ScienceDaily: Computational Biology News

Using math to kill cancer cells

Fri, 14 Jun 2013 08:26:26 EDT

Scientists have outlined how advanced mathematical modelling can be used in the fight against cancer. The technique predicts how different treatments and genetic modifications might allow cancer-killing, oncolytic viruses to overcome the natural defences that cancer cells use to stave off viral infection.

Math technique de-clutters cancer-cell data, revealing tumor evolution, treatment leads

Thu, 06 Jun 2013 19:09:09 EDT

Scientists have developed a mathematical method of simplifying and interpreting genome data bearing evidence of mutations, such as those that characterize specific cancers.

Advanced biological computer developed

Thu, 23 May 2013 18:03:03 EDT

Using only biomolecules, scientists have developed and constructed an advanced biological transducer, a computing machine capable of manipulating genetic codes, and using the output as new input for subsequent computations.

Bionimbus protected data cloud to enable researchers to analyze cancer data

Mon, 20 May 2013 08:32:32 EDT

The University of Chicago has launched the first secure cloud-based computing system that enables researchers to access and analyze human genomic cancer information without the costly and cumbersome infrastructure normally needed to download and store massive amounts of data.

Photonic quantum computers: A brighter future than ever

Mon, 13 May 2013 10:38:38 EDT

Harnessing the unique features of the quantum world promises a dramatic speed-up in information processing as compared to the fastest classical machines. Scientists have succeeded in prototyping a new and highly resource efficient model of a quantum computer -- the boson sampling computer.

Computer algorithms help find cancer connections

Wed, 01 May 2013 13:19:19 EDT

Using powerful algorithms developed by computer scientists, medical researchers have assembled the most complete genetic profile yet of acute myeloid leukemia, an aggressive form of blood cancer.

Modeling disease spread, including flu

Mon, 29 Apr 2013 16:46:46 EDT

A collaborative research network that formed nearly 10 years ago has pioneered the use of computational and mathematical models to prepare for, detect and respond to influenza, pertussis, West Nile disease, dengue fever, cholera and other infectious disease threats.

New keyboard for touchscreens enables faster thumb-typing

Wed, 17 Apr 2013 09:19:19 EDT

Scientists have created a new keyboard called KALQ that enables faster thumb-typing on touchscreen devices. They used computational optimization techniques in conjunction with a model of thumb movement to search among millions of potential layouts before identifying one that yields superior performance. A user study confirmed that, after a short amount of practice, users could type 34% faster than they could with a QWERTY layout.

Novel insights into the evolution of protein networks

Thu, 21 Mar 2013 11:09:09 EDT

System-wide networks of proteins are indispensable for organisms. Function and evolution of these networks are among the most fascinating research questions in biology. Researchers have reconstructed ancestral protein networks. The results are of high interest not only for evolutionary research but also for the interpretation of genome sequence data.

Molecular coordination in evolution

Tue, 05 Mar 2013 08:07:07 EST

Spanish researchers have published a review on the latest computational methods that, based on evolutionary principles, are revolutionizing the field of analysis and prediction of protein structure, function and protein-protein interactions, as well as the short- and long-term expectations for the field.

Taking the gamble out of DNA sequencing: How much can be learned in a large-scale experiment

Sun, 24 Feb 2013 14:28:28 EST

Scientists have developed an algorithm to predict how much can be learned in a large-scale DNA sequencing experiment -- with potential applications in every field of science.

Breakthrough architecture for quantum computers proposed

Sun, 17 Feb 2013 08:49:49 EST

Scientists have proposed a new computational model that may become the architecture for a scalable quantum computer.

Next lung cancer treatment advancement may come in the form of informatics

Thu, 31 Jan 2013 12:06:06 EST

Bioinformatic experts are creating a new model based on digital images and genomics to help improve survival rates in people with lung cancer, which is the leading cancer killer among men and women in the United States. The model - which will help clinicians select the treatment most likely to be successful - will base some of its data on a repository of 4,000 lung cancer samples from the Appalachian region, an area that has higher rates of lung cancer than anywhere else in the nation.

Protein origami: Quick folders are the best

Thu, 31 Jan 2013 08:44:44 EST

The evolutionary history of proteins shows that protein folding is an important factor. Especially the speed of protein folding plays a key role. This was the result of computer analysis. For almost four billions of years, there has been a trend towards faster folding.

Computer scientists develop new way to study molecular networks

Thu, 24 Jan 2013 14:07:07 EST

Computer scientists have developed a new approach to address the shortcomings in the computational analysis of the multiple ways interactions can occur within cells.

Novel gene-searching software improves accuracy in disease studies

Tue, 22 Jan 2013 16:21:21 EST

A novel software tool streamlines the detection of disease-causing CNVs through more sensitive detection methods and by automatically correcting for variations that reduce the accuracy of results in conventional software.

Vulnerabilities in security of personal genetic information

Thu, 17 Jan 2013 14:23:23 EST

Using only a computer, an Internet connection, and publicly accessible online resources, researchers have been able to identify nearly 50 individuals who had submitted personal genetic material as participants in genomic studies.

Soft nanoscale 'Lego' built in the computer

Thu, 17 Jan 2013 10:58:58 EST

Scientists have developed a new method for the construction of building blocks at the nanoscale.

When will genomic research translate into clinical care -- and at what cost? New study applies quantitative modeling to genomics

Fri, 04 Jan 2013 14:36:36 EST

Researchers find that the same tools that can successfully predict hurricanes and election outcomes can be applied to pharmacogenomics and clinical outcomes.

Toward a new model of the cell: Everything you always wanted to know about genes

Sun, 16 Dec 2012 13:25:25 EST

Turning vast amounts of genomic data into meaningful information about the cell is the great challenge of bioinformatics, with major implications for human biology and medicine. Researchers have proposed a new method that creates a computational model of the cell from large networks of gene and protein interactions, discovering how genes and proteins connect to form higher-level cellular machinery.

Best of both worlds: Hybrid approach sheds light on crystal structure solution

Tue, 11 Dec 2012 13:03:03 EST

Understanding the arrangement of atoms in a solid is vital to materials research -- but the problem can be difficult to solve in many important situations. Now, by combining the work of two different scientific camps, researchers have created an algorithm that makes crystal structure solution more automated and reliable.

Modeling the breaking points of metallic glasses

Mon, 26 Nov 2012 11:09:09 EST

Metallic glass alloys (or liquid metals) are three times stronger than the best industrial steel, but can be molded into complex shapes with the same ease as plastic. These materials are highly resistant to scratching, denting, shattering and corrosion. Mathematical methods developed by scientists will help explain why liquid metals have wildly different breaking points.

Computational medicine enhances way doctors detect, treat disease

Thu, 01 Nov 2012 11:10:10 EDT

Computational medicine, a fast-growing method of using computer models and sophisticated software to figure out how disease develops -- and how to thwart it -- has begun to leap off the drawing board and land in the hands of doctors who treat patients for heart ailments, cancer and other illnesses.

Predicting what topics will trend on Twitter: Algorithm offers new technique for analyzing data that fluctuate over time

Thu, 01 Nov 2012 11:06:06 EDT

Twitter's home page features a regularly updated list of topics that are "trending," meaning that tweets about them have suddenly exploded in volume. A position on the list is highly coveted as a source of free publicity, but the selection of topics is automatic, based on a proprietary algorithm that factors in both the number of tweets and recent increases in that number. Researchers have developed a new algorithm that can, with 95 percent accuracy, predict which topics will trend an average of an hour and a half before Twitter's algorithm puts them on the list -- and sometimes as much as four or five hours before.

Computational intelligence opens up new avenues in Alzheimer's research

Tue, 09 Oct 2012 10:16:16 EDT

Researchers have used machine learning and data mining techniques to compare gene expresssion levels in Alzheimer's disease (AD) patients in two key regions of the hippocampus: the dentate gyrus, where the disease appears to have little or no effect, and the entorhinal cortex, where Alzheimer's disease produces major neuronal damage. The results corroborate previous findings by other studies and set forth new working hypotheses for AD research.

Cutting through the genomic thicket in search of disease variants

Tue, 25 Sep 2012 09:18:18 EDT

Scientists and clinicians have turned to computer tools that sift meaningful genomic variants from the glut of mutations they face. Using a new tool researchers can now improve the accuracy of their analysis.

Most extensive pictures ever of an organism's DNA mutation processes

Mon, 17 Sep 2012 15:17:17 EDT

Biologists and informaticists have produced one of the most extensive pictures ever of mutation processes in the DNA sequence of an organism, elucidating important new evolutionary information about the molecular nature of mutations and how fast those heritable changes occur.

Who’s the most influential in a social graph? New software recognizes key influencers faster than ever

Fri, 07 Sep 2012 12:47:47 EDT

Determining the most influential person on a social media network is complex. Thousands of users are interacting about a single subject at the same time. New people are constantly joining the streaming conversation. Researchers have developed a new algorithm that quickly determines betweenness centrality for streaming graphs. The algorithm can identify influencers as information changes within a network.

Computational method for pinpointing genetic factors that cause disease

Wed, 05 Sep 2012 15:43:43 EDT

Researchers have developed a computational method of identifying "causal" genetic variants that lead to particular diseases, with wide application for genome-wide association studies.

First holistic view of how human genome actually works: ENCODE study produces massive data set

Wed, 05 Sep 2012 14:09:09 EDT

The Human Genome Project produced an almost complete order of the 3 billion pairs of chemical letters in the DNA that embodies the human genetic code -- but little about the way this blueprint works. Now, after a multi-year concerted effort by more than 440 researchers in 32 labs around the world, a more dynamic picture gives the first holistic view of how the human genome actually does its job.

Biologists create first predictive computational model of gene networks that control development of sea-urchin embryos

Wed, 29 Aug 2012 09:21:21 EDT

As an animal develops from an embryo, its cells take diverse paths, eventually forming different body parts -- muscles, bones, heart. In order for each cell to know what to do during development, it follows a genetic blueprint, which consists of complex webs of interacting genes called gene regulatory networks. Biologists have spent the last decade or so detailing how these gene networks control development in sea-urchin embryos. Now, for the first time, they have built a computational model of one of these networks.

Identifying aggressive breast cancers by interpreting the mathematical patterns in the cancer genome

Thu, 23 Aug 2012 09:09:09 EDT

It is now possible to identify aggressive breast cancers by interpreting the mathematical patterns in the cancer genome.

New computational technique relieves logjam from massive amounts of data

Wed, 01 Aug 2012 15:48:48 EDT

It's relatively easy to collect massive amounts of data on microbes. But the files are so large that it takes days to simply transmit them to other researchers and months to analyze once they are received. Researchers have now developed a new computational technique that relieves the logjam that these "big data" issues create.

Knee stress studied at tissue, cellular levels

Tue, 24 Jul 2012 16:10:10 EDT

Scientists are developing virtual models of human knee joints to better understand how tissues and their individual cells react to heavy loads – virtual models that someday can be used to understand damage mechanisms caused by the aging process or by debilitating diseases.

Researchers produce first complete computer model of an organism

Sat, 21 Jul 2012 09:14:14 EDT

In a breakthrough effort for computational biology, the world's first complete computer model of an organism has been completed, researchers report. A team used data from more than 900 scientific papers to account for every molecular interaction that takes place in the life cycle of Mycoplasma genitalium, the world's smallest free-living bacterium.

Angry Birds meets bioinformatics

Fri, 20 Jul 2012 10:33:33 EDT

Informatics researchers create an experimental framework for online, clinic-ready apps and ask others to embrace and expand it.

Evolutionary information improves discovery of mutations associated with diseases

Wed, 18 Jul 2012 09:07:07 EDT

Scientists have developed a statistical method using evolutionary information to significantly enhance the likelihood of identifying disease-associated alleles in the genome that show better consistency across populations.

New tools facilitate matching cancer drugs with gene targets

Mon, 16 Jul 2012 09:04:04 EDT

A new study details how a suite of web-based tools provides the research community with greatly improved capacity to compare data derived from large collections of genomic information against thousands of drugs. By comparing drugs and genetic targets, researchers can more easily identify pharmaceuticals that could be effective against different forms of cancer.

Searching genomic data faster: Biologists' capacity for generating genomic data is increasing more rapidly than computing power

Tue, 10 Jul 2012 13:29:29 EDT

In 2001, the Human Genome Project and Celera Genomics announced that after 10 years of work at a cost of some $400 million, they had completed a draft sequence of the human genome. Today, sequencing a human genome is something that a single researcher can do in a couple of weeks for less than $10,000. Since 2002, the rate at which genomes can be sequenced has been doubling every four months or so, whereas computing power doubles only every 18 months. Now a new algorithm drastically reduces the time it takes to find a particular gene sequence in a database of genomes.

Math experts question key ecological theory

Wed, 20 Jun 2012 13:31:31 EDT

Mathematicians say they have disproved a widely accepted theory underpinning the operation of complex networks of interactions in the natural world.

Molecular matchmaking for drug discovery

Tue, 05 Jun 2012 17:20:20 EDT

Computational drug discovery allows researchers to target a small group of possible molecules for therapeutic use, saving significant time and money. Scientists have now reported on advances in image reconstruction that allow his group to detect the secondary structures of proteins from single particle cryo-electron microscopy.

Google goes cancer: Search engine algorithm finds cancer biomarkers

Thu, 17 May 2012 19:31:31 EDT

The strategy used by Google to decide which pages are relevant for a search query can also be used to determine which proteins in a patient's cancer are relevant for the disease progression.

It's official: Physics is hard

Tue, 08 May 2012 10:38:38 EDT

Scientists have conducted scientific research on the difficulty –- from a computational complexity theory perspective -- of addressing some of the challenges of physics.

Forces among molecules: Tiny but important

Fri, 23 Mar 2012 13:46:46 EDT

Forces are not only associated with machines or muscles. You can also find them elsewhere, for instance between molecules. Theoretical chemists are familiar with that. However, they -- or rather their computers -- are not capable of calculating them with high accuracy and efficiency at the same time.

Carbon dioxide catchers: New tools for identifying effective carbon capture technologies

Thu, 01 Mar 2012 10:39:39 EST

Using techniques from drug discovery, and state-of-the-art advances in mathematics, computational algorithms and supercomputing, researchers have developed a tool for identifying the most efficient porous materials for CO2.

Researchers develop better control for DNA-based computations

Fri, 17 Feb 2012 14:57:57 EST

A chemist has found a way to give DNA-based computing better control over logic operations. His work could lead to interfacing DNA-based computing with traditional silicon-based computing.

Video games lead to new paths to treat cancer, other diseases

Thu, 16 Feb 2012 09:46:46 EST

The cure for cancer comes down to this: video games. Scientists have made highly realistic video game images that simulate the inner workings of human cells. Playing these 'games' helps medical researchers see exactly how cells live, divide and die. The research opens new paths for tumor-killing drugs to treat cancer and other diseases.

Computer sleuthing helps unravel RNA's role in cellular function

Wed, 15 Feb 2012 14:31:31 EST

Computer engineers may have just provided the medical community a new way of figuring out exactly how one of the three building blocks of life forms and functions. They have used a complex computer program to analyze RNA motifs – the subunits that make up RNA.

Chemist applies Google software to webs of the molecular world

Mon, 13 Feb 2012 18:58:58 EST

The technology that Google uses to analyze trillions of Web pages is being brought to bear on the way molecules are shaped and organized. Scientists have adapted Google's PageRank software to create moleculaRnetworks, which scientists can use to determine molecular shapes and chemical reactions without the expense, logistics and occasional danger of lab experiments.

Japan's 'K computer' ranks No. 1 in four benchmarks at HPC Challenge Awards

Wed, 16 Nov 2011 08:17:17 EST

RIKEN, the University of Tsukuba, and Fujitsu Limited have announced that they received top-ranking in all four benchmarks for the performance results of the "K computer" at the 2011 HPC Challenge Awards.

Clear vision despite a heavy head: Model explains the choice of simple movements

Wed, 09 Nov 2011 11:56:56 EST

The brain likes stereotypes -- at least for movements. Simple actions are most often performed in the same manner. A mathematical model explains why this is the case and could be used to generate more natural robot movements and to adapt prosthetic movements.

Galaxy DNA-analysis software is now available 'in the cloud'

Tue, 08 Nov 2011 20:15:15 EST

Galaxy -- an open-source, web-based platform for data-intensive biomedical and genetic research -- is now available as a "cloud computing" resource. The new technology will help scientists and biomedical researchers to harness such tools as DNA-sequencing and analysis software, as well as storage capacity for large quantities of scientific data.

New software models immune responses

Thu, 06 Oct 2011 13:29:29 EDT

New software lets researchers see how the immune system responds to pathogens that invade the bacteria-rich environment of the gut.

Computational modeling can help plan vaccine introduction, study finds

Thu, 29 Sep 2011 16:13:13 EDT

Proper planning before the introduction of new vaccines into a developing country's active immunization program could prevent storage problems and transportation bottlenecks that decrease the availability of existing vaccines by as much as two-thirds, according to a new study. Computational models can forecast the impact of new vaccine introduction and identify potential disruptions, concluded the study.

New targets for the control of HIV predicted using a novel computational analysis

Thu, 22 Sep 2011 18:00:00 EDT

Over 25 years of intensive research have failed to create a vaccine for preventing HIV. A new computational approach has predicted numerous human proteins that the human immunodeficiency virus requires to replicate itself -- "a powerful resource for experimentalists who desire to discover new targets."

Archivist in the sound library: New model for speech and sound recognition

Thu, 15 Sep 2011 11:36:36 EDT

A new mathematical model mimics the process of speech and noise recognition in the human brain efficiently. It may explain experimental findings that remained unclear so far.

Identifying correlations in electronic patient records

Thu, 25 Aug 2011 17:24:24 EDT

A new study demonstrates how text mining of electronic health records can be used to create medical term profiles of patients, which can be used both to identify co-occurrence of diseases and to cluster patients into groups with highly similar clinical features.

Computational method predicts new uses for existing medicines; Match-making program uses gene expression patterns

Wed, 17 Aug 2011 14:28:28 EDT

Scientists used computers and publicly available genomic information to predict new uses for existing medicines. The approach could save time and money compared to traditional drug discovery methods. Among the study's surprise findings: an anti-ulcer medicine that slowed the growth of lung cancer, and an anticonvulsant that might alleviate inflammatory bowel diseases.

Novel analysis method organizes genomic cancer data

Thu, 30 Jun 2011 13:18:18 EDT

The technology that allows scientists to profile the entire genome of individual tumors offers new hope for discovering ways to select the best treatment for each patient's particular type of cancer. However, these profiles produce huge amounts of data, and the volume alone creates unique analytical problems. In a new study, researchers describe a new analytical approach based on a concept called multiplicity, that can organize large amounts of varied genetic data.

Next-generation gene sequencing brings personal genomics closer, IDs mutation in new syndrome

Thu, 23 Jun 2011 13:01:01 EDT

Harnessing the new generation of rapid, highly accurate gene-sequencing techniques, a research team has identified the disease-causing mutation in a newly characterized rare genetic disease, by analyzing DNA from just a few individuals. The power and speed of the innovative bioinformatics tool marks a step toward personalized genomics -- discovering causative mutations in individual patients. The previously unknown lethal syndrome has affected infant boys in two unrelated families.