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Biometric Research Program (BRP)

Dr. Jianwen Fang

Computational Biologist, Computational & Systems Biology Branch

Research Interests

Integrated data analysis, data-mining algorithms, systems biology, protein bioinformatics, software and database development, computational drug discovery.

Selected Publications

Krushkal J, Negi S, Yee LM, Evans JR, Grkovic T, Palmisano A, Fang JW, Sankaran H, McShane LM, Zhao YD, O'Keefe BR. Molecular Genomic Features Associated with in Vitro Response of the NCI-60 Cancer Cell Line Panel to Natural Products. Molecular Oncology. 2021 Feb;15(2):381-406.

Fang JW*, A Critical Review of five Machine Learning Algorithms for Predicting Protein Stability Changes upon Mutations. Briefings in Bioinformatics (2019), bbz071.

Evans DM, Fang JW, Silvers T, Delosh R, Laudeman J, Ogle C, Reinhart R, Selby M, Bowles L, Connelly J, Harris E, Krushkal J, Rubinstein L, Doroshow JH, Teicher BA*. EXPOSURE TIME VERSUS CYTOTOXICITY FOR ANTICANCER AGENTS, Cancer Chemother Pharmacol (2019) 84: 359.

Monks A, Zhao Y, Hose C, Hamed H, Krushkal J, Fang JW, Sonkin D, Palmisano A, Polley E, Fogli L, Konate M, Miller S, Simpson M, Voth A, Li M-C, Harris E, Wu X, Connelly J, Rapisarda A, Teicher B, Simon R, Doroshow JH*.The NCI Transcriptional Pharmacodynamics Workbench: a tool to examine dynamic expression profiling of therapeutic response in the NCI-60 cell line panel. Cancer Research, 78: 6807-6817, 2018.

Fang, JW*, Tightly Integrated Genomic and Epigenomic Data Mining Using Tensor Decomposition, Bioinformatics (2018), 35 (1), 112-118.

Luo D, Wang SL*, Fang JW, Zhang W. MIMPFC: Identifying miRNA-mRNA regulatory modules by combining phase-only correlation and improved rough-fuzzy clustering, Journal of bioinformatics and computational biology (2018), 16 (01), 1750028.

Bender J, Fang JW, Simon R*. A computational study of the inhibition mechanisms of P-glycoprotein mediated paclitaxel efflux by kinase inhibitors. BMC Systems Biology (2017) 11:108. (co-first author)

Wang Y*, Fang JW, Chen S. Inference of drug responses in cancer cells from cancer genomic features and compound chemical and therapeutic properties. Scientific Reports 6, Article number: 32679 (2016) (co-first author).

Saeedipour S, Tai D, Fang JW*: ChemCom: A Software Program for Searching and Comparing Chemical Libraries. Journal of Chemical Information and Modeling 55(7): 1292-1296 (2015).

Zhan L, Liu HX, Fang Y, Kong B, He Y, Zhong X, Fang JW, Wan YJY*. Genome-Wide Binding and Transcriptome Analysis of Human Farnesoid X Receptor in Primary Human Hepatocytes. PloS one, 2014, 9 (9), e105930.

Fang YP, Gao S, Tai D, Middaugh CR, Fang JW*. Identification of properties important to protein aggregation using feature selection. BMC Bioinformatics 2013, 14:314.

Dasouki MJ*, Rafi SK, Olm-Shipman AJO, Wilson NR, Abhyankar S, Ganter B, Furness LM, Fang JW, Calado RT, and Saadi I*. Exome sequencing reveals a thrombopoietin ligand mutation in a Micronesian family with autosomal recessive aplastic anemia. Blood 122, no. 20 (2013): 3440-3449.

Thomas AM, Hart SN, Li GD, Lu H, Fang YP, Fang JW, Zhong XB, and Guo GL*. Hepatocyte Nuclear Factor 4 Alpha and Farnesoid X Receptor Co-regulates Gene Transcription in Mouse Livers on a Genome-Wide Scale. Pharmaceutical research (2013): 1-11.

Fang YP, and Fang JW*. Discrimination of soluble and aggregation-prone proteins based on sequence information. Mol. BioSyst. 9, no. 4 (2013): 806-811.

Thomas JC, O'Hara JM, Hu L, Gao FP, Joshi SB, Volkin DB, Robert N. Brey RN, Fang JW, Karanicolas J, Mantis NJ, and Middaugh CR*. Effect of single-point mutations on the stability and immunogenicity of a recombinant ricin chain subunit vaccine antigen. Human Vaccines & Immunotherapeutics 9:4, 1-9; April 2013.

Fang YP, Liu HX, Zhang N, Guo G, Wan YY, Fang JW*. NURBS: A Database of Experimental and Predicted Nuclear Receptor Binding Sites. 2013 Jan 15; 29(2):295-7.

Gao S, Xu S, Fang YP, Fang JW*. Prediction of Core Cancer Genes Using Multitask Classification Framework. J Theor Biol. 2012, 317, 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 and 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), 1926-1935.

Wang SL, Li XL, Fang JW*. Finding minimum gene subsets with heuristic breadth-first search algorithm for robust tumor classification. BMC Bioinformatics 2012, 13:178.

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.

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, 9, 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 Jun 1;8(2):107-11.

Cai S, Fang JW*, Li QS, Borchardt RT, Kuczera K, Middaugh CR, and Schowen RL. Comparative kinetics of cofactor association and dissociation for the human and trypanosomal S-adenosylhomocysteine hydrolases. 3. The role of lysyl and tyrosyl residues of the C-terminal extension. Biochemistry, 2010 Sep 28;49(38):8434-41.

Li Y, Fang JW.* Distance-dependent statistical potentials for discriminating thermophilic and mesophilic proteins. Biochem. Biophys. Res. Commun. 396, 3, 736-741, 2010.

Li Y, Middaugh CR, Fang JW.* A novel scoring function for discriminating hyperthermophilic and mesophilic proteins with application to predicting relative thermostability of protein mutants. BMC Bioinformatics. 2010 Jan 28;11(1):62.

Thomas AM, Hart SN, Kong B, Fang JW, Zhong XB, Guo GL. Genome-wide tissue-specific farnesoid X receptor binding in mouse liver and intestine. Hepatology. 51, 4, 1410-1419, 2009.

Fang JW, Koen YM, Hanzlik RP*. Bioinformatic analysis of xenobiotic reactive metabolite target proteins and their interacting partners. BMC Chem Biol. 2009 Jun 12;9(1):5.

Silva RA, Huang R, Morris J, Fang JW, Gracheva EO, Ren G, Kontush A, Jerome WG, Rye KA, Davidson WS. Structure of apolipoprotein A-I in spherical high density lipoproteins of different sizes. Proc Natl Acad Sci U S A. 2008 Aug 26;105(34):12176-81.

Hu C, Fang JW, Borchardt RT, Schowen RL, Kuczera K. Molecular dynamics simulations of domain motions of substrate-free S-Adenosyl-L-homocysteine hydrolase in solution. PROTEINS: Structure, Function, and Bioinformatics. 71(1), 131-143, 2008.

Fang JW*, Dong YH, Salamat-miller N, Middaugh CR. DB-PABP: a database of polyanion binding proteins. Nucleic Acid Research. 36(Database issue):D303-D306, 2008.

Salamat-Miller NS, Fang JW, Seidel C, Smalter A, Assenov Y, Albrecht M, Middaugh1 CR*. A Network-Based Analysis of Polyanion Binding Proteins Utilizing Yeast Protein Arrays. Molecular and Cellular Proteomics, 5, 12, 2263-2278, 2006.

Fang JW*, Dong YH, Lushington GH, Ye QZ, Georg GI. Support Vector Machines in HTS Data Mining: Type I MetAPs Inhibition Study. J. Biomolecular Screening 11 (2): 138-144, 2006.

Haasl RJ, Fang JW.* Mining protein-protein interaction data. Current Bioinformatics 1, 2: 197-205, 2006. (Invited review).

Fang, JW.*; Haasl, R.J.; Dong, Y.H.; Lushington, G. H. Discover protein sequence signatures from protein-protein interaction data. BMC Bioinformatics 6: 277, 2005.

Marchin M, Kelly PT and Fang JW* Tracker: continuous HMMER and BLAST searching. Bioinformatics 21: 388-389, 2005.

Dr. Jianwen Fang

Office Address:
Room 5W632
9609 Medical Center Dr
Rockville, MD 20850

Contact Information:
Tel: (240) 276-7672
Fax: (240) 276-7888