Friday, April 28, 2000

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Nature Open-source work even more vital to genome project than to software
"We note with dismay and alarm the controversy concerning access, distribution and patenting of the human genome sequence (Nature 404, 317; 2000 & Nature 404, 324; 2000). We wish to point out some analogies between the human genome sequencing efforts and 'open-source' software development, which have implications for the data-release policy of the public sequencing effort."

"The reasons why the Linux project could succeed against commercial wisdom have been analysed by Eric S. Raymond in his book The Cathedral and the Bazaar (O'Reilly, 1999). Most of these findings are of relevance to academic and commercial benefits arising from human genome sequencing." [via bioinformatics.org]

Thursday, April 27, 2000

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Individual.Com Incyte Genomics, Gene Logic, DoubleTwist on BioTalk's Look At Bioinformatics Today
"Incyte Genomics (Nasdaq: INCY), Gene Logic (Nasdaq: GLGC) and privately held DoubleTwist provide different examples of how bioinformatics -- computational tools and databases that support genomics research -- are revolutionizing approaches to drug-discovery on today's BioTalk radio show from InformedInvestors.com."

"Tune to the show from 11 a.m.-noon EDT at www.informedinvestors.com or www.broadcast.com/shows/biotech, or via analog dial at WMET 1150 AM in Gaithersburg, MD. Listeners can send questions in real-time via email during the show to cohost Tim Quast at tim@informedinvestors.com."

Wednesday, April 26, 2000

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BioInform $12.8M in NIH Grants Fund Work on Pharmacogenetics Database, Tools
"The US National Institutes of Health awarded $12.8 million to investigators at nine projects that will contribute to the creation of a public pharmacogenetics database. The tool could become available for public use within one year.

The bulk of the money will fund research that will generate the content of the database--information on drug responses in specific patient categories. But three investigators were awarded grants to create and apply bioinformatics tools that will make the data accessible.

Russ Altman of Stanford University was awarded $1.6 million to operate the Stanford Pharmacogenetics Knowledge Base (PharmGKB). NIH will give $421,000 to Yale University medical informatics professor Prakash Nadkarni to design web-based tools for incorporating existing pharmacogenetics knowledge into that database. And Richard Weinshilboum at the Mayo Foundation in Rochester, Minn., will use a $576,000 award to search for variations in genes encoding proteins already known to be important in the body's handling of an array of medicines, hormones, and chemical messengers."

"For the pharmacogenetics network, Nadkarni has proposed using the National Library of Medicine's Unified Medical Language System to design a "smarter" database search tool that scans text not just for matching phrases, but also for words with similar meanings. He explained, "Simple word indexing doesn't consult a thesaurus, but as it happens, there is a humongous thesaurus of all medical terms and quite a lot of bioinformatics terms in the Unified Medical Language System."

redux [03.30.00]
JAMIA Integration and Beyond: Linking Information from Disparate Sources and into Workflow
"The vision of integrating information—from a variety of sources, into the way people work, to improve decisions and process—is one of the cornerstones of biomedical informatics. Thoughts on how this vision might be realized have evolved as improvements in information and communication technologies, together with discoveries in biomedical informatics, and have changed the art of the possible. This review identified three distinct generations of "integration" projects. First-generation projects create a database and use it for multiple purposes. Second-generation projects integrate by bringing information from various sources together through enterprise information architecture. Third-generation projects inter-relate disparate but accessible information sources to provide the appearance of integration. The review suggests that the ideas developed in the earlier generations have not been supplanted by ideas from subsequent generations. Instead, the ideas represent a continuum of progress along the three dimensions of workflow, structure, and extraction. "

JAMIA Integration and Beyond: Panel Discussion
"I think one of the toughest things we all have to deal with is updating our dictionaries. In the simplest cases, the name of an organism is changed and we just have to do the maintenance. It is tougher, when, as with Citrobacter, they do genetic studies and say, "Oh, it's really six different organisms, not one." We have the human genome project coming very quickly. Even that is just the tip of the iceberg. We're not only going to see all the genes; we're then going to see clinical tests based on gene expression. Essentially, you'll be able to look at something on the order of 180,000 gene products and whether they're up or down regulated. How are we going to integrate such an incredible amount of data at a time when we're going to also be changing how we think about these processes? Classification and simple mapping are not going to work, because the lumpers and splitters are going to be arguing furiously on a daily basis."

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SF Gate Call It the Gene Rush -- Patent Stakes Run High
"After years of bickering, the patent office has proposed adding three simple words to its guidelines. To win a patent, applicants will have to describe a ``substantial, specific and credible'' use for their gene."

John Doll, who heads the patent office's biotech division, said the guidelines essentially group the huge backlog of 30,000 patent applications into three classes.

The first are genes isolated in a laboratory, whose purpose is likely to be known. Doll calls this ``wet biology.'' Government and academic scientists have used wet biology to patent genes for 20 years. These are not controversial.

Another class of applications cover ``naked DNA sequences.'' These were the sort of early, machine-generated gene discoveries that provoked alarm in the first place. The new guidelines rule them out.

The battleground is the large number of applications that fall in the middle. These are machine-discovered genes, but they aren't ``naked sequences.'' ."

"As the controversy over ``naked sequences'' festered, biotech companies got smarter about using their machines. When they discovered a new gene, they employed software that analyzed its structure and deduced its purpose. Doll called these ``in silico'' applications -- a reference to the fact that the gene's purpose was deduced through a computer analysis."

"``It's not important that you understand the function of the gene (to get a patent), it's only important that it have a commercial utility,'' Incyte's Scott said. "

Signals Homestead 2000: The Genome
""The analogy that I would use is that of a minefield," said Bob Levy, senior VP of science and technology for American Home Products. "We are spending an incredible amount of time now, when we find exciting targets and begin to validate them, in trying to define who has rights to what. And we're finding, in almost every product that we look at, that someone has patented the protein, the gene, a fragment, a diagnostic test." Levy noted that untangling patent rights, and determining which patents are dominant, are increasingly time-consuming and expensive tasks. And patent-holders must be paid. "The royalties that will be involved soon in some of the products that we are bringing to market, they're already up into the ten, fourteen, fifteen percent [range]," said Levy. "And that may increase with time.""

Tuesday, April 25, 2000

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UniSci Selfish Gene Theory Of Evolution Called Fatally Flawed
"In the current issue of Advances in Complex Systems (February-April), Dr. Yaneer Bar-Yam, president of the New England Complex Systems Institute and an expert on the application of mathematical analysis to complex systems, contends that the selfish-gene theory of evolution is fatally flawed.

If his mathematical proof gains general acceptance, it will shut the door on controversial "gene-centered" views of evolution.

Bar-Yam, in the upcoming article, proves that the "selfish gene" approach is not valid in the general case. He demonstrates that the gene-centered view, expressed in mathematical form, is only an approximation of the dynamics actually at work."

"The key to Bar-Yam's analysis lies in recognizing three levels of structure in nature: the gene, the organism and the group (or network) of organisms."

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Wired Handy DNA Analysis
"A biochip company is closer than ever to producing a handheld device to look at DNA in a doctor's office.

Clinical Micro Sensors Monday announced the results of a clinical trial showing its technology, called the eSensor biochip, could allow doctors to quickly and accurately diagnose or help tailor medications to patients according to their genetic make-up."

"The researchers said the technology, which consists of shooting electrons through the center of a DNA double helix, works as well as more laborious technology now used for analyzing genetic material. And eSensor can do it in one step, on the spot."

"...the eSensor technology will be instrumental in detecting SNPs. SNPs or singlenucleotide polymorphisms are tiny differences among individuals that can indicate that a patient is predisposed to a certain disease, or predict how an individual will respond to a specific drug."

redux [04.11.00]
The British Medical Journal Science, medicine, and the future: Pharmacogenetics
"Pharmacogenetic testing may provide the first example of a mechanism whereby DNA based testing can be applied to populations, but we are still a long way from having a pharmacogenetic DNA chip that general practitioners can use to identify all the drugs to which any particular patient is sensitive. However, there is increasing evidence that pharmacogenetics will be extremely important in the health service. One day it may be considered unethical not to carry out such tests routinely to avoid exposing individuals to doses of drugs that could be harmful to them. The ability to identify sensitive individuals, either before drug treatment or after an adverse drug response would also be of economic importance as it would avoid the empiricism associated with matching the most appropriate drug at its optimal dose for each patient. It might also substantially reduce the need for hospitalisation, and its associated costs, because of adverse drug reactions.

Our increasing knowledge of the mechanisms of drug action, the identification of new drug targets and the understanding of genetic factors that determine our response to drugs may allow us to design drugs that are specifically targeted towards particular populations or that avoid genetic variability in therapeutic response. The extent of genetic polymorphism in the human population indicates that pharmacogenetic variability will probably be an issue for most new drugs.

The development of pharmacogenetics provides at least one mechanism for taking prescription away from its current empiricism and progressing towards more "individualised" drug treatment. In view of the momentum that pharmacogenetics is developing, it is essential that the subject is taught as part of the medical student curriculum."

redux [04.16.00]
The New York Times Back to the Future: Medicine and Our Genes
[requires 'free' registration]
"SINCE the invention of the stethoscope by the French physician Réné Laennec in 1816, medicine has been troubled by a predicament: the technological advances that have enhanced our ability to diagnose and cure have also distanced us from our patients.

This problem was highlighted recently, when PE Celera Corporation, of Rockville, Md., announced that it had identified the three billion chemical letters of which human genes are made -- a feat accomplished by row upon row of tireless, automated gene-sequencing machines, like something out of Aldous Huxley's "Brave New World."

But this time technology has finally advanced far enough that it will enable medicine and medical research to return to some of its best, and most old-fashioned, traditions. In fact, the emerging gene sciences will reunite the patient, doctor and researcher in ways not seen since the 19th and early 20th centuries."

redux [04.16.00]
GeneLetter Genetics for all
"The topic of human genetics did not play a prominent role in the health care reform debates that began in the U.S. in the early 1990s. While participants recognized how progress in the field could revolutionize medicine and emphasize prediction and prevention in clinical practice, the reforms proposed for the multi-billion dollar health care industry did not utilize the "genetic card".

"While I am optimistic about technology providing us with new ways to attack important social problems, I do not think it is a cure-all. Making sure everyone can benefit from the new, genetically-informed medicine is a moral and political dilemma as much as a technological challenge. To be properly dealt with, it will require continued broad based, informed public debate and democratic action. "

Monday, April 24, 2000

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eurekalert! Genome annotation experts take standardized test
"Now that the age of the genome is upon us, scientists must find a way to spin mountains of DNA code into biological gold. To do it, they are building their own Rumpelstiltskins: powerful computer programs that automatically scrutinize the code and decipher its genetic elements. The April issue of Genome Research reports a new enterprise to test the state of the art in computer "genome annotation." Organized by a team from University of California, Berkeley, 12 international groups compared the power of their computer programs to predict gene elements within a 3 million base pair stretch of Drosophila DNA.

The groups compared the results of their programs against each other and against the results of an exhaustive experimental and computational effort to locate all the genes in this region (not available to the participants during the test).

When the results were in, many programs had detected the genes in the region with 95% accuracy compared to the experimental effort. Furthermore, the programs made predictions of genes that had not been found in that effort, which researchers are now investigating. However, the programs were less accurate in defining the exact boundaries of the genes within the code, and groups that attempted to find elements controlling gene activity (e.g., promoters) made a large number of false predictions."

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Conference Bioinformatics Open Source Conference
"The Bioinformatics Open Source Conference (BOSC) is the successor to the successful bioperl-99 conference. Like bioperl-99, BOSC is a satellite conference of ISMB, allowing people who are making the trip to San Diego to extend it for a couple of days and talk real code.

BOSC is designed to be open to all the open source efforts in bioinformatics, including Perl, Java, Python, C and C++ - even Fortran would be fun. We don't expect all attendees to be participating in a particular open source project (like, say, biojava), but we do expect that a lot of the people involved in the open source projects in bioinformatics will attend."

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Salon Lean, green gene-counting machine
"What the debate is really about is licensing strategy. It's not about patents at all. When people get upset about a patent, it's usually because they think they're going to be barred from using the information. But that only rarely happens. If you look at companies like Intel and Motorola, you'll find they have thousands of patents. But you very rarely hear anyone complain that they've been barred from doing something -- and that's because the high-tech companies generally just cross-license each other. They look at the patent system as a way of getting a financial return on their R&D. And that's exactly our approach. We license our patents broadly, not exclusively. And so far, drug companies have taken out over 30,000 licenses to our intellectual property. "

redux [03.29.00]
LinuxWorld Farming, Linux-Style
"Gone are the days when any pioneer with a bit of hardware, hard code, and hard work could run a small Linux farm and compete with the best plantations. The smart folks at biotech firm Incyte Genomics of Palo Alto, Calif., have just invented agribusiness. You remember everything you ever tried to tell your boss or colleagues about Linux's stability, price performance, and reliability? Well, Incyte has put those ideas to the test and come up grinning like a bandit.

To map the human genome, Incyte runs the world's largest commercial Linux farm, with more than 2,000 Linux processors chomping away on tens of millions of jobs per day. In its datacenter, laid out like a temple in the middle of Incyte's corporate headquarters, space costs a king's ransom -- but the company has come up with clever ways to address that problem..."

redux [03.18.00]
HMS Beagle Patenting Genes Is It Necessary and Is It Evil?
[requires 'free' registration]
"Last October, biologists' neck hair rose when J. Craig Venter announced his company, Celera, had filed 6,500 provisional patent applications for human genes. Henry Ford mass-produced automobiles - it seems evident we are now entering an era in which intellectual property is rolling off the assembly lines. Is this really the ultimate legacy of Watson and Crick's elegant double helix? And what does it portend for the future of biology?"

Friday, April 21, 2000

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Science Prime Pedigrees
[full text can be viewed for free once registered]
"Genetic counselors, investigators, and physicians who need to maintain pedigrees for genetic analysis will find a friend in Cyrillic 3. The software is simple to use and makes drawing pedigrees by hand a thing of the past. Retrieving and updating pedigree databases are also uncomplicated, thanks to useful tools in Cyrillic 3. With little practice, one can create, download, and analyze pedigrees easily."

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Science An Improved Tool for Molecular Biology
[full text can be viewed for free once registered]
"In 1998, Oxford Molecular Group released a comprehensive nucleic acid and protein sequence analysis package for the Windows platform. This package provided a significant resource for investigators who wished to have sequence analysis capabilities on their own PC. In its latest release, OMIGA 2.0, a number of new features have been included along with several fixes and improvements."

"This release of OMIGA improves the software product, which should continue to serve as a valuable resource to laboratories that require rapid sequence analyses and definition of strategies for such procedures as cloning and PCR primer design, as well as analysis of peptide and protein sequence properties."

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Science Modeling Population Genetics
[full text can be viewed for free once registered]
"Population genetics relies heavily on mathematical modeling to make quantitative predictions about the behavior of genes in populations. These models are based on the principles of classic Mendelian gene inheritance; the Hardy-Weinberg equilibrium law, which predicts the gene frequency in a population; and Darwin's theory of natural selection.

"PopGene version 1 is a simulation program that explores the parameters that affect the behavior of alternative forms of a gene (alleles) in a population. The program window is composed of three smaller windows specifying the parameters used, the calculated allele frequencies through each generation, and the graphical output of the calculations."

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GeneLetter Unusual polymorphisms in HIV-1 associated with slow or no disease progression
"Patients with nonprogressive HIV-1 infection exhibit difficult-to-revert polymorphisms in HIV-1 sequences, according to a report in the May issue of the Journal of Virology."

"Dr. Desrosiers and colleagues conclude, "Although we have not directly demonstrated that these deletions have contributed to [the patients'] rate of disease progression, they appear to be associated with the unusual clinical status of these individuals in an apparently nonrandom fashion."

Thursday, April 20, 2000

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The LA Times Biotech Firm's Mix-Up on Fly Genome Creates a Stir
"In a scientific mix-up that has gene researchers buzzing, the biotechnology company that deciphered the genetic code of the fruit fly inadvertently included stretches of human genetic material in data it posted on a public Web site.

The error by Maryland-based Celera Genomics was discovered by federal officials who monitor GenBank, the database where the codes of the fly and other creatures are freely available. The company retracted the information a few days ago, soon after being told of the error.

The mix-up, which is unlikely to cause any lasting scientific damage, has nonetheless become another issue dividing the scientific community at a time when Celera and a consortium of public genome centers are racing to complete and publish a working draft of the human genetic code. Scientists with the public Human Genome Project say that the discovery of human genetic code fragments and other more vexing errors in Celera's fly data are evidence of the company's rush to publish and the pressures of competition. Some wryly compare the mix-up to the plight of the genetically confused part-human, part-fly character in the classic horror movie "The Fly.""

Wednesday, April 19, 2000

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Conference DIMACS/IBM Workshop on Data Mining in the Internet Age
The objective of this workshop is to bring together premier researchers in the area of data mining for a workshop at IBM Almaden, May 1-2, 2000. As growing amounts of scientific and business data are warehoused in large data repositories, there is burgeoning interest in extracting valuable information latent in these warehouses. The growth of the internet has led to an explosion in the volume of information being gathered, as well as to the diversity of researchers from various backgrounds - from databases, statistics, machine learning and algorithms - attempting the advance the state of the art in data mining. "

[Program Includes]

"Simon Kasif, Compaq Cambridge Research Laboratory and MIT Genome Center Mining Biological Databases: From Gene Finding to Drug Discovery

"Shinichi Morishita, University of Tokyo" Association Rules, Boosting, and Genome Mining"

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Wired Biotech Can Be Fun
"Scientists should quit fretting about how to classify organisms and start figuring out how to make biology a unifying influence for researchers, doctors and their patients, biology pioneer Dr. Leroy Hood said Tuesday."

""I think we can revolutionize and transform the teaching of biology if we look at it as an informational science," said Hood, who began his career at Caltech, where he developed some of the first DNA sequencing machines."

"He said the most important place for that shift to take place is in medical schools."

Tuesday, April 18, 2000

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BioResearch Online Microarrays Used to Discover What Genes Are Regulated by Leptin
"In an article in the April 15 issue of the journal Genes & Development, Jeffrey M. Friedman, Howard Hughes Medical Institute investigator, and his colleagues at The Rockefeller University (New York) report that the “fat” hormone leptin alters gene expression in fat cells. Using expression arrays, the researchers found the pattern of expressed genes changed in fat cells following administration of leptin."

"To discover how exactly leptin causes weight loss, Friedman and colleagues took mRNA samples from the fat cells of normal mice and leptin minus mice given the hormone, and interrogated a chip array containing probes for thousands of genes. The researchers found that mice lacking leptin that were given the hormone had a different expression profile than those not given the hormone, indicating that at least some of leptin’s effects are due to effects on transcription."

Analyzing data from many such experiments with the mice, the scientists were able to group the expressed genes into clusters that appeared to behave similarly—increasing or decreasing in expression in tandem—as the mice were subjected to different regimes of leptin treatment or food restriction."

"We were able to find at least half a dozen distinct clusters of genes that were specifically regulated by leptin and that were not regulated in the same way by food restriction," said Friedman. "So leptin is doing a lot more than just leading to food intake restriction.""

Sunday, April 16, 2000

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The New York Times Back to the Future: Medicine and Our Genes
[requires 'free' registration]
"SINCE the invention of the stethoscope by the French physician Réné Laennec in 1816, medicine has been troubled by a predicament: the technological advances that have enhanced our ability to diagnose and cure have also distanced us from our patients.

This problem was highlighted recently, when PE Celera Corporation, of Rockville, Md., announced that it had identified the three billion chemical letters of which human genes are made -- a feat accomplished by row upon row of tireless, automated gene-sequencing machines, like something out of Aldous Huxley's "Brave New World."

But this time technology has finally advanced far enough that it will enable medicine and medical research to return to some of its best, and most old-fashioned, traditions. In fact, the emerging gene sciences will reunite the patient, doctor and researcher in ways not seen since the 19th and early 20th centuries."

GeneLetter Genetics for all
"The topic of human genetics did not play a prominent role in the health care reform debates that began in the U.S. in the early 1990s. While participants recognized how progress in the field could revolutionize medicine and emphasize prediction and prevention in clinical practice, the reforms proposed for the multi-billion dollar health care industry did not utilize the "genetic card".

"While I am optimistic about technology providing us with new ways to attack important social problems, I do not think it is a cure-all. Making sure everyone can benefit from the new, genetically-informed medicine is a moral and political dilemma as much as a technological challenge. To be properly dealt with, it will require continued broad based, informed public debate and democratic action. "

Saturday, April 15, 2000

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Bioresearch Online Free Genetic Analysis Software Available on Biowire.com
"Biowire.com (Mountain View, CA) has released its own genetic analysis software package, called Jellyfish, which it is making freely available to life science researchers through the Internet. According to a company release, the new package features easy-to-use tools, graphical sequence display for easy navigation, and one-click submission of sequences to genetic analysis web sites."

"Jellyfish provides a uniform Internet gateway that enables scientists to simultaneously submit and analyze information from multiple genetic databases. It performs the most often used data analyses, such as viewing DNA and protein sequence information, restriction enzyme analysis, and DNA/protein alignment."

"In addition to Jellyfish, Biowire.com, which was established in December of last year by four scientists with some venture capital backing, provides user-generated reviews of products for life science research."

Tools: biowire
"Biowire.com's mission is to become the definitive resource of knowledge and tools that bioresearchers need for efficient and successful science. Targeted to 400,000 life science researchers worldwide, the company's web site provides free, easy-to-use analytical tools and scientist-authored reviews of high-end, experiment-specific research products, such as enzymes, antibodies and reagent kits. Biowire.com has rapidly grown through a program of scientist-to-scientist referral to become one of the largest and most active Internet sites in the life sciences market. The web site now has over 17,000 registered users at more than 2,000 academic, commercial, and industrial organizations in 45 countries."

Friday, April 14, 2000

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The New York Times Energy Deptartment Experts Open Way to Gene Search in Genome Project
[requires 'free' registration]
"Biologists at the Department of Energy have gathered raw DNA data sufficient to search for genes on three human chromosomes, Secretary Bill Richardson said yesterday."

"The department's Joint Genome Institute, in Walnut, Calif., has now fulfilled, well ahead of deadline, its quota as part of the consortium's goal of achieving a "rough draft" of the human genome by the end of June."

Wednesday, April 12, 2000

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Conference: COMPUTER SCIENCE AND BIOLOGY- 2000
"The conference is one of the oldest (established 1985) and most traditional conferences in the rapidly expanding field of Bioinformatics and Computational Biology. The main focus of the conference is on current research in the theory and application of methods in bioinformatics that complement experimental research in the molecular biosciences. It seeks to expand its focus to various relevant aspects of computational biology such as theoretical biology, computational biochemistry, user-oriented representation and data-mining of biological data etc."

Tuesday, April 11, 2000

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BBC News Scientists target 'quiet' genes
"Researchers have developed a new way of hunting down the human genes which have so far evaded identification.

It is thought that these elusive genes are only active at very low levels or only in certain types of cells, at certain times. However, they could play key roles in how cells grow and develop and could be responsible for diseases such as cancer."

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The New York Times The Fly Frontiers of Genetics
[requires 'free' registration]
"The dung beetle was worshiped by the ancient Egyptians, and the honeybee has always had its admirers, but only one insect has a computer database, its own new CD-ROM and an international cult of 5,000 followers, each with a Ph.D."

"Even when roles have been assigned to all of the fly's presently predicted genes, Drosophilists will still be one major step away from the total definition of the fly. Imagine having a full list of parts for a Boeing 747 but not a single instruction for how to assemble them. Drosophila melanogaster has, perhaps, a fourth great gift of knowledge still concealed within its frail, miraculous body."

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The British Medical Journal Science, medicine, and the future: Pharmacogenetics
"Pharmacogenetic testing may provide the first example of a mechanism whereby DNA based testing can be applied to populations, but we are still a long way from having a pharmacogenetic DNA chip that general practitioners can use to identify all the drugs to which any particular patient is sensitive. However, there is increasing evidence that pharmacogenetics will be extremely important in the health service. One day it may be considered unethical not to carry out such tests routinely to avoid exposing individuals to doses of drugs that could be harmful to them. The ability to identify sensitive individuals, either before drug treatment or after an adverse drug response would also be of economic importance as it would avoid the empiricism associated with matching the most appropriate drug at its optimal dose for each patient. It might also substantially reduce the need for hospitalisation, and its associated costs, because of adverse drug reactions.

Our increasing knowledge of the mechanisms of drug action, the identification of new drug targets and the understanding of genetic factors that determine our response to drugs may allow us to design drugs that are specifically targeted towards particular populations or that avoid genetic variability in therapeutic response. The extent of genetic polymorphism in the human population indicates that pharmacogenetic variability will probably be an issue for most new drugs.

The development of pharmacogenetics provides at least one mechanism for taking prescription away from its current empiricism and progressing towards more "individualised" drug treatment. In view of the momentum that pharmacogenetics is developing, it is essential that the subject is taught as part of the medical student curriculum."

Wired Designer Drugs First HGP App
"New research reinforces that testing individuals to predict how they will respond to drugs will change the face of medicine in less than five years. A pair of British researchers claim that pharmacogenomics, the field of study that promises to measure, interpret, and understand variations in peoples' genes, will be one of the first practical applications to benefit from the Human Genome Project."

"In England, one in 15 hospital admissions is due to an adverse drug reaction, and in the United States, a study found that about 106,000 patients die and 2.2 million are injured every year by bad reactions to prescription drugs, according to the report."

Monday, April 10, 2000

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BBC News Gemini to patent disease data from Human Genome Project
"Gemini Genomics, the private biotechnology company, is expected to announce on Tuesday a multimillion dollar collaboration to trawl the Human Genome Project for disease-related data which it can patent."

"Gemini and Sequenom will focus their efforts on chronic diseases such as osteoporosis, diabetes and obesity. They plan to file broad patent claims covering the use of gene products in the diagnosis of disease, diagnostic tests and pharmacogenomics - the use of genetic information to match patients with the drugs most likely to be effective or to avoid potentially dangerous drug reactions."

Yahoo! News Gene Expert Says Industry Tries to 'Patent Rainbow'
"Scientists mapping the genetic blueprint of the human body believe that while patents on genes are necessary, they should not be used by industry hoping to profiteer by claiming ownership of basic science."

"Companies are trying to ``patent the rainbow'' by filing applications to patent gene sequences without a clear idea of their function or use, scientists said on Monday at a Human Genome Organization (HUGO) conference."

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BBC News Caution urged over genome hype
"Scientists have attempted to deflate what they see as the hype now surrounding the quest to decode the human genetic blueprint."

""You should not take at face value any claim by any group for at least two years that says 'we have finished sequencing a human genome sequence'. It will not be true," Dr Francis Collins told reporters prior to the start of the Human Genome Meeting 2000."

""All of us need to be very careful in our language. When somebody says 'done' or 'finished' or 'completed', you need to ask them what their definition is because the answers may be very interesting."

Friday, April 07, 2000

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The Washington Post Celera Hits Gene Map Milestone
""It would be a huge mistake to say that this company has sequenced a human genome," said Eric Lander, director of the Whitehead Center for Genome Research in Boston, which estimates it has contributed about 25 percent of the publicly available sequenced information so far. "People may have the misimpression that a private company has sequenced the human genome. Today more than 70 percent of the human sequence is already on the Web from the public sequencing project. We're proud of that and we're glad Venter has been able to use that data to help him get to where he is.""

The New York Times Analysis of Human Genome Is Said to Be Completed
[requires 'free' registration]
"Dr. J. Craig Venter told a Congressional committee today that his company, the Celera Corporation, had finished analyzing all necessary pieces of human DNA and would assemble the whole human genome within three to six weeks, far earlier than expected."

"Dr. Venter said that after the human genome was assembled, he would convene a conference of outside experts to annotate it, meaning to identify where the genes lie on the DNA and what they do. Annotation is achieved with computer programs that analyze the DNA sequence, pinpoint the components of genes, and guess their biological role from comparison with known genes of other species that are already in the databases.

Only 3 percent of the human genome codes for genes, and the methods for identifying them are far from perfect. Once the annotation experts have finished their task, sometime later this year, Celera will make its human genome sequence freely available to researchers, Dr. Venter said."

"Representative Sheila Jackson Lee, a Texas Democrat, asked in relation to decoding the human genome sequence: "Does this mean we can alter the race of people? Can we design who inhabits this earth?"

Wired Rivals to Celera: 'What-EVer'
"After Celera announced Thursday morning that it had finished the sequencing phase of one person's genetic code, its shares (CRA) skyrocketed, catching a host of other biotech stocks in its upstream.

But investors are being duped by the hype, say competitors."

""From a commercial point of view, it really is a non-event," said Roy Whitfield, CEO of Incyte Genomics, a private company that sells genes individually. "About 80 percent of what they say they have achieved is already public knowledge."

""It's science by press release. You can have hype and not substance and make your stock go up.""

The Register Alpha chip powers Celera genome burst
"Biotech firm Celera said yesterday that it has now finished sequencing 99 per cent of the human genetic pattern, and confirmed it will complete its corporate push during the course of this year.

Sources close to the firm's plans said it has used "mass quantities" of an as yet unreleased 667MHz Alpha processor, each of which includes 8Mb of cache*, incorporated in four way ES40 AlphaServers."

Thursday, April 06, 2000

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CBC News Newfoundland to regulate genetic research
"Newfoundland has become a favourite spot for genetic researchers because of the province's small "gene pool." It's become so popular the government will regulate research projects and discourage exploitation. "

""Newfoundland has a very interesting population," says Dr. Jane Green, a Memorial University geneticist who identified the gene that causes colon cancer. "It's valuable for genetic research because there was a relatively small number of people who came originally and so a smaller number of particular genes."

redux [02.14.00]
Yahoo! Finance Gemini Launches New Genetics Initiative In Newfoundland & Labrador
"Gemini Holdings plc, the clinical genomics company, today announced the signing of an agreement with Lineage Biomedical Inc., of St. John's, Newfoundland, to establish a joint venture for the purpose of identifying genes for common diseases using the unique population resources of Newfoundland. The joint venture, Newfound Genomics, will establish a genetics based research facility in Newfoundland and Labrador with the aim to identify disease-causing genes."

"The Canadian province of Newfoundland and Labrador has a population of around 550,000 people, primarily descended from a small 'founder' population of English, Scottish and Irish immigrants that populated the islands between the 1600s and the 1840s. The unique population history of Newfoundland and Labrador and the increased prevalence of certain diseases, such as psoriasis, rheumatoid arthritis and diabetes, represent a powerful resource for geneticists to identify genes that predispose to these diseases."

Wednesday, April 05, 2000

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HMS Beagle Are Computers Evolving in Biology?
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"I suspect that although the new enthusiasm for computers in biology is genuine, it overlooks some basic problems in implementation. The basic difficulty, as I see it, is that although biologists use computers, they do not trust everything that comes out of them. It is one thing to use them to print up nice-looking graphs, but it is an entirely different matter to use them to think better."

"Francis Crick was once quoted as saying that no biologist had ever made a discovery using a mathematical model. I would reply that no biologist has ever made a discovery by running an electrophoretic gel. They make discoveries by using their brains. Computers, like all scientific tools, are only as good as the person who uses them. If biologists don't understand how computer models are constructed, they won't know their strengths and limitations. Without some foundation of trust, biologists will be unlikely to utilize or accept this powerful method of data analysis."

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CBS MarketWatch Celera shares rocket on Clinton's clarification
"Shares of Celera Genomics soared 54 percent on Wednesday to lead gainers on the NYSE in percentage terms, fighting back after President Bill Clinton said companies conducting genetic research should have the right to patent their discoveries."

"Clinton reiterated his administration's policy that companies which discover applications for genomics information should be able to patent them."

redux [03.18.00]
HMS Beagle Patenting Genes Is It Necessary and Is It Evil?
[requires 'free' registration]
"Last October, biologists' neck hair rose when J. Craig Venter announced his company, Celera, had filed 6,500 provisional patent applications for human genes. Henry Ford mass-produced automobiles - it seems evident we are now entering an era in which intellectual property is rolling off the assembly lines. Is this really the ultimate legacy of Watson and Crick's elegant double helix? And what does it portend for the future of biology?"

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Wired Researcher Borrows from Napster
"A researcher working on the Human Genome Project is using Napster technology, and he's not looking for T3 connections to download Moby.

Dr. Lincoln Stein, an associate professor of bioinformatics at the Cold Spring Harbor Lab in New York, is investigating ways to use Napster-type technology to allow scientists to share their discoveries of the genome.

"I was very interested when I saw Napster," Stein said. "It has a similar architecture (to what we use now), but it allows for 'peer-to-peer' data exchange and it dawned on me that it would be marvelous for our annotation system.""

Tuesday, April 04, 2000

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Science When an Entire Country Is a Cohort
[summary - can be viewed for free once registered]
"Denmark has gathered more data on its citizens than any other country. Now scientists are pushing to make this vast array of statistics even more useful by easing restrictions on the use of data coded by personal identification numbers. But government officials are reluctant to do so, citing privacy concerns."

redux [02.25.00]
Science U.K. Plans Major Medical DNA Database
[summary - can be viewed for free once registered]
"Following the examples of Iceland, Sweden, and Estonia, the United Kingdom is drawing up plans to create a national database linking the DNA of 500,000 of its citizens to their medical records and lifestyle details. Its main goal is to tease apart the genetic and environmental components of conditions such as cardiovascular disease and cancer and, eventually, to come up with new drugs to treat--or even prevent--these conditions. An expert panel is currently hammering out a strategy for setting up the database and is due to report its recommendations next month.”

redux [02.13.00]
The Daily Davos Beyond the Genome
"By the spring of this year, the first draft of the human genome -- the sequence of all the genetic instructions needed to make up a human being -- will be published on the Web. But that is only the end of the beginning. Scientists still have very little idea of what most of the 100,000 or so human genes actually do, and finding out will take them into a very different area of research.

The raw material of the genome program has been anonymous samples of DNA, manipulated by complex laboratory machines that turn out information like a production line turns out widgets. But the new era of post-genome research involves analysing real people and their confidential medical records. The records are needed to match the genes that people carry with the diseases they may develop. Only then will gigabytes of genetic data into new treatments for cancer or heart disease. And that is why socialised healthcare is a vital part of post-genome research.

Countries such as the U.S., which provide healthcare through private enterprise, are useless for this sort of genetic inquiry. Only those countries which have organized the delivery of healthcare to their population in a way that is independent of the marketplace have built up the universal medical records necessary to make sense of the patterns of disease."

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Tools: The GeneMine Project
"GeneMine is a free sequence analysis and visualization program that makes full use of analysis servers across the Internet, to automate your sequence analysis needs and filter for meaningful results. GeneMine summarizes these results as graphical annotations on your sequence alignment, in a form that can be conveniently browsed, analyzed further, saved, and even published as web pages or presentations."

"GeneMine is the third generation of the commercial sequence/structure analysis and modeling package LOOK from Molecular Applications Group (now part of Celera). Developed by Dr. Christopher Lee, LOOK/GeneMine have been widely used in the pharmaceutical industry and academia from 1994 to the present for both modeling and gene functional analysis. This package includes modeling software developed by Dr. Michael Levitt of Stanford (SEGMOD, homology modeling) and Dr. Lee (CARA, mutant modeling).

Dr. Lee joined the faculty of the UCLA Department of Chemistry in 1998, and persuaded MAG to allow UCLA to distribute the GeneMine software free to non-commercial users beginning January 2000.

The GeneMine source code is now being actively developed at UCLA under the auspices of the GeneMine Project. Our goal is to make GeneMine the most useful tool for analyzing gene function and features for scientists around the world! "

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Yahoo! Finance Motorola Invests in World's First Virtual Tissue Bank; Web-based Technology Will Facilitate Drug Discovery and Tissue Engineering
"Motorola, Inc. (NYSE: MOT - news) announced today that it has made a strategic equity investment in TissueInformatics.Inc, a privately held, Pittsburgh-based bioinformatics company that is building the world's first Virtual Tissue Banks(TM)."

"TissueInformatics is developing Virtual Tissue Banks to facilitate drug discovery, tissue engineering and the scientific evaluation of human and plant tissues. These multi-dimensional databases will help researchers transform information into scientific knowledge by converting advanced microscopic images of tissue into quantitative analyses of tissue structure, function and genetic expression. Virtual Tissue Banks of normal and diseased tissues could eventually aid researchers in finding new treatments for diseases such as diabetes, breast cancer and Alzheimer's. Researchers at pharmaceutical, genomics and tissue engineering companies will gain proprietary access to these Web-based Virtual Tissue Banks via the Internet."

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Wired New Answers to Age-Old Question
""In order to come up with drugs, we need to understand [the aging] process. Before we didn't know where to aim our gun, but now we have a model," said Danith Ly, lead author of a study published Friday in Science that identified one common element in aging tissues throughout the body. "We've provided a general marker for identifying aging, and a model for explaining the process."

"The researchers examined 6,800 genes associated with aging by using DNA microarrays, or chips, to look at gene-expression patterns. The scientists placed bits of DNA from known genes on a fingernail-sized chip and exposed it to fluorescent light, highlighting the active genes.

Only 61 out of the 6,800 genes studied lit up, indicating that only a small number of genes are active in the aging process. That narrows the playing field for researchers. "

Saturday, April 01, 2000

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Conference: EBI The Second International Meeting on Microarray Data Standards, Annotations, Ontologies and Databases
"The goal of these meetings is to create a framework for developing standards for storing and communicating microarray based gene expression data. The particular discussion topics of the meetings define the minimal information about microarray experiments that laboratories should be encouraged to provide to ensure reproducibility and verifiability of results, identify where controlled vocabularies for annotating the samples and experiments are possible, and define the data communication standards. Another important issue addressed by the meetings is developing standards for cross-platform data comparison and normalisation"