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"... 36 D. S. Roos and others Mining the P. falciparum genome database any nucleated cell in any tissue within these organisms (Frenkel 1973). While the behaviour of these parasites is strikingly different, their basic biochemistry, genetics, and subcellular architecture are strikingly similar. All apico ..."
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36 D. S. Roos and others Mining the P. falciparum genome database any nucleated cell in any tissue within these organisms (Frenkel 1973). While the behaviour of these parasites is strikingly different, their basic biochemistry, genetics, and subcellular architecture are strikingly similar. All apicomplexan parasites synthesize pyrimidines de novo, making antifolate treatment a mainstay for anti-parasite chemotherapy; all are purine auxotrophs, raising interest in purine salvage enzymes as possible targets for new drug treatments (Ullman & Carter 1995). All replicate in haploid form, but undergo sexual recombination in the de � nitive host (mosquitoes for Plasmodium, cats for Toxoplasma, etc.) (Frenkel 1973; Levine 1988). All of these parasites exhibit a distinctive ‘apical complex ’ of organelles, for which the phylum Apicomplexa is named: including specialized secretory organelles (rhoptries and micronemes), and cytoskeletal elements (the conoid and associated structures of unknown composition or function) (Chobotar & Scholtyseck 1982). The precise function of these organelles is unknown, but they are thought to be involved in host cell attachment and invasion. Microneme contents are secreted upon host cell contact, and rhoptry contents are released coincident with the establishment of the intracellular parasitophorous vacuole within which replicating parasites reside (Carruthers & Sibley 1997). Apicomplexan parasites also harbour a variety of other unusual organelles. The inner membrane complex—a � attened patchwork of vesicles—is central to the peculiar mode of division observed in these parasites (endodyogeny, endopolyogeny, schizogeny) (Shef � eld &
unknown title
"... 36 D. S. Roos and others Mining the P. falciparum genome database any nucleated cell in any tissue within these organisms (Frenkel 1973). While the behaviour of these parasites is strikingly different, their basic biochemistry, genetics, and subcellular architecture are strikingly similar. All apico ..."
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36 D. S. Roos and others Mining the P. falciparum genome database any nucleated cell in any tissue within these organisms (Frenkel 1973). While the behaviour of these parasites is strikingly different, their basic biochemistry, genetics, and subcellular architecture are strikingly similar. All apicomplexan parasites synthesize pyrimidines de novo, making antifolate treatment a mainstay for anti-parasite chemotherapy; all are purine auxotrophs, raising interest in purine salvage enzymes as possible targets for new drug treatments (Ullman & Carter 1995). All replicate in haploid form, but undergo sexual recombination in the definitive host (mosquitoes for Plasmodium, cats for Toxoplasma, etc.) (Frenkel 1973; Levine 1988). All of these parasites exhibit a distinctive ‘apical complex ’ of organelles, for which the phylum Apicomplexa is named: including specialized secretory organelles (rhoptries and micronemes), and cytoskeletal elements (the conoid and associated structures of unknown composition or function) (Chobotar & Scholtyseck 1982). The precise function of these organelles is unknown, but they are thought to be involved in host cell attachment and invasion. Microneme contents are secreted upon host cell contact, and rhoptry contents are released coincident with the establishment of the intracellular parasitophorous vacuole within which replicating parasites reside (Carruthers & Sibley 1997). Apicomplexan parasites also harbour a variety of other unusual organelles. The inner membrane complex—a flattened patchwork of vesicles—is central to the peculiar mode of division observed in these parasites
Journal of Biomedical Informatics 40 (2007) 5–16 Methodological Review Data integration and genomic medicine www.elsevier.com/locate/yjbin
, 2005
"... Genomic medicine aims to revolutionize health care by applying our growing understanding of the molecular basis of disease. Research in this arena is data intensive, which means data sets are large and highly heterogeneous. To create knowledge from data, researchers must integrate these large and di ..."
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Genomic medicine aims to revolutionize health care by applying our growing understanding of the molecular basis of disease. Research in this arena is data intensive, which means data sets are large and highly heterogeneous. To create knowledge from data, researchers must integrate these large and diverse data sets. This presents daunting informatic challenges such as representation of data that is suitable for computational inference (knowledge representation), and linking heterogeneous data sets (data integration). Fortunately, many of these challenges can be classified as data integration problems, and technologies exist in the area of data integration that may be applied to these challenges. In this paper, we discuss the opportunities of genomic medicine as well as identify the informatics challenges in this domain. We also review concepts and methodologies in the field of data integration. These data integration concepts and methodologies are then aligned with informatics challenges in genomic medicine and presented as potential solutions. We conclude this paper with challenges still not addressed in genomic medicine and gaps that remain in data integration research to facilitate genomic medicine.
1 JIBtools: a Strategy to Reduce the Bioinformatics Analysis Gap
"... The aim of the Journal of Integrative Bioinformatics (JIB) is to provide a free-of-charge open access and peer-reviewed platform for original research articles in all aspects of integrative bioinformatics. Over the last ten years, the editorial board accompanied the process and trends in integrative ..."
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The aim of the Journal of Integrative Bioinformatics (JIB) is to provide a free-of-charge open access and peer-reviewed platform for original research articles in all aspects of integrative bioinformatics. Over the last ten years, the editorial board accompanied the process and trends in integrative bioinformatics and perceives a strong tendency towards a glut of tools and databases. As a consequence, a strategic decision was made to reduce the increasing Bioinformatics Analysis Gap by adding an additional focus to JIB as a platform for tool-related publications. 1.1 Data as Blessing and Curse The progress in molecular biology, ranging from experimental data acquisition on individual genes and proteins, over post-genomics technologies, such as RNA-seq, to phenotyping, proteomics, systems biology and integrative bioinformatics aims to capture the big picture of entire biological systems [1]. As a consequence of this revolution, the amount of data in the life sciences has exploded. The wave of new technologies, for example in genomics, is enabling data to be generated at unprecedented scales [2]. As of February 2013, NCBI Genbank provides access to more than 162 million sequences and PubMed comprises over 22 million citations for biomedical literature from MEDLINE, life science journals, and online books. The number of
Knowledge-Intensive Case-Based Support for Automated Explanation of Biological Phenomena
"... Abstract. The rapid growth of data stored in molecular biology-related databases has stimulated the development of integrative tools for retrieval and presentation of the data in the form of, e.g., biological association networks. We argue that a general and specific knowledge-based approach may pro ..."
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Abstract. The rapid growth of data stored in molecular biology-related databases has stimulated the development of integrative tools for retrieval and presentation of the data in the form of, e.g., biological association networks. We argue that a general and specific knowledge-based approach may provide substantial support for automated reconstruction of networks which otherwise tend to be large and, eventually, unreadable. This knowledge-based approach introduces a novel strategy with the potential to greatly enhance the explanatory power of automatically generated biological association networks. We discuss the motivation for a study of the process an expert employs while building a network, and suggest that a series of expert sessions be used as a case library for future reference. An example of a biological problem and the shape of its solution is described, and the types of knowledge involved are discussed. 1
by
, 2011
"... ii The bioinformatics applications often involve many computational components and massive data sets, which are very difficult to be deployed on a single computing machine. In this thesis, we designed a data-intensive computing platform for bioinformatics applications using virtualization technologi ..."
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ii The bioinformatics applications often involve many computational components and massive data sets, which are very difficult to be deployed on a single computing machine. In this thesis, we designed a data-intensive computing platform for bioinformatics applications using virtualization technologies and high performance computing (HPC) infrastructures with the concept of multi-tier architecture, which can seamlessly integrate the web user interface (presentation tier), scientific workflow (logic tier) and computing infrastructure (data/computing tier). We demonstrated our platform on two bioinformatics projects. First, we redesigned and deployed the cotton marker database (CMD)
