Software

RINalyzer

RINalyzer is a Java app/plugin for Cytoscape, a free open-source software platform for visualization and analysis of biomolecular networks. This plugin allows the simultaneous visualization and interactive analysis of residue interaction networks (RINs) together with the corresponding 3D protein structures displayed in UCSF Chimera. It also provides a comprehensive set of topological centrality measures to gain additional insights into the structural and functional role of interacting residues.
Reference: Doncheva, N.T., Klein, K., Domingues, F.S., Albrecht, M. (2011) Analyzing and visualizing residue networks of protein structures. Trends in Biochemical Sciences, 36(4):179-182. (Abstract)

NetworkAnalyzer

NetworkAnalyzer is a Java app/plugin for Cytoscape, a free open-source software platform for visualization and analysis of biomolecular networks. This plugin computes parameters describing the network topology and displays their distributions in diagrams.
Reference: Assenov, Y., Ramírez, F., Schelhorn, S.E., Lengauer, T., Albrecht, M. (2008) Computing topological parameters of biological networks. Bioinformatics, 24(2):282-284. (Abstract)

NetworkPrioritzer

NetworkPrioritzer is a Java plugin for Cytoscape, a free open-source software platform for visualization and analysis of biomolecular networks. This plugin ranks nodes according to centrality measures that quantify the node relevance for the connectivity between a set of seed nodes and the rest of the network. Furthermore, it provides tools to compare and aggregate different rankings. In particular, NetworkPrioritzer is suited for the integrative prioritization of candidate disease genes or other molecules.
Reference: Kacprowski, T., Doncheva, N.T., Albrecht, M. (2013) NetworkPrioritizer: a versatile tool for network-based prioritization of candidate disease genes or other molecules. Bioinformatics, 29(11):1471-1473. (Abstract)

DomainGraph

DomainGraph is the successor tool of DomainNetworkBuilder and works as Java plugin for Cytoscape, a free open-source software platform for visualization and analysis of biomolecular networks. This plugin decomposes protein interaction networks into domain-domain interactions and generates a new network of interacting domains. It also allows the integration of exon expression data measured using Affymetrix GeneChip microarrays or next-generation sequencing. This supports the visual analysis of alternative splicing events and the functional characterization of their effects on gene and protein interaction networks.
Reference: Emig, D., Salomonis, N., Baumbach, J., Lengauer, T., Conklin, B.R., Albrecht, M. (2010) AltAnalyze and DomainGraph: analyzing and visualizing exon expression data. Nucleic Acids Research, 38(Web Server issue):W755-W762. (Abstract)

ModuleGraph

ModuleGraph facilitates the identification, visualization, and investigation of functional modules and their interplay in molecular interaction networks. For instance, protein complexes form modules in protein networks. The modules are represented as extra nodes within the network. Additional edges in the network indicate the composition of modules and their overlap.
Reference: Foerster, S., Kacprowski, T., Dhople, V.M., Hammer, E., Herzog, S., Saafan, H., Bien-Mller, S., Albrecht, M., Vlker, U., Ritter, C.A. (2013) Characterization of the EGFR interactome reveals associated protein complex networks and intracellular receptor dynamics. Proteomics, 13(21):3131-3144, 2013. (Abstract)

BiLayout

BiLayout is a Java plugin for Cytoscape, a free open-source software platform for visualization and analysis of biomolecular networks. This plugin computes a bipartite network layout for two user-selected groups of nodes.

NeighborHighlight

NeighborHighlight is a simple Java plugin for Cytoscape that automatically highlights the neighbors and edges of a node when the user hovers the mouse over it.

Web Services


PSISCORE

PSISCORE complements the PSICQUIC protocol to exchange molecular interaction data with confidence scores. PSISCORE succeeds DASMI as distributed scoring approach based on a decentralized client-server architecture. Multiple scoring servers can be used to assess the quality of individual interactions.
Reference: Aranda, B., Blankenburg, H., ..., Albrecht, M., Hermjakob, H. (2011) PSICQUIC and PSISCORE: accessing and scoring molecular interactions. Nature Methods, 8(7):528-529. (Abstract)

DASMI &
DASMIweb

DASMI uses the DAS protocol to share experimental and predicted molecular interaction data. Our current DASMIweb client is focused on interactions of human proteins and Pfam domains. It also supports scoring the retrieved interactions with confidence values using different quality measures.
Reference: Blankenburg, H., Finn, R.D., Prlić, A., Jenkinson, A.M., Ramírez, F., Emig, D., Schelhorn, S.E., Büch, J., Lengauer, T., Albrecht, M. (2009) DASMI: exchanging, annotating and assessing molecular interaction data. Bioinformatics, 25(10):1321-1328. (Abstract)

FunSimMat

FunSimMat is a comprehensive functional similarity database as well as a web service for ranking genes and proteins by function. To this end, it provides different semantic similarity measures for Gene Ontology terms and offers precomputed functional similarity values for proteins contained in UniProtKB and for protein families and domains in Pfam and SMART. The web interface supports prioritizing disease gene candidates obtained by, e.g., GWAS and RNAi studies, and allows users to efficiently perform both semantic similarity searches with GO terms and functional similarity searches with proteins or protein families.
Reference: Schlicker, A., Albrecht, M. (2010) FunSimMat update: new features for exploring functional similarity. Nucleic Acids Research, 38(Database issue):D244-248. (Abstract)

GOTaxExplorer &
FSST

GOTax is a comparative genomics platform that integrates protein annotation with protein family classification and taxonomy. User-defined sets of proteins, protein families, annotation terms or taxonomic groups can be selected and compared in GOTaxExplorer, allowing for the analysis of distribution of biological processes and molecular activities over different taxonomic groups. Additionally, a functional similarity measure implemented in FSST is available for establishing functional relationships between proteins and protein families. FSST is also used by the functional similarity search in Pfam.
Reference: Schlicker, A., Rahnenführer, J., Albrecht, M., Lengauer, T., Domingues, F.S. (2007) GOTax: investigating biological processes and biochemical activities along the taxonomic tree. Genome Biology, 8(3):R33.1-10. (Abstract)

BioMyn

BioMyn is a comprehensive online resource that integrates information related to human genes and proteins from over a dozen external databases. It includes Gene Ontology annotations of human genes and proteins, sequence family classifications, protein domain architectures, metabolic and signaling pathways, protein interactions and protein complexes, and disease associations.
Reference: Ramírez, F., Lawyer, G., Albrecht, M. (2012) Novel search method for the discovery of functional relationships. Bioinformatics, 28(2):269-76, 2012. (Abstract)