A multilevel layout algorithm for visualizing physical and genetic interaction networks, with emphasis on their modular organization
Johannes Tuikkala,Heidi Vähämaa,Pekka Salmela,Olli S. Nevalainen,Tero Aittokallio,Tero Aittokallio +5 more
TL;DR: A modified layout plug-in is implemented, named Multilevel Layout, which applies the conventional layout algorithms within a multilevel optimization framework to better capture the hierarchical modularity of many biological networks.
read more
Abstract: Background
Graph drawing is an integral part of many systems biology studies, enabling visual exploration and mining of large-scale biological networks. While a number of layout algorithms are available in popular network analysis platforms, such as Cytoscape, it remains poorly understood how well their solutions reflect the underlying biological processes that give rise to the network connectivity structure. Moreover, visualizations obtained using conventional layout algorithms, such as those based on the force-directed drawing approach, may become uninformative when applied to larger networks with dense or clustered connectivity structure.
read more
Chat with Paper
AI Agents for this Paper
Find similar papers on Google Scholar, PubMed and Arxiv
Write a critical review of this paper
Analyze citations of this paper to find unaddressed research gaps
Citations
Structure and dynamics of molecular networks: A novel paradigm of drug discovery: A comprehensive review
Peter Csermely,Tamas Korcsmaros,Tamas Korcsmaros,Huba Kiss,Gábor London,Ruth Nussinov,Ruth Nussinov +6 more
TL;DR: It is shown how network techniques can help in the identification of single-target, edgetic, multi-target and allo-network drug target candidates and an optimized protocol of network-aided drug development is suggested, and a list of systems-level hallmarks of drug quality is provided.
916
Comprehensive metabolome analyses reveal N -acetylcysteine-responsive accumulation of kynurenine in systemic lupus erythematosus: implications for activation of the mechanistic target of rapamycin
Andras Perl,Robert Hanczko,Zhi-Wei Lai,Zachary Oaks,Ryan Kelly,Rebecca Borsuk,John M. Asara,Paul E. Phillips +7 more
TL;DR: The PPP-connected and NAC-responsive accumulation of kynurenine and its stimulation of mTOR are identified as novel metabolic checkpoints in lupus pathogenesis.
Genetic variants and their interactions in disease risk prediction – machine learning and network perspectives
Sebastian Okser,Sebastian Okser,Tapio Pahikkala,Tapio Pahikkala,Tero Aittokallio,Tero Aittokallio +5 more
TL;DR: The basic concepts and algorithms behind machine learning-based genetic feature selection approaches are described, their potential benefits and limitations in genome-wide setting, and how physical or genetic interaction networks could be used as a priori information for providing improved predictive power and mechanistic insights into the disease networks are described.
Force-directed algorithms for schematic drawings and placement: A survey:
Se-Hang Cheong,Yain-Whar Si +1 more
TL;DR: This survey provides a comprehensive summary of developments and a full roadmap for state-of-the-art force-directed algorithms in schematic drawings and placement.
A multilevel layout algorithm for visualizing physical and genetic interaction networks, with emphasis on their modular organization
Johannes Tuikkala,Heidi Vähämaa,Pekka Salmela,Olli S. Nevalainen,Tero Aittokallio,Tero Aittokallio +5 more
TL;DR: A modified layout plug-in is implemented, named Multilevel Layout, which applies the conventional layout algorithms within a multilevel optimization framework to better capture the hierarchical modularity of many biological networks.
References
Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction Networks
Paul Shannon,Andrew Markiel,Owen Ozier,Nitin S. Baliga,Jonathan T. Wang,Daniel Ramage,Nada Amin,Benno Schwikowski,Trey Ideker +8 more
TL;DR: Several case studies of Cytoscape plug-ins are surveyed, including a search for interaction pathways correlating with changes in gene expression, a study of protein complexes involved in cellular recovery to DNA damage, inference of a combined physical/functional interaction network for Halobacterium, and an interface to detailed stochastic/kinetic gene regulatory models.
Prokka: Rapid Prokaryotic Genome Annotation
TL;DR: Prokka is introduced, a command line software tool to fully annotate a draft bacterial genome in about 10 min on a typical desktop computer, and produces standards-compliant output files for further analysis or viewing in genome browsers.
Network biology: understanding the cell's functional organization
TL;DR: This work states that rapid advances in network biology indicate that cellular networks are governed by universal laws and offer a new conceptual framework that could potentially revolutionize the view of biology and disease pathologies in the twenty-first century.
ClueGO: a Cytoscape plug-in to decipher functionally grouped gene ontology and pathway annotation networks
Gabriela-Luana Bindea,Bernhard Mlecnik,Hubert Hackl,Pornpimol Charoentong,Marie Tosolini,Amos Kirilovsky,Wolf H. Fridman,Franck Pagès,Zlatko Trajanoski,Jérôme Galon +9 more
TL;DR: ClueGO is an easy to use Cytoscape plug-in that strongly improves biological interpretation of large lists of genes and creates a functionally organized GO/pathway term network.
An automated method for finding molecular complexes in large protein interaction networks.
TL;DR: A novel graph theoretic clustering algorithm, "Molecular Complex Detection" (MCODE), that detects densely connected regions in large protein-protein interaction networks that may represent molecular complexes is described.