http://www.sciencedaily.com/news/computers_math/computational_biology/ Computational biology and bioinformatics. Read the latest research from universities and research institutes around the world. Full text, images, free. en-us Fri, 16 May 2008 16:05:01 EDT Fri, 16 May 2008 16:05:01 EDT 60 http://www.sciencedaily.com/images/logosmall.gif http://www.sciencedaily.com/news/computers_math/computational_biology/ For more science articles, visit ScienceDaily. http://www.sciencedaily.com/releases/2008/05/080506115826.htm Scientists have developed a new method for simulating turbulent fluids, which will open up new perspectives in the field of astrophysics. Turbulence is worth studying, because of the fundamental role that it plays in astrophysics. Turbulence is frequently modelled by Large Eddy Simulations (LES), where the dynamics of turbulent eddies are computed on large scales, while a subgrid scale model approximates the influence of smaller eddies. In astrophysics the LES approach is challenged, because gravity and thermal processes break the scale-invariance employed in LES over a wide range of scales. Wed, 07 May 2008 02:00:00 EDT http://www.sciencedaily.com/releases/2008/05/080506115826.htm http://www.sciencedaily.com/releases/2008/04/080423131714.htm Using a multidisciplinary mix of geometry, biological research and techniques developed to solve problems on supercomputers, scientists have shown for the first time how a genome is organized in three-dimensional space. Fri, 25 Apr 2008 11:00:00 EDT http://www.sciencedaily.com/releases/2008/04/080423131714.htm http://www.sciencedaily.com/releases/2008/04/080407123839.htm Researchers have developed a new algorithm for ranking abnormal genes according to their likelihood of contributing to a cancer. They also show that a gene identified by the algorithm as a likely restrainer of tumor growth does indeed play that role in a common type of brain cancer, and is not a mere "bystander" to another restrainer gene. Thu, 10 Apr 2008 02:00:00 EDT http://www.sciencedaily.com/releases/2008/04/080407123839.htm http://www.sciencedaily.com/releases/2008/04/080410115425.htm A closer alliance between computational and experimental researchers is needed to make progress towards one of biology's most challenging goals, understanding how epigenetic marks contribute to regulation of gene expression. Thu, 10 Apr 2008 00:00:00 EDT http://www.sciencedaily.com/releases/2008/04/080410115425.htm http://www.sciencedaily.com/releases/2008/03/080328070108.htm As the scope of genome research expands on an almost daily basis, researchers confront increasingly large volumes of data. Now biologists are developing software that enables researchers to analyze millions of DNA sequences faster and with greater accuracy. Mon, 31 Mar 2008 14:00:00 EDT http://www.sciencedaily.com/releases/2008/03/080328070108.htm http://www.sciencedaily.com/releases/2008/03/080318212430.htm Computing grids have helped scientists shed light on how life on earth may have originated. Deep ocean hydrothermal vents have long been suggested as possible sources of biological molecules such as RNA and DNA but it was unclear how they could survive the high temperatures and pressures that occur round these vents. Wed, 19 Mar 2008 11:00:00 EDT http://www.sciencedaily.com/releases/2008/03/080318212430.htm http://www.sciencedaily.com/releases/2008/03/080317123237.htm Human diseases and social networks seem to have little in common. However, at the crux of these two lies a network, communities within the network, and farther even, substructures of the communities. Computer scientists and geneticists can now use a new computer program to automatically discover communities and their subtle structures in a variety of networks. Wed, 19 Mar 2008 11:00:00 EDT http://www.sciencedaily.com/releases/2008/03/080317123237.htm http://www.sciencedaily.com/releases/2008/02/080229090817.htm Brown applied mathematicians have found a new way to sift through mountains of data and draw reliable inferences from it -- a Holy Grail in science and technology. Their pioneering work, the development of a new class of statistical estimators, could lead to better methods for analyzing the large data sets that are increasingly common in fields from biology to business. Sun, 02 Mar 2008 14:00:00 EST http://www.sciencedaily.com/releases/2008/02/080229090817.htm http://www.sciencedaily.com/releases/2008/02/080215151207.htm For many years, Tomaso Poggio's lab at MIT ran two parallel lines of research. Some projects were aimed at understanding how the brain works, using complex computational models. Others were aimed at improving the abilities of computers to perform tasks that our brains do with ease. But recently Poggio has found that the two tasks have begun to overlap to such a degree, that it's now time to combine the two lines of research. Wed, 20 Feb 2008 23:00:00 EST http://www.sciencedaily.com/releases/2008/02/080215151207.htm http://www.sciencedaily.com/releases/2008/02/080215103312.htm Researchers have developed a new method that essentially does for the genetic pathways underlying cancer what social networking web sites can do for people: It finds the connections among them. The researchers first identified familiar sets of genes that work together to support the development of cancer by allowing uncontrolled growth or encouraging the development of blood vessels, for example. Then they used their new statistical techniques to look for relationships, or dependencies, that tie those separate gene sets together. Wed, 20 Feb 2008 02:00:00 EST http://www.sciencedaily.com/releases/2008/02/080215103312.htm http://www.sciencedaily.com/releases/2008/02/080205170602.htm Squeeze a crystal of manganese oxide hard enough, and it changes from an electrical insulator to a conductive metal. Researchers use computational modeling to show why this happens. The results represent an advance in computer modeling of these materials and could shed light on the behavior of similar minerals deep in the Earth. Wed, 06 Feb 2008 08:00:00 EST http://www.sciencedaily.com/releases/2008/02/080205170602.htm http://www.sciencedaily.com/releases/2008/01/080124233657.htm For years, scientists have been trying to teach computers how to see like humans, and recent research has seemed to show computers making progress in recognizing visual objects. A new study, however, cautions that this apparent success may be misleading because the tests being used are inadvertently stacked in favor of computers. Thu, 31 Jan 2008 11:00:00 EST http://www.sciencedaily.com/releases/2008/01/080124233657.htm http://www.sciencedaily.com/releases/2008/01/080124233635.htm A group of computational biologists have created a mathematical model of the process that regulates cell division in a common bacterium, confirming hypotheses, providing new insights, identifying gaps in what is understood so far, and demonstrating the role of computation in biology. Wed, 30 Jan 2008 20:00:00 EST http://www.sciencedaily.com/releases/2008/01/080124233635.htm http://www.sciencedaily.com/releases/2007/12/071227184008.htm A team of biologists have developed a model mapping the control circuit governing a whole free living organism. This is an important milestone for the new field of systems biology and will allow the researchers to model how the organism adapts over time in response to its environment. Sun, 30 Dec 2007 20:00:00 EST http://www.sciencedaily.com/releases/2007/12/071227184008.htm http://www.sciencedaily.com/releases/2007/12/071211232919.htm Early identification of adverse effects of drugs before they are tested in humans is crucial in developing new therapeutics, as unexpected effects account for a third of all drug failures during the development process. Now researchers at the University of California-San Diego have developed a novel technique using computer modeling to identify potential side effects of pharmaceuticals, and have used the technique to study a class of drugs that includes tamoxifen. Thu, 13 Dec 2007 08:00:00 EST http://www.sciencedaily.com/releases/2007/12/071211232919.htm http://www.sciencedaily.com/releases/2007/12/071208165846.htm Researchers are developing a biological map of how three tiny pathogens cause big losses for cattle producers each year. Using a newly developed technique called proteogenomic mapping, they have overcome the limitations inherent in computer modeling. They are using mass spectrometers to identify protein amino acid sequences and map them back onto the genome DNA sequences. Sun, 09 Dec 2007 14:00:00 EST http://www.sciencedaily.com/releases/2007/12/071208165846.htm http://www.sciencedaily.com/releases/2007/11/071121085715.htm A new model to predict the spread of emerging diseases has been developed. The model could give healthcare professionals advance warning of the path an emerging disease might take and so might improve emergency responses and control. Sun, 25 Nov 2007 08:00:00 EST http://www.sciencedaily.com/releases/2007/11/071121085715.htm http://www.sciencedaily.com/releases/2007/11/071109100207.htm The debate over the validity of genomic rearrangement 'hot spots' has its most recent addition in a new theory put forth by researchers at the UC-San Diego. The study holds that there are indeed rearrangement hot spots in the human genome. This study represents a major advance in the debate. Tue, 13 Nov 2007 05:00:00 EST http://www.sciencedaily.com/releases/2007/11/071109100207.htm http://www.sciencedaily.com/releases/2007/11/071109123201.htm Researchers have built a better plant, one that produces more leaves and fruit without needing extra fertilizer. The researchers accomplished this feat using a computer model that mimics the process of evolution. Theirs is the first model to simulate every step of the photosynthetic process. Sun, 11 Nov 2007 20:00:00 EST http://www.sciencedaily.com/releases/2007/11/071109123201.htm http://www.sciencedaily.com/releases/2007/11/071107091524.htm Most people have a few gigabytes of files on their PC. In the next decade, astronomers expect to be processing 10 million gigabytes of data every hour from the Square Kilometre Array telescope. Thu, 08 Nov 2007 17:00:00 EST http://www.sciencedaily.com/releases/2007/11/071107091524.htm http://www.sciencedaily.com/releases/2007/10/071003213607.htm An international team has opened a virtual bazaar, called PAZAR, which allows biologists to share information about gene regulation through individually managed 'boutiques' (data collections). According to research published in the online open access journal, Genome Biology, customers can access data without any charge from any boutique or extract information from the 'superstores' that aggregate data of similar types. Fri, 26 Oct 2007 05:00:00 EDT http://www.sciencedaily.com/releases/2007/10/071003213607.htm http://www.sciencedaily.com/releases/2007/10/071017131914.htm With the aid of more than 70,000 home computer users throughout the world, researchers have, for the first time, accurately predicted the 3-D structure of a small, naturally occurring globular protein using only its amino acid sequence. The accomplishment was achieved with a newly refined computational method for predicting protein structure. Thu, 18 Oct 2007 14:00:00 EDT http://www.sciencedaily.com/releases/2007/10/071017131914.htm http://www.sciencedaily.com/releases/2007/10/071009132043.htm A group of scientists, led by mathematicians, has taken on the challenge of building a common model of immune responses. Their work will radically improve our understanding of the human immune system by allowing all the scientific disciplines working on it to have a common reference point and language. Wed, 10 Oct 2007 11:00:00 EDT http://www.sciencedaily.com/releases/2007/10/071009132043.htm http://www.sciencedaily.com/releases/2007/09/070923193614.htm Researchers have developed a computer modeling approach that could improve a class of drugs based on antibodies, molecules key to the immune system. The model can predict structural changes in an antibody that will improve its effectiveness. Tue, 25 Sep 2007 23:00:00 EDT http://www.sciencedaily.com/releases/2007/09/070923193614.htm http://www.sciencedaily.com/releases/2007/08/070831093937.htm Scientists have developed a theoretical model that can explain the emergence of all orientation-specific cells that are known in rats and primates to date. To orient ourselves, we mainly need two pieces of information: where am I and in which direction am I heading? Every receptor in the eye only captures a very small section of the perceived image. Fri, 31 Aug 2007 17:00:00 EDT http://www.sciencedaily.com/releases/2007/08/070831093937.htm http://www.sciencedaily.com/releases/2007/08/070817132905.htm Most modern attempts to decipher how portions of genetic code are translated into physical characteristics are akin to a first-grader trying to sound out a word letter by letter -- or, in this case, base pair by base pair. Now researchers have developed a computational method that's more like reading whole words at a time. Tue, 21 Aug 2007 08:00:00 EDT http://www.sciencedaily.com/releases/2007/08/070817132905.htm http://www.sciencedaily.com/releases/2007/08/070809125812.htm Computer scientists have developed a way to generate images like smoke-filled bars, foggy alleys and smog-choked cityscapes without the computational drag and slow speed of previous computer graphics methods. Tue, 14 Aug 2007 20:00:00 EDT http://www.sciencedaily.com/releases/2007/08/070809125812.htm http://www.sciencedaily.com/releases/2007/07/070718001629.htm Sequence data for both chromosomes, can be inferred under the right circumstances through a new statistical method developed by USC biologists. Wed, 18 Jul 2007 11:00:00 EDT http://www.sciencedaily.com/releases/2007/07/070718001629.htm http://www.sciencedaily.com/releases/2007/07/070712135154.htm Researchers have developed a way to determine the function of some of the hundreds of thousands of proteins for which amino acid sequence data are available, but whose structure and function remain unknown. Tue, 17 Jul 2007 14:00:00 EDT http://www.sciencedaily.com/releases/2007/07/070712135154.htm http://www.sciencedaily.com/releases/2007/06/070628071618.htm Random Technologies, the newest start-up company to emerge from the University of Rochester Medical Center, launched its new statistical analysis software package at an international conference of drug industry professionals this week. The package is based on the open source software system "R" -- the most widely used statistical computing and graphics system in biomedical research. Fri, 06 Jul 2007 02:00:00 EDT http://www.sciencedaily.com/releases/2007/06/070628071618.htm http://www.sciencedaily.com/releases/2007/05/070523153056.htm A data-driven computational approach developed by a University of Illinois statistician is revealing secrets about inner Earth and discovering unique gene expressions in fruit flies, zebra fish and other living organisms. Fri, 25 May 2007 02:00:00 EDT http://www.sciencedaily.com/releases/2007/05/070523153056.htm http://www.sciencedaily.com/releases/2007/05/070518062419.htm Phillippy et al. describe a new computational system, called Insignia, that can identify DNA signatures of pathogens with a higher degree of accuracy than ever before. Fri, 18 May 2007 17:00:00 EDT http://www.sciencedaily.com/releases/2007/05/070518062419.htm http://www.sciencedaily.com/releases/2007/05/070518062424.htm By applying the techniques of computer engineering to a mechanistic diagram describing the development of the Nematode C. elegans, a group of researchers in Switzerland has been able to tease out how the crucial cross-talk between cellular signaling pathways takes place. Fri, 18 May 2007 14:00:00 EDT http://www.sciencedaily.com/releases/2007/05/070518062424.htm http://www.sciencedaily.com/releases/2007/04/070402153248.htm A mathematician at the University of York has been awarded a Research Leadership Award to study the geometry of viruses. Dr Reidun Twarock will study the structure and assembly of viruses, which will help to develop new anti-viral strategies. Wed, 04 Apr 2007 14:00:00 EDT http://www.sciencedaily.com/releases/2007/04/070402153248.htm http://www.sciencedaily.com/releases/2007/03/070323120004.htm Researchers will use bioinformatics, grid computing and networking infrastructure, as well as collaborative ties to Asian institutions to learn more about avian flu, in hopes of helping to head off a much-feared pandemic in the region of the world where the disease has already cost human lives. Sun, 25 Mar 2007 08:00:00 EDT http://www.sciencedaily.com/releases/2007/03/070323120004.htm http://www.sciencedaily.com/releases/2007/03/070315160953.htm As interest in the rising number of newly characterized microbial genomes mounts, powerful computational tools become critical for the management and analysis of these data to enable strategies for such challenges as harvesting the potential of carbon-neutral bioenergy sources and coping with global climate change. The Integrated Microbial Genomes (IMG) data management system developed by the U.S. Department of Energy Joint Genome Institute (DOE JGI) addresses this challenge with the release of version 2.1. Sat, 17 Mar 2007 17:00:00 EDT http://www.sciencedaily.com/releases/2007/03/070315160953.htm http://www.sciencedaily.com/releases/2007/02/070222160038.htm The Influenza Genome Sequencing Project, funded by the National Institute of Allergy and Infectious Diseases (NIAID), one of the National Institutes of Health (NIH), announced today that it has achieved a major milestone. The entire genetic blueprints of more than 2,000 human and avian influenza viruses taken from samples around the world have been completed and the sequence data made available in a public database. Mon, 26 Feb 2007 11:00:00 EST http://www.sciencedaily.com/releases/2007/02/070222160038.htm http://www.sciencedaily.com/releases/2007/02/070216113239.htm Certain cancer risks can be passed down through families, the result of tiny changes in a family's genetic code. But not all genetic changes are deadly. To help medical counselors and physicians identify the mutations that pose the greatest health risks, researchers have developed and validated a new computer tool. Sat, 17 Feb 2007 05:00:00 EST http://www.sciencedaily.com/releases/2007/02/070216113239.htm http://www.sciencedaily.com/releases/2007/02/070201144837.htm A new computational method to analyse environmental DNA samples, developed by researchers at the European Molecular Biology Laboratory (EMBL) in Heidelberg, now sheds light on the microbial composition of different habitats, from soil to water. The study, which will be published in this week's online issue of the journal Science, also reveals that microbes evolve faster in some environments than in others and that they rather rarely change their habitat preferences over time. Mon, 05 Feb 2007 05:00:00 EST http://www.sciencedaily.com/releases/2007/02/070201144837.htm http://www.sciencedaily.com/releases/2007/01/070125115707.htm Despite the fact that bees are one of the most beneficial insects in the world, much of their behavior remains a mystery -- even to the apiculturists who tend them. To better understand such fundamental processes as reproduction, and cope with problems such as bee mites and diseases, scientists are at work on a state-of-the-art genomics resource. Mon, 29 Jan 2007 11:00:00 EST http://www.sciencedaily.com/releases/2007/01/070125115707.htm http://www.sciencedaily.com/releases/2007/01/070128140422.htm An Indiana University School of Informatics-led team of researchers has constructed a model that predicts how an emerging pandemic influenza might spread across the globe by airliners. The study, "Modeling the Worldwide Spread of Pandemic Influenza: Baseline Case and Containment Intervention," appears in the January issue of the journal PLoS Medicine. The model they devised is said to be the world's largest-scale epidemic simulation of its kind. Mon, 29 Jan 2007 05:00:00 EST http://www.sciencedaily.com/releases/2007/01/070128140422.htm http://www.sciencedaily.com/releases/2006/12/061226134750.htm Computer scientists at the University of California, San Diego, and Brown University have created a software system that more accurately detects "microinversions," mutations that consist of tiny sequences of reversed DNA. The software gives biologists a powerful new tool to study genomic variation between and within species. The system is explained in the online edition of the Proceedings of the National Academy of Sciences. Sat, 30 Dec 2006 08:00:00 EST http://www.sciencedaily.com/releases/2006/12/061226134750.htm http://www.sciencedaily.com/releases/2006/12/061219095514.htm Researchers will reconstruct the process of evolution, determine relationships between species and build phylogenetic trees with greater accuracy thanks to new method for identifying extremely short strings of inverted nucleotides called "micro-inversions." This new work from researchers at UC-San Diego and Brown University will appear in the online version of PNAS on Dec. 18, 2006. Wed, 20 Dec 2006 17:00:00 EST http://www.sciencedaily.com/releases/2006/12/061219095514.htm http://www.sciencedaily.com/releases/2006/12/061201180429.htm A team of Vanderbilt and University of Dundee scientists envisions a future when computer simulations will be used to predict a tumor's clinical progression and formulate individualized treatment plans. The group has developed a mathematical model for cancer invasion powerful enough for this purpose. The result was published as an entirely theoretical paper in the journal Cell and represents a "sea change" in how biology is done. Mon, 04 Dec 2006 11:00:00 EST http://www.sciencedaily.com/releases/2006/12/061201180429.htm http://www.sciencedaily.com/releases/2006/11/061128084335.htm Breast cancer sufferers could eventually benefit from high-tuned, tailor-made drug treatments that minimize side effects as a result of a joint initiative between computer scientists in Edinburgh and cellular biologists in Japan. Thu, 30 Nov 2006 02:00:00 EST http://www.sciencedaily.com/releases/2006/11/061128084335.htm http://www.sciencedaily.com/releases/2006/10/061027081145.htm An Indiana University neuroscientist and University of Tokyo roboticist have figured out a way to model the popularly accepted idea that it takes all types of sensory information to help us make sense of our environments. Fri, 27 Oct 2006 08:00:00 EDT http://www.sciencedaily.com/releases/2006/10/061027081145.htm http://www.sciencedaily.com/releases/2006/07/060725074310.htm Researchers at the Virginia Bioinformatics Institute (VBI) at Virginia Tech have developed a computational model that allows scientists to better understand the metabolism and toxicity of the HIV/AIDS drug zidovudine (azidothymidine, AZT). Tue, 25 Jul 2006 02:00:00 EDT http://www.sciencedaily.com/releases/2006/07/060725074310.htm http://www.sciencedaily.com/releases/2006/05/060517175724.htm Computational chemists at the University of Georgia have discovered for the first time that when a proton is knocked off one of the pairs of bases that make up DNA, a chain of damage begins that causes "lesions" in the DNA. These lesions, when replicated in the copying mechanisms of DNA, can lead to serious disorders such as cancer. Wed, 17 May 2006 08:00:00 EDT http://www.sciencedaily.com/releases/2006/05/060517175724.htm