# overview
Dr. Ioerger's research interests are in the areas of Artificial Intelligence, Intelligent Agents, and Machine Learning. His work has covered diverse areas, from spatial reasoning, to simulating team-work, to modeling emotions. Currently, his primary focus is on designing multi-agent system architectures to simulate collaborative behavior and teamwork. He also applies AI and machine learning methods to various problems in the area of Bioinformatics, including the improvement of protein sequence alignments, molecular modeling, and X-ray crystallography. The latter research has lead to the development of an automated software system for protein model-building called TEXTAL, which is currently being used by crystallographers throughout the world.

# keywords[]
Alzheimer's Disease Including Alzheimer's Disease Related Dementias (ad/adrd)

# keywords[]
5 Development Of Treatments And Therapeutic Interventions

# keywords[]
4607 Graphics, Augmented Reality And Games

# keywords[]
5 Development Of Treatments And Therapeutic Interventions

# keywords[]
3404 Medicinal And Biomolecular Chemistry

# keywords[]
3404 Medicinal And Biomolecular Chemistry

# keywords[]
2.2 Factors Relating To The Physical Environment

# keywords[]
2.2 Factors Relating To The Physical Environment

# keywords[]
2.2 Factors Relating To The Physical Environment

# keywords[]
5 Development Of Treatments And Therapeutic Interventions

# keywords[]
3102 Bioinformatics And Computational Biology

# keywords[]
2.2 Factors Relating To The Physical Environment

# keywords[]
3102 Bioinformatics And Computational Biology

# keywords[]
5 Development Of Treatments And Therapeutic Interventions

# keywords[]
5 Development Of Treatments And Therapeutic Interventions

# keywords[]
3102 Bioinformatics And Computational Biology

# keywords[]
Networking And Information Technology R&d (nitrd)

# keywords[]
Machine Learning And Artificial Intelligence

# keywords[]
5 Development Of Treatments And Therapeutic Interventions

# keywords[]
Networking And Information Technology R&d

# keywords[]
5 Development Of Treatments And Therapeutic Interventions

# keywords[]
5 Development Of Treatments And Therapeutic Interventions

# keywords[]
1.1 Normal Biological Development And Functioning

# keywords[]
5 Development Of Treatments And Therapeutic Interventions

# keywords[]
2.2 Factors Relating To The Physical Environment

# keywords[]
Clustered Regularly Interspaced Short Palindromic Repeats

# keywords[]
5 Development Of Treatments And Therapeutic Interventions

# keywords[]
2.2 Factors Relating To The Physical Environment

# keywords[]
1.1 Normal Biological Development And Functioning

# keywords[]
2.2 Factors Relating To The Physical Environment

# keywords[]
2.2 Factors Relating To The Physical Environment

# keywords[]
5 Development Of Treatments And Therapeutic Interventions

# keywords[]
2.2 Factors Relating To The Physical Environment

# keywords[]
2.2 Factors Relating To The Physical Environment

# keywords[]
4607 Graphics, Augmented Reality And Games

# keywords[]
Networking And Information Technology R&d (nitrd)

# keywords[]
5 Development Of Treatments And Therapeutic Interventions

# keywords[]
2.2 Factors Relating To The Physical Environment

# keywords[]
2.2 Factors Relating To The Physical Environment

# keywords[]
5 Development Of Treatments And Therapeutic Interventions

# keywords[]
2.2 Factors Relating To The Physical Environment

# keywords[]
2.2 Factors Relating To The Physical Environment

# keywords[]
3102 Bioinformatics And Computational Biology

# keywords[]
Atp Binding Cassette Transporter, Subfamily B, Member 1

# keywords[]
3214 Pharmacology And Pharmaceutical Sciences

# keywords[]
2.2 Factors Relating To The Physical Environment

# keywords[]
Circadian Rhythm Signaling Peptides And Proteins

# educationAndTraining[].organization.label
Pennsylvania State University - (State College, Pennsylvania, United States)

# educationAndTraining[].organization.label
University of Illinois at Urbana Champaign - (Urbana, Illinois, United States)

# educationAndTraining[].organization.label
University of Illinois at Urbana Champaign - (Urbana, Illinois, United States)

# awardsAndHonors[].label
CSE Graduate Faculty Teaching Excellence Award

# publications[].label
PPE51 mediates uptake of trehalose across the mycomembrane of Mycobacterium tuberculosis.

# publications[].label
Developing synergistic drug combinations to restore antibiotic sensitivity in drug-resistant Mycobacterium tuberculosis.

# publications[].label
Large-scale chemical-genetics yields new M. tuberculosis inhibitor classes.

# publications[].label
FURL - A theory revision approach to learning fuzzy rules

# publications[].label
RNA sequencing for transcript 5'-end mapping in mycobacteria.

# publications[].label
Reinforcement Learning using EEG signals for Therapeutic Use of Music in Emotion Management.

# publications[].publisher
Institute of Electrical and Electronics Engineers (IEEE)

# publications[].label
Extracting fractal features for analyzing protein structure

# publications[].publisher
Institute of Electrical and Electronics Engineers (IEEE)

# publications[].label
Constructive induction and protein tertiary structure prediction.

# publications[].label
Intention is commitment with expectation

# publications[].label
Functional whole genome screen of nutrient-starved Mycobacterium tuberculosis identifies genes involved in antibiotic tolerance.

# publications[].label
Identification of a Series Containing a Pentafluorophenyl Moiety That Targets Pks13 to Inhibit Growth of Mycobacterium tuberculosis.

# publications[].label
An incremental approach to building a cluster hierarchy

# publications[].publisher
Institute of Electrical and Electronics Engineers (IEEE)

# publications[].label
Synthesis and StructureActivity Relationships of a New Class of Oxadiazoles Targeting DprE1 as Antitubercular Agents

# publications[].label
Air Traffic Conflict Negotiation and Resolution Using an Onboard Multi-Agent System

# publications[].publisher
Institute of Electrical and Electronics Engineers (IEEE)

# publications[].label
Crystallographic protein model-building on the web.

# publications[].label
Comprehensive analysis of iron utilization by Mycobacterium tuberculosis.

# publications[].label
Mutations in fbiD (Rv2983) as a Novel Determinant of Resistance to Pretomanid and Delamanid in Mycobacterium tuberculosis.

# publications[].label
Interstitial macrophages prevent tuberculosis relapse by restricting Mycobacterium tuberculosis immune evasion.

# publications[].label
Maturing Mycobacterium smegmatis peptidoglycan requires non-canonical crosslinks to maintain shape.

# publications[].label
Design criteria for minimalist mimics of protein-protein interface segments.

# publications[].label
Identification and Evaluation of dibasic piperidines as novel cell wall inhibitors against Mycobacterium tuberculosis

# publications[].label
Genetic requirements of Mycobacterium tuberculosis for survival under pathogen-specific immunity

# publications[].label
High-Throughput Differentiation and Screening of a Library of Mutant Stem Cell Clones Defines New Host-Based Genes Involved in Rabies Virus Infection.

# publications[].label
Global assessment of Mycobacterium avium subspecies hominissuis genetic requirement for growth and virulence

# publications[].label
An efficient heuristic bundle search algorithm for buyers in electronic markets

# publications[].label
Automatic generation of communication and teamwork within multi-agent teams

# publications[].label
Identifying essential genes in Mycobacterium tuberculosis by global phenotypic profiling.

# publications[].label
Transposon mutagenesis in Mycobacterium abscessus identifies an essential penicillin-binding protein involved in septal peptidoglycan synthesis and antibiotic sensitivity.

# publications[].label
Discovery of Antimicrobial Lipodepsipeptides Produced by a Serratia sp. within Mosquito Microbiomes.

# publications[].label
PRIMARY STRUCTURAL FEATURES OF THE SELF-INCOMPATIBILITY PROTEIN IN SOLANACEAE

# publications[].label
Crystal structure of Mycobacterium tuberculosis LrpA, a leucine-responsive global regulator associated with starvation response.

# publications[].label
A dose-response based model for statistical analysis of chemical genetic interactions in CRISPRi libraries.

# publications[].label
Analysis of Gene Essentiality from TnSeq Data Using Transit.

# publications[].label
Identifying NCS in electron density maps: a pattern recognition approach

# publications[].publisher
International Union of Crystallography (IUCr)

# publications[].label
Mutations in the Esx-3 secretion system confer resistance to multiple chemical scaffolds in Mycobacterium tuberculosis.

# publications[].label
Mycobacterial RNase E cleaves with a distinct sequence preference and controls the degradation rates of most Mycolicibacterium smegmatis mRNAs

# publications[].label
Behavioral and transcriptomic profiling of mice null for Lphn3, a gene implicated in ADHD and addiction.

# publications[].label
Synthesis and evaluation of the 2,4-diaminoquinazoline series as anti-tubercular agents.

# publications[].label
Chemical Genetic Interaction Profiling Reveals Determinants of Intrinsic Antibiotic Resistance in Mycobacterium tuberculosis.

# publications[].label
A Multifaceted Secondary Structure Mimic Based On Piperidinepiperidinones

# publications[].label
An improved statistical method to identify chemical-genetic interactions by exploiting concentration-dependence.

# publications[].label
Crystal structure of Mycobacterium tuberculosis polyketide synthase 11 (PKS11) reveals intermediates in the synthesis of methyl-branched alkylpyrones.

# publications[].label
Improved Phenoxyalkylbenzimidazoles with Activity against Mycobacterium tuberculosis Appear to Target QcrB.

# publications[].label
Deletion of Rv2571c confers resistance to arylamide compounds in Mycobacterium tuberculosis.

# publications[].label
Distinct Bacterial Pathways Influence the Efficacy of Antibiotics against Mycobacterium tuberculosis.

# publications[].label
Analysis of diversity of nucleotide and amino acid distributions in the VD and DJ joining regions in Ig heavy chains.

# publications[].label
A Hidden Markov Model for identifying essential and growth-defect regions in bacterial genomes from transposon insertion sequencing data.

# publications[].label
Efficient retrieval of electron density patterns for modeling proteins by X-ray crystallography

# publications[].publisher
Institute of Electrical and Electronics Engineers (IEEE)

# publications[].label
The context-dependence of amino acid properties.

# publications[].label
Evaluating selection at intermediate scales within genes provides robust identification of genes under positive selection in M. tuberculosis clinical isolates

# publications[].label
Reasoning about beliefs, observability, and information exchange in teamwork

# publications[].label
Metabolic Network for the Biosynthesis of Intra- and Extracellular -Glucans Required for Virulence of Mycobacterium tuberculosis.

# publications[].label
Extraction of rotation invariant signature based on fractal geometry

# publications[].publisher
Institute of Electrical and Electronics Engineers (IEEE)

# publications[].label
A decision-theoretic approach for designing proactive communication in multi-agent teamwork

# publications[].publisher
Association for Computing Machinery (ACM)

# publications[].label
The Mycobacterium tuberculosis Transposon Sequencing Database (MtbTnDB): A Large-Scale Guide to Genetic Conditional Essentiality.

# publications[].label
Functional Whole Genome Screen of Nutrient-Starved Mycobacterium tuberculosis Identifies Genes Involved in Rifampin Tolerance

# publications[].label
Developing synergistic drug combinations to restore antibiotic sensitivity in drug-resistant Mycobacterium tuberculosis

# publications[].label
Rectifying I: three point and continuous fit of the spatial autocorrelation metric, Moran's I, to ideal form

# publications[].label
Glyoxylate detoxification is an essential function of malate synthase required for carbon assimilation in Mycobacterium tuberculosis.

# publications[].publisher
Proceedings of the National Academy of Sciences

# publications[].label
Combining bundle search with buyer coalition formation in electronic markets: A distributed approach through explicit negotiation

# publications[].label
An Adaptive Planner Based on Learning of Planning Performance.

# publications[].label
A Compatibility Approach to Identify Recombination Breakpoints in Bacterial and Viral Genomes

# publications[].publisher
Association for Computing Machinery (ACM)

# publications[].label
Genome analysis of multi- and extensively-drug-resistant tuberculosis from KwaZulu-Natal, South Africa.

# publications[].label
GWAS for quantitative resistance phenotypes in Mycobacterium tuberculosis reveals resistance genes and regulatory regions.

# publications[].label
A formal model of responsibilities in agent-based teams

# publications[].publisher
Association for Computing Machinery (ACM)

# publications[].label
DEVELOPMENT OF NOVEL, NONTOXIC RIFAMYCINS THAT REVERSE DRUG RESISTANCE IN DIFFUSE LARGE BCELL LYMPHOMA (DLBCL)

# publications[].label
High throughput crystallography of TB drug targets.

# publications[].label
Multiplexed strain phenotyping defines consequences of genetic diversity in Mycobacterium tuberculosis for infection and vaccination outcomes

# publications[].label
Identifying genetic determinants of Mycobacterium tuberculosis acid growth arrest by transposon mutagenesis coupled with next-generation sequencing (Tn-seq).

# publications[].label
Resistance of Mycobacterium Tuberculosis to Indole 4-Carboxamides Occurs Through Alterations in Drug Metabolism and Alterations in Tryptophan Biosynthesis

# publications[].label
Recent developments in the PHENIX software for automated crystallographic structure determination.

# publications[].publisher
International Union of Crystallography (IUCr)

# publications[].label
Detecting feature interactions from accuracies of random feature subsets

# publications[].label
Weighting features to recognize 3D patterns of electron density in X-ray protein crystallography

# publications[].label
Automatic modeling of protein backbones in electron-density maps via prediction of Calpha coordinates.

# publications[].publisher
International Union of Crystallography (IUCr)

# publications[].label
Chlorflavonin Targets Acetohydroxyacid Synthase Catalytic Subunit IlvB1 for Synergistic Killing of Mycobacterium tuberculosis.

# publications[].label
Opposing reactions in coenzyme A metabolism sensitize Mycobacterium tuberculosis to enzyme inhibition.

# publications[].publisher
American Association for the Advancement of Science (AAAS)

# publications[].label
T-SEARCH: A program to identify and measure the geometry of cysteine-cysteine tryptophan (C-CW) triad motifs in immunoglobulin superfamily structures and other proteins

# publications[].label
Discovery of a cofactor-independent inhibitor of Mycobacterium tuberculosis InhA.

# publications[].label
An Entropy-based Adaptive Genetic Algorithm for Learning Classification Rules

# publications[].publisher
Institute of Electrical and Electronics Engineers (IEEE)

# publications[].label
Accurate identification of de novo genes in plant genomes using machine learning algorithms

# publications[].label
Inhibition of CorA-Dependent Magnesium Homeostasis Is Cidal in Mycobacterium tuberculosis.

# publications[].label
Evaluation of geometric & probabilistic distance measures to retrieve electron density patterns for protein structure determination

# publications[].label
TRANSIT--A Software Tool for Himar1 TnSeq Analysis.

# publications[].label
Diarylcoumarins inhibit mycolic acid biosynthesis and kill Mycobacterium tuberculosis by targeting FadD32.

# publications[].publisher
Proceedings of the National Academy of Sciences

# publications[].label
Automated structure determination with phenix

# publications[].label
Modeling and verifying multi-agent behaviors using predicate/transition nets

# publications[].publisher
Association for Computing Machinery (ACM)

# publications[].publisher
American Association for the Advancement of Science (AAAS)

# publications[].label
Correlations between secondary structure- and protein-protein interface-mimicry: the interface mimicry hypothesis.

# publications[].label
TEXTAL: a pattern recognition system for interpreting electron density maps.

# publications[].label
First Evaluation of GenoType MTBDRplus 2.0 Performed Directly on Respiratory Specimens in Central America.

# publications[].label
The 1.25 A resolution structure of phosphoribosyl-ATP pyrophosphohydrolase from Mycobacterium tuberculosis.

# publications[].publisher
International Union of Crystallography (IUCr)

# publications[].label
Sterilization of granulomas is common in active and latent tuberculosis despite within-host variability in bacterial killing.

# publications[].label
Tracking changes in user interests with a few relevance judgments

# publications[].publisher
Association for Computing Machinery (ACM)

# publications[].label
Phase variation as a major mechanism of adaptation in Mycobacterium tuberculosis complex.

# publications[].publisher
Proceedings of the National Academy of Sciences

# publications[].label
Functional genomics screening utilizing mutant mouse embryonic stem cells identifies novel radiation-response genes.

# publications[].label
Genetic models of latent tuberculosis in mice reveal differential influence of adaptive immunity.

# publications[].label
Correction for Shelton et al., "Deletion of Rv2571c Confers Resistance to Arylamide Compounds in Mycobacterium tuberculosis".

# publications[].label
Statistical Analysis of Variability in TnSeq Data Across Conditions Using Zero-Inflated Negative Binomial Regression

# publications[].label
Identification of cyclic hexapeptides natural products with inhibitory potency against Mycobacterium tuberculosis

# publications[].label
Distance Metric Learning through Optimization of Ranking

# publications[].publisher
Institute of Electrical and Electronics Engineers (IEEE)

# publications[].label
Tryptophan biosynthesis protects mycobacteria from CD4 T-cell-mediated killing.

# publications[].label
Identifying non-crystallographic symmetry in protein electron-density maps: a feature-based approach.

# publications[].publisher
International Union of Crystallography (IUCr)

# publications[].publisher
Association for Computing Machinery (ACM)

# publications[].label
TEXTAL system: artificial intelligence techniques for automated protein model building.

# publications[].label
Mutations in fbiD (Rv2983) as a novel determinant of resistance to pretomanid and delamanid in Mycobacterium tuberculosis

# publications[].label
Structural genomics approach to drug discovery for Mycobacterium tuberculosis.

# publications[].label
Training Teams with Collaborative Agents

# publications[].label
Structural Similarities and Differences between Two Functionally Distinct SecA Proteins, Mycobacterium tuberculosis SecA1 and SecA2.

# publications[].label
Integrating a spatial reasoner with a resolution theorem-prover

# publications[].label
Automated Conflict Resolution for Air Traffic Management Using Cooperative Multiagent Negotiation

# publications[].publisher
American Institute of Aeronautics and Astronautics (AIAA)

# publications[].label
A d-Phenylalanine-Benzoxazole Derivative Reveals the Role of the Essential Enzyme Rv3603c in the Pantothenate Biosynthetic Pathway of Mycobacterium tuberculosis.

# publications[].label
Variation among genome sequences of H37Rv strains of Mycobacterium tuberculosis from multiple laboratories.

# publications[].label
Use of whole genome sequencing to estimate the mutation rate of Mycobacterium tuberculosis during latent infection.

# publications[].label
A statistical method to identify recombination in bacterial genomes based on SNP incompatibility.

# publications[].label
On the use of intelligent agents as partners in training systems for complex tasks

# publications[].label
-Aminooxyacetic acid derivatives acting as pro-drugs against Mycobacterium tuberculosis

# publications[].label
Polymorphism at the self-incompatibility locus in Solanaceae predates speciation.

# publications[].publisher
Proceedings of the National Academy of Sciences

# publications[].label
Specificity normalization for identifying selective inhibitors in virtual screening

# publications[].label
An adaptive algorithm for learning changes in user interests

# publications[].publisher
Association for Computing Machinery (ACM)

# publications[].label
Combining bundle search with buyer coalition formation in electronic markets: A distributed approach through negotiation

# publications[].label
Biological Profiling Enables Rapid Mechanistic Classification of Phenotypic Screening Hits and Identification of KatG Activation-Dependent Pyridine Carboxamide Prodrugs With Activity Against Mycobacterium tuberculosis.

# publications[].label
A comprehensive characterization of PncA polymorphisms that confer resistance to pyrazinamide.

# publications[].label
Erratum for the Research Article "Opposing reactions in coenzyme A metabolism sensitize Mycobacterium tuberculosis to enzyme inhibition" by E. Ballinger, J. Mosior, T. Hartman, K. Burns-Huang, B. Gold, R. Morris, L. Goullieux, I. Blanc, J. Vaubourgeix, S. Lagrange, L. Fraisse, S. Sans, C. Couturier, E. Bacqu, K. Rhee, S. M. Scarry, J. Aub, G. Yang, O. Ouerfelli, D. Schnappinger, T. R. Ioerger, C. A. Engelhart, J. A. McConnell, K. McAulay, A. Fay, C. Roubert, J. Sacchettini, C. Nathan.

# publications[].publisher
American Association for the Advancement of Science (AAAS)

# publications[].label
Correction to: Natural brominated phenoxyphenols kill persistent and biofilm-incorporated cells of MRSA and other pathogenic bacteria.

# publications[].label
Altered Mycobacterium tuberculosis Cell Wall Metabolism and Physiology Associated With RpoB Mutation H526D.

# publications[].label
Transposon-sequencing across multiple Mycobacterium abscessus isolates reveals significant functional genomic diversity among strains.

# publications[].label
Exploiting Homoplasy in Genome-Wide Association Studies to Enhance Identification of Antibiotic-Resistance Mutations in Bacterial Genomes.

# publications[].label
Mutations in Rv2983 as a novel determinant of resistance to nitroimidazole drugs in Mycobacterium tuberculosis

# publications[].label
Genome-wide phenotypic insights into mycobacterial virulence using Drosophila melanogaster.

# publications[].label
Exploring key orientations at protein-protein interfaces with small molecule probes.

# publications[].label
MmpL3 is the cellular target of the antitubercular pyrrole derivative BM212.

# publications[].publisher
Institute of Electrical and Electronics Engineers (IEEE)

# publications[].label
Global Assessment of Mycobacterium avium subsp. hominissuis Genetic Requirement for Growth and Virulence.

# publications[].label
Determining protein structure from electron-density maps using pattern matching.

# publications[].publisher
International Union of Crystallography (IUCr)

# publications[].label
Erratum for Perkowski et al., "The EXIT Strategy: an Approach for Identifying Bacterial Proteins Exported during Host Infection".

# publications[].label
Forming resource-sharing coalitions: a distributed resource allocation mechanism for self-interested agents in computational grids

# publications[].publisher
Association for Computing Machinery (ACM)

# publications[].label
Cell cycle-associated expression patterns predict gene function in mycobacteria

# publications[].label
Capturing Uncertainty by Modeling Local Transposon Insertion Frequencies Improves Discrimination of Essential Genes.

# publications[].publisher
Institute of Electrical and Electronics Engineers (IEEE)

# publications[].label
TEXTAL - Crystallographic protein model building using AI and pattern recognition

# publications[].label
A proteomics approach for the identification of species-specific immunogenic proteins in the Mycobacterium abscessus complex.

# publications[].label
Modeling site-specific nucleotide biases affecting Himar1 transposon insertion frequencies in TnSeq datasets

# publications[].label
An adaptive planner based on learning of planning performance

# publications[].label
The conserved translation factor LepA is required for optimal synthesis of a porin family in Mycobacterium smegmatis.

# publications[].label
Evaluating minimalist mimics by exploring key orientations on secondary structures (EKOS).

# publications[].label
Perturbation of cytochrome c maturation reveals adaptability of the respiratory chain in Mycobacterium tuberculosis.

# publications[].label
The anti-tubercular callyaerins target the Mycobacterium tuberculosis-specific non-essential membrane protein Rv2113.

# publications[].label
Introduction to selected papers from the 8th International Conference on Bioinformatics and Computational Biology (BICOB 2016).

# publications[].label
Essential but Not Vulnerable: Indazole Sulfonamides Targeting Inosine Monophosphate Dehydrogenase as Potential Leads against Mycobacterium tuberculosis.

# publications[].label
Crystal structures of Mycobacterium tuberculosis S-adenosyl-L-homocysteine hydrolase in ternary complex with substrate and inhibitors.

# publications[].label
On Proactive Helping Behaviors In Teamwork

# publications[].label
MOPAC: motif finding by preprocessing and agglomerative clustering from microarrays.

# publications[].label
Conservation of cys-cys trp structural triads and their geometry in the protein domains of immunoglobulin superfamily members.

# publications[].label
Searching for Representations to Improve Protein Sequence Fold-Class Prediction

# publications[].publisher
Institute of Electrical and Electronics Engineers (IEEE)

# publications[].label
Analysis of protein-ligand interactions using localized stereochemical features

# publications[].label
SELF-INCOMPATIBILITY IN PETUNIA-INFLATA - ISOLATION AND CHARACTERIZATION OF CDNAS ENCODING 3 S-ALLELE-ASSOCIATED PROTEINS

# publications[].label
Anion- Interactions in Computer-Aided Drug Design: Modeling the Inhibition of Malate Synthase by Phenyl-Diketo Acids.

# publications[].label
Normalization of transposon-mutant library sequencing datasets to improve identification of conditionally essential genes.

# publications[].label
A quantitative model of capabilities in multi-agent systems

# publications[].label
SEARCHING FOR REPRESENTATIONS TO IMPROVE PROTEIN-SEQUENCE FOLD-CLASS PREDICTION

# publications[].label
A cytoplasmic peptidoglycan amidase homologue controls mycobacterial cell wall synthesis.

# publications[].label
THE MANIPULATION OF IMAGES TO HANDLE INDETERMINACY IN SPATIAL REASONING

# publications[].label
Genome wide association with quantitative resistance phenotypes in Mycobacterium tuberculosis reveals novel resistance genes and regulatory regions

# publications[].label
Normalization of transposon-mutant library sequencing datasets to improve identification of conditionally essential genes.

# publications[].label
The copper-responsive RicR regulon contributes to Mycobacterium tuberculosis virulence.

# publications[].label
Development of a Novel Lead that Targets M.tuberculosis Polyketide Synthase 13.

# publications[].label
The non-clonality of drug resistance in Beijing-genotype isolates of Mycobacterium tuberculosis from the Western Cape of South Africa.

# publications[].label
Chemical-genetic interaction mapping links carbon metabolism and cell wall structure to tuberculosis drug efficacy.

# publications[].publisher
Proceedings of the National Academy of Sciences

# publications[].label
TnSeq identifies genetic requirements of Mycobacterium tuberculosis for survival under vaccine-induced immunity.

# publications[].label
Front Cover: Discovery of Antimicrobial Lipodepsipeptides Produced by a Serratia sp. within Mosquito Microbiomes (ChemBioChem 15/2018)

# publications[].label
N-methylation of a bactericidal compound as a resistance mechanism in Mycobacterium tuberculosis.

# publications[].publisher
Proceedings of the National Academy of Sciences

# publications[].label
Ribosomal mutations promote the evolution of antibiotic resistance in a multidrug environment.

# publications[].label
A dose-response model for statistical analysis of chemical genetic interactions in CRISPRi screens.

# publications[].label
The myxobacterial antibiotic myxovalargin: Biosynthesis, structural revision, total synthesis and molecular characterization of ribosomal inhibition

# publications[].label
CAST: Collaborative Agents for Simulating Teamwork

# publications[].label
A conserved translation factor is required for optimal synthesis of a membrane protein family in mycobacteria

# publications[].label
Trehalose-6-Phosphate-Mediated Toxicity Determines Essentiality of OtsB2 in Mycobacterium tuberculosis In Vitro and in Mice.

# publications[].label
Improving discrimination of essential genes by modeling local insertion frequencies in transposon mutagenesis data

# publications[].publisher
Association for Computing Machinery (ACM)

# publications[].label
TEXTALTM: Artificial Intelligence Techniques for Automated Protein Structure Determination.

# publications[].label
2-Mercapto-Quinazolinones as Inhibitors of Type II NADH Dehydrogenase and Mycobacterium tuberculosis: Structure-Activity Relationships, Mechanism of Action and Absorption, Distribution, Metabolism, and Excretion Characterization.

# publications[].label
Reannotation of translational start sites in the genome of Mycobacterium tuberculosis.

# publications[].label
High-density transposon mutagenesis in Mycobacterium abscessus identifies an essential penicillin-binding lipo-protein (PBP-lipo) involved in septal peptidoglycan synthesis and antibiotic sensitivity

# publications[].label
A proteomics approach for the identification of species-specific immunogenic proteins in the Mycobacterium abscessus complex

# publications[].label
Leaderless Transcripts and Small Proteins Are Common Features of the Mycobacterial Translational Landscape.

# publications[].label
A multifaceted secondary structure mimic based on piperidine-piperidinones.

# publications[].label
TEXTAL: Al-based structural determination for X-ray protein crystallography

# publications[].publisher
Institute of Electrical and Electronics Engineers (IEEE)

# publications[].label
Multidrug-resistant tuberculosis in panama is driven by clonal expansion of a multidrug-resistant Mycobacterium tuberculosis strain related to the KZN extensively drug-resistant M. tuberculosis strain from South Africa.

# publications[].label
Determining relevant features to recognize electron density patterns in x-ray protein crystallography.

# publications[].label
Natural brominated phenoxyphenols kill persistent and biofilm-incorporated cells of MRSA and other pathogenic bacteria.

# publications[].label
Role-Based and Agent-Oriental Teamwork Modeling.

# publications[].label
SEQUENCE DIVERSITY OF PISTIL S-PROTEINS ASSOCIATED WITH GAMETOPHYTIC SELF-INCOMPATIBILITY IN NICOTIANA-ALATA

# publications[].label
Non-canonical peptidoglycan cross-linking is essential for Mycobacterium tuberculosis acid resistance.

# publications[].label
Structures of Mycobacterium tuberculosis FadD10 protein reveal a new type of adenylate-forming enzyme.

# publications[].label
Generating Parallel Based on Planning Graph Analysis of Predicate/Transition Nets.

# publications[].label
Learning user interest dynamics with a three-descriptor representation

# publications[].label
Introduction to selected papers from the 8th International Conference on Bioinformatics and Computational Biology (BICOB 2016).

# publications[].label
Automated structure solution with the PHENIX suite.

# publications[].label
Identification of cyclic hexapeptides natural products with inhibitory potency against Mycobacterium tuberculosis.

# publications[].label
Maturing Mycobacterial Peptidoglycan Required Non-canonical Crosslinks to Maintain Shape

# publications[].label
Frequently arising ESX-1-associated phase variants influence Mycobacterium tuberculosis fitness in the presence of host and antibiotic pressures.

# publications[].label
Comprehensive Essentiality Analysis of the Mycobacterium tuberculosis Genome via Saturating Transposon Mutagenesis.

# publications[].label
Mutations in pepQ Confer Low-Level Resistance to Bedaquiline and Clofazimine in Mycobacterium tuberculosis.

# publications[].label
Nature-Inspired (di)Azine-Bridged Bisindole Alkaloids with Potent Antibacterial In Vitro and In Vivo Efficacy against Methicillin-Resistant Staphylococcus aureus.

# publications[].label
Use of multiplex allele-specific polymerase chain reaction (MAS-PCR) to detect multidrug-resistant tuberculosis in Panama.

# publications[].label
Mycobacterial RNase E cleaves with a distinct sequence preference and controls the degradation rates of most Mycolicibacterium smegmatis mRNAs.

# publications[].label
Phase variation as a major mechanism of adaptation in Mycobacterium tuberculosis complex

# publications[].label
Drosophila melanogaster is a powerful host model to study mycobacterial virulence

# publications[].label
Modeling and analyzing multi-agent behaviors using predicate/transition nets

# publications[].label
Host-pathogen genetic interactions underlie tuberculosis susceptibility in genetically diverse mice.

# publications[].label
Reducing type i errors in Tn-Seq experiments by correcting the skew in read count distributions

# publications[].publisher
Institute of Electrical and Electronics Engineers (IEEE)

# publications[].label
Cell-Cycle-Associated Expression Patterns Predict Gene Function in Mycobacteria.

# publications[].label
Inhibitors of mycobacterium tuberculosis malate synthase, methods of making and uses thereof

# publications[].label
Peptidoglycan synthesis in Mycobacterium tuberculosis is organized into networks with varying drug susceptibility.

# publications[].publisher
Proceedings of the National Academy of Sciences

# publications[].label
Automated detection of disulfide bridges in electron density maps using linear discriminant analysis

# publications[].publisher
International Union of Crystallography (IUCr)

# publications[].label
Chemical-genetic interaction mapping links carbon metabolism and cell wall structure to tuberculosis drug efficacy

# publications[].label
IMAGERY AND CATEGORIES - THE INDETERMINACY PROBLEM

# publications[].label
A formal model of responsibilities in agent-based teamwork

# publications[].label
Genome-wide Phenotypic Profiling Identifies and Categorizes Genes Required for Mycobacterial Low Iron Fitness.

# publications[].label
Transposon-sequencing across multiple Mycobacterium abscessus isolates reveals significant functional genomic diversity among strains

# publications[].label
Statistical analysis of genetic interactions in Tn-Seq data.

# publications[].label
A Novel 6-Benzyl Ether Benzoxaborole Is Active against Mycobacterium tuberculosis In Vitro.

# publications[].label
A vitamin B transporter in Mycobacterium tuberculosis.

# publications[].label
The anti-tubercular callyaerins target the Mycobacterium tuberculosis -specific non-essential membrane protein Rv2113

# publications[].label
The EXIT Strategy: an Approach for Identifying Bacterial Proteins Exported during Host Infection.

# publications[].label
A mutant fitness assay identifies bacterial interactions in a model ocean hot spot.

# publications[].publisher
Proceedings of the National Academy of Sciences

# publications[].label
Weighting features to recognize 3D patterns of electron density in X-ray protein crystallography.

# publications[].publisher
Institute of Electrical and Electronics Engineers (IEEE)

# publications[].label
TnSeq of Mycobacterium tuberculosis clinical isolates reveals strain-specific antibiotic liabilities.

# publications[].label
The tuberculosis structural genomics consortium: a structural genomics approach to drug discovery.

# publications[].label
Collaborative agents for C2 teamwork simulation

# publications[].label
The Myxobacterial Antibiotic Myxovalargin: Biosynthesis, Structural Revision, Total Synthesis, and Molecular Characterization of Ribosomal Inhibition.

# publications[].label
Statistical analysis of variability in TnSeq data across conditions using zero-inflated negative binomial regression.

# publications[].label
Multiplexed Strain Phenotyping Defines Consequences of Genetic Diversity in Mycobacterium tuberculosis for Infection and Vaccination Outcomes.

# publications[].label
Global assessment of genomic regions required for growth in Mycobacterium tuberculosis.

# publications[].label
MALLET - A Multi-Agent Logic Language for Encoding Teamwork

# publications[].publisher
Institute of Electrical and Electronics Engineers (IEEE)

# publications[].label
FLAME - Fuzzy logic adaptive model of emotions

# publications[].label
Investigation of density and flow relationships in congested traffic with videogrammetric data

# publications[].label
Genetic variation/evolution and differential host responses resulting from in-patient adaptation of Mycobacterium avium

# publications[].label
Impact of immunopathology on the antituberculous activity of pyrazinamide.

# publications[].label
The Rip1 intramembrane protease contributes to iron and zinc homeostasis in Mycobacterium tuberculosis.

# publications[].label
High-resolution phenotypic profiling defines genes essential for mycobacterial growth and cholesterol catabolism.

# publications[].label
Selective Inactivity of Pyrazinamide against Tuberculosis in C3HeB/FeJ Mice Is Best Explained by Neutral pH of Caseum.

# publications[].label
A novel antimycobacterial compound acts as an intracellular iron chelator.

# publications[].label
Correction: TnSeq of Mycobacterium tuberculosis clinical isolates reveals strain-specific antibiotic liabilities.

# publications[].label
Structure-guided discovery of phenyl-diketo acids as potent inhibitors of M. tuberculosis malate synthase.

# publications[].label
Discovery of Novel Oral Protein Synthesis Inhibitors of Mycobacterium tuberculosis That Target Leucyl-tRNA Synthetase.

# publications[].label
The Manipulation of Images to Handle Indeterminacy in Spatial Reasoning

# publications[].label
Correction: Global Assessment of Genomic Regions Required for Growth in Mycobacterium tuberculosis

# publications[].label
Structures of Mycobacterium tuberculosis FadD10 protein reveal a new type of adenylate-forming enzyme (vol 288, pg 18473, 2013)

# publications[].label
High-throughput sequencing enhanced phage display identifies peptides that bind mycobacteria.

# publications[].label
Evaluating selection at intermediate scales within genes provides robust identification of genes under positive selection in M. tuberculosis clinical isolates.

# publications[].label
Mycobacterium tuberculosis dihydrofolate reductase is not a target relevant to the antitubercular activity of isoniazid.

# publications[].label
FURL - a Theory Revision Approach to Learning Fuzzy Rules

# publications[].publisher
Institute of Electrical and Electronics Engineers (IEEE)

# publications[].label
Modeling Site-Specific Nucleotide Biases Affecting Himar1 Transposon Insertion Frequencies in TnSeq Data Sets.

# publications[].label
Combining bundle search with buyer coalition formation in electronic markets: a distributed approach through explicit negotiation

# publications[].publisher
Association for Computing Machinery (ACM)

# publications[].label
Incentive compatible mechanism design for synthetic task allocation in virtual organizations

# publications[].publisher
Institute of Electrical and Electronics Engineers (IEEE)

# publications[].label
Resistance of Mycobacterium tuberculosis to indole 4-carboxamides occurs through alterations in drug metabolism and tryptophan biosynthesis.

# publications[].label
The Mycobacterium tuberculosis transposon sequencing database (MtbTnDB): a large-scale guide to genetic conditional essentiality

# publications[].label
Genetic Variation/Evolution and Differential Host Responses Resulting from In-Patient Adaptation of Mycobacterium avium.

# publications[].label
PHENIX: building new software for automated crystallographic structure determination.

# publications[].publisher
International Union of Crystallography (IUCr)

# publications[].label
The 7-phenyl benzoxaborole series is active against Mycobacterium tuberculosis.

# publications[].label
Abstract 410: Development of novel, non-toxic rifamycins that reverse drug resistance

# publications[].publisher
American Association for Cancer Research (AACR)

# publications[].label
Mutations in the anti-sigma H factor RshA confer resistance to econazole and clotrimazole in Mycobacterium smegmatis.

# publications[].label
Susceptibility of Mycobacterium tuberculosis Cytochrome bd Oxidase Mutants to Compounds Targeting the Terminal Respiratory Oxidase, Cytochrome c.

# publications[].label
Dual ICA to extract interacting sets of genes and conditions from transcriptomic data

# publications[].publisher
Association for Computing Machinery (ACM)

# publications[].label
Genomic and phenotypic insights into antibiotic resistance and virulence of Klebsiella pneumoniae from the environment in Southern Taiwan.

# publications[].label
Database approaches and data representation in structural bioinformatics

# publications[].publisher
Institute of Electrical and Electronics Engineers (IEEE)

# publications[].label
Proactive Information Exchange During Team Cooperation.

# publications[].label
Coalition formation meets information theory

# publications[].label
Identification of new drug targets and resistance mechanisms in Mycobacterium tuberculosis.

# publications[].label
PETEEI: a PET with evolving emotional intelligence

# publications[].publisher
Association for Computing Machinery (ACM)

# publications[].label
Discovery of novel nitrobenzothiazole inhibitors for Mycobacterium tuberculosis ATP phosphoribosyl transferase (HisG) through virtual screening.

# publications[].label
Improving amino-acid identification, fit and C(alpha) prediction using the Simplex method in automated model building.

# publications[].publisher
International Union of Crystallography (IUCr)

# publications[].label
Bayesian analysis of gene essentiality based on sequencing of transposon insertion libraries.

# publications[].label
Peptidoglycan synthesis in Mycobacterium tuberculosis is organized into networks with varying drug susceptibility

# publications[].label
Deletion of SenX3-RegX3, a key two-component regulatory system of Mycobacterium smegmatis, results in growth defects under phosphate-limiting conditions.

# publications[].label
Comparison of transposon and deletion mutants in Mycobacterium tuberculosis: The case of rv1248c, encoding 2-hydroxy-3-oxoadipate synthase.

# publications[].label
Mycobacterium smegmatis HtrA Blocks the Toxic Activity of a Putative Cell Wall Amidase.

# publications[].label
A knowledge-based approach for designing intelligent team training systems

# publications[].publisher
Association for Computing Machinery (ACM)

# publications[].label
FINDMOL: automated identification of macromolecules in electron-density maps.

# publications[].publisher
International Union of Crystallography (IUCr)

# publications[].label
THE TUBERCULOSIS STRUCTURAL GENOMICS CONSORTIUM: A STRUCTURAL GENOMICS APPROACH TO DRUG DISCOVERY

# publications[].label
Phylogeographic Analysis of Mycobacterium kansasii Isolates from Patients with M. kansasii Lung Disease in Industrialized City, Taiwan.

# publications[].publisher
Centers for Disease Control and Prevention (CDC)

# publications[].label
MEDI 204-Structure-based design, synthesis, and biological evaluation of novel inhibitors of Mycobacterium tuberculosis malate synthase

# publications[].label
Genetic models of latent tuberculosis in mice reveal differential control by adaptive immunity

# publications[].label
Crystal structure of circadian clock protein KaiA from Synechococcus elongatus.

# publications[].label
Modeling Capabilities and Workload in Intelligent Agents for Simulating Teamwork

# publications[].label
Learning User Interest Dynamics with a Three-Descriptor Representation

# researcherOn[].label
CDS&E: Cyclic Tetrapeptide Probes for Protein Binding

# researcherOn[].awardedBy.label
National Science Foundation - (Arlington, Virginia, United States)

# researcherOn[].label
Effective Exploitation Of Structural Data For Oncology

# researcherOn[].awardedBy.label
Cancer Prevention and Research Institute of Texas - (Austin, Texas, United States)

# streetAddress
Texas A&M University; Computer Science & Engineering; 3112 TAMU

# etdChairOf[].label
Wollkind, Steven Robert (2004-12). Using multi-agent negotiation techniques for the autonomous resolution of air traffic conflicts. Master's Thesis.

# etdChairOf[].label
Widyantoro, Dwi Hendratmo (2003-12). Concept drift learning and its application to adaptive information filtering. Doctoral Dissertation.

# etdChairOf[].label
DeJesus, Michael A. (2012-05). Bayesian Analysis of Transposon Mutagenesis Data. Master's Thesis.

# etdChairOf[].label
Palmer,  Victor (2007-08). Scaling reinforcement learning to the unconstrained multi-agent domain. Doctoral Dissertation.

# etdChairOf[].label
Gopal, Kreshna (2007-08). Efficient case-based reasoning through feature weighting, and its application in protein crystallography. Doctoral Dissertation.

# etdChairOf[].label
De Jesus Aneiro, Michael A. (2016-12). Statistical Analysis of Transposon Sequencing Data to Determine Essential Genes. Doctoral Dissertation.

# etdChairOf[].label
Pai Karkala, Reetal (2009-05). Fragment Based Protein Active Site Analysis Using Markov Random Field Combinations of Stereochemical Feature-Based Classifications. Doctoral Dissertation.

# etdChairOf[].label
Creel, James Silas (2005-05). Intention is commitment with expectation. Master's Thesis.

# etdChairOf[].label
Rozich, Ryan Timothy (2003-08). A practical method for proactive information exchange within multi-agent teams. Master's Thesis.

# etdChairOf[].label
Nelson, Eric James (2016-12). Learning to Control Linear Time-Invariant Systems with Discrete Time Reinforcement Learning. Master's Thesis.

# etdChairOf[].label
Childs, Kevin (2004-12). Combinatorial motif analysis in yeast gene promoters: the benefits of a biological consideration of motifs. Master's Thesis.

# etdChairOf[].label
He, Linli (2003-05). Mechanism design for distributed task and resource allocation among self-interested agents in virtual organizations. Doctoral Dissertation.