snowdeal.org > {bio,medical}informatics

ePrairie: University of Illinois at Chicago Bioinformatics Program a 'Well-Kept Secret'

2006-06-21T21:27:00.000-04:00

ePrairie University of Illinois at Chicago Bioinformatics Program a 'Well-Kept Secret'

"The University of Illinois at Chicago (UIC) is currently the only learning institution in the state that possesses an accredited bioinformatics program. UIC offers 12 credits in bioinformatics through a program called BiTmaP.

"It's a well-kept secret -- this program -- because the tuition is free," BiTmaP program director Ann Reed told ePrairie.

BiTmaP is a free training program sponsored by the U.S. Department of Labor through a $3 million grant awarded to the Chicago Technology Park. The program was created with the intent to bridge the growing gap between unemployed or underemployed IT professionals and the booming life sciences community."

eMaxHealth: Finding Gives Boost To Bioinformatics Use in Fighting Disease

2006-06-19T22:28:00.000-04:00

eMaxHealth Finding Gives Boost To Bioinformatics Use in Fighting Disease

"The use of computers to advance human disease research – known as bioinformatics - has received a major boost from researchers at the La Jolla Institute for Allergy & Immunology (LIAI), who have used it to successfully predict immune response to one of the most complex viruses known to man – the vaccinia virus, which is used in the smallpox vaccine. Immune responses, which are essentially how the body fights a disease-causing agent, are a crucial element of vaccine development."

"While bioinformatics – which uses computer databases, algorithms and statistical techniques to analyze biological information - is already in use as a predictor of immune response, the LIAI research team's findings were significant because they demonstrated an extremely high rate of prediction accuracy (95 percent) in a very complex pathogen – the vaccinia virus."

Nature: Peer Review Trial and Debate

2006-06-06T19:06:00.000-04:00

Nature Peer Review Trial and Debate

"Nature is undertaking a trial of a particular type of open peer review. In this trial, authors whose submissions to Nature are sent for peer review will also be offered the opportunity to participate in an open peer review process (see below for explanation). The trial is optional for authors; it will continue in parallel with Nature's usual procedures, and does not affect the likelihood of eventual publication of the submitted work. At the same time as the trial, Nature is running a web debate on peer review, to which we welcome comments from readers."

"The web debate contains a range of perspectives about peer review from those who believe it is working well, to those who prefer other options. What is the value of peer review, and how does it ensure quality? What are the ethical concerns? Are there viable alternatives, either technical or in terms of management of the process? And above all, what is the scientists' experience of the process, either as authors or as reviewers themselves? Nature's web debate provides a lively range of views, updated weekly."

redux [05.02.06]
The New York Times For Science's Gatekeepers, a Credibility Gap
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"Recent disclosures of fraudulent or flawed studies in medical and scientific journals have called into question as never before the merits of their peer-review system."

"Virtually every major scientific and medical journal has been humbled recently by publishing findings that are later discredited. The flurry of episodes has led many people to ask why authors, editors and independent expert reviewers all failed to detect the problems before publication."

redux [03.02.06]
The Scientist Is Peer Review Broken?
[requires 'free' registration]

"Despite a lack of evidence that peer review works, most scientists (by nature a skeptical lot) appear to believe in peer review. It's something that's held "absolutely sacred" in a field where people rarely accept anything with "blind faith," says Richard Smith, former editor of the BMJ and now CEO of UnitedHealth Europe and board member of PLoS. "It's very unscientific, really.

Indeed, an abundance of data from a range of journals suggests peer review does little to improve papers. "

redux [08.15.05]
The Boston Globe Flaws are found in validating medical studies
"Now, after a study that sent reverberations through the medical profession by finding that almost one-third of top research articles have been either contradicted or seriously questioned, some specialists are calling for radical changes in the system."

In advance of a world congress on peer review next month in Chicago, these specialists are suggesting that reviewers drop their anonymity and allow comments to be published."

""It would be lovely to start anew and to set up a trial of peer review against no peer review," Rennie said. "But no journal is willing to risk it.""

USA Today: Me, myself and my gut genome

2006-06-05T19:20:00.000-04:00

USA Today Me, myself and my gut genome

""Our body surfaces are home to microbial communities whose aggregate membership outnumbers our human somatic (functional) and germ (reproductive) cells by at least an order of magnitude," reports a research team led by Stephen Gill, who was with The Institute for Genomic Research in Rockville, Md., at the time the study was submitted to the current issue of the journal Science. The vast majority of these 10 to 100 trillion bugs live in the gut, most of them in the colon. And while the fancy-schmansy human genome got all the headlines a few years ago, Gill's team has succeeded in completing the first genetic analysis of this vast community of microbes living inside humanity's innards. At last.

Sort of like a very messy version of the Borg from Star Trek, these bugs and human beings rely on one another for survival, the team reports. Human genes don't produce some proteins that kick-start the chemistry needed to break down some foods — carbohydrates from plants, for example, something to think about the next time you eat a potato chip."

Nature: Mutant mice challenge rules of genetic inheritance

2006-05-24T17:50:00.000-04:00

Nature Mutant mice challenge rules of genetic inheritance

"In a discovery that rips up the rulebook of genetics, researchers in France have shown that RNA, rather than its more famous cousin DNA, might be able to ferry information from one generation of mice to the next."

"The new study in Nature thrusts RNA, DNA's sidekick, into the limelight. It suggests that sperm and eggs of mammals, perhaps including humans, can carry a cargo of RNA molecules into the embryo - and that these can change that generation and subsequent ones."

redux [12.07.05]
News-Medical.net MicroRNAs greatly influence the evolution of genes
"RNA continues to shed its reputation as DNA's faithful sidekick. Now, researchers in the lab of Whitehead Institute Member David Bartel have found that a class of small RNAs called microRNAs influence the evolution of genes far more widely than previous research had indicated.

"MicroRNAs are affecting the majority of protein-coding genes, either at a functional level or an evolutionary level," says Andrew Grimson, a post-doctoral fellow in Bartel's lab."

Wired News MicroRNA Is a Big Topic in Bio
"Researchers estimate there could be anywhere from 200 to 1,000 miRNAs -- the range is wide because miRNAs are so small, making them difficult to detect. Gary Ruvkun, a Harvard University researcher and pioneer of miRNA research, has called the tiny entities "the biological equivalent of dark matter, all around us but almost escaping detection.""

redux [09.13.05]
Palm Beach Post Scripps Florida scientists explore RNA
""We have to redefine the definition of a 'gene,' " said Claes Wahlestedt, pharmacogenomics director for The Scripps Research Institute in Jupiter.

It appears that DNA's sibling, RNA, or ribonucleic acid, plays a key role in the regulation of genes. Its molecules act as both management and labor within the cell, transcribing some genes into hardworking proteins while preventing the expression of others, Wahlestedt said."

"Scientists call a theory first advanced by Francis Crick the "central dogma" of biology. It said that DNA spelled out a gene, RNA read the gene and then RNA helped make the gene's protein. The latest research is forcing a much more complex view of biology.

"Taken together, it means the central dogma since the 1950s has to be rethought," Wahlestedt said."

Stanford Medicine Magazine Secret life of RNA
"Part of RNAi’s mystery is its very unexpectedness. RNA’s normal role in the cell is to carry a message from a gene to the cytoplasm where it directs a protein-making assembly line. That public life of RNA has been known for decades. In RNA’s covert life, it destroys those very messages and prevents proteins from being made. That’s like finding out your neighbor has a secret life destroying her own landscaping. It caught people off guard.

“This changed how people think about doing science,” says Aaron Straight, PhD, assistant professor of biochemistry. He says researchers can now look at the effects of every gene in an organism. “That’s an extraordinary advantage,” he says."

Science In the Forests of RNA Dark Matter
"For a long time, RNA has lived in the shadow of its more famous chemical cousin DNA and of the proteins that supposedly took over RNA's functions in the transition from the "RNA world" to the modern one. The shadow cast has been so deep that a whole universe (or so it seems) of RNA--predominantly of the noncoding variety--has remained hidden from view, until recently.

Nor is RNA quite so inert or structurally constrained as its cousin; its conformational versatility and catalytic abilities have been implicated at the very core of protein synthesis and possibly of RNA splicing."

ScienceDaily: Drug Discovery Team To Explore Newly Discovered Deep-sea Reefs

2006-05-23T19:30:00.000-04:00

ScienceDaily Drug Discovery Team To Explore Newly Discovered Deep-sea Reefs

"Harbor Branch scientists, along with colleagues from the University of Miami, will use the Harbor Branch Johnson-Sea-Link II submersible to explore for the first time newly discovered deep-sea reefs between Florida and the Bahamas. The reefs were discovered in 2,000 to 2,900 feet of water last December by a University of Miami team using advanced sonar techniques. A primary goal of the upcoming expedition, which is funded largely by the State of Florida's "Florida Oceans Initiative," will be to search for marine organisms that produce chemical compounds with the potential to treat human diseases such as cancer and Alzheimer's.

"We've found incredible and surprising diversity at other deepwater reefs near Miami and Bimini, and some promising potential disease treatments, so we're very excited about the chance to explore these new areas," says Amy Wright, director of the Harbor Branch Division of Biomedical Marine Research."

redux [05.10.06]
Bio-IT World Gilna to Captain CAMERA
"Later this summer, coinciding with the publication of the first peer-reviewed paper on results from J. Craig Venter’s worldwide voyage sampling ocean genomes, researchers will gain access to version 0.5 of CAMERA—the Community Cyberinfrastructure for Advanced Marine Microbial Ecology Research and Analysis—a platform replete with a wealth of data, analysis tools, and high-speed computational infrastructure.

“We’ll point readers to the portal from the paper,” says Paul Gilna, who was appointed executive director of CAMERA last month. Gilna is an experienced science program administrator who helped launch GenBank, worked on the protein data bank (PDB), and was a director of DOE’s Joint Genome Institute at Los Alamos National Laboratory. He hopes CAMERA will help jumpstart and grow the nascent field of metagenomics."

redux [05.08.06]
ABC Science Online Deep sea new site for 'lawless gold rush'
"Biotechnology companies are profiting from living resources found in the deep ocean without laws to ensure their actions are sustainable and fair, says an Australian environmental lawyer.

Dr David Leary of Macquarie University in Sydney says his research has revealed there are six companies selling products derived from the deep ocean and another eight developing them.

"They are the main players in the biotech industry; they're North American and European companies," he says."

"He says 70% of the ocean is beyond national jurisdiction and most of that is the area known as the deep seas or high seas, around 5 to 10 kilometres deep."

redux [04.30.02]
Washtech.Com A New Outlet for Venter's Energy
"Tapping a $100 million research endowment he is creating from his stock holdings, Venter plans to scour the world's deep ocean trenches for bacteria that might be able to convert carbon dioxide, the gas released when cars and power plants burn fuel, back into solid form without needing a lot of sunlight or other energy."

"Venter emphasized that from now on, his ventures will be set up as not-for-profit corporations. "I'm not in business anymore," he said."

Genomeweb: Genomic Tools Helped Drive 52-Percent Jump in R&D Success at Big Pharma; More Business Likely

2006-05-22T17:47:00.000-04:00

Genomeweb Genomic Tools Helped Drive 52-Percent Jump in R&D Success at Big Pharma; More Business Likely
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"Genomic technologies have helped to significantly increase the number of drug candidates that enter clinical trials at the world's biggest pharmas, according to a report released last week from the Tufts Center for the Study of Drug Development."

"Though the study did not seek to learn why R&D productivity increased or to address technological tools that might have helped enable it, TCSDD Director Kenneth Kaitin said discussions he has with officials from big pharma indicate that genomic technologies and methodologies have played "an increasingly important role" in driving the improvement. These tools and methods include mass spectrometry, genome sequencing, gene-expression, high-content screening, and SNP-genotyping.

The report also showed that the overall percentage of drugs that reach the clinic and go on to win US Food and Drug Administration approval - 20 percent - hasn't changed much in 30 years. But most of these candidates began life in the clinic before genomic tools were widely used, and big pharma, emboldened by the way these tools lifted their overall R&D productivity, may decide that investing more in new technologies might lead to better data and improved odds with regulators for the next crop of drug candidates."

redux [03.17.04]
Genomeweb Genomics Hasn't Solved Pharma's Pipeline Problem, But FDA Proposes a Solution
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"A new white paper from the US Food and Drug Administration outlines a new FDA initiative to translate the promise of biotechnology into improved healthcare by driving recent technological advances in early discovery through the later stages of the drug development pipeline.

Despite the rise of genomics, proteomics, bioinformatics, and other new technologies, the FDA notes that the number of new drug and biologic applications submitted to the agency has actually declined since 2000, and the number of medical device applications has also decreased. The primary problem, according to the report, is that "the applied sciences needed for medical product development have not kept pace with the tremendous advances in the basic sciences.""

redux [03.19.03]
BioMedNet Biotechnology: which way now?
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"Which approach is more likely to make a biotechnology company successful: a focus on novel technologies or on development of novel compounds?

Getting into clinical compounds has been portrayed as the route out of tough times like those the biotech industry is suffering through now, according to Mark G. Edwards, founder of Recombinant Capital, a California consulting firm and purveyor of biotech financial databases. But the data show, he says, that there doesn't seem to be any sure route out; companies specializing in compounds have fallen just like those specializing in technology."

redux [04.19.02]
The New York Times Despite Billions for Discoveries, Pipeline of Drugs Is Far From Full
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"This should be the golden age for pharmaceutical scientists. The deciphering of the human genome is laying bare the blueprint of human life. Medical research has increased understanding of disease. Robots and computers are turning drug discovery from a mixing of chemicals in a test tube to an industrialized, automated process."

"Instead of narrowing the list of compounds that might be useful in drugs, automation has broadened it -- greatly increasing the number of formulas tested without yet delivering commensurate growth in safe and effective drugs."

redux [12.14.01]
GenomeWeb Big Pharma, On the Ropes, Says it Knows What it Wants from Genomics. But Will That Spur a Turnaround?
"And although the drug industry remains the most profitable worldwide--it generated profits as a percentage of revenues four times the median rate for all Fortune 500 firms during the end of the last decade, according to a Kaiser Family Foundation report released that day--an editorial in this month's Nature Biotechnology by David Horrobin, CEO of Laxdale Research, in Stirling, Scotland, had this to say: "With rare exceptions, most of the top 20 multinational pharmaceutical companies are not generating in-house the new products needed to sustain the rates of growth they have enjoyed in the past.

"No serious industry onlooker could dispute this depressing picture," the commentary continues. "Although a few pharmaceutical companies may survive in their present form, most cannot.... A few brave companies are recognizing the obvious: large companies excel at sales and marketing but are hopeless at innovative research.""

redux [05.26.00]
Biospace Biotech Productivity: Myth or Method?
""The data suggest that the biotechnology industry used to be more productive than Big Pharma, but not any longer," said Rebecca Henderson, a professor at MIT's Sloan School of Management whose been studying the question for six years. "The public biotechs have declining productivity... and look as if they are running into the same problems as Big Pharma."

On every metric that Henderson has studied---number of scientific papers and patents per R&D dollar, cost per new drug--she found that biotech and Pharma productivity were quickly converging, and both were getting worse. After spending six years of studying the question, Henderson says she has found "no systematic evidence that small firms are more productive.""

redux [11.29.01]
The Scientist A Flood in Genomics
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"Glenn Giovanetti at Ernst & Young Life Sciences Industry Services, comments "You could really compare [today's situation] to a large degree with the first biotech boom in the late eighties and early nineties where the thought was, 'Hey, this is going to lead to better drugs faster,' and clearly that hasn't been the case." Having the genome in hand has brought about more drug targets, but, explains Ma, "People are getting more concerned that novel targets are going to have a higher rate of failures because there is less information on them." And when working in 10-year drug-development cycles, failures are costly.

Ma points to a trend of growth in clinical informatics that would effectively garner more information from expensive clinical trials instead of simply treating them as regulatory hurdles. "People are beginning to think through to how ... to take greater advantage of that information," he adds. But increasingly, the suppliers of genomic information have been looking to do the same thing.

Guardian Unlimited Books: Why I'm not a daffodil

2006-05-19T23:23:00.000-04:00

Guardian Unlimited Books Why I'm not a daffodil

"For most of the past 150 years, genetics has been the science of difference - what distinguishes a blue-eyed from a brown-eyed person, or both from a chimpanzee. By contrast, development has been the science of similarities: how is it that humans are so extraordinarily identical; nearly all of us growing up bilaterally symmetrical, with two arms and two legs, with exquisitely functioning though almost unimaginably complex brains? And while genetics became increasingly clever at accounting for such differences as blue versus brown eyes, it gulped and gave up the attempt to explain why, although humans are 98.8% genetically identical to chimpanzees, no one would mistake one for the other. What in this tiny 1.2% could account for the dramatic differences between two such closely related species? Meanwhile, generations of developmental biologists had studied in painstaking detail the seamless cellular cascade that leads, for instance, from the fertilised chick egg to the formation of its wings. But their work seemed to stall. It was time for the geneticists to come to the aid of the embryologists.

Yet despite valiant attempts to bring together these crucial pieces of the biological jigsaw, progress was painfully slow until the last couple of decades, when new insights into the mechanisms and control of gene action have begun to pour out of the molecular biology labs. It is these new findings that are contributing to what Sean Carroll, a distinguished researcher in the field, calls the Third Synthesis, of evolution, genetics and development, or, in the argot its practitioners so enjoy, Evo Devo."

redux [07.29.04]
Science & Theology News Accessible ‘Endless Forms’ shows the evolution of evolution
"The [ intelligent design ] people argue that the world is just too complex to have come about through blind law — intelligence must have intervened. However, evo-devo [ evolutionary development ] today is starting to fill in the gaps — the gaps that, in the opinion of Michael Behe and his friends, demand miracles. Existence is a miracle and life is a miracle, but increasingly it seems that the gaps do not need special miracles. Regular science can do the job.

More generally, I would go back to where I came in. The best of all arguments against the critics of science is the wonderful world that the best science reveals and explains. Offense is the best defense. Richard Dawkins is surely right when he argues against the cramped little medieval world of Genesis taken literally, and for the wonderful land of evolutionary studies. Sean Carroll’s book on evo-devo is a great passport to that land. "

Science & Theology News The problem with Darwinian solutions
"To sum up, developmental geneticists have found that the genes that seem to be most important in development are remarkably similar in many different types of animals, from worms to fruit flies to mammals.

Initially, this was regarded as evidence for genetic programs controlling development. But biologists are now realizing that it actually constitutes a paradox: if genes control development, why do similar genes produce such different animals? Why does a caterpillar turn into a butterfly instead of a barracuda?

If evo devo actually resolved the problems raised by these questions, then more power to it. Yet the real problem here is that Darwinian biologists like Carroll and Darwinian philosophers of biology like Ruse are pretending that evo devo has resolved fundamental problems of evolutionary biology when in fact it hasn’t.

2006-05-18T20:28:00.000-04:00

Nature Human genome completed (again)

"Chromosome 1 is the largest human chromosome, containing about 8% of the entire genome. That's six times longer than its smallest sibling, chromosome 21. Work on this monster started a couple of years after researchers cracked into some of the other chromosomes, says Simon Gregory of Duke University in Durham, North Carolina. Gregory led the project's team of more than 160 collaborators in their eight-year quest.

The task took so long, Gregory says, that it was regularly ridiculed in the annual pantomime at the Wellcome Trust Sanger Institute in Cambridge, UK, where much of the sequencing was done. "There's always friendly rivalry to get your chromosome out first," he says. Now it's finally done, "it's an incredible relief," he adds."

Medical News Today Genome Doesn't Start With ‘G' - Study Of The Largest And Last Chromosome Of The Human Genome Published
"The sequence of human chromosome 1 is 223,569,564 bases of genetic code - around 8% of our genome - and contains about twice as many genes as the average chromosome. “The size of chromosome 1 means its landscape spans extremes in gene content, with stretches of millions of bases of gene-rich oases and gene-poor deserts,” continued Dr Gregory, “as well as regions of the chromosome that are copied during early and late phases of cell division.”

But the sequence must be mined to be of benefit: for example, differences in the sequence between individuals will help develop an understanding of diseases associated with this chromosome. Almost 4500 single-letter changes in the genetic code (called SNPs) were identified that could lead to changes in protein activity. In addition, 90 SNPs were found that would result in a shortened - and possibly inactive - protein."

Nature: Chimpanzee and human ancestors may have interbred

2006-05-17T14:19:00.000-04:00

Nature Chimpanzee and human ancestors may have interbred

"The evolutionary split between humans and our nearest evolutionary cousins, chimpanzees, may have occurred more recently than we thought, according to a new comparison of the respective genetic sequences. What's more, it might have been a messy divorce rather than a clean break — leading to the controversial theory that our two sets of ancestors may have interbred many thousands of years after first parting company."

"If such a hybrid population really did exist, the question remains as to whether it died out, or whether modern humans or chimpanzees (or both) are its descendants. It's very difficult to say, admits Reich. "The fossil data suggest — very tenuously — that it may have been humans who are descended from the hybrid population."

redux [03.09.06]
BrightSurf.Com Most human-chimp differences due to gene regulation – not genes
"The vast differences between humans and chimpanzees are due more to changes in gene regulation than differences in individual genes themselves, researchers from Yale, the University of Chicago, and the Hall Institute in Parkville, Victoria, Australia, argue in the 9 March 2006 issue of the journal Nature.

The scientists provide powerful new evidence for a 30-year-old theory, proposed in a classic paper from Mary-Claire King and Allan Wilson of Berkeley. That 1975 paper documented the 99-percent similarity of genes from humans and chimps and suggested that altered gene regulation, rather than changes in coding, might explain how so few genetic changes could produce the wide anatomic and behavioral differences between the two."

redux [01.24.06]
Guardian Unlimited Closer to man than ape
"They already use basic tools, have rudimentary language and star in TV commercials, but now scientists have proof that chimpanzees are more closely related to humans than other great apes.

Genetic tests comparing DNA from humans, chimps, gorillas and orang-utans reveal striking similarities in the way chimps and humans evolve that set them apart from the others.

The finding adds weight to a controversial proposal to scrap the long-used chimp genus "Pan" and reclassify the animals as members of the human family. The move would give chimps a new place in creation's pecking order alongside humans, the only survivor of the genus Homo."

redux [09.27.05]
The Washington Post New Analyses Bolster Central Tenets of Evolution Theory
"When scientists announced last month they had determined the exact order of all 3 billion bits of genetic code that go into making a chimpanzee, it was no surprise that the sequence was more than 96 percent identical to the human genome. Charles Darwin had deduced more than a century ago that chimps were among humans' closest cousins.

But decoding chimpanzees' DNA allowed scientists to do more than just refine their estimates of how similar humans and chimps are. It let them put the very theory of evolution to some tough new tests."

redux [08.31.05]
MSNBC Chimp genetic code opens human frontiers
"Scientists unleashed a torrent of studies comparing the genetic coding for humans and chimpanzees on Wednesday, reporting that 96 percent of our DNA sequences are identical. Even more intriguingly, the other 4 percent appears to contain clues to how we became different from our closest relatives in the animal kingdom, they said."

"The researchers said the results confirmed the common evolutionary origin of humans and chimpanzees. Out of the 3 billion base pairs in the DNA coding for chimps and humans, about 35 million show single-base differences, and another 5 million DNA sites are different because of insertions or deletions of genetic code. Waterston estimated that 1 million of those coding changes are responsible for the functional differences between humans and chimps — thus defining our humanness."

redux [05.26.04]
Nature: Science Update Chimp chromosome creates puzzles
"What is the difference between a chimp and a human? There could be a lot more to the answer than scientists thought, according to the first accurate DNA sequence of a chimp chromosome."

"Because chimps and humans appear broadly similar, some have assumed that most of the differences would occur in the large regions of DNA that do not appear to have any obvious function. But that was not the case."

redux [04.05.04]
BBC New light shed on chimp genome
"A comparison of the chimp and human genomes casts new light on why the two species are so different despite having very similar genetic code."

"One of the leading scientists on the project says the answer lies in the process that orchestrates the genes as the chimpanzee is developing."

Biomedcentral.com Comparing relatives
"The latest experimental results have solidified evidence of a roughly 10% difference in gene expression from several regions of the brain."

"The researchers have confirmed their findings in four regions of the cerebral cortex, and in the cerebellum and the caudate nucleus. On the other hand, evidence relating to the linear accumulation of differences over time means "we are coming to believe that these are not all functionally relevant," Paabo added."

redux [12.12.03]
The New York Times Comparing Genomes Shows Split Between Chimps and People
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"In a preliminary screen, Dr. Clark and his colleagues have found that a large number of genes shows signs of accelerated evolution in the human lineage. Those are genes that, by a statistical test applied to changes in their DNA, appear to be under strong recent pressure of natural selection and so are likely to be those that make humans differ from chimpanzees.

A prominent set of accelerated human genes are those involved in hearing, particularly the gene that makes a protein called alpha-tectorin, a component of the tectorial membrane of the inner ear."

"Another group of selected genes is involved in brain development."

redux [12.10.03]
Nature: Science Update Chimp genome draft completed
"Researchers today released a draft version of the genetic sequence of our closest relative, the chimpanzee Pan troglodytes .

The differences between the chimp's genetic code and ours should reveal what makes us human, scientists hope. The disparities might, for example, lie in genes that control the development of the brain and language, or of human-specific diseases such as Alzheimer's, AIDS and malaria."

redux [05.20.03]
BBC Chimps genetically close to humans
"Scientists from the Wayne State University, School of Medicine, Detroit, US, examined key genes in humans and several ape species and found our "life code" to be 99.4% the same as chimps.

They propose moving common chimps and another very closely related ape, bonobos, into the genus, Homo, the taxonomic grouping researchers use to classify people in the animal kingdom."

redux [04.29.03]
Nature: Science Update Chimps expose humanness
"By studying chimpanzees, scientists are honing their genetic view of humanity, researchers told this week's meeting of the Human Genome Organisation in Cancun, Mexico."

"The data call for some revision of the estimated genetic similarity between us and our closest relatives. Previously, human and chimp genetic sequences were quoted as being nearly 99% identical, with a difference of only a few DNA's letters. In fact, the similarity may be as low as 94-95%, says Todd Taylor of the RIKEN Genomic Sciences Center in Yokohama, Japan.

redux [03.04.03]
Wired News You Can't Make a Monkey Out of Us
"Chimpanzees seem almost human, and scientists have maintained for decades that chimps are, in fact, 98.5 percent genetically identical to humans.

But the results of a new study call that figure into question, with a finding that there are actually large chunks of the human and chimp genomes that are vastly different."

Genomeweb How to Compare Us to Our Hairy Cousins? New Papers Provide Techniques
"It involves sampling data from select regions of many different related species, and then comparing them within the context of their phylogenetic relationships. In the research described in the Science paper, Rubin and colleagues sampled 17 primate species closely related to human and spanning 40 million years of evolution -- insufficient time for significant genetic divergence to have taken place.

According to Rubin, phylogenetic shadowing compensates for the failure of traditional comparative genomics techniques, which "invariably miss recent changes in DNA sequence that account for primate-specific biological traits." The approach overcomes the primary challenge of comparing genomes of closely related species: the difficulty in distinguishing functional from nonfunctional sequences."

InformationWeek: IBM Hopes Tech Will Unite Global Authorities In Battle Against Bird Flu

2006-05-16T22:43:00.000-04:00

InformationWeek IBM Hopes Tech Will Unite Global Authorities In Battle Against Bird Flu

"IBM, the Centers for Disease Control and Prevention, the World Health Organization, and several other public and private health care organizations from around the globe are getting together in an effort to control the spread of avian bird flu and other deadly diseases.

Researchers working under the Global Pandemic Initiative, as the project is being called, will combine information technology and health care science as they look for better ways to identify, track, and blunt the course of infectious outbreaks. "We want to see what we can do with IT to make sure the world is ready for the next pandemic," says Joseph Jasinski, IBM's program director for health care and life sciences. IBM disclosed the project on Monday."

redux [04.06.06]
New Scientist Avian flu modeled on supercomputer, explores vaccine and isolation options for thwarting a pandemic
"The large-scale, stochastic simulation model examines the nationwide spread of a pandemic influenza virus strain, such as an evolved avian H5N1 virus, should it become transmissible human-to-human. The simulation rolls out a city- and census-tract-level picture of the spread of infection through a synthetic population of 281 million people over the course of 180 days, and examines the impact of interventions, from antiviral therapy to school closures and travel restrictions, as the vaccine industry struggles to catch up with the evolving virus."

"The researchers noticed that the bills' move according to two mathematical rules, each known as a power law. One describes the distance travelled in each step of the journey, the other the length of time spent between journeys."

redux [01.26.06]
New Scientist Banknote tracking helps model spread of disease
"Tracking the movements of hundreds of thousands of banknotes across the US could provide scientists with a vital new tool to help combat the spread of deadly infectious diseases like bird flu."

"The researchers noticed that the bills' move according to two mathematical rules, each known as a power law. One describes the distance travelled in each step of the journey, the other the length of time spent between journeys."

redux [08.03.05]
National Geographic News "Bird Flu" Could Be Slowed at the Source, Study Says
"Experts from U.S. universities and Thailand's Ministry of Health used a computer model to simulate an outbreak in rural Southeast Asia—the most likely place for a new, more deadly avian influenza strain to emerge."

"Anthony Fauci directs the National Institute of Allergy and Infectious Diseases at the National Institutes of Health in Bethesda, Maryland. He called the model valuable but noted that "any model is only as good as the assumptions put into that model, and these really are only assumptions.""

HHMI News Computer Model Could Help Prevent Flu Pandemic
" In the scientists' computer model, a single resident of a rural village in Thailand was infected with a mutated H5N1 virus capable of human-to-human transmission. Scientists say that an avian flu pandemic would likely begin in southeast Asia, and the researchers chose Thailand because the type of national data they needed was easily accessible. Using information on past influenza pandemics, they calculated the number of secondary cases that would occur from the original infected individual, the normal incubation period of the illness, and the speed with which the pandemic would spread.

They then added demographic information such as regional and national population size and age; numbers of households, schools and large companies; and distances that people travel to work and school. This gave them a map of how the virus might spread."

redux [04.28.04]
The Oregonian Mathematical supermodels refine epidemic predictions
"Most modern disease models were developed about 100 years ago, she said, in response to malaria epidemics. They use statistics and a series of equations to define in general terms how epidemics progress. In graphic form, Crandall said, the models draw smooth, continuous curves.

The Reed model is notably different. Technically speaking, it relies on parametric relationships and fractals, not differential equations and curves, Crandall said. Simply put, the new model is "discrete," not "continuous." It considers millions of interactions event by event -- as represented by each tiny green speck in the virtual forest fire.

The difference is notable in disease outbreaks."

redux [04.17.03]
Stanford Medical Informatics Preprint Archive A Modular Framework for Automated Space-Time Surveillance Analysis of Public Health Data
"Public health surveillance is changing in response to concerns about bioterrorism, which have increased the pressure for early detection of epidemics. Rapid detection necessitates following multiple non-specific indicators, accounting for spatial structure, and quickly characterizing aberrancies. A single analytic method cannot meet these requirements, but there is no existing framework for the interoperation of surveillance methods. In this paper, we present such a framework and report on a preliminary implementation. Our framework consists of a decomposition of the surveillance analysis task into sub-tasks, and an ontology of surveillance analysis methods, which automate the sub-tasks. As an initial implementation, we use methods developed according to this framework to analyze 911 dispatch data from San Francisco."

redux [06.29.01]
EurekAlert GIS, bioinformatics collaborations offer promising new perspectives
"The merits of linking two fields seemingly as disparate as geographic information systems (GIS) and bioinformatics might not seem obvious, but Virginia Tech's recent symposium linking the twoaeand its roster of renowned participants from both fieldsaehas raised expectations "Applications of GIS to Bioinformatics" was the first major public forum to cross-pollinate the disciplines, helping to fortify a relatively new, yet highly promising investigative area."

""As a result of new dialog between the fields, as we've had at this conference, we are gaining an important mechanistic link between individual-level processes tracked by genomics and proteomics and population-level outcomes tracked by GIS and epidemiology. This will allow us to do a far better job of monitoring, quantifying, and predicting human-health consequences associated with the environment. The potential payoff in related fields such as those looking at climate change, emerging and resurgent infectious diseases, and environmental health is enormous.""

Applications of GIS to Bioinformatics Symposium Proceedings
"The meeting brings together researchers in two of the most dynamic analytical technologies-GIS and bioinformatics. The value of GIS analytical systems and data structures to bioinformatics are only now being recognized. Similarly, the methodologies used in bioinformatics can inform GIS scholars of new approaches to pattern recognition and analysis. The purpose of the symposium is to explore the potentials for using GIS as an analytical methodology in bioinformatics and to understand the opportunities bioinformatics presents to the GIS research community. The symposium, the first to focus on the interface between these two research areas, will afford scholars the opportunity to establish new research directions in both fields of investigation."

Bio-IT World: Human Variome Project Set to Launch

2006-05-15T20:38:00.000-04:00

Bio-IT World Human Variome Project Set to Launch

"“We’ve tried to get all the top people in the field, and the stakeholders,” Cotton says. “We hope that the meeting will affirm the name ‘Human Variome Project’, and the need for such a global body.” Another outcome might be an international committee, representing all stakeholders, to coordinate the project.

Cotton hopes the HVP will create a single, international database that will provide researchers and clinical geneticists with complete, accurate information on SNPs and mutations, linked to phenotype data from association studies. He envisages that governments and research funding agencies will also use the database."

Guardian Unlimited: US senators propose to make scientific research freely available

2006-05-12T14:45:00.000-04:00

Guardian Unlimited US senators propose to make scientific research freely available

"American legislators have proposed that scientific research paid for by US taxpayers should be freely available online to everyone. Analysts described the move as a "potential banana skin" for established scientific publishers such as Reed Elsevier, Springer and Informa."

""It will ensure that US taxpayers do not have to pay twice for the same research - once to conduct it and a second time to read it," Senator Cornyn told Congress."

redux [11.27.05]
Guardian Unlimited Keep science off web, says Royal Society
"The Royal Society, Britain's national academy of science, yesterday joined the debate about so-called open access to scientific research, warning that making research freely available on the internet as it is published in scientific journals could harm scientific debate.

The Royal Society fears it could lead to the demise of journals published by not-for-profit societies, which put out about a third of all journals. "Funders should remember that the primary aims should be to improve the exchange of knowledge between researchers and wider society," The Royal Society said."

"A spokesman for the Royal Society said: "We think it conceivable that the journals in some disciplines might suffer. Why would you pay to subscribe to a journal if the papers appear free of charge?""

redux [10.18.05]
Science Daily Online journal to cover clinical trials
"PLoS Clinical Trials, a new online journal, will be launched next spring to report results of all randomized controlled clinical trials on humans in all medical and public-health disciplines, its sponsor said Monday."

"PLoS will charge a publication fee to authors to offset the journal's costs, but the fee will be waived for authors with insufficient funds, the library said in a statement."

"Dr. Catherine DeAngelis, editor-in-chief of the Journal of the American Medical Association, said the entire scientific community is concerned about getting research information into the public domain.

"I think the idea of getting things out there is fine," DeAngelis told UPI, "but I'd like to see the (journal's) business plan. I think they will find this is a more expensive proposition than they thought.""

redux [09.28.05]
The Economist The paperless library
"IT USED to be so straightforward. A team of researchers working together in the laboratory would submit the results of their research to a journal. A journal editor would then remove the authors' names and affiliations from the paper and send it to their peers for review. Depending on the comments received, the editor would accept the paper for publication or decline it. Copyright rested with the journal publisher, and researchers seeking knowledge of the results would have to subscribe to the journal.

No longer. The internet—and pressure from funding agencies, who are questioning why commercial publishers are making money from government-funded research by restricting access to it—is making free access to scientific results a reality. This week, the Organisation for Economic Co-operation and Development (OECD) issued a report describing the far-reaching consequences of this. The report, by John Houghton of Victoria University in Australia and Graham Vickery of the OECD, makes heavy reading for publishers who have, so far, made handsome profits. But it goes further than that. It signals a change in what has, until now, been a key element of scientific endeavour."

redux [08.15.05]
The Boston Globe Flaws are found in validating medical studies
"Now, after a study that sent reverberations through the medical profession by finding that almost one-third of top research articles have been either contradicted or seriously questioned, some specialists are calling for radical changes in the system."

In advance of a world congress on peer review next month in Chicago, these specialists are suggesting that reviewers drop their anonymity and allow comments to be published."

""It would be lovely to start anew and to set up a trial of peer review against no peer review," Rennie said. "But no journal is willing to risk it.""

redux [06.25.04]
The New York Times A Quiet Revolt Puts Costly Journals on Web
[requires 'free' registration]

"More than money and success is at stake. Free and widespread distribution of new research has the potential to redefine the way scientific and intellectual developments are recorded, circulated and preserved for years to come.

"Society pays for science," said Dr. Nicolelis, whose article in the October issue of PLoS got worldwide attention. "We have the technology, we have the expertise. Why is it that the only thing that has remained the same for 50 years is the way we publish our results? The whole system needs overhaul.""

redux [11.22.03]
USA Today Upstart science journals take on the powerhouses
"Science's Rocky-style publishing battle starts its second round Monday when a groundbreaking journal releases its latest issue.

The challenger, the upstart Public Library of Science: Biology, packed a strong punch last month with its first issue, which featured a headline-grabbing report of monkeys getting brain implants to control robot arms. The upcoming issue spotlights newly discovered genes for obesity and osteoporosis."

redux [10.14.03]
The Star-Ledger Browsers swamp science Web site
"There are lots of scientific journals, and the debut of another one normally would not raise many eyebrows.

But yesterday's online launch of Public Library of Science Biology drew so many curious browsers -- half-a-million Web hits in the first eight hours -- that the swamped site had to divert many to a backup site."

"Led by heavyweights such as Nobel laureate Harold Varmus, former director of the National Institutes of Health, the PLoS project aims to shake up the world of scholarly publishing by freely sharing its monthly contents."

redux [10.10.03]
Guardian Unlimited Scientists take on the publishers in an experiment to make research free to all
"In the highly lucrative world of cutting-edge scientific research, it is nothing short of a revolution. A group of leading scientists are to mount an unprecedented challenge to the publishers that lock away the valuable findings of research in expensive, subscription-only electronic databases by launching their own journal to give away results for free.

The control of information on everything from new cancer treatments to space exploration is at stake, while caught in the crossfire are the world's publicly funded scientists, some of whom will soon face a choice between their career and their conscience."

redux [08.22.03]
The Scientist Economics of open access
[requires 'free' registration]

"Debate over open access to scientific articles is steadily moving into the mainstream, with the publication this month of an editorial in The New York Times, a recently introduced Congressional bill to promote open access publishing, and a television commercial sponsored by the Public Library of Science (PLoS), a California-based group that plans to launch an open-access journal in October.

As enthusiasm grows, however, some skeptics wonder whether open-access journals will succeed financially, since they charge relatively small "article processing fees," paid upfront by the researcher, instead of substantial fees for institutional library subscriptions."

redux [07.01.03]
Salon The free research movement
""It's ridiculous," Eisen said in this voice during a recent phone interview from Washington. "All these things we're so used to doing with information on the Internet, we're preventing clever entrepreneurial people from doing with works of science. The idea that a narrow profit motive would prevent the dissemination of this information -- it's insane!"

Eisen was in Washington to lend his support to a congressional effort he believes will make scientific publishing less insane and less ridiculous. Most scientific journals -- such as Science, Nature or the New England Journal of Medicine -- require researchers to turn over all rights to the reports selected for publication; the publications then charge institutions and individuals subscription fees to view these reports, a model that Eisen believes inhibits scientific progress. The approach is especially galling, Eisen says, when you consider that a great deal of the money that funds the research published in these journals comes from the federal government. The public is paying for science that it never gets to see, he says."

redux [12.16.02]
The New York Times New Premise in Science: Get the Word Out Quickly, Online
[requires 'free' registration]

"A group of prominent scientists is mounting an electronic challenge to the leading scientific journals, accusing them of holding back the progress of science by restricting online access to their articles so they can reap higher profits.

Supported by a $9 million grant from the Gordon and Betty Moore Foundation, the scientists say that this week they will announce the creation of two peer-reviewed online journals on biology and medicine, with the goal of cornering the best scientific papers and immediately depositing them in the public domain."

redux [11.15.02]
Federal Computer Week More sites targeted for shutdown
"Having persuaded the Energy Department to pull the plug on PubScience, a Web site that offered free access to scientific and technical articles, commercial publishers are taking aim at government-funded information services offering free legal and agricultural data.

"We're delighted with the decision [to shut down PubScience]," LeDuc said. "The administration has done a tremendous job of hearing our concerns and responding to what we've always considered to be our legitimate concern."

redux [09.24.02]
BioMedNet Adam Smith and science journals
[requires 'free' registration]

"The UK's Office of Fair Trading says that the prices for scientific, technical, and medical (STM) journals are too high because normal competitive forces have been suspended. Libraries are paying too much. The prices of STMs are rising faster than inflation, and the disparity between for-profit and not-for-profit journals is obvious. Part of the problem is that the journals compete on quality, not price, so libraries are prone to skip the cheaper journals for the better, more expensive ones. Bundling journals also skews the market.

Goodman, S. 2002. "Unusual forces" are pushing journal market off course. Nature 419(6904):239.

redux [09.05.01]
BioMedNet Profit vs. Public access
[requires 'free' registration]

"Publishers of established scientific journals have thus far resisted demands for freer access. In its campaign to make biomedical research literature available free online, Public Library of Science is now taking a new tack: It hopes to publish peer-reviewed, electronic journals.

"If we really want to change the publication of scientific research, we must do the publishing ourselves," says an announcement posted Sept. 1 on the group's Web site. "It is time for us to work together to create the journals we have called for."

redux [04.24.01]
Scientific American Publish Free or Perish
"When a molecular biologist or a biochemist has made a discovery - often after many months or even years of tedious experiments - they tell the rest of the world by publishing their results in a scientific journal. So far, these journals have controlled who can read them and who cannot - but maybe not for much longer.

E-mail, Internet discussion groups, electronic databases and pre- or e-print servers have already transformed the way scientists openly exchange their results. And in the life sciences, researchers are now demanding that their work be included in at least one free central electronic archive of published literature, challenging the traditional ownership of publishers. The demand has sparked widespread discussions among scientists, publishers, scientific societies and librarians about the future of scientific publishing. The outcome may be nothing short of a revolution in the scientific publishing world."

redux [09.20.00]
BioMedCentral Freedom of Information Conference: The impact of open access on biomedical research
"How should biomedical research be communicated? How should research be assessed and validated?"

"Below are abstracts, transcripts, and biographies from the conference. Some presentations did not lend themselves to transcription. Where possible we have supplemented them with editorials from the speakers.

We have also commissioned editorial articles from several speakers and delagates at the meeting."

The Philadelphia Enquirer: Science Anxiety

2006-05-11T14:36:00.000-04:00

The Philadelphia Enquirer Science Anxiety

"The moral standoff that will quickly come to characterize the 21st century is becoming clear. It is not the teaching of intelligent design vs. evolution in American schools. Almost no one but biblical literalists takes the ID position with any seriousness as science. Nor will it be the heated squabble over embryonic stem-cell research. That scrum is actually over as well: Many nations around the world are doing this type of research, so the question is only where not whether.

The real battle - the battle that will come to occupy the moral center stage of American politics, morality, law, public policy, editorial pages, and water-cooler discussions - will be waged over where genetic engineering ought to take us and whether we are satisfied to leave it to scientists to guide us there."

Bio-IT World: Gilna to Captain CAMERA

2006-05-10T15:17:00.000-04:00

Bio-IT World Gilna to Captain CAMERA

"Later this summer, coinciding with the publication of the first peer-reviewed paper on results from J. Craig Venter’s worldwide voyage sampling ocean genomes, researchers will gain access to version 0.5 of CAMERA—the Community Cyberinfrastructure for Advanced Marine Microbial Ecology Research and Analysis—a platform replete with a wealth of data, analysis tools, and high-speed computational infrastructure.

“We’ll point readers to the portal from the paper,” says Paul Gilna, who was appointed executive director of CAMERA last month. Gilna is an experienced science program administrator who helped launch GenBank, worked on the protein data bank (PDB), and was a director of DOE’s Joint Genome Institute at Los Alamos National Laboratory. He hopes CAMERA will help jumpstart and grow the nascent field of metagenomics."