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{bio,medical} informatics

Monday, February 13, 2006

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find related articles. powered by google. Genomeweb JGI Says Combining Sanger and 454 Sequencing is Best Approach for De Novo Microbial Sequencing

"454 Life Sciences' sequencer may show great potential for de novo sequencing of microbial genomes, but it can't replace Sanger sequencing completely, according to researchers from the Department of Energy's Joint Genome Institute."

""454 can generate high quality draft assemblies, not final finished sequences," Feng Chen, group leader of technology development at the Lawrence Berkeley National Laboratory, told GenomeWeb News. "The quality of [the] 454 assembly is reasonably high, but it is still lower than the required quality standard for [a] finished sequence.""

redux [01.27.06]
find related articles. powered by google. The Wall Street Journal Prize for DNA Decoding Aims to Fuel Innovation

"When inventor Burt Rutan's SpaceShipOne soared 63.6 miles above the Earth in October 2004, he captured the $10 million X Prize and helped inaugurate the era of commercial human space flight.

The X Prize Foundation, a nonprofit-education organization, is looking to spur a new adventure -- into human genes.

The Santa Monica, Calif., foundation plans to offer a $5 million to $20 million prize to the first team that completely decodes the DNA of 100 or more people in a matter of weeks, according to foundation officials and others involved.

Such speedy gene sequencing would represent a technology breakthrough for medical research. It could launch an era of "personal" genomics in which ordinary people can learn their complete DNA code for less than the cost of a wide-screen television."

redux [01.03.06]
find related articles. powered by google. Genomeweb As 454 Enabled Mammoth Project, Next-Generation Sequencers Will Drive Paleogenomics
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"As next-generation sequencing technologies emerge on the market, some experts believe they will be used for projects other than medical sequencing. This notion was reinforced two weeks ago when scientists announced the first genome sequences from a wooly mammoth, which became extinct about 10,000 years ago.

"Now some scientists say this project could signal the start of a sequencing trend in paleogenomics --- as well as a potential new market for emerging sequencing technologies, which enabled the wooly mammoth research, published in the Dec. 22 issue of Science."

redux [10.24.05]
find related articles. powered by google. The Wall Street Journal A Better Idea

"Gene sequencing -- the process of unlocking an individual's DNA -- could one day revolutionize medicine, allowing doctors to quickly identify someone's genetic makeup and craft individual treatments for such diseases as cancer and tuberculosis. But first, there has to be a way to speed the cumbersome, slow and expensive sequencing process."

"The genome-sequencing technique from 454 Life Sciences was selected as the Gold winner in The Wall Street Journal's 2005 Technology Innovation Awards competition. Innovative technologies from around the world were eligible for awards in categories including biotechnology, software, security, energy and the environment, among others."

redux [08.05.05]
find related articles. powered by google. Scientific American Recipe for D-I-Y DNA Decoding Revealed

"A thousand dollars can buy a lot of things. Scientists hope to soon add an individual's genetic sequence to that list. Full-genome DNA decoding, estimated to now cost $20 million, could soon be done for about $2.2 million, experts say, and will continue to drop in price as researchers develop new ways to conquer the task. A report published online yesterday by the journal Science suggests one such method: a technique that used off-the-shelf instruments and reagents to successfully sequence the E. coli genome."

find related articles. powered by google. Bio-IT World Harvard Group Develops Low-Cost DNA Sequencing Technique

"Unlike the 454 approach, the method developed by Church and colleagues is a form of DNA resequencing – that is, it requires a reference sequence with which to compare the new sequence, because each fragment of DNA sequenced is so short. Nevertheless, many likely lab applications – from genotyping haplotypes in a disease study, searching for mutations in cancer resistance, or as in the Science paper, identifying microbial strain variants – would fall into this category."

redux [08.01.05]
find related articles. powered by google. Nature Fast sequencing comes to light

"When Jonathan Rothberg's son was born six years ago, the baby was sent to the infant intensive care unit. Rothberg worried all night that something might be wrong with his child, and he found himself wishing he could just read the boy's genome to find out.

At the time that was impossible: it cost tens of millions of dollars and took more than a decade to decipher the first complete human genome, published in 2001 in Nature. But Rothberg's parental panic and frustration inspired him to design a faster, cheaper sequencing technique. Now Rothberg and his co-workers at the 454 Life Sciences Corporation, which he founded, report their success. "

find related articles. powered by google. The New York Times DNA Machine May Advance Genetic Sequencing for Patients
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""What they have done here is very significant," Dr. Ronaghi said, noting that the company had already sequenced 50 microbial genomes. "This is the first step toward $1,000 human genome sequencing," he said."

"Jonathan Rothberg, board chairman of 454 Life Sciences, said the company was already able to decode DNA 400 units at a time in test machines. It was working toward sequencing a human genome for $100,000, and if costs could be further reduced to $20,000 the sequencing of individual genomes would be medically worthwhile, Dr. Rothberg said."

redux [10.03.02]
find related articles. powered by google. Wired News Get Your Red-Hot Genome CD

"Mapping and reading J. Craig Venter's genome took 15 years, $5 billion and some of the world's most sophisticated computers.

Wouldn't you, too, like your genome decoded?

Venter says he plans to offer the service, with the goal of burning individual human's entire DNA sequences onto shiny compact discs."

find related articles. powered by google. Genomeweb Gene pioneer's next goal

"Tonight's plenary panel discussion at GSAC, "The Future of DNA Sequencing: Advancing Toward the $1,000 Genome," hosted by Craig Venter and Gerald Rubin, quickly turned into a genomics version of the game show "The Price is Right."

"I had to do a little better than the thousand-dollar genome," said VisiGen Biotechnologies CEO Susan Hardin, one of the panelists, about her company's efforts to develop a single-molecule sequencing method using both a modified polymerase and nucleotides. "So we're going for the $995 genome.""

[ rhetoric ]

Bioinformatics will be at the core of biology in the 21st century. In fields ranging from structural biology to genomics to biomedical imaging, ready access to data and analytical tools are fundamentally changing the way investigators in the life sciences conduct research and approach problems. Complex, computationally intensive biological problems are now being addressed and promise to significantly advance our understanding of biology and medicine. No biological discipline will be unaffected by these technological breakthroughs.


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