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Bioinformatics and Bioengineering Conference, 2001. Proceedings of the IEEE 2nd International Symposium on

Date 4-6 Nov. 2001

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  • Proceedings 2nd Annual IEEE International Symposium on Bioinformatics and Bioengineering (BIBE 2001)

    Publication Year: 2001
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  • Author index

    Publication Year: 2001 , Page(s): 278 - 279
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    Freely Available from IEEE
  • Utilizing multiple bioinformatics information sources: an XML database approach

    Publication Year: 2001 , Page(s): 73 - 80
    Cited by:  Papers (2)
    Save to Project icon | Request Permissions | Click to expandQuick Abstract | PDF file iconPDF (49 KB) |  | HTML iconHTML  

    Biological databanks have proven useful to bioscience researchers, especially in the analysis of raw data. Computational tools for sequence identification, structural analysis, and visualization have been built to access these databanks. This paper describes a way to utilize these resources (both data and tools) by integrating different biological databanks into a unified XML framework. An interface to access the embedded bioinformatic tools for this common model is built by leveraging the query language of XML database management system. The proposed framework has been implemented with the emphasis of reusing the existing bioinformatic data and tools. This paper describes the overall architecture of this prototype and some design issues View full abstract»

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  • Texture-based 3D brain imaging

    Publication Year: 2001 , Page(s): 136 - 143
    Cited by:  Papers (1)
    Save to Project icon | Request Permissions | Click to expandQuick Abstract | PDF file iconPDF (288 KB) |  | HTML iconHTML  

    Different modalities in biomedical imaging, like CT, MRI and PET scanners,, provide detailed cross-sectional views of the human anatomy. The imagery obtained from these scanning devices are typically large-scale data sets whose sizes vary from several hundred megabytes to about one hundred gigabytes, making them impossible to be stored on a regular local hard drive. San Diego Supercomputer Center (SDSC) maintains a high-performance storage system (HPSS) where these large-scale data sets can be stored. Members of the National Partnership for Advanced Computational Infrastructure (NPACI) have implemented a Scalable Visualization Toolkit (Vistools), which is used to access the data sets stored on HPSS and also to develop different applications on top of the toolkit. 2D cross-sectional images are extracted from the data sets stored oft HPSS using Vistools, and these 2D cross-sections are then transformed into smaller hierarchical representations using a wavelet transformation. This makes it easier to transmit them over the network and allows for progressive image refinement. The transmitted 2D cross-sections are then transformed and reconstructed into a 3D volume. The 3D reconstruction has been implemented using texture-mapping functions of Java3D. Sub-volumes that represent a region of interest are transmitted and rendered at a higher resolution than the rest of the data set View full abstract»

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  • PSST... the probabilistic sequence search tool

    Publication Year: 2001 , Page(s): 33 - 40
    Cited by:  Papers (1)
    Save to Project icon | Request Permissions | Click to expandQuick Abstract | PDF file iconPDF (443 KB) |  | HTML iconHTML  

    Whole genome comparison and clustering cannot be routinely performed without access to significant resources. If as expected, repositories continue to grow at the current rate, increasingly large and expensive systems will be required in order to maintain the status quo. The high-proportion of uncharacterised gene-sequences, combined with the fact that the majority of sequence analysis techniques are alignment-based, raises the possibility that alternative approaches might be able to identify relationships that have otherwise been missed. There is a need for alternative ways to predict function. PSST is an analysis tool with parallels to both pairwise algorithms and multiple motif-based pattern approaches. It is significantly faster than BLAST, and for some families including GPCRs, the tool is more sensitive and selective as well. For others it is worse. This paper describes the algorithm, its implementation, its evaluation against a diverse set of protein families, and discusses the reasons behind its behaviour View full abstract»

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  • Supporting remote user defined functions in heterogeneous biological databases

    Publication Year: 2001 , Page(s): 144 - 152
    Cited by:  Papers (1)
    Save to Project icon | Request Permissions | Click to expandQuick Abstract | PDF file iconPDF (357 KB) |  | HTML iconHTML  

    Similar to most scientific studies, biological analyses demand a great deal of computations and simulations involving sophisticated tools that are often found geographically distributed over the Internet. A worldwide effort in genomics research has resulted in a powerful collection of publicly available sequence analysis tools. These tools often require specialized local services and domain knowledge to function correctly, rendering them unlikely candidates for integration into remote database applications. Thus, integration of heterogeneous "functions" still remains an open problem. Providing a reasonable framework for seamless integration of these tools with database query engines will enable application developers to exploit and harness the power of these effective analysis tools. In this paper, we present an integration framework for such tools by enabling access to them in a user transparent way as part of database queries. In our system, such online tools are abstracted as remote user defined functions (RUDF). An extended SQL DDL language, called the Internet Function Definition Language (IFDL), is presented for the specification and definition of RUDFs. The interface between database system and the Internet is implemented using a layer based on a language called the Hypertext Query Language (HTQL). The separation of IFDL, DDL, HTQL and SQL DML offers several optimization opportunities and makes it possible to develop an architecture for interoperability of heterogeneous databases with RUDFs in more simple and efficient ways View full abstract»

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  • An algebra for semantic interoperability of information sources

    Publication Year: 2001 , Page(s): 174 - 182
    Cited by:  Papers (5)
    Save to Project icon | Request Permissions | Click to expandQuick Abstract | PDF file iconPDF (118 KB) |  | HTML iconHTML  

    Resolving heterogeneity among the various biological information systems is a crucial problem if we wish to gain value from the many distributed resources available to us. For example, information from multiple protein databases (e.g., Swiss-Prot and PDB) might need to be composed to answer queries posed by end-users. Problems of heterogeneity in hardware, operating systems, interfaces and data structures have been widely addressed, but issues of diverse semantics have been handled mainly in an ad-hoc fashion. This paper highlights the ONION (ONtology compositION) system that enables semantic interoperation among various information sources by articulating the ontologies associated with them. An articulation focuses on the semantically relevant intersection of information resources. Although the generation of articulations (semantic correspondences between the ontologies) cannot be fully automated, we take a semi-automatic approach. ONION uses heuristic algorithms for the automatic generation of suggested articulations. This paper outlines an algebra for ontology composition based on their articulations. We show the properties of the algebraic operators and how they depend upon the articulation functions that generate the articulations. Query optimization is enabled based on the properties of the algebraic operators View full abstract»

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  • Querying phylogenies visually

    Publication Year: 2001 , Page(s): 3 - 10
    Cited by:  Papers (1)  |  Patents (1)
    Save to Project icon | Request Permissions | Click to expandQuick Abstract | PDF file iconPDF (116 KB) |  | HTML iconHTML  

    Querying and visualization of phylogenetic databases remain a great challenge due to their inherent complex structures. Popular phylogenetic databases such as Tree of Life and TreeBASE do not support flexible querying through query languages for the exploration of their contents. The query facility employed in these databases is usually limited to complex interfaces or is too limited to be useful for many applications. The most striking shortcoming of these systems is that they do not treat phylogenies (trees) as first citizens. In this paper, we introduce a novel visual query language for phylogenetic databases in which trees are recognized as basic units. We also introduce a Web based query interface, based on this language, for querying any tree like structure, either on the Web (e.g. Tree of Life), or in traditional relational databases (e.g. TreeBASE). As an aside, the mapping technique used in our system makes it possible to interoperate between a variety of heterogeneous phylogenetic databases. Finally, we demonstrate that the basic tree manipulation operators proposed in this paper can be used to form unlimited types of tree queries that were not possible in popular phylogenetic databases until now View full abstract»

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  • Interrelated two-way clustering: an unsupervised approach for gene expression data analysis

    Publication Year: 2001 , Page(s): 41 - 48
    Cited by:  Papers (26)
    Save to Project icon | Request Permissions | Click to expandQuick Abstract | PDF file iconPDF (169 KB) |  | HTML iconHTML  

    DNA arrays can be used to measure the expression levels of thousands of genes simultaneously. Most research is focusing on interpretation of the meaning of the data. However, the majority of methods are supervised, with less attention having been paid to unsupervised approaches which are important when domain knowledge is incomplete or hard to obtain. In this paper we present a new framework for unsupervised analysis of gene expression data which applies an interrelated two-way clustering approach to the gene expression matrices. The goal of clustering is to find important gene patterns and perform cluster discovery on samples. The advantage of this approach is that we can dynamically use the relationships between the groups of genes and samples while iteratively clustering through both gene-dimension and sample-dimension. We illustrate the method on gene expression data from a study of multiple sclerosis patients. The experiments demonstrate the effectiveness of this approach View full abstract»

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  • Medical applications of radiation micro-force

    Publication Year: 2001
    Save to Project icon | Request Permissions | Click to expandQuick Abstract | PDF file iconPDF (623 KB) |  | HTML iconHTML  

    The general direction of this research is measurement of sound and vibration in response to a micro-force. The main hypothesis is that by measuring the sound and/or vibration resulting from such small forces we will be able to obtain important information about the object. The micro-force, which is in mN range, is produced by the radiation force of ultrasound, and the resulting vibration is in nanometer or angstrom range. The stress field is confined to a small region with a few hundred microns in diameter. We have shown that by measuring the acoustic field resulting from such vibrations, which are in low (kHz) frequency range, we can estimate some of the mechanical properties of objects. We have also used this method to image tissue at high resolutions and detect small particles. This imaging technology promises a wide range of medical applications, including imaging organs, detection of arterial calcifications and breast microcalcifications, and evaluation of the structural integrity of implants View full abstract»

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  • Investigation of ultrasound image based correction of intraoperative brain shift

    Publication Year: 2001 , Page(s): 254 - 261
    Save to Project icon | Request Permissions | Click to expandQuick Abstract | PDF file iconPDF (168 KB) |  | HTML iconHTML  

    Stereotactic navigational systems are being incorporated into an increasing number of neurosurgical procedures. Preoperatively acquired 3D images are used for planning the procedure, and are also employed in intraoperative navigations to help localize and resect brain lesions. However, as the operation progresses, multiple factors contribute to changes that limit the accuracy of the navigation based on pre-operative images alone. Our method to correct for brain shift involves the use of ultrasound intraoperatively to update patient specific pre-operative MRI scans using a physics based dynamic model. To validate the imaging and modeling process, a phantom was designed that simulates the brain and its shifting patterns resulting from several of the clinical factors present during a brain operation. MRI and ultrasound datasets were acquired for several permutations of phantom parameters. Deformation algorithms were then applied to the phantom data to demonstrate the efficacy of this approach as a method to effectively update the pre-operatively acquired MRI data during an operation View full abstract»

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  • GIMS-a data warehouse for storage and analysis of genome sequence and functional data

    Publication Year: 2001 , Page(s): 15 - 22
    Cited by:  Papers (2)
    Save to Project icon | Request Permissions | Click to expandQuick Abstract | PDF file iconPDF (166 KB) |  | HTML iconHTML  

    Effective analysis of genome sequences and associated functional data requires access to many different kinds of biological information. For example, when analysing gene expression data, it may be useful to have access to the sequences upstream of the genes, or to the cellular location of their protein products. Such information is currently stored in different formats at different sites in a way that does not readily allow integrated analyses. The Genome Information Management System (GIMS) is an object database that integrates genome sequence data with functional data on the transcriptome and on protein-protein interactions in a single data warehouse. We have used GIMS to store the Saccharomyces cerevisiae (yeast) genome and to demonstrate how the integrated storage of diverse kinds of genomic data can be beneficial for analysing data using context-rich queries and analyses. GIMS allows data to be stored in a way that reflects the underlying mechanisms in the organism, and permits complex questions to be asked of the data. This paper provides an overview of the GIMS system and describes some analyses that illustrate its use for analysing functional data sets for S. cerevisiae View full abstract»

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  • An XML application for genomic data interoperation

    Publication Year: 2001 , Page(s): 97 - 103
    Save to Project icon | Request Permissions | Click to expandQuick Abstract | PDF file iconPDF (166 KB) |  | HTML iconHTML  

    As the eXtensible Markup Language (XML) becomes a popular or standard language for exchanging data over the Internet/Web, there are a growing number of genome Web sites that make their data available in XML format. Publishing genomic data in XML format alone would not be that useful if there is a lack of development of software applications that could take advantage of the XML technology to process these XML-formatted data. This paper illustrates the usefulness of XML in representing and interoperating genomic data between two different data sources (Snyder's laboratory at Yale and SGD at Stanford). In particular, we compare the locations of transposon insertions in the yeast DNA sequences that have been identified by BLAST searches with the chromosomal locations of the yeast open reading frames (ORFs) stored in SGD. Such a comparison allows us to characterize the transposon insertions by indicating whether they fall into any ORFs (which may potentially encode proteins that possess essential biological functions). To implement this XML-based interoperation, we used NCBIs "blastall" (which gives an XML output option) and SGD's yeast nucleotide sequence dataset to establish a local blast server. Also, we converted the SGD's ORF location data file (which is available in tab-delimited formal) into an XML document based on the BIOML (BIOpolymer Markup Language) standard View full abstract»

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  • An intelligent assistant for navigation of visually impaired people

    Publication Year: 2001 , Page(s): 230 - 235
    Cited by:  Papers (4)  |  Patents (1)
    Save to Project icon | Request Permissions | Click to expandQuick Abstract | PDF file iconPDF (92 KB) |  | HTML iconHTML  

    This paper presents the navigation methodology employed by an intelligent assistant (agent) for people with disabilities. In particular, the intelligent assistant, called Tyflos, would help a visually impaired user to be partially independent and able to walk and work in a 3D dynamic environment. The Tyflos system carries two vision cameras and captures images from the surrounding 3D environment, either by the user's command or in a continuous mode (video), then it converts these images into verbal descriptions for each image into a verbal communication with the user. In other words the system plays the role of human assistant, who describes to the user the 3D visual environment View full abstract»

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  • Medical decision-making and collaborative reasoning

    Publication Year: 2001 , Page(s): 161 - 165
    Cited by:  Papers (1)
    Save to Project icon | Request Permissions | Click to expandQuick Abstract | PDF file iconPDF (98 KB) |  | HTML iconHTML  

    An overview is presented of different constraints in conventional medical decision-making for improving collaborative reasoning. When designing and implementing an effective assisted diagnoses system it is imperative to make a complete study of reasoning processes used by physicians every day. We are particularly interested in studying the process of conventional decision-making when, at the first stage, a physician faces a diagnosis decision and, later, when this decision is made by several physicians, that is, when collaborative medical reasoning is involved. The design of an architecture that supports the requirements of medical practices in this framework is presented View full abstract»

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  • PRECIS: an automated pipeline for producing concise reports about proteins

    Publication Year: 2001 , Page(s): 57 - 64
    Save to Project icon | Request Permissions | Click to expandQuick Abstract | PDF file iconPDF (58 KB) |  | HTML iconHTML  

    There have been several attempts at addressing the problem of annotating sequence data computationally. Annotation generation can be considered a pipeline of processes: first harvesting data from a variety of data sources, then distilling and transforming it into a form more appropriate for the end database. This task is usually performed by human annotators, a solution that is clearly not scaleable. There have been several attempts to mimic some of these pipelines in software. However, these have generally focused on low level annotation, such as database cross-references, or by harvesting data from computational techniques such as gene finding or similarity searches. Higher level annotation such as that seen in the PRINTS database is usually formed from data that is free text, or only partly structured. This presents a much greater computational challenge. Therefore we studied the pipeline that is used to generate annotation for the PRINTS database, and have developed prototype software that reflects and automates this pipeline. As this software operates primarily on data culled from the SWISS-PROT database, we have called it PRECIS (Protein Reports Engineered from Concise Information in SWISS-PROT). This software is currently being used to generate annotation for the prePRINTS database. As the output is a structured report detailing the function, structure and disease associations of a protein, and providing literature references and keywords we believe it will be of more generic use. The software is available on request from mitchell@bioinf.man.ac.uk View full abstract»

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  • An automated approach to modelling class II MHC alleles and predicting peptide binding

    Publication Year: 2001 , Page(s): 81 - 88
    Cited by:  Patents (3)
    Save to Project icon | Request Permissions | Click to expandQuick Abstract | PDF file iconPDF (208 KB) |  | HTML iconHTML  

    We present an automated method for constructing 3D models of class II MHC structures that uses constraint logic programming to select side-chain conformations. The resulting models are used by a "peptide threading" program that attempts to predict peptides from a protein sequence that will bind strongly to particular MHC alleles. This method follows a comparative modelling approach in basing the model structures on experimentally determined MHC-peptide structures. However, constraints are used to ease open the peptide binding groove so that the modelled MHC structure is a less specific fit for the co-crystallised peptide in the starting structure. Preliminary results indicate that MHC models that have been constructed in this way enable the peptide threading program to make binding predictions that are comparable with those obtained when using experimentally determined MHC structures View full abstract»

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  • Chemosensory adaptation in an electronic nose

    Publication Year: 2001 , Page(s): 223 - 229
    Cited by:  Papers (1)
    Save to Project icon | Request Permissions | Click to expandQuick Abstract | PDF file iconPDF (513 KB) |  | HTML iconHTML  

    This article presents a computational mechanism inspired by the process of chemosensory adaptation in the mammalian olfactory system. The algorithm operates on multiple subsets of the sensory space, generating a family of discriminant functions for different volatile compounds. A set of selectivity coefficients is associated to each discriminant function on the basis of its behavior in the presence of mixtures. These coefficients are employed to form a weighted average of the discriminant functions and establish a feedback signal that reduces the contribution of certain sensory inputs, inhibiting the overall selectivity of the system to previously detected analytes. The algorithm is validated on a database of organic solvents using an array of temperature-modulated metal-oxide chemoresistors View full abstract»

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  • Discovering common structural motifs from SSU 16 S ribosomal RNA secondary structures

    Publication Year: 2001 , Page(s): 104 - 111
    Save to Project icon | Request Permissions | Click to expandQuick Abstract | PDF file iconPDF (139 KB) |  | HTML iconHTML  

    Some structural motifs, like tetra-loops, in ribosomal RNA are known to functionally implicate in virtually every aspect of protein synthesis. Our aim in this study is to discover common structural motifs (CSMs), which are related to specific domains or functions, within the secondary structures of ribosomal RNAs in a data set constructed. After applying data mining techniques to mine the common structural motifs, a machine learning approach is used to find significant discriminating common structural motifs from groups of organisms. By applying to several data sets constructed in this study, it suggests that the CSMs can provide effective information to classify organisms and help biologists understand the functions of ribosomal RNA. From the experiments of the classification of organisms and the construction of phylogenetic trees by CSMs mined, we find our approach is promising View full abstract»

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  • Optimized seamless integration of biomolecular data

    Publication Year: 2001 , Page(s): 23 - 32
    Cited by:  Papers (3)
    Save to Project icon | Request Permissions | Click to expandQuick Abstract | PDF file iconPDF (75 KB) |  | HTML iconHTML  

    Today, scientific data is inevitably digitized, stored in a variety of heterogeneous formats, and is accessible over the Internet. Scientists need to access an integrated view of multiple remote or local heterogeneous data sources. They then integrate the results of complex queries and apply further analysis and visualization to support the task of scientific discovery. Building a digital library for scientific discovery requires accessing and manipulating data extracted from flat files or databases, documents retrieved from the Web, as well as data that is locally materialized in warehouses or is generated by software. We consider several tasks to provide optimized and seamless integration of biomolecular data. Challenges to be addressed include capturing and representing source capabilities; developing a methodology to acquire and represent metadata about source contents and access costs; and decision support to select sources and capabilities using cost based and semantic knowledge, and generating low cost query evaluation plans View full abstract»

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  • Development of a robotic device for MRI-guided interventions in the breast

    Publication Year: 2001 , Page(s): 201 - 208
    Cited by:  Papers (11)  |  Patents (1)
    Save to Project icon | Request Permissions | Click to expandQuick Abstract | PDF file iconPDF (379 KB) |  | HTML iconHTML  

    The objective of this work was to develop a robotic apparatus for MR-guided biopsy and therapeutic interventions in the breast. This device facilitates (i) conditioning of the breast, by setting the orientation and degree of compression, (ii) definition of the interventional probe trajectory, by setting the height and angulation of a probe guide and (iii) positioning of an interventional probe, by setting the depth of insertion. The apparatus is fitted with appropriate computer-controlled degrees of freedom for optimal approach for delivering and monitoring interventions with MR-guidance, such as diagnostic or therapeutic trans-cannula or subcutaneous minimally invasive procedures. The entire device is constructed of MR compatible material, i.e. non-magnetic and non-conductive, to eliminate artifacts and distortion of the local magnetic field. The apparatus is remotely controlled by means of ultrasonic actuators and a graphics user interface, providing real-time MR-guided planning and monitoring of the operation View full abstract»

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  • Gene classification using expression profiles: a feasibility study

    Publication Year: 2001 , Page(s): 191 - 200
    Cited by:  Papers (3)  |  Patents (1)
    Save to Project icon | Request Permissions | Click to expandQuick Abstract | PDF file iconPDF (144 KB) |  | HTML iconHTML  

    As various genome sequencing projects have already been completed or are near completion, genome researchers are shifting their focus to functional genomics. Functional genomics represents the next phase, that expands the biological investigation to studying the functionality of genes of a single organism as well as studying and correlating the functionality of genes across many different organisms. Recently developed methods for monitoring genome-wide mRNA expression changes hold the promise of allowing us to inexpensively gain insights into the function of unknown genes. In this paper we focus on evaluating the feasibility of using supervised machine learning methods for determining the function of genes based solely on their expression profiles. We experimentally evaluate the performance of traditional classification algorithms such as support vector machines and k-nearest neighbors on the yeast genome, and present new approaches for classification that improve the overall recall with moderate reductions in precision. Our experiments show that the accuracies achieved for different classes varies dramatically. In analyzing these results we show that the achieved accuracy is highly dependent on whether or not the genes of that class were significantly active during the various experimental conditions, suggesting that gene expression profiles can become a viable alternative to sequence similarity searches provided that the genes are observed under a wide range of experimental conditions View full abstract»

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  • Audio and vision-based evaluation of parkinson~s disease from discourse video

    Publication Year: 2001 , Page(s): 245 - 252
    Save to Project icon | Request Permissions | Click to expandQuick Abstract | PDF file iconPDF (255 KB) |  | HTML iconHTML  

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  • Comparing trees in a phylogenetic relationship repository

    Publication Year: 2001 , Page(s): 166 - 173
    Save to Project icon | Request Permissions | Click to expandQuick Abstract | PDF file iconPDF (328 KB) |  | HTML iconHTML  

    Scientists are able to use many different phylogenetic analysis tools to assist them in their research. The data collection and data analysis processes can take days or weeks to complete. Having this data available in a repository would reduce this process time and allow researchers to spend more time analyzing data instead of collecting it. We collected data for 21 completely sequenced genomes and created an intuitive interface for browsing the genomes. The interface allows users to search this data including the pre-calculated phylogenetic trees that are stored in the database. We have also developed a new method for comparing a large set of phylogenetic trees so users can search the database based on a user given hypothesis tree View full abstract»

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  • Applying data warehouse concepts to gene expression data management

    Publication Year: 2001 , Page(s): 65 - 72
    Cited by:  Papers (2)
    Save to Project icon | Request Permissions | Click to expandQuick Abstract | PDF file iconPDF (76 KB)  

    In this paper we present a method for applying data warehouse and on-line analytical processing concepts to gene expression data management. This method has been employed in developing the data management system that is used to host Gene Logic's GeneExpress(R) database products View full abstract»

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