Thomas R. Ioerger

According to our database, Thomas R. Ioerger authored at least 70 papers between 1993 and 2024.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of four.

2024

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

2023

Dual ICA to extract interacting sets of genes and conditions from transcriptomic data.

Sanjeevani Choudhery, Thomas R. Ioerger

Proceedings of the 14th ACM International Conference on Bioinformatics, 2023

2019

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, Sabine Ehrt, Dirk Schnappinger, Christopher M. Sassetti, Thomas R. Ioerger

BMC Bioinform., 2019

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

A statistical method to identify recombination in bacterial genomes based on SNP incompatibility.

Yi-Pin Lai, Thomas R. Ioerger

BMC Bioinform., 2018

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 Compatibility Approach to Identify Recombination Breakpoints in Bacterial and Viral Genomes.

Yi-Pin Lai, Thomas R. Ioerger

Proceedings of the 8th ACM International Conference on Bioinformatics, 2017

2016

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

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

TRANSIT - A Software Tool for Himar1 TnSeq Analysis.

Michael A. DeJesus, Chaitra Ambadipudi, Richard Baker, Christopher M. Sassetti, Thomas R. Ioerger

PLoS Comput. Biol., 2015

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

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

Improving discrimination of essential genes by modeling local insertion frequencies in transposon mutagenesis data.

Michael A. DeJesus, Thomas R. Ioerger

Proceedings of the ACM Conference on Bioinformatics, 2013

2008

Specificity Normalization for Identifying Selective Inhibitors in Virtual Screening.

Reetal Pai, James C. Sacchettini, Thomas R. Ioerger

Proceedings of the International Conference on Bioinformatics & Computational Biology, 2008

Analysis of Protein-Ligand Interactions Using Localized Stereochemical Features.

Reetal Pai, James C. Sacchettini, Thomas R. Ioerger

Proceedings of the International Conference on Bioinformatics & Computational Biology, 2008

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

Distance Metric Learning through Optimization of Ranking.

Kreshna Gopal, Thomas R. Ioerger

Proceedings of the Workshops Proceedings of the 7th IEEE International Conference on Data Mining (ICDM 2007), 2007

Intention Is Commitment with Expectation.

James Creel, Christopher Menzel, Thomas R. Ioerger

Proceedings of the Twentieth International Florida Artificial Intelligence Research Society Conference, 2007

Database Approaches and Data Representation in Structural Bioinformatics.

Kreshna Gopal, James C. Sacchettini, Thomas R. Ioerger

Proceedings of the 7th IEEE International Conference on Bioinformatics and Bioengineering, 2007

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

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

Coalition Formation Meets Information Theory.

Victor Palmer, Thomas R. Ioerger

Proceedings of the Nineteenth International Florida Artificial Intelligence Research Society Conference, 2006

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

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

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

Decision-theoretic proactive communication in multiagent teamwork.

Yu Zhang, Thomas R. Ioerger, Richard A. Volz

Proceedings of the IEEE International Conference on Systems, 2005

Forming resource-sharing coalitions: a distributed resource allocation mechanism for self-interested agents in computational grids.

Linli He, Thomas R. Ioerger

Proceedings of the 2005 ACM Symposium on Applied Computing (SAC), 2005

On Proactive Helping Behaviors In Teamwork.

Sen Cao, Richard A. Volz, Thomas R. Ioerger, Michael S. Miller

Proceedings of the 2005 International Conference on Artificial Intelligence, 2005

Observation-based proactive communication in team cooperation.

Yu Zhang, Richard A. Volz, Thomas R. Ioerger

Proceedings of the 4th International Joint Conference on Autonomous Agents and Multiagent Systems (AAMAS 2005), 2005

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

Proceedings of the Proceedings, 2005

2004

A decision-theoretic approach for designing proactive communication in multi-agent teamwork.

Yu Zhang, Richard A. Volz, Thomas R. Ioerger, John Yen

Proceedings of the 2004 ACM Symposium on Applied Computing (SAC), 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

Proceedings of the 2004 International Conference on Machine Learning and Applications, 2004

An Efficient Heuristic Bundle Search Algorithm for Buyers in Electronic Markets.

Linli He, Thomas R. Ioerger

Proceedings of the International Conference on Artificial Intelligence, 2004

Task-Oriented Computational Economic-Based Distributed Resource Allocation Mechanisms for Computational Grids.

Linli He, Thomas R. Ioerger

Proceedings of the International Conference on Artificial Intelligence, 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

Proceedings of the International Conference on Artificial Intelligence, 2004

Reasoning about Beliefs, Observability, and Information Exchange in Teamwork.

Thomas R. Ioerger

Proceedings of the Seventeenth International Florida Artificial Intelligence Research Society Conference, 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

Proceedings of the 3rd International IEEE Computer Society Computational Systems Bioinformatics Conference, 2004

Combining Bundle Search with Buyer Coalition Formation in Electronic Markets: A Distributed Approach through Negotiation.

Linli He, Thomas R. Ioerger

Proceedings of the 3rd International Joint Conference on Autonomous Agents and Multiagent Systems (AAMAS 2004), 2004

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

MOPAC: MOtif Finding by Preprocessing and Agglomerative Clustering from Microarrays.

R. Ganesh, Deborah A. Siegele, Thomas R. Ioerger

Proceedings of the 8th Pacific Symposium on Biocomputing, 2003

Collaborative Agents for C2 Teamwork Simulation.

Dianxiang Xu, Michael S. Miller, Richard A. Volz, Thomas R. Ioerger

Proceedings of the International Conference on Artificial Intelligence, 2003

A Quantitative Model of Capabilities in Multi-Agent Systems.

Linli He, Thomas R. Ioerger

Proceedings of the International Conference on Artificial Intelligence, 2003

TEXTAL^TM: Artificial Intelligence Techniques for Automated Protein Structure Determination.

Kreshna Gopal, Reetal Pai, Thomas R. Ioerger, Tod D. Romo, James C. Sacchettini

Proceedings of the Fifteenth Conference on Innovative Applications of Artificial Intelligence, 2003

Tracking changes in user interests with a few relevance judgments.

Dwi H. Widyantoro, Thomas R. Ioerger, John Yen

Proceedings of the 2003 ACM CIKM International Conference on Information and Knowledge Management, 2003

2002

Modeling and verifying multi-agent behaviors using predicate/transition nets.

Dianxiang Xu, Richard A. Volz, Thomas R. Ioerger, John Yen

Proceedings of the 14th international conference on Software engineering and knowledge engineering, 2002

Extracting Fractal Features for Analyzing Protein Structure.

Yu Tao, Thomas R. Ioerger, James C. Sacchettini

Proceedings of the 16th International Conference on Pattern Recognition, 2002

An Incremental Approach to Building a Cluster Hierarchy.

Dwi H. Widyantoro, Thomas R. Ioerger, John Yen

Proceedings of the 2002 IEEE International Conference on Data Mining (ICDM 2002), 2002

Proactive Information Exchange During Team Cooperation.

Yu Zhang, Richard A. Volz, Thomas R. Ioerger, Sen Cao, John Yen

Proceedings of the International Conference on Artificial Intelligence, 2002

Generating Parallel Based on Planning Graph Analysis of Predicate/Transition Nets.

Dianxiang Xu, Richard A. Volz, Thomas R. Ioerger

Proceedings of the International Conference on Artificial Intelligence, 2002

Role-Based and Agent-Oriental Teamwork Modeling.

Sen Cao, Richard A. Volz, Thomas R. Ioerger, Yu Zhang

Proceedings of the International Conference on Artificial Intelligence, 2002

FURL-A theory revision approach to learning fuzzy rules.

Ryan Rozich, Thomas R. Ioerger, Ronald R. Yager

Proceedings of the 2002 IEEE International Conference on Fuzzy Systems, 2002

2001

Learning user interest dynamics with a three-descriptor representation.

Dwi H. Widyantoro, Thomas R. Ioerger, John Yen

J. Assoc. Inf. Sci. Technol., 2001

Automatic Generation of Communication and Teamwork within Multi-Agent Teams.

Keith E. Biggers, Thomas R. Ioerger

Appl. Artif. Intell., 2001

CAST: Collaborative Agents for Simulating Teamwork.

John Yen, Jianwen Yin, Thomas R. Ioerger, Michael S. Miller, Dianxiang Xu, Richard A. Volz

Proceedings of the Seventeenth International Joint Conference on Artificial Intelligence, 2001

Extraction of rotation invariant signature based on fractal geometry.

Yu Tao, Thomas R. Ioerger, Yuan Yan Tang

Proceedings of the 2001 International Conference on Image Processing, 2001

A formal model of responsibilities in agent-based teams.

J. Colby Johnson, Thomas R. Ioerger

Proceedings of the Fifth International Conference on Autonomous Agents, 2001

2000

FLAME-Fuzzy Logic Adaptive Model of Emotions.

Magy Seif El-Nasr, John Yen, Thomas R. Ioerger

Auton. Agents Multi Agent Syst., 2000

Training Teams with Collaborative Agents.

Michael S. Miller, Jianwen Yin, Richard A. Volz, Thomas R. Ioerger, John Yen

Proceedings of the Intelligent Tutoring Systems, 5th International Conference, 2000

A knowledge-based approach for designing intelligent team training systems.

Jianwen Yin, Michael S. Miller, Thomas R. Ioerger, John Yen, Richard A. Volz

Proceedings of the Fourth International Conference on Autonomous Agents, 2000

An Adaptive Planner Based on Learning of Planning Performance.

Kreshna Gopal, Thomas R. Ioerger

Proceedings of the Seventeenth National Conference on Artificial Intelligence and Twelfth Conference on on Innovative Applications of Artificial Intelligence, July 30, 2000

1999

TEXTAL: A Pattern Recognition System for Interpreting Electron Density Maps.

Thomas R. Ioerger, Thomas Holton, Jon A. Christopher, James C. Sacchettini

Proceedings of the Seventh International Conference on Intelligent Systems for Molecular Biology, 1999

An Adaptive Algorithm for Learning Changes in User Interests.

Dwi H. Widyantoro, Thomas R. Ioerger, John Yen

Proceedings of the 1999 ACM CIKM International Conference on Information and Knowledge Management, 1999

Emotionally Expressive Agents.

Magy Seif El-Nasr, Thomas R. Ioerger, John Yen, Donald H. House, Frederic I. Parke

Proceedings of the Computer Animation 1999, 1999

PETEEI: A PET With Evolving Emotional Intelligence.

Magy Seif El-Nasr, Thomas R. Ioerger, John Yen

Proceedings of the Third Annual Conference on Autonomous Agents, 1999

Detecting Feature Interactions from Accuracies of Random Feature Subsets.

Thomas R. Ioerger

Proceedings of the Sixteenth National Conference on Artificial Intelligence and Eleventh Conference on Innovative Applications of Artificial Intelligence, 1999

1997

The Context-Dependence of Amino Acid Properties.

Thomas R. Ioerger

Proceedings of the 5th International Conference on Intelligent Systems for Molecular Biology, 1997

Integrating a Spatial Reasoner with a Resolution Theorem-Prover.

Thomas R. Ioerger

Proceedings of the Fourteenth National Conference on Artificial Intelligence and Ninth Innovative Applications of Artificial Intelligence Conference, 1997

1995

Searching for Representations to Improve Protein Sequence Fold-Class Prediction.

Thomas R. Ioerger, Larry A. Rendell, Shankar Subramaniam

Mach. Learn., 1995

1994

The Manipulation of Images to Handle Indeterminacy in Spatial Reasoning.

Thomas R. Ioerger

Cogn. Sci., 1994

1993

Constructive Induction and Protein Tertiary Structure Prediction.

Thomas R. Ioerger, Larry A. Rendell, Shankar Subramaniam

Proceedings of the 1st International Conference on Intelligent Systems for Molecular Biology, 1993