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Craig Liddell, Vice President of Informatics, Paradigm Genetics

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AT A GLANCE

PhD in plant pathology from the University of Sydney, Australia, in1986.

Prior to joining Paradigm in July 1998, served as associate professor of plant pathology and principal investigator at the computing research laboratory at New Mexico State University. Former senior editor of the journal Phytopathology.

Interests include hiking, camping, mountain biking, botany, travel to far-off places, and playing bass guitar in the newly formed Paradigm Genetics band known as GeneSmack.

QWhere will bioinformatics be in two years? Five years?

ABioinformatics will change fundamentally within five years from a predominantly technology-driven discipline into a scientific discipline, and within two years this change should be evident with the first scientific bioinformatics practitioners hitting the market.

The basic driver for this change is that the historical lack of good data management and data processing algorithms required bioinformatics experts to be knowledgeable about technology and not computational biology and biostatistics. In general, this is due to the service role of many bioinformatics experts working with and often reporting to domain specialists in all areas of biology, namely, cancer biology, stem cell research, plant biology, or microbial genomics. In addition, current bioinformatics specialists are often retrained biologists, who bring a relatively novice level of expertise to the field and who often retain a biology focus in their research questions. At the same time several significant IT-related technology issues are being solved with powerful new database technologies and data sharing and integration technologies that promise to help solve the integration, sharing, and management of the large amounts of data being produced.

However, these technologies alone cannot solve all the issues surrounding data interpretation. As the amount of data increases along with the ability to visualize and analyze the data, the need will grow for statistically rigorous and scientifically sound approaches to interpreting data. Essentially this means that bioinformatics scientists will become as involved in data generation as they currently are involved in data analysis, and the single biggest need will be for bioinformatics experts that are well-trained in biostatistics.

QWhat are the biggest challenges the bioinformatics sector faces?

AThe challenge in bioinformatics today is the generation of truly coherent data sets from cross-functional platforms that can be used for integrated discovery. This implies that bioinformatics experts must recognize that tools such as standard XML and standard ontologies, while important, are only tools to help solve the much bigger challenge of coherence in data sets.

The single biggest challenge in this process will be an inevitable but painful cultural paradigm shift that will occur as bioinformatics becomes a central part of the daily life of every biologist and bioinformatics experts become central players in every aspect of life science R&D programs. This type of cultural shift has occurred in earlier times in other sciences such as physics, astronomy, and chemistry. But history teaches that once the tidal wave of change begins, it takes only about one generation to complete the cultural change. The tidal wave in biology has begun.

QWhat do you see as the most important task for bioinformatics to address beyond genome sequencing?

AClearly the most significant technical task is to understand how to collect and manage coherent data from multiple high-throughput platforms. Bioinformatics must supply the tools and processes to maintain the coherence and integrity of multiple high-throughput data streams with the same level of quality that a highly experienced bench scientist applies to his or her own data.

QWith what companies do you have partnerships?

AAt the close of 2000, Paradigm had commercial partnerships valued at nearly $200 million with Bayer AG for herbicide discovery and development, Monsanto for agricultural biotechnology, and Lion Bioscience for software tools and database product development in metabolomics. Paradigm’s state-of-the-art Gene Function Factory went online in 2001 as the largest facility of its kind in the world with the capacity to determine the function of more than 200 genes per week.

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