Research graph
References from Ten practical tips and tricks to improve the effectiveness of biological network alignment. Local targets link to admitted publications; unresolved targets remain external evidence.
NAViGaTOR: network analysis, visualization and graphing Toronto
10.1093/bioinformatics/btp595 · 2009 · External reference
Cytoscape: a software environment for integrated models of biomolecular interaction networks
10.1101/gr.1239303 · 2003 · External reference
Semantic similarity in a taxonomy: an information-based measure and its application to problems of ambiguity in natural language
10.1613/jair.514 · 1999 · External reference
Investigating semantic similarity measures across the Gene Ontology: the relationship between sequence and annotation
10.1093/bioinformatics/btg153 · 2003 · External reference
Basic local alignment search tool
10.1016/s0022-2836(05)80360-2 · 1990 · External reference
The post-genomic era of biological network alignment
10.1186/s13637-015-0022-9 · 2015 · External reference
Survey of local and global biological network alignment: the need to reconcile the two sides of the same coin
2018 · External reference
Global alignment of multiple protein interaction networks with application to functional orthology detection
10.1073/pnas.0806627105 · 2008 · External reference
HubAlign: an accurate and efficient method for global alignment of protein-protein interaction networks
10.1093/bioinformatics/btu450 · 2014 · External reference
Gene and protein nomenclature in public databases
10.1186/1471-2105-7-372 · 2006 · External reference
The HUGO Gene Nomenclature Committee (HGNC)
10.1007/s00439-001-0615-0 · 2001 · External reference
OrthoDB v10: sampling the diversity of animal, plant, fungal, protist, bacterial and viral genomes for evolutionary and functional annotations of orthologs
10.1093/nar/gky1053 · 2019 · External reference
InParanoid 8: orthology analysis between 273 proteomes, mostly eukaryotic
2015 · External reference
Global network alignment using multiscale spectral signatures
10.1093/bioinformatics/bts592 · 2012 · External reference
MAGNA++: maximizing accuracy in global network alignment via both node and edge conservation
10.1093/bioinformatics/btv161 · 2015 · External reference
SANA: simulated annealing far outperforms many other search algorithms for biological network alignment
10.1093/bioinformatics/btx090 · 2017 · External reference
On the current failure—but bright future—of biological network alignment
2017 · External reference
Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles
10.1073/pnas.0506580102 · 2005 · External reference
PathDIP 5: improving coverage and making enrichment analysis more biologically meaningful
10.1093/nar/gkad1027 · 2024 · External reference
BioPAX-Parser: parsing and enrichment analysis of BioPAX pathways
10.1093/bioinformatics/btaa529 · 2020 · External reference
Global alignment of multiple protein interaction networks with application to functional orthology detection
10.1073/pnas.0806627105 · 2008 · External reference
A method based on temporal embedding for the pairwise alignment of dynamic networks
2023 · External reference
PyMulSim
External reference
Multilayer network alignment based on topological assessment via embeddings
10.1186/s12859-023-05508-5 · 2023 · External reference
Global network alignment
2010 · External reference
SUMONA: a supervised method for optimizing network alignment
10.1016/j.compbiolchem.2016.03.003 · 2016 · External reference
SPINAL: scalable protein interaction network alignment
10.1093/bioinformatics/btt071 · 2013 · External reference
10.1109/bibmw.2012.6470300
10.1109/bibmw.2012.6470300 · External reference
HubAlign: an accurate and efficient method for global alignment of protein-protein interaction networks
10.1093/bioinformatics/btu450 · 2014 · External reference
NETAL: a new graph-based method for global alignment of protein–protein interaction networks
10.1093/bioinformatics/btt202 · 2013 · External reference
MAGNA: maximizing accuracy in global network alignment via both node and edge conservation
10.1093/bioinformatics/btv161 · 2015 · External reference
IsoRankN: spectral methods for global alignment of multiple protein networks
2009 · External reference
Topological network alignment uncovers biological function and phylogeny
10.1098/rsif.2010.0063 · 2010 · External reference
Survey of local and global biological network alignment: the need to reconcile the two sides of the same coin
2018 · External reference
The post-genomic era of biological network alignment
2015 · External reference
10.1007/978-1-4614-0320-3_5
10.1007/978-1-4614-0320-3_5 · External reference
10.1109/sc.2014.68
10.1109/sc.2014.68 · External reference
A method based on temporal embedding for the pairwise alignment of dynamic networks
10.3390/e25040665 · 2023 · External reference
