Publications

Journal articles

Chen, B., McConnell, K., Wale, N., Wild, D.J. and Gifford, E. Comparing Bioassay Response and Similarity Ensemble Approaches to Probing Protein Pharmacology, Bioinformatics, Submitted June 2011

He, B., Tang, J., Ding, Y., Wang, H., Sun, Y., Shin, J.H., Chen, B., Moorthy, G., Qiu, J., Desai, P., Wild, D.J., Mining relational paths in in relational biomedical data PloS One, Submitted May 2011. 

Chen, B., Ding, Y., Wild, D.J. A query-driven web ontology for systems chemical biology and chemogenomics. Bioinformatics. Submitted May, 2011. 

Zhu, Q., Sun, Y., Challa, S., Ding, Y., Lajiness, M.S., Wild, D.J. Semantic inference using Chemogenomics Data for Drug Discovery. BMC Bioinformatics, 2011, 12, 256. 

Choi, J.Y., Bae, S.H., Qui, J., Chen, B., Wild, D.J. Browsing large scale cheminformatics data with dimension reduction. Currency and Computation: Practice and Experience. Published online May 2011. 

Wang, H., Ding, Y., Tang, J., Dong, X., He, B., Qiu, J., Wild, D.J. Finding complex biological relationships in recent PubMed articles using Bio-LDA. PLoS One, 2011, 6 (3), e17243 

Zhu, Q., Lajiness, M.S., Ding, Y., Wild, D.J. WENDI: A tool for finding non-obvious relationships between compounds and biological properties, genes, diseases and scholarly publications. Journal of Cheminformatics, 2010, 2, 6

Chen, B., Dong. X., Jiao, D., Wang, H., Zhu, Q., Ding, Y., Wild, D.J. Chem2Bio2RDF: a semantic framework for linking and data mining chemogenomic and systems chemical biology data. BMC Bioinformatics 2010, 11, 255. 

Guha, R., Gilbert, K., Fox, G., Pierce, M., Wild, D.J. and Yuan, H. Advances in Cheminformatics Methodologies and Infrastructure to Support the Data Mining of Large, Heterogeneous Chemical Datasets. Current Computer-Aided Drug Design. 2010; 6(1) pp 50-67

Chen, B. and Wild, D.J. PubChem BioAssays as a data source for predictive models, Journal of Molecular Graphics and Modeling. 2010; 28, 420-426.  

Chen, B., Wild, D.J., Guha, R. PubChem as a Source of Polypharmacology. Journal of Chemical Information and Modeling. 2009; 49(9), pp 2044-2055

Wild, D.J.  Mining large heterogenous datasets in drug discovery. Expert Opinion on Drug Discovery. 2009; 4(10), pp 995-1004

Wild, D.J. Grand Challenges for Cheminformatics, Journal of Cheminformatics, 2009, 1, 1.

Jiao, D. and Wild, D.J. Extraction of CYP Chemical Interactions from Biomedical Literature Using Natural Language Processing Methods, Journal of Chemical Information and Modeling, 2009; 49(2), pp 263-269

Hur, J. and Wild, D.J. PubChemSR: A search and retrieval tool for PubChem, Chemistry Central Journal, 2008, 2, 11.

Dutta, D., Guha, R., Wild, D., and Chen, T. Ensemble Feature Selection: Consistent Descriptor Subsets for Multiple QSAR Models,Journal of Chemical Information and Modeling, 2007; 47(3), pp 989 – 997

Guha, R., Dutta, D., Wild, D.J., Chen, T. Counting Clusters using R-NN Curves. Journal of Chemical Information and Modeling, 2007; 47(4) pp 1308-1318

Willighagen, E., O’Boyle, N.M., Gopalakrishnan H., Jiao, D., Guha,  R., Steinbeck, C. and Wild, D.J. Userscripts for the Life Sciences, BMC Bioinformatics, 2007, 8, 487.

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.

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

Wild, D.J. and Wiggins, D. Videoconferencing and Other Distance Education Techniques in Chemoinformatics Teaching and Research at Indiana University. Journal of Chemical Information & Modeling 2006; 46(2) pp 495 – 502

Wild, D.J. and Wiggins, G.D. Challenges for chemoinformatics education in drug discovery. Drug Discovery Today, 11, 9&10 (May 2006), pp436-439

Bohl, M., Dunbar, J., Gifford, E.M., Heritage, T., Wild, D.J., Willett, P., Wilton, D.J. Scaffold Searching: Automated Identification of Similar Ring Systems for the Design of Combinatorial Libraries. Quantitative Structure-Activity Relationships, 2002, 21, 6.

Wild, D.J., Blankley, C.J. Comparison of 2D Fingerprint Types and Hierarchy Level Selection Methods for Structural Grouping using Wards Clustering, Journal of Chemical Information and Computer Sciences, 2000, 40, 155-162.

Wild, D.J., Blankley, C.J. VisualiSAR: A Web-Based Application for Clustering, Structure Browsing and SAR Study, Journal of Molecular Graphics and Modelling, 1999, 17, 85-89.

Drayton, S.K., Edwards, K., Jewell, N., Turner, D.B., Wild, D.J., Willett, P., Wright, P. M., Simmons, K., Similarity Searching in Files of Three-Dimensional Chemical Structures: Identification Of Bioactive Molecules, Internet Journal of Chemistry (www.ijc.com); 1, 1998

Thorner, D.A., Wild, D.J., Willett, P., Wright, P.M. Calculation of Structural Similarity by the Alignment of Molecular Electrostatic Potentials, Perspectives in Drug Discovery and Design, 1998, 9/10/11, 301-320

Gillett, V.J., Wild, D.J., Willett, P., Bradshaw, J., Similarity and Dissimilarity Methods for Processing Chemical Structure Databases,The Computer Journal, 1998, 41, 547-558

Wild, D.J., Willett, P. Field-Based Similarity Searching in Databases of Three-Dimensional Chemical Structures, in Collier, H. (ed),Proceedings of the 1997 International Chemical Information Conference, Tetbury:Infonortics, 1997

Thorner, D.A., Wild, D.J., Willett, P., Wright, P.M. Similarity Searching in Files of Three-Dimensional Chemical Structures: Flexible Field-Based Searching of Molecular Electrostatic Potentials, Journal of Chemical Information and Computer Sciences, 1996, 36, 900-908.

Wild, D.J., Willett, P. Similarity Searching in Files of Three-Dimensional Chemical Structures: Alignment of Molecular Electrostatic Potential Field with a Genetic Algorithm, Journal of Chemical Information and Computer Sciences, 1996, 36, 159-167.

Wild, D.J., Willett, P. Similarity Searching in Files of Three-Dimensional Chemical Structures. Implementation of Atom Mapping on the Distributed Array Processor DAP-610, the MasPar MP-1104, and the Connection Machine CM-200. Journal of Chemical  Information and Computer Sciences, 1994, 34, 224-231.

Artymiuk, P.J., Bath, P.A., Grindley, H.M., Pepperrell, C.A., Poirrette, A.R., Rice, D.W., Thorner, D.A., Wild, D.J., Willett, P., Similarity Searching in Databases of Three-Dimensional Molecules and Macromolecules, Journal of Chemical Information and Computer Sciences, 1992, 32, 617-630.

Book chapters

Wild, D.J. and Beckman, R. The future of chemical information searching. In Banville, D. (ed). Chemical Information Mining: Facilitating Literature-Based Discovery. CRC Press 2008, pp 171-184.

Fox, G.C., Guha, R., McMullen, D.F., Mustacoglu, A.F., Pierce, M.E., Topcu, A.E., and Wild, D.J. Web 2.0 for Grids and eScience. In Grid Enabled Remote Instrumentation, Springer 2008.

Shankar, K., Wild, D.J., An, J., Narayanan, S., Shoulders, S. Information technology in times of crisis: Considering knowledge management for disaster management. In E. Bolisani (Ed.) Building the Knowledge Society on the Internet: Sharing and Exchanging Knowledge in Networked Environments. IGI Global, Hershey, 2008, pp 219-240

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. 

Published conference papers

Ding, Y., Sun, Y., Chen, B., Borner, K., Ding, L., Wild, D., Wu, M., DiFranzo, D., Fuenzalida, A. G., Li, D., Milojevic, S., Chen, S., Sankaranarayanan, M. & Toma, I. (2010). Semantic Web Portal: A Platform for Better Browsing and Visualizing Semantic Data. /Proceedings of the 2010 International Conference On Active Media Technology (AMT2010), Lecture Notes in Artificial Intelligence (LNAI), /Springer, Aug 28-30, Toronto, Canada,.

Chen, B., Ding, Y., Wang, H., Wild, D., Dong, X., Sun, Y., Zhu, Q., & Sankaranarayanan, M. Chem2Bio2RDF: A Linked Open Data Portal for Chemical Biology.Proceedings of the IEEE/WIC/ACM International Conference on Web Intelligence, 2010, 232-239, Toronto, Canada (Regular Paper, accept rate 16.6%).

Zhu, Q., Challa, S., Purohit, P., Lajiness, M., Wild, D., & Ding, Y. Using web technologies for integrative drug discovery. Proceedings of the IEEE/WIC/ACM International Conference on Web Intelligence, 2010, 232-239, Toronto, Canada (Short Paper, accept rate 22.7%)

Choi, J.Y. , Bae, S.H., Qiu, J., Fox, G., Chen, B., Wild. D.J. Browsing Large Scale Cheminformatics Data with Dimension Reduction. Proceedings of the 19th ACM International Symposium on High Performance Distributed Computing, 2010, Chicago IL.

Dong, X., Ding, Y., Wang, H., Chen, B., Wild, D.J. Chem2Bio2RDF Dashboard: Ranking Semantic Associations in Systems Chemical Biology Space. Future of the Web in Collaboratice Science (FWCS), WWW2010, Apr 26-30, 2010, Raleigh NC. Accepted (also to be published in Nature Precedings)

Challa, S., Wild, D.J., Ding, Y., Zhu, Qian. Semantic Rules on Drug Discovery Data. In Asunción Gómez-Pérez, Yong Yu, Ying Ding (Eds.): The Semantic Web, Fourth Asian Conference, ASWC 2009, Shanghai, China, December 6-9, 2009. Proceedings. Lecture Notes in Computer Science 5926 Springer 2009, ISBN 978-3-642-10870-9 pp362-364

Dong, X. and Wild, D.J. An Automatic Drug Discovery Workflow Generation Tool using Semantic Web Technologies, Proceedings of the 4th IEEE conference on eScience, Dec. 2008, p652-657. 

Academic and conference presentations

Furrer, S.M., Wild, D.J., Efficient core structure searches using various fingerprinting methodologies: advantages, peculiarities and pitfalls. American Chemical Society 241st National Meeting, March 2011, Anaheim, CA.

Wild, D.J. Algorithms for large scale chemogenomic data mining in drug discovery, Invited Presentation, Indiana University School of Medicine Center for Computational Biology and Bioinformatics, February 2011, Indianapolis, IN.

Pandit, Y., Zhu, Q., Choi, J., Bae, S.H., Wild, D.J. Exploring Activity Cliffs using Large Scale Semantic Analysis of PubChem. American Chemical Society 240th National Meeting, August 2010, Boston, MA.

Zhu, Q., Wild, D.J., Mining and Visualizing Chemical Compound Specific Chemical Gene/Disease/Pathway/Literature Relationships. American Chemical Society 240th National Meeting, August 2010, Boston, MA.

Wild, D.J. Data Mining and Querying of Integrated Chemical and Biological Information using Chem2Bio2RDF. American Chemical Society 240th National Meeting, August 2010, Boston, MA.

Wild. D.J. Big Data for Drug Discovery. NCSA Big Data for Science Workshop, July 2010, Bloomington, IN.

Jiao, D., Ding, Y., Wild, D.J. Contextual visualization of biological and chemical networks using linked open life science data. American Chemical Society 239th National Meeting, March 2010, San Francisco, CA.

Zhu, Q., Pierce, M.E., Fox, G.C., Wild, D.J. Integrative Data Mining For Drug Discovery Using the Semantic Web, Microsoft eScience Workshop 2009, Oct 15-17 2009, Pittsburgh PA.

Wild, D.J. An infrastructure for data mining public chemical & biological information. Eighth International Conference on Chemical Structures, June 1-5 2008, Noordwijkerhout, Netherlands.

Fox, G.; Guha, R.; Gilbert, K.E.; Pierce, M.; Wild, D.J. Highlights of the Indiana University Exploratory Chemical Informatics Center. American Chemical Society 235th National Meeting, April 6-10 2008, New Orleans, LA.

Wild, D.J. Developing a cheminformatics research and teaching center for the Web 2.0 world. American Chemical Society 235th National Meeting, April 6-10 2008, New Orleans, LA.

Guha, R; Fox, G; Gilbert, K; Pierce, M; Wild, D. I Don’t Care Where My Data and Methods Are: A Web-Service Approach for Distributed Access to Methods, Data and Models. 235th ACS National Meeting, April 6-10 2008, New Orleans, LA

Wild, D.J. A web service infrastructure for chemoinformatics. 4th Joint Conference on Chemoinformatics, June 2007, Sheffield, U.K.

Wild, D.J. A web service infrastructure for cheminformatics. CERMACS 2007, May 2007, Covington, KY.

Wild, D.J. Smart Mining of Drug Discovery Information and the Emerging Field of Chemoinformatics . University of Michigan Bioinformatics Seminar Series, March 2007, Ann Arbor, MI.

Guha, R., Dutta, D., Wild, D.J., Chen, T. Tiered Screening Protocol for the Discovery of Structurally Diverse HIV Integrase Inhibitors. American Chemical Society 233rd National Meeting, March 2007, Chicago, IL.

Dong, X; Wild, David J. Developing Semantic Web Service For Chemical Informatics. American Chemical Society 233rd National Meeting, March 2007, Chicago, IL.

Wild, D.J.  Integrating text and literature sources with traditional chemoinformatics tools. American Chemical Society 233rd National Meeting, March 2007, Chicago, IL. Also organizer of Advanced Mining of Life Science Information Symposium.

Dong, X. and Wild, D.J. An intelligent system for mining and integrating diverse chemical information and chemoinformatics tools, American Chemical Society 232nd National Meeting, September 2006, San Francisco, CA.

Wang, H. and Wild, D.J. An integrated Alzheimer’s Disease Information System, American Chemical Society 232nd National Meeting, September 2006, San Francisco, CA.

Wild, D.J. Advanced HTS data mining using web service workflows. American Chemical Society 232nd National Meeting, September 2006, San Francisco, CA.

Wild, D.J. Smart Mining Interfaces, Workflows, and Data Mining the NCI DTP Dataset, Joint Indiana University / University of Michigan / Eli Lilly Workshop, August 2006, Indianapolis, IN.

Wild, D.J. An agent-based chemistry mining tool for drug discovery. Microsoft eScience Workshop, April 2006, John Hopkins University, Baltimore, MD.

Cross, J.B., Jalaie, M., Gantt, S.L., Joshi, N.A., Wild, D.J., Snow, M.E., Narasimhan, L.S. Development and application of pfiscore: A filter function for reducing the false positive rate in docking and structure-based virtual screening. 227th American Chemical Society National Meeting, March 2004, Anaheim, CA.

Blankley, C.J. and Wild. D.J. Asymmetric similarity in action. 222nd American Chemical Society National Meeting, August 2001, Chicago, IL.

Bikker, J.A., Dunbar, J.B., Bornemeier, D., Wild, D.J., Calvet, A., Humblet, C. Needles in hayfields: Strategies for rapid HTS triage analysis, 222nd American Chemical Society National Meeting, August 2001, Chicago, IL.

Wild, D.J. and Gifford, E.M. Rapid 3D Similarity Searching for Scaffolds in Ring Databases. Daylight Chemical Information Systems 14th User Group Meeting, 22-25 February 2000, Santa Fe, NM.

Blankley, C.J. and Wild, D.J. Applications of VisualiSAR to structure-activity trend analysis. 217th American Chemical Society National Meeting, March 1999, Anaheim, CA.

Wild, D.J. and Blankley, C.J. VisualiSAR: A tool for visualizing topological commonalities in chemical datasets. 217th American Chemical Society National Meeting, March 1999, Anaheim. CA.

Wild, D.J. and Blankley, C.J. VisualiSAR: A web-based SAR tool. Daylight Chemical Information Systems 13th User Group Meeting, 23-26 February 1999, Santa Fe, NM.

Willett, P. and Wild, D.J. Database searching using molecular fields. 215th American Chemical Society National Meeting, September 1997, Las Vegas, NV.

Wild, D.J. and Willett, P. Field-based molecular similarity searching using a genetic algorithm. 209th American Chemical Society National Meeting, April 1995, Anaheim, CA.

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