Thomas R. Ioerger

71 papers A* 3A 7B 3C 5Misc 15Journal 22Unranked 16
YearRankTypeTitle / Venue / Authors
2024 J jnl
A dose-response model for statistical analysis of chemical genetic interactions in CRISPRi screens.
PLoS Comput. Biol.
Sanjeevani Choudhery, Michael A. DeJesus, Aarthi Srinivasan, Jeremy Rock, Dirk Schnappinger, Thomas R. Ioerger
2023 — conf
Dual ICA to extract interacting sets of genes and conditions from transcriptomic data.
BCB
Sanjeevani Choudhery, Thomas R. Ioerger
2019 J jnl
Statistical analysis of variability in TnSeq data across conditions using zero-inflated negative binomial regression.
BMC Bioinform.
Siddharth Subramaniyam, Michael A. DeJesus, Anisha Zaveri, Clare M. Smith, Richard Baker, Sabine Ehrt, Dirk Schnappinger, Christopher M. Sassetti, Thomas R. Ioerger
2018 J jnl
A statistical method to identify recombination in bacterial genomes based on SNP incompatibility.
BMC Bioinform.
Yi-Pin Lai, Thomas R. Ioerger
2018 J jnl
Anion-π Interactions in Computer-Aided Drug Design: Modeling the Inhibition of Malate Synthase by Phenyl-Diketo Acids.
J. Chem. Inf. Model.
Jill F. Ellenbarger, Inna V. Krieger, Hsiao-Ling Huang, Silvia Gómez-Coca, Thomas R. Ioerger, James C. Sacchettini, Steven E. Wheeler, Kim R. Dunbar
2017 — conf
A Compatibility Approach to Identify Recombination Breakpoints in Bacterial and Viral Genomes.
BCB
Yi-Pin Lai, Thomas R. Ioerger
2017 J jnl
Introduction to selected papers from the 8th International Conference on Bioinformatics and Computational Biology (BICOB 2016).
J. Bioinform. Comput. Biol.
Nurit Haspel, Thomas R. Ioerger, Hisham Al-Mubaid
2016 J jnl
Normalization of transposon-mutant library sequencing datasets to improve identification of conditionally essential genes.
J. Bioinform. Comput. Biol.
Michael A. DeJesus, Thomas R. Ioerger
2015 J jnl
Capturing Uncertainty by Modeling Local Transposon Insertion Frequencies Improves Discrimination of Essential Genes.
IEEE ACM Trans. Comput. Biol. Bioinform.
Michael A. DeJesus, Thomas R. Ioerger
2015 J jnl
TRANSIT - A Software Tool for Himar1 TnSeq Analysis.
PLoS Comput. Biol.
Michael A. DeJesus, Chaitra Ambadipudi, Richard Baker, Christopher M. Sassetti, Thomas R. Ioerger
2013 J jnl
A Hidden Markov Model for identifying essential and growth-defect regions in bacterial genomes from transposon insertion sequencing data.
BMC Bioinform.
Michael A. DeJesus, Thomas R. Ioerger
2013 J jnl
Bayesian analysis of gene essentiality based on sequencing of transposon insertion libraries.
Bioinform.
Michael A. DeJesus, Yanjia J. Zhang, Christopher M. Sassetti, Eric J. Rubin, James C. Sacchettini, Thomas R. Ioerger
2013 — conf
Improving discrimination of essential genes by modeling local insertion frequencies in transposon mutagenesis data.
BCB
Michael A. DeJesus, Thomas R. Ioerger
2008 — conf
Analysis of Protein-Ligand Interactions Using Localized Stereochemical Features.
BIOCOMP
Reetal Pai, James C. Sacchettini, Thomas R. Ioerger
2008 — conf
Specificity Normalization for Identifying Selective Inhibitors in Virtual Screening.
BIOCOMP
Reetal Pai, James C. Sacchettini, Thomas R. Ioerger
2007 J jnl
Crystallographic protein model-building on the web.
Bioinform.
Kreshna Gopal, Erik McKee, Tod D. Romo, Reetal Pai, Jacob N. Smith, James C. Sacchettini, Thomas R. Ioerger
2007 C conf
Database Approaches and Data Representation in Structural Bioinformatics.
BIBE
Kreshna Gopal, James C. Sacchettini, Thomas R. Ioerger
2007 — conf
Distance Metric Learning through Optimization of Ranking.
ICDM Workshops
Kreshna Gopal, Thomas R. Ioerger
2007 Misc conf
Intention Is Commitment with Expectation.
FLAIRS
James Creel, Christopher Menzel, Thomas R. Ioerger
2006 Misc conf
Coalition Formation Meets Information Theory.
FLAIRS
Victor Palmer, Thomas R. Ioerger
2006 J jnl
MALLET-A Multi-Agent Logic Language for Encoding Teamwork.
IEEE Trans. Knowl. Data Eng.
Xiaocong Fan, John Yen, Michael S. Miller, Thomas R. Ioerger, Richard A. Volz
2006 J jnl
TEXTAL: Crystallographic Protein Model Building Using AI and Pattern Recognition.
AI Mag.
Kreshna Gopal, Tod D. Romo, Erik McKee, Reetal Pai, Jacob N. Smith, James C. Sacchettini, Thomas R. Ioerger
2005 J jnl
Combining bundle search with buyer coalition formation in electronic markets: A distributed approach through explicit negotiation.
Electron. Commer. Res. Appl.
Linli He, Thomas R. Ioerger
2005 B conf
Decision-theoretic proactive communication in multiagent teamwork.
SMC
Yu Zhang, Thomas R. Ioerger, Richard A. Volz
2005 J jnl
Determining Relevant Features to Recognize Electron Density Patterns in X-ray Protein Crystallography.
J. Bioinform. Comput. Biol.
Kreshna Gopal, Tod D. Romo, James C. Sacchettini, Thomas R. Ioerger
2005 Misc conf
Forming resource-sharing coalitions: a distributed resource allocation mechanism for self-interested agents in computational grids.
SAC
Linli He, Thomas R. Ioerger
2005 A conf
Observation-based proactive communication in team cooperation.
AAMAS
Yu Zhang, Richard A. Volz, Thomas R. Ioerger
2005 Misc conf
On Proactive Helping Behaviors In Teamwork.
IC-AI
Sen Cao, Richard A. Volz, Thomas R. Ioerger, Michael S. Miller
2005 J jnl
TEXTAL: AI-Based Structural Determination for X-ray Protein Crystallography.
IEEE Intell. Syst.
Tod D. Romo, Kreshna Gopal, Erik McKee, Lalji Kanbi, Reetal Pai, Jacob N. Smith, James C. Sacchettini, Thomas R. Ioerger
2005 A* conf
TEXTAL™: Automated Crystallographic Protein Structure Determination.
AAAI
Kreshna Gopal, Tod D. Romo, Erik McKee, Kevin Childs, Lalji Kanbi, Reetal Pai, Jacob N. Smith, James C. Sacchettini, Thomas R. Ioerger
2004 Misc conf
A decision-theoretic approach for designing proactive communication in multi-agent teamwork.
SAC
Yu Zhang, Richard A. Volz, Thomas R. Ioerger, John Yen
2004 Misc conf
An Efficient Heuristic Bundle Search Algorithm for Buyers in Electronic Markets.
IC-AI
Linli He, Thomas R. Ioerger
2004 A conf
Combining Bundle Search with Buyer Coalition Formation in Electronic Markets: A Distributed Approach through Negotiation.
AAMAS
Linli He, Thomas R. Ioerger
2004 C conf
Combining bundle search with buyer coalition formation in electronic markets: a distributed approach through explicit negotiation.
ICEC
Linli He, Thomas R. Ioerger
2004 C conf
Efficient retrieval of electron density patterns for modeling proteins by X-ray crystallography.
ICMLA
Kreshna Gopal, Tod D. Romo, James C. Sacchettini, Thomas R. Ioerger
2004 Misc conf
Evaluation of Geometric & Probabilistic Distance Measures To Retrieve Electron Density Patterns for Protein Structure Determination.
IC-AI
Kreshna Gopal, Tod D. Romo, James C. Sacchettini, Thomas R. Ioerger
2004 Misc conf
Reasoning about Beliefs, Observability, and Information Exchange in Teamwork.
FLAIRS
Thomas R. Ioerger
2004 Misc conf
Task-Oriented Computational Economic-Based Distributed Resource Allocation Mechanisms for Computational Grids.
IC-AI
Linli He, Thomas R. Ioerger
2004 — conf
Weighting Features to Recognize 3D Patterns of Electron Density in X-Ray Protein Crystallography.
CSB
Kreshna Gopal, Tod D. Romo, James C. Sacchettini, Thomas R. Ioerger
2003 Misc conf
A Quantitative Model of Capabilities in Multi-Agent Systems.
IC-AI
Linli He, Thomas R. Ioerger
2003 Misc conf
Collaborative Agents for C2 Teamwork Simulation.
IC-AI
Dianxiang Xu, Michael S. Miller, Richard A. Volz, Thomas R. Ioerger
2003 Misc conf
MOPAC: MOtif Finding by Preprocessing and Agglomerative Clustering from Microarrays.
Pacific Symposium on Biocomputing
R. Ganesh, Deborah A. Siegele, Thomas R. Ioerger
2003 J jnl
Modeling and Analyzing Multi-Agent Behaviors Using Predicate/Transition Nets.
Int. J. Softw. Eng. Knowl. Eng.
Dianxiang Xu, Richard A. Volz, Thomas R. Ioerger, John Yen
2003 C conf
TEXTAL
IAAI
Kreshna Gopal, Reetal Pai, Thomas R. Ioerger, Tod D. Romo, James C. Sacchettini
2003 A conf
Tracking changes in user interests with a few relevance judgments.
CIKM
Dwi H. Widyantoro, Thomas R. Ioerger, John Yen
2002 A* conf
An Incremental Approach to Building a Cluster Hierarchy.
ICDM
Dwi H. Widyantoro, Thomas R. Ioerger, John Yen
2002 — conf
Extracting Fractal Features for Analyzing Protein Structure.
ICPR (2)
Yu Tao, Thomas R. Ioerger, James C. Sacchettini
2002 B conf
FURL-A theory revision approach to learning fuzzy rules.
FUZZ-IEEE
Ryan Rozich, Thomas R. Ioerger, Ronald R. Yager
2002 Misc conf
Generating Parallel Based on Planning Graph Analysis of Predicate/Transition Nets.
IC-AI
Dianxiang Xu, Richard A. Volz, Thomas R. Ioerger
2002 C conf
Modeling and verifying multi-agent behaviors using predicate/transition nets.
SEKE
Dianxiang Xu, Richard A. Volz, Thomas R. Ioerger, John Yen
2002 Misc conf
Proactive Information Exchange During Team Cooperation.
IC-AI
Yu Zhang, Richard A. Volz, Thomas R. Ioerger, Sen Cao, John Yen
2002 Misc conf
Role-Based and Agent-Oriental Teamwork Modeling.
IC-AI
Sen Cao, Richard A. Volz, Thomas R. Ioerger, Yu Zhang
2001 — conf
A formal model of responsibilities in agent-based teams.
Agents
J. Colby Johnson, Thomas R. Ioerger
2001 J jnl
Automatic Generation of Communication and Teamwork within Multi-Agent Teams.
Appl. Artif. Intell.
Keith E. Biggers, Thomas R. Ioerger
2001 A* conf
CAST: Collaborative Agents for Simulating Teamwork.
IJCAI
John Yen, Jianwen Yin, Thomas R. Ioerger, Michael S. Miller, Dianxiang Xu, Richard A. Volz
2001 — conf
Extraction of rotation invariant signature based on fractal geometry.
ICIP (1)
Yu Tao, Thomas R. Ioerger, Yuan Yan Tang
2001 J jnl
Learning user interest dynamics with a three-descriptor representation.
J. Assoc. Inf. Sci. Technol.
Dwi H. Widyantoro, Thomas R. Ioerger, John Yen
2000 — conf
A knowledge-based approach for designing intelligent team training systems.
Agents
Jianwen Yin, Michael S. Miller, Thomas R. Ioerger, John Yen, Richard A. Volz
2000 — conf
An Adaptive Planner Based on Learning of Planning Performance.
AAAI/IAAI
Kreshna Gopal, Thomas R. Ioerger
2000 J jnl
FLAME-Fuzzy Logic Adaptive Model of Emotions.
Auton. Agents Multi Agent Syst.
Magy Seif El-Nasr, John Yen, Thomas R. Ioerger
2000 B conf
Training Teams with Collaborative Agents.
Intelligent Tutoring Systems
Michael S. Miller, Jianwen Yin, Richard A. Volz, Thomas R. Ioerger, John Yen
1999 A conf
An Adaptive Algorithm for Learning Changes in User Interests.
CIKM
Dwi H. Widyantoro, Thomas R. Ioerger, John Yen
1999 — conf
Detecting Feature Interactions from Accuracies of Random Feature Subsets.
AAAI/IAAI
Thomas R. Ioerger
1999 — conf
Emotionally Expressive Agents.
CA
Magy Seif El-Nasr, Thomas R. Ioerger, John Yen, Donald H. House, Frederic I. Parke
1999 — conf
PETEEI: A PET With Evolving Emotional Intelligence.
Agents
Magy Seif El-Nasr, Thomas R. Ioerger, John Yen
1999 A conf
TEXTAL: A Pattern Recognition System for Interpreting Electron Density Maps.
ISMB
Thomas R. Ioerger, Thomas Holton, Jon A. Christopher, James C. Sacchettini
1997 — conf
Integrating a Spatial Reasoner with a Resolution Theorem-Prover.
AAAI/IAAI
Thomas R. Ioerger
1997 A conf
The Context-Dependence of Amino Acid Properties.
ISMB
Thomas R. Ioerger
1995 J jnl
Searching for Representations to Improve Protein Sequence Fold-Class Prediction.
Mach. Learn.
Thomas R. Ioerger, Larry A. Rendell, Shankar Subramaniam
1994 J jnl
The Manipulation of Images to Handle Indeterminacy in Spatial Reasoning.
Cogn. Sci.
Thomas R. Ioerger
1993 A conf
Constructive Induction and Protein Tertiary Structure Prediction.
ISMB
Thomas R. Ioerger, Larry A. Rendell, Shankar Subramaniam