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ResponseNet specifications

Information


Unique identifier OMICS_01562
Name ResponseNet
Interface Web user interface
Restrictions to use None
Computer skills Basic
Version 3.0
Stability Stable
Maintained Yes

Taxon


  • Plants and Fungi
    • Saccharomyces cerevisiae
  • Primates
    • Homo sapiens

Maintainer


  • person_outline Esti Yeger-Lotem

Publications for ResponseNet

ResponseNet citations

 (12)
library_books

Synucleins and Gene Expression: Ramblers in a Crowd or Cops Regulating Traffic?

2017
PMCID: 5508120
PMID: 28751856
DOI: 10.3389/fnmol.2017.00224

[…] 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 […]

library_books

Solving the influence maximization problem reveals regulatory organization of the yeast cell cycle

2017
PLoS Comput Biol
PMCID: 5495484
PMID: 28628618
DOI: 10.1371/journal.pcbi.1005591

[…] 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 […]

library_books

Utilizing somatic mutation data from numerous studies for cancer research: proof of concept and applications

2017
Oncogene
PMCID: 5485176
PMID: 28092680
DOI: 10.1038/onc.2016.489

[…] 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 […]

library_books

Network Based Protein Biomarker Discovery Platforms

2016
PMCID: 4838525
PMID: 27103885
DOI: 10.5808/GI.2016.14.1.2

[…] 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 […]

library_books

Pathways on demand: automated reconstruction of human signaling networks

2016
NPJ Syst Biol Appl
PMCID: 5516854
PMID: 28725467
DOI: 10.1038/npjsba.2016.2

[…] 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 . […]

library_books

Ubiquitin dependent proteolysis in yeast cells expressing neurotoxic proteins

2015
PMCID: 4357299
PMID: 25814926
DOI: 10.3389/fnmol.2015.00008

[…] 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 […]

Citations

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ResponseNet institution(s)
Department of Clinical Biochemistry and Pharmacology, Ben-Gurion University of the Negev, Beer-Sheva, Israel

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