Tool stats & trends
Looking to identify usage trends or leading experts?
|Interface||Web user interface|
|Restrictions to use||None|
Plants and Fungi
- Saccharomyces cerevisiae
- Homo sapiens
- person_outline Esti Yeger-Lotem
Publications for ResponseNet
Synucleins and Gene Expression: Ramblers in a Crowd or Cops Regulating Traffic?
[…] from yeast cells expressing various levels of α-synuclein. Usually genetic screens identify response regulators, whereas transcriptomic profiling assays reveal components of metabolic processes. The ResponseNet computational method combines data from the genetic screens and gene expression analyses with the comprehensive knowledge on protein (and gene) interaction information in public yeast data […]
Solving the influence maximization problem reveals regulatory organization of the yeast cell cycle
[…] problems where some quantity flows from source nodes, across the edges of a graph, draining in sink nodes. Various forms of network flow methodologies have found success in algorithms such as Hotnet, ResponseNet, resistor networks, and others [,,]. Diffusion, like the propagation of infection, does not follow algorithmically defined paths on graphs, such as shortest paths, but instead flows on all […]
Utilizing somatic mutation data from numerous studies for cancer research: proof of concept and applications
[…] ed subnetworks that harbor many mutated genes., Hofree et al. stratified patients by quantifying the impact of their mutations on how information propagates in a protein–protein interaction network. ResponseNet and xseq modeled the impact of mutations on the gene expression profiles., Liu et al. developed an ensemble method for detecting driver genes by integrating predictions from several appro […]
Network Based Protein Biomarker Discovery Platforms
[…] fy network modules or clusters each of which includes a set of the nodes densely connected in the network (). For network clustering or modularization, a number of methods, such as jActiveModules , ResponseNet , NetWalker , and clusterMaker , have been developed (). These methods can be categorized into two groups. One group, such as clusterMaker, searches for the node clusters based on th […]
Pathways on demand: automated reconstruction of human signaling networks
[…] We compared PATHLINKER with six other network-based algorithms (), including shortest path (SHORTESTPATHS, BOWTIEBUILDER), random walk with restarts (RWR), network flow (RESPONSENET), Steiner forest (PCSF), ANAT, and a greedy seed-based method (Ingenuity Pathway Analyzer (IPA). Brief descriptions of these methods and the user-defined parameters we selected appear in . […]
Ubiquitin dependent proteolysis in yeast cells expressing neurotoxic proteins
[…] e, and expression of the ERAD ubiquitin ligase Hrd1 suppressed α-synuclein-triggered cytotoxicity (Liang et al., ; Gitler et al., ). Bridging high-throughput genetic and transcriptional data with the ResponseNet algorithm predicted the AAA-ATPase Cdc48, also critically involved in ERAD, to be a modulator of α-synuclein-triggered cytotoxicity (Yeger-Lotem et al., ). Thus, the UPS in general, and sp […]
Looking to check out a full list of citations?
Be the first to review ResponseNet