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1.  Advanced significance analysis of microarray data based on weighted resampling: a comparative study and application to gene deletions in Mycobacterium bovis 
Bioinformatics (Oxford, England)  2004;20(3):357-363.
Motivation
When analyzing microarray data, non-biological variation introduces uncertainty in the analysis and interpretation. In this paper we focus on the validation of significant differences in gene expression levels, or normalized channel intensity levels with respect to different experimental conditions and with replicated measurements. A myriad of methods have been proposed to study differences in gene expression levels and to assign significance values as a measure of confidence. In this paper we compare several methods, including SAM, regularized t-test, mixture modeling, Wilk’s lambda score and variance stabilization. From this comparison we developed a weighted resampling approach and applied it to gene deletions in Mycobacterium bovis.
Results
We discuss the assumptions, model structure, computational complexity and applicability to microarray data. The results of our study justified the theoretical basis of the weighted resampling approach, which clearly outperforms the others.
Availability
Algorithms were implemented using the statistical programming language R and available on the author’s web-page.
doi:10.1093/bioinformatics/btg417
PMCID: PMC3128991  PMID: 14960462
2.  GO::TermFinder—open source software for accessing Gene Ontology information and finding significantly enriched Gene Ontology terms associated with a list of genes 
Bioinformatics (Oxford, England)  2004;20(18):3710-3715.
Summary
GO::TermFinder comprises a set of object-oriented Perl modules for accessing Gene Ontology (GO) information and evaluating and visualizing the collective annotation of a list of genes to GO terms. It can be used to draw conclusions from microarray and other biological data, calculating the statistical significance of each annotation. GO::TermFinder can be used on any system on which Perl can be run, either as a command line application, in single or batch mode, or as a web-based CGI script.
Availability
The full source code and documentation for GO::TermFinder are freely available from http://search.cpan.org/dist/GO-TermFinder/
Contact
sherlock@genome.stanford.edu
doi:10.1093/bioinformatics/bth456
PMCID: PMC3037731  PMID: 15297299
3.  Visualizing Information across Multidimensional Post-Genomic Structured and Textual Databases 
Bioinformatics (Oxford, England)  2004;21(8):1659-1667.
Motivation
Visualizing relations among biological information to facilitate understanding is crucial to biological research during the post-genomic era. Although different systems have been developed to view gene-phenotype relations for specific databases, very few have been designed specifically as a general flexible tool for visualizing multidimensional genotypic and phenotypic information together. Our goal is to develop a method for visualizing multidimensional genotypic and phenotypic information and a model that unifies different biological databases in order to present the integrated knowledge using a uniform interface.
Results
We developed a novel, flexible and generalizable visualization tool, called PhenoGenesviewer (PGviewer), which in this paper was used to display gene-phenotype relations from a human-curated database (OMIM) and from an automatic method using a Natural Language Processing tool called BioMedLEE. Data obtained from multiple databases were first integrated into a uniform structure and then organized by PGviewer. PGviewer provides a flexible query interface that allows dynamic selection and ordering of any desired dimension in the databases. Based on users’ queries, results can be visualized using hierarchical expandable trees that present views specified by users according to their research interests. We believe that this method, which allows users to dynamically organize and visualize multiple dimensions, is a potentially powerful and promising tool that should substantially facilitate biological research.
doi:10.1093/bioinformatics/bti210
PMCID: PMC2901923  PMID: 15598839
4.  Visualization of near-optimal sequence alignments 
Bioinformatics (Oxford, England)  2004;20(6):953-958.
Motivation
Mathematically optimal alignments do not always properly align active site residues or well-recognized structural elements. Most near-optimal sequence alignment algorithms display alternative alignment paths, rather than the conventional residue-by-residue pairwise alignment. Typically, these methods do not provide mechanisms for finding effectively the most biologically meaningful alignment in the potentially large set of options.
Results
We have developed Web-based software that displays near optimal or alternative alignments of two protein or DNA sequences as a continuous moving picture. A WWW interface to a C++ program generates near optimal alignments, which are sent to a Java Applet, which displays them in a series of alignment frames. The Applet aligns residues so that consistently aligned regions remain at a fixed position on the display, while variable regions move. The display can be stopped to examine alignment details.
Availability
Available at http://fasta.bioch.virginia.edu/ noptalign. For source code contact the authors at wrp@virginia.edu
Contact
wrp@virginia.edu
doi:10.1093/bioinformatics/bth013
PMCID: PMC2836811  PMID: 14751975
5.  Extracting multiple structural alignments from pairwise alignments: a comparison of a rigorous and a heuristic approach 
Bioinformatics (Oxford, England)  2004;21(7):1002-1009.
Motivation
Multiple structural alignments (MSTAs) provide position-specific information on the sequence variability allowed by protein folds. This information can be exploited to better understand the evolution of proteins and the physical chemistry of polypeptide folding. Most MSTA methods rely on a pre-computed library of pairwise alignments. This library will in general contain conflicting residue equivalences not all of which can be realized in the final MSTA. Hence to build a consistent MSTA, these methods have to select a conflict-free subset of equivalences.
Results
Using a dataset with 327 families from SCOP 1.63 we compare the ability of two different methods to select an optimal conflict-free subset of equivalences. One is an implementation of Reinert et al.’s integer linear programming formulation (ILP) of the maximum weight trace problem (Reinert et al., 1997, Proc. 1st Ann. Int. Conf. Comput. Mol. Biol. (RECOMB-97), ACM Press, New York). This ILP formulation is a rigorous approach but its complexity is difficult to predict. The other method is T-Coffee (Notredame et al., 2000) which uses a heuristic enhancement of the equivalence weights which allow it to use the speed and simplicity of the progressive alignment approach while still incorporating information of all alignments in each step of building the MSTA. We find that although the ILP formulation consistently selects a more optimal set of conflict-free equivalences, the differences are small and the quality of the resulting MSTAs are essentially the same for both methods. Given its speed and predictable complexity, our results show that T-Coffee is an attractive alternative for producing high-quality MSTAs.
Availability
The software for Resolver, our implementation of Reinert et al.’s ILP formulation, and the dataset used in this study are available at http://www.sbc.su.se/~erik/resolver
doi:10.1093/bioinformatics/bti117
PMCID: PMC2692033  PMID: 15531607
6.  VizStruct: exploratory visualization for gene expression profiling 
Motivation
DNA arrays provide a broad snapshot of the state of the cell by measuring the expression levels of thousands of genes simultaneously. Visualization techniques can enable the exploration and detection of patterns and relationships in a complex data set by presenting the data in a graphical format in which the key characteristics become more apparent. The dimensionality and size of array data sets however present significant challenges to visualization. The purpose of this study is to present an interactive approach for visualizing variations in gene expression profiles and to assess its usefulness for classifying samples.
Results
The first Fourier harmonic projection was used to map multi-dimensional gene expression data to two dimensions in an implementation called VizStruct. The visualization method was tested using the differentially expressed genes identified in eight separate gene expression data sets. The samples were classified using the oblique decision tree (OC1) algorithm to provide a procedure for visualization-driven classification. The classifiers were evaluated by the holdout and the cross-validation techniques. The proposed method was found to achieve high accuracy.
Availability
Detailed mathematical derivation of all mapping properties as well as figures in color can be found as supplementary on the web page http://www.cse.buffalo.edu/DBGROUP/bioinformatics/supplementary/vizstruct. All programs were written in Java and Matlab and software code is available by request from the first author.
doi:10.1093/bioinformatics/btg377
PMCID: PMC2607484  PMID: 14693813
7.  ESPD: a pattern detection model underlying gene expression profiles 
Bioinformatics (Oxford, England)  2004;20(6):829-838.
Motivation
DNA arrays permit rapid, large-scale screening for patterns of gene expression and simultaneously yield the expression levels of thousands of genes for samples. The number of samples is usually limited, and such datasets are very sparse in high-dimensional gene space. Furthermore, most of the genes collected may not necessarily be of interest and uncertainty about which genes are relevant makes it difficult to construct an informative gene space. Unsupervised empirical sample pattern discovery and informative genes identification of such sparse high-dimensional datasets present interesting but challenging problems.
Results
A new model called empirical sample pattern detection (ESPD) is proposed to delineate pattern quality with informative genes. By integrating statistical metrics, data mining and machine learning techniques, this model dynamically measures and manipulates the relationship between samples and genes while conducting an iterative detection of informative space and the empirical pattern. The performance of the proposed method with various array datasets is illustrated.
doi:10.1093/bioinformatics/btg486
PMCID: PMC2573998  PMID: 14751997
8.  MathSBML: a package for manipulating SBML-based biological models 
Bioinformatics (Oxford, England)  2004;20(16):2829-2831.
Summary: MathSBML is a Mathematica package designed for manipulating Systems Biology Markup Language (SBML) models. It converts SBML models into Mathematica data structures and provides a platform for manipulating and evaluating these models. Once a model is read by MathSBML, it is fully compatible with standard Mathematica functions such as NDSolve (a differential-algebraic equations solver). MathSBML also provides an application programming interface for viewing, manipulating, running numerical simulations; exporting SBML models; and converting SBML models in to other formats, such as XPP, HTML and FORTRAN. By accessing the full breadth of Mathematica functionality, MathSBML is fully extensible to SBML models of any size or complexity.
Availability: Open Source (LGPL) at http://www.sbml.org and http://www.sf.net/projects/sbml.
doi:10.1093/bioinformatics/bth271
PMCID: PMC1409765  PMID: 15087311
9.  Mining frequent patterns in protein structures: a study of protease families 
Bioinformatics (Oxford, England)  2004;20(Suppl 1):i77-i85.
Motivation
Analysis of protein sequence and structure databases usually reveal frequent patterns (FP) associated with biological function. Data mining techniques generally consider the physicochemical and structural properties of amino acids and their microenvironment in the folded structures. Dynamics is not usually considered, although proteins are not static, and their function relates to conformational mobility in many cases.
Results
This work describes a novel unsupervised learning approach to discover FPs in the protein families, based on biochemical, geometric and dynamic features. Without any prior knowledge of functional motifs, the method discovers the FPs for each type of amino acid and identifies the conserved residues in three protease subfamilies; chymotrypsin and subtilisin subfamilies of serine proteases and papain subfamily of cysteine proteases. The catalytic triad residues are distinguished by their strong spatial coupling (high interconnectivity) to other conserved residues. Although the spatial arrangements of the catalytic residues in the two subfamilies of serine proteases are similar, their FPs are found to be quite different. The present approach appears to be a promising tool for detecting functional patterns in rapidly growing structure databases and providing insights in to the relationship among protein structure, dynamics and function.
doi:10.1093/bioinformatics/bth912
PMCID: PMC1201446  PMID: 15262784

Results 1-9 (9)