Using graph theory to analyze biological networks
Understanding complex systems often requires a bottom-up analysis towards a systems
biology approach. The need to investigate a system, not only as individual components but …
biology approach. The need to investigate a system, not only as individual components but …
Combining complex networks and data mining: why and how
The increasing power of computer technology does not dispense with the need to extract
meaningful information out of data sets of ever growing size, and indeed typically …
meaningful information out of data sets of ever growing size, and indeed typically …
Compact integration of multi-network topology for functional analysis of genes
The topological landscape of molecular or functional interaction networks provides a rich
source of information for inferring functional patterns of genes or proteins. However, a …
source of information for inferring functional patterns of genes or proteins. However, a …
KG4SL: knowledge graph neural network for synthetic lethality prediction in human cancers
Motivation Synthetic lethality (SL) is a promising gold mine for the discovery of anti-cancer
drug targets. Wet-lab screening of SL pairs is afflicted with high cost, batch-effect, and off …
drug targets. Wet-lab screening of SL pairs is afflicted with high cost, batch-effect, and off …
Computational methods, databases and tools for synthetic lethality prediction
J Wang, Q Zhang, J Han, Y Zhao, C Zhao… - Briefings in …, 2022 - academic.oup.com
Synthetic lethality (SL) occurs between two genes when the inactivation of either gene alone
has no effect on cell survival but the inactivation of both genes results in cell death. SL …
has no effect on cell survival but the inactivation of both genes results in cell death. SL …
Genetic interaction networks: better understand to better predict
B Boucher, S Jenna - Frontiers in genetics, 2013 - frontiersin.org
A genetic interaction (GI) between two genes generally indicates that the phenotype of a
double mutant differs from what is expected from each individual mutant. In the last decade …
double mutant differs from what is expected from each individual mutant. In the last decade …
A semi-supervised learning approach to predict synthetic genetic interactions by combining functional and topological properties of functional gene network
Background Genetic interaction profiles are highly informative and helpful for understanding
the functional linkages between genes, and therefore have been extensively exploited for …
the functional linkages between genes, and therefore have been extensively exploited for …
Inferring synthetic lethal interactions from mutual exclusivity of genetic events in cancer
Background Synthetic lethality (SL) refers to the genetic interaction between two or more
genes where only their co-alteration (eg by mutations, amplifications or deletions) results in …
genes where only their co-alteration (eg by mutations, amplifications or deletions) results in …
Predicting synthetic lethal interactions using heterogeneous data sources
Motivation A synthetic lethal (SL) interaction is a relationship between two functional entities
where the loss of either one of the entities is viable but the loss of both entities is lethal to the …
where the loss of either one of the entities is viable but the loss of both entities is lethal to the …
On protocols and measures for the validation of supervised methods for the inference of biological networks
Networks provide a natural representation of molecular biology knowledge, in particular to
model relationships between biological entities such as genes, proteins, drugs, or diseases …
model relationships between biological entities such as genes, proteins, drugs, or diseases …