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!
Modern genetic sequencing tools give clearer picture of how corals are related
17.08.2017 | University of Washington
The irresistible fragrance of dying vinegar flies
16.08.2017 | Max-Planck-Institut für chemische Ökologie
Whether you call it effervescent, fizzy, or sparkling, carbonated water is making a comeback as a beverage. Aside from quenching thirst, researchers at the University of Illinois at Urbana-Champaign have discovered a new use for these "bubbly" concoctions that will have major impact on the manufacturer of the world's thinnest, flattest, and one most useful materials -- graphene.
As graphene's popularity grows as an advanced "wonder" material, the speed and quality at which it can be manufactured will be paramount. With that in mind,...
Physicists at the University of Bonn have managed to create optical hollows and more complex patterns into which the light of a Bose-Einstein condensate flows. The creation of such highly low-loss structures for light is a prerequisite for complex light circuits, such as for quantum information processing for a new generation of computers. The researchers are now presenting their results in the journal Nature Photonics.
Light particles (photons) occur as tiny, indivisible portions. Many thousands of these light portions can be merged to form a single super-photon if they are...
For the first time, scientists have shown that circular RNA is linked to brain function. When a RNA molecule called Cdr1as was deleted from the genome of mice, the animals had problems filtering out unnecessary information – like patients suffering from neuropsychiatric disorders.
While hundreds of circular RNAs (circRNAs) are abundant in mammalian brains, one big question has remained unanswered: What are they actually good for? In the...
An experimental small satellite has successfully collected and delivered data on a key measurement for predicting changes in Earth's climate.
The Radiometer Assessment using Vertically Aligned Nanotubes (RAVAN) CubeSat was launched into low-Earth orbit on Nov. 11, 2016, in order to test new...
A study led by scientists of the Max Planck Institute for the Structure and Dynamics of Matter (MPSD) at the Center for Free-Electron Laser Science in Hamburg presents evidence of the coexistence of superconductivity and “charge-density-waves” in compounds of the poorly-studied family of bismuthates. This observation opens up new perspectives for a deeper understanding of the phenomenon of high-temperature superconductivity, a topic which is at the core of condensed matter research since more than 30 years. The paper by Nicoletti et al has been published in the PNAS.
Since the beginning of the 20th century, superconductivity had been observed in some metals at temperatures only a few degrees above the absolute zero (minus...
16.08.2017 | Event News
04.08.2017 | Event News
26.07.2017 | Event News
17.08.2017 | Physics and Astronomy
17.08.2017 | Earth Sciences
17.08.2017 | Physics and Astronomy