Jianwen Fang

Summary

Affiliation: University of Kansas
Country: USA

Publications

  1. pmc Bioinformatic analysis of xenobiotic reactive metabolite target proteins and their interacting partners
    Jianwen Fang
    Department of Medicinal Chemistry, University of Kansas, Lawrence, KS 66045, USA
    BMC Chem Biol 9:5. 2009
  2. pmc Discrimination of soluble and aggregation-prone proteins based on sequence information
    Yaping Fang
    Applied Bioinformatics Laboratory, The University of Kansas, 2034 Becker Dr, Lawrence, Kansas 66047, USA
    Mol Biosyst 9:806-11. 2013
  3. pmc NURBS: a database of experimental and predicted nuclear receptor binding sites of mouse
    Yaping Fang
    Applied Bioinformatics Laboratory, University of Kansas, Lawrence, KS 66047, USA
    Bioinformatics 29:295-7. 2013
  4. pmc Using multitask classification methods to investigate the kinase-specific phosphorylation sites
    Shan Gao
    Applied Bioinformatics Laboratory, Kansas University, 2034 Becker Dr, Lawrence, KS 66047, USA
    Proteome Sci 10:S7. 2012
  5. pmc Discover protein sequence signatures from protein-protein interaction data
    Jianwen Fang
    Bioinformatics Core Facility, University of Kansas, Lawrence, KS 66045, USA
    BMC Bioinformatics 6:277. 2005
  6. ncbi request reprint Support vector machines in HTS data mining: Type I MetAPs inhibition study
    Jianwen Fang
    Bioinformatics Core Facility, University of Kansas, Lawrence, KS 66045, USA
    J Biomol Screen 11:138-44. 2006
  7. ncbi request reprint Evaluation of mutual information, genetic algorithm and SVR for feature selection in QSAR regression
    Jianwen Fang
    Applied Bioinformatics Laboratory, The University of Kansas, Lawrence, 66047, USA
    Curr Drug Discov Technol 8:107-11. 2011
  8. ncbi request reprint Feature selection in validating mass spectrometry database search results
    Jianwen Fang
    Bioinformatics Core Facility and Information and Telecommunication Technology Center, University of Kansas, 2099 Constant Dr, Lawrence, Kansas 66047, USA
    J Bioinform Comput Biol 6:223-40. 2008
  9. pmc The rationale for targeting the NAD/NADH cofactor binding site of parasitic S-adenosyl-L-homocysteine hydrolase for the design of anti-parasitic drugs
    Sumin Cai
    Department of Molecular Biosciences, The University of Kansas, Lawrence, Kansas, USA
    Nucleosides Nucleotides Nucleic Acids 28:485-503. 2009
  10. doi request reprint Comparative kinetics of cofactor association and dissociation for the human and trypanosomal S-adenosylhomocysteine hydrolases. 2. The role of helix 18 stability
    Qing Shan Li
    Department of Pharmaceutical Chemistry, The University of Kansas, Lawrence, Kansas 66047, USA
    Biochemistry 47:4983-91. 2008

Collaborators

Detail Information

Publications40

  1. pmc Bioinformatic analysis of xenobiotic reactive metabolite target proteins and their interacting partners
    Jianwen Fang
    Department of Medicinal Chemistry, University of Kansas, Lawrence, KS 66045, USA
    BMC Chem Biol 9:5. 2009
    ..non-target proteins and illuminate mechanisms connecting covalent binding to cytotoxicity...
  2. pmc Discrimination of soluble and aggregation-prone proteins based on sequence information
    Yaping Fang
    Applied Bioinformatics Laboratory, The University of Kansas, 2034 Becker Dr, Lawrence, Kansas 66047, USA
    Mol Biosyst 9:806-11. 2013
    ..Our results provide not only a reliable model for predicting protein solubility but also a list of features important to protein solubility. The predictive model is implemented as a freely available web application at ...
  3. pmc NURBS: a database of experimental and predicted nuclear receptor binding sites of mouse
    Yaping Fang
    Applied Bioinformatics Laboratory, University of Kansas, Lawrence, KS 66047, USA
    Bioinformatics 29:295-7. 2013
    ..NURBS also provides predicted binding sites using NR-HMM, a Hidden Markov Model (HMM) model...
  4. pmc Using multitask classification methods to investigate the kinase-specific phosphorylation sites
    Shan Gao
    Applied Bioinformatics Laboratory, Kansas University, 2034 Becker Dr, Lawrence, KS 66047, USA
    Proteome Sci 10:S7. 2012
    ....
  5. pmc Discover protein sequence signatures from protein-protein interaction data
    Jianwen Fang
    Bioinformatics Core Facility, University of Kansas, Lawrence, KS 66045, USA
    BMC Bioinformatics 6:277. 2005
    ..Mining these datasets for underlying biological knowledge has, however, remained a challenge...
  6. ncbi request reprint Support vector machines in HTS data mining: Type I MetAPs inhibition study
    Jianwen Fang
    Bioinformatics Core Facility, University of Kansas, Lawrence, KS 66045, USA
    J Biomol Screen 11:138-44. 2006
    ..A training set with 10,000 member compounds is likely the minimum size required to build a model with reasonable predictive power...
  7. ncbi request reprint Evaluation of mutual information, genetic algorithm and SVR for feature selection in QSAR regression
    Jianwen Fang
    Applied Bioinformatics Laboratory, The University of Kansas, Lawrence, 66047, USA
    Curr Drug Discov Technol 8:107-11. 2011
    ..In addition, we present a simple but very efficient iterative strategy for optimizing parameters for SVM-RFE algorithm. All three algorithms can effectively reduce the number of features and often achieve improved performance...
  8. ncbi request reprint Feature selection in validating mass spectrometry database search results
    Jianwen Fang
    Bioinformatics Core Facility and Information and Telecommunication Technology Center, University of Kansas, 2099 Constant Dr, Lawrence, Kansas 66047, USA
    J Bioinform Comput Biol 6:223-40. 2008
    ..The identified properties important to fragmentation and ionization can be either used in independent validation tools or incorporated into peptide sequencing and database search algorithms to improve existing software programs...
  9. pmc The rationale for targeting the NAD/NADH cofactor binding site of parasitic S-adenosyl-L-homocysteine hydrolase for the design of anti-parasitic drugs
    Sumin Cai
    Department of Molecular Biosciences, The University of Kansas, Lawrence, Kansas, USA
    Nucleosides Nucleotides Nucleic Acids 28:485-503. 2009
    ..Analogues of NAD and their reduced forms show significant selective inactivation of Tc-SAHH, confirming that this design approach is rational...
  10. doi request reprint Comparative kinetics of cofactor association and dissociation for the human and trypanosomal S-adenosylhomocysteine hydrolases. 2. The role of helix 18 stability
    Qing Shan Li
    Department of Pharmaceutical Chemistry, The University of Kansas, Lawrence, Kansas 66047, USA
    Biochemistry 47:4983-91. 2008
    ..Global unfolding of all fully reconstituted holoenzymes occurred around 63 degrees C, confirming that the kinetic transition temperatures did not arise from a major disruption of the protein structure...
  11. pmc The reactive metabolite target protein database (TPDB)--a web-accessible resource
    Robert P Hanzlik
    Department of Medicinal Chemistry, University of Kansas, Lawrence, KS 66045, USA
    BMC Bioinformatics 8:95. 2007
    ..The literature of this field is widely scattered but expanding rapidly, suggesting the need for a comprehensive, searchable database of reactive metabolite target proteins...
  12. pmc Comparative kinetics of cofactor association and dissociation for the human and trypanosomal S-adenosylhomocysteine hydrolases. 3. Role of lysyl and tyrosyl residues of the C-terminal extension
    Sumin Cai
    Department of Molecular Biosciences, The University of Kansas, Lawrence, Kansas 66047, USA
    Biochemistry 49:8434-41. 2010
    ....
  13. pmc Evaluation of NAD(H) analogues as selective inhibitors for Trypanosoma cruzi S-adenosylhomocysteine hydrolase
    Qing Shan Li
    Department of Pharmaceutical Chemistry, The University of Kansas, Lawrence, Kansas, USA
    Nucleosides Nucleotides Nucleic Acids 28:473-84. 2009
    ..None significantly inhibited Hs-SAHH while S-NADH and H-NADH (see Figure 1) reduced the catalytic activity of Tc-SAHH to < 10% in six minutes of exposure...
  14. pmc DB-PABP: a database of polyanion-binding proteins
    Jianwen Fang
    Bioinformatics Core Facility, Information and Telecommunication Technology Center, University of Kansas, Lawrence, KS 66047, USA
    Nucleic Acids Res 36:D303-6. 2008
    ..The DB-PABP is maintained at the University of Kansas. We encourage users to provide feedback and submit new data and references...
  15. pmc PROTS: a fragment based protein thermo-stability potential
    Yunqi Li
    Applied Bioinformatics Laboratory, The University of Kansas, Lawrence, Kansas 66047, USA
    Proteins 80:81-92. 2012
    ..In addition, this white-box predictor allows easy interpretation of the factors that influence mutation induced protein stability changes at the residue level...
  16. pmc In silico classification of proteins from acidic and neutral cytoplasms
    Yaping Fang
    Applied Bioinformatics Laboratory, The University of Kansas, Lawrence, Kansas, USA
    PLoS ONE 7:e45585. 2012
    ..To best of our knowledge, this work represents the first systematic comparative study of the acidostable proteins and their non-acidostable orthologs...
  17. pmc Identification of properties important to protein aggregation using feature selection
    Yaping Fang
    Applied Bioinformatics Laboratory, University of Kansas, 2034 Becker Drive, Lawrence, KS 66047, USA
    BMC Bioinformatics 14:314. 2013
    ..Such studies may result in not only accurately predicting peptide aggregation propensities and identifying aggregation prone regions in proteins, but also aid in discovering additional underlying mechanisms governing this process...
  18. doi request reprint Predicting residue-residue contacts using random forest models
    Yunqi Li
    Applied Bioinformatics Laboratory, The University of Kansas, Lawrence, KS 66047, USA
    Bioinformatics 27:3379-84. 2011
    ..Protein residue-residue contact prediction can be useful in predicting protein 3D structures. Current algorithms for such a purpose leave room for improvement...
  19. ncbi request reprint A network-based analysis of polyanion-binding proteins utilizing yeast protein arrays
    Nazila Salamat-Miller
    Department of Pharmaceutical Chemistry, University of Kansas, Lawrence, Kansas 66047, USA
    Mol Cell Proteomics 5:2263-78. 2006
    ..This investigation takes a first step toward achieving a better understanding of the nature of polyanion-protein interactions within cells and introduces an alternative way of thinking about intracellular organization...
  20. pmc PROTS-RF: a robust model for predicting mutation-induced protein stability changes
    Yunqi Li
    Applied Bioinformatics Laboratory, The University of Kansas, Lawrence, Kansas, United States of America
    PLoS ONE 7:e47247. 2012
    ..It also shows high levels of robustness in the tests using hypothetical reverse mutations. We demonstrate that testing datasets created based on physical principles can be highly useful for testing the robustness of predictive models...
  21. pmc Hepatocyte nuclear factor 4 alpha and farnesoid X receptor co-regulates gene transcription in mouse livers on a genome-wide scale
    Ann M Thomas
    Department of Pharmacology, Toxicology, and Therapeutics, University of Kansas Medical Center, Kansas City, Kansas, 66160, USA
    Pharm Res 30:2188-98. 2013
    ..Thus, we compared the genome-wide binding of Fxr and Hnf4α in the liver of mice and characterized their cooperative activity on binding to and activating target gene transcription...
  22. pmc Diagnostic prediction of complex diseases using phase-only correlation based on virtual sample template
    Shu Lin Wang
    Applied Bioinformatics Laboratory, The University of Kansas, 2034 Becker Drive, Lawrence, KS 66047, USA
    BMC Bioinformatics 14:S11. 2013
    ..However, it remains a major challenge to deal with the high dimensionality and small size of available complex disease gene expression datasets currently used for discovering gene expression patterns...
  23. doi request reprint Prediction of core cancer genes using multi-task classification framework
    Shan Gao
    Applied Bioinformatics Laboratory, The University of Kansas, 2034 Becker Drive, Lawrence, KS 66047, USA
    J Theor Biol 317:62-70. 2013
    ..Our strategy can be used as a general method to find important genes from large gene expression datasets on the genomic level. The selected genes can be used to predict cancers...
  24. pmc Filling and mining the reactive metabolite target protein database
    Robert P Hanzlik
    Department of Medicinal Chemistry and Bioinformatics Core Facility, University of Kansas, Lawrence, 66045 7582, USA
    Chem Biol Interact 179:38-44. 2009
    ....
  25. ncbi request reprint Large-scale Protein-Protein Interaction prediction using novel kernel methods
    Xue Wen Chen
    Electrical Engineering and Computer Science Department, The University of Kansas, Lawrence, KS 66045, USA
    Int J Data Min Bioinform 2:145-56. 2008
    ..Furthermore, we evaluate the problem of cross-species PPI prediction and the effect of the number of negative samples on the performance of PPI predictions, which are two fundamental problems in most in silico PPI methods...
  26. pmc A novel scoring function for discriminating hyperthermophilic and mesophilic proteins with application to predicting relative thermostability of protein mutants
    Yunqi Li
    Applied Bioinformatics Laboratory, The University of Kansas, Lawrence, KS 66047, USA
    BMC Bioinformatics 11:62. 2010
    ..Robust and accurate algorithms, however, remain elusive. One critical problem is the lack of reliable methods to estimate the relative thermostability of possible mutants...
  27. pmc Distance-dependent statistical potentials for discriminating thermophilic and mesophilic proteins
    Yunqi Li
    Applied Bioinformatics Laboratory, University of Kansas, Lawrence, KS 66047, USA
    Biochem Biophys Res Commun 396:736-41. 2010
    ..This approach revealed that the ability to distinct the subtle structural features responsible for protein thermostability may be effectively enhanced through rationally designed comparative study...
  28. ncbi request reprint Molecular dynamics simulations of domain motions of substrate-free S-adenosyl- L-homocysteine hydrolase in solution
    Chen Hu
    Department of Molecular Biosciences, The University of Kansas, Lawrence, Kansas, USA
    Proteins 71:131-43. 2008
    ..Overall, our simulation results complement the existing experimental data and provide important new insights into SAHH domain motions in solution, which play a crucial role in the catalytic mechanism of SAHH...
  29. ncbi request reprint Tracker: continuous HMMER and BLAST searching
    Madelaine Marchin
    Department of Molecular Biosciences, University of Kansas, Lawrence, KS 66045, USA
    Bioinformatics 21:388-9. 2005
    ..Tracker supports Boolean AND/OR operations on HMMER and BLASTP result sets to allow users to broaden or narrow protein searches...
  30. pmc Transcription activation by the DNA-binding domain of the AraC family protein RhaS in the absence of its effector-binding domain
    Jason R Wickstrum
    Department of Molecular Biosciences, 1200 Sunnyside Ave, University of Kansas, Lawrence, KS 66045, USA
    J Bacteriol 189:4984-93. 2007
    ..We conclude that RhaS-CTD contains all of the determinants necessary for transcription activation by RhaS...
  31. doi request reprint SymDex: increasing the efficiency of chemical fingerprint similarity searches for comparing large chemical libraries by using query set indexing
    David Tai
    Applied Bioinformatics Laboratory, University of Kansas, Lawrence, Kansas 66047, USA
    J Chem Inf Model 52:1926-35. 2012
    ..It can be adapted to most, if not all, existing indexing algorithms and shows potential for accelerating future similarity search algorithms for comparing chemical databases...
  32. pmc Genome-wide tissue-specific farnesoid X receptor binding in mouse liver and intestine
    Ann M Thomas
    Department of Pharmacology, Toxicology, and Therapeutics, University of Kansas Medical Center, Kansas City, KS, USA
    Hepatology 51:1410-9. 2010
    ..Furthermore, pathway analysis indicated that FXR may be extensively involved in multiple cellular metabolic pathways...
  33. ncbi request reprint Comparative kinetics of cofactor association and dissociation for the human and trypanosomal S-adenosylhomocysteine hydrolases. 1. Basic features of the association and dissociation processes
    Qing Shan Li
    Department of Pharmaceutical Chemistry, The University of Kansas, Lawrence, Kansas 66047, USA
    Biochemistry 46:5798-809. 2007
    ..The rate of loss of activity is equal to the rate of dissociation of the cofactor and thus 80-fold faster at 37 degrees C for Tc-SAHH...
  34. doi request reprint ChemCom: A Software Program for Searching and Comparing Chemical Libraries
    Sirus Saeedipour
    Applied Bioinformatics Laboratory, The University of Kansas, 2034 Becker Drive, Lawrence, Kansas 66047, United States
    J Chem Inf Model 55:1292-6. 2015
    ..It is approximately 11 times faster than the Open Babel FastSearch algorithm in our tests. ChemCom can be accessed free-of-charge via a user-friendly website at http://bioinformatics.org/chemcom/...
  35. ncbi request reprint A network-based analysis of polyanion-binding proteins utilizing human protein arrays
    Nazila Salamat-Miller
    Department of Pharmaceutical Chemistry, University of Kansas, Lawrence, Kansas 66047, USA
    J Biol Chem 282:10153-63. 2007
    ..Considering the crowded nature of cellular interiors, we propose that polyanion-binding proteins interact with a wide variety of polyanionic surfaces in cells in a functionally significant manner...
  36. ncbi request reprint The major vault protein is related to the toxic anion resistance protein (TelA) family
    Kathy A Suprenant
    Department of Molecular Biosciences, University of Kansas, Lawrence, KS 66045, USA
    J Exp Biol 210:946-55. 2007
    ..In addition, vaultosomes form independently from other stress-induced ribonucleoprotein complexes, stress granules and aggresomes. Vaultosome formation is therefore a unique cellular response to an environmental toxin...
  37. pmc Finding minimum gene subsets with heuristic breadth-first search algorithm for robust tumor classification
    Shu Lin Wang
    Applied Bioinformatics Laboratory, University of Kansas, 2034 Becker Drive, Lawrence, KS 66047, USA
    BMC Bioinformatics 13:178. 2012
    ....
  38. ncbi request reprint K-Screen: a free application for high throughput screening data analysis, visualization, and laboratory information management
    David Tai
    Applied Bioinformatics Laboratory, The University of Kansas, 2034 Becker Dr, Lawrence, KS 66047, USA
    Comb Chem High Throughput Screen 14:757-65. 2011
    ..Interfaces to external searches against PubChem and ZINC databases are also provided. We feel that these features make K-Screen a practical and effective alternative to other commercial or academic HTS LIMS systems...
  39. ncbi request reprint Canine cathelicidin (K9CATH): gene cloning, expression, and biochemical activity of a novel pro-myeloid antimicrobial peptide
    Yongming Sang
    Department of Anatomy, Kansas State University, Manhattan, KS 66506, USA
    Dev Comp Immunol 31:1278-96. 2007
    ..The potency and broad antimicrobial activity of K9CATH suggest that this peptide may act as a fundamental contributor to the innate immune responses in this carnivore species...
  40. ncbi request reprint Efficient chemoenzymatic synthesis of globotriose and its derivatives with a recombinant alpha-(1-->4)-galactosyltransferase
    Jianbo Zhang
    Department of Chemistry, Wayne State University, Detroit, MI 48202, USA
    Carbohydr Res 337:969-76. 2002
    ..Its acceptor specificity was carefully characterized. Then the purified enzyme was utilized in highly efficient syntheses of globotriose and a variety of alpha-(1-->4)-galactosylated derivatives as potential antibacterial agents...