Applied Bioinformatics Select Publications

For a complete list of publications, go to the Applied Bioinformatics website.


Fang YP, Liu HX, Zhang N, Guo G, Wan YY, Fang JW. NURBS: A Database of Experimental and Predicted Nuclear Receptor Binding Sites. Bioinformatics. accepted.

Zhan Q, Fang YP, He YQ, Liu HX, Fang JW, Wan YY*. Function annotation of hepatic retinoid x receptor α based on genome-wide DNA binding and transcriptome profiling. PLoSONE. 2012. 7(9): e50013.

Gao S, Xu S, Fang YP, Fang JW. Prediction of Core Cancer Genes Using Multitask Classification Framework. J Theor Biol. 2012, 317C: 62-70. 

Li Y, Fang JW. PROTS-RF: A Robust Model for Predicting Mutation Induced Protein Stability Change. PLoSONE, 2012, 7(10), e47247.

Fang YP, Middaugh CR, Fang JW. In silico classification of proteins from acidic and neutral cytoplasms. PLoSONE. 2012. 7(9): e45585.

Tai D, Fang JW. SymDex: Increasing the Efficiency of Chemical Fingerprint Similarity Searches for Comparing Large Chemical Libraries by Using Query Set Indexing. J. Chem. Inf. Model. 2012, 52 (8), pp 1926–1935.
Finding minimum gene subsets with heuristic breadth-first search algorithm for robust tumor classification. Wang SL, Li XL and Fang JW. BMC Bioinformatics 2012, 13:178

Gao S, Xu S, Fang YP, Fang JW. Using multitask classification methods to investigate the kinase-specific phosphorylation sites.Proteome Science 2012, 10(Suppl 1):S7.

Li Y, Zhang J, Tai D, Middaugh CR, Zhang Y, Fang JW. PROTS: A fragment based protein thermo-stability potential. Proteins: Structure, Function, and Bioinformatics. 2012, 80, 1, 81-92.


Li Y, Fang YP, Fang JW. Predicting Residue-Residue Contacts Using Random Forest Models. Bioinformatics. 2011, 27(24), 3379-3384.

Gao S, Xu S, Fang JW. Predicting Kinase-specific Phosphorylation Sites Using a Multitask Classification Framework. 2011 IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2011), Atlanta GA, 12-15 Nov 2011. In press. 

Gao S, Fang JW. Identification of Properties Important to Signal Peptides and Signal Anchors Using Feature Selection. 2011 International Conference on Computational Biology and Bioinformatics(CBB2011), Shanghai China, 28-30 October, 2011. In press. 

Tai D, Chaguturu R, Fang JW. K-Screen: A Free Application for High Throughput Screening Data Analysis, Visualization, and Laboratory Information Management. Comb Chem High Throughput Screen. 2011, 14, 757-765.

Fang JW, Tai D. Evaluation of Mutual Information, Genetic Algorithm and SVR for Feature Selection in QSAR Regression. Curr. Drug Discov. Technol.,2011, 8(2): 107-111.



Biochemistry & Protein Science

Bioinformatics & Modeling


Materials Characterization

Molecular Structures

Translational Biology

Ability to set up 24 NMR experiments at one time and eliminate periodic user intervention
Screen up to 100,000 compounds in two days for endpoint assays
Next-generation genome sequencing
Near-infrared and bioluminescence imaging instrumentation to track gene of interest and/or tumor growth
Expertise in the design and stability of various pharmaceutical dosage forms
More than 40 computational chemistry software programs and databases
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