MGM Lab Publications

2011
Xiaohong W., Smalter, A., Huan, J., Lushington, G. ​
Similarity Boosting for Label Noise Tolerance in Protein-Chemical Interaction Prediction. In Proceedings of the 2nd ACM Conference on Bioinformatics, Computational Biology and Biomedicine (ACM BCB'11), 2011.

Xiaohong W., W., Smalter, A., Huan, J., Lushington, G. ​​
G-hash: Towards Fast Kernel-based Similarity Search in Large Graph Databases. Graph Data Management: Techniques and Applications, Sherif Sakr and Eric Pardede edt, IGI Global, ISBN 161350053X, 2011

2010
Xiaohong W., Smalter, A., Huan, J., Lushington, G. ​​
GPD: A Graph Pattern Diffusion Kernel for Accurate Graph Classification with Applications in Cheminformatics. IEEE/ACM Transactions on Computational Biology and Bioinformatics, Vol. 7, No.2, pp. 197-207, 2010

Xiaohong W.,W., Smalter, A., Huan, J., Lushington, G. ​​
Application of Kernel Functions for Accurate Similarity Search in Large Chemical Databases. BMC Bioinformatics, Vol. 11 (Suppl. 3), 2010.

The MicroArray Quality Control (MAQC) Consortium.
The MAQC-II Project: A Comprehensive Study of Common Practices for the Development and Validation of Microarray-based Predictive Models. Nature Biotechnology, 2010.

2009
Xiaohong W., Smalter, A., Huan, J., Lushington, G. ​
Feature Selection in the Feature Tensor Product Space. Proceedings of the 9th IEEE International Conference on Data Mining (ICDM'09), 2009.

Xiaohong W., Smalter, A., Huan, J., Lushington, G. ​
GPD: A Graph Pattern Diffusion Kernel for Accurate Graph Classification with Applications in Cheminformatics. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2009.

Xiaohong W.​, Smalter, A., Huan, J., Lushington, G.
Feature Selection in the Feature Tensor Product Space. Proceedings of the 9th IEEE International Conference on Data Mining (ICDM'09), 2009.

Xiaohong W., Smalter, A., Huan, J., Lushington, G.
Graph Wavelet Alignment Kernels for Drug Virtual Screening. Journal of Bioinformatics and Computational Biology, Vol. 7 (3), pp. 473-497, 2009.

Xiaohong W., Smalter, A., Huan, J., Lushington, G.H.
Application of Kernel Functions for Accurate Similarity Search in Large Chemical Databases. In Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine (BIBM'09), 2009.

Xiaohong Wang,Smalter, A.​, Jun Huan, Lushington, G.H.​
G-Hash: Towards Fast Kernel-based Similarity Search in Large Graph Databases. In Proceedings of the 12th International Conference on Extending Database Technology, 2009.

Visvanathan, M., Pfeifer, B., Baumgartner, C., Tilg, B., Lushington, G.H.
Integrative Approach for Combining TNF ?-NF?B Mathematical Model to a Protein Interaction Connectivity Map. ISBRA 2009, LNBI 5542 proceedings. 2009, in press.

Visvanathan, M., Adagarla, B., Sittampalam, S., Lushington, G.H.
Finding Common Genes & Pathways for Multiple Cancer Types Using Hyper Geometric Distribution and Particle Swarm Optimization - Support Vector Machine. IEEE Proceedings of 2009 International Joint Conferences on System Biology, Bioinformatics and Intelligent Computing. 2009, in press.

Smalter, A.., Huan, J., Lushington, G.
G-Hash: Towards Fast Kernel-based Similarity Search in Large Graph Databases, Proceedings of the 12th International Conference on Extending Database Technology (EDBT'09). In press, 2009. NIHMSID #118201.

Gui, C., Wahlgren, B., Lushington, G.H., Hagenbuch, B.
Identification, Ki determination and CoMFA analysis of nuclear receptor ligands as competitive inhibitors of OATP1B1-mediated estradiol-17ß-glucuronide transport. Pharmacological Research. 60, 50-56 (2009). PMID: 19427586

DeVore, N.M., Smith, B.D., Wang, J.L., Lushington, G.H., and Scott, E.E.
Key residues controlling binding of diverse ligands to human cytochrome P450 2A enzymes. Drug Metabolism & Disposition. 37, 1319-1327 (2009). PMID: 19251817

Suryanarayana, S., Wang, J.L., Richter, M., Shen, Y., Tang, W.-T., Lushington, G.H., Seifert, R.
Distinct interactions of 2’- and 3’-O-(N-methyl)anthraniloyl)-isomers of ATP and GTP with the adenylyl cyclase toxin of Bacillus anthracis, edema factor. Biochem. Pharmacol., 78, 224-230 (2009).

Mathur, S., Visvanathan, M., Lushington, G.H., Smith, P.G.
GOAPhAR: An Integrative Discovery Tool for Annotation, Pathway Analysis. The Open Bioinformatics Journal. 2009, in press.

Larock, R., Cho, C.-H., Neuenswander, B., Lushington, G.
Solution-Phase Parallel Synthesis of a Multi-Substituted Benzo[b]thiophene Library. J. Comb. Chem. 2009, in press.

Li, Y., Dou, D., He, G., Lushington, G.H., Groutas, W.C.
Mechanism-Based Inhibitors of Serine Proteases with High Selectivity Through Optimization of S' Subsite Binding. Bioorg Med. Chem. 17, 3636-3542 (2009). PMID: 19394830

Rolfe, A., Young, K., Volp, K., Schoenen, F., Neuenswander, B., Lushington G. H., Hanson, P. R.
A One-Pot, 3-Component, Domino Heck-aza-Michael Approach to Libraries of Functionalized 1,1-Dioxido-1,2-benzisothiazoline-3-acetic acids. J. Comb. Chem. 11, 732-738 (2009).

Smalter, A., Huan, J., Lushington, G.
Graph Wavelet Alignment Kernels for Drug Virtual Screening. J. Bioinfo. Comput. Biol. 7, 473-497 (2009). NIHMSID #118199.

2002-2008
Feagan, L., Rohrer, J., Garrett, A., Amthauer, H., Komp, E., Johnson, D., Hock, A., Clark, T., Lushington, G., Minden G., Frost, V.
Bioinformatics process management: information flow via a computational journal. Source Code for Biology and Medicine. 2008, 2: 9. PMC2228283

Vedantham, P., Guerra, J.M., Schoenen, F., Huang, M., Gor, P.J., Georg, G.I., Wang, J.L., Neuenswander, B., Lushington, G.H., Mitscher, J.A., Ye, Q.-Z., Hanson, P.R.
Ionic immobilization, diversify and release: Application to the generation of a library of methionine aminopeptidase inhibitors. J. Comb. Chem., 10, 185-194 (2008). PMID: 18163595

Vedantham, P.,Zhang, M., Gor, P.J., Huang, M., Georg, G.I., Lushington, G.H., Mitscher, L.A., Ye, Q.-Z., Hanson, P.R.
Studies towards synthesis of methionine aminopeptidase inhibitors: Diversification utilizing a ROMP-derived coupling reagent. J. Comb. Chem., 10, 195-203 (2008). PMID: 18163594

Otrubova, K., Lushington, G., Vander Velde, D., McGuire, K.L., McAlpine, S.R.
A comprehensive study of Sansalvamide A derivatives and their structure-activity relationships against drug-resistant colon cancer cell lines. J. Med. Chem. 51, 530-544 (2008). PMID: 18186604

Fang, J., Dong, Y., Williams, T.D., Lushington, G.H.
Feature Selection in Validating Mass Spectrometry Database Search Results. J. Bioinf. Comp. Biol., 6, 233-240 (2008). PMID: 18324754

Zhang, L., Lushington, G., Neuenswander, B., Hershberger, J., Malinakova, H.
Solution-Phase Parallel Synthesis of Hexahydro-1H-isoindolone Libraries via Tactical Combination of Cu-Catalyzed Three-Component Coupling and Diels-Alder Reactions. J. Comb. Chem. 10, 285-302 (2008). PMID: 18237142

Lushington, G.H.
Comparative Modeling of Proteins. Methods in Molecular Biology 443, 199-212 (2008). PMID: 18446289

Theertham, B., Wang, J.L., Fang, J., Lushington, G.H.
Novel algorithms for the identification of biologically informative chemical diversity metrics. Curr. Comp.-Aided Drug Design. 4, 23-34 (2008). NIHMSID #118200.

Pinto, C., Papa, D., Hübner, M., Mou, T.-C., Lushington, G.H., Seifert, R.S.
Activation and Inhibition of Adenylyl Cyclase Isoforms by Forskolin Analogs, JPET. 325, 27-36 (2008). PMID: 18184830

Smalter, A., Huan, J., Lushington, G.
Structure-based Pattern Mining For Chemical Compound Classification, Proceedings of the 6th Asia Pacific Bioinformatics Conference (APBC), 39-48 (2008). NIHMSID #118197

Entwistle, R.A., Winefield, R.D., Foland, T.B., Lushington, G.H., Himes, R.H.
The paclitaxel site in tubulin probed by site-directed mutagenesis of Saccharomyces cerevisiae tubulin. FEBS Lett., 582, 2467-2470 (2008). PMID: 18570892

Stensrud, K.S., Adam, P.R., D. La Mar, C.D., Olive, A.J., Lushington, G.H., Sudharsan, R., Shelton, N.L., Givens, R.S., Picking, W.L., Picking, W.D.
Deoxycholate Interacts with IpaD of Shigella flexneri in Inducing the Recruitment of IpaB to the Type III Secretion Apparatus Needle Tip. J. Biol. Chem., 283, 18646-18654 (2008). PMID: 18450744

Linde, A., Lushington, G.H., Blecha, F., Melgarejo, T.
Rat cardiomyocytes express a classical epithelial beta-defensin. Am. J. Animal & Vet. Sci. 3, 1-6 (2008).

Waldo, J., Mehta, S., Neuenswander, B., Lushington, G., Larock, R.
Solution Phase Synthesis of a Diverse Library of Highly Substituted Isoxazoles. J. Comb. Chem., 10, 658-663 (2008).

Brown, N., Gao, G., Minatoya, M., Xie, B., Vander Velde, D., Lushington, G., Perchellet, J.-P., Perchellet, E., Buszek, K., Crow, K.
Design and Synthesis of Medium-Ring Lactam Libraries Inspired by Octalactin A. A Convergent-Divergent Approach. J. Comb. Chem., 10, 628-631 (2008). PMID: 18693764

Smalter, A., Huan, J., Lushington, G.
A Graph Pattern Diffusion Kernel for Chemical Compound Classi?cation. Proceedings of the 8th IEEE International Conference on Bioinformatics and BioEngineering (BIBE'08), 2008. NIHMSID #118198.

Winefield , R.D., Entwistle , R.A, Foland , T.B., Lushington , G.H., Himes , R.H.
Differences in Paclitaxel and Docetaxel Interactions with Tubulin Detected by Mutagenesis of Yeast Tubulin . Chem . Med. Chem . 3, 1844-1847 (2008). PMID : 18988212

Cho, C.-H., Larock, R., Neunswander, B., Lushington, G.
Parallel Synthesis of a Multi-Substituted Benzo[b]furan Library. J. Comb. Chem., 10, 941-947 (2008). PMID: 18937516

Ahn, Y.M., Vogeti, L., Liu, C.J., Santhapuram, H.K.R., White, J.M., Vasandani, V., Mitscher, L.A., Lushington, G.H., Hanson, P.R., Powell, D.C., Himes, R.H., Roby, K.F., Ye, Q.-Z., Georg, G.I.
"Design, Synthesis, Antiproliferative and CDK2-Cyclin A Inhibitory Activity of Novel Flavopiridol Analogues." Bio-org. Med Chem. 15: 702-713, 2007. PMC1876666

Manyem, S., Sibi, M.P., Lushington, G.H., Neuenswander, B., Schoenen, F., Aubé, J.
"Solution-Phase Parallel Synthesis of a Library of ?2-Pyrazolines." J. Comb. Chem. 9: 20-28, 2007. PMC2562233

Suprenant, K.A., Bloom, N., Fang, J., Lushington, G.H.
"The major vault protein is related to the prokaryotic toxic anion resistance protein family, TelA." J. Exp. Biol., 210: 946-55, 2007. PMID: 17337707

Wang, J.L., Guo, J.-X., Zhang, Q.-Y., Wu, J.J.Q., Seifert, R., Lushington, G.H.
"A Conformational Transition in the Adenylyl Cyclase Catalytic Site Yields Different Binding Modes for Ribosyl-Modified and Unmodified Nucleotide Inhibitors." Bio-org. Med. Chem., 15: 2993-3002, 2007. PMC2023969

Chaudhry, P., Schoenen, F., Neuenswander, B., Lushington, G.H., Aube, J.
"One-Step Synthesis of Oxazoline and Dihydrooxazine Libraries. " J. Comb. Chem. 9: 473-476, 2007. PMC2539067

Smith, B.D., Sanders, J.L., Porubsky, P.R., Lushington, G.H., Stout, C.D., Scott, E.E.
Structure of the Human Lung Cytochrome P450 2A13. J. Biol. Chem. 2007, 282: 17306-17313. PMID: 17428784

Lushington, G.H., Guo, J.-X., Wang, J.L.,
"Whither COMBINE? New Opportunities for Receptor-Based QSAR." Current Med. Chem., 2007, 14: 1863-1877. PMID: 17627522

Wang, J.L., Datta, A., Lushington, G.H.
"Structure-based Quantitative Structure Activity Relationship Analysis of Omuralide Analogs in the 20S Proteasome: A Covalent Inhibitor COMBINE Study." Lett. Drug Design Disc., 2007, 4: 417-421.

Sang, Y., Teresa Ortega, M., Rune, K., Xiau, W., Zhang, G., Soulages, J.L., Lushington, G.H., Fang, J.W., Williams, T.D., Blecha, F., Melgarejo, T.
Canine cathelicidin (K9CATH): Gene cloning, expression, and biochemical activity of a novel pro-myeloid antimicrobial peptide. Dev. Comp. Immunol. 2007, 31: 1278-1296. PMID: 17462733

Day, V. W., Hossain, M.D.,A., Kang, S.O., Powell, D., Lushington, G., Bowman-James, K.
Encircled Proton. J. Am. Chem. Soc. 2007, 129: 8692-8693. PMID: 17585768

Guo, J.-X., Wood, S.J., David, S.A., Lushington, G.H.
"Molecular Modeling Analysis of the Interaction of Novel Bis-cationic Ligands with the Lipid A Moiety of Lipopolysaccharide." Bioorg. Med. Chem. Lett. 16: 714-717, 2006. PMID: 16266804

Lushington, G.H.
"Computational Approaches in Medicinal Chemistry: Surveys, Case Studies and Future Directions." Curr. Topics Med. Chem. 6: 1-2, 2006 (editorial). PMID: 16454753

Lushington, G.H., Guo, J.-X., Hurley, M.M.
" Acetylcholinesterase : Molecular Modeling with the Whole Toolkit." Curr . Topics Med. Chem . 6: 57-73, 2006. PMID : 16454758

Guo, J.-X., Wu, J.-Q., Wright, J.B., Lushington, G.H.
"Mechanistic Insight into Acetylcholinesterase Inhibition and Acute Toxicity of Organophosphorus Compounds: a Molecular Modeling Study." Chem. Res. Toxicol. 19: 209-216, 2006. PMID: 16485896

Holovics, T.C., Robinson, R.E. Weintrob, E.C., Toriyama, M., Lushington, G.H., Barybin, M.V.
The 2,6-Diisocyanoazulene Motif: Synthesis and Efficient Mono-and Heterobimetallic Complexation with Controlled Orientation of the Azulenic Dipole. J. Am. Chem. Soc. 128: 2300-2309, 2006. PMID: 16478185

Fang, J., Dong, Y., Lushington, G.H., Ye, Q.-Z., Georg, G.I.
"Support Vector Machines in HTS Data Mining: Type I MetAPs Inhibition Study." ​ J. Biomolecular Screening. 11: 138-144, 2006. PMID: 16418315

Blackman, B., Georg, G.I., Lushington, G.H.
"CoMSIA / QSAR Models for Vacuolar (H+) ATPase Inhibition by Selected Benzoate and Benzolactone Species." Lett. Drug Design & Disc. 3; 104-107, 2006.

Talebizadeh, Z., Lam, D.Y., Theodoro, M.F., Bittel, D.C., Lushington, G.H., Butler, M.G.
"Novel splice isoforms for NLGN3 and NLGN4 with possible implications in autism." J. Medical Genetics. 43: e21, 2006. PMC2564526

Wood, S.J., Miller, K.A., Lushington, G.H., Burns, M.R., David, S.A.
"Anti-Endotoxin Agents. 3. Rapid Identification of High-Affinity Lipopolysaccharide-Binding Compounds in a Substituted Polyamine Library." Comb. Chem. High Throughput Screening. 9,10: 27-36, 2006. PMID: 16454684

Houndonougbo, Y., Guo, J.-X., Lushington, G.H., Laird, B.
"Monte Carlo Simulations of CO2-expanded Acetonitrile." Mol. Phys. 104: 2955-2960, 2006.

Wang, J., Lushington, G.H., Mezey, P.
"Stability and Electronic Properties of Nitrogen Nanoneedles and Nanotubes." J. Chem. Inf. Model. 46: 1965-1971, 2006. PMID: 16995727

Priestman, M.A., Healy, M.L., Becker, A., Alberg, D.G., Bartlett, P.A., Lushington, G.H., Schönbrunn, E.
"Interaction of Phosphonate Analogues of the Tetrahedral Reaction Intermediate with 5-Enolpyruvylshikimate-3-phosphate Synthase in Atomic Detail." Biochemistry. 44: 3241-3248, 2005. PMID: 15736934

Ramanathan, S.K., Keeler, J., Lee, H.-L., Reddy, D.S., Lushington, G., Aubé, J.
"Modular Synthesis of Cyclic Peptidomimetics Inspired by ?-Turns." Org. Lett., 7: 1059-1062, 2005. PMID: 15760138

Unruh, J.R., Gokulrangan, G., Lushington, G.H., Johnson, C.K., Wilson, G.S.
"Orientational Dynamics and Dye-DNA Interactions in a Dye-Labeled DNA Aptamer." Biophys. J. 88: 3455-3465, 2005. PMC1305492

Robinson, R.E., Holovics, T.C., Deplazes, S.F., Powell, D.R., Lushington, G.H., Thompson, W.H., Barybin, M.V.
"Five Possible Isocyanoazulenes and Electron-Rich Complexes Thereof: A Quantitative Organometallic Approach for Probing Electronic Inhomogeneity of the Azulenic Framework." Organometallics. 24: 2386-2397, 2005.

Lushington, G.H., Zaidi, A., Michaelis, M.L.
"Theoretically Predicted Structures of Plasma Membrane Ca2+-ATPase and their Susceptibilities to Oxidation." J. Mol. Graphics & Modeling. 24: 175-185, 2005. PMID: 16169758

Gille, A., Guo, J.-X., Mou, T.-C., Doughty, M.B., Lushington, G.H., Seifert, R.
"Differential interactions of G-proteins and adenylyl cyclase with nucleoside 5’-triphosphates, nucleoside 5’-[?-thio]triphosphates and nucleoside 5’-[?,?-imido]triphosphates." Biochem. Pharmacol. 71: 89-97, 2005. PMID: 16271707

Hurley, M.M., Balboa, A., Lushington, G.H., and Guo, J.-X.
"Interactions of Organophosphorus and Related Compounds with Cholinesterases, a Theoretical Study." Chemico-Biological Interactions. 157-158: 321-325, 2005. PMID: 16289061

Krogmeier S.L., Reddy D.S., Vander Velde D., Lushington G.H., Siahaan T.J., Middaugh C.R., Borchardt R.T., Topp E.M.
"Deamidation of model beta-turn cyclic peptides in the solid state." J. Pharmaceutical Sciences. 94: 2616-2631, 2005. PMID: 16258986

Fang, J., Haasl, R.J., Dong, Y., Lushington, G.H.
"Discover Protein Sequence Signatures from Protein-Protein Interaction Data." BMC Bioinformatics. 6: 277, 2005. PMC1310605

Lushington, G.H., Cowley, A.B., Silchenko, S., Lukat-Rodgers, G.S., Rodgers, K.R., and Benson D.R.
“Comparison of Thioethers and Sulfoxides as Axial Ligands for N-Acetylmicroperoxidase-8: Implications for Oxidation of Methionine-80 in Cytochrome c.” Inorg. Chem. 42: 7550, 2004. PMID: 14606851

MacBeth, C.E., Gupta, R., Mitchell-Koch, K.R., Young, V.G. Jr., Lushington, G.H., Thompson, W.H., Hendrich, M.P., Borovik, A.S.
"Utilization of Hydrogen Bonds To Stabilize M-O(H) Units: Synthesis and Properties of Monomeric Iron and Manganese Complexes with Terminal Oxo and Hydroxo Ligands.” J. Am. Chem. Soc. 126: 2556, 2004.

Gille, A., Lushington, G.H., Mou, T.-C., Doughty, M.B., Johnson, R.A., Seifert, R.
"Differential inhibition of adenylyl cyclase isoforms and soluble guanylyl cyclase by purine and pyrimidine nucleotides." J. Biol . Chem . 279: 19955, 2004. PMID : 14981084

Lushington, G.H.
"Ab Initio Calculations of g-Tensors, in Quantum Chemical Calculation of NMR and EPR Parameters”. V. Malkin , M. Kaupp , eds . Wiley VCH Verlag , Weinheim , 2004.

Lushington , G.H.
"The Effective Spin Hamiltonian Concept” in Quantum Chemical Calculation of NMR and EPR Parameters. V. Malkin , M. Kaupp , eds ., Wiley VCH Verlag , Weinheim , 2004.

Holovics, T.C., Deplazes, S.F., Toriyama, M., Powell, D.R., Lushington, G.H., Barybin, M.V.
"Organometallic Isocyanocyclopentadienides: A Combined Synthetic, Spectroscopic, Structural, Electrochemical and Theoretical Investigation." Organometallics. 23: 2927, 2004.

Guo, J., Hurley, M.M., Wright, J.B., Lushington, G.H.
"A Docking Score Function for Estimating Ligand-Protein Interactions: Applications to Acetylcholinesterase Inhibition." J. Med. Chem. 47: 5492, 2004. PMID: 15481986

Hurley, M.M., Wright, J.B., Lushington, G.H. and White, W.E.
“Mixed QM/MM Studies of Model Nerve Agents with Acetylchonlinesterase.” Theor. Chem. Acct. 109:160 2003.

Wright, J.B., Hurley, M.M., Lushington, G.H. and White, W.E.
“Hydrolysis of Phosphorus Esters: A Computational Study.” NATICK/TR-03/024, Unclassified, May 2003.

Robinson, R.E., Barybin, M.V., Holovics, T.C., Deplazes, S.F., Lushington, G.H., and Powell, D.R.
“First Isocyanoazulene and its Homoleptic Complexes.” J. Am. Chem. Soc. 125: 4432, 2003. PMID: 12683808

Slaughter, B., Lushington, G.H., and Johnson, C.
"Theoretical Design of Optically Active Peptides.” J. Phys. Chem. 107: 5670, 2003.

Luo, Q-L., Li, J-Y., Liu, Z-Y., Chen, L-L., Li, J., Qian, Z., Shen, Q., Li, Y., Lushington, G.H., Ye, Q-Z., and Nan, F-J.
"Discovery and Structural Modification of Inhibitors of Methionine Aminopeptidases from Escherichia coli and Saccharomyces cerevisiae.” J. Med. Chem. 46: 2631, 2003. PMID: 12801227

Hurley, M.M., Wright, J.B., Balboa, A., Lushington, G.H.
"Defense Against Chemical Warfare Agents and Toxic Industrial Chemicals." IEEE Proceedings of the 2003 User Group Conference (DoD UGC'03), Bellevue, Washington, June 9-13, 2003.

Barybin , M.V., Holovics , T.C., Deplazes , S.F., Lushington , G.H., and Powell, D.R.
“First Homoleptic Complexes of Isocyanoferrocene.” J. Am. Chem . Soc . 124: 13668, 2002. PMID : 12431084

Eschenburg, S., Healy, M.L., Priestman, M.A., Lushington, G.H., and Schönbrunn, E.
“How the Mutation Glycine96 to Alanine Confers Glyphosate Insensitivity to 5-Enolpyruvyl Shikimate-3-Phosphate Synthase (EPSP Synthase) from Escherichia Coli.” Planta 216: 129, 2002. PMID: 12430021


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