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Defining a Systematic Approach


Your editorial “A Systematic Approach, and a Fond Farewell” (Genome Technology, Jan/Feb 2004) aptly brings out the problems created by the multitude of definitions for systems biology. As eloquently pointed out, the definition embraced is related to the potential to create new drugs. Some associate the term with the integration and assimilation of genomic, proteomic, and metabolomic data; and to others, it means utilization of concepts from systems science and engineering to understand biology.

A more comprehensive definition that does away with particulars is this: The study of biology at multiple temporal and spatial scales taking advantage of the recent advances in science at the molecular level, e.g., high-throughput techniques, imaging, and nanotechnology.

Drug manufacturers consider systems biology worthwhile only if it can expand target space, help in creating new drugs, and shorten the timeline for drug development. Quantitative and mechanistic knowledge of biological systems promised by systems biology will also lead to the development of diagnostic tools and therapeutic devices. Therefore, it’s not only about drugs but about being empowered to manipulate natural phenomena precisely.

Well-funded multidisciplinary centers are required to realize the potential of systems biology in improving health and wellness. As with any partially comprehensible and rapidly developing technology, the issues related to business practice, patenting, and license protection pose as spectral behemoths.

Shwetal Patel
Postdoctoral Researcher
The University of Texas Southwestern Medical Center at Dallas


Array of Data

I was pleased to see the results of the array survey in this month’s issue of Genome Technology (April 2004). I am not at all surprised that cost, for either the software or for the slides themselves, is still a major barrier for some researchers. In general, the summary of results could have been more useful, however, had you shown the results broken down according to the type of institution (university labs, not-for-profit labs, industry labs, etc.).

Drosophila researchers at not-for-profit institutions can take heart about the cost of microarrays: the NIH-funded Drosophila Genomics Resource Center ( will begin accepting orders in April 2004 for spotted cDNA microarrays at a cost of $100 per slide.

Jennifer Steinbachs, PhD
Deputy Director
The Center for Genomics and Bioinformatics
Indiana University



In the March 2004 issue of Genome Technology, the following quote appeared in the article “Hot Rod Homology Heaven”: “With an unlimited budget, of course, researchers could spring for tailor-made supercomputers or a cluster of PCs — or even a so-called dedicated hardware system, a commercial version of a PC/FPGA configuration offered by the likes of TimeLogic or Paracel.”

Please note that while Paracel’s GeneMatcher2 is a dedicated system, it is actually based on ASIC technology combined with a Linux cluster.

Lisa Rehfeld, Paracel


Genome Technology thanks the members of its advisory panel, who have agreed to be a sounding board for the magazine.

David Clemmer, Indiana University

Mark Cockett, Bristol-Myers Squibb

Dalia Cohen, Novartis Institutes for Biomedical Research

Claire Fraser, The Institute for Genomic Research

Sandra Glucksmann, Millennium Pharmaceuticals

Rod MacKenzie, Pfizer Discovery Technology Center

Jill Mesirov, Eli & Edythe L. Broad Institute, MIT and Harvard

Emanuel Petricoin, FDA-NCI Clinical Proteomics Program

Gerald Rubin, Howard Hughes Medical Institute

Tom Tuschl, Rockefeller University


The Scan

Study Finds Sorghum Genetic Loci Influencing Composition, Function of Human Gut Microbes

Focusing on microbes found in the human gut microbiome, researchers in Nature Communications identified 10 sorghum loci that appear to influence the microbial taxa or microbial metabolite features.

Treatment Costs May Not Coincide With R&D Investment, Study Suggests

Researchers in JAMA Network Open did not find an association between ultimate treatment costs and investments in a drug when they analyzed available data on 60 approved drugs.

Sleep-Related Variants Show Low Penetrance in Large Population Analysis

A limited number of variants had documented sleep effects in an investigation in PLOS Genetics of 10 genes with reported sleep ties in nearly 192,000 participants in four population studies.

Researchers Develop Polygenic Risk Scores for Dozens of Disease-Related Exposures

With genetic data from two large population cohorts and summary statistics from prior genome-wide association studies, researchers came up with 27 exposure polygenic risk scores in the American Journal of Human Genetics.