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Examples of Recent and Ongoing Projects at the ABL

KU Research
About research at KU

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Proteimcs/genomics Data mining
Salamat-Miller, N. S.; Fang, J. W.; Seidel, C.; Smalter, A.; Assenov, Y.; Albrecht, M.; Middaugh1, C. R. A Network-Based Analysis of Polyanion Binding Proteins Utilizing Yeast Protein Arrays. Molecular and Cellular Proteomics, 5, 12, 2263-2278, 2006. (Our contribution: proteomics data mining)

Salamat-Miller, N.; Fang, J.W.; Seidel, C.; Smalter, A.; Assenov, Y.; Albrechat, M.; Middaugh, C.R. A Network-Based Analysis of Polyanion Binding Proteins Utilizing Human Protein Arrays. J. Biol. Chem. 282, 14, 10153-10163, 2007. (Our contribution: proteomics data mining)

Rider, V.; Isuzugawa, K.; Twarog, M.; Jones, S.; Cameron, B.; Imakawa, K.; Fang, J. W. Progesterone Initiates Wnt-ß-Catenin Signaling But Estradiol Is Required For Nuclear Activation and Synchronous Proliferation of Rat Uterine Stromal Cells. J. Endocrinology, 191(3):537-48, 2006. (Our contribution: MicroArray data analysis and mining)
Cheminformatics
Fang, J.W.; Grzymala-Busse, J.W. "Predicting Penetration Across the Blood-Brain Barrier - a Rough Set Approach". Proceedings of 2007 IEEE International Conference on Granular Computing, IEEE Computer Society Press, pp. 231-236. (Our contribution: QSAR)

Chen. D.C.; Fang, J.W.; Yu, J.W. "Predicting Blood-Brain Barrier Penetration by Stochastic Discrimination". The International Conference on BioMedical Engineering and Informatics (BMEI2008). Accepted. (Our contribution: QSAR)

Fang, J. W.; Dong, Y. H.; Lushington, G. H.; Ye, Q. Z.; Georg, G. I. “Support Vector Machines in HTS Data Mining: Type I MetAPs Inhibition Study.” Journal of Biomolecular Screening 11 (2): 138-144, 2006. (Our contribution: HTS data mining)
Databases (click banners to access the databases)

Tracker was developed and maintained by KU bioinformatics facility. This is a system for monitoring the following: protein searches using HMMER and Blast-P, nucleotide searches using Blast-N, and literature searches of the PubMed databases. Your searches will be run against new information to keep you up to date. If there are results on your searches, you will be notified by email and will then be able to access results and link to more information on the NCBI site. You will be able to monitor, edit, or delete your searches on this website using the buttons on the lefthand menu. Tracker is available for download. Click here for more detail. A paper on the system was published in Bioinformatics Journal recently (Bioinformatics 2005 21(3):388-389).

The Target Protein Database is an attempt to catalog in a convenient, searchable fashion the publicly available information about the identities of mammalian proteins that become covalently adducted by chemically-reactive metabolites of xenobiotic agents.

DB-PABP is an attempt to document the publicly available experimentally determined PABPs. The purpose of the database is to provide life scientists who are interested in PA/PABP interactions with a comprehensive data repository, as well as computer scientists with a publicly available dataset to perform knowledge discovery and datamining studies. The database is manually curated. It uses protein annotations from NCBI protein database and literature information is retrieved from PubMed. Whenever applicable, links to NCBI protein database and PubMed are provided so users may access additional information available in these public databases.


Pro-LIMS was developed to facilitate Mass Spectrometry data manegement/analysis/validation for the proteomics efforts at the University of Kansas. It is a joint project of the Applied Bioinformatics Lab, K-INBRE Bioinformatics Core (BCF) and the Analytical Proteomics Laboratory (APL).

The KU-HTS Data Management System was developed to facilitate high throughput screening data mangement/analysis for the HTS efforts at the University of Kansas. The system consists of a web-browser based interface written in PHP, a MySQL database as the backend.

Virtual Freezer, a web accessible relational database, was designed to facilitate tracking and sharing animal models and tissues for the Program Project on Aging.


Protein structure/sequence/domain analysis and homology modeling
Li, Q.-S.; Cai, S.; Fang, J.W.; Borchardt, R.T; Kuczera, K.; Middaugh, C.R.; and Schowen, R.L. "Comparative kinetics of cofactor association and dissociation for the human and trypanosomal S-adenosylhomocysteine hydrolases. 2. The role of helix 18 stability". Biochemistry. Accepted. (Our contribution: protein sequence and structure analysis)

R. A. Gangani D. Silva, George M. Hilliard, Jianwen Fang, Stephen Macha and W. Sean Davidson. "A Three Dimensional Molecular Model of Lipid-free Apolipoprotein A-I Determined by Cross-linking/Mass Spectrometry and Sequence Threading", Biochemistry, 2005, 44: 2759-2769.. (Our contribution: homology modeling)

Suprenant, K.A.; Nathan Bloom1, N.; Fang, J.W.; Lushington, G.H. The Major Vault Protein is Related to the Toxic Anion Resistance Protein (TELA) Family. J. Exp. Biol. 210, 946-955, 2007 (Our contribution: protein sequence and structure analysis)

Phylogenetic analysis
Sang Y, Teresa Ortega M, Rune K, Xiau W, Zhang G, Soulages JL, Lushington GH, Fang J.W., Williams TD, Blecha F, Melgarejo T. Canine cathelicidin (K9CATH): Gene cloning, expression, and biochemical activity of a novel pro-myeloid antimicrobial peptide. Dev Comp Immunol. Developmental and Comparative Immunology 31 (2007) 1278–1296