Publications

Thomas R. Ioerger



Peer-Reviewed Publications

2015

Long, J.E., DeJesus, M., Ward, D., Baker, R.E., Ioerger, T.R. and Sassetti, C.M. (2015). Identifying essential genes in Mycobacterium tuberculosis by global phenotypic profiling. in: Methods in Molecular Biology: Gene Essentiality, (Long Jason Lu, ed.), vol. 1279.

2014

DeJesus, M.A. and Ioerger, T.R. (2014). Capturing uncertainty by modeling local transposon insertion frequencies improves discrimination of essential genes. IEEE Transactions on Computational Biology and Bioinformatics, to appear.

Xin, D., Perez, L.M., Ioerger, T.R., and Burgess, K. (2014). A multi-faceted secondary structure mimic based in piperidine-piperidinones. Angewandte Chemie, 53(14):3594-8. pubmed

Shi, X., Festa, R.A., Ioerger, T.R., Butler-Wu, S., Sacchettini, J.C. Darwin, K.H. and Samanovic, M.I. (2014). The copper-responsive RicR regulon contributes to Mycobacterium tuberculosis virulence. mBio, e00876-13. pubmed

Lin, P.L., Ford, C.B, Coleman, M.T., Myers, A., Gawande, R., Ioerger, T.R., Sacchettini, J.C., Fortune, S.M. and Flynn, J.L. (2014). Sterilization of granulomas is common in both active and latent tuberculosis despite extensive within-host variability in bacterial killing. Nature Medicine, 20(1):75-9. pubmed

2013

Zhang, Y.J., Reddy, M.C., Ioerger, T.R., Rothchild, A.C., Dartois, V., Schuster, B.M., Trauner, A., Wallis, D.E., Galaviz, S., Huttenhower, C., Saccettini, J.C., Behar, S.M., and Rubin, E.J. (2013). Tryptophan biosynthesis protects mycobacteria from CD4 T cell-mediated killing. Cell, 155(6):1296-308. pubmed

Ngubane, N.Q.C, Gresh, L., Ioerger, T.R., Sacchettini, J.C., Zhang, Y.J., Rubin, E.J., Pym, A. and Khati, M. (2013). High-throughput sequencing enhanced phage display identifies peptides that bind mycobacteria. PLOS ONE, e77844. pubmed

Xin D, Ko E, Perez LM, Ioerger TR, Burgess K. (2013). Evaluating minimalist mimics by exploring key orientations on secondary structures (EKOS). Organic and Biomolecular Chemistry, 11(44):7789-801. pubmed

DeJesus, M.A. and Ioerger, T.R. (2013). A Hidden Markov Model for identifying essential and growth-defect regions in bacterial genomes from transposon insertion sequencing data. BMC Bioinformatics, 14:303. pubmed

Ioerger, T.R., O'Malley, T., Liao, R., Guinn, K.M., Hickey, M.J., Mohaideen, N., Murphy, K.C., Boshoff, H.I.M., Mizrahi, V., Rubin, E.J., Sassetti, C.M., Barry, C.E., Sherman, D.R., Parish, T., and Sacchettini, J.C. (2013). Identification of new drug targets and resistance mechanisms in Mycobacterium tuberculosis. PLOS ONE, 8(9):e75245. pubmed

Small, J.L., Park, S.W., Kana, B., Ioerger, T.R., Sacchettini, J.C. and Ehrt, S. (2013). Perturbation of cytochrome C maturation reveals adaptability of the respiratory chain in Mycobacterium tuberculosis. mBio, 4(5):e00475-13. pubmed

Lanzas, F., Karakousis, P.K, Sacchettini, J.C. and Ioerger, T.R. (2013). Multidrug-resistant tuberculosis in Panama is driven by clonal expansion of an MDR-TB strain related to the KZN XDR-TB strain from South Africa. Journal of Clinical Microbiology, 51(10):3277-3285. pubmed

DeJesus, M.A. and Ioerger, T.R. (2013). Improving discrimination of essential genes by modeling local insertion frequencies in transposon mutagenesis data. ACM Conference on Bioinformatics, Computational Biology, and Biomedical Informatics (ACM-BCB), Washington, DC, Sept 22-25, 2013. pdf   Best paper award!

Stanley, S.A., Kawate, T., Iwase, N., Shimizu, M., Clatworthy, A., Kazyanskaya, E., Sacchettini, J.C., Ioerger, T.R., Siddiqi, N., Minami, S., Aquadro, J.A., Grant, S.S., Rubin, E.J. and Hung, D.T. (2013). Diarylcoumarins inhibit mycolic acid biosynthesis and kill M. tuberculosis by targeting FadD32. Proceedings of the National Academy of Sciences (PNAS), 110(28):11565-70. pubmed

Liu Z, Ioerger TR, Wang F, Sacchettini JC. (2013). Structures of Mtb FadD10 reveal a new type of adenylate-forming enzyme. Journal of Biological Chemistry, 288(25):18473-83. pubmed

Gokulan, K., O'Leary, S.E., Russell, W.K., Russell, D.H., Lalgondar, M., Begley, T.P., Ioerger, T.R., and Sacchettini, J.C. (2013). Crystal structure of Mycobacterium tuberculosis PKS11 reveals intermediates in the synthesis of methyl-branched alkylpyrones. Journal of Biological Chemistry, 288(23):16484-94. pubmed

Gopinath, K., Venclovas, C., Ioerger, T.R., Sacchettini, J.C., McKinney, J.D., Mizrahi, V. and Warner, D.F. (2013). A vitamin B12 transporter in Mycobacterium tuberculosis. Open Biology, 3(2):120175. pubmed

DeJesus, M.A., Zhang, Y.J., Sassettti, C.M., Rubin, E.J., Sacchettini, J.C., and Ioerger, T.R. (2013). Bayesian analysis of gene essentiality based on sequencing of transposon insertion libraries. Bioinformatics, 29(6):695-703. pubmed

Ko, E., Raghuraman, A., Perez, L., Ioerger, T.R. and Burgess, K. (2013). Exploring key orientations at protein-protein interfaces with small molecule probes. Journal of the American Chemical Society, 135(1):167-73. pubmed

DeJesus, M.A., Sacchettini, J.C., and Ioerger, T.R. (2013). Reannotation of translational start sites in the genome of Mycobacterium tuberculosis. Tuberculosis, 93:18-25. pubmed

2012

Krieger, I., Freundlich, J., Gawandi, Vijay, Roberts, J., Gawandi, Vidya, Sun, Q., Owen, J., Fraile, M., Huss, S., Duncan, K., Lavandera, J.-L., Ioerger, T.R., and Sacchettini, J.C. (2012). Structure-guided discovery of phenyl diketo-acids as potent inhibitors of M. tuberculosis malate synthase. Chemistry & Biology, 19(12):1556-1567. pubmed

James, J.N., Hasan, Z., Ioerger, T.R., Brown, A.C., Personne, Y., Carroll, P., Ikeh, M., Tilston-Lunel, N.L., Palavecino, C., Sacchettini, J.C., and Parish, T. (2012). Deletion of SenX3-RegX3, a key two component regulatory system of Mycobacterium smegmatis, results in growth defects under phosphate-limiting conditions. Microbiology, 158(Pt 11):2724-31. pubmed

Zhang, Y.J., Ioerger, T.R., Huggenhower, C., Chen, X., Mohaideen, N., Long, J., Sassetti, C.M., Sacchettini, J.C. and Rubin, E.J. (2012). Global assessment of genomic regions required for growth in Mycobacterium tuberculosis. PLoS Pathogens, 8(9):e1002946. pubmed

Chia, B.-S., Lanzas, F., Rifat, D., Herrera, A., Kim, E.Y., Sailer, C., Torres-Chavolla, E., Narayanaswamy, P., Einarsson, V., Bravo, J., Pascale, J.M., Ioerger, T.R., Sacchttini, J.C. and Karakousis, P.C. (2012). Use of multiplex allele-specific polymerase chain reaction (MAS-PCR) to detect multidrug-resistant Tuberculosis in Panama. PLoS ONE, 7(7):e40456. pubmed

Ford, C., Yusim, K., Ioerger, T.R., Feng, S., Chase, M., Greene, M., Korber, B., and Fortune, S. (2012). Mycobacterium tuberculosis: Heterogeneity revealed through whole genome sequencing. Tuberculosis, 92(3):194-201. pubmed

La Rosa, V., Poce, G., Canseco, J.O., Buroni, S., Pasca, M.R., Biava, M., Raju, R.M., Porretta, C. Alfonso, S. Battilocchio, C., Javid, B., Sorrentino, F., Ioerger, T., Sacchettini, J., Manetti, F., Botta, M., De Logu, A., Rubin, E., and De Rossi, E. (2012). MmpL3 is the cellular target of the antitubercular pyrrole derivative BM212. Antimicrobial Agents and Chemotherapy, 56(1):324-31. pubmed

2011

Griffin, J.E., Gawronski, J.D., DeJesus, M.A., Ioerger, T.R., Akerley, B.J., Sassetti, C.M. (2011). High-resolution phenotypic profiling defines genes essential for mycobacterial survival and cholesterol catabolism. PLoS Pathogens, 7(9):e1002251. pubmed

Raghuraman, A., Ko, E., Perez, L., Ioerger, T.R., and Burgess, K. (2011). Pyrrolinone-pyrrolidine oligomers as universal peptidomimetics. Journal of the American Chemical Society, 133(32):12350-3. pubmed

Ford, C.B., Lin, P.L., Chase, M., Shah, R.R., Iartchouk, O., Galagan, J., Mohaideen, N., Ioerger, T.R., Sacchettini, J.C., Lipsitch, M., Flynn, J.L., and Fortune, S.M. (2011). Use of whole genome sequencing to estimate the mutation rate of Mycobacterium tuberculosis during latent infection. Nature Genetics, 43:482.486. pubmed

2010

Ioerger, T.R., Feng, Y., Chen, X., Dobos, K.M., Victor, T.C., Streicher, E.M., Warren, R.M., Gey van Pittius, N.C., Van Helden P.D. and Sacchettini, J.C. (2010). The non-clonality of drug resistance in Beijing-genotype isolates of Mycobacterium tuberculosis from the Western Cape of South Africa. BMC Genomics, 11(1):670. pubmed

Wang, F., Jain, P., Gulten, G., Liu, Z., Feng, Y., Ganesula, K., Motiwala, A.S., Ioerger, T.R., Alland, D., Vilcheze, C., Jacobs, W.R. and Sacchettini1, J.C. (2010). Mycobacterium tuberculosis dihydrofolate reductase is not a target relevant to the anti-tubercular activity of isoniazid. Antimicrobial Agents and Chemotherapy, 54(9):3776-3782. pubmed

Ioerger, T.R., Feng, Y., Ganseula, K., Chen, X., Dobos, K.M., Fortune, S., Jacobs, W.R., Mizrahi, V., Parish, T., Rubin, E., Sassetti, C. and Sacchettini, J.C. (2010). Variation among genome sequences of H37Rv strains of M. tuberculosis from multiple laboratories. Journal of Bacteriology, 192(14):3645-3653. pubmed

2009

Ioerger, T.R., Koo, S., No, E.-G., Chen, X., Larsen, M.H., Jacobs, W.R., Pillay, M., Sturm, A.W., and Sacchettini, J.C. (2009). Genome analysis of multi- and extensively-drug-resistant Tuberculosis from KwaZulu-Natal, South Africa. PLoS ONE, 4(11):e7778. pubmed

Ioerger, T.R. and Sacchettini, J.C. (2009). Structural genomics approach to drug discovery for Mycobacterium tuberculosis. Current Opinion in Microbiology, 12:318-325. pubmed

2008

Reddy, C.M.C., Kuppan, G., Shetty, N.D., Owen, J.L., Ioerger, T.R., Sacchettini, J.C. (2008). Crystal structures of Mycobacterium tuberculosis S-adenosyl-L-homocysteine hydrolase in ternary complex with substrate and inhibitors. Protein Science, 17(12):2134-2144. pubmed

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. pubmed

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. pubmed

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. pubmed

2007

Gopal, K. and Ioerger, T.R. (2007). Distance Metric Learning through Optimization of Ranking. Seventh IEEE International Conference on Data Mining (ICDM) Workshops, pp.201-206. PDF

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. pubmed

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.

2006

Romo, T.D., Sacchettini, J.C., and Ioerger, T.R. (2006). Improving amino acid identification, fit, and C-alpha prediction using the Simplex method in automated model building. Acta Crystallographica, D62(11):1401-1406. pubmed

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.

2005

Romo, T.D., Gopal, K., McKee, E., Kanbi, L., Pai, R., Smith, J., Sacchettini, J.C., and Ioerger, T.R. (2005). TEXTAL: AI-based Structural Determination for X-ray Protein Crystallography. IEEE Intelligent Systems, 20(6):59-63.

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. pubmed

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. pubmed, PDF

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%)

2004

Adams PD, Gopal K, Grosse-Kunstleve RW, Hung LW, Ioerger TR, McCoy AJ, Moriarty NW, Pai RK, Read RJ, Romo TD, Sacchettini JC, Sauter NK, Storoni LC, Terwilliger TC. (2004). Recent developments in the PHENIX software for automated crystallographic structure determination. Journal of Synchrotron Radiation, 11:53-55.

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. pubmed

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%)

2003

Xu, D., Volz, R.A., Ioerger, T.R., and Yen, J. (2003). Modeling and Analyzing Multi-Agent Behaviors Using Predicate/Transition Nets. International Journal of Software Engineering and Knowledge Engineering, 13(1):103-124. abstract

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

2002

Ioerger, T.R. and Sacchettini, J.C. (2002). Automatic Modeling of Protein Backbones in Electron Density Maps via Prediction of C-alpha Coordinates. Acta Crystallographica, D58(12):2043-2054. abstract

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

2001

Biggers, K.E. and Ioerger, T.R. (2001). Automatic Generation of Communication and Teamwork within Multi-Agent Systems. Applied Artificial Intelligence, 15(10):875-916. abstract

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

2000

Holton, T.R., Christopher, J.A., Ioerger, T.R., and Sacchettini, J.C. (2000). Determining protein structure from electron density maps using pattern matching. Acta Crystallographica, D56:722-734. abstract, full text in PDF

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

1999

Ioerger, T.R., Du, C., and Linthicum, D.S. (1999). Conservation of Cys-Cys-Trp Structural Triads and their Geometry in the Protein Domains of Immunoglobulin Superfamily Members. Molecular Immunology, 36:373-386. abstract

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

1997

Ioerger, T.R. (1997). The context-dependence of amino acid properties. Proceedings of the Fifth International Conference on Intelligent Systems for Molecular Biology, (ISMB-97), pp. 157-166. 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

1995

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

1994

Ioerger, T.R. (1994). The manipulation of images to handle indeterminacy in spatial reasoning. Cognitive Science, 18:551-593. abstract

1993

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.

1991

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.

1990

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.



Book Chapters

Long, J.E., DeJesus, M., Ward, D., Baker, R.E., Ioerger, T.R. and Sassetti, C.M. (2015). Identifying essential genes in Mycobacterium tuberculosis by global phenotypic profiling. in: Methods in Molecular Biology: Gene Essentiality, (Long Jason Lu, ed.), vol. 1279.

Musa, T.L., Ioerger, T.R., and Sacchettini, J.C. (2009). The Tuberculosis Structural Genomics Consortium: A Structural Genomics Approach to Drug Discovery. Advances in Protein Chemistry and Structural Biology, Volume 77, pp. 41-76.

Zwart PH, Afonine PV, Grosse-Kunstleve RW, Hung LW, Ioerger TR, McCoy AJ, McKee E, Moriarty NW, Read RJ, Sacchettini JC, Sauter NK, Storoni LC, Terwilliger TC, Adams PD. (2008). Automated structure solution with the PHENIX suite. Methods in Molecular Biology, vol. 426, pp. 419-35.

Ioerger, T.R. and Sacchettini, J.C. (2003). The TEXTAL System: Artificial Intelligence Techniques for Automated Protein Model Building. in Methods in Enzymology. C. Carter and R. Sweet (eds.). vol. 374, pp. 244-270.

Ioerger, T.R. (1999). Indeterminacy in spatial reasoning. Encyclopedia of Microcomputers. Marcel Dekker: New York. volume 22, pages 193-213.



Other Work

Smith, J., Jarvi, J. and Ioerger, T.R. (2006). A parametrized iterator request framework for generic libraries. In Workshop of Library-Centric Software Design at OOPSLA'06, Portland Oregon, pp. 107-112. (proceedings)

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.