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Sifting Through Systems Biology Dean Bottino, Novartis Institutes for BioMedical Research Christopher Portier, chief, Laboratory of Computational Biology and Risk Analysis, NIEHS Arnold Levine, director, Center for Systems Biology, Institute for Advanced Study, Princeton University Andrea Califano, director of bioinformatics, Columbia University Genome Center In late February, four systems biology experts braved a harsh winter (and 10 inches of snow) to gather at the Genome Technology office in New York City and hash…
Genomics Inside the FDA By John S. MacNeil The US Food and Drug Administration is under a lot of pressure these days after issues like the uproar over findings that Vioxx is less safe than previously assumed. But not all changes taking place within the agency today are reactions to such pressure. In fact, FDA administrators in recent years have made efforts to update their review process to take advantage of new technologies…
Markers
Systems Biology New Guise for Beyond Genomics Not only does Beyond Genomics have a new CEO, but now the Cambridge, Mass.-based purveyor of integrated biology services also has a new name. From here on out, according to Pieter Muntendam, who took over as CEO in December of last year, Beyond Genomics will be known as BG Medicine. “The paradox of being called Beyond Genomics is that to investors the focus is on genomics, and that’s a…
Bioinformatics Harvard Tempts Quackenbush Away from TIGR After eight years at The Institute for Genomic Research, John Quackenbush moved last month to take a dual appointment at the Harvard School of Public Health and the Dana-Farber Cancer Institute in Cambridge. “I’d been looking around to see how I could grow my research,” Quackenbush says, “and [Harvard] had an attractive offer. They have capacities there in bioinformatics, animal models, cancer, human disease — the opportunities there are…
Conference report At Marco Island, Gordon Tells Us We re Mostly Bugs When the sixth annual Advances in Genome Biology and Technology conference opened in Marco Island, Fla., this February, some 200 attendees may have been surprised to hear that they were composed almost entirely of bacteria. The conference kicked off with a session on microbial genomics, opening with Jeffrey Gordon of Washington University speaking on “The Human Intestinal Microbiota and its Microbiome: Terra Incognita Becomes More Cognita.” Gordon, who…
Microarrays With new array CGH tool, Agilent targets cancer research market When Agilent decided to release its latest array tool — arrays for comparative genomic hybridization, or CGH — early this year, the company didn’t waste time figuring out which research field to target. Cancer research, says Lou Welebob, marketing program manager for integrated biological solutions, “is the largest addressable market” for this kind of technology. …
Collaborations Monsanto Sequencers Urge Teaming Up with Academics When Nancy Miller gave a talk at the Advances in Genome Biology and Technology conference this February extolling the benefits of public/private collaborations to get genomes sequenced, she’d come a long way from the early days of trying to convince her own company, Monsanto, of the same thing. …
Protein analysis INCAPS Represents Indiana, Wery Represents as CsO As one of many communities vying for the reputation as an upcoming hotbed of biotechnology research, one of central Indiana’s claims to fame is the Indiana Centers for Applied Protein Sciences. Founded in January 2004 with $7.2 million, including over $3 million from Indianapolis neighbor Eli Lilly and with pledges for business from other regional life science companies and universities, INCAPS — as the laboratories are known — has…
Expression Studies Sloan-Kettering: Array Analysis for Prostate Cancer To William Gerald, a pathologist and researcher at Memorial Sloan-Kettering Cancer Center in New York, it’s clear that any effort to understand and defeat cancer will involve more than just analyzing gene expression data derived from microarray experiments. In fact, the 13-year veteran of Sloan-Kettering is already making forays into what he describes as comprehensive molecular analysis by integrating his microarray results with data from gene copy number and…
Short Reads/Markers DOE’s Joint Genome Institute kicked off Integrated Microbial Genomes, its public online microbial genome database featuring more than 200 organisms. JGI produces nearly 25 percent of the number of microbial genome projects worldwide and expects to add another 200 genomes to the database in 2005. …
Informatics Insider
Sorting Out Statistics The outcome of many biomedical experiments comes down to two questions: 1) Is it statistically significant? and 2) Is it biomedically meaningful? The answer to the latter, of course, determines the importance to the researcher and the biomedical community, but it is closely linked to the answer to the former — at least with quantitative data. Biomedical research is becoming more quantitative, and statistical theory and practice is becoming…
Pattern Recognition
Grants for Cancer The National Cancer Institute has an extramural budget of $3.7 billion, and a sizable portion of that goes to researchers involved in systems biology. For the list of grants below, Genome Technology searched the NCI grants database for those that included the word “genome.” Then we narrowed the list to include the larger and more technology-focused of the grants. This list is not comprehensive and is meant to be a…
Technology Spotlight
Can Dxs Thin Down Microarrays for the Clinics? “This is the counterrevolution against systems biology, and it’s thin slicing,” Francis Barany, keynote speaker at the Feb. 17 Clinical Genomics meeting, said. By that comment, Barany, a professor of Microbiology and Immunology at Cornell University’s Weill College of Medicine, summarized what he sees as a step critical to getting molecular diagnostics for tumors into the clinic and the minds of doctors. The term “thin slicing,” popularized by author…
Bacterial Genomes Culled From Drosophila Sequence While finishing sequencing the genomes of seven species of Drosophila last year, a team of researchers at the University of California, Berkeley, inadvertently sequenced the genes of several bacteria that secretly live in fruit fly embryos. These bacteria, which belong to the Wolbachia genus, reside in the Drosophila gene database, where they lived quietly, and, until now, unnoticed, according to Michael Eisen, a Berkeley assistant professor of molecular and…
Ocimum Eyes Chip Market with MWG s Array Unit Ocimum Biosolutions has agreed to acquire the core microarray assets of MWG Biotech, giving the Hyderabad, India-based provider of microarray analysis services a new role as a supplier of chips and amplification kits. The MWG assets include custom and catalog microarrays, including a 40K human genome chip; the ExpressArt mRNA Amplification Kits; a hybridization service; a bioinformatics service; and an online gene index for all of the catalog…
PITTCON: Software, Peptide Scoring, Search Engines Novel and upgraded software for proteomic analysis, new peptide-scoring methods, and new ways to optimize existing search engines made a splash at this year’s PITTCON conference, held in Orlando early last month. In a session on informatics methods used to mine mass-spectrometry data, Morgan Giddings, an assistant professor at the University of North Carolina at Chapel Hill, described her strategy for connecting genomic sequence with protein function. …
Sigma-Aldrich to Buy Proligo; RNAi IP Key to Deal Sigma-Aldrich announced this February that it has signed a definitive agreement to acquire Proligo from specialty chemical giant Degussa, further advancing a wave of consolidation that has been sweeping the RNAi reagent market recently. According to Sigma-Aldrich, Proligo, which has about 300 employees, racked up sales of $40 million in 2004. Depending on when the acquisition closes, as much as nine months of Proligo’s operating results will be added…
Microsoft Modifies Software for HIV Research Turns out that Microsoft isn’t only concerned with viruses of the electronic variety. In March the company announced that machine-learning software developed within its research labs may help design more effective vaccines to fight HIV. In a collaboration with the University of Washington and Australia’s Royal Perth Hospital, computer scientists at Microsoft Research are adapting software originally designed for computer vision and spam blocking to sift through large genetic…
Calendar & Deadlines
Calendar of Meetings, Deadlines & Workshops CONFERENCES April 3 — Analytical and Life Science Systems Association, Palm Beach, Fla. April 5 — EmTech 2005: Emerging Technologies for Drug Discovery, San Francisco April 8 — Keystone Symposia: Proteomics and Bioinformatics, Keystone, Colo. April 13 — International Conference on Microbial Genomes, Halifax, Nova Scotia …
Where Are They Now
Mass market, Shamrock, sequencers In Genome Technology a year ago, our cover story featured what we call “next-generation genomics” — a series of marketplace applications in which genomics has already made a mainstream appearance. Those areas included anti-counterfeiting measures, personalized skin care, and improved artificial flavors, among others. In the year since, those organizations have continued to make strides; genetically personalized skin care products, for one, have been prominently featured in consumer media. …
Primer
The Cancer Issue In most issues of this magazine, we strive to give you an overview of as many fields as possible. You tell us that this helps you see the big picture of large-scale biology, and we’re glad to do it. But for this issue, we’re trying something different. …
Blunt End
The Dark Side of Metagenomics GenomeWeb Intelligence Network GenomeWeb,LLC PO Box 998, Peck Slip Station, New York, NY 10272 USA Attn: J. Craig Venter Institute From: GenomeWeb News Team Dear Craig, Congratulations on your recent announcement that the Venter Institute will be sequencing the microorganisms in New York City air. As residents of this wonderful city, we’d like to ask one teensy favor when you’ve completed your work: please don’t publish it. There’s no need…
Other
New Lab & IT Products for Integrated Biology BIOINFORMATICS Gene Logic Genesis Enterprise System 2.5 Version 2.5 of Gene Logic’s Genesis Enterprise System further expands and accelerates researchers'' ability to assess drug risks using genomics and toxicogenomics data and related clinical information. Users can now use the software to import and analyze their own Affymetrix GeneChip array data and annotate their samples. The latest software update reflects significant customer input regarding group-share abilities for a collaborative, secure…
Here Comes the NIH Consulting Ban Much has already been written about the controversy at NIH around its relatively laissez-faire approach to overseeing potential conflicts of interest on the part of its scientists. It seems clear that either the code of ethics itself, or NIH’s lax enforcement of the code, is responsible for some of the more ostensibly blatant examples of conflict of interest that so famously raised the ire of Congressman James Greenwood (R) from…
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