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Five Septembers of Systems Biology


2000 Five years ago, Genome Technology launched its first issue with a cover story looking into Lee Hood’s latest brainstorm — a new institute he would build after leaving the University of Washington. The Institute for Systems Biology, begun with a $5 million anonymous donation, would hope to raise $200 million, Hood said, and would allow for interdisciplinary science in a way that wasn’t happening anywhere else.

Today, the ISB is going strong, though by all accounts the $200 million goal is still beyond Hood, who has become irreversibly associated with the concept of systems biology, a frequent subject of his talks at conferences. Ruedi Aebersold, who cofounded ISB with Hood, has since left for a position at the Swiss Federal Institute of Technology in Zurich.

Our first issue included a feature story on Incyte, one of the industry drivers at the time relying on a genomics database business model. That model foundered in the years since, and Incyte has reshaped itself into more of a pharmaceutical company, selling off its genomic and proteomic units to companies such as Ingenium and Biobase.

Also in the September 2000 issue, GT provided a sneak peek into GSAC, the mega-conference known for its massive exhibit hall and lavish parties. Since then, GSAC has downsized and rebranded away from its sequence-heavy roots. After years of dropping attendance, the conference will no longer be hosted by TIGR and has been reincarnated as the “Genomes, Medicine, and the Environment” conference run by the J. Craig Venter Institute. Coming full circle, the meeting —known years ago for being an intimate, science-heavy conference — will be held this year in Hilton Head, SC.


2001 In September 2001, GT’s cover story looked at the growth in popularity of protein crystallography using synchrotrons —which has enabled truly high-throughput structural genomics. In the years since, the trend has continued: just this year, a new $5.7 million X-ray beamline opened at the Synchrotron Radiation Source at Daresbury Laboratory in the UK. The facility will allow researchers to study protein structures and will be available some of the time to external scientists in the UK.

Four years ago, we also looked into Perlegen Sciences, the Affymetrix spinoff launched with $100 million in private funding and a staff of 50. The company’s technology was a high-density wafer able to scan the whole genome for SNPs. In the years between then and now, evolving technology has allowed for whole-genome scanning without the wafer-size chips: major array manufacturers offer a whole-human-genome chip. That hasn’t stopped Perlegen, though, which has formed partnerships with several academic institutions to use its technology to perform association studies for dozens of major diseases.


2002 Three years ago, Genome Technology introduced readers to a new nonprofit venture in Arizona led by Jeff Trent, a former scientific director with NHGRI. The Translational Genomics Research Institute, better known as TGen, was started in Arizona and works through alliances with state universities. TGen has continued to grow in the time since, and today has announced collaborations with the Mayo Clinic, Kronos, Lokoya, and Children’s Memorial Institute, among others.

Also in the 2002 issue we profiled Evan Eichler, a scientist who made a name for himself studying genetic duplication anomalies. Eichler, then at Case Western Reserve University, has continued to fill out the body of research in this niche. In the meantime, he moved to the University of Washington, where he’s an associate professor in the genome sciences department. Eichler was also named this year as one of the Howard Hughes Medical Institute’s new investigators.


2003 Our cover story in September 2003 looked at the latest academic institution trend in systems biology: new multidisciplinary centers with loads of funding, all aimed at finding the sweet spot of large-scale biology. With so many new centers, and no track record on which to base the many predictions of revolutionary science, it wasn’t clear that these places would be able to make it. GT profiled new centers at Stanford, MIT, Princeton, Duke, the University of Michigan, the Universities of California, and Cornell. In the time since then, these centers have continued ramping up. At the University of Michigan, the Life Sciences Institute has moved into a brand-new facility and is still in the process of filling faculty positions. Duke lured Hunt Willard from Case Western and has continued opening new centers within its Institute for Genome Sciences and Policy.

Another article in the ’03 issue looked into early indications that NIH was considering funding research further down the drug-discovery pipeline than the institutes usually considered their realm. A little over a year later, the multi-institute chemical genomics initiative would grace our cover, and just recently news came out that NIH awarded close to $90 million to a group of nine centers participating in the small-molecule screening effort (see p. 11).


2004 Last year, GT checked out the hot new pairing of RNAi with microarrays — a technology coupling that pharma scientists said was making inroads into applying gene silencing studies into the discovery phase. According to experts, using RNAi with high-throughput arrays was turning up promising targets that hadn’t been found with the traditional means.

We’re finding that RNA interference is a thoroughly adaptable technology, and in the current issue we look into another pairing: RNAi with cell-based assays. It’s another way of trying to make gene silencing a high-throughput science. Check that story out on p. 23.

GT’s September 2004 issue also looked in on cheap sequencing technologies. The $1,000 genome has long been a goal for this market, and after years of developing tools to get closer to the mark, it looks like this field is finally approaching commercial status, although the $1,000 price tag is still out of reach. In the year since we checked in, 454 Life Sciences made strides by placing its instruments at the Broad Institute, Baylor’s genome center, and the Joint Genome Institute. Meantime, the startups continue: Helicos BioSciences recently emerged from stealth mode with claims that it has a technology to do faster and cheaper sequencing than competitors. The company may place an instrument with beta testers as early as the end of this year.

— Meredith Salisbury

Coming Up
Next Month in GT

Career focus: Academic/industry crossover. For years, readers have been asking us about whether the grass is really greener on the other side of the public/private divide. In this feature, GT clears the air about switching from public to private sector (or vice versa) and back again — how it works, the pay and perk ramifications, and whether it has a long-term impact on your career.

Protein informatics: Proteomics scientists are thwarted by terabytes of incompatible data from the various platforms they need in their labs, and also by software that lags as each new instrument is introduced to the market. We offer a tour of solutions.


The Scan

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A JAMA Otolaryngology — Head & Neck Surgery study says polygenic risk scores associated with hearing loss in older adults is also associated with hearing decline in younger groups.

Genome-Wide Analysis Sheds Light on Genetics of ADHD

A genome-wide association study meta-analysis of attention-deficit hyperactivity disorder appearing in Nature Genetics links 76 genes to risk of having the disorder.

MicroRNA Cotargeting Linked to Lupus

A mouse-based study appearing in BMC Biology implicates two microRNAs with overlapping target sites in lupus.

Enzyme Involved in Lipid Metabolism Linked to Mutational Signatures

In Nature Genetics, a Wellcome Sanger Institute-led team found that APOBEC1 may contribute to the development of the SBS2 and SBS13 mutational signatures in the small intestine.