Now showing items 1-13 of 13

    • Cloud Computing for Comparative Genomics 

      Wall, Dennis Paul; Kudtarkar, Parul; Fusaro, Vincent Alfred; Pivovarov, Rimma; Patil, Prasad; Tonellato, Peter J (BioMed Central, 2010)
      Background: Large comparative genomics studies and tools are becoming increasingly more compute-expensive as the number of available genome sequences continues to rise. The capacity and cost of local computing infrastructures ...
    • COSMOS: Python library for massively parallel workflows 

      Gafni, Erik; Luquette, Lovelace J.; Lancaster, Alex K.; Hawkins, Jared B.; Jung, Jae-Yoon; Souilmi, Yassine; Wall, Dennis P.; Tonellato, Peter J. (Oxford University Press, 2014)
      Summary: Efficient workflows to shepherd clinically generated genomic data through the multiple stages of a next-generation sequencing pipeline are of critical importance in translational biomedical science. Here we present ...
    • The future of genomics in pathology 

      Wall, Dennis Paul Paul; Tonellato, Peter J (Faculty of 1000 Ltd, 2012)
      The recent advances in technology and the promise of cheap and fast whole genomic data offer the possibility to revolutionise the discipline of pathology. This should allow pathologists in the near future to diagnose disease ...
    • Genotator: A Disease-Agnostic Tool for Genetic Annotation of Disease 

      Wall, Dennis Paul Paul; Pivovarov, Rimma; Tong, Mark; Jung, Jae-Yoon; Fusaro, Vincent Alfred; DeLuca, Todd; Tonellato, Peter J (BioMed Central, 2010)
      Background: Disease-specific genetic information has been increasing at rapid rates as a consequence of recent improvements and massive cost reductions in sequencing technologies. Numerous systems designed to capture and ...
    • Histopathologic Alterations Associated with Global Gene Expression Due to Chronic Dietary TCDD Exposure in Juvenile Zebrafish 

      Liu, Qing; Spitsbergen, Jan M.; Cariou, Ronan; Huang, Chun-Yuan; Jiang, Nan; Goetz, Giles; Hutz, Reinhold J.; Tonellato, Peter J.; Carvan, Michael J. (Public Library of Science, 2014)
      The goal of this project was to investigate the effects and possible developmental disease implication of chronic dietary TCDD exposure on global gene expression anchored to histopathologic analysis in juvenile zebrafish ...
    • MC-GenomeKey: a multicloud system for the detection and annotation of genomic variants 

      Elshazly, Hatem; Souilmi, Yassine; Tonellato, Peter J.; Wall, Dennis P.; Abouelhoda, Mohamed (BioMed Central, 2017)
      Background: Next Generation Genome sequencing techniques became affordable for massive sequencing efforts devoted to clinical characterization of human diseases. However, the cost of providing cloud-based data analysis of ...
    • Personalized cloud-based bioinformatics services for research and education: Use cases and the elasticHPC package 

      El-Kalioby, Mohamed; Abouelhoda, Mohamed; Krüger, Jan; Giegerich, Robert; Sczyrba, Alexander; Wall, Dennis Paul; Tonellato, Peter J (BioMed Central, 2012)
      Background: Bioinformatics services have been traditionally provided in the form of a web-server that is hosted at institutional infrastructure and serves multiple users. This model, however, is not flexible enough to cope ...
    • RNA-Seq of the Caribbean reef-building coral Orbicella faveolata (Scleractinia-Merulinidae) under bleaching and disease stress expands models of coral innate immunity 

      Anderson, David A.; Walz, Marcus E.; Weil, Ernesto; Tonellato, Peter; Smith, Matthew C. (PeerJ Inc., 2016)
      Climate change-driven coral disease outbreaks have led to widespread declines in coral populations. Early work on coral genomics established that corals have a complex innate immune system, and whole-transcriptome gene ...
    • Scalable and cost-effective NGS genotyping in the cloud 

      Souilmi, Yassine; Lancaster, Alex K.; Jung, Jae-Yoon; Rizzo, Ettore; Hawkins, Jared B.; Powles, Ryan; Amzazi, Saaïd; Ghazal, Hassan; Tonellato, Peter J.; Wall, Dennis P. (BioMed Central, 2015)
      Background: While next-generation sequencing (NGS) costs have plummeted in recent years, cost and complexity of computation remain substantial barriers to the use of NGS in routine clinical care. The clinical potential of ...
    • A Simulation Platform to Examine Heterogeneity Influence on Treatment 

      Chi, Chih-Lin; Fusaro, Vincent Alfred; Patil, Prasad; Crawford, Matthew A.; Content, Charles F.; Tonellato, Peter J. (American Medical Informatics Association, 2012)
      Although a protocol aims to guide treatment management and optimize overall outcomes, the benefits and harms for each individual vary due to heterogeneity. Some protocols integrate clinical and genetic variation to provide ...
    • Streaming Support for Data Intensive Cloud-Based Sequence Analysis 

      Issa, Shadi A.; Kienzler, Romeo; El-Kalioby, Mohamed; Tonellato, Peter J.; Wall, Dennis; Bruggmann, Rémy; Abouelhoda, Mohamed (Hindawi Publishing Corporation, 2013)
      Cloud computing provides a promising solution to the genomics data deluge problem resulting from the advent of next-generation sequencing (NGS) technology. Based on the concepts of “resources-on-demand” and “pay-as-you-go”, ...
    • Systems Analysis of Inflammatory Bowel Disease Based on Comprehensive Gene Information 

      Suzuki, Satoru; Takai-Igarashi, Takako; Fukuoka, Yutaka; Wall, Dennis Paul; Tanaka, Hiroshi; Tonellato, Peter J. (BioMed Central, 2012)
      Background: The rise of systems biology and availability of highly curated gene and molecular information resources has promoted a comprehensive approach to study disease as the cumulative deleterious function of a collection ...
    • The Translational Medicine Ontology and Knowledge Base: Driving Personalized Medicine By Bridging The Gap Between Bench And Bedside 

      Luciano, Joanne S; Andersson, Bosse; Batchelor, Colin; Bodenreider, Olivier; Denney, Christine K; Domarew, Christopher; Gambet, Thomas; Harland, Lee; Jentzsch, Anja; Kashyap, Vipul; Kos, Peter; Kozlovsky, Julia; Lebo, Timothy; Marshall, Scott M; McCusker, James P; McGuinness, Deborah L; Ogbuji, Chimezie; Pichler, Elgar; Samwald, Matthias; Schriml, Lynn; Whetzel, Patricia L; Stephens, Susie; Dumontier, Michel; Clark, Timothy William; Prud'hommeaux, Eric; Tonellato, Peter J; Zhao, Jun (BioMed Central, 2011)
      Background: Translational medicine requires the integration of knowledge using heterogeneous data from health care to the life sciences. Here, we describe a collaborative effort to produce a prototype Translational Medicine ...