Now showing items 1-15 of 15

    • Autworks: a Cross-Disease Network Biology Application for Autism and Related Disorders 

      Nelson, Tristan; Jung, Jae-Yoon; DeLuca, Todd; Hinebaugh, Byron Kent; St Gabriel, Kristian Che; Wall, Dennis Paul Paul (BioMed Central, 2012)
      Background: The genetic etiology of autism is heterogeneous. Multiple disorders share genotypic and phenotypic traits with autism. Network based cross-disorder analysis can aid in the understanding and characterization of ...
    • 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 ...
    • Cloud Computing for Comparative Genomics with Windows Azure Platform 

      Kim, Insik; Jung, Jae-Yoon; DeLuca, Todd; Nelson, Tristan; Wall, Dennis Paul Paul (Libertas Academica, 2012)
      Cloud computing services have emerged as a cost-effective alternative for cluster systems as the number of genomes and required computation power to analyze them increased in recent years. Here we introduce the Microsoft ...
    • Cross-Pollination of Research Findings, Although Uncommon, May Accelerate Discovery of Human Disease Genes 

      Duda, Marlena; Nelson, Tristan; Wall, Dennis Paul Paul (BioMed Central, 2012)
      Background: Technological leaps in genome sequencing have resulted in a surge in discovery of human disease genes. These discoveries have led to increased clarity on the molecular pathology of disease and have also ...
    • 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 ...
    • Identification of Autoimmune Gene Signatures in Autism 

      Jung, J-Y; Kohane, Isaac Samuel; Wall, Dennis Paul Paul (Nature Publishing Group, 2011)
      The role of the immune system in neuropsychiatric diseases, including autism spectrum disorder (ASD), has long been hypothesized. This hypothesis has mainly been supported by family cohort studies and the immunological ...
    • 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 ...
    • Phylogenetically informed logic relationships improve detection of biological network organization 

      Cui, Jike; DeLuca, Todd; Jung, Jae-Yoon; Wall, Dennis Paul Paul (BioMed Central, 2011)
      Background: A "phylogenetic profile" refers to the presence or absence of a gene across a set of organisms, and it has been proven valuable for understanding gene functional relationships and network organization. Despite ...
    • Reply to the “Letter to the Editors” by Steven Buyske 

      Abu-Elneel, K.; Liu, T.; Gazzaniga, F. S.; Nishimura, Y.; Wall, Dennis Paul Paul; Geschwind, D. H.; Lao, K.; Kosik, K. S. (Springer-Verlag, 2009)
    • Roundup 2.0: Enabling Comparative Genomics for over 1800 Genomes 

      DeLuca, Todd F.; Cui, Jike; Jung, Jae-Yoon; St. Gabriel, Kristian Che; Wall, Dennis Paul Paul (Oxford University Press, 2012)
      Summary: Roundup is an online database of gene orthologs for over 1800 genomes, including 226 Eukaryota, 1447 Bacteria, 113 Archaea, and 21 Viruses. Orthologs are inferred using the Reciprocal Smallest Distance algorithm. ...
    • 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 ...
    • Use of Artificial Intelligence to Shorten the Behavioral Diagnosis of Autism 

      Wall, Dennis Paul; Dally, Rebecca; Luyster, Rhiannon; Jung, Jae-Yoon; DeLuca, Todd (Public Library of Science, 2012)
      The Autism Diagnostic Interview-Revised (ADI-R) is one of the most commonly used instruments for assisting in the behavioral diagnosis of autism. The exam consists of 93 questions that must be answered by a care provider ...
    • Use of Machine Learning to Shorten Observation-based Screening and Diagnosis of Autism 

      Wall, Dennis Paul; Kosmicki, Jack Alphonse; DeLuca, Todd; Harstad, Elizabeth Borges; Fusaro, Vincent Alfred (Nature Publishing Group, 2012)
      The Autism Diagnostic Observation Schedule-Generic (ADOS) is one of the most widely used instruments for behavioral evaluation of autism spectrum disorders. It is composed of four modules, each tailored for a specific group ...