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Chi-Ren Shyu

Chi-Ren Shyu

Professor and Director
MU Informatics Institute

E-mail: shyuc at missouri dot edu
Web site: MU Informatics Institute
Office address: 243 Engineering Building West
Office phone: 573-882-3884

I oversee the work of a crew of students and post-docs on a variety of research projects in such areas as biomedical informatics, geospatial informatics, data mining, and computer vision. Extramural funders of our research include the National Science Foundation, the National Institutes of Health (National Library of Medicine), the National Geospatial-Intelligence Agency, and the U.S. Department of Education as well as a number of for-profit and not-for-profit organizations.

My lab currently has two plant-related bioinformatics projects currently underway. The first project is plant phenotype information analysis and retrievals ( This ongoing project is a continuous effort for my NSF CAREER project (2005-2010) titled "Linking Visual Phenotypes with Genotypes in Plants: Content Management, Knowledge Sharing, and Database Retrievals." We provide a unique way for plant phenotype modeling using various biologically-driven visual cues. There are several new approaches that may foster inter-site phenotypic information exchange through a computable ontology and multi-source/ontology-based phenotype retrievals. My lab is also working on temporal modeling of Maize mutant phenotypic expressions and multi-dimensional scoring in QTL. To bring worldwide experts in plant phenotypes and repot updates of phenotypes from major plant genomics databases, I co-chair a recurring workshop in plant phenotypes at the PAG conference since 2009.

The second project is a NSF-funded (2010-2013) collaborative research with seven other institutions (Carnegie Mellon, OHSU, Illinois, Florida State, U.C. Irvine, Virginia Tech, and Wash U) to develop a framework to represent, analyze and interpret shapes extracted from images, supporting a wide range of biological investigations. The primary objectives are: (1) to develop a mathematical framework and computational tools for the quantification and analysis of shapes; (2) to integrate these computational models with machine learning and statistical inference methods to enable new discoveries, transforming imaging data into biological knowledge; (3) to deliver novel quantitative methodologies for shape analysis that start from a biological premise, rather than a purely geometric one. Shape-based phenotypes in plant model organisms are one of our targets.

In addition to my research in bioinformatics, I also manage MU Informatics Institute, a campus-wide doctoral program in informatics, supported by 40 core faculty members from 15 academic units and seven colleges/schools.


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J Green, J Harnsomburana, C Lawrence, M Schaeffer, and CR Shyu. Multi-Source and Ontology-Based Retrieval Engine for Maize Mutant Phenotypes. Database - Journal of Biological Databases and Curation, Oxford, 2011: 10.1093/database/bar012.

Jaturon Harnsomburana, JM Green, AS Barb, M Schaeffer, L Vincent and CR Shyu. Computable visually observed phenotype ontological framework for plants. BMC Bioinformatics 2011;12:260 doi:10.1186/1471-2105-12-260

Zhao N, Pang B, Shyu CR, and Korkin D. Charged residues at protein interaction interfaces: Unexpected conservation and orchestrated divergence. Protein Science 2011;20(7):1275-1284.

Chan LWC, Liu Y, Shyu CR, and Benzie IFF. A SNOMED supported ontological vector model for subclinical disorder detection using EHR similarity. Engineering Applications of Artificial Intelligence. Article in Press.

Zhao N, Pang B, Shyu CR, and Korkin D. Structural similarity and classification of protein interaction interfaces. PLoS ONE 2011;6(5): art. no. e19554.

Scott GJ, Klaric MN, Davis CH, and Shyu CR. Entropy-balanced bitmap tree for shape-based object retrieval from large-scale satellite imagery databases. IEEE Transactions on Geoscience and Remote Sensing 2011;49(5), art. no. 5669345:1603-1616.

Wang X, Erdelez S, Alen C, Anderson B, Cao H, and Shyu CR. Medical image describing behavior: A comparison between an expert and novice. ACM International Conference Proceeding Series 2011;792-793.

Han J, Shin DV, Arthur GL, and Shyu CR. Multi-resolution tile-based follicle detection using color and textural information of follicular lymphoma IHC slides. 2010 IEEE International Conference on Bioinformatics and Biomedicine Workshops; BIBMW 2010, art. no. 5703949:866-867.

Klaric M, Scott G, and Shyu CR. Progressive spatial clustering of content-based satellite imagery retrieval results. International Geoscience and Remote Sensing Symposium (IGARSS) 2010;art. no. 5651582:36-39.

Barb AS and Shyu CR. Visual information mining and ranking using graded relevance assessments in satellite image databases. International Geoscience and Remote Sensing Symposium (IGARSS) 2010; art. no. 5650173:3398-3401.

Zhao N, Pang B, Shyu CR, and Korkin D. An accurate classification of native and non-native protein-protein interactions using supervised and semi-supervised learning approaches. Proceedings - 2010 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2010, art. no. 5706560:185-189.

Shyu CR, Pang B, Chi PH, Zhao N, Korkin D, and Xu D. ProteinDBS v2.0: A web server for global and local protein structure search. Nucleic Acids Research 2010;38(SUPPL. 2):W53-W58.

Barb AS and Shyu CR. Visual-semantic modeling in content-based geospatial information retrieval using associative mining techniques. IEEE Geoscience and Remote Sensing Letters 2010;7(1):38-42.

Chi P-H, Pang B, Korkin D, and Shyu C-R. Efficient SCOP-fold classification and retrieval using index-based protein substructure alignments. Bioinformatics 2009;25(19):2559-2565.

Liu Y, Chan LW-C, and Shyu CR. Editorial for the special issue of knowledge discovery and management in biomedical information systems. Information Systems Frontiers 2009;11(4):345-347.

Taft LM, Evans RS, Shyu CR, Egger MJ, Chawla N, Mitchell JA, Thornton SN, Bray B, and Varner M. Countering imbalanced datasets to improve adverse drug event predictive models in labor and delivery. Journal of Biomedical Informatics 2009;42(2):356-364.

He W, Erdelez S, Wang F-K, and Shyu CR. The effects of conceptual description and search practice on users' mental models and information seeking in a case-based reasoning retrieval system. Information Processing and Management 2008;44(1): 294-309.

Scott G and Shyu CR. Knowledge-driven multidimensional indexing structure for biomedical media database retrieval. IEEE Transactions on Information Technology in Biomedicine 2007:11(3):320-331.

Wan XF, Wu X, Lin G, Holton S, Desmone RA, Shyu CR, Guan Y, and Emch M. Computational identification of reassortments in avian influenza viruses. Avian Diseases 2007;51:434-439.

Shyu CR, Green J, Lun DPK, Kazic T, Schaeffer M, and Coe E. Image analysis for mapping immeasurable phenotypes in maize. IEEE Signal Processing Magazine 2007;24(3):116-119.

Shyu CR, Harnsomburana J, Green J, Barb A, Kazic T, Schaeffer M, and Coe E. Searching and mining visually-observed phenotypes of maize mutants. Journal of Bioinformatics and Computational Biology 2007;5(6):1193-1213.

Shyu CR, Klaric M, Scott G, Barb A, Davis C, and Palaniappan K. GeoIRIS: Geospatial Information Retrieval and Indexing System - content mining, semantics modeling, and complex queries. IEEE Transactions on Geoscience and Remote Sensing 2007;45(4):839-852.

Chi P-H, Shyu CR, and Xu D. A fast SCOP fold classification system using content-based E-Predict algorithm. BMC Bioinformatics 2006;7:362.

Chi P-H, Scott G, and Shyu CR. A fast protein structure retrieval system using image-based distance matrices and multidimensional index. International Journal of Software Engineering and Knowledge Engineering 2005;15(3):527-545.

Reneker J and Shyu CR. Refined repetitive sequence searches utilizing a fast hash function and cross species information retrievals. BMC Bioinformatics 2005;6:111.

Barb A, Shyu CR, and Sethi Y. Knowledge representation and sharing using visual semantic modeling for diagnostic medical image databases. IEEE Transactions on Information Technology in BioMedicine 2005;9(4): 538-553.

Shyu CR, Chi P-H, Scott G, and Xu D. ProteinDBS: A content-based retrieval system for protein structure database. Nucleic Acids Research 2004;32: W572-W575.

Reneker J, Shyu CR, Zeng P, Polacco J, and Gassmann W. ACMES: Fast multiple-genome searches for short repeat sequences with concurrent cross-species information retrieval. Nucleic Acids Research 2004;32: W649-W653.

Johnson ED, Pancoast PE, Mitchell JA, and Shyu CR. Evaluation of a PDA-based alerting service for clinicians. Journal of the Medical Library Association 2004;92(4):438-444.

Aisen AM, Broderick LS, Winer-Muram H, Brodley CE, Kak AC, Pavlopoulou C, Dy J, Shyu CR, and Marchiori A. Automated storage and retrieval of medical images to assist diagnosis: Implementation and preliminary assessment. Radiology 2003;228(1):265-270.

Kazic T, Coe E, Polacco M, and Shyu C-R. Whither biological database research. OMICS: A Journal of Integrative Biology 2003;7(1):61-65.

Shyu C-R, Pavlopoulou C, Kak AC, Brodley CE, and Broderick LS. Using human perceptual categories for content-based retrieval from a medical image database. Computer Vision and Image Understanding 2002;88(3):119-151.

Wei S, Chen C-M, Strathdee G, Harnsomburana J, Shyu C-R, Rahmatpanah F, Shi H, Ng S-W, Yan PS, Nephew KP, Brown R, and Huang TH-M. Methylation microarray analysis of late-stage ovarian cancinomas distinguishes progression-free survival in patients and identifies candidate epigenetic markers. Clinical Cancer Research 2002;8(7):2246-2252.

Shyu C-R, Brodley CE, Kak AC, Kosaka A, Aisen AM, and Broderick LS. ASSERT: A physician-in-the-loop content-based retrieval system for HRCT image databases. Computer Vision and Image Understanding 1999;75(1/2):111-132.


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  • National Science Foundation CAREER Award (2005)
  • Excellence in Teaching Award - MU College of Engineering (2008)
  • Faculty Research Award - MU College of Engineering (2005)
  • Teaching Awards - MU Computer Science Department (2001-2006)
  • Adjunct/Clinical Faculty member in MU Sinclair School of Nursing, MU School of Information Science and Learning Technologies, MU Electrical and Computer Engineering, and University of Utah Biomedical Informatics Department.
  • Senior Member: IEEE


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