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2020 – today
- 2023
[c49]Sanjeevani Choudhery
, Thomas R. Ioerger:
Dual ICA to extract interacting sets of genes and conditions from transcriptomic data. BCB 2023: 8:1-8:13
2010 – 2019
- 2019
- [j21]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): 603:1-603:15 (2019) - 2018
- [j20]Yi-Pin Lai, Thomas R. Ioerger:
A statistical method to identify recombination in bacterial genomes based on SNP incompatibility. BMC Bioinform. 19(1): 450:1-450:15 (2018) - [j19]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): 2085-2091 (2018) - 2017
- [j18]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): 1702002:1-1702002:2 (2017) - [c48]Yi-Pin Lai, Thomas R. Ioerger:
A Compatibility Approach to Identify Recombination Breakpoints in Bacterial and Viral Genomes. BCB 2017: 11-20 - 2016
- [j17]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): 1642004:1-1642004:20 (2016) - 2015
- [j16]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) - [j15]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): 92-102 (2015) - 2013
- [j14]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): 695-703 (2013) - [j13]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: 303 (2013) - [c47]Michael A. DeJesus, Thomas R. Ioerger:
Improving discrimination of essential genes by modeling local insertion frequencies in transposon mutagenesis data. BCB 2013: 144
2000 – 2009
- 2008
- [c46]Reetal Pai, James C. Sacchettini, Thomas R. Ioerger:
Analysis of Protein-Ligand Interactions Using Localized Stereochemical Features. BIOCOMP 2008: 666-673 - [c45]Reetal Pai, James C. Sacchettini, Thomas R. Ioerger:
Specificity Normalization for Identifying Selective Inhibitors in Virtual Screening. BIOCOMP 2008: 787-793 - 2007
- [j12]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): 375-377 (2007) - [c44]Kreshna Gopal, James C. Sacchettini, Thomas R. Ioerger:
Database Approaches and Data Representation in Structural Bioinformatics. BIBE 2007: 425-432 - [c43]James Creel, Christopher Menzel, Thomas R. Ioerger:
Intention Is Commitment with Expectation. FLAIRS 2007: 50-55 - [c42]Kreshna Gopal, Thomas R. Ioerger:
Distance Metric Learning through Optimization of Ranking. ICDM Workshops 2007: 201-206 - 2006
- [j11]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): 15-24 (2006) - [j10]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): 123-138 (2006) - [c41]Victor Palmer, Thomas R. Ioerger:
Coalition Formation Meets Information Theory. FLAIRS 2006: 98-99 - 2005
- [j9]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): 329-344 (2005) - [j8]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): 59-63 (2005) - [j7]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): 645-676 (2005) - [c40]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: 1483-1490 - [c39]Yu Zhang, Richard A. Volz, Thomas R. Ioerger:
Observation-based proactive communication in team cooperation. AAMAS 2005: 1321-1322 - [c38]Sen Cao, Richard A. Volz, Thomas R. Ioerger, Michael S. Miller:
On Proactive Helping Behaviors In Teamwork. IC-AI 2005: 974-980 - [c37]Linli He, Thomas R. Ioerger:
Forming resource-sharing coalitions: a distributed resource allocation mechanism for self-interested agents in computational grids. SAC 2005: 84-91 - [c36]Yu Zhang, Thomas R. Ioerger, Richard A. Volz:
Decision-theoretic proactive communication in multiagent teamwork. SMC 2005: 3903-3908 - 2004
- [c35]Linli He, Thomas R. Ioerger:
Combining bundle search with buyer coalition formation in electronic markets: a distributed approach through explicit negotiation. ICEC 2004: 95-104 - [c34]Linli He, Thomas R. Ioerger:
Combining Bundle Search with Buyer Coalition Formation in Electronic Markets: A Distributed Approach through Negotiation. AAMAS 2004: 1440-1441 - [c33]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: 255-265 - [c32]Thomas R. Ioerger:
Reasoning about Beliefs, Observability, and Information Exchange in Teamwork. FLAIRS 2004: 430-435 - [c31]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: 427-432 - [c30]Linli He, Thomas R. Ioerger:
Task-Oriented Computational Economic-Based Distributed Resource Allocation Mechanisms for Computational Grids. IC-AI 2004: 462-468 - [c29]Linli He, Thomas R. Ioerger:
An Efficient Heuristic Bundle Search Algorithm for Buyers in Electronic Markets. IC-AI 2004: 729-735 - [c28]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: 380-387 - [c27]Yu Zhang, Richard A. Volz, Thomas R. Ioerger, John Yen:
A decision-theoretic approach for designing proactive communication in multi-agent teamwork. SAC 2004: 64-71 - 2003
- [j6]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): 103-124 (2003) - [c26]Dwi H. Widyantoro, Thomas R. Ioerger, John Yen:
Tracking changes in user interests with a few relevance judgments. CIKM 2003: 548-551 - [c25]Kreshna Gopal, Reetal Pai, Thomas R. Ioerger, Tod D. Romo, James C. Sacchettini:
TEXTALTM: Artificial Intelligence Techniques for Automated Protein Structure Determination. IAAI 2003: 93-100 - [c24]Dianxiang Xu, Michael S. Miller, Richard A. Volz, Thomas R. Ioerger:
Collaborative Agents for C2 Teamwork Simulation. IC-AI 2003: 723-729 - [c23]Linli He, Thomas R. Ioerger:
A Quantitative Model of Capabilities in Multi-Agent Systems. IC-AI 2003: 730-736 - [c22]R. Ganesh, Deborah A. Siegele, Thomas R. Ioerger:
MOPAC: MOtif Finding by Preprocessing and Agglomerative Clustering from Microarrays. Pacific Symposium on Biocomputing 2003: 41-52 - 2002
- [c21]Ryan Rozich, Thomas R. Ioerger, Ronald R. Yager:
FURL-A theory revision approach to learning fuzzy rules. FUZZ-IEEE 2002: 791-796 - [c20]Yu Zhang, Richard A. Volz, Thomas R. Ioerger, Sen Cao, John Yen:
Proactive Information Exchange During Team Cooperation. IC-AI 2002: 341-346 - [c19]Dianxiang Xu, Richard A. Volz, Thomas R. Ioerger:
Generating Parallel Based on Planning Graph Analysis of Predicate/Transition Nets. IC-AI 2002: 440-446 - [c18]Sen Cao, Richard A. Volz, Thomas R. Ioerger, Yu Zhang:
Role-Based and Agent-Oriental Teamwork Modeling. IC-AI 2002: 1190- - [c17]Dwi H. Widyantoro, Thomas R. Ioerger, John Yen:
An Incremental Approach to Building a Cluster Hierarchy. ICDM 2002: 705-708 - [c16]Yu Tao, Thomas R. Ioerger, James C. Sacchettini:
Extracting Fractal Features for Analyzing Protein Structure. ICPR (2) 2002: 482-485 - [c15]Dianxiang Xu, Richard A. Volz, Thomas R. Ioerger, John Yen:
Modeling and verifying multi-agent behaviors using predicate/transition nets. SEKE 2002: 193-200 - 2001
- [j5]Keith E. Biggers, Thomas R. Ioerger:
Automatic Generation of Communication and Teamwork within Multi-Agent Teams. Appl. Artif. Intell. 15(10): 875-916 (2001) - [j4]Dwi H. Widyantoro, Thomas R. Ioerger, John Yen:
Learning user interest dynamics with a three-descriptor representation. J. Assoc. Inf. Sci. Technol. 52(3): 212-225 (2001) - [c14]J. Colby Johnson, Thomas R. Ioerger:
A formal model of responsibilities in agent-based teams. Agents 2001: 157-158 - [c13]Yu Tao, Thomas R. Ioerger, Yuan Yan Tang:
Extraction of rotation invariant signature based on fractal geometry. ICIP (1) 2001: 1090-1093 - [c12]John Yen, Jianwen Yin, Thomas R. Ioerger, Michael S. Miller, Dianxiang Xu, Richard A. Volz:
CAST: Collaborative Agents for Simulating Teamwork. IJCAI 2001: 1135-1144 - 2000
- [j3]Magy Seif El-Nasr, John Yen, Thomas R. Ioerger:
FLAME-Fuzzy Logic Adaptive Model of Emotions. Auton. Agents Multi Agent Syst. 3(3): 219-257 (2000) - [c11]Kreshna Gopal, Thomas R. Ioerger:
An Adaptive Planner Based on Learning of Planning Performance. AAAI/IAAI 2000: 1073 - [c10]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: 427-434 - [c9]Michael S. Miller, Jianwen Yin, Richard A. Volz, Thomas R. Ioerger, John Yen:
Training Teams with Collaborative Agents. Intelligent Tutoring Systems 2000: 63-72
1990 – 1999
- 1999
- [c8]Thomas R. Ioerger:
Detecting Feature Interactions from Accuracies of Random Feature Subsets. AAAI/IAAI 1999: 350-357 - [c7]Magy Seif El-Nasr, Thomas R. Ioerger, John Yen:
PETEEI: A PET With Evolving Emotional Intelligence. Agents 1999: 9-15 - [c6]Magy Seif El-Nasr, Thomas R. Ioerger, John Yen, Donald H. House, Frederic I. Parke:
Emotionally Expressive Agents. CA 1999: 48-57 - [c5]Dwi H. Widyantoro, Thomas R. Ioerger, John Yen:
An Adaptive Algorithm for Learning Changes in User Interests. CIKM 1999: 405-412 - [c4]Thomas R. Ioerger, Thomas Holton, Jon A. Christopher, James C. Sacchettini:
TEXTAL: A Pattern Recognition System for Interpreting Electron Density Maps. ISMB 1999: 130-137 - 1997
- [c3]Thomas R. Ioerger:
Integrating a Spatial Reasoner with a Resolution Theorem-Prover. AAAI/IAAI 1997: 145-152 - [c2]Thomas R. Ioerger:
The Context-Dependence of Amino Acid Properties. ISMB 1997: 157-166 - 1995
- [j2]Thomas R. Ioerger, Larry A. Rendell, Shankar Subramaniam:
Searching for Representations to Improve Protein Sequence Fold-Class Prediction. Mach. Learn. 21(1-2): 151-175 (1995) - 1994
- [j1]Thomas R. Ioerger:
The Manipulation of Images to Handle Indeterminacy in Spatial Reasoning. Cogn. Sci. 18(4): 551-593 (1994) - 1993
- [c1]Thomas R. Ioerger, Larry A. Rendell, Shankar Subramaniam:
Constructive Induction and Protein Tertiary Structure Prediction. ISMB 1993: 198-206
Coauthor Index
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