An important application of CRISPR interference (CRISPRi) technology is for identifying chemical-genetic interactions (CGIs). Discovery of genes that interact with exposure to antibiotics can yield insights to drug targets and mechanisms of action or resistance. The objective is to identify CRISPRi mutants whose relative abundance is suppressed (or enriched) in the presence of a drug when the target protein is depleted, reflecting synergistic behavior. Different sgRNAs for a given target can induce a wide range of protein depletion and differential effects on growth rate. The effect of sgRNA strength can be partially predicted based on sequence features. However, the actual growth phenotype depends on the sensitivity of cells to depletion of the target protein. For essential genes, sgRNA efficiency can be empirically measured by quantifying effects on growth rate. We observe that the most efficient sgRNAs are not always optimal for detecting synergies with drugs. sgRNA efficiency interacts in a non-linear way with drug sensitivity, producing an effect where the concentration-dependence is maximized for sgRNAs of intermediate strength (and less so for sgRNAs that induce too much or too little target depletion). To capture this interaction, we propose a novel statistical method called CRISPRi-DR (for Dose-Response model) that incorporates both sgRNA efficiencies and drug concentrations in a modified dose-response equation. We use CRISPRi-DR to re-analyze data from a recent CGI experiment in Mycobacterium tuberculosis to identify genes that interact with antibiotics. This approach can be generalized to non-CGI datasets, which we show via an CRISPRi dataset for E. coli growth on different carbon sources. The performance is competitive with the best of several related analytical methods. However, for noisier datasets, some of these methods generate far more significant interactions, likely including many false positives, whereas CRISPRi-DR maintains higher precision, which we observed in both empirical and simulated data.

BACKGROUND: Deep sequencing of transposon mutant libraries (or TnSeq) is a powerful method for probing essentiality of genomic loci under different environmental conditions. Various analytical methods have been described for identifying conditionally essential genes whose tolerance for insertions varies between two conditions. However, for large-scale experiments involving many conditions, a method is needed for identifying genes that exhibit significant variability in insertions across multiple conditions. RESULTS: In this paper, we introduce a novel statistical method for identifying genes with significant variability of insertion counts across multiple conditions based on Zero-Inflated Negative Binomial (ZINB) regression. Using likelihood ratio tests, we show that the ZINB distribution fits TnSeq data better than either ANOVA or a Negative Binomial (in a generalized linear model). We use ZINB regression to identify genes required for infection of M. tuberculosis H37Rv in C57BL/6 mice. We also use ZINB to perform a analysis of genes conditionally essential in H37Rv cultures exposed to multiple antibiotics. CONCLUSIONS: Our results show that, not only does ZINB generally identify most of the genes found by pairwise resampling (and vastly out-performs ANOVA), but it also identifies additional genes where variability is detectable only when the magnitudes of insertion counts are treated separately from local differences in saturation, as in the ZINB model.

BACKGROUND: Phylogeny estimation for bacteria is likely to reflect their true evolutionary histories only if they are highly clonal. However, recombination events could occur during evolution for some species. The reconstruction of phylogenetic trees from an alignment without considering recombination could be misleading, since the relationships among strains in some parts of the genome might be different than in others. Using a single, global tree can create the appearance of homoplasy in recombined regions. Hence, the identification of recombination breakpoints is essential to better understand the evolutionary relationships of isolates among a bacterial population. RESULTS: Previously, we have developed a method (called ACR) to detect potential breakpoints in an alignment by evaluating compatibility of polymorphic sites in a sliding window. To assess the statistical significance of candidate breakpoints, we propose an extension of the algorithm (ptACR) that applies a permutation test to generate a null distribution for comparing the average local compatibility. The performance of ptACR is evaluated on both simulated and empirical datasets. ptACR is shown to have similar sensitivity (true positive rate) but a lower false positive rate and higher F1 score compared to basic ACR. When used to analyze a collection of clinical isolates of Staphylococcus aureus, ptACR finds clear evidence of recombination events in this bacterial pathogen, and is able to identify statistically significant boundaries of chromosomal regions with distinct phylogenies. CONCLUSIONS: ptACR is an accurate and efficient method for identifying genomic regions affected by recombination in bacterial genomes.

TnSeq has become a popular technique for determining the essentiality of genomic regions in bacterial organisms. Several methods have been developed to analyze the wealth of data that has been obtained through TnSeq experiments. We developed a tool for analyzing Himar1 TnSeq data called TRANSIT. TRANSIT provides a graphical interface to three different statistical methods for analyzing TnSeq data. These methods cover a variety of approaches capable of identifying essential genes in individual datasets as well as comparative analysis between conditions. We demonstrate the utility of this software by analyzing TnSeq datasets of M. tuberculosis grown on glycerol and cholesterol. We show that TRANSIT can be used to discover genes which have been previously implicated for growth on these carbon sources. TRANSIT is written in Python, and thus can be run on Windows, OSX and Linux platforms. The source code is distributed under the GNU GPL v3 license and can be obtained from the following GitHub repository: https://github.com/mad-lab/transit.

Transposon mutagenesis experiments enable the identification of essential genes in bacteria. Deep-sequencing of mutant libraries provides a large amount of high-resolution data on essentiality. Statistical methods developed to analyze this data have traditionally assumed that the probability of observing a transposon insertion is the same across the genome. This assumption, however, is inconsistent with the observed insertion frequencies from transposon mutant libraries of M. tuberculosis. We propose a modified Binomial model of essentiality that can characterize the insertion probability of individual genes in which we allow local variation in the background insertion frequency in different non-essential regions of the genome. Using the Metropolis-Hastings algorithm, samples of the posterior insertion probabilities were obtained for each gene, and the probability of each gene being essential is estimated. We compared our predictions to those of previous methods and show that, by taking into consideration local insertion frequencies, our method is capable of making more conservative predictions that better match what is experimentally known about essential and non-essential genes.

Abstract Motivation: Next-generation sequencing affords an efficient analysis of transposon insertion libraries, which can be used to identify essential genes in bacteria. To analyse this high-resolution data, we present a formal Bayesian framework for estimating the posterior probability of essentiality for each gene, using the extreme-value distribution to characterize the statistical significance of the longest region lacking insertions within a gene. We describe a sampling procedure based on the Metropolis–Hastings algorithm to calculate posterior probabilities of essentiality while simultaneously integrating over unknown internal parameters. Results: Using a sequence dataset from a transposon library for Mycobacterium tuberculosis, we show that this Bayesian approach predicts essential genes that correspond well with genes shown to be essential in previous studies. Furthermore, we show that by using the extreme-value distribution to characterize genomic regions lacking transposon insertions, this method is capable of identifying essential domains within genes. This approach can be used for analysing transposon libraries in other organisms and augmenting essentiality predictions with statistical confidence scores. Availability: A python script implementing the method described is available for download from http://saclab.tamu.edu/essentiality/. Contact: [email protected] or [email protected] Supplementary information: Supplementary data are available at Bioinformatics online.

BACKGROUND: Knowledge of which genes are essential to the survival of an organism is critical to understanding the function of genes, and for the identification of potential drug targets for antimicrobial treatment. Previous statistical methods for assessing essentiality based on sequencing of tranposon libraries have usually limited their assessment to strict 'essential' or 'non-essential' categories. However, this binary view of essentiality does not accurately represent the more nuanced ways the growth of an organism might be affected by the disruption of its genes. In addition, these methods often limit their analysis to open-reading frames. We propose a novel method for analyzing sequence data from transposon mutant libraries using a Hidden Markov Model (HMM), along with formulas to adapt the parameters of the model to different datasets for robustness. This approach allows for the clustering of insertion sites into distinct regions of essentiality across the entire genome in a statistically rigorous manner, while also allowing for the detection of growth-defect and growth-advantage regions. RESULTS: We evaluate the performance of a 4-state HMM on a sequence dataset of M. tuberculosis transposon mutants. We also test the HMM on several synthetic datasets representing different levels of transposon insertion density and sequence coverage. We show that the HMM produces results that are highly correlated with previous assignments of essentiality for this organism. We also show that it detects growth-defect and growth-advantage genes previously shown to impair or enhance growth when disrupted. CONCLUSIONS: A 4-state HMM provides an improved way of analyzing Tn-seq data and assessing different levels of essentiality that enables not only the characterization of essential and non-essential genes, but also genes whose disruption leads to impairment (or enhancement) of growth.

Database approaches are widely used in structural bioinformatics, since ab initio techniques are often computationally prohibitive, and the structure of biological macromolecules are typically derived from a limited set of motifs. There are several issues and challenges that arise when developing methods to enable efficient database retrieval. For example, how can complex data be represented efficiently, and what should be the size and composition of the database? In this work, we discuss some of these challenges, based on a crystallographic protein model-building program called TEXTAL. In particular, we discuss how structural information on amino acids is represented (as numeric features), how difficult it is to recognize amino acids (based on 3D electron density patterns), and what types of examples (and how many of them) need to be stored in the database. These insights are potentially useful in many other related applications, such as structure-based drug design, protein-protein interaction, discriminating nucleic acids and proteins in hybrid complexes, etc.

UNLABELLED: X-ray crystallography is the most widely used method to determine the 3D structure of protein molecules. One of the most difficult steps in protein crystallography is model-building, which consists of constructing a backbone and then amino acid side chains into an electron density map. Interpretation of electron density maps represents a major bottleneck in protein structure determination pipelines, and thus, automated techniques to interpret maps can greatly improve the throughput. We have developed WebTex, a simple and yet powerful web interface to TEXTAL, a program that automates this process of fitting atoms into electron density maps. TEXTAL can also be downloaded for local installation. AVAILABILITY: Web interface, downloadable binaries and documentation at http://textal.tamu.edu

MALLET, a multi-agent logic language for encoding teamwork, is intended to enable expression of teamwork emulating human teamwork, allowing experimentation with different levels and forms of inferred team intelligence. A consequence of this goal is that the actual teamwork behavior is determined by the level of intelligence built into the underlying system as well as the semantics of the language. In this paper, we give the design objectives, the syntax, and an operational semantics for MALLET in terms of a transition system. We show how the semantics can be used to reason about the behaviors of team-based agents. The semantics can also be used to guide the implementation of various MALLET interpreters emulating different forms of team intelligence, as well as formally study the properties of team-based agents specified in MALLET. We have explored various forms of proactive information exchange behavior embodied in human teamwork using the CAST system, which implements a built-in MALLET interpreter.

Despite the significant progress in multi-agent communication decision, existing research does not address two important issues: 1) how to optimize timing and currency of communication when dealing with dynamically changing information, and 2) what kinds of communication decision interdependency exist in a team and how this interdependency impacts a single agent's communication decision. To provide a more comprehensive solution to the communication problem, we present a new model, DTPC (decision-theoretic proactive communication), which uses statistical analysis of information production and need of team members and a dynamic decision-theoretic determination of communication policies. We show experimentally how DTPC decreases communication load while improving performance of distributed teamwork.

In electronic markets, both bundle search and buyer coalition formation are profitable purchasing strategies for buyers who need to buy small amount of goods and have no bargaining power. It is valuable to combine these two purchasing strategies for buyers to obtain greater discounts based on the different discount policies of multiple sellers. In this paper, we present a distributed mechanism that allows buyers to use both purchasing strategies. The mechanism includes a very efficient heuristic bundle search algorithm and a distributed coalition formation scheme, which is based on an explicit negotiation protocol. The resulting coalitions are stable in the core. The simulation results show that the cost to buyers is close to the optimal cost. Increasing the number of buyers who are involved in the coalition formation process does not increase the communication load caused by the negotiation between two buyers.

Inefficient case retrieval is a major problem in many case-based reasoning systems, especially when case matching is expensive and the case-base is large. In this paper, we present a two-phase approach where an inexpensive feature-based method is used to jind a set of potential matches and a more expensive and accurate case matching method is used to make the jinal selection. This approach has been successfully employed in TEXTALTM, a system that retrieves previously solved 3D patterns of electron density from a database to determine the structure of proteins. Electron density patterns are characterized by numeric features and an appropriate distance measure is used to efficiently jilter good matches through an exhaustive search of the database. These matches are then examined using a computationally expensive density correlation procedure based on jinding an optimal superposition between 3D patterns. We provide an empirical and theoretical analysis of some of the keys issues related to this method. In particular, we dejine a model for estimating how approximate various featurebased similarity measures are (relative to an objective matching metric), and determine its relation to the number of cases that should be jiltered from a given database to make the approach effective.

Keeping track of changes in user interests from a document stream with a few relevance judgments is not an easy task. To tackle this problem, we propose a novel method that integrates (1) pseudo-relevance feedback mechanism, (2) assumption about the persistence of user interests and (3) incremental method for data clustering. This approach has been empirically evaluated using Reuters-21578 corpus in a setting for information filtering. The experiment results reveal that it significantly improves the performances of existing user-interest-tracking systems without requiring additional, actual relevance judgments.

How agents accomplish a goal task in a multi-agent system is usually specified by multi-agent plans built from basic actions (e.g. operators) of which the agents are capable. The plan specification provides the agents with a shared mental model for how they are supposed to collaborate with each other to achieve the common goal. Making sure that the plans are reliable and fit for the purpose for which they are designed is a critical problem with this approach. To address this problem, this paper presents a formal approach to modeling and analyzing multi-agent behaviors using Predicate/Transition (PrT) nets, a high- level formalism of Petri nets. We model a multi-agent problem by representing agent capabilities as transitions in PrT nets. To analyze a multi-agent PrT model, we adapt the planning graphs as a compact structure for reachability analysis, which is coherent to the concurrent semantics. We also demonstrate that one can analyze whether parallel actions specified in multi-agent plans can be executed in parallel and whether the plans can achieve the goal by analyzing the dependency relations among the transitions in the PrT model.

Fuzzy rules have been shown to be very useful in modeling relationships between variables that have a high degree of uncertainty or ambiguity. A major question in regards to learning fuzzy rule bases is how to handle interactions between rules of overlapping coverage. Structures, such as Yager's (1993, 1998) HPS (hierarchical prioritized structure), have been proposed to answer this question. In this paper, we present our system of learning a hierarchical fuzzy rule base named FURL (for Fuzzy Rule Learner). FURL takes advantage of the properties of HPS to learn hierarchical levels of fuzzy rules. FURL applies machine-learning techniques from theory revision such as credit assignment and repair to fuzzy rules. We also discuss the results of testing FURL on multiple benchmark datasets and finally discuss our results.

In this paper we present a novel incremental hierarchical clustering (IHC) algorithm. Our approach aims to construct a hierarchy that satisfies homogeneity and monotonicity properties. Working in a bottom-up fashion, a new instance is placed in the hierarchy and a sequence of hierarchy restructuring processes is performed only in regions that have been affected by the presence of the new instance. The experimental results on a variety of domains demonstrate that our algorithm is not sensitive to input ordering, can produce a quality cluster hierarchy, and is efficient in terms of computational time.

In a multi-agent system, how agents accomplish a goal task is usually specified by multi-agent plans built from basic actions (e.g. operators) of which the agents are capable. A critical problem with such an approach is how can the designer make sure the plans are reliable. To tackle this problem, this paper presents a formal approach for modeling and analyzing multi-agent behaviors using Predicate/Transition (PrT) nets, a high-level formalism of Petri nets. We construct a multi-agent model by representing agent capabilities as transitions. To verify a multi-agent PrT model, we adapt the planning graphs as a compact structure for the reachability analysis. We also demonstrate that, based on the PrT model, whether parallel actions specified in multi-agent plans can be executed in parallel and whether the plans guarantee the achievement of the goal can be verified by analyzing the dependency relations among the transitions.

A new method of feature extraction with a rotation invariant property is presented. One of the main contributions of this study is that a rotation invariant signature of 2D contours is selected based on fractal theory. The rotation invariant signature is a measure of the fractal dimensions, which is rotation invariant based on a series of central projection transform (CPT) groups. As the CPT is applied to a 2D object, a unique contour is obtained. In the unfolding process, this contour is further spread into a central projection unfolded curve, which can be viewed as a periodic function due to the different orientations of the pattern. We consider the unfolded curves to be non-empty and bounded sets in IR/sup n/, and the central projection unfolded curves with respect to the box computing dimension are rotation invariant. Some experiments with positive results have been conducted. This approach is applicable to a wide range of areas such as image analysis, pattern recognition etc.

Learning users' interest categories is challenging in a dynamic environment like the Web because they change over time. This article describes a novel scheme to represent a user's interest categories, and an adaptive algorithm to learn the dynamics of the user's interests through positive and negative relevance feedback. We propose a three-descriptor model to represent a user's interests. The proposed model maintains a long-term interest descriptor to capture the user's general interests and a short-term interest descriptor to keep track of the user's more recent, faster-changing interests. An algorithm based on the three-descriptor representation is developed to acquire high accuracy of recognition for long-term interests, and to adapt quickly to changing interests in the short-term. The model is also extended to multiple three-descriptor representations to capture a broader range of interests. Empirical studies confirm the effectiveness of this scheme to accurately model a user's interests and to adapt appropriately to various levels of changes in the user's interests.

The ability to express emotions is important for creating believable interactive characters. To simulate emotional expressions in an interactive environment, an intelligent agent needs both an adaptive model for generating believable responses, and a visualization model for mapping emotions into facial expressions. Recent advances in intelligent agents and in facial modeling have produced effective algorithms for these tasks independently. We describe a method for integrating these algorithms to create an interactive simulation of an agent that produces appropriate facial expressions in a dynamic environment. Our approach to combining a model of emotions with a facial model represents a first step towards developing the technology of a truly believable interactive agent which has a wide range of applications from designing intelligent training systems to video games and animation tools.

In this paper, we describe a new scheme to learn dynamic user's interests in an automated information filtering and gathering system running on the Internet. Our scheme is aimed to handle multiple domains of long-term and short-term user's interests simultaneously, which is learned through positive and negative user's relevance feedback. We developed a 3-descriptor approach to represent the user's interest categories. Using a learning algorithm derived for this representation, our scheme adapts quickly to significant changes in user interest, and is also able to learn exceptions to interest categories.