Discovering functional interaction patterns in protein-protein interaction networks

Download

index.pdf

Date

2008-06-11

Author

Turanalp, Mehmet E.
Can, Tolga

Metadata

Show full item record

This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License.

Item Usage Stats

230
views

49
downloads

Background: In recent years, a considerable amount of research effort has been directed to the analysis of biological networks with the availability of genome-scale networks of genes and/or proteins of an increasing number of organisms. A protein-protein interaction (PPI) network is a particular biological network which represents physical interactions between pairs of proteins of an organism. Major research on PPI networks has focused on understanding the topological organization of PPI networks, evolution of PPI networks and identification of conserved subnetworks across different species, discovery of modules of interaction, use of PPI networks for functional annotation of uncharacterized proteins, and improvement of the accuracy of currently available networks.

Subject Keywords

Biochemistry, Applied Mathematics, Molecular Biology, Structural Biology, Computer Science Applications

URI

https://hdl.handle.net/11511/47646

Journal

BMC BIOINFORMATICS

DOI

https://doi.org/10.1186/1471-2105-9-276

Collections

Department of Computer Engineering, Article

Suggestions

OpenMETU
Core

MicroarrayDesigner: an online search tool and repository for near-optimal microarray experimental designs Sacan, Ahmet; Ferhatosmanoglu, Nilgun; Ferhatosmanoglu, Hakan (Springer Science and Business Media LLC, 2009-9-22) Background: Dual-channel microarray experiments are commonly employed for inference of differential gene expressions across varying organisms and experimental conditions. The design of dual-channel microarray experiments that can help minimize the errors in the resulting inferences has recently received increasing attention. However, a general and scalable search tool and a corresponding database of optimal designs were still missing. Description: An efficient and scalable search method for finding nea...
Development and application of a modified dynamic time warping algorithm (DTW-S) to analyses of primate brain expression time series Yuan, Yuan; Chen, Yi-Ping Phoebe; Ni, Shengyu; Xu, Augix Guohua; Tang, Lin; Vingron, Martin; Somel, Mehmet; Khaitovich, Philipp (Springer Science and Business Media LLC, 2011-08-18) Background: Comparing biological time series data across different conditions, or different specimens, is a common but still challenging task. Algorithms aligning two time series represent a valuable tool for such comparisons. While many powerful computation tools for time series alignment have been developed, they do not provide significance estimates for time shift measurements.
JOA: Joint Overlap Analysis of multiple genomic interval sets Otlu, Burcak; Can, Tolga (Springer Science and Business Media LLC, 2019-03-08) BackgroundNext-generation sequencing (NGS) technologies have produced large volumes of genomic data. One common operation on heterogeneous genomic data is genomic interval intersection. Most of the existing tools impose restrictions such as not allowing nested intervals or requiring intervals to be sorted when finding overlaps in two or more interval sets.ResultsWe proposed segment tree (ST) and indexed segment tree forest (ISTF) based solutions for intersection of multiple genomic interval sets in parallel...
Isolation of High-Quality RNA from Pichia pastoris Öztürk, Sibel; Demir, İrem; Çalık, Pınar (Wiley, 2019-12-01) Analysis of RNA structuromes provides new insights into cellular processes, enabling systems biology and biotechnology researchers to calculate promoter and terminator strengths and to directly observe how differing circuit states impact host gene expression and the burdens imposed by the circuits. Such analysis, however, is crucially dependent on the availability of highly pure, intact RNA isolated from fresh or frozen cell cultures. RNA extraction from the yeast Pichia pastoris requires specific pretreatm...
ImaGene: a convolutional neural network to quantify natural selection from genomic data Torada, Luis; Lorenzon, Lucrezia; Beddis, Alice; Isildak, Ulas; Pattini, Linda; Mathieson, Sara; Fumagalli, Matteo (Springer Science and Business Media LLC, 2019-11-22) Background: The genetic bases of many complex phenotypes are still largely unknown, mostly due to the polygenic nature of the traits and the small effect of each associated mutation. An alternative approach to classic association studies to determining such genetic bases is an evolutionary framework. As sites targeted by natural selection are likely to harbor important functionalities for the carrier, the identification of selection signatures in the genome has the potential to unveil the genetic mechanisms...

Citation Formats

M. E. Turanalp and T. Can, “Discovering functional interaction patterns in protein-protein interaction networks,” BMC BIOINFORMATICS, pp. 0–0, 2008, Accessed: 00, 2020. [Online]. Available: https://hdl.handle.net/11511/47646.