Physical Sciences and Mathematics Commons^™

A New Essential Protein Discovery Method Based On The Integration Of Protein-Protein Interaction And Gene Expression Data, Min Li, Hanhui Zhang, Jian-Xin Wang, Yi Pan

Computer Science Faculty Publications

The article offers information on a study conducted on the essential protein discovery method, PeC, which is based on the integration of protein-protein interaction and gene expression data. It states that PeC was developed on the basis of the definitions of edge clustering coefficient (ECC) and Pearson's correlation coefficient (PCC). It mentions that a list of essential proteins of Saccharomyces cerevisiae were collected.

Background: Identification of essential proteins is always a challenging task since it requires experimental approaches that are time-consuming and laborious. With the advances in high throughput technologies, a large number of protein-protein interactions are available, which have …

Towards The Identification Of Protein Complexes And Functional Modules By Integrating Ppi Network And Gene Expression Data, Min Li, Xuehong Wu, Jianxin Wang, Yi Pan

Computer Science Faculty Publications

Background: Identification of protein complexes and functional modules from protein-protein interaction (PPI) networks is crucial to understanding the principles of cellular organization and predicting protein functions. In the past few years, many computational methods have been proposed. However, most of them considered the PPI networks as static graphs and overlooked the dynamics inherent within these networks. Moreover, few of them can distinguish between protein complexes and functional modules.

Results: In this paper, a new framework is proposed to distinguish between protein complexes and functional modules by integrating gene expression data into protein-protein interaction (PPI) data. A series of time-sequenced subnetworks …

Trip: A Method For Novel Transcript Reconstruction From Paired-End Rna-Seq Reads, Serghei Mangul, Adrian Caciula, Dumitru Brinza, Ion I. Măndoiu, Alexander Zelikovskiy

Computer Science Faculty Publications

Preliminary experimental results on synthetic datasets generated with various sequencing parameters and distribution assumptions show that TRIP has increased transcriptome reconstruction accuracy compared to previous methods that ignore fragment length distribution information.

Guest Editors' Introduction, Jianer Chen, Ion Măndoiu, Raj Sunderraman, Jianxin Wang, Alexander Zelikovskiy

Computer Science Faculty Publications

This Supplement includes a selection of papers presented at the 7th International Symposium on Bioinformatics Research and Application (ISBRA), which was held on May 27-29, 2011 at Central South University in Changsha, China. The technical program of the symposium included 36 extended abstracts presented orally and published in volume 6674 of Springer Verlag’s Lecture Notes in Bioinformatics series. Additionally, the program included 38 short abstracts presented either orally or as posters. Authors of both extended and short abstracts presented at the symposium were invited to submit full versions of their work to this Supplement. Following a rigorous review process, 19 …