploring online nuclear segmentation on large fluorescence brain tumor images using CometCloud”, The Six High Performance Computing Workshop Associated with The 16th International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI), Vol. 1, pp. 50-58, 2013
  6. Fuyong Xing, Hai Su, Lin Yang, “An integrated framework for automatic Ki-67 scoring in pancreatic neuroendocrine tumor”, The 16th International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI), Vol. 8149, pp. 436-443, 2013
  7. Fuyong Xing, Lin Yang, “Robust Selection-based Sparse Shape Model for Lung Cancer Image Segmentation”, The 16th International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI), Vol. 8151, pp. 404-412, 2013
  8. Fuyong Xing, Lin Yang, “Robust cell segmentation for non-small cell lung cancer”, 2013 International Symposium on Biomedical Imaging (ISBI), Vol. 1, pp. 386-389, 2013
  9. Hai Su, Fuyong Xing, Jonah Lee, Charlotte Peterson, Lin Yang, “Learning based automatic detection of myonuclei in isolated single skeletal muscle fibers using multi-focus image fusion”, 2013 International Symposium on Biomedical Imaging (ISBI), Vol. 1, pp. 432-435, 2013
  10. Xin Qi, Rebekah H. Gensure, David J. Foran, Lin Yang, "Content-based white blood cell retrieval on bright-field pathology images", SPIE International Symposium on Medical Imaging (SPIE), Vol. 8676, pp. 100-110, 2013
  11. Fuyong Xing, Baiyang Liu, Xin Qi, David J. Foran, Lin Yang, "Digital tissue microarray classification using sparse reconstruction", SPIE International Symposium on Medical Imaging (SPIE), Vol. 8314, pp. 50-60, 2012
  12. Xin Qi, Fuyong Xing, Meghana Ghadge, Ivan Rodero, Moustafa Abdelbaky, Manish Parashar, Evita Sadimin, David Foran, Lin Yang , “Content-based image retrieval on imaged peripheral blood smear specimens using high performance computation”, Data- and Compute-intensive Clinical and Translation Imaging associated with the International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI), Vol. 1, pp. 11-19, 2012
  13. Fuyong Xing, Xin Qi, David J. Foran, Tahsin Kurc, Joel Saltz, Lin Yang , “Content-based parallel sub-image retrieval”, Data- and Compute-intensive Clinical and Translation Imaging associated with the International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI), Vol. 1, pp. 31-40, 2012
  14. Baiyang Liu, Junzhou Huang, Lin Yang, Casimir Kulikowski. "Robust tracking using local sparse appearance model and K-Selection", Proc. IEEE International Conference on Computer Vision and Pattern Recognition (CVPR), Vol. 1, pp. 1-8, 2011
  15. Xin Qi, Fuyong Xing, David J. Foran and Lin Yang, "Comparative performance analysis of stained histopathology specimens using RGB and multispectral Imaging", SPIE International Symposium on Medical Imaging(SPIE), Vol. 7963, pp. 120-128, 2011
  16. Lin Yang, Hyunjoo Kim, Manish Parashar and David Foran, "High throughput landmark based image registration using Cloud computing", High Performance Computing (HP) workshop associated with Proc. International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI), Vol. 1, pp. 21-29, 2011
  17. Xin Qi, Hyunjoo Kim, Fuyong Xing, Manish Parashar, David Foran and Lin Yang, "The analysis of image texture feature robustness using CometCloud", High Performance Computing (HP) workshop associated with Proc. International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI), Vol. 1, pp. 80-88, 2011
  18. Xin Qi, Fuyong Xing, David J. Foran and Lin Yang, "GPU enabled parallel touching cell segmentation using mean shift based seed detection and repulsive level set", High Performance Computing (HP) workshop associated with Proc. International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI), Vol. 1, pp. 30-40, 2010
  19. Tahsin Kurc, Patrick Widener, Wenjin Chen, Fusheng Wang, Lin Yang, Jun Hu, Vijay Kumar, Vicky Chu, Lee Cooper, Jun Kong, Ashish Sharma, Tony Pan, Joel Saltz, David Foran, "Grid-enabled, high-performance microscopy image analysis", High Performance Computing (HP) workshop associated with Proc. International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI), Vol. 1, pp. 11-20, 2010
  20. Baiyang Liu, Lin Yang, Junzhou Huang, P. Meer, Leiguang Gong, Casimir Kulikowski, "Robust and fast visual tracking with two stage sparse optimization", 11th European Conference on Computer Vision (ECCV), Vol. 6314, pp. 624-637, 2010
  21. Baiyang Liu, Lin Yang, Casimir Kulikowski, Jinghao Zhou, Leiguang Gong, David J. Foran, Salma J. Jabbour and Ning J. Yue. "An adaptive tracking algorithm of lung tumors in fluoroscopy using online learned collaborative trackers ", IEEE International Symposium on Biomedical Imaging (ISBI), Vol. 1, pp. 209-212, 2010
  22. Hyunjoo Kim, Manish Parashar, David J. Foran and Lin Yang, "Investigating the use of automatic cloudbursts for high-throughput medical image registration", IEEE International Conference on Grid Computing (GRID), Vol. 1, pp. 34-41, 2009.
  23. Lin Yang, Leiguang Gong, Hong Zhang, John L. Nosher and David J. Foran, "A parallel point matching algorithm for landmark based image registration using multicore platform", 2009 European Conference on Parallel Computing (Euro-par), Vol. 5704, pp. 936-947, 2009
  24. Lin Yang, Salma Jabbour, Jinghao Zhou, Bruce Haffty, David J. Foran and Ning J. Yue, "A fast and robust dynamic tracking method of the moving deformable targets in the fluoroscopy image sequence for image guided radiotherapy", the 51th American Association of Physicists in Medicine, 2009
  25. David J. Foran, Lin Yang, Oncel Tuzel, Wenjin Chen, Jun Hu, Tahsin Kurc, Renato Ferreira, Joel Saltz, "A caGrid-enabled, learning based image segmentation method for histopathology specimens", Proc. IEEE International Symposium on Biomedical Imaging (ISBI), Vol. 1, pp. 1306-1309, 2009.
  26. Hong Zhang, Lin Yang, David J. Foran, John Nosher, Peter Yim, "3D segmentation of the liver using free-form deformation based on boosting and deformation gradients", Proc. IEEE International Symposium on Biomedical Imaging (ISBI), Vol. 1, pp. 494-497, 2009.
  27. Lin Yang, Leiguang Gong, Hong Zhang, John L. Nosher and David J. Foran, "A multicore based parallel image registration method", Proc. International Conference on Engineering in Medicine and Biology Society (EMBS), Vol. 1, pp. 98-101, 2009.
  28. Lin Yang, Oncel Tuzel, Peter Meer and David J. Foran, "Automatic image analysis of histopathology specimens using concave vertex graph", Proc. International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI), Vol. 11, pp. 833-841, 2008..
  29. Lin Yang, Bogdan Georgescu, Yefeng Zheng, Peter Meer and Dorin Comaniciu, "3D Ultrasound tracking of the left ventricle using one-step forward prediction and data fusion of collaborative trackers", Proc. IEEE International Conference on Computer Vision and Pattern Recognition (CVPR), Vol. 1, pp. 1-8, 2008.
  30. Lin Yang, Bogdan Georgescu, Yefeng Zheng, David J. Foran and Dorin Comaniciu. "A fast and accurate tracking algorithm of left ventricles in 3D echocardiography", Proc. International Symposium on Biomedical Imaging (ISBI) , Vol. 5, pp. 221-224, 2008.
  31. Lin Yang, Wenjin Chen, Peter Meer, Gratian Salaru, Michael D. Feldman and David J. Foran, "High throughput analysis of breast cancer specimens on the Grid", Proc. International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI), Vol. 10, pp. 617-625, 2007
  32. Lin Yang, Peter Meer and David J. Foran, "Multiple class segmentation using a unified framework over mean-shift patches", Proc. IEEE International Conference on Computer Vision and Pattern Recognition (CVPR), Vol. 1, pp. 1-8, 2007.
  33. Lin Yang and David J. Foran. "A variational framework for partially occluded image segmentation using coarse to fine shape alignment and semi-parametric density approximation", Proc. IEEE International Conference on Image Processing (ICIP), Vol. 1, pp. 137-140, 2007.
  34. Dazhang Gu, Lin Yang and Lonnie R. Welch. "A predictive, decentralized load balancing approach", 19th Proc. IEEE International Parallel and Distributed Processing Symposium (IPDPS), Vol. 1, pp. 131-140, 2005.
  35. Lin Yang, Jundong Liu, Charles D. Cavanaugh and Lonnie R. Welch, "A L2E-based QoS forecasting technique for dynamic, distributed real-time systems", Proc. International Conference on Parallel and Distributed Processing Techniques and Applications, Vol. 1, pp. 100-104, 2003.
  36. Lin Yang, Jundong Liu, Charles D. Cavanaugh and Lonnie R. Welch, "A robust QoS forecasting algorithm for a dynamic, distributed real-time testbed", Proc. IEEE International Workshop on Computer Architectures for Machine Perception, Vol. 1, pp. 96-100, 2003

Book Chapters:

  1. Lin Yang and David J. Foran, Parametric and geometric deformable models: An application in biomaterials and medical imaging . Suri/Farag, eds, Vol. 2, Chapter 4, pp. 95-122, Springer, ISBN: 0-387-31204-8,2006.
  2. Xiaoping Shen and Lin Yang, Handbook of medical image analysis: segmentation and registration models, Suri/Wilson/Laxminarayan, eds, Vol. 1, Chapter 1, 47 pp., Kluwer, ISBN: 0306485508, 2005

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