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 Wed, 25 Nov 2009 09:05:01 EST Wed, 25 Nov 2009 09:05:01 EST 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/2009/11/091119121306.htm A new statistical technique allows scientists to scan a genome for specific gene-regulatory regions without requiring prior knowledge of the relevant transcription factors. The technique has been experimentally validated in both the mouse genome and the fruit fly genome. Thu, 19 Nov 2009 00:00:00 EST http://www.sciencedaily.com/releases/2009/11/091119121306.htm http://www.sciencedaily.com/releases/2009/11/091110065917.htm Natural history plans to chart life on earth, yet the discipline risks being buried under a landslide of painstakingly collected data that isn't always used. Now researchers at London's Natural History Museum have created a social networking tool called "Scratchpads" where natural historians can get together and share their data. Thu, 12 Nov 2009 17:00:00 EST http://www.sciencedaily.com/releases/2009/11/091110065917.htm http://www.sciencedaily.com/releases/2009/10/091027103109.htm Electronic tools and technology applications for consumers can help improve health care processes, such as adherence to medication and clinical outcomes like smoking cessation, according to a new report. The analysis of consumer health informatics was based on an examination of 146 published research studies of patient-focused electronic tools. It is among the first to explore the potential value of consumer health informatics. Tue, 27 Oct 2009 00:00:00 EDT http://www.sciencedaily.com/releases/2009/10/091027103109.htm http://www.sciencedaily.com/releases/2009/09/090930165034.htm Researchers have started using computational models of the brain, making it easier to study the brain's connections. An electrical and computer engineering doctoral student has discovered new evidence on how the brain reacts to fear, including important findings that could help victims of post-traumatic stress disorder. Thu, 01 Oct 2009 05:00:00 EDT http://www.sciencedaily.com/releases/2009/09/090930165034.htm http://www.sciencedaily.com/releases/2009/09/090922160104.htm Researchers are utilizing computational models to study how the brain's chemicals and synaptic mechanisms, or connections between neurons, react to cocaine addiction and what this could mean for future therapies. Wed, 23 Sep 2009 14:00:00 EDT http://www.sciencedaily.com/releases/2009/09/090922160104.htm http://www.sciencedaily.com/releases/2009/09/090917111615.htm Researchers in Spain have revealed the process by which proteins with a tendency to cause conformational diseases such as amyotrophic lateral sclerosis, familial amyloidotic polyneuropathy, familial amyloidotic cardiomyopathy, finally end up causing them. The researchers carried out an analysis of their 3D structure and studied why these proteins finally become toxic although they are correctly folded, an indicator that they are functioning correctly. Sun, 20 Sep 2009 05:00:00 EDT http://www.sciencedaily.com/releases/2009/09/090917111615.htm http://www.sciencedaily.com/releases/2009/09/090914111100.htm A new study has demonstrated that researchers trying to model a range of processes could use the power and capabilities of a particular XBox chip as a much cheaper alternative to other forms of parallel processing hardware. Tue, 15 Sep 2009 17:00:00 EDT http://www.sciencedaily.com/releases/2009/09/090914111100.htm http://www.sciencedaily.com/releases/2009/08/090830192032.htm A new computational method has proven its usefulness in counting duplicated sequences in human genomes and in initially assessing their content. Duplicated segments have been linked with several types of diseases, including intellectual impairment, schizoprhenia, lupus, Crohn's, psoriasis and macular degeneration. They have also been found in resistance to certain diseases, like HIV infections. Determining the number, content, and location of segmental duplications is vital to understanding their health implications. Sun, 06 Sep 2009 05:00:00 EDT http://www.sciencedaily.com/releases/2009/08/090830192032.htm http://www.sciencedaily.com/releases/2009/09/090901172836.htm Engineers have devised innovative computer software that can sift through hundreds of genetic mutations and highlight the DNA changes that are most likely to promote cancer. Wed, 02 Sep 2009 23:00:00 EDT http://www.sciencedaily.com/releases/2009/09/090901172836.htm http://www.sciencedaily.com/releases/2009/08/090813202124.htm Scientists have developed a quantitative, mathematical model of DNA replication and cell division for the bacterium Caulobacter crescentus. Sat, 22 Aug 2009 17:00:00 EDT http://www.sciencedaily.com/releases/2009/08/090813202124.htm http://www.sciencedaily.com/releases/2009/07/090729121706.htm Scientists have created a two-step computer simulation (using an important process called the Wang-Landau algorithm) that sheds light on how a crucial protein -- glycophorin A -- becomes an active part of living cells. The new use of Wang-Landau could lead to a better understanding of the controlling mechanisms behind protein folding. Tue, 11 Aug 2009 02:00:00 EDT http://www.sciencedaily.com/releases/2009/07/090729121706.htm http://www.sciencedaily.com/releases/2009/07/090730141605.htm As mathematics continues to become an increasingly important component in undergraduate biology programs, a more comprehensive understanding of the use of algebraic models is needed by the next generation of biologists to facilitate new advances in the life sciences, according to researchers. Mon, 03 Aug 2009 08:00:00 EDT http://www.sciencedaily.com/releases/2009/07/090730141605.htm http://www.sciencedaily.com/releases/2009/07/090723142048.htm Much as meteorologists predict the path and intensity of hurricanes, some researchers believe we will one day predict with unprecedented foresight, specificity and scale such things as the economic and social effects of billions of new Internet users in China and India, or the exact location and number of airline flights to cancel around the world in order to halt the spread of a pandemic. Fri, 24 Jul 2009 14:00:00 EDT http://www.sciencedaily.com/releases/2009/07/090723142048.htm http://www.sciencedaily.com/releases/2009/06/090617105048.htm Computer scientists have developed a framework for studying the arrangement of tissue networks created by cell division across a diverse set of organisms, including fruit flies, tadpoles and plants. Fri, 03 Jul 2009 20:00:00 EDT http://www.sciencedaily.com/releases/2009/06/090617105048.htm http://www.sciencedaily.com/releases/2009/06/090616103205.htm Gene regulatory networks in cell nuclei are similar to cloud computing networks, such as Google or Yahoo!, researchers report in the journal Molecular Systems Biology. The similarity is that each system keeps working despite the failure of individual components, whether they are master genes or computer processors. Wed, 17 Jun 2009 11:00:00 EDT http://www.sciencedaily.com/releases/2009/06/090616103205.htm http://www.sciencedaily.com/releases/2009/05/090505100648.htm A lattice of vanadium dioxide molecules just six atoms thick in which electrons appear to be guided by conflicting laws of physics depending on their direction of travel has been modeled by a team of physicists. Its unique properties could open up a new world of possibilities in the emerging field of spintronics technology, which takes advantage of the magnetic as well as the electric properties of electrons in the design of novel electronic devices. Thu, 07 May 2009 14:00:00 EDT http://www.sciencedaily.com/releases/2009/05/090505100648.htm http://www.sciencedaily.com/releases/2009/05/090504122107.htm A new approach to analyzing social networks could help homeland security find the covert connections between the people behind terrorist attacks. The approach involves revealing the nodes that act as hubs in a terrorist network and tracing back to individual planners and perpetrators. Tue, 05 May 2009 05:00:00 EDT http://www.sciencedaily.com/releases/2009/05/090504122107.htm http://www.sciencedaily.com/releases/2009/04/090410100940.htm Researchers have developed a set of free tools called ViPDAC (virtual proteomics data analysis cluster), for use in combination with Amazon's inexpensive "cloud computing" service, providing the option to rent processing time on its powerful servers; and free software, to put this very expensive and promising field within reach of scientists everywhere. Mon, 13 Apr 2009 23:00:00 EDT http://www.sciencedaily.com/releases/2009/04/090410100940.htm http://www.sciencedaily.com/releases/2009/02/090211082359.htm Scientists have used a computer simulation to predict what the very early universe would have appeared like 500 million years after the "Big Bang." Wed, 11 Feb 2009 17:00:00 EST http://www.sciencedaily.com/releases/2009/02/090211082359.htm http://www.sciencedaily.com/releases/2009/02/090205214412.htm Molecular and cellular biologists have made tremendous scientific advances by dissecting apart the functions of individual genes, proteins, and pathways. Researchers are looking to expand that understanding by putting the pieces back together, mathematically. Tue, 10 Feb 2009 20:00:00 EST http://www.sciencedaily.com/releases/2009/02/090205214412.htm http://www.sciencedaily.com/releases/2008/11/081124203705.htm A team of lecturers in French have developed the Annotathon -- an innovative bioinformatics teaching approach that appeals to undergraduate biology students. With an increasing interest in metagenomics -- the decoding of not just a single genome, but of an entire microbial ecosystem -- the amount of data produced is more than a biologist can keep up with. Mon, 24 Nov 2008 00:00:00 EST http://www.sciencedaily.com/releases/2008/11/081124203705.htm http://www.sciencedaily.com/releases/2008/11/081119140714.htm Computational neuroscientists have developed a computational model that provides insight into the function of the brain's visual cortex and the information processing that enables people to perceive contours and surfaces, and understand what they see in the world around them. Thu, 20 Nov 2008 08:00:00 EST http://www.sciencedaily.com/releases/2008/11/081119140714.htm http://www.sciencedaily.com/releases/2008/11/081112074901.htm Human disease research produces an enormous amount of data from different sources such as animal models, high throughput genetic screening of human tissue, and in vitro laboratory experiments. This data operates at different levels and scales including genes, molecules, cells, tissues and whole organs, embodying a huge amount of potentially valuable insight that current computer modeling approaches often fail to exploit properly. Fri, 14 Nov 2008 23:00:00 EST http://www.sciencedaily.com/releases/2008/11/081112074901.htm http://www.sciencedaily.com/releases/2008/11/081107071822.htm The evolution of novel characteristics within organisms can be enhanced when environments change in a systematic manner, according to a new study. Researchers suggest that in environments that vary over time in a non-random way, evolution can learn the rules of the environment and develop organisms that can readily generate novel useful traits with only a few mutations. Mon, 10 Nov 2008 05:00:00 EST http://www.sciencedaily.com/releases/2008/11/081107071822.htm http://www.sciencedaily.com/releases/2008/10/081031102642.htm Sequence alignments are the basic tools of genomics research. Researchers introduce a statistical method for assessing the quality of protein sequence alignments. Fri, 31 Oct 2008 00:00:00 EDT http://www.sciencedaily.com/releases/2008/10/081031102642.htm http://www.sciencedaily.com/releases/2008/10/081029084044.htm In less time than the blink of an eye, the Translational Genomics Research Institute's new supercomputer at Arizona State University can do operations equal to every dollar in the recent Wall Street bailout. That would be 700 billion computations in less than 1/60th of a second. Thu, 30 Oct 2008 05:00:00 EDT http://www.sciencedaily.com/releases/2008/10/081029084044.htm http://www.sciencedaily.com/releases/2008/10/081028121025.htm Around 150 thousand people per year get the parasitic disease African sleeping sickness, but the only medicines to treat it are either difficult to administer, expensive, or toxic. Now a team of scientists has put computers to work to find a solution. Wed, 29 Oct 2008 20:00:00 EDT http://www.sciencedaily.com/releases/2008/10/081028121025.htm http://www.sciencedaily.com/releases/2008/10/081023222250.htm When reaching for an object, the brain prepares neural commands sent to the target muscles to minimize energy expenditure, according to a new study. Sun, 26 Oct 2008 14:00:00 EDT http://www.sciencedaily.com/releases/2008/10/081023222250.htm http://www.sciencedaily.com/releases/2008/10/081023222252.htm Researchers have put forward a simple model of development and gene regulation that is capable of explaining patterns observed in the distribution of morphologies and body plans (or, more generally, phenotypes). Sat, 25 Oct 2008 20:00:00 EDT http://www.sciencedaily.com/releases/2008/10/081023222252.htm http://www.sciencedaily.com/releases/2008/10/081016132839.htm Computer scientists are cracking the code on the metabolism of human diseases. Scientists know that different normal and diseased tissues behave differently. But a method that tells them just how they do so may one day give medical science a new way to fight obesity, hypertension, diabetes and other dangerous disorders of the metabolism. Fri, 17 Oct 2008 11:00:00 EDT http://www.sciencedaily.com/releases/2008/10/081016132839.htm http://www.sciencedaily.com/releases/2008/10/081016124039.htm After spending years developing a computational model to help illuminate cell signaling pathways, a team of MIT researchers decided to see what would happen if they "broke" the model. The results reveal new ways in which cells process chemical information and could indicate how to maximize the effectiveness of disease treatments such as chemotherapy. Thu, 16 Oct 2008 23:00:00 EDT http://www.sciencedaily.com/releases/2008/10/081016124039.htm http://www.sciencedaily.com/releases/2008/09/080929104601.htm Researchers have developed a computer program that trains itself to predict genes in the DNA sequences of fungi. The software will be freely available for academic researchers. Tue, 07 Oct 2008 02:00:00 EDT http://www.sciencedaily.com/releases/2008/09/080929104601.htm http://www.sciencedaily.com/releases/2008/09/080904102747.htm Computer scientists are generating new "petascale" computer models depicting detailed climate dynamics, which will build the foundation for the next generation of complex climate models. The project offers a golden opportunity for climate simulation and prediction scientists to dramatically advance Earth system science and help to improve quality of life on the planet. Thu, 04 Sep 2008 00:00:00 EDT http://www.sciencedaily.com/releases/2008/09/080904102747.htm http://www.sciencedaily.com/releases/2008/07/080728193231.htm The information technology industry consumes as much energy and has roughly the same carbon "footprint" as the airline industry. Now scientists and engineers are building an instrument to test the energy efficiency of computing systems under real-world conditions -- with the ultimate goal of getting computer designers and users in the scientific community to rethink the way they do their jobs. Mon, 04 Aug 2008 20:00:00 EDT http://www.sciencedaily.com/releases/2008/07/080728193231.htm http://www.sciencedaily.com/releases/2008/07/080722192341.htm A new computer language for modeling biological phenomenon can "think" like cells and molecular mechanisms think, thereby simulating the dynamics of biological phenomenon. Through incorporating basic principles of engineering, the new language, called Little b, surpasses current biological modeling software in that it goes beyond simply representing biological information. It allows biologists to create programs that can reason about biological knowledge and thereby help overcome the barrier of complexity. Fri, 25 Jul 2008 08:00:00 EDT http://www.sciencedaily.com/releases/2008/07/080722192341.htm http://www.sciencedaily.com/releases/2008/07/080717225716.htm Researchers have developed an intelligent computational model of the descriptive grammar of the Spanish language. This opens up new possibilities for the computational representation of languages and natural language processing applications. Tue, 22 Jul 2008 05:00:00 EDT http://www.sciencedaily.com/releases/2008/07/080717225716.htm http://www.sciencedaily.com/releases/2008/07/080702141425.htm Medical researchers are using high-powered computers to determine how substances known as recombinant immunotoxins can best be modified in order to attack and kill malignant tumors while doing minimal harm to a patient's healthy cells. Mon, 07 Jul 2008 20:00:00 EDT http://www.sciencedaily.com/releases/2008/07/080702141425.htm http://www.sciencedaily.com/releases/2008/07/080702121148.htm A group of undergraduate students have forged a new area of bioinformatics that may improve genomic and proteomic annotations and unlock a collection of stubborn biological mysteries. Their work will be published in the journal Genome Research. Sat, 05 Jul 2008 20:00:00 EDT http://www.sciencedaily.com/releases/2008/07/080702121148.htm http://www.sciencedaily.com/releases/2008/06/080630173945.htm Myoglobin is responsible for oxygen storage in cells. But how does oxygen travel through the solid protein wall to be anchored by an iron atom deep within the protein? Scientists have now provided a computational solution to the decades-old puzzle. Sat, 05 Jul 2008 14:00:00 EDT http://www.sciencedaily.com/releases/2008/06/080630173945.htm http://www.sciencedaily.com/releases/2008/05/080529141354.htm Scientists have taken an important step toward understanding how the human brain codes the meanings of words by creating the first computational model that can predict the unique brain activation patterns associated with names for things that you can see, hear, feel, taste or smell. The model predicts brain activation patterns for thousands of concrete nouns. Mon, 02 Jun 2008 05:00:00 EDT http://www.sciencedaily.com/releases/2008/05/080529141354.htm http://www.sciencedaily.com/releases/2008/05/080522210025.htm A statistical approach to studying genetic variation promises to shed new light on the history of human migration. Application of the method has already turned up such surprising findings as a strong Mongolian contribution to the genes of the Native American Pima people and gene flow from the north of Europe to Eastern Siberia. Sat, 24 May 2008 08:00:00 EDT http://www.sciencedaily.com/releases/2008/05/080522210025.htm 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