Publications
2008
- Guha, R.; Van Drie, J.H.; "Assessing How Well a Modeling
Protocol Captures a Structure-Activity Landscape",
J. Chem. Inf. Model., submitted
- Jur, H.; Wild, D.J.; "PubChemSR: A search and retrieval tool
for PubChem", Chemistry Central Journal, 2008, in
press
- Guha, R.; Wiggins, G.D.; Wild, D.J.; Baik, M.-H.; Pierce,
M.E.; Fox, G.. "Improving usability and accessibility of
cheminformatics tools for chemists through cyberinfrastructure and
education", Cheminformatics, 2008, in press
- Guha, R.; Schurer, S.; "Utilizing High Throughput Screening
Data for Predictive Toxicology Models: Protocols and Application
to MLSCN Assays", J. Comp. Aid. Molec. Des., 2008,
ASAP
- Guha, R.; Van Drie, J.H.; "The Structure-Activity Landscape
Index: Identifying and Quantifying Activity-Cliffs",
J. Chem. Inf. Model., 2008, 48, 646-658
- Guha, R.; "A Flexible Web Service Infrastructure for the
Development and Deployment of Predictive Models",
J. Chem. Inf. Model., 2008, 48, 456-464
- Fox, G.; "Parallel
Data Mining from Multicore to Cloudy Grids", International
Advanced Research Workshop On High Performance Computing And Grids
, 2008
- Qiu, X.; Fox, G.; Yuan, H.; Bae, S.-H.; Chrysanthakopoulos,,
G.; Nielsen, H.; "Parallel
Clustering And Dimensional Scaling On Multicore Systems",
High Performance Computing & Simulation Conference,
2008
- Qiu, X.; Fox, G.C.; Yuan, H.; Bae, S.-H.; "Parallel
Datamining on Multicore Systems", Technical Report,
2008
- Qiu, X.; Fox, G.C.; Yuan, H.; Bae, S.-H.;
Chrysanthakopoulos,, G.; Nielsen, H.; "Performance
of Multicore Systems on Parallel Data Clustering with
Deterministic Annealing", ICCS 2008: "Advancing Science
through Computation" Conference; ACC CYFRONET and Institute of
Computer Science AGH University of Science and Technology Krak�w,
POLAND; June 23-25, 2008
2007
- Guha, R.; "Chemical Informatics Functionality in R",
J. Stat. Soft, 2007, 18
- Dutta, D.; Guha, R.; Chen, T.; Wild, D.
J. "Ensemble Feature Selection: Consistent Descriptor Subsets for
Multiple QSAR Models", J. Chem. Inf. Model., 2007,
47, 989-997
- Guha, R.; Dutta, D.; Chen, T.; Wild, D.J.; "Counting Clusters
Using R-NN Curves", J. Chem. Inf. Model., 2007,
47, 1303-1318
- Dong, X., Gilbert, K.E., Guha, R., Heiland, R., Kim, J., Pierce, M.E. Pierce, Fox, G.C. and Wild, D.J. Web service infrastructure for chemoinformatics, Journal of Chemical Information and Modeling, 2007; 47(4) pp 1303-1307.
- Wang, H., Klinginsmith, J., Dong, X., Lee, A.C., Guha, R., Wu,
Y., Crippen, G.M., and Wild, D.J. Chemical Data Mining of the NCI Human Tumor Cell Line Database, Journal of Chemical Information and Modeling, 2007; 47(6), 2063-2076.
- Willighagen, E.L.; O'Boyle, N.; Gopalakrishnan, H.; Jiao, D.;
Guha, R.; Steinbeck, C.; Wild, D.J.; "Userscripts for the Life
Sciences", BMC Bioinformatics, 2007, 8, 487
- Aktas, M.S.; Fox, G.; Pierce, M.E.; "Fault tolerant high
performance Information Services for dynamic collections of Grid
and Web services", Future Generation Comp. Syst.,
2007 23(3), 317-337
- Gadgil, H.; Fox, G.; Pallickara, S.; Pierce, M.; "Scalable,
Fault-tolerant Management in a Service Oriented Architecture.",
High Performance Distributed Computing (HPDC), 2007,
in review
- Fox, G.; Pierce, M.; "Grids
meet Too much Computing, Too much Data and never Too much
Simplicity", White Paper, 2007
- Qiu, X.; Fox, G.C.; Yuan, H.; Bae, S.-H.; Chrysanthakopoulos,,
G.; Nielsen, H.; "High
Performance Multi-Paradigm Messaging Runtime Integrating Grids and
Multicore Systems", Proc. of eScience 2007, Bangalore,
India
- Pallickara, S.; Ekanayake, J.; Fox, G.; "A Scalable Approach
for the Secure and Authorized Tracking of the Availability of
Entities in Distributed Systems", Proc. 21st IEEE Intl
Parallel & Distributed Processing Symposium (IPDPS 2007), Long
Beach, California.
- Fox, G.; Pierce, M.; "Grids
Challenged by a Web 2.0 and Multicore Sandwich", Special Issue
of Concurrency & Computation: Practice & Experience
, on Seventh IEEE International Symposium on Cluster Computing
and the Grid - CCGrid 2007, Keynote Talk Rio de Janeiro Brazil May
15 2007
- Stewart, C.A.; Link, M.; Rodgers, G.; Turner, G.; Hancock,
D.; Repasky, R.; Saied, F.; Pierce, M.; Aiken, R.;
"Implementation, performance, and science results from a 20.441
TFLOPS IBM BladeCenter cluster", International Supercomputer
Conference ISC, 2007, submitted
- Brad C. Bailey, Hongjun Fan, John C. Huffman, Mu-Hyun Baik and Daniel J. Mindiola.
"Intermolecular C-H Bond Activation of Hydrocarbons Promoted by
Transient Titanium Alkylidynes. Synthesis, Reactivity, Kinetic and
Theroretical Studies of the Ti[triplebond]C Linkage",
J. Am. Chem. Soc., 2007, 129, 8781-8793
- Ferdaus Hossain, Matthew A. Rigsby, Cole T. Duncan, Paul
L. Milligan, Jr., Richard L. Lord, Mu-Hyun Baik and Franklin
A. Schultz. "Synthesis, Structure and Properties of Low-Spin
Manganese(III)-Poly(pyrazolyl)borate Complexes.",
Inorg. Chem., 2007 , 46, 2596-2603
- Yogita Mantri, Stephen J. Lippard and Mu-Hyun
Baik. "Bifunctional Binding of Cisplatin to DNA: Why Does
Cisplatin Form 1,2-Intrastrand Crosslinks with AG, But Not with
GA?" J. Am. Chem. Soc., 2007, 129, 5023-5030
2006
- Guha, R.; Dutta, D.; Jurs, P.C.; Chen, T.; "Local Lazy
Regression: Making Use of the Neighborhood to Improve QSAR
Predictions.", J. Chem. Inf. Model., 2006,
46, 1836-1847
- Guha, R.; Dutta, D.; Jurs, P.C; Chen, T.; "R-NN Curves: An
Intuitive Approach to Outlier Detection Using a Distance Based
Method", J. Chem. Inf. Model., 2006, 46,
1713-1722
- Guha, R.; Howard, M.T.; Hutchison, G.R.; Murray-Rust, P.;
Rzepa, H.; Steinbeck, C.; Wegner, J.; Willighagen, E.L.; "The Blue
Obelisk--Interoperability in Chemical Informatics",
J. Chem. Inf. Model., 2006, 46, 991-998
- Dutta, D.; Guha, R.; Jurs, P.C.; Chen, T.; "Scalable
Partitioning and Exploration of Chemical Spaces using Geometric
Hashing", J. Chem. Inf. Model., 2006, 46,
321-333
- Steinbeck, C.; Hoppe, C.; Kuhn, S.; Floris, M.; Guha, R.;
Willighagen, E.L., "Recent Developments of the Chemistry
Development Kit (CDK) - An Open-Source Java Library for Chemo- and
Bioinformatics", Curr. Pharm. Des., 2006, 12,
2110-2120
- Wild, D.J.; "Strategies for Using Information Effectively in
Early-stage Drug Discovery." in Ekins, S. (ed), Computer
Applications in Pharmaceutical Research and
Development. Wiley-Interscience, Hoboken, 2006
- Wild, D.J.; Wiggins, G.D.; "Challenges for chemoinformatics
education in drug discovery.", Drug Discovery Today, 2006, 11(9-10),
436-439.
- Wild, D.J.; Wiggins, G.D.; "Videoconferencing and Other
Distance Education Techniques in Chemoinformatics Teaching and
Research at Indiana University", J. Chem. Inf. Model.,
2006, 46, 495-502.
- Bramley, R.; Chiu, K.; Devadithya, T.; Gupta, N.; Hart, C.;
Huffman, J.C.; Huffman, K.; Ma, Y.; McMullen, D.F. "Instrument
Monitoring, Data Sharing, and Archiving Using Common Instrument
Middleware Architecture (CIMA)." J. Chem. Inf. Model.,
2006, 46, 1017-1025
- Sunnie Myung, K. Patrick Lorton, Samuel I. Merenbloom, Marco
Fioroni, Mu-Hyun Baik and D. E. Clemmer. "Evidence for Spontaneous
Resolution of Icosahedral Proline" J. Am. Chem. Soc.,
2006, 128, 15988-15989
- Richard L. Lord, Mario Vieweger, Huijun Wang and Mu-Hyun
Baik."What difference one double bond makes: Electronic structure
of saturated and unsaturated n-heterocyclic carbene ligands in
Grubbs 2nd generation catalysts", J. Organometal. Chem.,
2006, 691, 5505-5512
- Mi Hee Lim, Brian A. Wong, William H. Pitcock, Deepa
Mokshagundam, Mu-Hyun Baik and Stephen J. Lippard. "Direct Nitric
Oxide Detection In Aqueous Solution by Copper(II) Fluorescein
Complexes", J. Am. Chem. Soc., 2006, 128,
14364-14373
- Sunnie Myung, Marco Fioroni, Ryan R. Julian, Stormy
L. Koeniger, Mu-Hyun Baik and D. E. Clemmer. "Chirally Directed
Formation of Nanometer Scale Proline Clusters",
J. Am. Chem. Soc., b> 2006, 128, 10833-10839
- D. R. Williams, Janathan T. Reeves, Partha P. Nag, William
H. Pitcock, Jr. and Mu-Hyun Baik "Studies of the Generation and
Pericyclic Behavior of Cyclic Pentadienyl Carbanions. Alkylation
Reactions As An Efficient Route to Functionalized
cis-Bicyclo[3.3.0]octenes", J. Am. Chem. Soc., 2006,
128, 12339-12348
- Brad C. Bailey, Hongjun Fan, John C. Huffman, Mu-Hyun Baik and
Daniel J. Mindiola "Room Temperature Ring-Opening Metathesis of
Pyridines by a Transient Ti[triplebond]C Linkage",
J. Am. Chem. Soc., 2006, 128, 6798-6799
- Alison R. Fout, Falguni Basuli, Hongjun Fan, John Tomaszewski,
John C. Huffman, Mu-Hyun Baik and Daniel J. Mindiola. "A Co2N2
Diamond-Core Resting State of Cobalt(I): A Three-Coordinate Co(I)
Synthon Invoking an Unusual Pincer-Type Rearrangement",
Ange. Chemie Intl. Ed. Eng, 2006, 45,
3291-3295
- Xiaofan Yang and Mu-Hyun Baik. "Cis,cis-[(bpy)2RuVO]2O4+
Catalyzes Water Oxidation formally via in situ Generation of
radicaloid RuIV-O(dot)", J. Am. Chem. Soc., 2006,
128, 7476-7485
2005
- Guha, R.; Stanton, D.T.; Jurs, P.C.; "Interpreting
Computational Neural Network QSAR Models: A Detailed Interpretation
of the Weights and Biases", J. Chem. Inf. Model.,
2005, 45, 1109-1121
- Guha, R.; Jurs, P.C.; "Interpreting Computational Neural
Network QSAR Models: A Measure of Descriptor Importance",
J. Chem. Inf. Model., 2005, 45, 800-806
- Guha, R.; Jurs, P.C.; "Determining the Validity of a QSAR
Model--A Classification Approach", J. Chem. Inf. Model.,
2005, 45, 65-73
- B. C. Bailey, H. Fan, E. W. Baum, J. C. Huffman, M.-H. Baik,
D. Mindiola. "Intermolecular C-H Activation Promoted by a Titanium
Alkylidyne", J. Am. Chem. Soc., 2005, 127,
16016-16017
