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  • Ohio Biosciences Library
    Visualization Blue Collar Computing Computational Science Engineering Research Applications Networking Research Systems Research Research Report Ralph Regula School Computational Chemistry Grid Summer Institute Young Women s Summer Institute HPC and Software Training Current Training and Events Educators Online OCS Lecture Series Press Releases Headlines Calendar of Events About OSC Media Kit OSC Media Contacts Staff Directory Visit OSC Supercomputing Support Networking Support Research Blue Collar Computing Analytics Bioinformatics Biomedical Sciences and Visualization Computational Science Engineering Research Cyberinfrastructure and Software Development Systems Research Research Archive Related Links Collaborations Get an Account Research Partners Research Video Library Research Reports 2010 Research Highlights 2009 Research Highlights 2008 Research Report 2007 Research Report Bioinformatics Software Development Projects Ohio Biosciences Library Principal Investigator Eric Stahlberg OSC Funding Source Internal Research and Development An HPC software library for use in developing bioinformatics analysis programs built on the foundations of CBL and PCBL The Ohio Biosciences Library is a suite of high performance bioinformatics applications designed for use on large memory SMP and cluster computing systems alike The library provides an ability to conduct application level performance and benchmark evaluations of HPC systems used in bioinformatics and computational biology research The Ohio Biosciences Library employs routines from

    Original URL path: http://archive.osc.edu/research/bioinformatics/projects/obl/index.shtml (2013-06-13)
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  • Genome-wide Location Analysis of b-catenin/TCF Target Genes using Custom Human Promoter Microarray
    Series Press Releases Headlines Calendar of Events About OSC Media Kit OSC Media Contacts Staff Directory Visit OSC Supercomputing Support Networking Support Research Blue Collar Computing Analytics Bioinformatics Biomedical Sciences and Visualization Computational Science Engineering Research Cyberinfrastructure and Software Development Systems Research Research Archive Related Links Collaborations Get an Account Research Partners Research Video Library Research Reports 2010 Research Highlights 2009 Research Highlights 2008 Research Report 2007 Research Report Bioinformatics Software Development Projects Genome wide Location Analysis of b catenin TCF Target Genes using Custom Human Promoter Microarray Principal Investigator Chunming Liu University of Texas Medical Branch Funding agency UTMB start up fund Wnt b catenin signaling plays essential roles in both development and tumorigenesis Moon et al 2004 Wnt signaling is mediated by b catenin which binds T cell factor TCF in the nucleus and activates gene transcription In the absence of Wnt stimulation a protein complex consisting of Glycogen synthase kinase 3 GSK 3 Casein kinase I alpha CKIa and tumor suppressor proteins Axin and Adenomatous polyposis coli APC phosphorylates b catenin Liu et al 2002 The phosphorylated b catenin is degraded by the ubiquitin proteasome pathway Liu et al 1999 However mutations in the Wnt b catenin signaling pathway prevent b catenin degradation Liu et al 2002 Accumulated b catenin enters the nucleus and forms a complex with TCF and activates TCF target genes that ultimately lead to tumor formation e g colorectal cancers Although gene expression microarray studies have revealed some b catenin TCF related genes many of them are actually not regulated by b catenin TCF directly To identify the complete direct target genes that b catenin TCF transcribes a custom human promoter array has been designed locating all possible candidate TCF binding sites throughout the human genome 60 mer probes are specifically designed based

    Original URL path: http://archive.osc.edu/research/bioinformatics/projects/bcatenin/index.shtml (2013-06-13)
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  • DIMSA Project
    Computational Science Engineering Research Cyberinfrastructure and Software Development Systems Research Research Archive Related Links Collaborations Get an Account Research Partners Research Video Library Research Reports 2010 Research Highlights 2009 Research Highlights 2008 Research Report 2007 Research Report Bioinformatics Software Development Projects DIMSA Project Principal Investigator Michael Frietas Funding Agency TBD Duration October 2005 December 2005 The DIMSA Data Intensive Mass Spect Analysis project aims to automate the process of Mass Spect data analysis pipeline which is an integral part of the proteomics research The DIMSA project includes all steps of the MS MS analysis pipeline input file conversion database searching output file conversion and integrative analysis of the result XML based the DIMSA project is easily extensible to additional search engines and analysis modules A prototype of the pipeline is currently under implementation This will have all the primitive components of the pipeline It will include Input user interface for input parameter selection data file upload and submission of the searching jobs Output user interface for displaying the results from several search engines The first page should present a comprehensive look of the results which could be a table that lists all the protein hits in the first column and

    Original URL path: http://archive.osc.edu/research/bioinformatics/projects/dimsa/index.shtml (2013-06-13)
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  • Genome-wide identification of Arabidopsis coiled-coil proteins and establishment of the ARABI-COIL database
    Educators Online OCS Lecture Series Press Releases Headlines Calendar of Events About OSC Media Kit OSC Media Contacts Staff Directory Visit OSC Supercomputing Support Networking Support Research Blue Collar Computing Analytics Bioinformatics Biomedical Sciences and Visualization Computational Science Engineering Research Cyberinfrastructure and Software Development Systems Research Research Archive Related Links Collaborations Get an Account Research Partners Research Video Library Research Reports 2010 Research Highlights 2009 Research Highlights 2008 Research Report 2007 Research Report Bioinformatics Software Development Projects Genome wide identification of Arabidopsis coiled coil proteins and establishment of the ARABI COIL database Principal Investigator Iris Meier Ohio State University CoPI Eric Stahlberg OSC Funding Agency National Science Foundation Description Increasing evidence demonstrates the importance of long coiled coil proteins for the spatial organization of cellular processes Although several protein classes with long coiled coil domains have been studied in animals and yeast our knowledge about plant long coiled coil proteins is very limited The repeat nature of the coiled coil sequence motif often prevents the simple identification of homologs of animal coiled coil proteins by generic sequence similarity searches As a consequence counterparts of many animal proteins with long coiled coil domains like lamins golgins or microtubule organization center components have not been identified yet in plants Here all Arabidopsis proteins predicted to contain long stretches of coiled coil domains were identified by applying the algorithm MultiCoil to a genome wide screen A searchable protein database ARABI COIL http www coiled coil org arabidopsis was established that integrates information on number size and position of predicted coiled coil domains with subcellular localization signals transmembrane domains and available functional annotations ARABI COIL serves as a tool to sort and browse Arabidopsis long coiled coil proteins to facilitate the identification and selection of candidate proteins of potential interest for specific research areas

    Original URL path: http://archive.osc.edu/research/bioinformatics/projects/coiled-coil/index.shtml (2013-06-13)
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  • Investigating Coiled-coil Proteins in the Arabidopsis ORFeome
    2007 Research Report Bioinformatics Software Development Projects Investigating Coiled coil Proteins in the Arabidopsis ORFeome Principal Investigator Iris Meier Ohio State University CoPI Eric Stahlberg OSC Funding Agency National Science Foundation Duration 09 2002 09 2005 Description Proteins containing long coiled coil domains have been found in animals and yeast to be involved in attaching signaling molecules to the large solid state components of the cell such as membrane systems centromeres centrosomes or the nuclear scaffold There is growing evidence that they play an important role in the spatial and temporal regulation of protein positioning in the cell In contrast this group of proteins has been barely investigated in plants The goal of this Arabidopsis 2010 project is to identify all Arabidopsis proteins that contain long stretches of coiled coil domains and to functionally characterize a subgroup that has been implicated in plant nuclear envelope targeting Preliminary research has identified over 1000 predicted coiled coil proteins in the Arabidopsis genome almost 70 of which are unknown proteins Examples of coiled coil proteins with sorting signals for all major compartments of the plant cell have been identified To begin a functional investigation of this large and uncharacterized protein class in Arabidopsis a twofold approach will be taken 1 An automated computational platform will be established on a multi processor cluster that will allow a to identify all long 50 amino acids or longer coiled coil proteins in Arabidopsis by structural prediction algorithms b to integrate the output with a battery of sequence and structure analysis programs to establish predicted nuclear organellar and membrane localization family relationships functional domains and other relevant features and c to create a publicly available searchable database of Arabidopsis coiled coil proteins to which experimental data such as subcellular location protein protein interactions and mutant phenotypes will

    Original URL path: http://archive.osc.edu/research/bioinformatics/projects/arabidopsis/index.shtml (2013-06-13)
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  • FPGA Assisted Equine Gene Annotation and Custom Microarray (Genechip®)
    Account Research Partners Research Video Library Research Reports 2010 Research Highlights 2009 Research Highlights 2008 Research Report 2007 Research Report Bioinformatics Software Development Projects FPGA Assisted Equine Gene Annotation and Custom Microarray Genechip Principal Investigator Alicia Bertone Ohio State Unviersity Funding agency Ohio State University Duration 5 2002 4 2004 DNA microarrays are small solid supports containing thousands of gene sequences that are immobilized or attached at fixed locations This technologic advance has revolutionized the basic approach to research as hundreds to thousands of genes can be analyzed simultaneously under identical conditions to assess various biological models including disease therapy or experimental manipulation Mammalian commercial microarrays currently exist for human mouse and rat but not for the horse Sequence selection and probe design are crucial for the reliability sensitivity and specificity of DNA microarrays The completed human genome consists of 3 000 mega bases and 35 000 genes distributed across 23 chromosomes The mouse genome is in similar size and gene number except with 3 fewer chromosomes These genetic data are good templates in comparative analysis to annotate gene information of other organisms However huge computation is involved in sequence similarity comparisons Currently a public nucleotide sequence database maintained at the National Center for Biotechnology Information NCBI contains 20 000 equine related sequences which are sufficient for the generation of the first equine DNA microarray Several challenges exist for the equine DNA microarray design 1 There is no public algorithm and software available for DNA microarray design 2 Not all available equine sequence data are suitable for DNA microarray 3 There is significant data redundancy and replication in the equine public database Hence the data need to be pruned 4 Significant equine gene data with unknown function need to be annotated by comparative analysis against the annotated human and mouse

    Original URL path: http://archive.osc.edu/research/bioinformatics/projects/horse_gene/index.shtml (2013-06-13)
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  • SignalSleuth Software
    Get an Account Renew Project Bioinformatics Biomedical Sciences and Visualization Blue Collar Computing Computational Science Engineering Research Applications Networking Research Systems Research Research Report Ralph Regula School Computational Chemistry Grid Summer Institute Young Women s Summer Institute HPC and Software Training Current Training and Events Educators Online OCS Lecture Series Press Releases Headlines Calendar of Events About OSC Media Kit OSC Media Contacts Staff Directory Visit OSC Supercomputing Support Networking Support Research Blue Collar Computing Analytics Bioinformatics Biomedical Sciences and Visualization Computational Science Engineering Research Cyberinfrastructure and Software Development Systems Research Research Archive Related Links Collaborations Get an Account Research Partners Research Video Library Research Reports 2010 Research Highlights 2009 Research Highlights 2008 Research Report 2007 Research Report Bioinformatics Software Development Projects SignalSleuth Software Principal Investigator Quinn Li Miami University Funding Source NSF An application for detecting frequent patterns in upstream regions SignalSleuth is a high performance application employing the CBL libraries and their PCBL counterparts for conducting rapid yet exhaustive genome wide pattern analysis The application originated as the result of a multi way partnership between Dave Strenski of Cray Inc Quinn Li and Johnny Loke of Miami University and OSC to identify key patterns in the near and

    Original URL path: http://archive.osc.edu/research/bioinformatics/projects/sig_sleuth/index.shtml (2013-06-13)
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  • Expression Profile of Genes Involved in Angiopoietin 2-induced Astrocytoma Invasion
    and Events Educators Online OCS Lecture Series Press Releases Headlines Calendar of Events About OSC Media Kit OSC Media Contacts Staff Directory Visit OSC Supercomputing Support Networking Support Research Blue Collar Computing Analytics Bioinformatics Biomedical Sciences and Visualization Computational Science Engineering Research Cyberinfrastructure and Software Development Systems Research Research Archive Related Links Collaborations Get an Account Research Partners Research Video Library Research Reports 2010 Research Highlights 2009 Research Highlights 2008 Research Report 2007 Research Report Bioinformatics Software Development Projects Expression Profile of Genes Involved in Angiopoietin 2 induced Astrocytoma Invasion Principal Investigator Shiyuan Cheng University of Pittsburgh Funding agency National Institute of Health Malignant astrocytomas have the ability to diffusely invade into surrounding brain tissues making them incurable by surgical removal even when combined with adjuvant radiation chemotherapy and or immunotherapy We have previously reported that the overexpression of angiopoietin 2 Ang2 leads to the acquisition of invasiveness in engineered U87MG intracranial astrocytomas in mice through the activation of MMP 2 However U87MG as well as other established astrocytoma cell lines contain genetic mutations alterations in pathways such as p53 and PTEN rendering the precise determination of the molecular mechanisms of invasion difficult Therefore we have utilized a minimally genetically altered human astrocyte cell line that stably expresses Ang2 and forms invasive tumors resembling human WHO grade III anaplastic astrocytomas in the murine brain To begin to explore the mechanisms of Ang2 induced astrocytoma invasion we employed Affymetrix GeneChip HG U133A to identify genes differentially expressed in both U87MG and the constructed astrocytic model systems parental versus Ang2 expressing clones Shared alterations and unique differences in genes and pathways involved in the induction of tumor invasion were identified in the two model systems Ang2 promotes glioma cell invasion in the brain of animals demonstrated by two genetically distinct orthotopic models

    Original URL path: http://archive.osc.edu/research/bioinformatics/projects/angio/index.shtml (2013-06-13)
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