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Chapter
Motif Finding Algorithms: A Performance Comparison
Network motifs are subgraphs of a network that occur more frequently than expected, according to some reasonable null model. They represent building blocks of complex systems such as genetic interaction networ...
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Article
Open AccessTemporalRI: subgraph isomorphism in temporal networks with multiple contacts
Temporal networks are graphs where each edge is associated with a timestamp denoting when two nodes interact. Temporal Subgraph Isomorphism (TSI) aims at retrieving all the subgraphs of a temporal network (cal...
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Chapter and Conference Paper
TemporalRI: A Subgraph Isomorphism Algorithm for Temporal Networks
Temporal networks are graphs where each edge is associated with a timestamp or an interval indicating when an interaction between two nodes happens. The Temporal Subgraph Isomorphism (TSI) problem aims at iden...
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Article
Open AccessEstablish the expected number of induced motifs on unlabeled graphs through analytical models
Complex networks are usually characterized by the presence of small and recurrent patterns of interactions between nodes, called network motifs. These small modules can help to elucidate the structure and the ...
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Chapter and Conference Paper
Establish the Expected Number of Injective Motifs on Unlabeled Graphs Through Analytical Models
Network motifs have a central role in explaining the functionality of complex systems. Establishing motif significance requires the computation of the expected number of their occurrences according to a random...
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Article
Fast Subgraph Matching Strategies Based on Pattern-Only Heuristics
Many scientific applications entail solving the subgraph isomorphism problem, i.e., given an input pattern graph, find all the subgraphs of a (usually much larger) target graph that are structurally equivalent...
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Chapter and Conference Paper
Simple Pattern-only Heuristics Lead to Fast Subgraph Matching Strategies on Very Large Networks
A wide range of biomedical applications entails solving the subgraph isomorphism problem, i.e. finding all the possible subgraphs of a target graph that are structurally equivalent to an input pattern graph. T...
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Protocol
Computational Methods to Investigate the Impact of miRNAs on Pathways
Pathway analysis is a wide class of methods allowing to determine the alteration of functional processes in complex diseases. However, biological pathways are still partial, and knowledge coming from posttrans...
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Article
Open AccessINBIA: a boosting methodology for proteomic network inference
The analysis of tissue-specific protein interaction networks and their functional enrichment in pathological and normal tissues provides insights on the etiology of diseases. The Pan-cancer proteomic project, ...
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Article
Fast analytical methods for finding significant labeled graph motifs
Network motif discovery is the problem of finding subgraphs of a network that occur more frequently than expected, according to some reasonable null hypothesis. Such subgraphs may indicate small scale interact...
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Chapter
gLabTrie: A Data Structure for Motif Discovery with Constraints
Motif discovery is the problem of finding subgraphs of a network that appear surprisingly often. Each such subgraph may indicate a small-scale interaction feature in applications ranging from a genomic interac...
