Computational Strategies for Scalable Genomics Analysis.

The revolution in next-generation DNA sequencing technologies is leading to explosive data growth in genomics, posing a significant challenge to the computing infrastructure and software algorithms for genomics analysis. Various big data technologies have been explored to scale up/out current bioinformatics solutions to mine the big genomics data. In this review, we survey some of these exciting developments in the applications of parallel distributed computing and special hardware to genomics. We comment on the pros and cons of each strategy in the context of ease of development, robustness, scalability, and efficiency. Although this review is written for an audience from the genomics and bioinformatics fields, it may also be informative for the audience of computer science with interests in genomics applications

Talking Glossary of Genomics Terminology: A Genomics Education Module for American Indian Communities

This paper describes the development of an audio visual genomics glossary that was designed as an education tool for American Indian communities. This “Talking Glossary of Genomics Terminology” is a multimedia DVD that was modeled on the “Talking Glossary of Genetics,” which was developed by the National Human Genome Research Institute (NHGRI). The NHGRI Glossary was modified and expanded with content designed to increase awareness among American Indians about cancer, genomics, and personalized medicine. Partners on the project include the Inter Tribal Council of Arizona, Inc., Phoenix Indian Medical Center, Arizona Cancer Center at the University of Arizona, the Translational Genomics Research Institute, as well as Arizona State University and University of Arizona graduate students

The Governance of Genomic Information: Will It Come of Age?

The completion of the Human Genome Project has opened up unprecedented possibilities in healthcare, but also ethical and social dilemmas in terms of how these can be achieved. Genomic information can be seen as a 'global public good' (GPG), in that it is represented by knowledge in the public domain and across national boundaries. Lack of investment, infrastructure and expertise in developing countries means that they are unable to take advantage of these GPG characteristics to address their health needs, fuelling fears of a growing 'genomics divide'. Some have suggested an international knowledge sharing and capacity building network, a Global Genomics Initiative, as a means to harness the potential of genomics to reduce inequalities in health between North and South. Three UNESCO declarations also call for cooperation between developed and developing countries in genomics research and science and technology in general. Using international relations theories around global governance and networks as a conceptual framework, this paper examines whether these initiatives are likely to succeed in providing effective governance of genomics

<i>Medicago truncatula</i> functional genomics: an invaluable resource for studies on agriculture sustainability

Legume functional genomics has moved many steps forward in the last two decades thanks to the improvement of genomics technologies and to the efforts of the research community. Tools for functional genomics studies are now available in Lotus japonicus, Medicago truncatula and soybean. In this chapter we focus on M.truncatula, as a model species for forage legumes, on the main achievements obtained due to the reported resources and on the future perspectives for the study of gene function in this species

Revisiting digital technologies: envisioning biodigital bodies

In this paper the contemporary practices of human genomics in the 21st century are placed alongside the digital bodies of the 1990s. The primary aim is to provide a trajectory of the biodigital as follows: First, digital bodies and biodigital bodies were both part of the spectacular imaginaries of early cybercultures. Second, these spectacular digital bodies were supplemented in the mid-1990s by digital bodywork practices that have become an important dimension of everyday communication. Third, the spectacle of biodigital bodies is in the process of being supplemented by biodigital bodywork practices, through personal or direct-to-consumer genomics. This shift moves a form of biodigital communication into the everyday. Finally, what can be learned from putting the trajectories of digital and biodigital bodies together is that the degree of this communicative shift may be obscured through the doubled attachment of personal genomics to everyday digital culture and high-tech spectacle.Keywords: genomics, biodigital, bodies, spectacle, everyda

The emergence of commercial genomics: analysis of the rise of a biotechnology subsector during the Human Genome Project, 1990 to 2004.

BackgroundDevelopment of the commercial genomics sector within the biotechnology industry relied heavily on the scientific commons, public funding, and technology transfer between academic and industrial research. This study tracks financial and intellectual property data on genomics firms from 1990 through 2004, thus following these firms as they emerged in the era of the Human Genome Project and through the 2000 to 2001 market bubble.MethodsA database was created based on an early survey of genomics firms, which was expanded using three web-based biotechnology services, scientific journals, and biotechnology trade and technical publications. Financial data for publicly traded firms was collected through the use of four databases specializing in firm financials. Patent searches were conducted using firm names in the US Patent and Trademark Office website search engine and the DNA Patent Database.ResultsA biotechnology subsector of genomics firms emerged in parallel to the publicly funded Human Genome Project. Trends among top firms show that hiring, capital improvement, and research and development expenditures continued to grow after a 2000 to 2001 bubble. The majority of firms are small businesses with great diversity in type of research and development, products, and services provided. Over half the public firms holding patents have the majority of their intellectual property portfolio in DNA-based patents.ConclusionsThese data allow estimates of investment, research and development expenditures, and jobs that paralleled the rise of genomics as a sector within biotechnology between 1990 and 2004