Shann-Ching Chen
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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 |
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EDUCATION & TRAINING |
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The
Scripps Research Institute, Postdoctoral Research Associate in Department of
Cell Biology
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Ph.D. in Biomedical Engineering
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M.S. in Electrical and Computer Engineering |
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B.S. in Computer Science and Information Engineering |
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HONORS |
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Outstanding Engineering Student Prize, Chinese
Institute of Engineers+ May 1999 |
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Presidential Award* of |
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Mayor’s Awardw of Taipei Municipal Chien Kuo Senior High
School June 1995 |
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RESEARCH INTERESTS |
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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. |
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RESEARCH EXPERIENCE |
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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.
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Identify morphodynamic parameters and perform statistical
analysis of cell migration.
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Examine the migration of individual cancer cells
and the migration of border cells in the Drosophila ovary.
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Graduate
Research Assistant, ·
Designed machine learning
methodologies to classify protein subcellular location patterns in multi-cell
images.
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Proposed a novel approximate
inference algorithm on probabilistic graphical models.
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Investigated a new image
segmentation algorithm for budding yeast images.
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Re-annotated subcellular location patterns of
protein in the whole yeast genomes computationally.
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Programmed utilities
on the Protein Subcellular
Localization Image Database (PSLID).
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Pre-Doctoral
Fellow, ·
Utilized data mining
algorithms to discover frequent patterns in
protein families.
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Incorporated proteins’ dynamic,
biochemical, and geometrical features for pattern analysis.
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Graduate
Research Assistant, ·
Developed an efficient algorithm to retrieve
similar structures in the protein structural database.
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Adapted geometric hashing
algorithms to find similar protein substructures.
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PUBLICATIONS |
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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 |
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BOOK CHAPTER |
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Zhao T., Chen S.-C., and Murphy R.F. Location
Proteomics. In: Introduction to Systems Biology. (S. Choi, ed.) 2006 |
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PATENT |
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Patent, Tip-Free Pad for Paper Cups, Patent No.
146940, |
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ORAL AND POSTER PRESENTATIONS |
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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, ·
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 |
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TEACHING EXPERIENCE |
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Undergraduate
Research ·
Kyle Chang, Automated Classification of Cellular
Protein Localization Patterns in tissue-like CaCO2 cell images (2006)
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Ashley Gonzalez, Image Acquisition for
Heterogeneous Protein Location Pattern Analysis (2006)
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Lori Dansie, Computer Analysis of Butons and Spines
in the Neural Network (2005)
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Amber Reed, Analysis of Subcellular Location
Patterns on effects of Ras Oncogene on in NIH 3T3 Cells (2005)
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Yenixsa Rivera-Sierra, Skeletonization by
Morphological Thinning for Protein Subcellular Location Patterns (2004)
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Teaching
Assistant ·
Computational Biology (2005, 2006)
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Grader ·
Physiology (2005)
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WORK EXPERIENCE |
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Software Engineer, eFunda Inc., CA
May 2002 – June 2002 ·
Designed and implemented web-based utilities using
SQL.
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Developed a unit exchange software using Embedded
VC on the WinCE platform.
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Second Lieutenant, ·
Led 30 soldiers to maintain the security of a
military airport.
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Assumed responsibility for routine training and
platoon scheduling.
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TECHNICAL SKILLS |
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Image Analysis ·
Image Segmentation
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Multi-Cell Image Classification
Probabilistic Graphical Model Approaches ·
Graph Construction
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Approximate Inference Algorithms
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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
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Fluorescence Microscopy
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EXTRACURRICULAR ACTIVITIES |
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Second Runner-Up, Men’s Single, National Taiwan
University Table-Tennis Tournament,
April 1999 |
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President of Student Council, Dept. of Comp. Sci.
and Info. |
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Vice-President of Creative Intelligent Club, |
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+ Chinese Institute of Engineers is the leading
engineering society in * Presidential Award in NTU is similar to the “Dean's
List” of universities in the w Mayor's Award is the most honorable award granted in
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