Forum for Science, Industry and Business

Sponsored by:     3M 
Search our Site:

 

Virginia Tech computer scientists develop new way to study molecular networks

25.01.2013
In biology, molecules can have multi-way interactions within cells, and until recently, computational analysis of these links has been "incomplete," according to T. M. Murali, associate professor of computer science in the College of Engineering at Virginia Tech.

His group authored an article on their new approach to address these shortcomings, titled "Reverse Engineering Molecular Hypergraphs," that received the Best Paper Award at the recent 2012 ACM Conference on Bioinformatics, Computational Biology and Biomedicine.

Intricate networks of connections among molecules control the processes that occur within cells. The "analysis of these interaction networks has relied almost entirely on graphs for modeling the information. Since a link in a graph connects at most two molecules (e.g., genes or proteins), such edges cannot accurately represent interactions among multiple molecules. These interactions occur very often within cells," the computer scientists wrote in their paper.

To overcome the limitations in the use of the graphs, Murali and his students used hypergraphs, a generalization of a graph in which an hyperedge can connect multiple molecules.

"We used hypergraphs to capture the uncertainty that is inherent in reverse engineering gene to gene networks from systems biology datasets," explained Ahsanur Rahman, the lead author on the paper. "We believe hypergraphs are powerful representations for capturing the uncertainty in a network's structure."

They developed reliable algorithms that can discover hyperedges supported by sets of networks. In ongoing research, the scientists seek to use hyperedges to suggest new experiments. By capturing uncertainty in network structure, hyperedges can directly suggest groups of genes for which further experiments may be required in order to precisely discover interaction patterns. Incorporating the data from these experiments might help to refine hyperedges and resolve the interactions among molecules, resulting in fruitful interplay and feedback between computation and experiment.

Murali, and his students Ahsanur Rahman and Christopher L. Poirel, both doctoral candidates, and David L. Badger, a software engineer in Murali's group, all of Blacksburg, Va., and all in the computer science department, used funding from the National Institutes of Health and the National Science Foundation to better understand this uncertainty in these various forms of interactions.

Murali is also the co-director of the Institute for Critical Technology and Applied Science's Center for Systems Biology of Engineered Tissues and the associate program director for the computational tissue engineering interdisciplinary graduate education program at Virginia Tech.

Lynn Nystrom | EurekAlert!
Further information:
http://www.vt.edu

More articles from Life Sciences:

nachricht Show me your leaves - Health check for urban trees
12.12.2017 | Gesellschaft für Ökologie e.V.

nachricht Liver Cancer: Lipid Synthesis Promotes Tumor Formation
12.12.2017 | Universität Basel

All articles from Life Sciences >>>

The most recent press releases about innovation >>>

Die letzten 5 Focus-News des innovations-reports im Überblick:

Im Focus: Long-lived storage of a photonic qubit for worldwide teleportation

MPQ scientists achieve long storage times for photonic quantum bits which break the lower bound for direct teleportation in a global quantum network.

Concerning the development of quantum memories for the realization of global quantum networks, scientists of the Quantum Dynamics Division led by Professor...

Im Focus: Electromagnetic water cloak eliminates drag and wake

Detailed calculations show water cloaks are feasible with today's technology

Researchers have developed a water cloaking concept based on electromagnetic forces that could eliminate an object's wake, greatly reducing its drag while...

Im Focus: Scientists channel graphene to understand filtration and ion transport into cells

Tiny pores at a cell's entryway act as miniature bouncers, letting in some electrically charged atoms--ions--but blocking others. Operating as exquisitely sensitive filters, these "ion channels" play a critical role in biological functions such as muscle contraction and the firing of brain cells.

To rapidly transport the right ions through the cell membrane, the tiny channels rely on a complex interplay between the ions and surrounding molecules,...

Im Focus: Towards data storage at the single molecule level

The miniaturization of the current technology of storage media is hindered by fundamental limits of quantum mechanics. A new approach consists in using so-called spin-crossover molecules as the smallest possible storage unit. Similar to normal hard drives, these special molecules can save information via their magnetic state. A research team from Kiel University has now managed to successfully place a new class of spin-crossover molecules onto a surface and to improve the molecule’s storage capacity. The storage density of conventional hard drives could therefore theoretically be increased by more than one hundred fold. The study has been published in the scientific journal Nano Letters.

Over the past few years, the building blocks of storage media have gotten ever smaller. But further miniaturization of the current technology is hindered by...

Im Focus: Successful Mechanical Testing of Nanowires

With innovative experiments, researchers at the Helmholtz-Zentrums Geesthacht and the Technical University Hamburg unravel why tiny metallic structures are extremely strong

Light-weight and simultaneously strong – porous metallic nanomaterials promise interesting applications as, for instance, for future aeroplanes with enhanced...

All Focus news of the innovation-report >>>

Anzeige

Anzeige

Event News

See, understand and experience the work of the future

11.12.2017 | Event News

Innovative strategies to tackle parasitic worms

08.12.2017 | Event News

AKL’18: The opportunities and challenges of digitalization in the laser industry

07.12.2017 | Event News

 
Latest News

Long-lived storage of a photonic qubit for worldwide teleportation

12.12.2017 | Physics and Astronomy

Multi-year submarine-canyon study challenges textbook theories about turbidity currents

12.12.2017 | Earth Sciences

Electromagnetic water cloak eliminates drag and wake

12.12.2017 | Power and Electrical Engineering

VideoLinks
B2B-VideoLinks
More VideoLinks >>>