{bio,medical} informatics
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TechWhack News
Sergey Brin and Larry Page are Financial Times men of the year
"Google’s IPO has also made big news this year as their current stock position places the net worth of the company at an amazing USD 130 billion. This brings them close to the giants of the industry IBM and is only trailed by biggest like Intel and Microsoft. However, the Google guys are not resting on their laurels, as they believe that there is much more to be done and achieved.
"Brin said in a statement: “It’s clear there’s a lot of room for improvement, there’s no inherent ceiling we’re hitting up on. Google has a large computational infrastructure – that could be very useful for microbiology or computational biology. I don’t think we particularly restrict ourselves or have a 20-year vision or anything like that. I don’t think we’re averse to doing something new.”"
redux [11.29.05]
"SERGEY BRIN and Larry Page have ambitious long-term plans for Google’s expansion into biology and genetics through the fusion of science, medicine and technology."
"Over dinner and plenty of wine in February, Brin discussed the prospects for genetics with Craig Venter, the maverick biologist who decoded the human genome.
Despite millions of dollars in funding and thousands of hours of computing time from America’s federal Department of Energy, Venter needed more help to unlock the molecular mysteries of life. It seemed to him that Google’s mathematicians, scientists, technologists, and computing power had the potential to vault his research forward. He pressed Brin hard to get Google involved."
"Not long after the dinner, Brin and Page teamed up with Venter."
redux [11.08.05]
"By the end of next year, Google intends to open an engineering center in the Valley that will employ 600. The company has said it wants to be in a place with a strong quality of life for its employees, with access to public transportation and amenities."
"Downtown Phoenix offers perfect geography, housing and the public transit amenities that Google wants, said John Chan, deputy director of the downtown development office."
"Downtown is the Valley’s financial center and it also has a growing cluster of biotechnology companies. That may interest Google, since the company is said to be intrigued by bioinformatics, the use of computers to characterize the molecular components of living things."
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Flags and Lollipops
Golden rules for bioinformatics web applications
"Continuing yesterday's well executed web applications theme I've drafted a list of common sense "golden rules" for bioinformatics web application interfaces. After all, the underlying algorithm might be fantastic but if nobody can use it then you may as well have kept it to yourself.
When I say "golden rule", of course, I mean "generally, and in my opinion". If you've got more to add, or disagree with any of them, add a comment and I'll check it out."
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EurekAlert
New view of cancer: 'Epigenetic' changes come before mutations
"A Johns Hopkins researcher, with colleagues in Sweden and at the Fred Hutchinson Cancer Research Center, suggests that the traditional view of cancer as a group of diseases with markedly different biological properties arising from a series of alterations within a cell's nuclear DNA may have to give way to a more complicated view. In the January issue of Nature Reviews Genetics, available online Dec. 21, he and his colleagues suggest that cancers instead begin with "epigenetic" alterations to stem cells.
"We're not contradicting the view that genetic changes occur in the development of cancers, but there also are epigenetic changes and those come first," says lead author Andrew Feinberg, M.D., M.P.H., King Fahd Professor of Medicine and director of the Center for Epigenetics in Common Human Disease at Johns Hopkins."
redux [12.15.05]
"Although the human genome was sequenced more than five years ago, it can provide scientists with comparatively few clues to the origins and treatment of disease.
The bulk of that information lies buried in the "epigenome" -- from the Greek epi, meaning "in addition to." The epigenome consists of chemical "amendments" to strings of DNA that spell out the human genetic code.
Now, an international group of 40 leading cancer scientists are proposing a new effort -- the Human Epigenome Project -- to map these chemical modifications.
And it would appear some of these altered genes are passed on to future generations with a range of studies emerging to support the idea.
redux [11.30.05]
"What we eat may influence our health by changing specific genes, researchers believe.
Several studies in rodents have shown that nutrients and supplements can change the genetics of animals by switching on or off certain genes."
redux [08.18.05]
"The more we learn about the human genome, the less DNA looks like destiny.
As scientists discover more about the "epigenome," a layer of biochemical reactions that turns genes on and off, they're finding that it plays a big part in health and heredity.
By mapping the epigenome and linking it with genomic and health information, scientists believe they can develop better ways to predict, diagnose and treat disease."
redux [07.02.04]
[requires 'free' registration]
"In a written commentary, evolutionary biologist Massimo Pigliucci said that Ruden's experiment was "one of the most convincing pieces of evidence that epigenetic variation is far from being a curious nuisance to evolutionary biologists." Pigluicci doesn't go so far as to say that the heritable changes caused by Hsp90 alterations are Lamarckian, but Ruden does. "Epigenetics has always been Lamarckian. I really don't think there's any controversy," he says.
Not that Mendelian genetics is wrong; far from it. The increased understanding of epigenetic change and the recent evidence indicating its role in inheritance and development doesn't give epigenetics greater importance than DNA. Genetics and epigenetics go "hand in hand," says Ohlsson. In the case of disease, says Reik, "there are clearly genetic factors involved, but there are also other factors involved. My suspicion is that it will be a combination of genetic and epigenetic factors, as well as environmental factors, that determine all these diseases.""
redux [10.07.03]
"The Human Epigenome Project will look for patterns in our "life code" that are associated with gene regulation but are also implicated in causing disease."
"Researchers at Epigenomics AG in Berlin and the Sanger Institute in Cambridge will take part in the five-year study."
"The announcement follows the completion of an HEP pilot project that studied methylation patterns within the Major Histocompatibility Complex in chromosome 6 to determine the methylation status of over 100,000 sites. Data from the pilot study, which was funded by the European Union, was released today on the HEP's website."
"The methylation data will be integrated with the human genome sequence using the Ensembl interface and publicly released at www.epigenome.org and at www.sanger.ac.uk/epigenome."
redux [10.06.03]
[requires 'free' registration]
"With the help of some fat yellow mice, scientists have discovered exactly how a mother's diet can permanently alter the functioning of genes in her offspring without changing the genes themselves."
"The research is a milestone in the relatively new science of epigenetics, the study of how environmental factors like diet, stress and maternal nutrition can change gene function without altering the DNA sequence in any way."
redux [09.13.01]
[requires 'free' registration]
"The term was introduced by Conrad H. Waddington in 1942.1 To paraphrase an erudite epistolary exchange in Science, he is said to contrast genetics with epigenetics , the study of the processes by which genotype gives rise to phenotype. In 1942 we had barely any clue as to what those processes are, so "epigenetic" had no connotation of the underlying chemical mechanism, whatever it was that modulated cell differentiation.
In 1994, as cited in the same issue of Science, Robin Holliday voiced a commonly apprehended drift in meaning, and redefined epigenetic as "Nuclear inheritance which is not based on differences in DNA sequence." These two memes are freely circulating and can cause muddle or mischief mainly when they recombine, namely when epigenetic-H is automatically applied to epigenetic-W."
"This neology of nucleic, epinucleic, extranucleic, has attracted few followers, I think largely because so few people had really thought through the distinctions. There is much merit in Ben Johnson's caution about unbridled proliferation of terms: "A man coins not a new word without some peril, and less fruit; for if it happen to be received, the praise is but moderate; if refus'd, the scorn is assur'd." But is a polysemy to be preferred, with thought-muddling as a further peril?"
redux [08.16.01]
[ summary can be viewed for free once registered ]
"Some of the weirdest genetic phenomena have very little to do with the genes themselves. True, as the units of DNA that define the proteins needed for life, genes have played biology's center stage for decades. But whereas the genes always seem to get star billing, work over the past few years suggests that they are little more than puppets. An assortment of proteins and, sometimes, RNAs, pull the strings, telling the genes when and where to turn on or off."
""The unit of inheritance, i.e., a gene, [now] extends beyond the sequence to epigenetic modifications of that sequence," explains Emma Whitelaw, a biochemist at the University of Sydney, Australia."
""[Epigenetic effects] give you a mechanism by which the environment can very stably change things," says Rudolph Jaenisch, a developmental biologist at the Whitehead Institute for Biomedical Research in Cambridge, Massachusetts. Researchers are hoping to harness these effects to design drugs that correct cancer and other diseases brought on by gene misregulation."
redux [07.11.00]
"Genes are tricksters. They can be turned on or off -- and whether they're on or off decides whether the gene-owner will develop disease.
Gene researchers have embarked on a new field of research, called epigenomics, to determine whether genes are in the on or off position. This type of marker could prove an important diagnostic or therapeutic tool for all types of cancer.
"At Johns Hopkins, researchers are performing clinical trials on about 15 patients with leukemia and other cancers to find out if epigenomics might give pharmaceutical companies a lead for developing cancer drugs.
The research, like all epigenomics research, is studying a chemical found in everyone's DNA called cytosine. Cytosine is the only chemical of the four that make up human DNA (the others are adenine, thymine, and guanine) that is prone to a phenomenon called methylation. When cytosine is methylated, it tuns off its gene."
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The New York Times
Global Trend: More Science, More Fraud
[requires 'free' registration]
"The South Korean scandal that shook the world of science last week is just one sign of a global explosion in research that is outstripping the mechanisms meant to guard against error and fraud.
Experts say the problem is only getting worse, as research projects, and the journals that publish the findings, soar."
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The Atlanta Journal-Constitution
Disease prediction on the horizon
"Emory University and Georgia Tech will launch a multiyear, multimillion-dollar project Monday to remake U.S. health care — a bold effort that plays to the schools' strengths in biomedical and engineering research but carries wide ethical, legal and economic complications.
The project, dubbed the Predictive Health Initiative, combines genetics, nanotechnology, information technology and cutting-edge patient care into a new type of medicine that aims to stop disease before it starts."
"The initiative and conference will explore a discipline that is so new its leading researchers cannot agree what to call it — predictive, personalized, preventive or pre-emptive — and that relies on scientific specialties most Americans may not recognize: proteomics, epigenetics, bioinformatics and computational biology."
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The Washington Post
Scientists Find A DNA Change That Accounts For White Skin
"Scientists said yesterday that they have discovered a tiny genetic mutation that largely explains the first appearance of white skin in humans tens of thousands of years ago, a finding that helps solve one of biology's most enduring mysteries and illuminates one of humanity's greatest sources of strife."
"[For] better or worse, the finding's most immediate impact may be an escalating debate about the meaning of race."
redux [11.11.05]
[requires 'free' registration]
"In a finding that is likely to sharpen discussion about the merits of race-based medicine, an Icelandic company says it has detected a version of a gene that raises the risk of heart attack in African-Americans by more than 250 percent."
"Dr. Kari Stefansson, the company's chief executive, said he would consult with the Association of Black Cardiologists and others as to whether to test a new heart attack drug specifically in a population of African-Americans."
"Last year a drug called BiDil evoked mixed reactions after it was shown to sharply reduce heart attacks among African-Americans, first in a general study and then in a targeted study, after it failed to show efficacy in the general population. The drug, invented by Dr. Jay N. Cohn, a cardiologist at the University of Minnesota, prompted objections that race-based medicine was the wrong approach."
redux [10.26.05]
"Gattaca, a science-fiction movie released in 1997, portrays a dystopian future in which a person's place in society is determined by an analysis of his or her DNA, and the likelihood of disease is ascertained at birth. The movie would seem to have little connection with reality -- except that an international consortium has just completed the groundwork for a version of this future. Ultimately, an individual's DNA could be decoded at an early age to spot a predisposition to illness. And here's where life improves on art: The goal will be to counter the risk of disease, not pigeonhole the person."
"And HapMap shows how differences between ethnic groups can be very subtle."
"But although the absolute differences between the various ethnic backgrounds are tiny, there are genetic trends that differ between ethnic groups. A given set of SNPs may be linked in one way in Asian populations for example, but in a different way in Europeans. Over the whole genome there are more differences between individuals than there are between ethnic groups, but such trends are still thought to be useful for targeting drugs.
Hudson stresses that not all people within an ethnic group share the same SNP pattern, so pharmaceutical companies should bear this in mind. "We would want to give a drug not based on the colour of someone's skin but based on the presence or absence of the genetic markers," he says."
redux [07.27.05]
"So, what's in it for me? That question probably crossed many minds five years ago following the news that scientists had successfully assembled the first draft of the human genome -- the genetic blueprint of a human being. The answer for most of us was ''not much."
What a difference five years can make. Today, we are witnessing a revolution in the understanding of health and disease, spurred on by the sequencing of the human genome and the subsequent creation of a map of human genetic variation. And, like most historic movements, this revolution has been given a name: personalized medicine."
"Will access to genomic technologies be equitable? Will knowledge of human genetic variation reduce prejudice or increase it? What boundaries will need to be placed on this technology, particularly when applied to enhancement of traits rather than prevention or treatment of disease? Will we succumb to genetic determinism, neglecting the role of the environment and undervaluing the power of the human spirit?"
redux [07.12.03]
[requires 'free' registration]
"Genetics increasingly shows that racial and ethnic distinctions are real -- but often fuzzy and greatly exaggerated. Genetics will increasingly show that most humans are mongrels, and it will make a mockery of racism.
"There are meaningful distinctions among groups that may have implications for disease susceptibility," said Harry Ostrer, a genetics expert at the New York University School of Medicine. "The right-wing version of this is `The Bell Curve,' and that's pseudoscience -- that's not real. But there can be a middle ground between left-wing political correctness and right-wing meanness.""
redux [05.28.03]
"Howard University officials yesterday announced plans to create the first large-scale collection of genetic profiles of African Americans, an endeavor they described as a bid for a "place at the table in genetic research" and a pathway to improved medical care for blacks."
"However, other genetics experts question the premise that the program can help as much as Howard officials say."
redux [05.13.03]
"The use--and often misuse--of genetics to explain racial and ethnic differences is, of course, nothing new. But the HapMap, together with a series of powerful genomic tools developed over the last several years, will make it possible to spell out in great detail the genetic differences between peoples from different parts of the world. Sociologists, bioethicists, and anthropologists worry that the genetic data could be manipulated to give an air of biological credence to ethnic stereotypes, to revive discredited racial classifications, and even to fuel bogus claims of fundamental genetic differences between groups."
redux [01.25.03]
"Race doesn't exist, the mantra went. The DNA inside people with different complexions and hair textures is 99.9 percent alike, so the notion of race had no meaning in science. At a National Human Genome Research Institute (NHGRI) meeting five years ago, geneticists were all nodding in agreement. Then sociologist Troy Duster pulled a forensics paper out of his briefcase. It claimed that criminologists could find out whether a suspect was Caucasian, Afro-Caribbean or Asian Indian merely by analyzing three sections of DNA.
"It was chilling," recalls Francis S. Collins, director of the institute. He had not been aware of DNA sequences that could identify race, and it shocked him that the information can be used to investigate crimes. "It stopped the conversation in its tracks.""
redux [12.20.02]
"Inuit or Basque, Laotian or Pashtun: we're much more similar than we are different, says the most detailed analysis of human genetic variation to date.
When it comes to sensitivity to drugs or diseases, the analysis also suggests that a person's account of their ethnic origin is almost as reliable an indicator as intrusive genetic tests.""
redux [11.01.02]
"In response to early concerns about racial profiling, scientists at the Human Genome Project went out of their way to downplay ethnic variations. Humans are 99.9 per cent alike, the sequencing showed, a figure that was leveraged into a call for global harmony. "The concept of race has no genetic or scientific basis," said Francis Collins, head of the Human Genome Project, at the White House ceremony to celebrate the genome completion.
Yet a great deal of controversy is now brewing over that 0.1 per cent. A growing number of scientists want to use such information as a way to find cures for devastating diseases. If we know more about the genes that cause susceptibility to cystic fibrosis in whites, or sickle cell anaemia in blacks, they argue, we will move closer to a solution for these illnesses. "Ancestry is imperative to biomedical research," says Mark Shriver, an anthropologist at Pennsylvania State University."
redux [10.30.01]
"Race should not influence drug prescriptions, warn geneticists. Genetic differences between individuals give a better indication of who will respond well to a medicine, a new study shows."
Geneticists have known this for a while. "It's no surprise that skin pigment is a lousy predictor of physiology," says Howard McLeod of Washington University School of Medicine in St Louis, Missouri. This study is the first to prove it."
redux [07.20.01]
[requires 'free' registration]
"Scientists planning the next phase of the human genome project are being forced to confront a treacherous issue: the genetic differences between human races."
"With the decoding of the human genome largely complete, government scientists are beginning to construct a special kind of genetic map that would provide a shortcut to locating the variant human genes that predispose people to common diseases."
"The question the scientists face is whether that map should chart possible differences that may emerge among the principal population groups, those of Africans, Asians and Europeans."
redux [03.18.01]
"Genetics research is demonstrating that the differences in appearance among groups are profoundly incidental, but these differences do have a genetic basis. And although it's true that all people have inherited the same genetic legacy, the genetic differences among groups have important implications for our understanding of history and for biomedical research. These complications in an otherwise reassuring story have thoroughly spooked the leaders of the public and private genome efforts. The NIH has been collecting information about genetic variants from different ethnic groups in the United States, but it has refused to link specific variants with ethnicity. Celera has been sequencing DNA from an Asian, a Hispanic, a Caucasian, and an African-American, but it, too, declines to say which DNA is which.
This strategy of avoiding the issue is almost sure to backfire. It seems to imply that geneticists have something to hide. But the message emerging from laboratories around the world should be hailed, not muzzled. It is one of great hope and promise for our species."
redux [06.11.01]
[requires 'free' registration]
"Scientists have long suspected that the racial categories recognized by society are not reflected on the genetic level.
But the more closely that researchers examine the human genome -- the complement of genetic material encased in the heart of almost every cell of the body -- the more most of them are convinced that the standard labels used to distinguish people by "race" have little or no biological meaning.""
""Ethnicity is a broad concept that encompasses both genetics and culture," Dr. Anand said. "Thinking about ethnicity is a way to bring together questions of a person's biology, lifestyle, diet, rather than just focusing on race. Ethnicity is about phenotype and genotype, and, if you define the terms of your study, it allows you to look at differences between groups in a valid way."
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Sci-Tech News
Human Epigenome Project Could Help Cure Disease
"Although the human genome was sequenced more than five years ago, it can provide scientists with comparatively few clues to the origins and treatment of disease.
The bulk of that information lies buried in the "epigenome" -- from the Greek epi, meaning "in addition to." The epigenome consists of chemical "amendments" to strings of DNA that spell out the human genetic code.
Now, an international group of 40 leading cancer scientists are proposing a new effort -- the Human Epigenome Project -- to map these chemical modifications.
And it would appear some of these altered genes are passed on to future generations with a range of studies emerging to support the idea.
redux [11.30.05]
"What we eat may influence our health by changing specific genes, researchers believe.
Several studies in rodents have shown that nutrients and supplements can change the genetics of animals by switching on or off certain genes."
redux [08.18.05]
"The more we learn about the human genome, the less DNA looks like destiny.
As scientists discover more about the "epigenome," a layer of biochemical reactions that turns genes on and off, they're finding that it plays a big part in health and heredity.
By mapping the epigenome and linking it with genomic and health information, scientists believe they can develop better ways to predict, diagnose and treat disease."
redux [07.02.04]
[requires 'free' registration]
"In a written commentary, evolutionary biologist Massimo Pigliucci said that Ruden's experiment was "one of the most convincing pieces of evidence that epigenetic variation is far from being a curious nuisance to evolutionary biologists." Pigluicci doesn't go so far as to say that the heritable changes caused by Hsp90 alterations are Lamarckian, but Ruden does. "Epigenetics has always been Lamarckian. I really don't think there's any controversy," he says.
Not that Mendelian genetics is wrong; far from it. The increased understanding of epigenetic change and the recent evidence indicating its role in inheritance and development doesn't give epigenetics greater importance than DNA. Genetics and epigenetics go "hand in hand," says Ohlsson. In the case of disease, says Reik, "there are clearly genetic factors involved, but there are also other factors involved. My suspicion is that it will be a combination of genetic and epigenetic factors, as well as environmental factors, that determine all these diseases.""
redux [10.07.03]
"The Human Epigenome Project will look for patterns in our "life code" that are associated with gene regulation but are also implicated in causing disease."
"Researchers at Epigenomics AG in Berlin and the Sanger Institute in Cambridge will take part in the five-year study."
"The announcement follows the completion of an HEP pilot project that studied methylation patterns within the Major Histocompatibility Complex in chromosome 6 to determine the methylation status of over 100,000 sites. Data from the pilot study, which was funded by the European Union, was released today on the HEP's website."
"The methylation data will be integrated with the human genome sequence using the Ensembl interface and publicly released at www.epigenome.org and at www.sanger.ac.uk/epigenome."
redux [10.06.03]
[requires 'free' registration]
"With the help of some fat yellow mice, scientists have discovered exactly how a mother's diet can permanently alter the functioning of genes in her offspring without changing the genes themselves."
"The research is a milestone in the relatively new science of epigenetics, the study of how environmental factors like diet, stress and maternal nutrition can change gene function without altering the DNA sequence in any way."
redux [09.13.01]
[requires 'free' registration]
"The term was introduced by Conrad H. Waddington in 1942.1 To paraphrase an erudite epistolary exchange in Science, he is said to contrast genetics with epigenetics , the study of the processes by which genotype gives rise to phenotype. In 1942 we had barely any clue as to what those processes are, so "epigenetic" had no connotation of the underlying chemical mechanism, whatever it was that modulated cell differentiation.
In 1994, as cited in the same issue of Science, Robin Holliday voiced a commonly apprehended drift in meaning, and redefined epigenetic as "Nuclear inheritance which is not based on differences in DNA sequence." These two memes are freely circulating and can cause muddle or mischief mainly when they recombine, namely when epigenetic-H is automatically applied to epigenetic-W."
"This neology of nucleic, epinucleic, extranucleic, has attracted few followers, I think largely because so few people had really thought through the distinctions. There is much merit in Ben Johnson's caution about unbridled proliferation of terms: "A man coins not a new word without some peril, and less fruit; for if it happen to be received, the praise is but moderate; if refus'd, the scorn is assur'd." But is a polysemy to be preferred, with thought-muddling as a further peril?"
redux [08.16.01]
[ summary can be viewed for free once registered ]
"Some of the weirdest genetic phenomena have very little to do with the genes themselves. True, as the units of DNA that define the proteins needed for life, genes have played biology's center stage for decades. But whereas the genes always seem to get star billing, work over the past few years suggests that they are little more than puppets. An assortment of proteins and, sometimes, RNAs, pull the strings, telling the genes when and where to turn on or off."
""The unit of inheritance, i.e., a gene, [now] extends beyond the sequence to epigenetic modifications of that sequence," explains Emma Whitelaw, a biochemist at the University of Sydney, Australia."
""[Epigenetic effects] give you a mechanism by which the environment can very stably change things," says Rudolph Jaenisch, a developmental biologist at the Whitehead Institute for Biomedical Research in Cambridge, Massachusetts. Researchers are hoping to harness these effects to design drugs that correct cancer and other diseases brought on by gene misregulation."
redux [07.11.00]
"Genes are tricksters. They can be turned on or off -- and whether they're on or off decides whether the gene-owner will develop disease.
Gene researchers have embarked on a new field of research, called epigenomics, to determine whether genes are in the on or off position. This type of marker could prove an important diagnostic or therapeutic tool for all types of cancer.
"At Johns Hopkins, researchers are performing clinical trials on about 15 patients with leukemia and other cancers to find out if epigenomics might give pharmaceutical companies a lead for developing cancer drugs.
The research, like all epigenomics research, is studying a chemical found in everyone's DNA called cytosine. Cytosine is the only chemical of the four that make up human DNA (the others are adenine, thymine, and guanine) that is prone to a phenomenon called methylation. When cytosine is methylated, it tuns off its gene."
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The Atlanta Journal-Constitution
Georgia Tech lands biotech research 'star'
"A biotech "rock star" who headed a $200 million research center at the University of Buffalo is joining the faculty at Georgia Tech and bringing a band of 19 scientists with him.
Jeffrey Skolnick, a scientist in systems biology — a field that uses supercomputers to break down information in the genetic code in a quest to create new drugs — also will bring $1.5 million in grant funding to Tech.
Skolnick's arrival in Buffalo, N.Y., made headlines. The Center of Excellence in Bioinformatics, which he led, was regarded as a symbol of hope for the struggling upstate economy. He was regarded as the academic equivalent of a celebrity."
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The Financial Express
Q&A, Samir K Brahmachari
"The international bioinformatics sector is clearly dominated by Indian scientists. Be it the research labs or bioinformatics firms in the US, Europe or Japan, there is always an Indian spearheading the research. However, the country is facing a shortage of bioinformatics professionals. Indian capabilities are noticed globally in bioinformatics, though we are not leading the foray. I hope that by 2010, we emerge as a significant contributor to the global bioinformatics sector. The basic infrastructure — high performance computing machines — has just arrived in the country at IISc, IITs, TIFR and CSIR laboratories. "
redux [03.22.04]
"It was touted as one of the biggest markets Indian software companies could address. But somewhere along the way, the market scenario has changed and today only a few focused companies are still looking at bioinformatics as the next big opportunity, says Srikanth R P."
"While the market potential for bioinformatics is huge few Indian companies have the skill sets or the ability to capture a significant share of the market."
redux [02.23.04]
"Indian pharmas are also waking up to the fact that 'ripping off' patented drugs is becoming more difficult with 'legit piracy' no longer a real option. It's in this changed scene that India plans to make a splash.
A well-developed base industry such as pharma gives India a distinct advantage over others in the biotech boom. It already has a good network of research labs and scores of bioinformatic units have been set up by IT companies across the country. Add to these a rich biodiversity and access to diverse disease populations, and India is ready to ride the wave. At the forefront of this 'petri-dish revolution' will be drug companies -- especially those that manage to add bioinformatics to the already existing arsenal of molecule'n'mortar process."
redux [02.11.04]
"Software major Sun Microsystems would set up a Centre of Excellence (CoE) for medical bio-informatics at Centre for DNA Fingerprinting Analysis and Development (CDFD) here. The CoE would help in analysis, storage of biological research in areas like genomics, structural biology and molecular evolutionary genetics."
"The proposed CoE is the ninth major medical bio-informatics centre established by Sun in the world and first in India."
redux [10.20.03]
"Tata Consultancy Services (TCS) is on track to launch it's biotech software package 'Bio-Suite' by April '04. The software, which will be used in analysing and accelerating drug discovery processes, is being developed in partnership with the Council for Scientific and Industrial Research (CSIR)."
"The software consists of eight 'blocks' covering all aspects of computational biology ranging from genomics to structure-based drug design. In all, Bio-Suite encompasses more than 200 individual algorithms, and is designed to be highly modular so that new algorithms can be added as scientific advances take place."
redux [08.07.03]
"Sun Microsystems has made a proposal to the department of biotechnology to invest in bioinformatics projects in India and to collaborate with various R&D institutions under the department in this burgeoning area. DBT's Task Force on bioinformatics has asked to multinational to specify the quantum of investment and the specific areas of bioinformatics wherein alliances could be forged with Indian institutes."
Official sources said that the Centre for DNA Fingerprinting & Diagnostics, Hyderabad which has an alliance with software services major Tata Consultancy Services, would possibly be a nodal centre for the joint venture project with Sun."
redux [07.14.03]
"The report estimates that currently up to 10 per cent of investment in R&D is IT-related, and hence there is huge potential for Indian biotech and IT companies to enter into collaborative bioinformatics research with global pharma majors in the near term.
The report, however, indicated that despite India's IT capabilities, it may be difficuly to replicate this success in biotechnology as biotechnology differs from IT in many ways. Avendus suggests that Indian players will have to leverage upon the lower costs of infrastructure and human resources. The cost of setting up and running a bioinformatics company in India is a fraction of the cost in the US."
redux [03.18.03]
"Despite several strengths inherent, India's biotechnology industry is not able to take a quantum jump mainly due to lack of capital and low R&D spending, absence of industry-academic partnership and the mismatch between strategic research, product planning and effective collaboration.
The Associated Chambers of Commerce and Industry of India (Assocham) paper on Business of Biotechnology has pointed out that India has several options with the main focus on informatics. Bioinformatics is crucial for the advancement of the biotech industry by cutting the timeframe and costs in developing a product tremendously."
"Everyone in the room, from Sen. Hillary Rodham Clinton to Buffalo Mayor Anthony Masiello, was beaming at last week's announcement.
The news was that Asia's largest computer consultant has become a deep-pocket partner of the University at Buffalo. Under an agreement signed Monday, Tata Consultancy Services of India will partner with local researchers and help transform their discoveries into money-making products."
"But some in the tech community voiced concern that the state's $100 million-plus bioinformatics investment will wind up boosting the economy in Bombay instead of Buffalo."
redux [12.13.02]
[requires 'free' registration]
"India is set to reap substantial rewards in the field of functional genomics, thanks to an invaluable genetic resource and highly advanced IT expertise, predicts Samir Brahmachari, director of the country's Institute of Genomics and Integrative Biology in Delhi."
"Brahmachari sees India's genetic resource - not the biological samples themselves, but the associated information - as a tradable commodity. Data can be processed using India's unparalleled IT expertise, he says: The country's IT industry generated about $10 billion in revenues this year, and has continued to grow by 50% each year over the past decade. The information, once processed, represents an "intellectual-property protectable" commodity, he says."
redux [06.23.02]
"Also, India's success in information technology provides excellent opportunities in the field of bioinformatics.
"Traditional IT companies are translating their strong capabilities in data mining and warehousing to business models based on biological data," says the report, citing examples of IBM's India Research Lab and Satyam's five-year agreement with the Center for Cellular and Molecular Biology, Hyderabad."
redux [02.13.02]
"India's biotech boom could even dwarf software in coming years if you trust the most optimistic projections. Much of our $2.5-billion biotech market relies on low-end products like vaccines, but experts predict that as more start-ups come up, that could change dramatically."
"The need to dive into this ocean of genetic data for hidden treasures has created a whole new discipline--bio-informatics, the science of using information technology (IT) to decipher the genomic jumble. Thanks to a flourishing IT industry, bioinformatics is today the darling of venture capitalists, drug firms, and, of course, IT majors. So, Satyam Computers has signed a five-year alliance with CCMB to create, store, and annotate genetic databases, and it is angling for contracts from global bigpharma to sequence genes and build protein catalogs. Strand Genomics, a Bangalore-based bio-informatics start-up, is designing tools to accelerate drug discovery."
redux [09.17.01]
"India has the potential to garner 8-10 per cent of the global software market in the next few years from the current levels of just 1.5 per cent, but the country?s planners need to focus on improving computer penetration and use of Indian made software in the industry.
This was the view of FC Kohli, chairman, Tata Consultancy Services, while speaking at Connect 2001, an international conference and exhibition on information technology, communication technologies and bioinformatics, which opened on Thursday. Currently, India's IT exports are about $8.7 billion."
redux [08.27.01]
"THE mood is one of caution as far as bioinformatics is concerned. The beginning of the year saw hype building up around the fledgling industry as the next big gold rush for India.
But six months after the first bioinformatics seminar in the country, with the IT industry's lesson on hype fresh in mind, things are moving at a more sedate pace."
"In India, bioinformatics training institutes have already begun to mushroom. Bangalore and Hyderabad have around five private training institutes between them. However, the industry is sceptical about the quality of manpower these centres can supply because most of them have short-term courses offering basic skills, says Dr. Sabharwal. In all fairness to them she adds, "We need to wait for a few months to see the outcome of it all.""
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Palm Beach Post
Scripps fever contagious - at Scripps
"In one of the great scenes from The Graduate, a boozy middle-aged man corrals the Dustin Hoffman character and tells him, "I just want to say one word to you." The word? "Plastics."
That was 1967. Today, the word would be: "Bioinformatics.""
redux [11.04.05]
[requires 'free' registration]
"Lion Bioscience reported a 42-percent year-over-year decline in revenues for its second fiscal quarter today, but the company's bioinformatics business -- which is in the process of being sold to an undisclosed buyer -- posted a profit for the first time in Lion's history.
Lion's total revenues for the quarter ended Sept. 30 fell to €1.5 million ($1.8 million), from €2.6 million ($3.1 million) in the prior-year period. All of the revenues reported for the second quarter of 2005 came from the bioinformatics business, which the company has listed under discontinued operations."
redux [10.04.05]
[requires 'free' registration]
"The lessons of bioinformatics' recent boom and bust cycle have not been lost on Rainer Fuchs, vice president of research informatics and operations at Biogen Idec.
Fuchs, who spoke at Cambridge Healthtech Institute's inaugural Bridging Discovery and IT conference here last week, said that he's "seeing a shift from lofty expectations" about what bioinformatics can accomplish "to more realistic, smaller projects with a better [return on investment]."
Fuchs asked for a show of hands from those attendees who saw "significant cost savings" in drug discovery from their investment in informatics over the last several years.
Not one hand was raised."
redux [08.13.03]
"Those charged with hearing pitches from software vendors who want to sell wares to biotechnology companies don't like these words: "enterprise-wide solution." They don't want to hear the generic wonders of the "solution" being pitched, they don't want to hear marketing buzzwords or that the software will revolutionize the pharmaceutical business. They won't believe that kind of approach and they will show the software vendor the door, perhaps within minutes, without an invitation back."
"But perhaps the largest issue has little to do with technology, but with getting recalcitrant scientists excited about tools available to them."
redux [04.28.03]
"Leading executives speaking at several recent seminars, however, suggested that this cross-tech hybrid is not generating the gains that proponents initially projected.
One challenge to the effectiveness of bioinformatics is that independent software developers have not been able to develop useful products for life sciences companies looking to save time and money.
“Very few companies, if any, can give us a turnkey solution,” said Mark Murcko, chief technical officer at Vertex Pharmaceuticals, at a recent panel discussion."
redux [03.08.03]
""We have great technology - perhaps ahead of its time," Molecular Mining president and CEO Evan Steeg said yesterday.
Steeg refused to go into details about the company's demise, citing legal reasons. He said it was hard to make things work for the biotechnology and information technology hybrid in an economy where corporations in both sectors have tightened their belts."
"The market for bioinformatics firms like Molecular Mining is "brutal," Molloy said."
redux [02.24.03]
"To some extent, the life sciences market, which relies heavily on computational biology, has lived up to the promise. Research centers in both the private and public sectors placed orders last year for thousands of servers and storage systems capable of handling terabytes of the new genomic, proteomic, drug, and health care data generated hourly.
That's the good news. The bad news is that, during the past year, companies that develop software tools for managing and exploiting all of the new data struggled mightily. Red ink, consolidation, and layoffs were the norm. Welcome to the tumultuous world of ''bioinformatics,'' the underachieving wonder child of a genomics revolution-in-waiting."
redux [12.12.02]
"Bioinformatics: In life-sciences establishments around the world, the laboratory rat is giving way to the computer mouse--as computing joins forces with biology to create a bioinformatics market that is expected to be worth nearly $40 billion within three years."
"Welcome to the world of bioinformatics--a branch of computing concerned with the acquisition, storage and analysis of biological data. Once an obscure part of computer science, bioinformatics has become a linchpin of biotechnology's progress. In the struggle for speed and agility, bioinformatics offers unparalleled efficiency through mathematical modelling. In the quest for new drugs, it promises new ways to look at biology through data mining. And it is the only practical way of making sense of the ensuing deluge of data."
redux [11.30.02]
"Bioinformatics as a business, not to be confused with bioinformatics as a field of study, is at an interesting crossroads. As an academic branch of learning, bioinformatics remains mostly what it always was -- a cross-disciplinary endeavor between computer science and molecular biology. But bioinformatics as a money-making proposition has different criteria for success, and it has received a lot of bad press lately, some of it deserved."
"During this golden age, bioinformaticists developed software that computational biologists could use to make biological discoveries based on genomic data. But the industry swerved off course by selling expensive systems that focused on the individual pieces of a solution, without heeding downstream processes that were the actual bread-and-butter of our customers. Bioinformatics has always been about integrating data and converting it into information. When it loses that focus, it loses its value to the customer."
redux [11.05.02]
[requires 'free' registration]
"The biotechnology industry is facing one of its worst financial squeezes ever. The prices of many biotechnology stocks have plummeted, and Wall Street's vaults have snapped nearly shut, making it almost impossible for capital-hungry companies to finance themselves."
"Another sector that has suffered is bioinformatics, which uses computers to analyze masses of genetic data. Several young companies have gone out of business or been acquired for a pittance after sales did not meet expectations."
redux [07.09.02]
"Most agree that venture money is there for companies -- but the pressure must seem insurmountable for entrepreneurs, who probably feel like they have to give the perfect business pitch to venture capitalists just to get a foot in the door.
"If people aren't rethinking their models, they're nuts; if they were waiting for Viaken to be their wake-up call, they're nuts," Nelson says."
redux [04.18.02]
""Bioinformatics is heterogeneous, but many bioinformatics [tools] fulfill a narrow niche," said Williamson. "There is room for someone to consolidate, but I don't know if that is needed or necessary. Plus there's always an academic coming up with the next thing. So it's a hard business to sustain."
Bioinformatics "is great for smaller companies," he went on. And there are "people who can tie the islands of analysis together, and who have the resources to pull it off, but is that a business? That's the million dollar question. And will anyone buy it if you can pull it together? Everybody wants to be the Microsoft Office of bioinformatics, but I'm not sure that's going to happen.""
redux [03.11.02]
"The emerging field of bioinformatics, the use of computers to analyze the inner workings of biology, is transforming an industry that just a decade ago relied on the manual labor of chemists and biologists. But even as it does so, bioinformatics is floundering as a business.
Shares of public companies that sell biological data or software are trading at a fraction of what they did two years ago. Dozens of companies have crowded into the field. Some have folded; others have survived only by morphing into drug-discovery companies.
''It's a hard market to build a business around,'' said Oliver Fetzer, a vice president at Boston Consulting Group."
redux [02.11.02]
"LIKE EVERY BUBBLE, this one had to burst. Stock prices of many bioinformatics firms have fallen sharply in recent years. LION Biosciences of Germany went public at $40 a share and now trades at about $13. Iceland's DeCode is worth a fourth of its former high. Even Celera, the U.S. firm that helped decode the human genome, is off its peak.
Falling stock prices are a symptom of a greater disappointment in bioinformatics. A few years ago the laborious and quirky process of drug discovery seemed on the verge of giving way to new streamlined, data-driven methods. Some firms organized the blizzard of genetic data into databases that researchers could mine with search engines from still other firms. Software companies built computer programs that modeled what goes on in human cells and even whole organs. Many investors came to believe that bioinformatics would open a new avenue to the discovery of drugs. But this avenue simply hasn't materialized. Says biotech analyst Earling Refsum at Nomura Bank in London: "Bioinformatics has not helped Big Pharma get more drugs into the pipeline.""
redux [01.03.02]
"Inside the laboratories of the world's major pharmaceutical companies and biotechnology start-ups, an emerging science is quietly transforming the drug industry. Bioinformatics -- the use of computers to analyze the inner workings of biology -- is helping researchers pinpoint the roots of diseases and design sophisticated medicines to treat them.
But even as it becomes a vital part of drug research, bioinformatics as a business is losing favor with investors. Shares of publicly traded firms that sell biological data and software tools are slumping, and venture capitalists are increasingly wary of investing in such companies.
redux [12.18.01]
"There comes a point in the life cycle of every organism when it must change or perish. For bioinformatics, the time for metamorphosis is now. Though computational biology is already an intrinsic part of the drug discovery process, the business models adopted by most bioinformatics firms have failed to produce profits. Competition -- from the IT industry and big pharma itself -- is growing and investors, both public and private, are unimpressed. While some companies are hoping persistence pays off, many are pursuing new business models that should allow them to retain a bigger share of the profits they are helping to create."
redux [03.14.01]
"The story proclaimed in its lead, "Move over Information Age. Make room for the age of bioinformation." You could picture bleary eyes opening all over the Bay Area. The story went on to note that a San Jose consulting firm was predicting a 10 percent annual growth in the bioinformatics market for years to come; and that the National Science Foundation estimated that 20,000 new jobs in the field would be created in the field in just the next four years.
If that wasn't enough, the rest of the section was filled with page after page of biotech firms listing job openings - in powerful juxtaposition to the endless lists of dot-com layoffs just a few pages earlier. Picture Starbucks spit-takes from Marin to Santa Cruz.
Wow! Rewrite that resume to emphasize that biology course you took in college. Roll your Aeron chair down to the nearest lab. Trade that black turtleneck for a white lab coat..."
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Buffalo News
Skolnick resigning UB biotech center post
"Jeffrey Skolnick, the prominent scientist hailed as the "rock star" of bioinformatics research when he arrived at the University at Buffalo in 2002, is leaving UB for a job at the Georgia Institute of Technology.
Skolnick has submitted a resignation letter, effective Jan. 10, and will take a position as director of a center focusing on systems-biology research.
This brings an end to Skolnick's rocky term at the UB bioinformatics center, which received more than $200 million in financial support and generated high expectations as an economic engine. "His tenure's been disappointing in the sense that [he] was trumpeted as a rock star, and there weren't many concerts to attend," said Assembly Majority Leader Paul A. Tokasz, D-Cheektowaga."
redux [04.15.04]
"Two years ago, Jeffrey Skolnick arrived as the leader of the University at Buffalo's new bioinformatics center and the next great hope for the region's struggling economy.
Last week, UB issued a three-page news release announcing a restructuring and expansion of the bioinformatics center that includes a new executive director.
Skolnick's name did not appear anywhere in that document."
redux [03.29.04]
"Bioinformatics star Jeffrey Skolnick has created a stir at the University at Buffalo by criticizing his Dell supercomputer -- announced with fanfare in 2002 -- and switching his allegiance to rival IBM Corp.
The highly public flap has prompted UB administrators to come to the defense of Dell, a deep-pocketed research partner."
redux [12.08.03]
""Unfortunately, I think there's unreal expectations," said Skolnick, the Buffalo center director. Still, he said, the center "can play a role, and perhaps a significant role" in an economic turnaround.
Even so, not everybody is on board. At Ulrich's Tavern, which calls itself Buffalo's oldest and is sandwiched between the center and an old windshield-wiper factory, an elderly man nursed a midafternoon beer and said he'd never even heard of bioinformatics.
The bar's proprietor, Jim Daley Jr., was plenty aware of it.
"I think it's the most underrated thing in Buffalo," he said. "Most people talk about the casino.""
redux [07.14.03]
"If any doubts lingered among scientists, politicians or business executives about the future prospects for the University at Buffalo Center of Excellence in Bioinformatics, they were erased last Friday as nearly 200 scientists representing the U.S., Canada, India, the Netherlands, the United Kingdom, Italy and Japan gathered in the Adams Mark Hotel in Buffalo for the first annual "Frontiers in Bioinformatics" symposium."
"The day's events amounted to a grand show of support for the center of excellence, which was founded in 2001 by Gov. George E. Pataki"
redux [06.06.03]
"Despite the media barrage surrounding her new book, Senator Hillary Rodham Clinton made a brief appearance in Buffalo on Friday, June 6, to praise the University of Buffalo (UB)'s ambitious Bioinformatics Center of Excellence initiative."
""It has taken a lot of work to make the case to fund bioinformatics," Clinton said. "When we started, the response was, 'What's that?' " Despite this, Clinton and Reynolds have helped to earmark more than $9 million in federal funding for the project."
redux [03.02.03]
"Jeff Skolnick didn't sign up for all this hype.
He did not apply to the following posting:
Savior wanted: A wunderkind in cutting-edge technology who can help build a new economy and carry the hopes of a Rust Belt region of 1.2 million people.
He just took a job heading a new academic program, the University at Buffalo's Center of Excellence in Bioinformatics."
redux [07.26.02]
"New York's U.S. Senators Charles Schumer and Hillary Rodham Clinton jointly announced that the Senate Appropriations Committee has approved $1 million in funding for Buffalo's planned Center of Excellence in Bioinformatics.
The $1 million was included as part of a an appropriations measure for the Departments of Veterans Affairs and Housing and Urban Development."
redux [05.01.02]
"An optimistic Pataki declared the center "will transform western New York into a 21st Century economy."
The lofty predictions come as upstate's largest city struggles to reinvent itself from a past-its-peak industrial center losing not only jobs but people: U.S. Census figures show the population has dropped to under 300,000, down from a 1950s peak of 580,000."
redux [12.07.01]
"Buffalo will be the site of a Center of Excellence for Bioinformatics thanks to a $200 million collaboration between the public and private sectors.
Gov. George Pataki announced during a swing through Buffalo on Dec. 6 that the state will contribute $50 million to help establish the 150,000 square-foot facility to be located adjacent to the emerging Buffalo Niagara Medical Campus. It is part of Pataki's $1 billion high-tech and biotech Centers of Excellence planned for across the state."
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National Geographic News
Dog Genome Mapped, Shows Similarities to Humans
"Scientists had previously found that about 5 percent of the human genome sequence appears in the mouse genome. The new study shows that 5 percent of the human genome is also shared with dogs.
Significantly, the sequences that are conserved in all three species are virtually the same.
"[This] indicates that there is a core set of noncoding sequences needed to make a mammal.""
redux [10.08.03]
"Building on the newly finished draft of the dog genome, a team at the University of Illinois is conducting a study of the nexus between diet and gene expression in dogs, the University said today."
""Genome sequencing allows us to understand health across animals," Schook said in a statement. "Dogs, like humans, get diseases associated with lifestyles. Thus not exercising and over-eating can result in obesity and diabetes. Information about human diseases can be used to treat dogs, and understanding dog diseases can be used to treat humans.""
redux [09.29.03]
"The dog is the latest animal to have its genome sequenced. Shadow belongs to Craig Venter, the researcher whose privately funded project sequenced the human genome using his own DNA."
"The new sequence reveals that 18,473 dog genes have human equivalents. This already surpasses the 18,311 known from the mouse sequence. The team also found genes related to a dog's life: they have many more that are linked to smell than we do."
"The researchers assembled 6.22 million sequences of canine DNA for 1.5X coverage, or 78 percent, of the genome."
""In little more than a decade genomics has advanced greatly and we now have approximately 150 completed genomes, including the human, mouse and fruit fly, in the public domain," Craig Venter, president of TCAG and the J. Craig Venter Science Foundation, which paid for the dog genome research, said in the statement. "Our new method is an efficient and effective way of sequencing that will allow more organisms to be analyzed while still providing significant information.""
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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."
"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]
""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."
"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."
"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."
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BMJ
Mad, Bad and Dangerous: The Scientist and the Cinema
"Fictional narratives in literature, film, and television help shape public perception of scientists and doctors, their values, and how they behave; they also promote a shared self identity among professionals. Cultural commentators and medical historians' interest in how clinicians and medical scientists are represented in feature films has developed in parallel with the use of films in teaching, which is now a popular means of stimulating debate on biomedical ethics and professional conduct, in undergraduate medicine and medical history courses.
Christopher Frayling's book characterises several thematic variations in the portrayal of scientists and doctors in Western cinema, from silent movies to modern blockbusters. He has cast his net widely, studying posters and publicity stills as well as films and scripts, and compiled an entertaining survey. The only disappointment is the staid selection of illustrations."
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UB Reporter
Bioinformatics project goes to next level
"An effort to introduce local high school students to the emerging field of bioinformatics—and hopefully inspire some to pursue studies, and eventually jobs, in the field—is moving to the next level with a workshop designed to help high school teachers incorporate the topic into their own curriculums.
The "Next Generation Scientists: Training Students and Teachers" project, a program developed by UB's Center for Computational Research and funded by Verizon Corp., has been working for several years with teachers and students at Mt. St. Mary Academy in Kenmore and Orchard Park High School to provide coursework in bioinformatics for students at those schools."
"Bioinformatics "is not typically" covered as part of the high school curriculum, Pitman said, adding that he is not aware of any other formal bioinformatics programs in place at a secondary school nationwide."
redux [07.29.05]
"In response to the soaring demand for computational power by the hundreds of researchers who depend on it, UB has expanded the computing capacity of the Center for Computational Research in its New York State Center of Excellence in Bioinformatics and Life Sciences with the installation of a new Dell high-performance computing cluster.
The cluster, with 1,668 processors, nearly doubles the Center of Excellence's computing capacity. If this cluster was listed on the current top 500 list of the world's fastest supercomputers, (http://www.top500.org), it would be among the 40 fastest individual machines."
redux [04.15.04]
"Two years ago, Jeffrey Skolnick arrived as the leader of the University at Buffalo's new bioinformatics center and the next great hope for the region's struggling economy.
Last week, UB issued a three-page news release announcing a restructuring and expansion of the bioinformatics center that includes a new executive director.
Skolnick's name did not appear anywhere in that document."
redux [03.29.04]
"Bioinformatics star Jeffrey Skolnick has created a stir at the University at Buffalo by criticizing his Dell supercomputer -- announced with fanfare in 2002 -- and switching his allegiance to rival IBM Corp.
The highly public flap has prompted UB administrators to come to the defense of Dell, a deep-pocketed research partner."
redux [03.25.04]
"The University at Buffalo Center of Excellence in Bioinformatics has installed an IBM Corp. supercomputer built on blades and also will work with IBM researchers who will provide algorithms to aid protein pattern and correlation discovery, the company and the center announced Thursday."
"The new supercomputer that will handle the intensive computational work will have a peak performance of more than 1.32T flops and will consist of a cluster of 266 IBM eServer BladeCenter HS20 systems running Red Hat Advance Server 2.1 Linux."
redux [12.08.03]
""Unfortunately, I think there's unreal expectations," said Skolnick, the Buffalo center director. Still, he said, the center "can play a role, and perhaps a significant role" in an economic turnaround.
Even so, not everybody is on board. At Ulrich's Tavern, which calls itself Buffalo's oldest and is sandwiched between the center and an old windshield-wiper factory, an elderly man nursed a midafternoon beer and said he'd never even heard of bioinformatics.
The bar's proprietor, Jim Daley Jr., was plenty aware of it.
"I think it's the most underrated thing in Buffalo," he said. "Most people talk about the casino.""
redux [07.14.03]
"If any doubts lingered among scientists, politicians or business executives about the future prospects for the University at Buffalo Center of Excellence in Bioinformatics, they were erased last Friday as nearly 200 scientists representing the U.S., Canada, India, the Netherlands, the United Kingdom, Italy and Japan gathered in the Adams Mark Hotel in Buffalo for the first annual "Frontiers in Bioinformatics" symposium."
"The day's events amounted to a grand show of support for the center of excellence, which was founded in 2001 by Gov. George E. Pataki"
redux [06.06.03]
"Despite the media barrage surrounding her new book, Senator Hillary Rodham Clinton made a brief appearance in Buffalo on Friday, June 6, to praise the University of Buffalo (UB)'s ambitious Bioinformatics Center of Excellence initiative."
""It has taken a lot of work to make the case to fund bioinformatics," Clinton said. "When we started, the response was, 'What's that?' " Despite this, Clinton and Reynolds have helped to earmark more than $9 million in federal funding for the project."
"Scientists on the cutting edge of drug development were comparing notes in Buffalo Friday during a symposium aimed at introducing the city's developing bioinformatics center to the scientific world."
"In Buffalo, bioinformatics is viewed as perhaps the best hope to generate jobs lost with the demise of its steel and grain-milling industries. But with several other cities around the country also investing heavily in life sciences, the center's directors are well aware of the competition for staff and resources."
redux [03.02.03]
"Jeff Skolnick didn't sign up for all this hype.
He did not apply to the following posting:
Savior wanted: A wunderkind in cutting-edge technology who can help build a new economy and carry the hopes of a Rust Belt region of 1.2 million people.
He just took a job heading a new academic program, the University at Buffalo's Center of Excellence in Bioinformatics."
redux [07.26.02]
"New York's U.S. Senators Charles Schumer and Hillary Rodham Clinton jointly announced that the Senate Appropriations Committee has approved $1 million in funding for Buffalo's planned Center of Excellence in Bioinformatics.
The $1 million was included as part of a an appropriations measure for the Departments of Veterans Affairs and Housing and Urban Development."
redux [05.01.02]
"An optimistic Pataki declared the center "will transform western New York into a 21st Century economy."
The lofty predictions come as upstate's largest city struggles to reinvent itself from a past-its-peak industrial center losing not only jobs but people: U.S. Census figures show the population has dropped to under 300,000, down from a 1950s peak of 580,000."
redux [12.07.01]
"Buffalo will be the site of a Center of Excellence for Bioinformatics thanks to a $200 million collaboration between the public and private sectors.
Gov. George Pataki announced during a swing through Buffalo on Dec. 6 that the state will contribute $50 million to help establish the 150,000 square-foot facility to be located adjacent to the emerging Buffalo Niagara Medical Campus. It is part of Pataki's $1 billion high-tech and biotech Centers of Excellence planned for across the state."
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Nature
Let data speak to data
"Web tools now allow data sharing and informal debate to take place alongside published papers. But to take full advantage, scientists must embrace a culture of sharing and rethink their vision of databases."
"Scientists may be justified in retaining privileged access to data that they have invested heavily in collecting, pending publication — but there are also huge amounts of data that do not need to be kept behind walls. And few organizations seem to be aware that by making their data available under a Creative Commons licence (see http://creativecommons.org/license), they can stipulate both rights and credits for the reuse of data, while allowing its uninterrupted access by machines."
redux [01.28.04]
"Many academic scientists see nothing wrong with making their commercial brethren pay for access. After all, they reason, industry has lots of money. Why not make them pay?"
"When you choose the "soak industry" option, you are implicitly expressing the following beliefs: (1) Your database is so useful for drug development that companies will pay handsomely for it. And (2) you're willing to delay the drug developers until the company comes up with the scratch. To hell with the patients who might benefit from the drug in question! Do you really believe this?"
redux [06.13.02]
"But Celera's rival published its version free of charge on the internet, a move which damaged Celera's commercial prospects. "That has had an impact," says Bennett. "Any stand-alone information business will be challenged because the value of information degrades," he adds.
But he denies that the venture has been a failure. "We have 250 subscribers, both commercial and non-commercial," says Bennett. The business even makes a profit, but the company will not discuss the impact of the free genome data on profits."
redux [04.08.02]
"Jim Kent was a graduate student in biology at the University of California, Santa Cruz (UCSC), when he wrote the program that allowed the public human genome team to assemble its fragments just before Celera's private, commercial effort. His program ensured that the human genome data would remain in the public domain. Kent wrote the 10,000-line program in a month, because he didn't want to see the genome data locked up by commercial patents."
"Kent's work illustrates the need to think about more than just open source code; in the scientific community there is a growing awareness of the importance of open data."
redux [03.20.02]
[requires 'free' registration]
"The genomics revolution and the Internet have changed science in ways impossible to imagine 20 years ago. Among other advances, these forces have allowed the latest research to be routinely gathered, organized, and disseminated, typically at little or cost, through online biological information databases.
Arduous to use and filled with mostly unanalyzed data early on, these computer databases are now packed with valuable, up-to-date information made easily accessible with improved search engines. They have become so ubiquitous and integral to science today that almost every molecular biologist consults one when initiating research projects. "It would be impossible to do molecular biology properly these days without access to them."
redux [03.07.02]
"''I humbly have to admit that between only 15 to 20 percent of my requests are fulfilled. I cannot afford to do anything else,'' said Tak Mak, a leading genetics researcher at the University of Toronto.
"In fact, according to a recent study published in the Journal of the American Medical Association and led by doctors at Massachusetts General Hospital, nearly 50 percent of surveyed geneticists at major US academic institutions said that another faculty member had denied them at least one request for information in the past three years. The study also found that geneticists are vastly more likely to believe that sharing has decreased in their field over the past decade than that it has increased - a startling figure given how much easier the Internet has made the transfer of information."
redux [01.23.02]
[requires 'free' registration]
"Nearly half the academic geneticists who asked for additional information, data, or materials related to a published research report were denied their requests, a new survey reports today. Are geneticists being unfairly pilloried?"
"Because they were denied access to data, 28% of geneticists reported that they had been unable to confirm published research. Other reported consequences were delays in publications, abandonment of a promising line of research, and the collapse of collaborations."
redux [02.27.02]
"For the scientists working on the Human Genome Project, the data defining who we are is too important to be left to Celera -- or any other company. David Haussler, a team leader at the University of California at Santa Cruz who helped Kent and others put the genome online, expresses the credo of a data liberator succinctly: "Information about the human genome is better in public hands than secretly locked up somewhere."
"But it's not just the research data itself that is at the center of the tug of war between corporations and scientists. When working with data as complex and vast as the human genome, the software tools necessary to manipulate that data are as important as the genetic code itself."
"It's really clear that there are some real issues here, but there are people taking up the guerdon on behalf of openness as well as those who are working for secrecy and private advantage. So I'm hopeful that in the end, openness will win.
Especially in a field like bioinformatics, the natural advantages of open source really do outweigh the advantages of secrecy. No one controls all the data. Talk after talk at the conference focused on the way that matching up data from other researcher's databases is the key to making sense out of your own data."
redux [05.09.01]
"It may seem surprising, considering the amount of publicity the Human Genome Project has garnered over the past year, but a recent Wellcome Trust survey indicates that only half of biomedical researchers using genome databases are familiar with the services provided by Ensembl and other freely available options.
Although the number of hits on the Ensembl website has doubled since the publication of the Human Genome Project's findings in Nature in February, a questionnaire sent to 777 individuals funded by the Wellcome Trust found that only 82 used Ensembl regularly, 189 used it occasionally, and only 50 percent of those who used DNA databases regularly used Ensembl at all.
Even more surprising was the finding that of those who didn't use Ensembl, 50 percent had never heard of it.""
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Nature
COMIC 1. Adventures in Synthetic Biology
"Setting -- (Dude is squatting close to a river of cells) little amorphous, faceless, bacterial cells burbling along replicating and racing from the distant past into the distant future (let's call this the River of Life?). The first half of Hardy's poem Heredity about the "family face" sets the mood. Sally and Dude stand overlooking the burbling river of replicating cells. Dude wants to get the cells to do something. Sally does too, but she's feeling more circumspect about taking responsibility for the consequences of success."
redux [08.17.05]
[requires 'free' registration]
""You can sit down at a computer, and you can design experiments, and you can see the performance of this thing, and then you can figure out why it's done what it's done," Dr. Ellison said. "You're not going to recognize the full return of the biological revolution until you can simulate a living organism."
In the past few years this fantasy has become plausible and now Dr. Ellison is part of an international team of biologists who are now trying to make it a reality. They have chosen to recreate Escherichia coli, the humble resident of the human gut that has been the favorite species for biology experiments for decades."
redux [11.14.03]
"For now, "this is basic science at the most basic level with lots of unknowns".
But he added: "The ability to construct synthetic genomes may lead to extraordinary advances in our ability to engineer micro-organisms for many vital energy and environmental purposes"."
[requires 'free' registration]
"Venter also said during the press conference that his team would not commercialize PCA, nor would he file patents on it. "We'd rather wait till the next stage when there's a clear cut application: for instance if we have something that produces hydrogen that might hold some value." Asked how the PCA technology will be made available to other scientists he said "By reading our paper."
redux [11.26.02]
[requires 'free' registration]
"Craig Venter's "minimal genome" project announced Wednesday is not about creating a new life form and probably doesn't pose much of a biowarfare threat, researchers say. The high-profile project was just funded by the US Department of Energy (DOE) with $3 million going to the Institute for Biological Energy Alternatives (IBEA), one of the non-profit research institutes Venter founded after leaving the newly profit-minded Celera Genomics early this year.
According to some scientists, the new project won't even define the minimal genomethe basic gene set required for lifebecause there can be no single minimal genome."
"Several years ago, Venter first looked at this mycoplasma as the best such model, because the organism is a record-holder of sorts: the self-replicating life form with the smallest known complement of genetic material. Unlike the human genome with its 30,000 to 50,000 genes, M. genitalium gets by with only 517. But remarkably, nearly half of even that minimal set is extra baggage. Under some laboratory conditions, as few as 300 of the genes can fulfill its definition as a lifeform that feeds and divides.
As it turns out, what is the definition of life itself? and also exactly what is its minimal genetic set? have been hotly contested. Gene size is one of the main limits to what could be the final and minimal cell size, and thus may set a limit on possible targets for creating life from scratch.
But what structures are too small or too simple to be considered "life"?"
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“Bioinformatics will be at the core of biology in the 21st century. In fields ranging from structural biology to genomics to biomedical imaging, ready access to data and analytical tools are fundamentally changing the way investigators in the life sciences conduct research and approach problems. Complex, computationally intensive biological problems are now being addressed and promise to significantly advance our understanding of biology and medicine. No biological discipline will be unaffected by these technological breakthroughs.”
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