Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Experiment Videos

Faspad: fast signaling pathway detection.

Falk Hüffner1, Sebastian Wernicke, Thomas Zichner

  • 1Institut für Informatik, Friedrich-Schiller-Universität Jena, Ernst-Abbe-Platz 2, D-07743 Jena, Germany. hueffner@minet.uni-jena.de

Bioinformatics (Oxford, England)
|April 28, 2007
PubMed
Summary
This summary is machine-generated.

Related Concept Videos

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

SHACLens: a visualization workflow for SHACL violation exploration in knowledge graphs.

Frontiers in bioinformatics·2026
Same author

Finding the most promising indications for novel treatments in oncology.

NPJ precision oncology·2026
Same author

Coral: a web-based visual analysis tool for creating and characterizing cohorts.

Bioinformatics (Oxford, England)·2021
Same author

PD-1 and LAG-3 Dominate Checkpoint Receptor-Mediated T-cell Inhibition in Renal Cell Carcinoma.

Cancer immunology research·2019
Same author

SMARCA2-deficiency confers sensitivity to targeted inhibition of SMARCA4 in esophageal squamous cell carcinoma cell lines.

Scientific reports·2019
Same author

Ordino: a visual cancer analysis tool for ranking and exploring genes, cell lines and tissue samples.

Bioinformatics (Oxford, England)·2019
Same journal

Cross-Domain Transfer Learning from Peptides to Metabolites Using a Multi-Property Fine-Tuned LLM.

Bioinformatics (Oxford, England)·2026
Same journal

Biomedical Concept Recognition with Error-aware Negative-enhanced Ranking Framework.

Bioinformatics (Oxford, England)·2026
Same journal

TEDLH: Domain HMMs for sensitive detection of remote homologues.

Bioinformatics (Oxford, England)·2026
Same journal

PLNFGL: Joint Estimation of Multi-Condition Gene Networks from Single-cell RNA-seq Data.

Bioinformatics (Oxford, England)·2026
Same journal

MCFST: Spatial domain identification method based on multi-view graph convolutional network and graph fusion network.

Bioinformatics (Oxford, England)·2026
Same journal

SpaBiT: Enhancing Spatial Transcriptomics Resolution via Bidirectional Attention Transformers.

Bioinformatics (Oxford, England)·2026
See all related articles

Faspad is a new tool that quickly finds linear signaling pathways in protein networks. It identifies potential pathways with high accuracy and displays them graphically for analysis.

Area of Science:

  • Computational Biology
  • Bioinformatics

Background:

  • Linear signaling pathway detection is crucial for understanding cellular processes.
  • Identifying these pathways in large protein interaction networks is computationally challenging.

Purpose of the Study:

  • To introduce Faspad, a user-friendly tool for detecting linear signaling pathway candidates.
  • To leverage recent algorithmic advancements for efficient pathway identification.

Main Methods:

  • Faspad employs an algorithm based on Scott et al. (2006) for pathway detection.
  • The tool utilizes recent algorithmic insights to address the NP-hard nature of the problem.
  • It offers graphical visualization of identified pathway candidates and network context.

Main Results:

Related Experiment Videos

  • Faspad efficiently identifies linear signaling pathway candidates in protein networks.
  • For networks with thousands of nodes, pathways up to 13 proteins long are found in seconds.
  • The tool achieves a 99.9% probability of optimality for detected pathways.

Conclusions:

  • Faspad provides a fast and accurate solution for identifying linear signaling pathways.
  • The software is user-friendly and suitable for analyzing large-scale protein interaction networks.
  • Faspad facilitates pathway evaluation and comparison through graphical displays.