11 years 6 months ago
Reconstructing Boolean Models of Signaling
Abstract. Since the first emergence of protein-protein interaction networks, more than a decade ago, they have been viewed as static scaffolds of the signaling-regulatory events ...
Roded Sharan, Richard M. Karp
211views Computer Vision» more  NAR 2011»
12 years 7 months ago
DIMA 3.0: Domain Interaction Map
Domain Interaction MAp (DIMA, available at http:// is a database of predicted and known interactions between protein domains. It integrates 5807 struct...
Qibin Luo, Philipp Pagel, Baiba Vilne, Dmitrij Fri...
212views Computer Vision» more  NAR 2011»
12 years 7 months ago
Phospho.ELM: a database of phosphorylation sites - update 2011
The Phospho.ELM resource ( .org) is a relational database designed to store in vivo and in vitro phosphorylation data extracted from the scientific literature...
Holger Dinkel, Claudia Chica, Allegra Via, Cathryn...
235views Computer Vision» more  NAR 2011»
12 years 7 months ago
P2CS: a database of prokaryotic two-component systems
P2CS ( is a specialized database for prokaryotic two-component systems (TCSs), virtually ubiquitous signalling proteins which regulate a wide range of physiolo...
Mohamed Barakat, Philippe Ortet, David E. Whitwort...
213views Bioinformatics» more  BCB 2010»
12 years 11 months ago
Markov clustering of protein interaction networks with improved balance and scalability
Markov Clustering (MCL) is a popular algorithm for clustering networks in bioinformatics such as protein-protein interaction networks and protein similarity networks. An important...
Venu Satuluri, Srinivasan Parthasarathy, Duygu Uca...
134views more  IJBRA 2010»
13 years 2 months ago
Deterministic graph-theoretic algorithm for detecting modules in biological interaction networks
—Accumulating evidence suggests that biological systems exhibit modular organization. Accurate identification of modularity is vital for understanding this organization. A recen...
Roger L. Chang, Feng Luo, Stuart Johnson, Richard ...
146views more  EXPERT 2002»
13 years 4 months ago
The Frame-Based Module of the SUISEKI Information Extraction System
names in the same abstract already indicates a relation between them. Because of its simplicity, we can apply this approach to large amounts of text and establish interaction netwo...
Christian Blaschke, Alfonso Valencia
133views Education» more  CORR 2004»
13 years 4 months ago
Information theory, multivariate dependence, and genetic network inference
We define the concept of dependence among multiple variables using maximum entropy techniques and introduce a graphical notation to denote the dependencies. Direct inference of in...
Ilya Nemenman
149views more  BIB 2005»
13 years 4 months ago
Biomolecular Interaction Network Database
The Biomolecular Interaction Network Database (BIND) ( archives biomolecular interaction, reaction, complex and pathway information. Our aim is to curate the detail...
Don Gilbert
119views more  BMCBI 2006»
13 years 4 months ago
A methodology for the structural and functional analysis of signaling and regulatory networks
Background: Structural analysis of cellular interaction networks contributes to a deeper understanding of network-wide interdependencies, causal relationships, and basic functiona...
Steffen Klamt, Julio Saez-Rodriguez, Jonathan A. L...