davidjwild

        Assistant Professor, IU School of Informatics and Computing.
        Director, IU Cheminformatics Program.
        Editor-in-Chief, Journal of Cheminformatics.
        CoPI, CICC / ChemBioGrid

SUMMARY

I am an Assistant Professor of Informatics and Computing at Indiana University School of Informatics. I lead the Cheminformatics & Chemogenomics Research Group (CCRG), consisting of approximately 10 students and 1 postdoc. My research focus is on the development of algorithms and tools for large scale integrative data mining of drug discovery, chemical & biological data. I am active in the emerging fields of chemogenomics, systems chemical biology and the Semantic Web and edit the Journal of Cheminformatics. For an overview of emerging work at the intersection of these fields, see our recent Drug Discovery Today paper Systems Chemical Biology and the Semantic Web: what they mean for the future of drug discovery research.

Here are a selection of my latest presentations (all PDF format unless indicated otherwise):

Accelerating Drug Discovery with Chemogenomics & Large Scale Integrated Data Mining, Industry Presentation, July 2011
Integrative algorithms for cheminformatics & chemogenomics GLBIO2011 Tutuorial, May 2011 (Wiki Format)
Algorithms for Chemogenomic Data Mining in Drug Discovery, IU School of Medicine, February 2011
Exploring Activity Cliffs using Large Scale Semantic Analysis of PubChem, Boston ACS, August 2010
Mining and Visualizing Chemical Compound Specific Chemical Gene/Disease/Pathway/Literature Relationships, Boston ACS, August 2010
Exploring Activity Cliffs using Large Scale Semantic Analysis of PubChem, Boston ACS Meeting, August 2010

For a formal overview of my work and publications, see my Curriculum Vitae.

TOOLS CREATED IN OUR LAB

Chem2Bio2RDF - A semantic systems chemical biology / chemogenomic network linking chemical compounds with genes, diseases, targets, pathways and adverse effects that allows cross-domain querying using SPARQL. Developed in conjunction with Prof. Ying Ding in the School of Library & Information Science. Chem2Bio2RDF is described in our recent paper Chen, B. et al., BMC Bioinformatics 2010, 11, 255.

Semantic Link Association Prediction (SLAP). A missing-link prediction tool derived from social networking that uses the Chem2Bio2RDF network to predict association between compounds and gene targets. You can supply both a compound and a gene to view the network of interactions between them, just a compound to find the most strongly associated targets (and drugs that have a similar target association to the compound), or just a target to find the most strongly associated compounds. The algorithm and its validation will be described in a paper in review at PLoS Computational Biology.

Bioterm Semantic Association Predictor (BSAP). Predicts association between genes, drugs and diseases from data mining of recent PubMed scholarly journal articles using a BioLDA Topic Model, a Language model, and a combination of the two. You can specify a start node (e.g. a gene), and intermediate and end node types, and the tool will produce a list of the most strongly associated end node types (e.g. drugs). The BioLDA algorithm is described in our recent paper Wang, H. et al., PLoS One, 2011, 6(3), e17243.

ChemBioSpace Association Search - A tool for finding and ranking associations between any two drugs, diseases, genes, side effects or metabolic pathways using a pathfinding algorithm on a subset of the Chem2Bio2RDF data. Paths are ranked using the BioLDA literature association scores. Click on the question mark in the top right hand corner for information about using this tool. The algorithm and tool are described in our recent paper He et al., PLoS One, 2011, 6(12), e27506

WENDI - a tool for finding non-obvious relationships between chemical compounds and biology that aggregates information from databases, extracted from the literature, and computational predictions. Funded by Eli Lilly. Extended to use an RDF inference engine to make predictions of compound-disease relationships using a rule-base. For more information, see our recent papers Zhu et al., Journal of Cheminformatics , 2010, 2:6 and Zhu et al., BMC Bioinformatics, 2011, 12, 256.

PlotViz - The SALSA HPC lab at IU developed a high dimensional visualization tool called PlotViz. We collaborated with the lab to enable its use on huge chemical datasets to allow contextualization of compounds and drugs in chemical similarity space. PlotViz is fully integrated with Chem2Bio2RDF (SPARQL querying) and WENDI. For more information see our ECMLS conference paper.

ChemViz - a cheminformatics plug-in for Cytoscape developed by Dazhi Jiao as part of the Google Summer of Code

PubChemSR - A desktop PC tool for downloading and extracting information from the PubChem database. For more information, see our Hur, J. and Wild, D.J., Chemistry Central Journal, 2008, 2, 11.

ICEP - A repository of freely accessible cheminformatics educational materials developed as part of the distance education cheminformatics program at Indiana University

ChemBioGrid - An integrative web service framework for cheminformatics, funded by an NIH grant. For more information, see our Journal of Chemical Information and Modeling paper.

LATEST PUBLICATIONS

These are the most recent publications: for a full list see my Curriculum Vitae. You can also take a look at my ResearcherID Homepage for citation statistics on papers that are indexed.

2011

Yu, P. and Wild, D.J. Associative classification mining on chemical datasets. Journal of Chemical Information and Modeling. In review, December 2011.
Chen, B., Ding, Y., Wild, D.J. Assessing Drug Target Association using Semantic Linked Data. PLoS Computational Biology. In review, December 2011.
Chen, B., Ding, Y., Wild, D.J. Improving Integrative Searching of Systems Chemical Biology data using Semantic Annotation. Journal of Cheminformatics. In review, December 2011
Wild, D.J., Ding, Y., Sheth, A.P., Harland, L., Gifford, E.M., Lajiness, M.S. Systems Chemical Biology and the Semantic Web: what they mean for the future of drug discovery research, Drug Discovery Today, in press, available online Dec 29, 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 biomedical data PloS One, 2011, e27506.
Chen, B., McConnell, K., Wale, N., Wild, D.J. and Gifford, E. Comparing Bioassay Response and Similarity Ensemble Approaches to Probing Protein Pharmacology, Bioinformatics, 2011, 27(21), 3044-3049.
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, 6 (3), e17243

2010

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
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. (2010). 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.
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.

2009

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

2008

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

2007

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.
Guha, R., Wiggins, G.D., Wild, D.J., Baik, M.H., Pierce, M.E., and Fox, G.C. Improving usability and accessibility of cheminformatics tools for chemists through cyberinfrastructure and education, Cheminformatics, Accepted September 2007.
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.
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
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

CONFERENCE/INVITED PRESENTATIONS & CONFERENCE LEADERSHIP

2011

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.

2010

Qiu, J., Wild, D.J. Analyzing large-scale cheminformatics and chemogenomics datasets through dimension reduction. NIPS Workshop, December 11, 2010, Vancouver, Canada.
Second IEEE International Conference on Cloud Computing Technology and Science, Nov 30-Dec 3 2010, Indianapolis, IN. Program Committee
Pandit, Y., Zhu, Q., Choi, J., Bae, S.H., Qiu, J., 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., Lajiness, M.S., 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 in Drug Discovery. NCSA Big Data for Science Workshop, July 2010, Bloomington, IN.
Emerging Computational Methods for the Life Sciences Workshop, ACM Symposium for High Performance Distributed Computing, Jun 21-25, 2010, Chicago IL. Program Committee Member.
5th Joint Conference on Chemoinformatics, June 2010, Sheffield, U.K. Organizing Committee Member
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.
Wild, D.J. NSF/JSMF Workshop on Mapping of Science and Semantic Web, Mar 4-5, 2010. Bloomington, IN. Invited Participant.

2009

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.
Integrative, Compound-Centric Data Mining for Drug Discovery, presentation given to industry, July 2009.

2008

4th IEEE International Conference on eScience, December 7-12, 2008, Indianapolis, Indiana. Organizer for eScience for Cheminformatics and Drug Discovery workshop.
20th Bicentennial Conference on Chemical Education, July 2008, Bloomington, Indiana. Symposium chair for Advanced Informatics in Chemistry Education.
8th International Conference on Chemical Structures, June 1-5 2008, Noordwijkerhout, Netherlands. Poster presentation: An infrastructure for data mining public chemical & biological information.
American Chemical Society 235th National Meeting, April 6-10 2008, New Orleans. Presentation: Developing a cheminformatics research and teaching center for the Web 2.0 world

2007

4th Joint Conference on Chemoinformatics, June 2007, Sheffield, U.K. Organizing Committee Member. Session chair for clustering session. Presentation: A web service infrastructure for chemoinformatics
CERMACS 2007, May 2007, Covington, KY. Presentation: A web service infrastructure for cheminformatics,
University of Michigan Bioinformatics Seminar Series, March 2007, Ann Arbor, Mich. Presentation: Smart Mining of Drug Discovery Information and the Emerging Field of Chemoinformatics, (video available)
American Chemical Society 233rd National Meeting, March 2007, Chicago. Organizer of Advanced Mining of Life Science Information Symposium. Presentation: Integrating text and literature sources with traditional chemoinformatics tools

2006

American Chemical Society 232nd National Meeting, September 2006, San Francisco. Presentation: Advanced HTS data mining using web service workflows
Microsoft eScience Workshop, April 2006, John Hopkins University. Presentation: An agent-based chemistry mining tool for drug discovery