Navigation Links
Virginia Tech computer scientists develop new way to study molecular networks
Date:1/24/2013

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.


'/>"/>

Contact: Lynn Nystrom
tansy@vt.edu
540-231-4371
Virginia Tech
Source:Eurekalert  

Related biology news :

1. Virginia Tech announces 2012 football helmet ratings; 2 more added to the 5-star mark
2. Biology professor secures grant to save West Virginias primary natural history collection
3. Virginia Tech and University of Tuscia lead team to unravel origin of devastating kiwifruit bacterium
4. Scientific meeting at Virginia Tech will make more than $2 million economic impact
5. Old deeds, witness trees offer glimpse of pre-settlement forest in West Virginia
6. TESARO and Virginia G. Piper Cancer Center announce first patient in clinical trial of TSR-011
7. Computer simulations help explain why HIV cure remains elusive
8. Patel recognized with NSF Career Award for computer-modeling research on cell membranes
9. Computer scientists develop an interactive field guide app for birders
10. Computer model pinpoints prime materials for efficient carbon capture
11. 2 NASA visualizations selected for computers graphics showcase
Post Your Comments:
*Name:
*Comment:
*Email:
Related Image:
Virginia Tech computer scientists develop new way to study molecular networks
(Date:4/4/2017)... April 4, 2017   EyeLock LLC , a ... the United States Patent and Trademark Office (USPTO) has ... the linking of an iris image with a face ... represents the company,s 45 th issued patent. ... very timely given the multi-modal biometric capabilities that have ...
(Date:3/30/2017)... -- The research team of The Hong Kong Polytechnic ... by adopting ground breaking 3D fingerprint minutiae recovery and matching technology, ... accuracy for use in identification, crime investigation, immigration control, security of ... ... A research team led by Dr ...
(Date:3/28/2017)... 28, 2017 The report "Video ... Monitors, Servers, Storage Devices), Software (Video Analytics, VMS), and ... Global Forecast to 2022", published by MarketsandMarkets, the market ... is projected to reach USD 75.64 Billion by 2022, ... The base year considered for the study is 2016 ...
Breaking Biology News(10 mins):
(Date:10/11/2017)... ... October 11, 2017 , ... Disappearing forests and increased emissions are the ... million people each year. Especially those living in larger cities are affected by air ... one of the most pollution-affected countries globally - decided to take action. , “I ...
(Date:10/10/2017)... ... October 10, 2017 , ... ... pharmaceutical company advancing targeted antibody-drug conjugate (ADC) therapeutics, today confirmed licensing rights ... (Hybrid Polymerized Liposomal Nanoparticle), a technology developed in collaboration with Children’s Hospital ...
(Date:10/10/2017)... Oct. 10, 2017 SomaGenics announced the receipt ... to develop RealSeq®-SC (Single Cell), expected to be the ... RNAs (including microRNAs) from single cells using NGS methods. ... need to accelerate development of approaches to analyze the ... "New techniques for measuring levels of mRNAs in ...
(Date:10/9/2017)... Jupiter, FL (PRWEB) , ... October 09, 2017 , ... ... episode, scheduled to broadcast first quarter 2018. American Farmer airs Tuesdays at 8:30aET on ... Agriculture industry is faced with the challenge of how to continue to feed a ...
Breaking Biology Technology: