Publications

Articles are listed in reverse chronological order. For a hyperlinked list of publications, see David Wild's Google Scholar page.

Journal articles

54. Passi, A., Rajput, N.K., Wild, D.J., Bhardwaj, A. RepTB: a gene ontology based drug repurposing approach for tuberculosis. Journal of Cheminformatics, 2018, 10:24
53. Correia, R.B., de Araújo, L.P., Mattos, M.M.,Wild, D., Rocha, L.M. City-wide Analysis of Electronic Health Records Reveals Gender and Age Biases in the Administration of Known Drug-Drug Interactions. arXiv:1803.03571 2018/3.
52. Djokic-Petrovic, M., Cvjetkovic, V., Yang, J., Marko Zivanovic, M., Wild, D.J. PIBAS FedSPARQL: a web-based platform for integration and exploration of bioinformatics datasets. Journal of Biomedical Semantics, 2017, 8(1) 42.
51. Kulkarni, V.S., Wild, D.J. An activity canyon characterization of the pharmacological topography. Journal of Cheminformatics, 2016, 8:1, 41.
50. Lee, J.A., Shinn, P., Jaken, S., Oliver, S., Willard, F.S., Heidler, S., Peery, R.B., Oler, J., Chu, S., Southall, N., Dexheimer, T.S., Smallwood, J., Huang, R., Guha, R., Jadhav, A., Cox, K., Austin, C.P., Simeonov, A., Sittampalam, G.S., Husain, S., Franklin, N., Wild, D.J., Yang, J.J., Sutherland, J.J., Thomas, C. Novel phenotypic outcomes identified for a public collection of approved drugs from a publicly accessible panel of assays. PLoS One, 2015, DOI:10.1371/journal.pone.0130796
49. Seal, A., Ahn, Y.Y., Wild, D.J. Optimizing drug-target interaction prediction based on random walk on heterogeneous networks. Journal of Cheminformatics, 2015, 7:40
48. Chen, B., Wang, H., Ding, Y., Wild, D. Semantic Breakthrough in Drug Discovery. Synthesis Lectures on the Semantic Web: Theory and Technology, Morgan & Claypool, 2014, 4(2) p1-142.
47. Joshi, H., Parihar, A., Jiao, D., Murali, S., Wild, D.J. A possible gut microbiota basis for weight gain side effects of antipsychotic drugs. Eprint arXiv:1401.2389, 2014/1
46. Chen, B., Wild, D.J. Practice and challenges of building a semantic framework for chemogenomics research. Molecular Informatics, 2013, 32(11-12), 1000-1008
45. Machina, H.K., Wild, D.J., Dey, P., Merchant, M. Effective integration of informatics tools to enhance the drug discovery process. Industrial & Engineering Chemistry Research, 2013, 52(47) pp16547-16554.  
44. Wild, D.J. Cheminformatics for the masses: a chance to increase educational opportunities for the next generation of cheminformaticians. Journal of Cheminformatics, 2013, 5:32
43. Willighagen E., Waagmeester, A., Spjuth, O., Ansell, P., Williams, A.J., Tkachenko, V., Hastings, J., Chen, B. and Wild, D.J. The ChEMBL database as linked open data. Journal of Cheminformatics, 2013, 5:23
42. Machina, H.K. and Wild, D.J. Electronic laboratory notebooks: progress and challenges in implementation. Journal of Laboratory Automation, 2013, in press.
41. Seal, A., Yogeeswari, P., Sriram, D., Wild, D.J. Enhanced ranking of PknB inhibitors using data fusion methods. Journal of Cheminformatics, 2013, 5:3.
40. Machina, H.K. and Wild, D.J. Laboratory informatics tools integration strategies for drug discovery, Journal of Laboratory Automation, 2013, 18(2), 126-136.
39. Yu, P. and Wild, D.J. Fast rule-based bioactivity prediction using Associative Classification Mining, Journal of Cheminformatics, 2012, 4:29
38. Yu, P. and Wild, D.J. Discovering Associations in Biomedical Datasets by Link-based Associative Classifier (LAC), PLoS One, 2012, 7(12), e51018
37. Dumontier, M., Wild, D.J. Linked data in drug discovery. IEEE Internet Computing, 2012, 16(6), 68- 71
36. Chen, B., Ding, Y., Wild, D.J. Assessing Drug Target Association using Semantic Linked Data. PLoS Computational Biology, 2012, 8(7), e1002574
35. Seal, A., Passi, A., Jaleel, U.C., Wild, D.J. In silico predictive mutagenicity model generation using supervised learning approaches. Journal of Cheminformatics, 2012, 4:10
34. Chen, B., Ding, Y., Wild, D.J. Improving Integrative Searching of Systems Chemical Biology data using Semantic Annotation. Journal of Cheminformatics, 2012, 4:6
33. 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, 2012, 17, 469-474.
32. 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.
31. 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 association paths in relational biomedical data PLoS One, 2011, 6(12), e27506.  
30. 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.
29. 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, 2011, 23(17), 2315-2325.
28. 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
27. 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
26. 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.
25. 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
24. 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.  
23. 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
22. Wild, D.J.  Mining large heterogenous data sets in drug discovery. Expert Opinion on Drug Discovery. 2009; 4(10), pp 995-1004
21. Wild, D.J. Grand Challenges for Cheminformatics, Journal of Cheminformatics, 2009, 1, 1.
20. 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
19. Hur, J. and Wild, D.J. PubChemSR: A search and retrieval tool for PubChem, Chemistry Central Journal, 2008, 2, 11.
18. 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
17. 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
16. 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.  
15. 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.
14. 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
13. 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
12. Wild, D.J. and Wiggins, G.D. Challenges for chemoinformatics education in drug discovery. Drug Discovery Today, 11, 9&10 (May 2006), pp436-439
11. 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.
10. 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.
9. 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.
8. 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 1998, 1
7. 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
6. 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
5. 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
4. 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.
3. 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.
2. 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.
1. 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.

Books and book chapters

B7. Wild, D.J. Surviving and helping in disasters in a global technology age. Lulu Enterprises eBook, 2014.  
B6. Wild, D.J. Introducing Cheminformatics: an intensive self-study guide. Lulu Enterprises eBook, 2012.  
B5. Wild, D.J. Chem2Bio2RDF: a semantic resource for systems chemical biology and drug discovery. In Harland, L. and Forster, M. (eds).  Open source software in life science research: Practical solutions to common challenges. Woodhead Publishing, 2012.
B4. 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.  
B3. 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.
B2. 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
B1. 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.

Conference papers

C12. Gao Z., Ding, Y. and Wild, D. Learning Semantics on Complex Networks in Health Care Domain. The 17th International Semantic Web Conference, 2018, Submitted.
C11. Correia, R., Pereira de Araújo, L., Mattos, M.M., Wild, D.J., Rocha, L.M. City-wide Analysis of Drug-Drug-Interactions. Translational Bioinformatics Conference, 2017, Accepted.
C10. Fox, G., Maini, S., Rosenbaum, H., Wild, D.J. Data Science and Online Education. IEEE 7th International Conference on Cloud Computing Technology and Science (CloudCom), 2015, 582-8587.
C9. Henschel, R., Seal, A., Yang, J.J., Wild, D.J., Ding, Y., Thota, A., Michael, S., Gianni, M., Maltby, J. Applications of the YarcData Urika in Drug Discovery and Healthcare. Proceedings of the Cray User Group, 2014.
C8. Kong, X., Yu, P.S., Ding, Y., Wild, D.J. Meta Path-based Classification on Heterogeneous Information Networks. In Proceedings of the 21st ACM International Conference on Information and Knowledge Management (CIKM 2012), 2012, Oct 29-Nov 2, Maui (Short paper, acceptance rate 14.3%)
C7. 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. 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, 2010, Toronto, Canada,.
C6. 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, acceptance rate 16.6%).
C5. 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, acceptance rate 22.7%)
C4. 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.
C3. 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 Collaborative Science (FWCS), WWW2010, Apr 26-30, 2010, Raleigh NC.
C2. Challa, S., Wild, D.J., Ding, Y., Zhu, Qian. Semantic Rules on Drug Discovery Data. In Asunción Gómez-Pérez, Yong Yu, Ying Ding (Eds.): Proceedings of 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
C1. 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.