Now showing items 1-10 of 19
A compound graph layout algorithm for biological pathways
(Springer, Berlin, Heidelberg, 2004-09-10)
We present a new compound graph layout algorithm based on traditional force-directed layout scheme with extensions for nesting and other application-specific constraints. The algorithm has been successfully implemented ...
A constrained, force-directed layout algorithm for biological pathways
(Springer, Berlin, Heidelberg, 2004-09)
We present a new elegant algorithm for layout of biological signaling pathways. It uses a force-directed layout scheme, taking into account directional and regional constraints enforced by different molecular interaction ...
PATIKA: an integrated visual environment for collaborative construction and analysis of cellular pathways
(American Society for Biochemistry and Molecular Biology(ASBMB), 2002-09)
PATIKAweb: a Web service for querying, visualizing and analyzing a graph-based pathway database
(ISCB Org, 2005-06)
PATIKAweb provides a Web service for retrieving and analyzing biological pathways in PATIKA database, which currently contains data integrated from popular public pathway databases like Reactome. It features a user-friendly ...
Microarray data analysis and pathway activity inference in PATIKA
(ISCB Org, 2004)
Pathway activity inference attempts to infer differential activity of cellular networks, given a qualitative state - transition model of the network and an expression profile of RNA molecules. We present an efficient ...
Pathway activity inference using microarray data
(Bilkent Center for Bioinformatics (BCBI), 2004)
Motivation: Microarray technology provides cell-scale expression data; however, analyzing this data is notoriously difficult. It is becoming clear that system-oriented methods are needed in order to best interpret this ...
PATIKA: An informatics infrastructure for cellular networks
(ISCB Org, 2004)
The PATIKA Project aims for an informatics infrastructure to cope with the inherently complex cellular pathway data and provides software tools with sophisticated visualization technology around a central database using ...
ChiBE: interactive visualization and manipulation of BioPAX pathway models
(Oxford University Press, 2010-02-01)
SUMMARY: Representing models of cellular processes or pathways in a graphically rich form facilitates interpretation of biological observations and generation of new hypotheses. Solving biological problems using large ...
Algorithms for effective querying of compound graph-based pathway databases
(BioMed Central Ltd., 2009-11-16)
Background: Graph-based pathway ontologies and databases are widely used to represent data about cellular processes. This representation makes it possible to programmatically integrate cellular networks and to investigate ...
Discovering modulators of gene expression
(Oxford University Press, 2010-09-01)
Proteins that modulate the activity of transcription factors, often called modulators, play a critical role in creating tissue- and context-specific gene expression responses to the signals cells receive. GEM (Gene Expression ...