Show/Hide Menu
Hide/Show Apps
Logout
Türkçe
Türkçe
Search
Search
Login
Login
OpenMETU
OpenMETU
About
About
Open Science Policy
Open Science Policy
Open Access Guideline
Open Access Guideline
Postgraduate Thesis Guideline
Postgraduate Thesis Guideline
Communities & Collections
Communities & Collections
Help
Help
Frequently Asked Questions
Frequently Asked Questions
Guides
Guides
Thesis submission
Thesis submission
MS without thesis term project submission
MS without thesis term project submission
Publication submission with DOI
Publication submission with DOI
Publication submission
Publication submission
Supporting Information
Supporting Information
General Information
General Information
Copyright, Embargo and License
Copyright, Embargo and License
Contact us
Contact us
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
217
views
45
downloads
Cite This
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
IEEE
ACM
APA
CHICAGO
MLA
BibTeX
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.