Constructive Induction and Protein Tertiary Structure Prediction. - Thomas R. Ioerger; Larry A. Rendell; Shankar Subramaniam (ISMB, 1993)

The Manipulation of Images to Handle Indeterminacy in Spatial Reasoning. - Thomas R. Ioerger (Cogn. Sci., 1994)

Searching for Representations to Improve Protein Sequence Fold-Class Prediction. - Thomas R. Ioerger; Larry A. Rendell; Shankar Subramaniam (Mach. Learn., 1995)

Integrating a Spatial Reasoner with a Resolution Theorem-Prover. - Thomas R. Ioerger (AAAI/IAAI, 1997)

The Context-Dependence of Amino Acid Properties. - Thomas R. Ioerger (ISMB, 1997)

Detecting Feature Interactions from Accuracies of Random Feature Subsets. - Thomas R. Ioerger (AAAI/IAAI, 1999)

PETEEI: A PET With Evolving Emotional Intelligence. - Magy Seif El-Nasr; Thomas R. Ioerger; John Yen (Agents, 1999)

Emotionally Expressive Agents. - Magy Seif El-Nasr; Thomas R. Ioerger; John Yen; Donald H. House; Frederic I. Parke (CA, 1999)

An Adaptive Algorithm for Learning Changes in User Interests. - Dwi H. Widyantoro; Thomas R. Ioerger; John Yen (CIKM, 1999)

TEXTAL: A Pattern Recognition System for Interpreting Electron Density Maps. - Thomas R. Ioerger; Thomas Holton; Jon A. Christopher; James C. Sacchettini (ISMB, 1999)

An Adaptive Planner Based on Learning of Planning Performance. - Kreshna Gopal; Thomas R. Ioerger (AAAI/IAAI, 2000)

A knowledge-based approach for designing intelligent team training systems. - Jianwen Yin; Michael S. Miller; Thomas R. Ioerger; John Yen; Richard A. Volz (Agents, 2000)

Training Teams with Collaborative Agents. - Michael S. Miller; Jianwen Yin; Richard A. Volz; Thomas R. Ioerger; John Yen (Intelligent Tutoring Systems, 2000)

FLAME-Fuzzy Logic Adaptive Model of Emotions. - Magy Seif El-Nasr; John Yen; Thomas R. Ioerger (Auton. Agents Multi Agent Syst., 2000)

A formal model of responsibilities in agent-based teams. - J. Colby Johnson; Thomas R. Ioerger (Agents, 2001)

Extraction of rotation invariant signature based on fractal geometry. - Yu Tao 015; Thomas R. Ioerger; Yuan Yan Tang (ICIP (1), 2001)

CAST: Collaborative Agents for Simulating Teamwork. - John Yen; Jianwen Yin; Thomas R. Ioerger; Michael S. Miller; Dianxiang Xu; Richard A. Volz (IJCAI, 2001)

Automatic Generation of Communication and Teamwork within Multi-Agent Teams. - Keith E. Biggers; Thomas R. Ioerger (Appl. Artif. Intell., 2001)

Learning user interest dynamics with a three-descriptor representation. - Dwi H. Widyantoro; Thomas R. Ioerger; John Yen (J. Assoc. Inf. Sci. Technol., 2001)

FURL-A theory revision approach to learning fuzzy rules. - Ryan Rozich; Thomas R. Ioerger; Ronald R. Yager (FUZZ-IEEE, 2002)

Role-Based and Agent-Oriental Teamwork Modeling. - Sen Cao; Richard A. Volz; Thomas R. Ioerger; Yu Zhang 150 (IC-AI, 2002)

Generating Parallel Based on Planning Graph Analysis of Predicate/Transition Nets. - Dianxiang Xu; Richard A. Volz; Thomas R. Ioerger (IC-AI, 2002)

Proactive Information Exchange During Team Cooperation. - Yu Zhang 150; Richard A. Volz; Thomas R. Ioerger; Sen Cao; John Yen (IC-AI, 2002)

An Incremental Approach to Building a Cluster Hierarchy. - Dwi H. Widyantoro; Thomas R. Ioerger; John Yen (ICDM, 2002)

Extracting Fractal Features for Analyzing Protein Structure. - Yu Tao; Thomas R. Ioerger; James C. Sacchettini (ICPR (2), 2002)

Modeling and verifying multi-agent behaviors using predicate/transition nets. - Dianxiang Xu; Richard A. Volz; Thomas R. Ioerger; John Yen (SEKE, 2002)

Tracking changes in user interests with a few relevance judgments. - Dwi H. Widyantoro; Thomas R. Ioerger; John Yen (CIKM, 2003)

TEXTALTM: Artificial Intelligence Techniques for Automated Protein Structure Determination. - Kreshna Gopal; Reetal Pai; Thomas R. Ioerger; Tod D. Romo; James C. Sacchettini (IAAI, 2003)

A Quantitative Model of Capabilities in Multi-Agent Systems. - Linli He; Thomas R. Ioerger (IC-AI, 2003)

Collaborative Agents for C2 Teamwork Simulation. - Dianxiang Xu; Michael S. Miller; Richard A. Volz; Thomas R. Ioerger (IC-AI, 2003)

MOPAC: MOtif Finding by Preprocessing and Agglomerative Clustering from Microarrays. - R. Ganesh; Deborah A. Siegele; Thomas R. Ioerger (Pacific Symposium on Biocomputing, 2003)

Modeling and Analyzing Multi-Agent Behaviors Using Predicate/Transition Nets. - Dianxiang Xu; Richard A. Volz; Thomas R. Ioerger; John Yen (Int. J. Softw. Eng. Knowl. Eng., 2003)

Combining Bundle Search with Buyer Coalition Formation in Electronic Markets: A Distributed Approach through Negotiation. - Linli He; Thomas R. Ioerger (AAMAS, 2004)

Weighting Features to Recognize 3D Patterns of Electron Density in X-Ray Protein Crystallography. - Kreshna Gopal; Tod D. Romo; James C. Sacchettini; Thomas R. Ioerger (CSB, 2004)

Reasoning about Beliefs, Observability, and Information Exchange in Teamwork. - Thomas R. Ioerger (FLAIRS, 2004)

Evaluation of Geometric & Probabilistic Distance Measures To Retrieve Electron Density Patterns for Protein Structure Determination. - Kreshna Gopal; Tod D. Romo; James C. Sacchettini; Thomas R. Ioerger (IC-AI, 2004)

Task-Oriented Computational Economic-Based Distributed Resource Allocation Mechanisms for Computational Grids. - Linli He; Thomas R. Ioerger (IC-AI, 2004)

An Efficient Heuristic Bundle Search Algorithm for Buyers in Electronic Markets. - Linli He; Thomas R. Ioerger (IC-AI, 2004)

Efficient retrieval of electron density patterns for modeling proteins by X-ray crystallography. - Kreshna Gopal; Tod D. Romo; James C. Sacchettini; Thomas R. Ioerger (ICMLA, 2004)

A decision-theoretic approach for designing proactive communication in multi-agent teamwork. - Yu Zhang 150; Richard A. Volz; Thomas R. Ioerger; John Yen (SAC, 2004)

TEXTAL™: Automated Crystallographic Protein Structure Determination. - Kreshna Gopal; Tod D. Romo; Erik McKee; Kevin Childs; Lalji Kanbi; Reetal Pai; Jacob N. Smith; James C. Sacchettini; Thomas R. Ioerger (AAAI, 2005)

Observation-based proactive communication in team cooperation. - Yu Zhang 150; Richard A. Volz; Thomas R. Ioerger (AAMAS, 2005)

On Proactive Helping Behaviors In Teamwork. - Sen Cao; Richard A. Volz; Thomas R. Ioerger; Michael S. Miller (IC-AI, 2005)

Forming resource-sharing coalitions: a distributed resource allocation mechanism for self-interested agents in computational grids. - Linli He; Thomas R. Ioerger (SAC, 2005)

Decision-theoretic proactive communication in multiagent teamwork. - Yu Zhang 150; Thomas R. Ioerger; Richard A. Volz (SMC, 2005)

Combining bundle search with buyer coalition formation in electronic markets: A distributed approach through explicit negotiation. - Linli He; Thomas R. Ioerger (Electron. Commer. Res. Appl., 2005)

TEXTAL: AI-Based Structural Determination for X-ray Protein Crystallography. - Tod D. Romo; Kreshna Gopal; Erik McKee; Lalji Kanbi; Reetal Pai; Jacob N. Smith; James C. Sacchettini; Thomas R. Ioerger (IEEE Intell. Syst., 2005)

Determining Relevant Features to Recognize Electron Density Patterns in X-ray Protein Crystallography. - Kreshna Gopal; Tod D. Romo; James C. Sacchettini; Thomas R. Ioerger (J. Bioinform. Comput. Biol., 2005)

Coalition Formation Meets Information Theory. - Victor Palmer; Thomas R. Ioerger (FLAIRS, 2006)

TEXTAL: Crystallographic Protein Model Building Using AI and Pattern Recognition. - Kreshna Gopal; Tod D. Romo; Erik McKee; Reetal Pai; Jacob N. Smith; James C. Sacchettini; Thomas R. Ioerger (AI Mag., 2006)

MALLET-A Multi-Agent Logic Language for Encoding Teamwork. - Xiaocong Fan; John Yen; Michael S. Miller; Thomas R. Ioerger; Richard A. Volz (IEEE Trans. Knowl. Data Eng., 2006)

Database Approaches and Data Representation in Structural Bioinformatics. - Kreshna Gopal; James C. Sacchettini; Thomas R. Ioerger (BIBE, 2007)

Intention Is Commitment with Expectation. - James Creel; Christopher Menzel; Thomas R. Ioerger (FLAIRS, 2007)

Distance Metric Learning through Optimization of Ranking. - Kreshna Gopal; Thomas R. Ioerger (ICDM Workshops, 2007)

Crystallographic protein model-building on the web. - Kreshna Gopal; Erik McKee; Tod D. Romo; Reetal Pai; Jacob N. Smith; James C. Sacchettini; Thomas R. Ioerger (Bioinform., 2007)

Analysis of Protein-Ligand Interactions Using Localized Stereochemical Features. - Reetal Pai; James C. Sacchettini; Thomas R. Ioerger (BIOCOMP, 2008)

Specificity Normalization for Identifying Selective Inhibitors in Virtual Screening. - Reetal Pai; James C. Sacchettini; Thomas R. Ioerger (BIOCOMP, 2008)

Improving discrimination of essential genes by modeling local insertion frequencies in transposon mutagenesis data. - Michael A. DeJesus; Thomas R. Ioerger (BCB, 2013)

Bayesian analysis of gene essentiality based on sequencing of transposon insertion libraries. - Michael A. DeJesus; Yanjia J. Zhang; Christopher M. Sassetti; Eric J. Rubin; James C. Sacchettini; Thomas R. Ioerger (Bioinform., 2013)

A Hidden Markov Model for identifying essential and growth-defect regions in bacterial genomes from transposon insertion sequencing data. - Michael A. DeJesus; Thomas R. Ioerger (BMC Bioinform., 2013)

TRANSIT - A Software Tool for Himar1 TnSeq Analysis. - Michael A. DeJesus; Chaitra Ambadipudi; Richard Baker 007; Christopher M. Sassetti; Thomas R. Ioerger (PLoS Comput. Biol., 2015)

Capturing Uncertainty by Modeling Local Transposon Insertion Frequencies Improves Discrimination of Essential Genes. - Michael A. DeJesus; Thomas R. Ioerger (IEEE ACM Trans. Comput. Biol. Bioinform., 2015)

Normalization of transposon-mutant library sequencing datasets to improve identification of conditionally essential genes. - Michael A. DeJesus; Thomas R. Ioerger (J. Bioinform. Comput. Biol., 2016)

A Compatibility Approach to Identify Recombination Breakpoints in Bacterial and Viral Genomes. - Yi-Pin Lai; Thomas R. Ioerger (BCB, 2017)

Introduction to selected papers from the 8th International Conference on Bioinformatics and Computational Biology (BICOB 2016). - Nurit Haspel; Thomas R. Ioerger; Hisham Al-Mubaid (J. Bioinform. Comput. Biol., 2017)

A statistical method to identify recombination in bacterial genomes based on SNP incompatibility. - Yi-Pin Lai; Thomas R. Ioerger (BMC Bioinform., 2018)

Anion-π Interactions in Computer-Aided Drug Design: Modeling the Inhibition of Malate Synthase by Phenyl-Diketo Acids. - Jill F. Ellenbarger; Inna V. Krieger; Hsiao-Ling Huang; Silvia Gómez-Coca; Thomas R. Ioerger; James C. Sacchettini; Steven E. Wheeler; Kim R. Dunbar (J. Chem. Inf. Model., 2018)

Statistical analysis of variability in TnSeq data across conditions using zero-inflated negative binomial regression. - Siddharth Subramaniyam; Michael A. DeJesus; Anisha Zaveri; Clare M. Smith; Richard Baker 007; Sabine Ehrt; Dirk Schnappinger; Christopher M. Sassetti; Thomas R. Ioerger (BMC Bioinform., 2019)

Dual ICA to extract interacting sets of genes and conditions from transcriptomic data. - Sanjeevani Choudhery; Thomas R. Ioerger (BCB, 2023)

A dose-response model for statistical analysis of chemical genetic interactions in CRISPRi screens. - Sanjeevani Choudhery; Michael A. DeJesus; Aarthi Srinivasan; Jeremy Rock; Dirk Schnappinger; Thomas R. Ioerger (PLoS Comput. Biol., 2024)