Cho, Y., Ioerger, T.R. and Sacchettini, J.C. (2008). Discovery of Novel Nitrobenzothiazole Inhibitors for M. tuberculosis ATP Phosphoribosyl Transferase (HisG) through Virtual Screening. Journal of Medicinal Chemistry, 51(19):5984-5992.
Pai, R., Sacchettini, J.C., and Ioerger, T.R. (2008). Specificity normalization for identifying selective inhibitors in virtual screening. Proc. of the International Conference on Bioinformatics and Computational Biology (BIOCOMP'08). (acceptance rate = 27%) PDF
Pai, R., Sacchettini, J.C., and Ioerger, T.R. (2008). Analysis of protein-ligand interactions using localized stereochemical features. Proc. of the International Conference on Bioinformatics and Computational Biology (BIOCOMP'08). (acceptance rate = 27%) PDF
Javid-Majd, F., Yang, D., Ioerger, T.R., and Sacchettini, J.C. (2008). The 1.25 A resolution structure of phosphoribosyl-ATP pyrophosphohydrolase from Mycobacterium tuberculosis. Acta Crystallographica, D:64(6):627-635.
Reddy C.M., Gokulan, K., Jacobs, W.R., Ioerger, T.R., and Sacchettini, J.C. (2008). Crystal structure of Mycobacterium tuberculosis LrpA, a leucine-responsive global regulator associated with starvation response. Protein Science, 17(1):159-170.
Gopal, K., Sacchettini, J.C., and Ioerger, T.R. (2007). Database Approaches and Data Representation in Structural Bioinformatics. IEEE 7th International Symposium on BioInformatics and BioEngineering (BIBE'07), 425-434. (acceptance rate = 65/500 = 13%)
Murillo, A.C., Alber, T.C., Baker, E.N., Berger, J.M., Cherney, L.T., Cherney, M.M., Eisenberg, D., Garen, C.R., Hung, L.W., Ioerger, T.R., Jacobs, W.R., James, M.N.G., Kim, C., Kriger, I., Li, H., Lott, J.S., Sankaranarayanan, R., Segelke, B.R., Terwilliger, T.C., Wang, F., and Sacchettini, J.C. (2007). High Throughput Crystallography of TB Drug Targets. Infectious Disorders - Drug Targets, 7(2):127-139.
Gopal, K., McKee, E., Romo, T., Pai, R., Smith, J., Sacchettini, J.C. and Ioerger, T.R. (2007). Crystallographic Protein Model-Building on the Web. Bioinformatics, 23:375-377.
Creel, J., Menzel, C., and Ioerger, T.R. (2007). Intention is Commitment with Expectation. 20th International Conference of the Florida Artificial Intelligence Research Society (FLAIRS'07), 50-55.
Gopal, K., Romo, T.D., McKee, E.W., Pai, R., Smith, J.N., Sacchettini, J.C. and Ioerger, T.R. (2006). TEXTAL: Crystallographic Model Building Using AI and Pattern Recognition. AI Magazine, 27(3):15-24.
Pai, R., Sacchettini, J.C. and Ioerger, T.R. (2006). Identifying non-crystallographic symmetry in protein electron-density maps: a feature-based approach. Acta Crystallographica, D62(9):1012-1021.
Fan, X., Yen, J., Miller, M., Ioerger, T.R. and Volz, R.A. (2006). MALLET - A Multi-Agent Logic Language for Encoding Teamwork. IEEE Transactions on Knowledge and Data Engineering, 18(1):123-138.
McKee, E.W., Kanbi, L.D., Childs, K.L., Grosse-Kunstleve, R.W., Adams, P.D., Sacchettini J.C. and Ioerger, T.R. (2005). FINDMOL: Automated Identification of Macromolecules in Electron Density Maps. Acta Crystallographica, D61(11):1514-1520.
He, L. and Ioerger, T.R. (2005). Combining bundle search with buyer coalition formation in electronic markets: A distributed approach through explicit negotiation. Electronic Commerce Research and Applications, 4(4):329-344.
Gopal, K., Romo, T., Sacchettini, J.C., and Ioerger, T.R. (2005). Determining Relevant Features to Recognize Electron Density Patterns in X-ray Protein Crystallography. Journal of Bioinformatics and Computational Biology, 3(3):645-676.
Ioerger, T.R. (2005). Automated detection of disulfide bridges in electron density maps using linear discriminant analysis. Journal of Applied Crystallography, 38(1):121-125.
Cao, S., Volz, R.A, Ioerger, T.R. and Miller M. (2005). On Proactive Helping Behaviors In Teamwork. International Conference on Artificial Intelligence (IC-AI). Las Vegas.
Gopal, K., Romo, T., McKee, E., Childs, K., Pai, R., Smith, J., Sacchettini, J., and Ioerger, T. (2005). TEXTAL: Automated Crystallographic Protein Structure Determination. Proc. 17th Conference on Innovative Applications in Artificial Intelligence (IAAI-05), 1483-1490. (acceptance rate = 18/48 = 38%)
He, L. and Ioerger, T.R. (2005). Forming Resource-Sharing Coalitions: A Distributed Resource Allocation Mechanism for Self-Interested Agents in Computational Grids. Symposium on Applied Computing (SAC), special track on Agents, Interactions, Mobility, and Systems (AIMS), 84-91. (acceptance rate = 29%)
Ye S, Vakonakis I, Ioerger TR, LiWang AC, Sacchettini JC. (2004). Crystal structure of circadian clock protein KaiA from Synechococcus elongatus. Journal of Biological Chemistry, 279(19):20511-20518.
Gopal, K., Romo, T., Sacchettini, J.C., and Ioerger, T.R. (2004). Efficient Retrieval of Electron Density Patterns for Modeling Proteins by X-ray Crystallography. Proc. International Conference on Machine Learning and Applications (ICMLA'04), 380-387. (acceptance rate = 67/93 = 72%)
He, L. and Ioerger, T.R. (2004). Combining Bundle Search with Buyer Coalition Formation in Electronic Markets: A Distributed Approach through Explicit Negotiation. Sixth International Conference on Electronic Commerce (ICEC'04). Oct. 25-27, Delft, The Netherlands. PDF
Gopal, K., Romo, T.D., Sacchettini, J.C., and Ioerger, T.R. (2004). Weighting Features to Recognize 3D Patterns of Electron Density in X-ray Protein Crystallography. Computational Systems Bioinformatics Conference (CSB 2004), 255-265. Stanford, CA, Aug 16-19. (acceptance rate = 30/202 = 15%) PDF
Gopal, K., Romo, T.D., Sacchettini, J.C., and Ioerger, T.R. (2004). Evaluation of Geometric and Probabilistic Distance Measures to Retrieve Electron Density Patterns for Protein Structure Determination. Proceedings of the International Conference on Artificial Intelligence, 427-432. June 21-24, Las Vegas. (acceptance rate = 20% for RRPs) PDF
Wollkind, S., Valasek, J., and Ioerger, T.R. (2004). Automated Conflict Resolution for Air Traffic Management Using Cooperative Multiagent Negotiation. AIAA Guidance, Navigation, and Control Conference. Aug, 16-19, Providence, RI. PDF
Ma, N.K. and Ioerger, T.R. (2004). Distributed Command and Organizational Situation Awareness. Command and Control Research and Technology Symposium. June 15-17, San Diego. PDF
He, L. and Ioerger, T.R. (2004). An Efficient Heuristic Bundle Search Algorithm for Buyers in Electronic Markets. Proceedings of the International Conference on Artificial Intelligence, 729-735. June 21-24, Las Vegas. (acceptance rate = 33% for RRRs) PDF
He, L. and Ioerger, T.R. (2004). Task-Oriented Computational Economic-Based Distributed Resource Allocation Mechanisms for Computational Grids. Proceedings of the International Conference on Artificial Intelligence, 462-468. June 21-24, Las Vegas. (acceptance rate = 20% for RRPs) PDF
Ioerger, T.R. (2004). Reasoning about Beliefs, Observability, and Information Exchange in Teamwork. 17th International Conference of the Florida Artificial Intelligence Research Society (FLAIRS'04). (acceptance rate = 158/286 = 55%) PDF
Zhang, Yu, Ioerger, T.R., Volz, R.A., and Yen, J. (2004). A Decision-Theoretic Approach for Designing Proactive Communication in Multi-Agent Teamwork. ACM Symposium on Applied Computing, special track on Agents, Interactions, Mobility, and Systems, pp. 64-71. March 14-17, Nicosa, Cyprus. PDF (acceptance rate = 10/34 = 29%)
Widyantoro, D., Ioerger, T.R., and Yen, J. (2003). Tracking Changes in User Interests with a Few Relevance Judgements. Proceedings of the Twelfth International Conference on Information and Knowledge Management, 548-551. (CIKM'03) PDF
Ioerger, T.R., Sims, J., Volz, R.A, Workman, J., and Shebilske, W.L. (2003). On the Use of Intelligent Agents as Partners in Training Systems for Complex Tasks. Proceedings of the 25th Annual Meeting of the Cognitive Science Society (CogSci'03). text&info
Ioerger, T.R. and He, L. (2003). Modeling Command and Control in Multi-Agent Systems. 8th International Command and Control Research and Technology Symposium (ICCRTS). Washington, DC, June 17-19, 2003. text&info
Gopal, K., Pai, R., Ioerger, T.R., Romo, T., and Sacchettini, J.C. (2003). TEXTAL: Artificial Intelligence Techniques for Automated Protein Structure Determination. Proceedings of the Fifteenth Conference on Innovative Applications of Artificial Intelligence (IAAI), 93-100. text&info
He, L. and Ioerger, T.R. (2003). A Quantitative Model of Capabilities in Multi-Agent Systems. International Conference on Artificial Intelligence (ICAI), 730-736. Las Vegas. PDF
Xu, D., Miller, M., Volz, R.A., and Ioerger, T.R. (2003). Collaborative Agents for C2 Teamwork Simulation. International Conference on Artificial Intelligence (ICAI), 723-729. Las Vegas. PDF
Rajagopalan, G., Siegele, D., and Ioerger, T.R. (2003). MOPAC: MOtif-finding by Preprocessing and Agglomerative Clustering from Microarrays. Pacific Symposium on Biocomputing (PSB), 41-52. Kauai, Hawaii. January 2003. text&info
Adams, P.D., Grosse-Kunstleve, R.W., Hung, L.W., Ioerger, T.R., McCoy, A.J., Moriarty, N.W., Read, R.J., Sacchettini, J.C., Sauter, N.K., and Terwilliger, T.C. (2002). PHENIX: Building New Software for Automated Crystallographic Structure Determination. Acta Crystallographica, D58:1948-1954. abstract
Widyantoro, D., Ioerger, T.R., and Yen, J. (2002). An Incremental Approach to Building Concept Hierarchies. IEEE International Conference on Data Mining, 705-708. PDF
Xu, D., Volz, R.A., Ioerger, T.R., and Yen, J. (2002). Modeling and Verifying Multi-Agent Behaviors Using Predicate/Transition Nets. Proc. 14th International Conference on Software Engineering and Knowledge Engineering (SEKE), 193-200. PDF
Rong, J., Valasek, J., Geng, S., and Ioerger, T.R. (2002). Air Traffic Conflict Negotiation and Resolution Using an OnBoard Multi-Agent System. 21st Digital Avionics Systems Conference (DASC), Irvine, CA. October 2002. paper
Ioerger, T.R., He, L., Lord, D., and Tsang, P. (2002). Modeling Capabilities and Workload in Intelligent Agents for Simulating Teamwork. Proceedings of the Twenty-Fourth Annual Conference of the Cognitive Science Society (CogSci'02), 482-487. text&info
Zhang, Y., Volz, R.A., Ioerger, T.R., Cao S., and Yen, J. (2002). Proactive Information Exchange During Team Cooperation. International Conference on Artificial Intelligence (IC-AI'2002), 341-346.
Cao, S., Volz, R.A., Ioerger, T.R., Zhang, Y. and Yen, J. (2002). Role-Based and Agent-Oriented Teamwork Modeling. International Conference on Artificial Intelligence (IC-AI'2002), 1190-1196.
Xu, D., Volz, R.A., and Ioerger, T.R. (2002). Generating Parallel Plans Based on Planning Graph Analysis of Predicate/Transition Nets. International Conference on Artificial Intelligence (IC-AI'2002), 440-446.
Tao, Y., Ioerger, T.R., and Sacchettini, J.C. (2002). Extracting Fractal Features for Analyzing Protein Structure. IEEE Conference on Pattern Recognition (ICPR'02), 482-485. text&info
Rozich, R., Ioerger, T.R., and Yager, R. (2002). FURL - A Theory Revision Approach to Learning Fuzzy Rules. Proc. IEEE International Conference on Fuzzy Systems,791-796. text&info
Ioerger, T.R., Meeks, J.H., and Nelson, P. (2001). Investigation of Density and Flow Relationships in Congested Traffic Using Videogrammetric Data. Transportation Research Record, 1776:167-177.
Linthicum, D.S., Tetin, S.Y., Anchin, J.M., and Ioerger, T.R. (2001). Antibody-Ligand Interactions: Computational Modeling and Correlation with Biophysical Measurements. Combinatorial Chemistry and High Throughput Screening, 4(5):439-449. abstract
Hofle, M., Linthicum, D.S., and Ioerger, T.R. (2001). Analysis of diversity of nucleotide and amino acid distribution in the VD and DJ joining regions in Ig heavy chains. Molecular Immunology, 37(14):827-835. abstract
Widyantoro, D.W., Ioerger, T.R., and Yen, J. (2001). Learning User Interest Dynamics with a Three-Descriptor Representation. Journal of the American Society for Information Science, 52(3):212-225.
Yen, J., Yin, J., Ioerger, T.R., Miller, M., Xu, D., and Volz, R.A. (2001). CAST: Collaborative Agents for Simulating Teamwork. Proceedings of the Seventeenth International Joint Conference on Artificial Intelligence (IJCAI-01), 1135-1142. text&info
Ioerger, T.R. and Johnson, J.C. (2001). A Formal Model of Responsibilities in Agent-Based Teamwork. Proceedings of the International Conference on Artificial Intelligence (IC-AI'2001), 58-64. text&info
Zhang, Y., He, L., Biggers, K., Yen, J., and Ioerger, T.R. (2001). Simulating Teamwork and Information Flow in Tactical Operations Centers using Multi-Agent Systems. Proceedings of the Tenth Conference on Computer Generated Forces (10th CGF), 529-539. text&info
Zhang, Y., Biggers, K., He, L., Reddy, S.K., Sepulvado, D., Yen, J. and Ioerger, T.R. (2001). A Distributed Intelligent Agent Architecture for Simulating Aggregate-Level Behavior and Interactions on the Battlefield. Proceedings of the Fifth World Multi-Conference on Systemics, Cybernetics, and Informatics (SCI-2001), 58-63.text&info
Tao, Y., Ioerger, T.R., and Tang, Y.Y. (2001). Extraction of Rotation Invariant Signature Based on Fractal Geometry. IEEE International Conference on Image Processing, 1090-1093. text&info
Yang, L., Widyantoro, D.H., Ioerger, T.R. and Yen, J. (2001). Entropy-based Adaptive Genetic Algorithm for Learning Classification Rules. Proceedings, Congress on Evolutionary Computation, 790-796. text&info
Ioerger, T.R., Meeks, J.H., and Nelson, P. (2001). Investigation of Density and Flow Relationships in Congested Traffic Using Videogrammetric Data. Proceedings of the 80th Annual Meeting of the Transportation Research Board, CD-ROM. Washington, DC. text&info
El-Nasr, M.S., Yen, J., and Ioerger, T.R. (2000). FLAME: Fuzzy Logic Adaptive Model of Emotions. Autonomous Agents and Multi-Agent Systems, 3(3):219-257. abstract
Gopal, K. and Ioerger, T.R. (2000). An Adaptive Planner Based on Learning of Planning Performance. Proceedings of the International Conference on Artificial Intelligence (IC-AI'2000), 1017-1023. text&info
Ioerger, T.R., Volz, R.A., and Yen, J. (2000). Modeling Cooperative, Reactive Behaviors on the Battlefield Using Intelligent Agents. Proceedings of the Ninth Conference on Computer Generated Forces (9th CGF), 13-23. text&info
Miller, M., Yin, J., Volz, R.A., Ioerger, T.R., Yen, J. (2000). Training teams with collaborative agents. Proceedings of the Fifth International Conference on Intelligent Tutoring Systems, (ITS-2000), 63-72. text&info
Yin, J., Miller, M., Ioerger, T.R., Yen, J., and Volz, R.A. (2000). A knowledge-based approach for designing intelligent team training systems. Proceedings of the Fourth International Conference on Autonomous Agents, (AGENTS-2000), 427-434. text&info
Ioerger, T.R. and Linthicum, D.S. (1999). T-SEARCH: A program to identify and measure the geometry of cysteine-cysteine tryptophan (C-CW) triad motifs in immunoglobulin superfamily structures and other proteins. Biotechnology Software and Internet Journal , vol. 16(3), pp. 26-31. related web page
Widyantoro, D.H., Ioerger, T.R., and Yen, J. (1999). An adaptive algorithm for learning changes in user interests. Proceedings of the Eighth International Conference on Information and Knowledge Management, (CIKM-99), 405-412. text&info
Ioerger, T.R., Holton, T.R., Christopher, J.A., and Sacchettini, J.C. (1999). TEXTAL: A pattern recognition system for interpreting electron density maps. Proceedings of the Seventh International Conference on Intelligent Systems for Molecular Biology, (ISMB-99), pp. 130-137. text&info
Ioerger, T.R. (1999). Detecting feature interactions from accuracies of random feature subsets. Proceedings of the Sixteenth National Conference on Artificial Intelligence, (AAAI-99), pp. 350-357. text&info
Seif El-Nasr, M., Ioerger, T.R., Yen, J., House, D. and Parke, F. (1999). Emotionally expressive agents. Proceedings of Computer Animation '99, (CA-99), pp. 48-57. text&info
Seif El-Nasr, M., Ioerger, T.R., and Yen, J. (1999). PETEEI: A pet with evolving emotional intelligence. Proceedings of the Third International Conference on Autonomous Agents, (AGENTS-99), pp. 9-15. text&info
Ioerger, T.R. (1997). Integrating a spatial reasoner with a resolution theorem-prover. Proceedings of the Fourteenth National Conference on Artificial Intelligence, (AAAI-97), pp. 145-152. text&info
Ioerger, T.R., Rendell, L., and Subramaniam, S. (1995). Searching for representations to improve protein sequence fold-class prediction. Machine Learning, 21:151-175. abstract
Ioerger, T.R. (1994). The manipulation of images to handle indeterminacy in spatial reasoning. Cognitive Science, 18:551-593. abstract
Ioerger, T.R., Rendell, L., and Subramaniam, S. (1993). Constructive induction and protein tertiary structure prediction, Proceedings of the First International Conference on Intelligent Systems for Molecular Biology, (ISMB-93), pp. 198-206.
Ioerger, T.R. (1991). Imagery and categories: The Indeterminacy Problem. Proceedings of the Thirteenth Annual Meeting of the Cognitive Science Society, (CogSci-91), pp. 37-42.
Ioerger, T.R., Gohlke, J., Xu, B., and Kao, T.H. (1991). Primary structural features of the self-incompatibility protein in Solanaceae. Sexual Plant Reproduction, 4:81-87.
Ioerger, T.R., Clark, A., and Kao, T.H. (1990). Polymorphism at the self-incompatibility locus in Solanaceae predates speciation. Proceedings of the National Academy of Sciences USA, 87:9732-9735. PubMed
Kheyr-Pour, A., Bintrim, S., Ioerger, T.R., Remy, R., Hammond, S., and Kao, T.H. (1990). Sequence diversity of pistil S-proteins associated with gametophytic self-incompatibility in Nicotiana alata. Sexual Plant Reproduction, 3:88-97.
Yunjun, A., Singh, A., Coleman, C., Ioerger, T.R., Kheyr-Pour, A., and Kao, T.H. (1990). Self-incompatibility in Petunia inflata: Isolation and characterization of cDNAs encoding three S-allele-associated proteins. Sexual Plant Reproduction, 3:130-138.
Ioerger, T.R. (1999). Indeterminacy in spatial reasoning. Encyclopedia of Microcomputers. Marcel Dekker: New York. volume 22, pages 193-213.
Palmer, V. and Ioerger, T.R. (2006). Coalition Formation Meets Information Theory. Florida AI Research Society Conference (FLAIRS'06), 98-99.
Zhang, Y., Volz, R.A., and Ioerger, T.R. (2004). Observation-based proactive communication in team cooperation. Proc. 3rd International Joint Conference on Autonomous Agents and Multiagent Systems, 1321-1322.
Binas, A. and Ioerger, T.R. (2004). Multi-Agent Belief Reasoning in a First-Order Logic Back-Chainer. Technical report TSSTI-TR-10-04, Training System Science and Technology Initiative, Texas A&M University.
He, L. and Ioerger, T.R. (2004). Combining Bundle Search with Buyer Coalition Formation in Electronic Markets: A Distributed Approach. Third International Joint Conference on Autonomous Agents and Multi-Agent Systems (AAMAS'04), accepted as poster/2-page abstract. (acceptance rate = 26%) PDF
Ioerger, T.R. (2003). Literature Review: Modeling Teamwork as Part of Human Behavior Representation. Technical report TSSTI-TR-10-03, Training System Science and Technology Initiative, Texas A&M University.
Johnson, J.C. and Ioerger, T.R. (2001). A Formal Model of Responsibilities in Agent-Based Teamwork. Proceedings of the Fifth International Conference on Intelligent Agents, 157-158. 2-page abstract and poster presentation.
Gopal, K. and Ioerger, T.R. (2000). An Adaptive Planner Based on Learning of Planning Performance. Proceedings of the Seventeenth National Conference on Artificial Intelligence, (AAAI-2000, Austin, TX), p. 1073 (student abstract). text and poster presentation
Seif El-Nasr, M., Ioerger, T.R., and Yen, J. (1999). A Web of Emotions. Proceedings of Workshop on Emotion-Based Agent Architectures (in conjunction with Autonomous Agents '99).
Seif El-Nasr, M., Ioerger, T.R., and Yen, J. (1998). Learning and Emotional Intelligence in Agents. AAAI Fall Symposium on Emotional Intelligence.
Ioerger, T.R. (1996). Change of Representation in Machine Learning, and an Application to Protein Structure Prediction. PhD dissertation. Department of Computer Science, University of Illinois.
Ioerger, T.R. (1992). A Method of Default Reasoning for Reasoning about Spatial Prepositions. MS thesis. Department of Computer Science, University of Illinois.
Ioerger, T.R. (1992). Diagrammatic semantics for spatial prepositions. AAAI Spring Symposium on Reasoning with Diagrammatic Representations, working notes, 194-197.
Ioerger, T.R. (1985). Alcohol dehydrogenase activity in a temperature-sensitive mutant of Drosophila melanogaster. Journal of the Pennsylvania Governor's School for the Sciences, 3:55-61.