Shann-Ching Chen

Laboratory for Computational Cell Biology, The Scripps Research Institute Email: shanncc AT Scripps DOT edu 10550 North Torrey Pines Road, La Jolla, CA, 92037 Phone: 412.519.3783
EDUCATION & TRAINING
	The Scripps Research Institute, La Jolla, CA October 2007 - present Postdoctoral Research Associate in Department of Cell Biology
	Carnegie Mellon University, Pittsburgh, PA September 2007 Ph.D. in Biomedical Engineering
	Carnegie Mellon University, Pittsburgh, PA December 2002 M.S. in Electrical and Computer Engineering
	National Taiwan University, Taipei, Taiwan June 1999 B.S. in Computer Science and Information Engineering
	Taipei Municipal Chien Kuo Senior High School, Taipei, Taiwan June 1995
HONORS
	Outstanding Engineering Student Prize, Chinese Institute of Engineers^+ May 1999
	Presidential Award^* of National Taiwan University 1995, 1996
	Mayor’s Award^w of Taipei Municipal Chien Kuo Senior High School June 1995
RESEARCH INTERESTS
	Bioimage Informatics and Computational Cell Biology. Automated image analysis for protein subcellular location patterns in multi-cell images. Computational modeling on cell migration in 3D images.
RESEARCH EXPERIENCE
	Postdoctoral Research Associate, The Scripps Research Institute Oct. 2007 – present (Advisor: Gaudenz Danuser) · Develop image analysis software to track cell morphodynamics in 2D and 3D spaces. · Identify morphodynamic parameters and perform statistical analysis of cell migration. · Examine the migration of individual cancer cells and the migration of border cells in the Drosophila ovary.
	Graduate Research Assistant, Carnegie Mellon University Jan. 2004 – Sep. 2007 (Advisor: Robert F. Murphy) · Designed machine learning methodologies to classify protein subcellular location patterns in multi-cell images. · Proposed a novel approximate inference algorithm on probabilistic graphical models. · Investigated a new image segmentation algorithm for budding yeast images. · Re-annotated subcellular location patterns of protein in the whole yeast genomes computationally. · Programmed utilities on the Protein Subcellular Localization Image Database (PSLID).
	Pre-Doctoral Fellow, School of Medicine, University of Pittsburgh Jan. 2003 – Dec. 2003 (Advisor: Ivet Bahar) · Utilized data mining algorithms to discover frequent patterns in protein families. · Incorporated proteins’ dynamic, biochemical, and geometrical features for pattern analysis.
	Graduate Research Assistant, Carnegie Mellon University Aug. 2001 – Dec. 2002 (Advisor: Tsuhan Chen) · Developed an efficient algorithm to retrieve similar structures in the protein structural database. · Adapted geometric hashing algorithms to find similar protein substructures.
PUBLICATIONS
	· Chen S.-C., Gordon G.J., and Murphy R.F. Graphical Models for Structured Classification, with an Application to Interpreting Images of Protein Subcellular Location Patterns. Journal of Machine Learning Research, 9, pp.651-682 2008 · Chen S.-C., Zhao T, Gordon G.J., and Murphy R.F. Automated Image Analysis of Protein Localization in Budding Yeast. Bioinformatics 23:i66-i71 2007 · Chen S.-C., and Murphy R.F. A graphical model approach to automated classification of protein subcellular location patterns in multi-cell images. BMC Bioinformatics 7:90 2006 · Yang L.-W., Rader A.J., Liu X., Jursa C.J., Chen S.-C., Karimi H., and Bahar I. oGNM: A protein dynamics online calculation engine using the Gaussian Network Model. Nucleic Acids Research, 34, W24-31 2006 · Chen S.-C., and Bahar I. Mining frequent patterns in proteins: A study of serine proteinases. Bioinformatics 20,  i77-i85 2004 · Chen S.-C., Zhao T., Gordon G.J., and Murphy R.F. A Novel Graphical Model Approach to Segmenting Cell Images. Proceedings of the 2006 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, pp.1079-1086 2006 · Chen S.-C., Gordon G.J., and Murphy R.F. A Novel Approximation Inference Approach to Automated Classification of Protein Subcellular Location Pattern in Multi-cell Image. Proceedings of the 2006 IEEE International Symposium on Biomedical Imaging, pp.558-561 2006 · Chen S.-C., and Chen T. Retrieval of 3D Protein Structure. Proceedings of the 2002 International Conference on Image Processing, pp.933-936 2002 · Chen S.-C., and Chen T. Protein Retrieval by Matching 3D Surfaces. Proceedings of the 2002 Workshop on Genomic Signal Processing and Statistics, pp. CP2-09: 1-4 2002
BOOK CHAPTER
	Zhao T., Chen S.-C., and Murphy R.F. Location Proteomics. In: Introduction to Systems Biology. (S. Choi, ed.) 2006
PATENT
	Patent, Tip-Free Pad for Paper Cups, Patent No. 146940, Taiwan May 1999 to April 2009
ORAL AND POSTER PRESENTATIONS
	· Graphical model approaches to automated classification of protein subcellular location patterns in multicell image. In: Howard Hughes Medical Institute’s 2007 Predoctoral Fellows Meeting · Automated Image Analysis of Protein Localization in Budding Yeast. In: National Technology Centers for Networks and Pathways 2007 All-Hands Meeting, National Institutes of Health, Bethesda, MD · A Novel Graphical Model Approach to Segmenting Cell Images. In: Biomedical Engineering Society (BMES) Annual Meeting 2006 · A Novel Graphical Model Approach to Segmenting Cell Images. In: Proc of the 2006 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology · A Novel Approximation Inference Approach to Automated Classification of Protein Subcellular Location Pattern in Multi-cell Image. In: Bioimaging Day 2006, Carnegie Mellon University, Pittsburgh, PA · A Novel Approximation Inference Approach to Automated Classification of Protein Subcellular Location Pattern in Multi-cell Image. In: Proc 2006 IEEE Intl Symp Biomed Imaging · A Novel Graphical Model Method to Automated Classification of Protein Subcellular Location Patterns. In: Biomedical Engineering Society (BMES) Annual Meeting 2005 · Protein Retrieval by Matching 3D Surfaces. In: Workshop on Genomic Signal Processing and Statistics 2002
TEACHING EXPERIENCE
	Undergraduate Research Mentor · Kyle Chang, Automated Classification of Cellular Protein Localization Patterns in tissue-like CaCO2 cell images (2006) · Ashley Gonzalez, Image Acquisition for Heterogeneous Protein Location Pattern Analysis (2006) · Lori Dansie, Computer Analysis of Butons and Spines in the Neural Network (2005) · Amber Reed, Analysis of Subcellular Location Patterns on effects of Ras Oncogene on in NIH 3T3 Cells (2005) · Yenixsa Rivera-Sierra, Skeletonization by Morphological Thinning for Protein Subcellular Location Patterns (2004)
	Teaching Assistant · Computational Biology (2005, 2006)
	Grader · Physiology (2005)
WORK EXPERIENCE
	Software Engineer, eFunda Inc., CA May 2002 – June 2002 · Designed and implemented web-based utilities using SQL. · Developed a unit exchange software using Embedded VC on the WinCE platform.
	Second Lieutenant, Air Force, Taiwan July 1999 – March 2001 · Led 30 soldiers to maintain the security of a military airport. · Assumed responsibility for routine training and platoon scheduling.
TECHNICAL SKILLS
	Image Analysis · Image Segmentation · Multi-Cell Image Classification Probabilistic Graphical Model Approaches · Graph Construction · Approximate Inference Algorithms · Parameter Learning Data mining · Frequent Pattern Discovery Protein Dynamics · Gaussian Network Model Programming Skills · Matlab, Java, Java Server Pages, C, C++, 80X86 Assembly, SQL, Pascal, VC++, MFC, Embedded VC Cell Biology · Cell Culture · Fluorescence Microscopy
EXTRACURRICULAR ACTIVITIES
	Second Runner-Up, Men’s Single, National Taiwan University Table-Tennis Tournament, April 1999
	President of Student Council, Dept. of Comp. Sci. and Info. Eng., National Taiwan Univ., June 1997 – May 1998
	Vice-President of Creative Intelligent Club, National Taiwan University, September 1996 – June 1997
^+Chinese Institute of Engineers is the leading engineering society in Taiwan. Each year it grants the outstanding engineering student prize to ten students majoring in engineering disciplines, with excellent performance both in academic work and extracurricular leadership. Each university can nominate only one senior engineering student as a candidate every year to compete this award. As a result the ten most outstanding students are elected as the winners. ^*Presidential Award in NTU is similar to the “Dean's List” of universities in the U.S. Each semester the university grants this award to the top 5% students in each department to acknowledge their academic performance. ^wMayor's Award is the most honorable award granted in Taiwan's grade schools. A student with best academic performance in his/her class during the whole school years will be granted this award upon graduation.