Thomas R. Ioerger

Publication Activity (10 Years)

Years Active: 1993-2023
Publications (10 Years): 7

Top Topics

Capsule Endoscopy

Dagstuhl Castle

Bayesian Analysis

Escherichia Coli

Top Venues

J. Bioinform. Comput. Biol.

Publications

Sanjeevani Choudhery, Thomas R. Ioerger
Dual ICA to extract interacting sets of genes and conditions from transcriptomic data. BCB (2023)
Siddharth Subramaniyam, Michael A. DeJesus, Anisha Zaveri, Clare M. Smith, Richard Baker, Sabine Ehrt, Dirk Schnappinger, Christopher M. Sassetti, Thomas R. Ioerger
Statistical analysis of variability in TnSeq data across conditions using zero-inflated negative binomial regression. BMC Bioinform. 20 (1) (2019)
Jill F. Ellenbarger, Inna V. Krieger, Hsiao-Ling Huang, Silvia Gómez-Coca, Thomas R. Ioerger, James C. Sacchettini, Steven E. Wheeler, Kim R. Dunbar
Anion-π Interactions in Computer-Aided Drug Design: Modeling the Inhibition of Malate Synthase by Phenyl-Diketo Acids. J. Chem. Inf. Model. 58 (10) (2018)
Yi-Pin Lai, Thomas R. Ioerger
A statistical method to identify recombination in bacterial genomes based on SNP incompatibility. BMC Bioinform. 19 (1) (2018)
Nurit Haspel, Thomas R. Ioerger, Hisham Al-Mubaid
Introduction to selected papers from the 8th International Conference on Bioinformatics and Computational Biology (BICOB 2016). J. Bioinform. Comput. Biol. 15 (3) (2017)
Yi-Pin Lai, Thomas R. Ioerger
A Compatibility Approach to Identify Recombination Breakpoints in Bacterial and Viral Genomes. BCB (2017)
Michael A. DeJesus, Thomas R. Ioerger
Normalization of transposon-mutant library sequencing datasets to improve identification of conditionally essential genes. J. Bioinform. Comput. Biol. 14 (3) (2016)
Michael A. DeJesus, Thomas R. Ioerger
Capturing Uncertainty by Modeling Local Transposon Insertion Frequencies Improves Discrimination of Essential Genes. IEEE ACM Trans. Comput. Biol. Bioinform. 12 (1) (2015)
Michael A. DeJesus, Chaitra Ambadipudi, Richard Baker, Christopher M. Sassetti, Thomas R. Ioerger
TRANSIT - A Software Tool for Himar1 TnSeq Analysis. PLoS Comput. Biol. 11 (10) (2015)
Michael A. DeJesus, Yanjia J. Zhang, Christopher M. Sassetti, Eric J. Rubin, James C. Sacchettini, Thomas R. Ioerger
Bayesian analysis of gene essentiality based on sequencing of transposon insertion libraries. Bioinform. 29 (6) (2013)
Michael A. DeJesus, Thomas R. Ioerger
Improving discrimination of essential genes by modeling local insertion frequencies in transposon mutagenesis data. BCB (2013)
Michael A. DeJesus, Thomas R. Ioerger
A Hidden Markov Model for identifying essential and growth-defect regions in bacterial genomes from transposon insertion sequencing data. BMC Bioinform. 14 (2013)
Reetal Pai, James C. Sacchettini, Thomas R. Ioerger
Specificity Normalization for Identifying Selective Inhibitors in Virtual Screening. BIOCOMP (2008)
Reetal Pai, James C. Sacchettini, Thomas R. Ioerger
Analysis of Protein-Ligand Interactions Using Localized Stereochemical Features. BIOCOMP (2008)
Kreshna Gopal, James C. Sacchettini, Thomas R. Ioerger
Database Approaches and Data Representation in Structural Bioinformatics. BIBE (2007)
James Creel, Christopher Menzel, Thomas R. Ioerger
Intention Is Commitment with Expectation. FLAIRS Conference (2007)
Kreshna Gopal, Erik McKee, Tod D. Romo, Reetal Pai, Jacob N. Smith, James C. Sacchettini, Thomas R. Ioerger
Crystallographic protein model-building on the web. Bioinform. 23 (3) (2007)
Kreshna Gopal, Thomas R. Ioerger
Distance Metric Learning through Optimization of Ranking. ICDM Workshops (2007)
Victor Palmer, Thomas R. Ioerger
Coalition Formation Meets Information Theory. FLAIRS Conference (2006)
Kreshna Gopal, Tod D. Romo, Erik McKee, Reetal Pai, Jacob N. Smith, James C. Sacchettini, Thomas R. Ioerger
TEXTAL: Crystallographic Protein Model Building Using AI and Pattern Recognition. AI Mag. 27 (3) (2006)
Xiaocong Fan, John Yen, Michael S. Miller, Thomas R. Ioerger, Richard A. Volz
MALLET-A Multi-Agent Logic Language for Encoding Teamwork. IEEE Trans. Knowl. Data Eng. 18 (1) (2006)
Kreshna Gopal, Tod D. Romo, Erik McKee, Kevin Childs, Lalji Kanbi, Reetal Pai, Jacob N. Smith, James C. Sacchettini, Thomas R. Ioerger
TEXTAL™: Automated Crystallographic Protein Structure Determination. AAAI (2005)
Sen Cao, Richard A. Volz, Thomas R. Ioerger, Michael S. Miller
On Proactive Helping Behaviors In Teamwork. IC-AI (2005)
Linli He, Thomas R. Ioerger
Forming resource-sharing coalitions: a distributed resource allocation mechanism for self-interested agents in computational grids. SAC (2005)
Linli He, Thomas R. Ioerger
Combining bundle search with buyer coalition formation in electronic markets: A distributed approach through explicit negotiation. Electron. Commer. Res. Appl. 4 (4) (2005)
Kreshna Gopal, Tod D. Romo, James C. Sacchettini, Thomas R. Ioerger
Determining Relevant Features to Recognize Electron Density Patterns in X-ray Protein Crystallography. J. Bioinform. Comput. Biol. 3 (3) (2005)
Yu Zhang, Thomas R. Ioerger, Richard A. Volz
Decision-theoretic proactive communication in multiagent teamwork. SMC (2005)
Yu Zhang, Richard A. Volz, Thomas R. Ioerger
Observation-based proactive communication in team cooperation. AAMAS (2005)
Tod D. Romo, Kreshna Gopal, Erik McKee, Lalji Kanbi, Reetal Pai, Jacob N. Smith, James C. Sacchettini, Thomas R. Ioerger
TEXTAL: AI-Based Structural Determination for X-ray Protein Crystallography. IEEE Intell. Syst. 20 (6) (2005)
Linli He, Thomas R. Ioerger
An Efficient Heuristic Bundle Search Algorithm for Buyers in Electronic Markets. IC-AI (2004)
Linli He, Thomas R. Ioerger
Combining Bundle Search with Buyer Coalition Formation in Electronic Markets: A Distributed Approach through Negotiation. AAMAS (2004)
Linli He, Thomas R. Ioerger
Task-Oriented Computational Economic-Based Distributed Resource Allocation Mechanisms for Computational Grids. IC-AI (2004)
Linli He, Thomas R. Ioerger
Combining bundle search with buyer coalition formation in electronic markets: a distributed approach through explicit negotiation. ICEC (2004)
Kreshna Gopal, Tod D. Romo, James C. Sacchettini, Thomas R. Ioerger
Weighting Features to Recognize 3D Patterns of Electron Density in X-Ray Protein Crystallography. CSB (2004)
Kreshna Gopal, Tod D. Romo, James C. Sacchettini, Thomas R. Ioerger
Efficient retrieval of electron density patterns for modeling proteins by X-ray crystallography. ICMLA (2004)
Kreshna Gopal, Tod D. Romo, James C. Sacchettini, Thomas R. Ioerger
Evaluation of Geometric & Probabilistic Distance Measures To Retrieve Electron Density Patterns for Protein Structure Determination. IC-AI (2004)
Thomas R. Ioerger
Reasoning about Beliefs, Observability, and Information Exchange in Teamwork. FLAIRS Conference (2004)
Yu Zhang, Richard A. Volz, Thomas R. Ioerger, John Yen
A decision-theoretic approach for designing proactive communication in multi-agent teamwork. SAC (2004)
Linli He, Thomas R. Ioerger
A Quantitative Model of Capabilities in Multi-Agent Systems. IC-AI (2003)
Kreshna Gopal, Reetal Pai, Thomas R. Ioerger, Tod D. Romo, James C. Sacchettini
: Artificial Intelligence Techniques for Automated Protein Structure Determination. IAAI (2003)
Dwi H. Widyantoro, Thomas R. Ioerger, John Yen
Tracking changes in user interests with a few relevance judgments. CIKM (2003)
Dianxiang Xu, Michael S. Miller, Richard A. Volz, Thomas R. Ioerger
Collaborative Agents for C2 Teamwork Simulation. IC-AI (2003)
R. Ganesh, Deborah A. Siegele, Thomas R. Ioerger
MOPAC: MOtif Finding by Preprocessing and Agglomerative Clustering from Microarrays. Pacific Symposium on Biocomputing (2003)
Dianxiang Xu, Richard A. Volz, Thomas R. Ioerger, John Yen
Modeling and Analyzing Multi-Agent Behaviors Using Predicate/Transition Nets. Int. J. Softw. Eng. Knowl. Eng. 13 (1) (2003)
Yu Tao, Thomas R. Ioerger, James C. Sacchettini
Extracting Fractal Features for Analyzing Protein Structure. ICPR (2) (2002)
Dwi H. Widyantoro, Thomas R. Ioerger, John Yen
An Incremental Approach to Building a Cluster Hierarchy. ICDM (2002)
Yu Zhang, Richard A. Volz, Thomas R. Ioerger, Sen Cao, John Yen
Proactive Information Exchange During Team Cooperation. IC-AI (2002)
Sen Cao, Richard A. Volz, Thomas R. Ioerger, Yu Zhang
Role-Based and Agent-Oriental Teamwork Modeling. IC-AI (2002)
Ryan Rozich, Thomas R. Ioerger, Ronald R. Yager
FURL-A theory revision approach to learning fuzzy rules. FUZZ-IEEE (2002)
Dianxiang Xu, Richard A. Volz, Thomas R. Ioerger
Generating Parallel Based on Planning Graph Analysis of Predicate/Transition Nets. IC-AI (2002)
Dianxiang Xu, Richard A. Volz, Thomas R. Ioerger, John Yen
Modeling and verifying multi-agent behaviors using predicate/transition nets. SEKE (2002)
J. Colby Johnson, Thomas R. Ioerger
A formal model of responsibilities in agent-based teams. Agents (2001)
Keith E. Biggers, Thomas R. Ioerger
Automatic Generation of Communication and Teamwork within Multi-Agent Teams. Appl. Artif. Intell. 15 (10) (2001)
Yu Tao, Thomas R. Ioerger, Yuan Yan Tang
Extraction of rotation invariant signature based on fractal geometry. ICIP (1) (2001)
John Yen, Jianwen Yin, Thomas R. Ioerger, Michael S. Miller, Dianxiang Xu, Richard A. Volz
CAST: Collaborative Agents for Simulating Teamwork. IJCAI (2001)
Dwi H. Widyantoro, Thomas R. Ioerger, John Yen
Learning user interest dynamics with a three-descriptor representation. J. Assoc. Inf. Sci. Technol. 52 (3) (2001)
Jianwen Yin, Michael S. Miller, Thomas R. Ioerger, John Yen, Richard A. Volz
A knowledge-based approach for designing intelligent team training systems. Agents (2000)
Michael S. Miller, Jianwen Yin, Richard A. Volz, Thomas R. Ioerger, John Yen
Training Teams with Collaborative Agents. Intelligent Tutoring Systems (2000)
Kreshna Gopal, Thomas R. Ioerger
An Adaptive Planner Based on Learning of Planning Performance. AAAI/IAAI (2000)
Magy Seif El-Nasr, John Yen, Thomas R. Ioerger
FLAME-Fuzzy Logic Adaptive Model of Emotions. Auton. Agents Multi Agent Syst. 3 (3) (2000)
Thomas R. Ioerger
Detecting Feature Interactions from Accuracies of Random Feature Subsets. AAAI/IAAI (1999)
Dwi H. Widyantoro, Thomas R. Ioerger, John Yen
An Adaptive Algorithm for Learning Changes in User Interests. CIKM (1999)
Magy Seif El-Nasr, Thomas R. Ioerger, John Yen, Donald H. House, Frederic I. Parke
Emotionally Expressive Agents. CA (1999)
Magy Seif El-Nasr, Thomas R. Ioerger, John Yen
PETEEI: A PET With Evolving Emotional Intelligence. Agents (1999)
Thomas R. Ioerger, Thomas Holton, Jon A. Christopher, James C. Sacchettini
TEXTAL: A Pattern Recognition System for Interpreting Electron Density Maps. ISMB (1999)
Thomas R. Ioerger
The Context-Dependence of Amino Acid Properties. ISMB (1997)
Thomas R. Ioerger
Integrating a Spatial Reasoner with a Resolution Theorem-Prover. AAAI/IAAI (1997)
Thomas R. Ioerger, Larry A. Rendell, Shankar Subramaniam
Searching for Representations to Improve Protein Sequence Fold-Class Prediction. Mach. Learn. 21 (1-2) (1995)
Thomas R. Ioerger
The Manipulation of Images to Handle Indeterminacy in Spatial Reasoning. Cogn. Sci. 18 (4) (1994)
Thomas R. Ioerger, Larry A. Rendell, Shankar Subramaniam
Constructive Induction and Protein Tertiary Structure Prediction. ISMB (1993)